Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_035073
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 687482
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.27
Found at i:20246 original size:42 final size:42
Alignment explanation
Indices: 20187--20275 Score: 178
Period size: 42 Copynumber: 2.1 Consensus size: 42
20177 ACAGTCTTCA
20187 CCAAGACAGCTGGAAGGCATAGAGTCAAGACAAAAAGGAAAG
1 CCAAGACAGCTGGAAGGCATAGAGTCAAGACAAAAAGGAAAG
20229 CCAAGACAGCTGGAAGGCATAGAGTCAAGACAAAAAGGAAAG
1 CCAAGACAGCTGGAAGGCATAGAGTCAAGACAAAAAGGAAAG
20271 CCAAG
1 CCAAG
20276 CCAGGAATGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.47, C:0.18, G:0.28, T:0.07
Consensus pattern (42 bp):
CCAAGACAGCTGGAAGGCATAGAGTCAAGACAAAAAGGAAAG
Left flanking sequence: Indices 19687 -- 20186
CGGTTTTTTCCAAGCAAGATTGTATCAGGAGTAGTAGCAGTAGGAGTGGGAGATTGAAAGCTAGC
TCCTGACTCGAGGGGAGAAGGAATAGTCTATGAAAGAGATAGTCTTAGTACACCCGAAGGAAGAG
GGAAATTTAGGCCTAGTAGCACGGTTGAAGTCCAATCCGTGTGAGTATGAGTGCCAGCCAAGCCG
CTTTCAAGCTCTCCAACGCTAGCAGTGCAGTAAGGGTTCATTCAAAGCGAACCAGTAGCAAAGCG
GTTGAAAGCAGTCTGTCGGTCTAAGTCCTGGTATTCCGGGCAAGCCAGTCGATGGTAGTCATTCC
GGTGCTTCTAGTGACTTTCTTGCCTGTCTCCTGTCTGTTTACGAATCGGATGTGAGGTTTTCCTT
ATATCCTTATATAAAGAGATCTTGCCCTCGGTCTTTCTGCCGCAAAGAAGCAAGCGAAAGAGATA
TTCAATCAACCCAGCAAAGAACCGATACCACTACCACAGTCTTCA
Right flanking sequence: Indices 20276 -- 20775
CCAGGAATGAGAGCGGAAAAGGCGTTAATCAAGAGAATACCCTGTACATGAAAAGGGCTCAGAAT
AGACTCTTTGCTTGAATGGCTTGTTTGCAGGTTTGACATTCTCTTTAGCAAAGAAGAAAGCACTA
CTTCATGGGAAGTTTCCAAAGGTAAGTCCGACGTCTCCTTAAGGTAAGGCAGTTCACTCGTAAGG
CCTCATTCATCTCTTACCCGACAAAGGCCTCTCTCATCCCTTGCTTATGCTGAATCGATATTTTC
TTGGTCTTCTTTGACCCTCGAGTTGAATAAGCTCTTCTTCCTCAAGCTTTTAGCTTGGAACAAGA
ATGGATAGAGTTGACTCAGCTGCGATTGCTCTTGTTCTCTTTGCTCTTTATAAAATGGTTTCTGT
GAACAAGGAAGAGGGGCTGCCATTGAATCAGTTTCATTTGGTTAGAAATATCATAAGAGAAGAAA
GATCGTAGCGTAGAAAAGAAAGAACGTTTTGATTCGCCTTTACGA
Found at i:20257 original size:24 final size:24
Alignment explanation
Indices: 20188--20260 Score: 77
Period size: 24 Copynumber: 3.3 Consensus size: 24
20178 CAGTCTTCAC
20188 CAAGACAGCTGGAAGGCATAGAGT
1 CAAGACAGCTGGAAGGCATAGAGT
** *
20212 CAAGACA---AAAAGG-A-A-AGC
1 CAAGACAGCTGGAAGGCATAGAGT
20230 CAAGACAGCTGGAAGGCATAGAGT
1 CAAGACAGCTGGAAGGCATAGAGT
20254 CAAGACA
1 CAAGACA
20261 AAAAGGAAAG
Statistics
Matches: 37, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
18 9 0.24
19 1 0.03
20 1 0.03
21 8 0.22
22 1 0.03
23 1 0.03
24 16 0.43
ACGTcount: A:0.45, C:0.18, G:0.29, T:0.08
Consensus pattern (24 bp):
CAAGACAGCTGGAAGGCATAGAGT
Left flanking sequence: Indices 19688 -- 20187
GGTTTTTTCCAAGCAAGATTGTATCAGGAGTAGTAGCAGTAGGAGTGGGAGATTGAAAGCTAGCT
CCTGACTCGAGGGGAGAAGGAATAGTCTATGAAAGAGATAGTCTTAGTACACCCGAAGGAAGAGG
GAAATTTAGGCCTAGTAGCACGGTTGAAGTCCAATCCGTGTGAGTATGAGTGCCAGCCAAGCCGC
TTTCAAGCTCTCCAACGCTAGCAGTGCAGTAAGGGTTCATTCAAAGCGAACCAGTAGCAAAGCGG
TTGAAAGCAGTCTGTCGGTCTAAGTCCTGGTATTCCGGGCAAGCCAGTCGATGGTAGTCATTCCG
GTGCTTCTAGTGACTTTCTTGCCTGTCTCCTGTCTGTTTACGAATCGGATGTGAGGTTTTCCTTA
TATCCTTATATAAAGAGATCTTGCCCTCGGTCTTTCTGCCGCAAAGAAGCAAGCGAAAGAGATAT
TCAATCAACCCAGCAAAGAACCGATACCACTACCACAGTCTTCAC
Right flanking sequence: Indices 20261 -- 20760
AAAAGGAAAGCCAAGCCAGGAATGAGAGCGGAAAAGGCGTTAATCAAGAGAATACCCTGTACATG
AAAAGGGCTCAGAATAGACTCTTTGCTTGAATGGCTTGTTTGCAGGTTTGACATTCTCTTTAGCA
AAGAAGAAAGCACTACTTCATGGGAAGTTTCCAAAGGTAAGTCCGACGTCTCCTTAAGGTAAGGC
AGTTCACTCGTAAGGCCTCATTCATCTCTTACCCGACAAAGGCCTCTCTCATCCCTTGCTTATGC
TGAATCGATATTTTCTTGGTCTTCTTTGACCCTCGAGTTGAATAAGCTCTTCTTCCTCAAGCTTT
TAGCTTGGAACAAGAATGGATAGAGTTGACTCAGCTGCGATTGCTCTTGTTCTCTTTGCTCTTTA
TAAAATGGTTTCTGTGAACAAGGAAGAGGGGCTGCCATTGAATCAGTTTCATTTGGTTAGAAATA
TCATAAGAGAAGAAAGATCGTAGCGTAGAAAAGAAAGAACGTTTT
Found at i:124191 original size:15 final size:15
Alignment explanation
Indices: 124171--124200 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
124161 CCAGTATATT
124171 ATTTTATTTCACTTA
1 ATTTTATTTCACTTA
124186 ATTTTATTTCACTTA
1 ATTTTATTTCACTTA
124201 GCCTGCCTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.13, G:0.00, T:0.60
Consensus pattern (15 bp):
ATTTTATTTCACTTA
Left flanking sequence: Indices 123671 -- 124170
TTTTTCATTTAAAATTGAAGTTTGACTCTGATTAGATCCTTAGCGCAAGCGCTAAGTAAGCAAGC
TACCTTATGTAATGTAAAAAAAACCGAGGAAAATAACGTCAAGTAGAAACGAACAAGGTCTTACG
GCACGATCGATCACTATATCTTTTCTTTTTTTTTTTTTTTTTATGGAAAGAGGGGATGATACGTG
GCGTGGTATACCTAATCGTTTGGTCAACGAGACGTACGTAAGTCGACATAGCTCCATGTATATGT
TCTTTGGAGCTAGAACCCATAAATAGAATGAAATAATGGTGAGCCTAGGGCGACGAATATGGCTC
AAGGGTGTCTATACAAAGCCCTTCTCTTATTCATTCAAAGGGCCAATGCACCAGCCAGCCGGTGT
GGTGGCGAACACGCTGTGCTGTAAGCCAAGCTGTTCACCTTGTAGACGGAGGAGATATAGAAAGT
GTGCCGTGCGTGATTCAAAAGATTCTATAGTAGCACCAGTATATT
Right flanking sequence: Indices 124201 -- 124700
GCCTGCCTCCCCCATGACTTTCCGGACCAACCAACCCAGATCTGCCCTCGCAAGTCTCTCTGCAT
TTTGGGAGCAGAGCATGCAAAATCGATCGAGCAATGGATGGATCTTAGAAGAATTCCACTTTGAA
CGGCACGACTCTTTCTATTTTTTCGCTGGAATTCATTTTGTCTCCCCTCCTCTTTCAATCGACAC
ACTCGACGCAGATAGCTCCGGTGGCCCCGGCTTCTGCCTCTATCAGGCGGCGGCAGCCCCCACCT
CCACAGCCACAGCATGGAGGAGCAGCTCCTTAATCCGCACTACAACCAATCCAAATTATCTCCGG
ATCGATATATGATGATGCTAAACCGAGACCGAGATAGAGAAAGAGGGCTGTCCCTTTGTTGGCTT
TTCGAAAAAAAGCACTCATAGGAATGGTGCGAATTCCCATGTTCTTTTTAGTCTCGCTTGGTTTC
GAGAGCCTCCCCCTCCCCGTCTCTTACTCGTCTTTTGAAAGCCGT
Found at i:137039 original size:19 final size:19
Alignment explanation
Indices: 137015--137056 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
137005 CTTCAGATAT
137015 TTTTATTTCTTTTA-TTTTA
1 TTTTATTT-TTTTACTTTTA
*
137034 TTTTATTTTTTTACTTTTC
1 TTTTATTTTTTTACTTTTA
137053 TTTT
1 TTTT
137057 GGTGCTGCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.12, C:0.07, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTATTTTTTTACTTTTA
Left flanking sequence: Indices 136515 -- 137014
TGAAGCAGCCTAGCATCACTTTAGATAGAAGCAGAATGGATAACTTACAACTGAAAGTAAGTTCT
TCGGATCGATATCTCGTACGACGTAATGGAGATCTTGGTCTAGATCCGGTGGTTCGCAGAATTCG
GGACCTAACGATGTTCGGTTCGTCCCATGAACGGGAGCGGACAATTCCCTTTTCGGGGAATGGCT
GCAATCACAAGCAAGTGATTGAATGAGTGGGGGGCTCCGAAAGCACATGCGGGATAAGCAGGTAT
TTCAGGAGACGGTCTAAAAATGGGTCCGATTCAAAAAAAAAAAAGAGAACTCTCAACAAGCTGGA
ACTAATCAAGATCAATAGGAAGAGGAGTTAGCTAGGAATCTATTGACAAAGTTCATGCACCTATA
TGGAAGGGCTGTTTTGTTGATGTATTCCTGTCGAGAATGAAGAAGAAGAAAAAGAGCCTTTTCAA
CCGGCCCAGATCTATTATCACGAACCCTAAAATTTCTTCAGATAT
Right flanking sequence: Indices 137057 -- 137556
GGTGCTGCTACTGTTCAACTCCATACTAACATTTTTTAATTCCTATCATCATCGTCGCAGCTTGC
GAGTTTGAGGAAGATAAGGTCGATTCGATGGAGGTGCAGCAAGCCCTCCCCCCGGTGCCGGAAGC
TTCTGAGCCACTACCACTAGCTCAGGAGCCTGTTTCTCCTTCGTTTGAAATCCAAGCTGCTGAAG
TCAACCAAGAGGACATCTGGAGGGAGTTGGAGCAGCAGGAGCAACCGGCACCAACGGGTGGAGCT
AAGCTAACAAGGCCTCACATATGCGAAAGCTCACCCCATTGGAAAATCAGGTAGCTGACCTTATT
ATCGATTTACGAAAATCCGAAGTACCCTCACCTAATAAGATTCAACAAATCGTCGAAATGCTCGA
AGAAGAAAGAATATGGTCTGGAAAAGCTGCGCACAATCAAAAAGCACAACCAACAATATGGCAGA
AAGAGTGTATTTTTTAGGAACTCCAAGGAGTGCTTTAATATGTTC
Found at i:227172 original size:2 final size:2
Alignment explanation
Indices: 227165--227201 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
227155 ATTATAAAAG
*
227165 TA TA TA TA CTA TA TA TA TA TA TA TA TT TA TA TA TA TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
227202 CTAAAAAGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Left flanking sequence: Indices 226665 -- 227164
TTTCCGAAAGCGCAGTGCCCCACGGATAGAAGACGACTCCCCTGATTTGGTGTCGCCCATTTTTG
ATATTTATGGGGTTTACACCGTCGTGCACTAATGCTGTTTCTATCTTTTTTTCTAGCAGCATCCG
CTTTTCCAGAACACTAAAAAATGCTGACACCTCGTGGTGTCTCCCGACAAAATGCACTGCTAAGC
GGTCGAACAGTTCCATCCTTCTCGTGTGATCCGGCATCAGGGGTTGCTCGAGAATCGGGACGAGA
ACAGCCTGTGCTATTTCAGGATCAGTCAGGGGCCTCGGGAGCGCGCGGTTGGACCGCTTGATGGA
AATCCGCTGCGCCAGACGGGGAACCACTTCTTACGTCGCACATGGCTATCTCCAGGAGGGGCCCC
TGACTGATTATTCCAACGATAGATAGAATAAGACCCAGAAGTTGGATGGGACTGCCATGAAAGAT
CTCCTCCGGGATTGGATCCCGGTGAAAAGAGATCCATTATAAAAG
Right flanking sequence: Indices 227202 -- 227701
CTAAAAAGGTGGATTTCGCCCTGCAATCCTAAGGGCCAGGATTCAATCTCCACTGGAGCCATTGT
GAGGAATAACCATTCTAGAACAATCATTTGGTTTGTTTCATTCTTTTTTTGTTCTGCTCCCCCCA
AAAAAAAGGGAGACTTCCTCAGGAAATCGCTGGTTTTTCCAACCCAACCGAGGATTTCCGACAAG
TCCTTCTTCATTTTTAGAGCAAGAAGGGGAACTATAGAGATTCAATGAACAGTGTTTCTTACGAT
TACGCCCAGCCCAAAAAAGCCCTTCGGAGTTGAACCGAAAAAAAAGCCTATTACTTAGGGCCCTT
CAAGAAGTTTGTGTTAAGCATATAGCCGGGCCCTCTTTCTGAGCCAGGATCAAACTCTTCTTTTT
TTACTATGATTGGGCCCTGCAGACGTACTACTTTCAATCAAACCTTTTCTTTCCTTTCCTTAAGA
TATATATGTTACCCACCATATTAATAAGGCACCAAACGCGCACTG
Found at i:236463 original size:14 final size:14
Alignment explanation
Indices: 236444--236474 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
236434 TATCTAAACT
236444 ATTGGATTAGCGGC
1 ATTGGATTAGCGGC
*
236458 ATTGGATTAGTGGC
1 ATTGGATTAGCGGC
236472 ATT
1 ATT
236475 ATAATTCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.10, G:0.32, T:0.35
Consensus pattern (14 bp):
ATTGGATTAGCGGC
Left flanking sequence: Indices 235944 -- 236443
AAGAAAAGCTTTTTCAGATGTTAAAAAAAGCATTGTAGGATAATCGGCATCTGTCCCTCGAGAAA
GAGTAAGATAGGCAAAAAGGCATAGAGACTACAGCGGTAATGCCGCATCTCTCGATGAGAAGGAA
TCCTGGAAAGAAGAGCAAAGAAAAGCCCTTCTTCTTCTGCCTTTTGACTCTATCTTGCCCTTTCT
TTAGGGAATTGCGGAGTGAATGAGTGCAACAAAACAAGGAAAGAAGGCTATAAGCTGCCTACATG
GAATTACTCTTCATGCACATTTCCCAGAAAGAGTATATTGCGATAATCGGATGCTAAGTCTCCCT
GGCTTCCTTCCTCCAGCGGATCTGTGGGCATTAAAAGAAGAAAGACTTTCAGGTTCTTCGCCACA
TTCCTTCTTAGGAAAGAAAGGCTCCCGTTCGTGCCCTGTAAGAAGGAAAATTAGAAAGGAAGGCA
TAGTCGAAAAGACTAGCAGCTTCTCTGTGCATGGATATCTAAACT
Right flanking sequence: Indices 236475 -- 236974
ATAATTCAAAAAGACTTTCGCGAAGCAGGAAAACAATCAGGTAATCAGGAAAGGCAGAAAGGGTA
GAGCCTTAGTTACCCGCAGCTCAAATAGCCAAGGTCGGTGGAAAAGGAATAGTACAGCTTGTTTG
GATAAAGGAAGCATTCATACTCGACCCGCGTCTGGACGCCCCTCTCGGGCTCACTTCCTGACAAC
CCAGCCCACAACAGGAAATGGACAGGCATTGACAAAAGCCGAAGCCTCTAACGATTTTTAAGCTG
GGTAACGGGTACCCTATCGGAAAGGGGTTTTCGTCTACCTCCCAAGCATATGGCGGGCTTATAGG
GCGCTGGTCTCCGTTAGGCTTTGAGTCTAGGAGTATAGCGATGGCTTCATCCACCGGTCCTACCA
TGGAACGAGTTTCTTCGCGCTTGGCCTTGAAATTTCGAGGCATCTTTCCCAAGACAAGAAGCGGC
GTCGGATCCCGGTAGTGCGGTAGTACGCCCAGCAGAATGTCGTAG
Found at i:245019 original size:26 final size:26
Alignment explanation
Indices: 244990--245042 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
244980 GACACGCTAT
244990 GATCGCCGTCAAAGACAGGATTCGAG
1 GATCGCCGTCAAAGACAGGATTCGAG
245016 GATCGCCGTCAAAGACAGGATTCGAG
1 GATCGCCGTCAAAGACAGGATTCGAG
245042 G
1 G
245043 CCTTTGTCCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.23, G:0.32, T:0.15
Consensus pattern (26 bp):
GATCGCCGTCAAAGACAGGATTCGAG
Left flanking sequence: Indices 244490 -- 244989
GTGGTAGTGGCTCTATTGACTATAGCCGTCCCAATGTGAAATATAGTATTCAGTAGACGCAAATG
CAGATACTATCCCCTACGGAATAAAACTTTCTTTCATTCCGTAGGGGTAAGACTCTTCAAATAAA
ACTCAAAATTCACCTAGGACTTTTTTCTTTTATAGGGACTTCTGGCTCTGATCCTTCTATAGTAG
GAAGACAAGATCGCAAGGGAATCACTAGTTCGAGTTCCATGCCTTCCTTCTGGTCCCAAACACTG
GGTTATTAACCGATGAGTTAATTTTCCCCTTACCCATTTCTTGTCCATGTGTCCCTTGCTTCTTA
GTGCTCCGTTGGACGGGGACTCCTTCTTCATTTGAATGCTTTGATGCTGGCCAACTGGGAGTAGG
TTCTGGCTGCTCTTTCTGTGATGCTATTTCGACCTCGTAAAGATATTAGGACTTTCACACTGACA
TTGAGACAGAAAACATTCGATCAGTTTCCCAGCGTGACACGCTAT
Right flanking sequence: Indices 245043 -- 245542
CCTTTGTCCCCATTGCTTGTTAGTTAAGTAGGGAGAGAGAACGCCCCATCTCTTGATTACGAAGA
TCACTTTCACAGCAAGCACGAAGCTTAACTATTATGTAAATTGAAACGATCTCCCCAGGAAAGCA
TGATGCCTGACTTGCCCCTGCTTTCCAAAACGGTAGACCAAAAGCACTGAAATGAATATGAGAAA
TGTGGCCTATCTATGGAAGGAATCTTTCGTTACTAGAACCCCTTCCTAGTGACTGTAAGCGAAAT
GCATTTAGCGAACGCCTGGGGGTACTGAGTTCCATATTTTTTATTATAGAAATGTTATCTCTATC
TAAACGACTAAGTCTTCCAGTGATCTCTCCCCCACCCAAAACCATCCCTTCCAGCGTTAGCGCAC
AAGAAGGAGCTTTTGGCAGTGAGTCGAAAGTCTTAGTGAGAAGCCCTCTTAGGACTCTTTCCACT
CTTCTCTGAGTGCCTTCAACAGTGCTTAGGTAGCGCTCACTGCGA
Found at i:272108 original size:17 final size:17
Alignment explanation
Indices: 272065--272110 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
272055 GCAGTAAATG
*
272065 GAATAAACTAAGCAAGA
1 GAATAAACTAACCAAGA
*
272082 G-ATCAACTAACCAAGA
1 GAATAAACTAACCAAGA
*
272098 GAATGAACTAACC
1 GAATAAACTAACC
272111 CCAAGGGATG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.56
17 11 0.44
ACGTcount: A:0.52, C:0.20, G:0.15, T:0.13
Consensus pattern (17 bp):
GAATAAACTAACCAAGA
Left flanking sequence: Indices 271565 -- 272064
TAAGCAGCCAAGGCCAAGAGCAAGCAGGAGTAGTCCTATCTGCCTATAAGGATTCGATAAAGAAA
GAGAATGTGAGTGGGCAGGAGATCAATAAACACAGAAAGCGAAGAGCAAAAGGAGCAGAAGACAC
TCAGTTGTTTATGTGAAATCAAGGAGCAGCAGGTTACACTTTTACACTTTCCCAAAGCAAAGAGA
GCTCAAAGCAATAAGATGAAAGCTGGGATGAGATGCTAGCCTTAGCTAGGAAGATCCATCATTGA
GCCTTAGGCCACTACCGAGCAGAAATGGAGGATCATAACACTTGAGAGATGATCCCTACTTGAAA
AGGCGGAGACAATACCTCTTGTTGCGACAAATCGAGTTTCAAAAGCCCATTTATCAATCACATTT
TCAGGCACACCAGTCAAAGAGCCATCGGACCCATTAAAGTCCCCTTTTTTACTAATATACAAGGC
CTTTGCCAGGATGTCTTTCATCAAGCAAAAGAGGGGCAGTAAATG
Right flanking sequence: Indices 272111 -- 272610
CCAAGGGATGATCTCGGATTGAAATCCAAGGCATGGTCCCATTGAAAGCCCAGGGATAAATTCCT
AAAACAGAAAATTAAAGTAAAGTCCAAGGGGGTATGATCCCAATAAAGATAGGATGGATTTTAAG
TCATTTTGGACGAAGCAGCGGGCATACCAGAAATGGCTTGTCAGGAATGGTAGATGGAGCAAGAA
TGCATAGCAGGCTTAAAACACGACACAAGTAGGACGCACTGAGGCCGAGCTTTCCTCTACTACTC
ATTGGAGCTAGCATACGAAATTATCCGTTGAAGGGTTCAACTCTCAGGGCGGCCATTGCGAGCGA
TATTCACTTTCAAGAATCATCGAGCCTACGCCTATTTCATTACTCTCGAAGAGCTCATCAAAGAG
CTAAGGCTAAGGGATGAGAAAAAAAAAGGAGGAGGTGGAATTTCTTTCAACTATAACATTTATTA
CAACACTTAATATTACAGACAGAGAATTCGGTAAGGGGATAGAAG
Found at i:343141 original size:15 final size:14
Alignment explanation
Indices: 343121--343175 Score: 74
Period size: 15 Copynumber: 3.7 Consensus size: 14
343111 TCATTAGAAG
343121 AACCAGCGGTAGCTA
1 AACCAGCGGTAGC-A
*
343136 AACCAGCGATAGCAA
1 AACCAGCGGTAGC-A
343151 AACCAGCGGTAGCA
1 AACCAGCGGTAGCA
343165 GAACCAGCGGT
1 -AACCAGCGGT
343176 TTTTGGCCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
14 1 0.03
15 35 0.97
ACGTcount: A:0.36, C:0.27, G:0.27, T:0.09
Consensus pattern (14 bp):
AACCAGCGGTAGCA
Left flanking sequence: Indices 342621 -- 343120
TAAAAAGCTTAAAAAATGTATCCCATTTCTTTGAAATCCCACTATAGTAATGCCAATAAAAAGAG
AAAATGAGAGACCCAAAGTAATGAGAAAATGACTTGTAACTGTGAAGCTATAAGGTATCATACCC
TGGGGATTACGAAATAACGAAAAAGTAAAAGTGACCGAGATGCAAGGGAAATACTTTTGTTTCAC
ATTACTGGAAAGACCGCCTATTTGTTCGTTTACCGGGTTCAGCACGAAATCATAAATAAGCTCTA
CCAAGGATTGCCAAGCATTTGGTACTAACTTTCCTCCTCCCTTTTTAGTAACAAAATGAACCAGA
AGTAGGAACAAACTGAGAGTTAGCAGCATAAACAAAGATGGATTTGTGAATGAGAAATACAAGTT
TCCAATCTTCAAATCAATCAATGGCACAATCTCAAATTGCTCAAGGGGGCTGGGGACGATGGGTG
GTTGGGGTGGTTCCATTTGCCCCCCCACCCCCAGGTCATTAGAAG
Right flanking sequence: Indices 343176 -- 343675
TTTTGGCCAAGGCCAAGACAAACATTTTGAAAAAAAATCTTTTGAATTTTGAATAGCCGTGGTCA
TTTTTCTTTCATTCTTTTCATTCTCCGCTCCCCCCAAAAAAAGGAGAGACTTCATTTTCACTGTA
CGAGTAGTGAAAAACTATAGTTTACTTTTATTGGTTGTTGACCAACGGAAAGCATGGGAGTCTTT
GGGCATTTCTTCTTCTCTTACGATATTTCTAATTACCTAATAGAATAAATACTTTAGTTCGAACT
AGTTTTTAGCTTGAACGTGGCGAATGCTATCTCTTTCCCGCAACTCGACTGTTTAACAGGATGGT
ACGAATCCGCTCTTTGACTTAGTTAAGGAAGGAAGCAATTGTTCTCTTTGCGTTTAGCTGGGCAA
AGCAAAGTGAAGGGAAGGATGAATCGCTCCCGAAAAGGAATCTATTGATTCTCTCCCAATTGGTT
GGACCGTAGGTGCGATGATTTACTTCACGGGCGAGGTCTCTGGTT
Found at i:459656 original size:24 final size:24
Alignment explanation
Indices: 459614--459662 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
459604 ATTCGGATTC
* *
459614 GTTACTTGGGGCTGATGAGGATGA
1 GTTACTTCGGGCTCATGAGGATGA
* *
459638 GTTACTTCGGGCTCCTGAGGGTGA
1 GTTACTTCGGGCTCATGAGGATGA
459662 G
1 G
459663 GAATCCGTTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.16, C:0.14, G:0.41, T:0.29
Consensus pattern (24 bp):
GTTACTTCGGGCTCATGAGGATGA
Left flanking sequence: Indices 459114 -- 459613
CAAAAAGTTTAAATTGTCAGTTTCATCCTCTTTATGAGCCTGAGATCATAATCATATGGGTCAAC
AATTCTCATTTCTTAGTTACAGAAAGCCCTTCTCAAGGAAGTAAGCCAAAAGCCACTCATCTGAG
CCAGCGGATTCTCATTCTGCTGTGCCGGTGCGCAAAGCAAGCACGCTTAGACTGCGATGTGCAAT
CTTTGGTCTGCCTATCATTGTCCATTAAGGGCTGACTCCGCTAGGCAAGAGGACCACTACTGGGA
TTATTCAACTACTAACTGATGACCAGGGGACTACTCTGCTTCTTCCACTACTGATATTGACCGAC
CTGTTGAGAGGATAGCAACAGGAGAAAGAAAAAAAAGAAGTAGAGTTAGGTTCTGTTCTAGTATG
TAAGCATCTCTTTCCTCGGTCGATTCGTCTGCTCATTCAGCGTATGATTCTTATCCTACTTCCGA
TAAGTCTTATGAAACGAATTCGGCTGGAGATAGGCATTCGGATTC
Right flanking sequence: Indices 459663 -- 460162
GAATCCGTTGTTTCGGGATAAACTTGATATGTTAGTTCGGCCTCGGCTTCTTAGGATGATGCCTG
TGCAATGTATGATCCATCGGATTCTTTTTATTCTATTCTCGGTGCGTTGTTCTTCAGCGAATGAA
AGAAACCGCTGATTCCAAAGTTCCTTCATCAGATTTGGGTGCTTTTGAAAGAGCTGCTTCTGCGA
ATGACTCAACTGATACTACTCAAAAATTTCCCACATGGAAGGAAATGGGATTTTTGAGAAAAGGG
GTTGGGAACCATCGAAGGACTAGCAACCTGACAGTCCTAAGCAACCTTGAACCAACAACGTTACA
TATACCATACTGCTATAGAAGACATGAGTACCAGTTAGACTACGGGACGCGTACACCCGAAATTG
GTGAGCTACTTACTGCCCCTTAAGTCAAGAGAATAATAGTACTTTCAGCAAAGGATATCGTAACT
ATGGCGAATACGTTTTTCTTGCTTTCCACATACCCGGAATGCGAA
Found at i:477031 original size:26 final size:26
Alignment explanation
Indices: 476997--477054 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 26
476987 TTCCATACTT
* *
476997 AGAGAAAGATTTTAAGTTAAGAGAAG
1 AGAGAAAGATTTTAAGTCAAGAAAAG
477023 AGAGAAAGATTTTAAGTCAAGAAAAG
1 AGAGAAAGATTTTAAGTCAAGAAAAG
477049 A-AGAAA
1 AGAGAAA
477055 ACTGCCTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
25 5 0.17
26 25 0.83
ACGTcount: A:0.55, C:0.02, G:0.24, T:0.19
Consensus pattern (26 bp):
AGAGAAAGATTTTAAGTCAAGAAAAG
Left flanking sequence: Indices 476497 -- 476996
CTATCCGTCCCTTTTGCTAGAGTAAGTAATTCCCTTCCCTTTTGTTTGCCAGCGTAGCGCATTGA
TCATTGAAGTGGGGGCTAGGCGAGGGCATGGTCTACTTTTTGTTCTGAAATGACTAAGTACGGCT
TGGCTTCAGCTCGTGGGACTGGTTCTCTAGAAAAAGTCCCAAACCCCACATCCTGCAGTCCGCCT
GGATTCGATTCGCTTTTAGTAATTATATTACATTATATATATAAGTAATTAGAAGCTAAAGAGAA
ATTCAATATTACCATATTCTACCGCTCAACTAACGCTATGTGATCCGGTCAAGATGAATCGATCG
AATTTCACAGCTGAGGAGGCAAAGGGAGGCAAAGCGAGAGGTTCTGAAAGAAAAGACTTTATAGA
ACCTTACTCACACGATACGGGGATGGGCCTACACAAGCAGAAGGAAGAGCTATTAGCTTGTCGGC
GTAACGAATGAACTATCGGATGGTAGGCTAACTGCTTCCATACTT
Right flanking sequence: Indices 477055 -- 477554
ACTGCCTTTTTTTTGAATTGAAGGAGGAGTCGCGCATTCGTCTGCAGCGTATAGTATAGTAGCTT
CAATGGAAATCCGTTTGAATTGATGATTTTTCACCTGATTCCCCCAAAACCGTAGAAGCTCAGAT
CGGGGTTTAGCGATAACCTGAGATCCTTTATTCTGTCTCCACTTCTGAGCCGACCGAGCCTGAAG
CCAATATGTATGAAAGAAACCAATCAACGCAGGAATGGAGTTCGTAGCGAGAAGATAAAGTTCCT
CGCCTGAGAAGCACTTCACTGGGTAATAAAAAAAGCTACCTAAAAGATCTTATTACCTTTACTCT
AAGATGCTATAAGATAATTGGGAATCTTTTAGCCGCTATTCCCGCACTATTGTAAACCAGCTTGA
TAAAGGGTAGTGGTAGAGTCTCAGTACCACTGAAAGTGCGATAGTCGGGCAAACAATCTCCTCTT
TTTATCATATCATATAAGGTAGGGTATTGTATATATGGAAATTCA
Found at i:527807 original size:19 final size:19
Alignment explanation
Indices: 527780--527821 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
527770 TAGCAGCACC
527780 AAAAGAAAAGTAAAA-AAAT
1 AAAAGAAAA-TAAAAGAAAT
*
527799 AAAATAAAATAAAAGAAAT
1 AAAAGAAAATAAAAGAAAT
527818 AAAA
1 AAAA
527822 ATATCTGAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 5 0.24
19 16 0.76
ACGTcount: A:0.81, C:0.00, G:0.07, T:0.12
Consensus pattern (19 bp):
AAAAGAAAATAAAAGAAAT
Left flanking sequence: Indices 527280 -- 527779
GAACATATTAAAGCACTCCTTGGAGTTCCTAAAAAATACACTCTTTCTGCCATATTGTTGGTTGT
GCTTTTTGATTGTGCGCAGCTTTTCCAGACCATATTCTTTCTTCTTCGAGCATTTCGACGATTTG
TTGAATCTTATTAGGTGAGGGTACTTCGGATTTTCGTAAATCGATAATAAGGTCAGCTACCTGAT
TTTCCAATGGGGTGAGCTTTCGCATATGTGAGGCCTTGTTAGCTTAGCTCCACCCGTTGGTGCCG
GTTGCTCCTGCTGCTCCAACTCCCTCCAGATGTCCTCTTGGTTGACTTCAGCAGCTTGGATTTCA
AACGAAGGAGAAACAGGCTCCTGAGCTAGTGGTAGTGGCTCAGAAGCTTCCGGCACCGGGGGGAG
GGCTTGCTGCACCTCCATCGAATCGACCTTATCTTCCTCAAACTCGCAAGCTGCGACGATGATGA
TAGGAATTAAAAAATGTTAGTATGGAGTTGAACAGTAGCAGCACC
Right flanking sequence: Indices 527822 -- 528321
ATATCTGAAGAAATTTTAGGGTTCGTGATAATAGATCTGGGCCGGTTGAAAAGGCTCTTTTTCTT
CTTCTTCATTCTCGACAGGAATACATCAACAAAACAGCCCTTCCATATAGGTGCATGAACTTTGT
CAATAGATTCCTAGCTAACTCCTCTTCCTATTGATCTTGATTAGTTCCAGCTTGTTGAGAGTTCT
CTTTTTTTTTTTTGAATCGGACCCATTTTTAGACCGTCTCCTGAAATACCTGCTTATCCCGCATG
TGCTTTCGGAGCCCCCCACTCATTCAATCACTTGCTTGTGATTGCAGCCATTCCCCGAAAAGGGA
ATTGTCCGCTCCCGTTCATGGGACGAACCGAACATCGTTAGGTCCCGAATTCTGCGAACCACCGG
ATCTAGACCAAGATCTCCATTACGTCGTACGAGATATCGATCCGAAGAACTTACTTTCAGTTGTA
AGTTATCCATTCTGCTTCTATCTAAAGTGATGCTAGGCTGCTTCA
Found at i:540656 original size:15 final size:15
Alignment explanation
Indices: 540636--540665 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
540626 GGAGGCAGGC
540636 TAAGTGAAATAAAAT
1 TAAGTGAAATAAAAT
540651 TAAGTGAAATAAAAT
1 TAAGTGAAATAAAAT
540666 AATATACTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.60, C:0.00, G:0.13, T:0.27
Consensus pattern (15 bp):
TAAGTGAAATAAAAT
Left flanking sequence: Indices 540136 -- 540635
ACGGCTTTCAAAAGACGAGTAAGAGACGGGGAGGGGGAGGCTCTCGAAACCAAGCGAGACTAAAA
AGAACATGGGAATTCGCACCATTCCTATGAGTGCTTTTTTTCGAAAAGCCAACAAAGGGACAGCC
CTCTTTCTCTATCTCGGTCTCGGTTTAGCATCATCATATATCGATCCGGAGATAATTTGGATTGG
TTGTAGTGCGGATTAAGGAGCTGCTCCTCCATGCTGTGGCTGTGGAGGTGGGGGCTGCCGCCGCC
TGATAGAGGCAGAAGCCGGGGCCACCGGAGCTATCTGCGTCGAGTGTGTCGATTGAAAGAGGAGG
GGAGACAAAATGAATTCCAGCGAAAAAATAGAAAGAGTCGTGCCGTTCAAAGTGGAATTCTTCTA
AGATCCATCCATTGCTCGATCGATTTTGCATGCTCTGCTCCCAAAATGCAGAGAGACTTGCGAGG
GCAGATCTGGGTTGGTTGGTCCGGAAAGTCATGGGGGAGGCAGGC
Right flanking sequence: Indices 540666 -- 541165
AATATACTGGTGCTACTATAGAATCTTTTGAATCACGCACGGCACACTTTCTATATCTCCTCCGT
CTACAAGGTGAACAGCTTGGCTTACAGCACAGCGTGTTCGCCACCACACCGGCTGGCTGGTGCAT
TGGCCCTTTGAATGAATAAGAGAAGGGCTTTGTATAGACACCCTTGAGCCATATTCGTCGCCCTA
GGCTCACCATTATTTCATTCTATTTATGGGTTCTAGCTCCAAAGAACATATACATGGAGCTATGT
CGACTTACGTACGTCTCGTTGACCAAACGATTAGGTATACCACGCCACGTATCATCCCCTCTTTC
CATAAAAAAAAAAAAAAAAAGAAAAGATATAGTGATCGATCGTGCCGTAAGACCTTGTTCGTTTC
TACTTGACGTTATTTTCCTCGGTTTTTTTTACATTACATAAGGTAGCTTGCTTACTTAGCGCTTG
CGCTAAGGATCTAATCAGAGTCAAACTTCAATTTTAAATGAAAAA
Found at i:586382 original size:21 final size:21
Alignment explanation
Indices: 586356--586402 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
586346 TTAAGGGATG
586356 TAACAGAAGTTTCAAGAGAAC
1 TAACAGAAGTTTCAAGAGAAC
586377 TAACAGAAGTTTCAAGAGAAC
1 TAACAGAAGTTTCAAGAGAAC
586398 TAACA
1 TAACA
586403 ATCGATGGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.49, C:0.15, G:0.17, T:0.19
Consensus pattern (21 bp):
TAACAGAAGTTTCAAGAGAAC
Left flanking sequence: Indices 585856 -- 586355
TTAAGACTGTTGCAATTGGTACAACTGCTTCAATGGGATAGAAGGAAACTGGCTAAAAAGGATTA
GAAATGGACTAGTAAGAGACTCCAATGTAACCTCAAACTAAAATTGGAACCCTAGGAGGGGCAAC
TTCCACTCTTTTTTTCACTCTTTCCATTGTCGTTTACTTTACGAAGCGAAGGAAATCAAAAGGTA
TGCCCATTTTATCGAGGAGAGGAATTACTAGCTCGCAGGCTTAAAAATGATAACTTCCTTCCTTG
CCCTCGAACCGACTATCCAACGGCATGGAACACTTAGCATTGGCCTATAACTCAAATTCCATTTT
ATAGCACGCCAACAGGAGGGGCTTCTTACAAAAGCACTCCAACAACTCGCTTGAACTTGAAGAGA
GAAGCAACTACTACTTCTCCATCAAAGGAAAAACAAGCATCGACTAAATAGAAGGCCCTTGAATC
TTATCGTTAGAGCGCTATCTACCCTTAAGACTTACTTAAGGGATG
Right flanking sequence: Indices 586403 -- 586902
ATCGATGGACTGGAAGGGCGAGAGACAGAAGAGCAAAGAGAACTCAATCTAGAATTTCCACTCCT
TCTAAAACCCCAACCCCAAGTACGGCATTAGCAATTGAAGAGCTTAGTTAGGATGGGTGGAACTA
CAACCCCTCGAACAGGCTCGATAAAGTCTGGGAGATTAGATAAGCTGGCTAGGTATTTTTATATT
CTTTTTACTGAAAATGCACCGAAGGCAACTGCCATTGAAACTATATAGCTTTATATATAAAAGGG
AGAATTCCGCTCGAAAACCAGCCCTCTTCACACCAGTACCTCTGTCCCGACATTTGGTGAGATAG
GGGTAATGCCTACCAAAGGTAAAGGGGAGCCTTCATGCAAATCTATTGAAGGGTCACCTACGTTA
GCTGGTGCCCACAGTGCCAAAGTTTCAACCAAGATCCTTTGGCTCCGTGCTGGTAGCCGGCTTGT
TACTCCAGATTTTAGTGACAAGAACGTCTGTCACGTGCGTCCCTA
Found at i:685350 original size:17 final size:17
Alignment explanation
Indices: 685330--685365 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
685320 ATATCCTTAG
685330 CTTTCCTGTATCTCTTT
1 CTTTCCTGTATCTCTTT
* *
685347 CTTTCTTGTCTCTCTTT
1 CTTTCCTGTATCTCTTT
685364 CT
1 CT
685366 CTATCTTCCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.03, C:0.31, G:0.06, T:0.61
Consensus pattern (17 bp):
CTTTCCTGTATCTCTTT
Left flanking sequence: Indices 684830 -- 685329
GGCAAGAAATGAAATCGAATAATTGTATGCCGATCGCGCCCTCTCTTTCAATTGAGCTGATCCCC
TCGCTTCTTTACCCGGTGACTTAAATTTCTATTCATTACTGGGCTATTCCCACGTACTCACTGAC
GAACTGTACTAATTGGTGGGTTGATCCAGGTAGCTCAGATCTGGGAATGTACTACAGGGAGCATC
CTGACTAGTCTCATTGACATTTAAATGAGCATCCTGTTCCCTTCTGCTTCAGCATAGTAGACCTA
TTCTCCGAGAAGGAAGACCCTGTCCAGAAAAGTGGATTTCCCTGCTGTAGTATGAGTTGAGAGGA
TCAGACTTACGGGGGAACCTTCTCTAGTCTAGGAGCATTTCCACTATGTCTGTGTTCTTTCAATG
CCCCTTCCCAAAGCAAAGCAGGAAGAAACCTATGGCGCATTCTTCTCTTTCAAAAAAGCTTTGGT
ATTGCGCCTTTCTGTGCTCCCTTTCGCCCTTCGTTATATCCTTAG
Right flanking sequence: Indices 685366 -- 685865
CTATCTTCCCATTCCTTGTAAGAAGTCCTAGGAGCCAAGACAGTAAGTAAGCCAGTCTTTGGTCT
TTTAGTAAGTCTTTCCCTTCCTTGTACTAAGTAAGTAGGGGATCCTTTCTTTCTTTTTAATATTC
TTTCTCTCCAGGCAAGCAAGGAAGTAAGCAAGTAAGGAAGGGGGTCTGTGATTAATAGGTAAGCC
TGTGCTGCTAGTGTTAAGCTAGTGGTAAGGCAGCAGTAGGCCAATAATCCTTCTTTATAAGAGTC
CTAAATCCTAGGGTCCTCGTAGTCCATTAGGAAGAAGGCAAAAGAGCTTACCTCTGAAGACTGAA
GGAACAAGCGATTACTCTAAACCAAAGCGAACGCGAAGGGGTATCGGTAGTCCCTTTACTTTATT
CCTTGGCAGGAATAGCGGAAATGGTAACTCCAAACCCTTGAGTGGCTGGTTGAATGGATTTGGGC
GTATCTTAAATAAGGTAATTGATTGATTGAGTTGTTTCTGGATAA
Done.