Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_053927
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: 219198
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Found at i:40876 original size:9 final size:9
Alignment explanation
Indices: 40861--40907 Score: 58
Period size: 9 Copynumber: 5.2 Consensus size: 9
40851 TGTAGTTTTG
40861 CCCTGAGAA
1 CCCTGAGAA
*
40870 TCCTGAGAA
1 CCCTGAGAA
*
40879 CCCTGTGAA
1 CCCTGAGAA
*
40888 CCCTGTGAA
1 CCCTGAGAA
*
40897 GCCTGAGAA
1 CCCTGAGAA
40906 CC
1 CC
40908 TGGAGATCCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.28, C:0.32, G:0.23, T:0.17
Consensus pattern (9 bp):
CCCTGAGAA
Left flanking sequence: Indices 40361 -- 40860
GGCTAGCTGGCCCCTCCGTCGAATTCGAAACTTTATTACCGTGGGGTACGGGCCCTGCATCGGCA
GAAGCGGTCGAGGCGCCCTCCGTTGGTGTTTCGGGAAATGGCTCCATCAACACTCCTATCGAGAA
CGAATCTTCGTTCGAGTGTGATGGTCCCCCGGAACCTGAATTGGAAGGGATTATTTCCCCACCCG
ACGGATTCATCATATTGGCTCCGACCCCCGCAGTGACGAGCGCTCGAAAAGCACAGCCTATCACT
GAGGCCAGAGCGGAGGAGCAGCCCATCTTGCTAAAAAGCAAAGAGAGGGCCTTCACCCCTATGAA
GCCTGCTACCTTTGAGAGAACAGAAAACAAAAACGAGATTCCCCCTATCGAAAGACAGAGAAGAT
AGAAAAGCATCAGAAGAGCGAGAAAAGGAATGAACGCCCTAGCACTGCGAAAGAAATGCATTCTC
ACTGAAGACGAAACCGTTTTACAGAAGTTTTTCATTGTAGTTTTG
Right flanking sequence: Indices 40908 -- 41407
TGGAGATCCATTATGGTCATGATTGCTACTAAAATCTCTTGTCATGCAAATACCCAAGTCTACAA
TTTGTCTATTCATGCAAATCTTTCTACGTGTCCAAATACCCGTCCCGGTCCCCACCATAATGTTC
ATTTGTAACATTAGCATTCTAGTTTTCTTTTCTTTGCTGATTCCTCTCAATTCCATTTTCCATGT
TGCACTAAGTTACTTACGGATGTATGCATGCAGTCCGGGAACACTTTGGGGTAAACACCCATCCA
AACAACTCCAACAAGAAAAGGTATAAATATGAAAACTTCTCTACCATTTAGATCGGATAATTTAT
GGAGGAAATCCGGTTTTAAATTCCCAGAAACCACACGATTATATAGCCAAAGGGAATACGCCGCG
CCTAAAATCATCCCAAGCGCTGCTAATGTGGCTACTAAGCTATTTCTTTGGAAAGCTCCTACTAA
GATGAGAAATTCCCCGATAAAGCTGCTAGTACCAGGTAAACTCAT
Found at i:52661 original size:18 final size:18
Alignment explanation
Indices: 52640--52682 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
52630 CAACCTTGTT
52640 GACTATGACAACAG-TCGC
1 GACTATGA-AACAGATCGC
52658 GACTAT-AAACAGACTCGC
1 GACTATGAAACAGA-TCGC
52676 GACTATG
1 GACTATG
52683 GCAGGGCGGT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.23
17 1 0.05
18 16 0.73
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.19
Consensus pattern (18 bp):
GACTATGAAACAGATCGC
Left flanking sequence: Indices 52140 -- 52639
TACCGTCTAGCCGTTGGTACTCCGCATCTTCACGGAGAATTCAATTTCACCGGGTCCATGTCGGA
GACAGCGGGGCAGTCGTTACACCATTCGTGCAGGTCGCTACTTATGCGACAAGGAATTTCGCTAC
CTTAGGACAGTTAGAGTTACTGCCGCCGTTTACCGGGGCTTCCATTCAAAGCTTATAACACTTCT
CCTTCCGACTTTCCAGCACCGGGCAGGTGTCAGACTCTATACATCGTGTTACCACTTAGCAGAGT
CCTGTGTTTTTAATAAACAGTCGCTACCCCCTGGTATGTGCCGCTTTCCTAATCAAAAGATAGGA
GAGCACCCCTTCTCCCGAAGTTACGGGGTCATTTTGCCGAGTTCCTTCGACATGGTTCTCTCAAG
CGCCCTAGTATACTCTACTTGTTCACCTGTGTCGGTTTGGGGTACGGTCAGTTCACCGGGAGGAT
CGCCCTCCCAATTCGAAGTTTTTTCCTGGAAGTTTCAACCTTGTT
Right flanking sequence: Indices 52683 -- 53182
GCAGGGCGGTACGCTCTGCTCTCTCGCGACCCCTACTCTAATCAAAAGACTAAAGGCCCCTACTG
AAGATTCAAAGGGCGAGCACTGAAATGAGAAAGGCTTGTAGACTCGTGACGCTGAACGAGACATT
CGAAAACTAAAGCGCACACTAGAAAGTGCTTCGAAAGGTGTCAGCAGGTGCGCGGAGCCGGAGCC
CGGCATGTTCGCCCGCTGGGCCGAGTGTTCGCCCACTTCCGAGTCTTCGCCTTTAGATAACAAAA
AGTGTCCGCCCCTTAGGTCGCCAAACTACGACGAGAGTTTCGCCTTTTGAAGCGCCAGTCGCGTA
GGGCGACCGGGCCAGGCCGAGTCAGAAAGGCTTTGATGACTCAAGGTTCATATTAGGGAAAGGAG
AGTGAGGGGAAGAGGGGGCAGCCCTCGGCCCGATCATCCAATTCGCTCCAACAGACAGGCATGGT
TCTGTAGTCAAAGCAACTTCGTCACTTTCGTGTACCCATCGGACG
Found at i:88664 original size:23 final size:23
Alignment explanation
Indices: 88634--88681 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
88624 GAGAAAGATG
*
88634 CCCACCATCCTCTGTAACTCAAA
1 CCCACCATCCTCCGTAACTCAAA
*
88657 CCCACCATCTTCCGTAACTCAAA
1 CCCACCATCCTCCGTAACTCAAA
88680 CC
1 CC
88682 AACTTGCCCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.29, C:0.46, G:0.04, T:0.21
Consensus pattern (23 bp):
CCCACCATCCTCCGTAACTCAAA
Left flanking sequence: Indices 88134 -- 88633
TCGGTCCTCCATTCATCCGACCGGAGGTGTGGATAACGAGGCCACCTTCACAACCTTCTCCCTTC
TGTCCTTATGTTGTAGTAAGGTAGGGCGGTTCGCTTGAGTTGCTCAACCGCCCCTTAGCCCGGTG
CTCATGACGCGCTACGGAACCTCCACCGTGCCGGGGGACCAAGCAGGGCATAGCTAGCGGCATAG
GAGCCGACTTGGCATCAGCGGCTTCGTGCCGCACTGGAGTGATCCAATATGTGGTTCCGCACGTT
CCACCACTTCTCCGTTCATTTCCAATACTGATCGTGAAACACCATGAGCAGCAGGATGTTGAGGT
CCGAAATTCGAAGTGAAATTTTTGATTTGCCCGTTCCTAGTCGTCATGGGAAAGAAAGGCAGAAA
GAAGAAAGAAATGATTCCCTTTTTTCTTGTCCAATACCACCAGTACCAGAAATGCATCTCCTTCG
CCCGCGCGAGATACTTATTGAACCCGAAAAGAAGGGAGAAAGATG
Right flanking sequence: Indices 88682 -- 89181
AACTTGCCCTTCCCCAAACCGTACCTTCGATCCGAGCTCAATCGTCATTTAAAATAATATTATAG
CGACGAAAGAGAATAGTATGGTTATGAATTGCCCGCAGAACGCGCCTATAAGGAACGCTTTCGCG
GGTTCCAAGCGTTCCCCGCGTCACACCAGGCGATGACAGGCTGTAAAATGCCTCCCGCTATTATC
AATACAAAAAAGCAGAACCAGAAGAGCAAGGGAGAACTATAGTAAAGCCGTAAATCAGACCGCGA
TCTGAAGACAAGAATCGTCGATACGATTAAAGAAAGCAGGATACACCTAAGATCATGGTGTAATC
CCATGAAAAACGAATACATATTGAAGCGAAAGCACGAAGCGGAGCGAAGTAAAGTCTTCAAAAAT
ACTGAATCCCATTCTGTTGGAGCAATTGTGAGGAATAGCCATTCTAGAGCATCTATAGAACTCAT
CCACTCCCCCAATTTTGCTAGTATAAAAGATAGAAATATCATAAT
Found at i:89219 original size:27 final size:27
Alignment explanation
Indices: 89184--89235 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
89174 ATCATAATAT
89184 AATTCAAATGTTAACATCCTAACCATA
1 AATTCAAATGTTAACATCCTAACCATA
89211 AATTCAAATGTTAACATCCTAACCA
1 AATTCAAATGTTAACATCCTAACCA
89236 AGGCTTTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.44, C:0.23, G:0.04, T:0.29
Consensus pattern (27 bp):
AATTCAAATGTTAACATCCTAACCATA
Left flanking sequence: Indices 88684 -- 89183
CTTGCCCTTCCCCAAACCGTACCTTCGATCCGAGCTCAATCGTCATTTAAAATAATATTATAGCG
ACGAAAGAGAATAGTATGGTTATGAATTGCCCGCAGAACGCGCCTATAAGGAACGCTTTCGCGGG
TTCCAAGCGTTCCCCGCGTCACACCAGGCGATGACAGGCTGTAAAATGCCTCCCGCTATTATCAA
TACAAAAAAGCAGAACCAGAAGAGCAAGGGAGAACTATAGTAAAGCCGTAAATCAGACCGCGATC
TGAAGACAAGAATCGTCGATACGATTAAAGAAAGCAGGATACACCTAAGATCATGGTGTAATCCC
ATGAAAAACGAATACATATTGAAGCGAAAGCACGAAGCGGAGCGAAGTAAAGTCTTCAAAAATAC
TGAATCCCATTCTGTTGGAGCAATTGTGAGGAATAGCCATTCTAGAGCATCTATAGAACTCATCC
ACTCCCCCAATTTTGCTAGTATAAAAGATAGAAATATCATAATAT
Right flanking sequence: Indices 89236 -- 89735
AGGCTTTCTTTGCCTTGTTTACATCAGGGGCTCTGGGACTCGAACCCAATTCTTTCCGCGACCCC
CCCTAGAGAGCAAACTTTTCTCTTCTCTTTTCTACGATCATTTCTGCTTCGCTACTTTTCTACTA
TACAGCTACGCTACGATCTTTCTTCTCTTATGAAATTTCTGGTGACGGTACACTTCACTTCATTG
CACTACACTCTACTCTCCATTCTTGCTGAAGCCTCTTGCCATCCGGGTTCCACGGCATGAAGAAG
TTCATTGATCATGATTTTTGGTTGAGATAAAGAAAATCCCTCCTTAAGTCCGTCAAGCCTGTAGG
AGTAGTGAATAAATATAGAGAGTTTTGTTGTGGAAAAAAGAAAAAGAAAACCACTACTCACCAGT
TTCGAATCAAACAAGTATCAACAACAGCCCCTTCTTTGCTTTTCTGATTTCATTCTGGAAGTACC
GTAGGCACCTTATCTATGCAATAATGAACTCGCTCTTCAAGACAG
Found at i:122094 original size:18 final size:18
Alignment explanation
Indices: 122071--122106 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
122061 AGGGCTTCCT
122071 TCTTTATCTAAACGACTA
1 TCTTTATCTAAACGACTA
*
122089 TCTTTATCTAAGCGACTA
1 TCTTTATCTAAACGACTA
122107 ATAGGCTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.22, G:0.08, T:0.39
Consensus pattern (18 bp):
TCTTTATCTAAACGACTA
Left flanking sequence: Indices 121571 -- 122070
GATTACTGAATCCATCCATAAACCTAGACCCCGATAACCTTCGTAACCAAAGTGTCACGACAACA
TCCAAAGGTCATGGATTCTTAGGGGGGCAAGGAAGAGGCTGTTATGTTAGTTGTAGCGCGCCTTC
CCTCTTTATAACACTTCGGAAAGATTTTGCATTGCATTTCTTATGATGACCTGGTCGAGAGAGTA
CAATACATCGGTGTAAAAGATTGATCATGCAGTATGAGCCTAAAGGAGTTCCAAGCAACCGAGCC
ACCAGGTTTGAGAATAAGGTGGGATCCACAGATGTAGTGGCTGGTGAACCGCTTCTTCTTCTTCC
ACGAAGATTCACACAAAACCGAGCTTGGATGGAACTGATGCTACACCTTGGGGCCGCAGTCCCTT
CTTCTTAGCACGGATGTCCCTCTTCAATCCCCTGCTCCTACCATTGAAACAGCTAGGGGCTAGTA
AGTCCTGCCAATATCAGGGAAAGAATAGCTCCCGAAGGGCTTCCT
Right flanking sequence: Indices 122107 -- 122606
ATAGGCTTGGGTGGCTAGGGCACATGCTATCGAGGTTACACGCCTGGTCCCGAAACCACATCTGG
CAGATGCGATTCCTGGATGTAGTTGGATGTGATTATCGGTGAAAGCATAGAAGGATCTCCTGTCA
ATAGTCACAGGGAATTACACTATAGCTTTAGGACCTGACCTGTAATAGGTGGTGTAAATGTCCTT
ATTTATTATAGAAGATGATTCACTCACCAAGAAGACCGTCTACTCGAGCAGTCAGAGTTGATATC
AAGATGAAAGGGAAAGACAATAAGAAAGATTCAAGATAAAGACTAGAAGAAGGGGCTTTCTTAGA
AGAATTCCCACTTGGACTGGTAGTGAGAACCCGATCTCCAGAAGCTAATTGGCAAGGTTCGACTT
GACCGGAGCGGATCGCAACTCAAGCACAACTAGAGTTCACTCACCCACGTGCCCAATACTTGATG
TGATGACTCTAGCCCCATGTCGGCTTCATTGACGAGTCATGATGC
Found at i:125793 original size:15 final size:16
Alignment explanation
Indices: 125761--125795 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
125751 CATTTTCTAT
*
125761 TTTTATATATTTTATC
1 TTTTATATATTATATC
125777 TTTTATATA-TATATC
1 TTTTATATATTATATC
125792 TTTT
1 TTTT
125796 TAATATGCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.69
Consensus pattern (16 bp):
TTTTATATATTATATC
Left flanking sequence: Indices 125261 -- 125760
AAACAGAAAGTATCATAGTACGTCGTCCTTCCCTGTTCTAGTGCTTGCAGATACACTTATATACC
CGAATTTCGCCGGTTTGTAGGAATGATAACTGATCATTTGATCAGAAAACTAAGGGAGCCTGGGC
ATAAAGAAACTGGAAAAAGGTTTCTAAGCAAAGTTGCTGAGTATAGGTCTCGTGTGCTTGCTATA
GAAAGTACATATACGAGTCACGAGTAAGAGGAGTCGATGGATGTTCATATTTGAGTATTTGCTGA
CGGAATGCCTCACATCAAGGTGACAGGATTCGAACCTATGGCCCTCTGTACCCAAAACAGATGCG
CTGACCAGACTGCGCTACACCTCGTCTCACCACCCCGGAGCATATAGATCCACCCGATCGATGAA
CACTCAAACCGAACTCACCCATCCTTTTGGGCACAGGGACGCGAGAACCTAAGAAACAGCTTTTT
TCTTTTATTTCTTTTCATTTTGAATGAAAAATTTTCATTTTCTAT
Right flanking sequence: Indices 125796 -- 126295
TAATATGCCTCCAGCAAGATAGGGCGACGCAAAAAAGCCGTATAGTGCAGGAGCGCTCACATTTT
TTGGCTTACTCTTGCACTTGAATTTCCAAATCCGGCCTTTGGACCCTTGGCCCGCTTAGAAGTGG
ATTCGAACCACTGACACAAGGATTTTCAGTCCTTTGCTCTAACCAGCTGAGCTACCTGAACCACT
TTCCTAAAAGATGTTTTATTCATCGAATAGCGCCCTACCTTACCACTTGACTAGTAAAAAGCCCT
GGTACTAAAAAAATAGAATCTAATCTATATATAGGCCTCTTCGTCAAGCTTTCGAGCAGCTCTTT
CAACTGCCGCCTAATCCCCCTCAAGAACCGAGAGCCGCCCAGCCCCTGGACAGCCGGAGGGAGCT
TGCTTATAGAAAGAAGATAGGCCGATCAAACAAAAAGAACGCGCAAAGGTCTCTCCGCTCCTAGT
CACTAAGTAGTGCTATTCTGGGGGGGCTGGACTCCACCAAGAGGT
Found at i:125796 original size:16 final size:16
Alignment explanation
Indices: 125760--125801 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
125750 TCATTTTCTA
*
125760 TTTTTATATATTTTATC
1 TTTTTATATA-TATATC
125777 -TTTTATATATATATC
1 TTTTTATATATATATC
125792 TTTTTA-ATAT
1 TTTTTATATAT
125802 GCCTCCAGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
15 9 0.39
16 14 0.61
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTTATATATATATC
Left flanking sequence: Indices 125260 -- 125759
AAAACAGAAAGTATCATAGTACGTCGTCCTTCCCTGTTCTAGTGCTTGCAGATACACTTATATAC
CCGAATTTCGCCGGTTTGTAGGAATGATAACTGATCATTTGATCAGAAAACTAAGGGAGCCTGGG
CATAAAGAAACTGGAAAAAGGTTTCTAAGCAAAGTTGCTGAGTATAGGTCTCGTGTGCTTGCTAT
AGAAAGTACATATACGAGTCACGAGTAAGAGGAGTCGATGGATGTTCATATTTGAGTATTTGCTG
ACGGAATGCCTCACATCAAGGTGACAGGATTCGAACCTATGGCCCTCTGTACCCAAAACAGATGC
GCTGACCAGACTGCGCTACACCTCGTCTCACCACCCCGGAGCATATAGATCCACCCGATCGATGA
ACACTCAAACCGAACTCACCCATCCTTTTGGGCACAGGGACGCGAGAACCTAAGAAACAGCTTTT
TTCTTTTATTTCTTTTCATTTTGAATGAAAAATTTTCATTTTCTA
Right flanking sequence: Indices 125802 -- 126301
GCCTCCAGCAAGATAGGGCGACGCAAAAAAGCCGTATAGTGCAGGAGCGCTCACATTTTTTGGCT
TACTCTTGCACTTGAATTTCCAAATCCGGCCTTTGGACCCTTGGCCCGCTTAGAAGTGGATTCGA
ACCACTGACACAAGGATTTTCAGTCCTTTGCTCTAACCAGCTGAGCTACCTGAACCACTTTCCTA
AAAGATGTTTTATTCATCGAATAGCGCCCTACCTTACCACTTGACTAGTAAAAAGCCCTGGTACT
AAAAAAATAGAATCTAATCTATATATAGGCCTCTTCGTCAAGCTTTCGAGCAGCTCTTTCAACTG
CCGCCTAATCCCCCTCAAGAACCGAGAGCCGCCCAGCCCCTGGACAGCCGGAGGGAGCTTGCTTA
TAGAAAGAAGATAGGCCGATCAAACAAAAAGAACGCGCAAAGGTCTCTCCGCTCCTAGTCACTAA
GTAGTGCTATTCTGGGGGGGCTGGACTCCACCAAGAGGTTCTTTC
Found at i:170462 original size:17 final size:16
Alignment explanation
Indices: 170440--170471 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
170430 TTCCTTATTA
170440 AATAAAAAAAAGAATAT
1 AATAAAAAAAA-AATAT
170457 AATAAAAAAAAAATA
1 AATAAAAAAAAAATA
170472 AGAAAATGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (16 bp):
AATAAAAAAAAAATAT
Left flanking sequence: Indices 169940 -- 170439
TTCTGTCCGGCTTGAAACTAGAATTCGATAAGTATAGTACGCAGGGAAGTACCTATCTGAAAGGA
AGGTAACGGCTGGCACATAGGGACATCGGTTTAAGCTCCCTCAATGGGTAGCTAGCTCATATGGA
ATAGGTCTCTGGCTTGCTCCTGTCTGCTCTTTGGTTATCTATCGGAAAGAGTCGTAATCTTTCCT
TTCTGTCTACAAAGAAATTCTTTCTATTGATTCCCGCGAATCTGGAATCTCTGTAACTATGGAAA
AGGGTCATAGCGTTCTGATAAGGAAAGAAGATACGTAAGCCTATTTTTTTTTCCTTTCTTTTAGG
ATCTATCTTTCTTATTTATACAATAAAAAGAGGAAAATTAGATCTTTATTTGCGGTGCCCCGACA
GAGAAGAGGTCCTTCAAATCATGGCTGAAGTCCCGGATATATCACAGAAGTTGGTTTTTATTTTG
ACTTGAAAAGCACGGGAAAAGCAGACAGTTTGCCCTTCCTTATTA
Right flanking sequence: Indices 170472 -- 170971
AGAAAATGATAGGATTCCTTGTAGGCTACTTCTTTACTATCAGAAAAAGTTCATTGTTTAAGGAT
GCAGCTCCATCCTCTTTTTCTCTTGTCCCTTATCTGATTATCTTATCTGATTGACTTTCCTCTCT
CTTTAGGGATTAGGGTGGTGTGCTCTTCTGAGTGGGAGTGTGTGTTGTGCCAGAAGGCTTGCGTA
TAGTATATATAGAAAGATTCGGAAAATAGTTCTCGAGGATGCATCTCCATCTCCTCGTTCAAAGC
AGCGTGGTAGATCAACACGCTTATCTTATATAAGAAATAAAATAAGCAGGGGAGCCAAGAAGCTC
AAAGAGAGTCTGAGAAGCTTAGGCAAAAGCATACGCTTCAGACGTTTCTAGGGCTTTAGTTCCTT
TTCTATATCCTTTTCTCTATGGTAGATAGAATATGCATTTTGTTCTTCTTCTTGTGATTCTTTCG
GCTGTGAACCTGAGCTAATTCTTTTCTCTATTGTAGCTGAATCTC
Found at i:186809 original size:10 final size:10
Alignment explanation
Indices: 186790--186823 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
186780 AAATACCGGA
*
186790 CTTTTCCTTT
1 CTTTTTCTTT
186800 CTTTTTCTTT
1 CTTTTTCTTT
186810 CTTTTTTCTTT
1 C-TTTTTCTTT
186821 CTT
1 CTT
186824 GCTTGATTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (10 bp):
CTTTTTCTTT
Left flanking sequence: Indices 186290 -- 186789
AAAGCGTGTTCCAGACGCACCGTAGGCCATCCTCGGCCTTCTTCGTTTTCGATGAAAAAGAAAAT
CTCGATCTCCGAAAGCCTTTTCCTTCCCCCGCCGCATCTCCCTCCCTTCGTCGAGCCTTTCCTTT
CATGGTTGGGGGAAGCATTCCCTTATCTGAACTTGGCGGGCATTCTTTCCAGCCTGACTCAAATA
GGAGGTGGTTTTGTTTGGTTTGAACATAGGCTCAAACATGATTTGAAGGGTCCTAGCTACGCCAT
GCGTTCAATAAACAATCTGGAAAGGAAAGCTGCAGGGATGACAAAAAGAGAGCGCTTTCCTGCAC
TGAAAAAGAAAGAAAAAGAAAGAATACGTCTTCTCTTATTCCTCCCGCGCCCGCCGCCGTCCGGC
CCGCGTTAGAGGGGAAGAAAAATGGAGAGAGAAAGAGCAGATGGATTCTATCCCCTATATCGAAC
ACTCATTCCTATCTATTGATAGAAAGATCTTCGTCAAATACCGGA
Right flanking sequence: Indices 186824 -- 187323
GCTTGATTTATTATTCTTTTTTATAATTCCTCATATCCAAGGCAGCTTATCACAAGCACCCCACC
CCATACGACTTGTTGGGGGGCCGTTCGCCTTTTGAATCAAACAAAGTAAGTAGTAGGGGCTTCAT
AGCAACTTTCATTCTAAAGGAAAGCGAAGAACCCACTTTTAGTCAATAAGAGCCCTACTTCCCTC
GAAAAACCTCATCACTGAAATTCAAGCGCAACCCTTCTTAGTCACCGGGCTGAGCGCACCTTTGG
TACTTCAGTCGAGCTCTTTGATAGTGACTTCTTTCGGGGCGACGAAAGGCTACTTCAATCTAGAA
AACAGCCGGAAACTCGAGAGGGTCGCCTTTGGGAGCGTTCGCCGGTAACCATCACGACAACATAA
AAAGGAAGGAGTGAGGCTGACTGAATCCAATCCATAAACCCGGAAACGAAACTAAGTTCGTTCCC
TTTCGTCAAGTAGGTAAAGTAGGCATACGAACCACTTTATTTGCC
Found at i:186815 original size:11 final size:11
Alignment explanation
Indices: 186791--186823 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
186781 AATACCGGAC
*
186791 TTTTCCTTTC-
1 TTTTTCTTTCT
186801 TTTTTCTTTCT
1 TTTTTCTTTCT
186812 TTTTTCTTTCT
1 TTTTTCTTTCT
186823 T
1 T
186824 GCTTGATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTCTTTCT
Left flanking sequence: Indices 186291 -- 186790
AAGCGTGTTCCAGACGCACCGTAGGCCATCCTCGGCCTTCTTCGTTTTCGATGAAAAAGAAAATC
TCGATCTCCGAAAGCCTTTTCCTTCCCCCGCCGCATCTCCCTCCCTTCGTCGAGCCTTTCCTTTC
ATGGTTGGGGGAAGCATTCCCTTATCTGAACTTGGCGGGCATTCTTTCCAGCCTGACTCAAATAG
GAGGTGGTTTTGTTTGGTTTGAACATAGGCTCAAACATGATTTGAAGGGTCCTAGCTACGCCATG
CGTTCAATAAACAATCTGGAAAGGAAAGCTGCAGGGATGACAAAAAGAGAGCGCTTTCCTGCACT
GAAAAAGAAAGAAAAAGAAAGAATACGTCTTCTCTTATTCCTCCCGCGCCCGCCGCCGTCCGGCC
CGCGTTAGAGGGGAAGAAAAATGGAGAGAGAAAGAGCAGATGGATTCTATCCCCTATATCGAACA
CTCATTCCTATCTATTGATAGAAAGATCTTCGTCAAATACCGGAC
Right flanking sequence: Indices 186824 -- 187323
GCTTGATTTATTATTCTTTTTTATAATTCCTCATATCCAAGGCAGCTTATCACAAGCACCCCACC
CCATACGACTTGTTGGGGGGCCGTTCGCCTTTTGAATCAAACAAAGTAAGTAGTAGGGGCTTCAT
AGCAACTTTCATTCTAAAGGAAAGCGAAGAACCCACTTTTAGTCAATAAGAGCCCTACTTCCCTC
GAAAAACCTCATCACTGAAATTCAAGCGCAACCCTTCTTAGTCACCGGGCTGAGCGCACCTTTGG
TACTTCAGTCGAGCTCTTTGATAGTGACTTCTTTCGGGGCGACGAAAGGCTACTTCAATCTAGAA
AACAGCCGGAAACTCGAGAGGGTCGCCTTTGGGAGCGTTCGCCGGTAACCATCACGACAACATAA
AAAGGAAGGAGTGAGGCTGACTGAATCCAATCCATAAACCCGGAAACGAAACTAAGTTCGTTCCC
TTTCGTCAAGTAGGTAAAGTAGGCATACGAACCACTTTATTTGCC
Found at i:190829 original size:14 final size:13
Alignment explanation
Indices: 190810--190844 Score: 61
Period size: 14 Copynumber: 2.6 Consensus size: 13
190800 CAGGCCCCTT
190810 TTCTATTATATATA
1 TTCTATTATAT-TA
190824 TTCTATTATATTA
1 TTCTATTATATTA
190837 TTCTATTA
1 TTCTATTA
190845 GTCAAGCGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60
Consensus pattern (13 bp):
TTCTATTATATTA
Left flanking sequence: Indices 190310 -- 190809
CCCAAACAAAGGCGCTACCAAGCTGCGCTACATCCCTTTCAATTGGTCTACAGTGTCATTGTAGA
GAATCCCTGCCCTGTTTTCCACATCGGCAATGCACCTCCATCGATATTCAATTTATCTTGCCATT
TCTTCTTTATTGATTGATTTATATACTCATCATCATCCCGCCGATCCCACCAACGCTTTCTTACT
TATCTTATGAGCAAGGTTCTAAATAATCATGGAATTGAATAAGCGAGGCTTTCCCGATAGAAAGA
TTTGCATGTGACAGAGATCCCAATTCCGTGTATCCGGTTAAGCAAGCCCCGCCGCCAGCTTCCAC
CCAGACAAAAAAAGTGAGCGCCTAGCGCGAAAGGTTGCTTTACTAAGTAATATAACGTTAGCGCT
TTAGTTTGTTTGATTGCTCGTTAGTTTCGTTTTCAATAAGGGGCGGAGCTTGAAGAAGCGAGCCT
AGAGTAGCAGCGCAGCCTATTACGTTTACGTTTTTCAGGCCCCTT
Right flanking sequence: Indices 190845 -- 191344
GTCAAGCGCTAGCGCCCCTATAGAGTCAGGATATTCTGCTATCAATGAGAAAGAAAGAAAAAAAC
AAGTGCCTTTCGTATAGATCGAGACTTGTAGCTTGATTCTTTACTCATTCCATACTGGGAAGAAT
TGCAGGCGATAACACTTCTTCCTATTTCTTTCTCAATGATATCCGACGATCAAGACAATTCCCTT
TCATAGAAGTGAATTCTTATTCTTACGAAGCAAATTACATTTCCTATTGATTTGTCCCCTGGACC
TATTCTGATTCTGAATTATCCGTCGCTACGCTGTTCCCAAGGACTAGCAGAATCGAAATAGCGAA
ATTCTTGGGTCATCTCAATGGGTTCAGAAACCACACGTTTCTCTGGATCATCATAGCGTACTTCC
ACATATCCACTCAGAGGAAGGTCTTTTCGTAATGGATGACCCTCGAAACCATAATCTGTTGATAT
ACGGCGTAGATCTGGATGATTGATGGAAGAAACACCAAACATATC
Found at i:204734 original size:17 final size:17
Alignment explanation
Indices: 204712--204756 Score: 90
Period size: 17 Copynumber: 2.6 Consensus size: 17
204702 CAGGGGGAGA
204712 AGCTTCGCTTCGTAGAC
1 AGCTTCGCTTCGTAGAC
204729 AGCTTCGCTTCGTAGAC
1 AGCTTCGCTTCGTAGAC
204746 AGCTTCGCTTC
1 AGCTTCGCTTC
204757 CTCGTCGCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.16, C:0.31, G:0.22, T:0.31
Consensus pattern (17 bp):
AGCTTCGCTTCGTAGAC
Left flanking sequence: Indices 204212 -- 204711
GGTAGAACATCATAGAAACTTCGCTGACTTTCTCATAAACCTTGATTTCGCTACGCTCAATAAGA
AGCCGGAATAGCTGAAATTGGTTCGTGTTCCGTTTCCAAAGTCAGTCGTCTTTACCCAAGTGTGA
ACTTCAGACGACTCTCAAGCGGTTCCATTCCTTCTTACTGTACTTCTGGGTCAACCCGAATGGGA
AGAAGGGGGTCAGCCAAACAGCGGTCCACTTTGTACGTTTGCTGAGCAGACCAATCAGGCATTTT
TTCTTTTTTAGAAAAGGAAGGGAACTTCTCACCGAAGGAGGCAGTAGGAATGAAGGAGGCGGGAA
GCTACCGCGGTTGCTTATCCTTTTTTTTAGAGCGTATCGCTATGAAAAAGAAAAGAAAAAGTTTA
TGTAATCGGAAAAAGGGTTACGGTTGCGGAAACCAGAGAAAGTCGGGAACCATCGCTTTTGATTT
GAATCAAAGTAGCGACGAGCCGAGTATTACGACTACAGGGGGAGA
Right flanking sequence: Indices 204757 -- 205256
CTCGTCGCTTCTTTCTAGCGACCAGCTTCTCAAGTGGGAAGCAAGCTACCTTCAGCATCGGTAAA
ATCCCTATAATAGGCCGGAATGGTGGGGAAGGAAGCCCTCCCTACTTCAATGGAAAGGGGGGAAG
AGCCCTTTCACAGCCGCTCCACTACCTTTCGCCCAACATGATCACGAACGAAGACAGAGAATTGC
GTAGATAGGAGGACGAAACGAACCAACCCACTTGTCCTGATCGGAACGATTGAAGAAAGAAAGAG
AATGGTGTCCCCTTTCGCCCAGGGGACATCGTCGGAGAACAATGTCGGGGACAGGGTGAGAACCT
TCCGTTGCTTACACCCTTTAAGTGTTGGTTCTTCCGGGGATAGATCTGGTTTCAAGATCTATGAA
CAAGAGAGATCCCTAAATCGCCATTTTAAAAAAGAGATGAATAGATAAGGCGAAGCCAGCTGGGC
GCTAACGCGCAACGGCTTTCCTTTCTCTGATAGAGGCTCGCTTCT
Found at i:218014 original size:39 final size:39
Alignment explanation
Indices: 217960--218038 Score: 149
Period size: 39 Copynumber: 2.0 Consensus size: 39
217950 CTATTTTCTA
217960 TTCACTCATGATCTGGCCTAGTCGACCCAATCATGATAT
1 TTCACTCATGATCTGGCCTAGTCGACCCAATCATGATAT
*
217999 TTCACTCATGATCTGGCCTGGTCGACCCAATCATGATAT
1 TTCACTCATGATCTGGCCTAGTCGACCCAATCATGATAT
218038 T
1 T
218039 GAAGGATGGG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.24, C:0.28, G:0.16, T:0.32
Consensus pattern (39 bp):
TTCACTCATGATCTGGCCTAGTCGACCCAATCATGATAT
Left flanking sequence: Indices 217460 -- 217959
CACCTGTGTAGAGTGGATCGTTCAACACCTGCGGCACAAACCCATTTTATTTTTGACCTATTGGT
CCTAGTATCATAGGCGACCGAACGGCCGCCCCTTAATTACTAGACCGACCTGCTATAATAATTCC
ATAAACACCTAGCGAAGATATGGCAAACAAATAAAGTAGCCCTATGTTCGGATCTGACAATACCA
TACCATAATCAAAAGGTACAACGGCCCGAGCGACCAGACTTAACATAAATGTAGCCACTGGAGCC
ATTCTAAAAAGGGAGAAATTTGCACTACTTGGTGAAATAGGTTCTTTTATAATCAATTTAAAACC
ATCTGCTAGAGGTTGTAACAATCCAAACGATCCCACTACATCAGGACCCTTTCGACGTTGCACAA
AAGCCATTACTTTACGTTCAGCTAGCACTAAAAAGGCTACTCCTAGTAGAAGTGGTAGAATTATT
CCAAGTATTTCAGCTGGAACTGCTATGTACATTTTCTATTTTCTA
Right flanking sequence: Indices 218039 -- 218538
GAAGGATGGGACCTTTTCTCGAACTCGAAAAATCCTGCCGACATACGGGCATTCTTTTTTGTACC
TTAGTACACTGAACACCAACCCCCGGAAAAAAGAAAACTACAAGCAATCATGAAACTGGCAAAGC
TTGATAACCATTTTCTCATGACGAGCACGTTGGATCATTTTAACAATTTTGATCGCGCATCAGCT
CTGCCTTAACCCTTTTTCCGCTCCAGGTAAAGAAAGAGGTAGAATTCGTTATCGGAGTATCCTCC
GCCAACTAACCTGAGCATGCTCTCTAACATCACATACGAGATTCTTTGTCTGGCTTTTATAACTC
CTTAAGGAAGTGTCTCTTCCGAGTATTTTCTCACTTGCTTTCCTAAGCTAAGTCAGACATTCAAA
TCAAGGAAAGCGAATGAGAAACCTTCTTGGAATCAGTTCGTTCGGGAGGGTGTGTTAGTGCCAGT
ACGGGGTGTGGTGCTGGTTCTCATTTCCTGGTTTGGATTTCAGTG
Done.