Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_050334
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: 482343
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Found at i:20107 original size:22 final size:24
Alignment explanation
Indices: 20071--20132 Score: 76
Period size: 22 Copynumber: 2.7 Consensus size: 24
20061 GGATCACTAA
20071 CTAATACTAATCTAATATAATAGT
1 CTAATACTAATCTAATATAATAGT
20095 CTAATA-T-ATCTAATATAATAG-
1 CTAATACTAATCTAATATAATAGT
** *
20116 AAAATACTAATATAATA
1 CTAATACTAATCTAATA
20133 GAAAAGAACT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
21 4 0.12
22 15 0.45
23 8 0.24
24 6 0.18
ACGTcount: A:0.52, C:0.10, G:0.03, T:0.35
Consensus pattern (24 bp):
CTAATACTAATCTAATATAATAGT
Left flanking sequence: Indices 19571 -- 20070
CCCCTATCGGAAATAGGATTGACTACCGATTCCGAAGGAACTGGAGTTACATCTCTTTTCCATTC
AAGAGTTCTTATGCGTTTCCACGCCCCTTTGAGACCCCGAAAAATGGACAAATTCCTTTTCTTAG
GAACACATACAAGATTCGTCACTACAAAACGGATAATGGTAACCCTACCATTAACTACTTCATTT
ATGAATTTCATAGTAATAGAAATACATGTCCTACCGAGACAGAATTTGGAACTTGCTATCCTCTT
GCCTAGCAGGCAAAGATTTACCTCCGTGGAAAGGATGATTCATTCGGATCGACATGAGAGTCCAA
CTACATTACCAGAATCCATGTTGTATATTTGAAAGAGGTTGACCTCCTTGCTTCTCTCATGGTAC
ACTCCTCTTCCCGCCGAGCCCCCTTTCTCCTCGGTCCACAGAGACAAAATGTAGGACTGGTGCCA
ACAGTTCATCACGGAAGAAAGGACTCACTAAGTCGGGATCACTAA
Right flanking sequence: Indices 20133 -- 20632
GAAAAGAACTGTCTTTTCTGTATACTTTCCCCGGTTCCGTTGCTACCGCGGGCTTTACGCAATCG
ATCGGATTAGATAGATATCCCTTCAACATAGGTCATCGAAAGGATCTCGGAGACCCACCAAAGTA
CGAAAGCCAGGATCTTTCAGAAAACGGATTCCTATTCAAAGAGTGCATAACCGCATGGATAAGCT
CACACTAACCCGTCAATTTGGGATCCAAATTAGAGATTTTCCTTGGGAGGTATCGGGAAGGATTT
GGAATGGAATAATATCGATTCATACAGAAGAAAAGGTTCTCTATTGATTCAAACACTGTACCTAT
GGGATAGGGATCGAGGAAGGGGAAAAACCGAAGATTTCACATGGTACTTTTATCAATCTGATTTA
TTTCGTACCTTTCGTTCAATGAGAAAATGGGTCAAATTCTACAGGATCAAACCTATGGGACTTAA
GGAATGATATAAAAAAAAGAGAGGGAAAATATTCATATTAAATAA
Found at i:40853 original size:12 final size:12
Alignment explanation
Indices: 40836--40860 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40826 GCAGAATGCC
40836 TTTGAGATTCAA
1 TTTGAGATTCAA
40848 TTTGAGATTCAA
1 TTTGAGATTCAA
40860 T
1 T
40861 CAATGCGAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (12 bp):
TTTGAGATTCAA
Left flanking sequence: Indices 40336 -- 40835
CGCAGCCAGTTCAATGTCAGCTATATTCTTCCACGTTCAAATCTAAGTCAAGCAGTCCAGCAGAG
ACTACCGGAATAAAAAGAATGACATCCGTAAAAGATAAAAAGGCACTCTTTAGGCCTAATCAATT
AAGATTAAATTAAGGAAGCATTCCAATATTTTCAAAACCTTATTGTTATTTTTCATCGGATAGGC
AAAGTTTGAATCAAAGCCAGGCGGCTGGATGGAATGAAGCTCTCCCCTTTGGATAGGGCTCGACT
GACCAGAAAGAGAGTCCCCTATCCTATATTGTTATATTGTCTATTTGATTTTCAGGGCTTTGCAC
TTGAAAGAGATTCCCTTATTATTAGCTTGGGTACACCTTACTTTATGCTAGCTCTGGATGGAAGA
CTGCCTTATCTTATATTTATTGTATTTCTTCCCGGATGGGTGACCACTTTTTCTTTGAGAATACG
AAAGGCCACTGCCGAATCCTTATCCTTGCTTAAGTGCAGAATGCC
Right flanking sequence: Indices 40861 -- 41360
CAATGCGAATTGATTTACCTAGGCTTGACGGATTGTCCTAGCTTTTCATATACGTGGAATGAAAT
ATGAATTAGTAATTCTTGATCCAATCCTGAACAAATGAACAATTGACTTAGGTCCTTGTACGCCG
CGGCTCACCATTTTAGGTTAGGAATAAGGGTGAATCCCGCTTGAAGTCAACTAAGTAAGCCTGGA
AGCGAGAGGTACGAAGGTCACTCGACAGGGGATAAAGTCGCTCGACATAGAGTTGCATCGGATCC
TTCTCCAAAAGAGTGCCTTTGCCCGGCTATCGGTTTTTCTCGAAATAACGCCTTTGAAAAAAAAG
AATGCTACTTACCAAGGCGACTCTAGAGATTCCAGAAAGTAAGAAGAAGCGTCCGACTATCTATC
TCATACCTGTCCATCAATCCGATAAGGGGCTATCTTCCTCTATCAAAGAGCGTATTCTCTAACAC
CCCTCAAGGCAATTTCCCCATACTTTTTTTTCCCATGAGCATGGT
Found at i:124725 original size:9 final size:9
Alignment explanation
Indices: 124711--124737 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
124701 ATATTTTCAA
124711 AAGTAGTAG
1 AAGTAGTAG
124720 AAGTAGTAG
1 AAGTAGTAG
124729 AAGTAGTAG
1 AAGTAGTAG
124738 GGTCCAGACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.33, T:0.22
Consensus pattern (9 bp):
AAGTAGTAG
Left flanking sequence: Indices 124211 -- 124710
CTTTTGTTTAACATTTCCGGAAAGACCACCTATTTGTTCGTTTACCGGGTTCAGCACGAAATCAT
AAATAAGCTCTACCAAGGATTGCCAAGCATTTGGTACTGAGTTTCCTCCTCCCTTTTTAGTAACA
AAATAAACCAAAAGTAGGACCAAACTGAGAGTTAGTAGCATAAACAAAGATGGATTTGTGAATGA
GAAATAGAAGTTTCCTATTTTCATAGGAATCAATGGGATTATTTCAAATTGTTCAAGTGGACTGG
TGATCGTCGGAGGTGTCCCCCCTACAATCACGTTAAATTGTTTTAGGGCAAAGTCATAGTGCTCA
CCCTGTTTGTCTTTTAAATGTTCTAAAATTTCTCTTAGAAAACCCGTGCTGTCTTCATCATTATG
CAAATTTTCGCTGATTGCGAGTAATTTGTTTTCATCTGAACAATGATTTTGGAAGACTTTTTGAA
CGGACTCAAAGATTTCACCCCTTAGGTAGTCCGCTATATTTTCAA
Right flanking sequence: Indices 124738 -- 125237
GGTCCAGACCTTCAAAAATACCATGATTATTCGAAATACTCGAACCACTCCCATCAACCTGAGTA
CTGGACGACCGAAGACTAAAATCGTGAATAGTCGTAGTAGATTGATTCGTAGGATTTTGAATCCC
AGTACTACTAGTTCCGAATGAACTACTAGACGAAGTCGAAGCTATATTACTGGAACTTGAGTTCA
GACTAGCTTCATCAAAGCGGAAAATTCGTTGCACCGTATTTTGATTTTTTAAGATGATTCCCTCA
ATACAGCTTAACTCCGTCAAGCCTGTACGAGTAGTGAAGAAGTCTAGAGATTTTCGTTGGTTGTT
GACCAACGGAAAGCATGGGATCAAAAAAGATGCACAAACGAAACTGGAAACAACGAATTTCTCAG
GAGCAATATCAACTACCTAGACCGACCTGCTAAAAGAATTCCATAAACACCTAGCGAAGATACTG
TACTGAATGACTGGATCGATCGTACTAGATAGATAGTCTCAGATA
Found at i:127795 original size:22 final size:22
Alignment explanation
Indices: 127767--127808 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
127757 GACTTATTCG
127767 CTTCGCTACGCTTCGC-TCTTAC
1 CTTCGCTACG-TTCGCATCTTAC
*
127789 CTTCGCTTCGTTCGCATCTT
1 CTTCGCTACGTTCGCATCTT
127809 GCATCGGGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.07, C:0.38, G:0.14, T:0.40
Consensus pattern (22 bp):
CTTCGCTACGTTCGCATCTTAC
Left flanking sequence: Indices 127267 -- 127766
AGGGACAATGTAGTGTATTTCTCGAACGAAACGAGTTCCTTGTGATGTGTTGAATCTTCAATGAA
CTTCCATCAGCACTTCAGATTGATCTTGAGGAAGAACGTCTCGCGGATCTCTCCTTGCTTGTTAG
AGAACCTTGGAGAATACTATGTAGTTGATCCCTTCTTGTGATCGATTTTAGCACTAGCATGGTTC
GCTTCGGCCGTGTCATTAGCGTCAATGATGATCTTTCCGTCTCTCACCAACGTCATGATCTTCTC
CTTTAAGACGAAGCATCTTGCTGTAGGGTGACTGACGATGCGGTGATATTTGCAATACTTGGGAT
CATCGACTTTGTTGGCTTCATCAGGTCGCTTTGACTCTGGAAGGTCAATGACTTTCTTGGCCAGC
AACTCGTCGAGAATCGCGGGGACGTCAGAATCAGGGAAAGGATAGGCCTTCGCTTCTAACTCCTT
CAAAGTTGGCTGGCTTTTCTCTTCTCTCGGCCGCCGACTTATTCG
Right flanking sequence: Indices 127809 -- 128308
GCATCGGGCTTGGCATCTTCGCCTAACGGTCCAGTCTTTTAGTTCCCCATCATGATCTGGAAAAA
CCCTTACTCAACTTCATGATTTGCTTCACTCATTGAAGATTCGTCACTTTCGGAAAAATAAAGAA
TTCCAATACCTTTTCGGACGAGGCATCGAAGCGCCCGGAGGGAGCAGCTATACTAGAGTCTAGAA
CACTCTCCTATTCTATCTAAAGGTCCCACTCAGACATTCAGACACACACAAAGACAAAACAAAGA
TTACCTTTGACGAGCAAGTTCATCTGTCTTTTTGAGTTGTTAGTTGATCGGTTTTCAAAGTAGCT
TCATCGCGTATTGGAAAAAGATATCAATTGCATTTTAGAACTTAGGGGTGGATCCAATGATTCCT
AGTTGCATTCCAGACTCCATTCCTACCTCCTCCTTGAATCAGGCAGGGCAGACACGAACAACTGG
CAGAAAACCCCCGAGTTGGTTCTGTACCAGGTCATGCTAGATACC
Found at i:129675 original size:24 final size:24
Alignment explanation
Indices: 129643--129689 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
129633 CCATTTCTTC
* *
129643 GGAATTGTCCGCTCATAGCACGAT
1 GGAAGTGTCCGATCATAGCACGAT
*
129667 GGAAGTGTCCGATTATAGCACGA
1 GGAAGTGTCCGATCATAGCACGA
129690 CGCGCTGCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (24 bp):
GGAAGTGTCCGATCATAGCACGAT
Left flanking sequence: Indices 129143 -- 129642
ATATCGATCGAAGGAACATTATGACCTTTCTTTTCATCATTTTTTGATTGATTTTCATTTTCTTC
AAATGCACATGCACTGAGTTACTTAAGGAATCTCAAAGAGTCGTCCAAGAGCACAACGTTCGACT
TGCATGTGTTAAGCATATAGCTAGCGTTCCTTCTATTCCTAGAAAATGCAAAAAAGAATTGGCAG
CTATGAAAGTCAGCAAGGTAAAAAAATAACGAATGATAGTTATCATGATGGTTTGTCTTGTACAT
TATTTCGGTACGACCACCGAACGAACTTGGTTGACGAACATAGTTTATGCGCCGCTAATGTAGCG
GCTTGACGAGCATTTGACAAACTCACACCATCCATTTCAAATAGGATTTGTCCCCTGGACACACG
AGCAATCCAACCCGTAGGATTTCCTTTTCCTCTTCCCATTCTTACTTCTGTAGGTTTCCCGGTAA
TAGGGATATCTGCGAGAACTCTTACCCATATCTTACCATTTCTTC
Right flanking sequence: Indices 129690 -- 130189
CGCGCTGCTTCAATGGCTCGATATGAAAGACGACCAGCTCTACAACTTTGAGTGCCATATCTTCC
AAAACCAAGTTGTGTACCGTCCGGTTTGCAACCCCTACTACATCTGCCTTTACGATATTTACGAA
ATTTCGTACGTTTCGGATATAGCATGTCCCCCCTTTTTTTGACTATATGAAATCCACACTTTGAC
ACCTGAGATTCCGTAACGAGTAGATACTTCCGCAGGAGCATAATCTATTTTCTGGTTAAATACAT
TACGAGATGTTTTTCCATACTTTCCGCATTCAGTTCTAGCTATTTCTGCACCTTCTAATCGACCT
GAACAACATATACGGATCCCCTCCACCCCCTTTTTCATTACTAATGGAATATCCTTCACTATTTT
ACGAAAAATGGAACGAAATGATCTTGTTTTGTTCCTCGGTTGAAAAGAGATGTCTTGAGCAATCG
GAGAAGCACTTTGATAAACAGATTTGATCTTGACCGATTCAATTA
Found at i:192179 original size:18 final size:18
Alignment explanation
Indices: 192111--192170 Score: 93
Period size: 18 Copynumber: 3.3 Consensus size: 18
192101 GTCACGATCG
*
192111 ATATCGTCACTAGCATCA
1 ATATCGTCACTATCATCA
* *
192129 AGATTGTCACTATCATCA
1 ATATCGTCACTATCATCA
192147 ATATCGTCACTATCATCA
1 ATATCGTCACTATCATCA
192165 ATATCG
1 ATATCG
192171 ATCTCATCAA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.33, C:0.25, G:0.10, T:0.32
Consensus pattern (18 bp):
ATATCGTCACTATCATCA
Left flanking sequence: Indices 191611 -- 192110
TACTAATCGATAGGACCTCATTGGTAAGTGCTACAAGATCTCGTGCATTGGAACCCATGGTTATG
GACCCGAATCCGTTAGTATGGAACATTTTCTTTTCCAAGTGAAATCCCCTAGTATATGAAAGAGT
GAAAAAGTGCTTTCGTTGTTGTGGAATAAGAAGCCTTCGTATCTTAATGCACGTATTTAATTTAT
TCGGAGCTATTAGAGCGGGATCTACTTTTTGGGGAATATGAGTCGAAGCAATAACAAGAATATTT
CTAGTAGAACATCTTTCACAATCCCTGGAGAGATGGTTCACTAATAGACCGAGGGATAAGTCATT
CGACTCATTCACATCCAGATCATGAATGTTTGGAATCCATATTATGCAAGGAGACATTGCTTTTG
CTAATTCGAATTGAAGGGTGATATAAAATCGGTCTATTTCCGGCATCATATCCACAGTTAGCCCA
TTCATCCTAGTTAGCAGTTCCAGCTCCGTATCAAGGTCACGATCG
Right flanking sequence: Indices 192171 -- 192670
ATCTCATCAAGAAGAAAACCTTTAGACTTGTTATCCAGGAACTTGTTCAGAAATACCGTAATGAA
AGGAACATAGGAGTTTGTCGCTAGGTATTTGACCAAATAGGATCGTCCAGTTCCTATAGAACCTA
TCACTAAAATACCCCTAGAGGGGGATAAGGCTAAGCGGAGCGAAAAGGGTTTTCCATGAGATGGG
AAATGAAAACTATTTTCCCCACACGAAGTTTGTGAATAAGTGATTGTCTGATAATGAGCAAGGAA
TATCCGTCTTTCTGCTAAACAGGATGGATTGAACTCATAATTCATTAGATGCTTTTTATGAATGT
CAACTAAGTATCGTAAGTAAATTGCTCCCGGTTGTTCAATCATTTGATAACCAGAGTCATTCTTT
GATAAATGATCACTATGAGTCAGACTCAATAGAATTTGATCAATCCTATTTTCTGTCGTTAAGGT
GGAGAAATGAACCAAGAATTCTTTTTCTTCATCATCAATCGAATC
Found at i:194604 original size:24 final size:22
Alignment explanation
Indices: 194523--194612 Score: 85
Period size: 21 Copynumber: 4.1 Consensus size: 22
194513 ACTCACACAG
* * *
194523 AAAAAAGGAAGTGAGTTAGACA
1 AAAAAAAGAAGTGACTTGGACA
* **
194545 AAAATAA-AAGCAACTTGGAC-
1 AAAAAAAGAAGTGACTTGGACA
194565 AAAAAAAGAAGTGACTTGGACA
1 AAAAAAAGAAGTGACTTGGACA
*
194587 AAAAGAAACGAAGTGACTTAGACA
1 AAAA-AAA-GAAGTGACTTGGACA
194611 AA
1 AA
194613 TCTTTTTTGT
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
20 6 0.11
21 20 0.37
22 9 0.17
23 3 0.06
24 16 0.30
ACGTcount: A:0.56, C:0.10, G:0.21, T:0.13
Consensus pattern (22 bp):
AAAAAAAGAAGTGACTTGGACA
Left flanking sequence: Indices 194023 -- 194522
GTCCATACGTAAAATCCGAATTATTGATACGGGCCTTTTCCACAGAAAAGGGGAATCTTGTGTTC
CAATAGAAGCAGAAGTGATGTGGATTATTCAAGAATCGAAGTCGATTTGCTTTATAAAAAGAAGA
TATCAATGAACTTCTATGAAATGGTTTCACGGGATTCAGCCAATTGTCTTGATCGTGGAATATCA
TTGAGAAATAGGAATCCGGGCTATCAAAGGATTTCCTGCGATTATTTCGAGTATGGAATGAGTCA
ATCATCCACTTTGGTATCTTATTGAACAAAAATGGTGATATTGTTCCTCCATTGATCAAGAATTT
CGATTTTTGGGAAGTATCATGATCGTCCAATAAGAAGGGTTTCAATTTTTTCAAATGAACAATTT
GAAGACCTATTGATTCTAACAACTGATTGCAGAGTTGATCATTCGGACCTTTCAATTCATAGATG
TAGATCTCGGACCTATGAATGGGGATATTTCCGAAACTCACACAG
Right flanking sequence: Indices 194613 -- 195112
TCTTTTTTGTCGATAACCTCAGACCAATCAATCGAATATTGATTAATACGTAATCGATCGAACAC
TACTTGAAAACGGCTCTTCTGCTCCGAAACGGACTGTTCCAAATGTTCCTGGAAATTCTTGCTCC
CATTGGACCATTTGTATCTATATGCATCAGGATCCCGATTCATGGATCTCTCGGTTCGAGAAATC
AAAATAAGAGGCTCGAACCATTTCTTCTGACTCTTTTTCAAATTCGATAAATATTGGTTGATCGT
ATATTTCATTATAGTTCTATGATTCAGAGTATCCTTTCCTATTTGATCCCTTTGAATTCCATATT
CGAAGTTGCGATCGGATCTATTCATTAAAAAGAATCGATTCAATACATTTCTTATGTACCCATAG
GTACTATATTGGATTTGAATCAGATTTCGGATCAATCTATATTGAGTGACTGCCTCCATTATGTT
GTTGCTAGCAAATAGTGCCTCTGGAATTATGAAATCCTCTTCTAG
Found at i:196948 original size:17 final size:17
Alignment explanation
Indices: 196915--196948 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
196905 CGCTCCTGAC
* *
196915 TATTCATATTCACGGCT
1 TATTCATAATCAAGGCT
196932 TATTCATAATCAAGGCT
1 TATTCATAATCAAGGCT
196949 CTAACCTCCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (17 bp):
TATTCATAATCAAGGCT
Left flanking sequence: Indices 196415 -- 196914
GGCCTTGAGGGTAATGTCGGAGCCTCTGCCTAGCCCACACCAAGGCGAGGCACGTCTTTTCCAAG
GTCGAATATGACGACTCGTAGTCCGTCAGCTTATTTCTCAGGTAGTAATCTTTCCTTTCTTCCCC
TTTCATCATGCTGGCCTAAGACGCATCTCATGGAGTTTTCCGTGACCGAGAGGTATAGCAAGAGG
GTTCTTCCCTTAATAAAAAAAGTACCAAGACCGGAGAATCAAAAAGATAGGTCTTAATCTTCTCG
AAAGCACTCTGCATAGTCAGTCTAGGGCATCGTTCTACTCCTTTTCTTCTTCCTCAAGAGCTTGA
AAATGGGCTCGCAAAAGGGAGTGAGCTGTGCGATGAACCTGCTGATATACTACCCAAGAATCCTC
TTCTTTCTTTCCTTTCTATCCCTTTCCTTTCTCGGGGAATGAGCACACCTTCAACTAGTCACCAG
TGCCCAGATTTTCTGTCTCTGCCAGCTCGTAACCTCGCTCCTGAC
Right flanking sequence: Indices 196949 -- 197448
CTAACCTCCTAATCAAGGAGTGGAATTCTCTGCTCCCCTCGGAAAACTCCATTGCTTTGACCATC
CTCAATGACCTGAGGATGCTTCTAGCCTTCAAAGAAGACCAATTGACCACTACTACTATAATGGA
GAAAGGACAATCTGCCTTCTAACCCGAGGTCCAGGTATTCCGGCCCCAGAGAGAGAGCGTGCCAA
AGCCCGATGAATAGACAGGGGATGGACAGTCCTTGGAGCCGTACCACCAAGAAGAAGATCAAGGG
AATCTCTACCATCAGGCTTCGAATCTGAGGTTGAGGTCTAGCCTCTCTTTTCAGTGGAAGTTGAG
CTCGTCGGATCTGCTGCCCGTGACGTGAGTGATCCTTAACCCTGCCCCTTCTTATTGCTATTTGT
GACATCGAGTGCTTAAGTGAGATCAGCGGTCTGGCAGGTCCTTGGACGCTGGCCCTTATAGTCTA
GTCTATTCGGACCTCTACTAGGGCTAGAGCTAGCCGGAAAAAGAA
Found at i:287119 original size:27 final size:27
Alignment explanation
Indices: 287081--287164 Score: 168
Period size: 27 Copynumber: 3.1 Consensus size: 27
287071 TTCGACCTAC
287081 AGGTACGAAGTCTCTGCGCTTGCGCAG
1 AGGTACGAAGTCTCTGCGCTTGCGCAG
287108 AGGTACGAAGTCTCTGCGCTTGCGCAG
1 AGGTACGAAGTCTCTGCGCTTGCGCAG
287135 AGGTACGAAGTCTCTGCGCTTGCGCAG
1 AGGTACGAAGTCTCTGCGCTTGCGCAG
287162 AGG
1 AGG
287165 GAGAGTGGAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 57 1.00
ACGTcount: A:0.19, C:0.25, G:0.35, T:0.21
Consensus pattern (27 bp):
AGGTACGAAGTCTCTGCGCTTGCGCAG
Left flanking sequence: Indices 286581 -- 287080
CATAGGACCACTCCATGTGGTTACCCTACAAGGAGGTACGTAGGGGAGAAGGGTAGACCCCAGTT
TTTCAATCCTTTACTAGATACAGATGATGTAGACAGAATACGAAGATTCTCCAGGGTCCGCGATA
AGTAAATTGGAAAATTCCCATCATCTTCAACTTAGCCGGTTCTCGCTCTTTATAGCAGCTTAGCC
CGCTTCGACCAGGAATCTGTCAAGTTAGTAGCTAATAGTAGCTAATAAGAGAGTCTCACCCTCCC
GCGTGATCCCGCAGCGCAAGCATCTCCATAAGGAAGTCATCACCTTCTAACAGAAAAGTAACCCA
CAAGGTAAGGAAAGAAAGCAGAAATAAAAGGCGAGAGCATAGTGATCACCGGCGCTTTTCGTGGG
GGAAGCAGAGGTACGAAGTCGTTTGTTCGTTTTTACCTATGTGAAGTTGAACATAGTACAGAGAT
TCGTTTCAAACGTTTACAACGAATAGTTCAACTCATTCGACCTAC
Right flanking sequence: Indices 287165 -- 287664
GAGAGTGGATGTTATCGGTTACTAGATTTGGGCCAAGTAAATAATTTTTGGTAAATATAAGAGAA
TTTTATTATGATTTTGACAAAGTTATTTTCAAATGCAGAGAAGGTCACCCTAATATCTTGGCGTG
GTATCTTTGAAGGTACCAGACGGCTAAAGGGATTACTCTTGCGAGTCCCTTTAGTCGTTCTATCA
GTTTAAGTTGGACTTCATTTTCGCGAACTGTTGTTAGAATGGGACGAAAGTCTGGTTTCATTATA
TTGAAAGCAGTGTGGCGTAAGTCTTCAGCGATACTATGCTTCCAAACATGATCAGCTTTCTAGGG
CTACCTGTGGTCATTCCTTCTTATGTCCGAAAGGTTATTAGAAGGCATGACTCCAGGTCTGATCA
GTGGGTCATAATTGGTTTGGTATTTGTAGAATCATACCTTTGGCGAAGAAAGTTTCTTCGTCACT
GTTTGAATCTATAACTACTCCATCAAGTGATATTGATTCTGTAAA
Found at i:289268 original size:9 final size:9
Alignment explanation
Indices: 289254--289287 Score: 68
Period size: 9 Copynumber: 3.8 Consensus size: 9
289244 CCGGATCTAC
289254 TACTAGATA
1 TACTAGATA
289263 TACTAGATA
1 TACTAGATA
289272 TACTAGATA
1 TACTAGATA
289281 TACTAGA
1 TACTAGA
289288 GGTCAAGCGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.32
Consensus pattern (9 bp):
TACTAGATA
Left flanking sequence: Indices 288754 -- 289253
AGGACTGTGCTCCGTAATTGGATGTCACAGTGGCTTGATTGGGTCTATTGGTACTATTCGACTGA
GACAGTGTCCATTGAGGTACGAAGTCACTCGACCGTAAGGTCGAGGGGCTACCGCCAACTCATTC
TGTTCAACGAATCTTTCAATTGCAGTCGACCAAACCGATTGAAGCAAGCATGAGTAGTATCCCTT
CCTTCGTTGTCCCTTTCTTATTTAGAATATCTCTTTGGCTACCAACTCAAAGGCGGTAAGATTTG
GAACCCAGAGAAAAATCCGAAATAACATCTGAATCGGATATTCAGTTGTTCAATCTGCGGGTGCT
TTGAAAAGCTTTATTCCCGTGTAGACATTATTTGACGAATTCGGAAGAAAGGGAATAAAAATAAT
CCACAGAGTCGACTGATGCATCTATACTATTGAGTTGAGAGAAAGAAAAGATGGGACTAGTTTGC
TACTCCTACTAATAAGAACCTAACAGAAGATCCATCCGGATCTAC
Right flanking sequence: Indices 289288 -- 289787
GGTCAAGCGGCTCCCCTTACGTAGATAGATGGTCCCTGCTTGTCTGGCGAACTAGGCAATTTCCT
TGGGTACGGTTCATTCTAAACGATTTTGCACCCTCTGGTCAATGATAGTCTATATGGCAAAACGC
TATAGGAGACACGTGTACACCGACGGAATACCTTCTGCGACTATCATGGCTAGGGTAATAATTCG
TATATAACAACATCTAATTGCGTATATCCTAAGTCCAATGTGAATGAGAATGGATAAGAGGCTCG
TGGGATTGACGTGAGGGGGCAGGGATGGCTATATTTATGAACTCCGGGCGAATATGAAGCGCATG
GGTAGAAATTCCGAATTCGCTTTGTCTACGAACAACTCATTTTCAACTATGTTACAGAAATGAGT
ATCAAAACGAACAACGAATAGTTCAACTCATTTCGTGTAACTATGTTACACTCATTTCGTACCTT
AGTTGCCACTGATCGATTCATCTATAGCCTAGGCTTCATCCATGC
Found at i:327433 original size:7 final size:7
Alignment explanation
Indices: 327421--327448 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
327411 TCGAACCGCT
327421 TTAAGCA
1 TTAAGCA
327428 TTAAGCA
1 TTAAGCA
327435 TTAAGCA
1 TTAAGCA
327442 TTAAGCA
1 TTAAGCA
327449 AGAGCCTACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (7 bp):
TTAAGCA
Left flanking sequence: Indices 326921 -- 327420
TAGCTTTAGATGTTATATGAACCCCTAACAAGGAACCGTAGGCATAGAGCTATCGGGTCATAACT
CTTCTCACTCTGGCCTTAGGGTTCTTCTTTCAACAATCAAAAATCCTTTCTTCATTTACAAACAC
TTATGTGATAATATTCCTAACAAAGATTCCGTTTGACTTGACCGTAGGACATCACCTTCCTCAAT
GCAATGGAAAACTAGGAGCACGGAAGCGATGAAAGCATGCCCACTTTCGCCGGCTAACACAATGG
ATCAATACAGGGGAAACTGGCCGAGAAGCCTAAGCTAGCTATCAGCTGCCCTAGCGAACGAAGTC
TAGTCTTCTTATCGAGATGAGCATGAGTGGTCAAGCCCTGCAATGAGATCATGCGCCCTAACCTA
AGCCTGGGCTACTGTTGTGTGTTCCGATCCTTCTAGTGAGAGCTTGTGACCATCGCAGTGACCGC
AAGCTAGCAACAACGAAAGAATGAGCGAGAGCAGCTCGAACCGCT
Right flanking sequence: Indices 327449 -- 327948
AGAGCCTACCTCTACCCGAAAGCAGCGGCGAGGCGGACATTGATTTTGCAGAAAGGCTGGCTGCC
TTGCAGGGTCGCTTGCCTAGTTCACCGGTACTAGGCTATGAGAGGCTCAACATCGGGTCCAATGT
AAAGCAAGCCTTGCGAATGATGGTGGCTCCATACGGGTAGACGTAGGCCCTGAAACCATAACAAA
GACAAGACAATTACAGGGAGGACGTACGTGTTCTCGGGCGAGTGCGGACTCGGTTAGTATACAAG
ATCATCAACATAGTAATAGGATGCATCTGCTGAAGCCAAGACTCATGTAACAACAAGCTGGACCG
AAGCTCAGCCATAGTTGGTTTTGGTCGTTGAAGCTTCGCCGTAGTGACAAAGCTTTCATACTCCG
AAGGCAGGCCAGCAAGAAGGAATGTAAACATATCAGATTGGGACACCGGTGCATTGATAGATGCC
AAGGAGTCACAACTGTTCTTGAATGTACGAAGGTAAGCCGCCATA
Found at i:405473 original size:20 final size:20
Alignment explanation
Indices: 405448--405485 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
405438 AATCAATAAG
*
405448 TATCAATCTATGGGAGATTA
1 TATCAACCTATGGGAGATTA
*
405468 TATCAACCTCTGGGAGAT
1 TATCAACCTATGGGAGAT
405486 ATTAATAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.32
Consensus pattern (20 bp):
TATCAACCTATGGGAGATTA
Left flanking sequence: Indices 404948 -- 405447
CCAACTGTCTACTATACAAACAAGGAATAGCGCATCCGGGAATGAATGCATTTCAAAATGAAAGA
GAGAAGAAGCAGCTAATGCATCATCAATGAAAGCCGCTGAATCAACTGATGCAGTGTTATACGCC
AAGGTCAAGGTATATGCATTCGCCAAGTCAAGGGCTAAAGCATCTCCTTGAACAGAAGATTCACT
TCCTTCTTAACGTGAGATACTCGGCTTTTCAAAATTACAATAATAGGTCACTAATAGATCGGCTT
CAAACGGTACCATGCATGCCCAGCAGCAGCAGACGCACACCCCAGGTGCTTTCCCACAATAGCTT
TGAGACTACATATTGACCCCTTTTGCTCACCCGAAGTGCCTGCCTGCCCTAGGCTGATTTAGAGC
CCCCCTCCCTTACTGATACTGAATGAATCCCTCACAGGCTGAACCAGTACCGATATCGACCGACC
TGTTGTCAATCTTAAGGCAGGCCCCCTTTACTGGAAATCAATAAG
Right flanking sequence: Indices 405486 -- 405985
ATTAATAATTATCAACTGCAGAATCGAGACTACGTGACACATTTCTTCCACTGACGAGCTTTATC
GCGCCCTGAGCATCCCCTCCTGTATGTAAAGGGCTCTATCAAAAGCCCTGTATTTTAACTGCTTT
TTCGATTATCAAATGCCGGTGTAGTTCCTCCTTAGAGGCGTTCCAACGTGTAGCCCATTATCTGA
ACCTCCCTTTTCTCGCAGCCCAACACGACTTTGACTTAATTGTCTGTTTGAACTCCTTCCGTACC
TGTTCAGCCGTGAACCACTTGGCTTCTGTTACCACCTAAATGACTACTCAAAACAACACACTTTC
TTGGTTGAGCTGATGGAGACGATTCAAGAATCCTAGCTTATCCCCCGGATCTTACTCAGAAAGAA
AGCGCTAGGACAGAACTAAAAGTGCGGAATCCCCTCCTGCTGCAGGGATTGGAAATTGCGGAATA
TCAGGATTTAGGCGAAGGCAATTCATTCGTAGTAGGATATTGAAA
Found at i:409286 original size:19 final size:19
Alignment explanation
Indices: 409262--409322 Score: 77
Period size: 19 Copynumber: 3.2 Consensus size: 19
409252 TGCAGCCTCC
* *
409262 GTAGGAAGTTCCTCAACCT
1 GTAGGAAGTTCCACGACCT
* * *
409281 GTAGGAAGCTGCACGACCC
1 GTAGGAAGTTCCACGACCT
409300 GTAGGAAGTTCCACGACCT
1 GTAGGAAGTTCCACGACCT
409319 GTAG
1 GTAG
409323 ATCTTGCTAA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (19 bp):
GTAGGAAGTTCCACGACCT
Left flanking sequence: Indices 408762 -- 409261
TAACGAACGAGAGTTGTTGAAACTAGCATATTGGAAGATCAATCGGCCAAAATAATTATGAGCAG
CTACGATATTATAAGTTTATTCCTCTTGACCGAGTGAAGTAACAGCAGGACAACCATCATAGGCA
AAAATCAAAAAGGTCTTGTCACGAGCTGGATTCGAACCAGCGCTTCCCAGATCCGCGAAAACACC
GGATTGAAACGATCGTGACTTTAAAAAATAAAGAAGAGATAGAATGGGGAGTGGAGTTGGTGGTT
GCTTGCTTACCAAGCGATCCTGGCTTTGCACTCCTCTCCCGGCCAATCGAGTCTGCTTCGTTCAT
CTCTAGCCAATAGCGCAGGTAAGAATAGTCCAAGCCAAATAATCGTAGAATCACAACAACAACCA
CACCACGGAAACTTTTGTCTTTCTGGCGATGCTTCAGGGGAATCCTATCAATACAGATTGATCAG
TTTCTTCTACTCACGTCATTAATGGACGCTTTCAATGCAGCCTCC
Right flanking sequence: Indices 409323 -- 409822
ATCTTGCTAATTACATGTTCTCTTATCCCATATTCTATTTGGCATAAAAAAATACACATACACAA
ATTCTTTGTATTACTTGTGTGGATGTTAGCAAATGCGGACTTTAATATGGCCAACCAAATGTTGT
ATTAAATTATGCAGTTGCATTCCATTTATGTATTCCTTTTTATGCAAGTTAAATAAGTCTGTGTT
ACAGTAAAAACCGGGGTCCTATTCCACTATACTTATTCTACTAGGTAATTCTACAATTTGCAGAA
CTTCATGTTTGACTTCTTCTTTCTTGTTTTCCTTTCATTTTTCCAGGTTGTTGCCGAGAAGCAAT
TGCTGAAGCATTTACAAAAGGAAGTTTCCAGACTTGAAGCAGAGCTTCGAAGTCCTGACCCTTCT
GCCTCCCCATGTTTAAGATCTCTACTAATGGAGAAAGAGCGGAAAATCCAACAGGTACCACTAAT
GCTTTTCAGGACTCCCAGCATCATTTTAGCTATAGCTAAAGAGAG
Found at i:422143 original size:20 final size:20
Alignment explanation
Indices: 422118--422155 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
422108 CCGCGGAAGC
*
422118 CGGTGTGAACAAGCACCGAA
1 CGGTGTGAACAAACACCGAA
422138 CGGTGTGAACAAACACCG
1 CGGTGTGAACAAACACCG
422156 GCTTCTTGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.26, G:0.29, T:0.11
Consensus pattern (20 bp):
CGGTGTGAACAAACACCGAA
Left flanking sequence: Indices 421618 -- 422117
TTGAAGTGAGTCTAACTAGTATAACGAGTAAGACAACGAGTACTAGAGCTCCCTACTCTCAGTGG
ACTACTTATAGGAGGATAGGGAAAAGCTGCGTGCAGTTCAAGAGAGATCGACCAAAATCAAAGGG
GGGATAGAGCAAGGGCTCCACGCTCAAGGGACGGGCTATTTTACATAATACGGATCGGCGTATAG
CCTTTTTCTTCTTACGATCCTCTCCTTTCTGCTTCAGCGGAATATTCTGATTCGGCTTTAGCTGC
TTCGTCTGTATCTTCACATTATTCAAATGATCCTGAAGCGGACCTTTCCTTTGTGTTTGTTGTAG
CTCGCCCTTACTTAGCTTCCTTCCCTGAGCTAACCTCCTCTACCACGTTTCTATATGCCATTAGG
AGAAGTCAGTCTGCGCAATCCGCAATCATGAACCCGGCTCTGCACTAAAGAAAGGTGCGTCTGTA
TTCACTTTCATTCAGAACAAGCAACGGCTGAGCTACCGCGGAAGC
Right flanking sequence: Indices 422156 -- 422655
GCTTCTTGCCGGTGTGCGTTAGTGAAGCTAATAGTTCGGATGCGCATACCTTTTCTTGCTCCGTT
TCCTTGGTACCCGAACCGGAGAACTATCCACAAGACCGCTTCATGCTCCAAACTCGAGAAGAAGC
TTTCGAAGGCGCGTGTACCATTACTTGTACTTGTTATTCCACTAGTTATTTTTGGCAAGATCAAT
ATATAGTGATCAGTTATGATTGCTCAAACTACGGTACATAGTTTCAAGTTAGGCCTTACTTCAGT
CTGGTCTCCTCTCCCAGGTCTCAGCTTCAGGCTCCCACTGAAAAACGTATGAAAACGGCAAGGCA
AGCAAATGCACGAACGTATTGGAGGCTTTCTCTCATAAGAATCTTCTTTTCATCAGTATACGCCT
GATCGGCGAGTTCAGTCACACCTATAGGTCCGCTACTTCAAAGGCATCGCCTCACTTAGATCGCC
GGGGTTGGAGCTTCTTCGACCTCTAGCCATGACACTCCTCCCTTA
Found at i:427463 original size:19 final size:19
Alignment explanation
Indices: 427439--427476 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
427429 TCGGTGCGAC
*
427439 CACTAAAGAATTGCTTATA
1 CACTAAAGAACTGCTTATA
*
427458 CACTAAAGAGCTGCTTATA
1 CACTAAAGAACTGCTTATA
427477 TACGTTTACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.29
Consensus pattern (19 bp):
CACTAAAGAACTGCTTATA
Left flanking sequence: Indices 426939 -- 427438
AAGAGTCAAGACCAGGCTACCTAATGGAATGTTTAACCGATCCATTCCGGATCGACCGAATTGGT
ACGGAAGTTGTAACATGGGAAAACCACGGAAAACACGACTTATTTGAATAACCCGGTGACCTACC
AATTGTAGAAGTAGGATTTTTGGCAAGCAATAAGCACTTAAATAATACAATTCAAGTGTACCATC
TTCTTTCTCATTTCGAGGAAAAGGTGCGGAAGGAAAAGGAAACAACGGAGGGATCCGAATCGGAC
CTAAATGGGAATGACATGAAAAGTCTTTTTCAAAACCTAGCATTAAGGGCGTTACGACGATATAC
GAGAGGAATAGAGAAAAACTCGTGATTGGTGTGGAGGGGAAGATCTGTTTATGATATAGTTCAAG
AAAGAGTCGTCTCATTTCCTTACTTCTTTATAATTCATTCACTTCAAGACTGGTTCTGAACGCCG
CGTAACATCATCTTCAACCAACCTCCACCGTACTTTCGGTGCGAC
Right flanking sequence: Indices 427477 -- 427976
TACGTTTACTAAAAGACTGACTTTCATTCATTATCATTAGTCCAGCGTGAAACTAAGAAAGAGAG
ATGTGCCTAAGGCGGCATGTAAGCAAACTGTGCACGCTAAGAGAAGAGGAGAGATGTTCGCAATT
ACTACCACAAGAAAGCCGCCCCCTATCTTCTAAAGGGGCCCGTCACTTCGTTCGTACCTTCTTGG
CTTAGGCTTCCAACTGAACAACATGGCCTTGCCGCCCCGCCACTAGCAGAAGCTAAGCGCTTGAA
AAGCGCGCTAAGAAAGGTTGCTTCTGTCGCCCTTTCTGTGCAACAGTCCACCAGTAGCGGAAGAG
AGGGTTACCGTACATACAAGAGTCTTCCAGTTCTTACGGAAGCTCTTTCTTACCAGTCAATCAAG
TAGTACAAGAACTCTATCTTATCTTATAGCCCGGCGCGGCGGGTCGCCTTTTAAATTAATGTTGT
AGATAGAAGAAAGTATTAAATAGATAAGGAGTAGATGAGTGAGTG
Done.