Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_042756
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: 363324
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Found at i:13045 original size:21 final size:21
Alignment explanation
Indices: 13021--13064 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
13011 TCTTTGAGAG
*
13021 CATAAAGAGGGCCTTATAATT
1 CATAAAGAGGGCCTTAGAATT
*
13042 CATAAAGAGGGTCTTAGAATT
1 CATAAAGAGGGCCTTAGAATT
13063 CA
1 CA
13065 AACTAGATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (21 bp):
CATAAAGAGGGCCTTAGAATT
Left flanking sequence: Indices 12521 -- 13020
GGGGAGATTCCCCTTTCGATTGGAGTTCTACGGTGGGAAAGAAAGTAAGGAGTTAGAGCTCGGAA
GTGAGAACTAGCTTATAGGAGCGAAGCCACTCGACCTACGGGAGAGGAATGAGTACTCTCTCTCC
TCATTCAAAGAAGATAGAGGAATTCCCCAGGACTGCTATAACTATAGGGGGAGAAGTGAGAACTA
GCTAGACCATATTGACTTTTATATAGGCTCGACCTTCAAAGAGGGAGTAAAAACTGACTTATAGG
GGTTGCCAGTCATAGCTATAGGAAGAGGGAATCCAACTATCGCAATTCAATCATAGGGCTAAACT
GTGCTTGATTAGTACCGGCTTTCGTTGAACTGAACAAGCGAAATGAGAATGTCAGTCTAGTGCTA
AAAAGGGCGAATAGCAATCGGGCTAAATGCATGGCTTCTACTCCTAATTCTACCTTGAAAGGGCT
TCGTTTCGGCCTATGGAATCTCAGTTCTGTAAAAGTCTTTGAGAG
Right flanking sequence: Indices 13065 -- 13564
AACTAGATATCGGATGAAAGTGGTATGACAACCTCAAACCCCGGTCCCATGGGGAGAGTTTTCTA
TTTGAGTTTCGGAAAAGAAAGGAGAAAGGACTTTTGAAGCTTGCTGACTAGGGTTGGAAGCTAAA
TTCAGTCTTATAATAACATAAGAAAGTCGTGGAGTGCATAAGCCCCTTTAGAGATAGGGGCTACT
TTCTTGTGGTAGTCATTGCGAATGAGCAAGTAGGGGGCGGCAACTAAAGAGGTAGCGAGACTGAC
CGCAATTGCAGGAATAGGTTGACTTTCTTTCATTTTGGTTATGGAAAGTGAAAGTTCTTTCGTTT
AGTACGAGATCGCTTCACACCTCGCGGTGCTTACACCTCTCGCCTATCGAAGTTCTGTTCAAAAA
CCTCGTCCGAGAACTTGTATAGAGAAGGATTTCCCGCGGCGCAGCAGTTCTTCCATACCAACTTA
GCTGCCCGGCGCTGCTATTGGCATAACAACCGGTACACCATAGGT
Found at i:14696 original size:18 final size:18
Alignment explanation
Indices: 14675--14717 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
14665 CAACCTTGTT
14675 GACTATGACAACAG-TCGC
1 GACTATGA-AACAGATCGC
14693 GACTAT-AAACAGACTCGC
1 GACTATGAAACAGA-TCGC
14711 GACTATG
1 GACTATG
14718 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 14175 -- 14674
TACCGTCTAGCCGTTGGTACTCCGCATCTTCACGGAGAATTCAATTTCACCGGGTCCATGTCGGA
GACAGCGGGGCAGTCGTTACACCATTCGTGCAGGTCGCTACTTATGCGACAAGGAATTTCGCTAC
CTTAGGACAGTTAGAGTTACTGCCGCCGTTTACCGGGGCTTCCATTCAAAGCTTATAACACTTCT
CCTTCCGACTTTCCAGCACCGGGCAGGTGTCAGACTCTATACATCGTGTTACCACTTAGCAGAGT
CCTGTGTTTTTAATAAACAGTCGCTACCCCCTGGTATGTGCCGCTTTCCTAATCAAAAGATAGGA
GAGCACCCCTTCTCCCGAAGTTACGGGGTCATTTTGCCGAGTTCCTTCGACATGGTTCTCTCAAG
CGCCCTAGTATACTCTACTTGTTCACCTGTGTCGGTTTGGGGTACGGTCAGTTCACCGGGAGGAT
CGCCCTCCCAATTCGAAGTTTTTTCCTGGAAGTTTCAACCTTGTT
Right flanking sequence: Indices 14718 -- 15217
GCAGGGCGGTACGCTCTGCTCTCTCGCGACCCCTACTCTAATCAAAAGACTAAAGGCCCCTACTG
AAGATTCAAAGGGCGAGCACTTAAATGAGAAAGGCTTGTAGACTCGTGACGCTGAACGAGACATT
CGAAAACTAAAGCGCACACTAGAAAGTGCTTCGAAAGGTGTCAGCAGGTGCGCGGAGCCGGAGCC
CGGCATGTTCGCCCGCTGGGCCGAGTGTTCGCCCACTTCAGAGTCTTCGCCTTTAGATAACAAAA
AGTGTCCGCCCCTTAGGTCGCCAAACTACGACGAGAGTTTCGCCTTTTGAAGCGCCAGTCGCGTA
GGGCGACCGGGCCAGGCCGAGTCAGAAAGGCTTTGATGACTCAAGGTTCATATTAGGGAAAGGAG
AGTGAGGGGAAGAGGGGGCAGCCCTCGGCCCGATCATCCAATTCGCTCCAACAGACAGGCATGGT
TCTGTAGTCAAAGCAACTTCGTCACTTTCGTGTACCCATCGGACG
Found at i:25696 original size:27 final size:27
Alignment explanation
Indices: 25658--25709 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
25648 ACTTGTCAAT
*
25658 AAACAATTCTATGTTCAATTTGACTAC
1 AAACAATTCTATGTTCAACTTGACTAC
*
25685 AAACAATTCTATGTTCCACTTGACT
1 AAACAATTCTATGTTCAACTTGACT
25710 CCTACCCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.35, C:0.21, G:0.08, T:0.37
Consensus pattern (27 bp):
AAACAATTCTATGTTCAACTTGACTAC
Left flanking sequence: Indices 25158 -- 25657
AATGATCACTGGCCGGAACGATCTATGATAGCTATTAACTAGTGCCATGGAGTCAGTCAGTCTAA
ACTCTATAGCTCAACAGTCTAGTGCAGCTAATGTACGAAGGAAGCAAGAAGTCAGCTAAAAAGTA
TGAGAATCTCCACTGTTCAATCAACAACAACAGGGAGGGATGCCCCCGAGGGCATCCCGATCGAT
TCAATCAACAAAGCAAGTGTTGTGAGCCCACCGGCGAGTGAGGGCTAAACGGTATTTATAGATTG
AAACTAGAAAACCTTAATTCCTGAACTAGCCTCATGAACAAGCCAGTCTCAACTTTCCTGTTCAA
CTTTCTAGTGCGTCTATCTAAGGATAGATCTCGGTATCTGTGGAGAGGAAAAGAATGAATCCTAC
TAATGCGTCAAAATCTAAAAAACATTTATCTGTATTCCCCTTTCTTTATAGGTCTCGTGTTCCCC
CTATTGAACGAAATGCAAAAACCACATACCCACAAACTTGTCAAT
Right flanking sequence: Indices 25710 -- 26209
CCTACCCATACCGTGTTCAATTTGTATAGTTCCCATACCGTGTTCAATTGTACAACTACCAATTC
AATCTTGAGATTTAGTAAGAATAGCAGACGGTATACTAGTCAGGACTCTTCTTTTCTACGAACAA
GTCAGTACTCGCACTATTGGGAGAACATGCGTCAAAGAAGGTCGTTTTCTTTTCCGTCCTCGCAC
TATTGTACGAATTTATCCCTGTACCTAAAAAAGTCTTTATTTCACGCTGGAGCATTTGTAAGCGA
CGGGATCTTAGCAGCTTCTTCCCGAGTTGCATTAGCTAAAGTGGATCTACGATCACGGGAACTAA
TCAATCGGTCTGTTCTGCCCCATAAGCATCTGGATGGTCTACGATCAGTGCTATTCGTACACCCT
ATGCCTGATTTCGCAACTTCAACCCTTTCCCGCTGTAACTGCGCCTTATTGGCTTCTTTTCAGGC
TTGAACAAGCAAGTACGCAAACAGCCTTCGGTTCCTAACAAGCTA
Found at i:30695 original size:28 final size:28
Alignment explanation
Indices: 30655--30710 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
30645 ATCCATAGCT
30655 AAATGGTTCAACATTTGAAGTTCTTTCC
1 AAATGGTTCAACATTTGAAGTTCTTTCC
30683 AAATGGTTCAACATTTGAAGTTCTTTCC
1 AAATGGTTCAACATTTGAAGTTCTTTCC
30711 TTGGTCTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (28 bp):
AAATGGTTCAACATTTGAAGTTCTTTCC
Left flanking sequence: Indices 30155 -- 30654
CTTGAAAATGACATCTTCGTGAAATAGAGAAAGCCGCCCCGTCTCCAACTGAGGTCTTCTCGCCC
GCTGCCAGGAAGATTCGATCCCAACGACCGCCTCGCAAGACCTCTGTACTTTTTTCTTGCCTTTC
CTTATTTTCATTTCAGGAAATCCACTTCTTTACTAGAGAGAACTCGATTTGAAGCTTTCATTCCT
CTTCGGGTGGTTTGCTTTCTCTTTATTTAGCTATTGAGCAAAAAGAGTTCGCTACCTTTCTGCGT
CAATCTTGTTTTCGGGGGGTTCGTAAGCTGCAAGAAAGGAGAGAGAGGCAGGCTATCTCTTTTTT
GAAGTCAGTGCTTGTATTTGGTCGTCCAGTTCTTCCGGGAGGAAAGGGGCATTCTTCACTCCTTC
GCGACGCCTCTATGTACTACATAAGGGGCGGACTAAGGGCCCATTGGTTCTACCTTCTTTTCTTT
GTCGGCGACAAGGGATCTCTCAACCCCCGCTAAGCATCCATAGCT
Right flanking sequence: Indices 30711 -- 31210
TTGGTCTTCATTCAGTGAAAGGAGTGAAGCTTTCCGCAGCTGGAAAGCGGAGACCCACGAAGGCG
AGATGATCCCAAAGCGAGAATGAAGCTAGAGCCATTACTTGACCAAGAACGTGAGAGGATTGAAC
ACACCTTCCCCGGACCGGGTGGATACACTTTTTGACCCTTCCCAGGATTGAACTACGGGATCGAT
CTCTTATTTACCAAGATATGAAAGCCACGAGCCACTTTCTTTCGATGTGCTGTCATGATCACATT
CTCAGTTTCGTACGAGATTCCCAGTTTAGCTTACGGGGTCAAAGTCTTCTTTGGACTTTTCCAAT
TCTATTTCTTTTTCATCAATCGGGGCGAGAGGGAGCTGCTTCGAGGAGGCGACACCCACTAGTTT
TGTCCGGATCAAACTCTCCCCAAAGCAGGTAGGTGAGAAGGGCTCGGCTCCATGCAGGTCTTTCA
CCAACGGCTGGCACTGAATTAGCGCGATGCGAAAGAGTCCGGGCT
Found at i:36401 original size:39 final size:39
Alignment explanation
Indices: 36346--36424 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
36336 CCCATCCTTC
*
36346 AATATCATGATTGGGTCGACCAGGCCAGATCATGAGTGA
1 AATATCATGATCGGGTCGACCAGGCCAGATCATGAGTGA
*
36385 AATATCATGATCGGGTCGACTAGGCCAGATCATGAGTGA
1 AATATCATGATCGGGTCGACCAGGCCAGATCATGAGTGA
36424 A
1 A
36425 TAGAAAATAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.32, C:0.18, G:0.28, T:0.23
Consensus pattern (39 bp):
AATATCATGATCGGGTCGACCAGGCCAGATCATGAGTGA
Left flanking sequence: Indices 35846 -- 36345
GGAAGCCGGCTTGTGCTGGATTCCTGCATACCTCTGGCAGGCATCGCAGCTCTTAGCATGTGCTA
TGTAATCTGCAAGGACCGTAGGCCAGTAGTGGCCATGTCTCCGGATCTCTCGAATTTCCCTCAGC
GCGCTCGATCTACCTATCTTTCTGAGTTTGATTGGTTTTCGCTCCAGCTGACCTTTCCATTTAAT
CACTGACAAAACCTACCTTTCCATTTTTCTTACCCTATGAGCTTTCAGCAAAGGACAGATTTCTT
GGTCCATTGACATCGATCAACGAAATAGACCTCCTTCTTTCACTTTTGTCGTTGTCTTCCAATTC
AAATAGCCCCATTAAGTGAGTGTTCCGCGAGAAAAGAGAGGCTGACATCTTTTCTTATCTATCTA
TTTTCGTAAATGAAGAAGATAAGTGAGAGCTTACTGACTGCATCTTCTAAGAAGGGCTTGGAAGA
AGAAATAGAATCTCCTTTCTTTTTCGAGAAAAGGTCCCATCCTTC
Right flanking sequence: Indices 36425 -- 36924
TAGAAAATAGAAAATGTACATAGCAGTTCCAGCTGAAATACTTGGAATAATTCTACCACTTCTAC
TAGGAGTAGCCTTTTTAGTGCTAGCTGAACGTAAAGTAATGGCTTTTGTGCAACGTCGAAAGGGT
CCTGATGTAGTGGGATCATTTGGATTGTTACAACCTCTAGCAGATGGTTTTAAATTGATTATAAA
AGAACCTATTTCACCAAGTAGTGCAAATTTCTCCCTTTTTAGAATGGCTCCAGTGGCTACATTTA
TGTTAAGTCTGGTCGCTCGGGCCGTTGTACCTTTTGATTATGGTATGGTATTGTCAGATCCGAAC
ATAGGGCTACTTTATTTGTTTGCCATATCTTCGCTAGGTGTTTATGGAATTATTATAGCAGGTCG
GTCTAGTAATTAGGGGGCGGCCGTTCGGTCGCCTATGATACTAGGACCAATAGGTCAAAAATGGG
TTTGTGCCGCAGGTGTTGAACGATCCACTCTACACAGGTGTGGGC
Found at i:42266 original size:12 final size:12
Alignment explanation
Indices: 42231--42266 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
42221 CCCTTTATCG
42231 TCATCGTCGCTA
1 TCATCGTCGCTA
* *
42243 TCATAGTTGCTA
1 TCATCGTCGCTA
42255 TCATCGTCGCTA
1 TCATCGTCGCTA
42267 AAGCTCCTCC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.36
Consensus pattern (12 bp):
TCATCGTCGCTA
Left flanking sequence: Indices 41731 -- 42230
CTTGCTGCCAAACAACCTATTGCTATTGACAAGAGTCGGTCAATGCCATTCAATGTCCAGCCAAT
AACCAATTGAGGAAGCAAGCCGAATCCTTATATACGAGAGAATAAAGGGATCATAGCGGTGAAGG
AGGACGACCGGAGAGAGGAGCTTACGAAAATAAGCTACTAAAAGCGACGAGGGCAGCATGTCTTT
ACTGGGGAAAGCTGCCAAATCATTCATATTATCGGAAGCTCTTGTCAAAGGATTTTACCTCTGTT
GGACCTAAAGCTTTCAAATCGGAACCTGAAAGGTAAGGCGCGTTGGTTAAGTATCTCATTCCACA
AAAGTTGCACAAATCTCTTAAGACATGAGAATAGGAAGGCGTATACCTTACGTACTTTTTATTAG
CCGGTGTGTTGATGATCCTCGTGTTATAATTTCTATCTATTAGTTGATGATCGAGCTCTTTATGA
TTGAATGAAGTGAAAGATCAAACTCAAAGGGCTCTCCCTTTATCG
Right flanking sequence: Indices 42267 -- 42766
AAGCTCCTCCACTTTCCTCCTTCCTTTGCTAACGCTCCTCCCTTTGACCAAAAACACAAAAGACG
GTGCATGAGGGAGAGAAAGATGTTGCTCTCATACCAGATGCTTTGAGCAAACTAGCCTATCTCTC
GGCAGGATGGTGTGCCCAAACTGTCATTTCATTCGAGGCGGGATCGGAGTAAGGGGCGAAGTCTC
GAGCATCGGTACTCGCAGCCTTTAGGTTTAGGTAATCGTCAGATTTCCAAAGCCGACAGGCCTTC
ACGCCCCGACCCTCAGATGCGGGGTTCACTGAGCAAAGGAGTCGGCAGATGTTACATTTTTTTAG
ACTCCACCTTCGCGAAACTACTAAAGAGAAGGCTAACAGTCTTTAGCGCAGCTTATTAGGGATTT
CCCAACGGAAAGGCTTTGTCGAACCCTCTTACGTTAACCTACCTTCTTGCCAGCGAAATAAAATT
TGAGGTCGCGCATTCAATGACTGCTCTAGAGCCGACTTATTCGGG
Found at i:81464 original size:16 final size:16
Alignment explanation
Indices: 81439--81478 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
81429 AAAGTGGAAA
*
81439 CTTTCCGCGGGATCCT
1 CTTTCTGCGGGATCCT
*
81455 CTTTCTGCGGGATGCT
1 CTTTCTGCGGGATCCT
81471 CTTT-TGCG
1 CTTTCTGCG
81479 CTACGATGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.05, C:0.30, G:0.28, T:0.38
Consensus pattern (16 bp):
CTTTCTGCGGGATCCT
Left flanking sequence: Indices 80939 -- 81438
GGGCACTACTAACCAAGCCAAGCCCAGTTCCCGCCGATAGGCGCAGGTAGCTTGCTTCCAAGCCT
TGCCTTATATGATAGTTGTGGCCATGGCCCGAAGGAGCCTTAAGCACTTGTACAATGCTTCAAGT
CAAGGCTCCCCCCCACTCGTTGCCCAGAGCCTTTACTTTCCATGTTTTTAGTCAAATGCGCGCTA
GCGCGCTACAACTAGCACTTTTTTCTCTGAGAGGCTCGCTTCTTCCCGCCCCTTATTGAAAAAAA
AAGCGCGTTAGCGCTTTTACTTTTATTTATTATATAATACCTTCTTTCTACTTCTTTCTCAAAGT
AAAGCAAGCAACCTTTCGCCTTTATTTTTTTGAGGAGATATAAAAAGAAGCAACCTTACTAAGCA
AACGTAGGCTTGGGCTCGAAAGCAAGAAGCAACGGCTTTCGCGCTTGTTGGAGCTATTAAGCATC
TTAGACTATTCCATTCCATTTTGCAGCTGGACAGAAAAGTGGAAA
Right flanking sequence: Indices 81479 -- 81978
CTACGATGGATTTTTTTACTCTTTAAGTGCGCCACTCCTTCTTTTGTCCTGTATCTGTAGCTGCT
TTTCCCGCACTCTCTTTTATCCCGCCGAAGGTCCCCCTTACGTAATAGGGGTTAAGTTAAGGGGG
GTGCACACCGTGGTCAAATCTGCATGAAAAACCGCGGGGAATCCTTAGTATTAAGTATTATGCTC
CCGCACCCCCTATCTCTTAAAGGCTCTGCGCTCCCGCATTCTGATTGATCCTGTGCAATGTTGTA
ATCCTGCTGTTCCTTTATCCCCCGCTCCGCAGCTGCTGGAGACTTAGTCAGATTTTTAGCCTTTT
GCGGTACTGATTGATGTTATGGGGGATTACTTGGGTTGGCCGGACTGTTTGTTTGCGAAGGCCGA
AGGACTAAAAAATGAGGTTTTTGATGTTATTGGACAGAATTGGTGCCGTTTTCCCACGCCTCCTT
TTCCATAATATGATTATGAGCTGCAGAACGCTTGAAGCTGGAATT
Found at i:126013 original size:21 final size:21
Alignment explanation
Indices: 125989--126032 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
125979 TCTTTGAGAG
*
125989 CATAAAGAGGGCCTTATAATT
1 CATAAAGAGGGCCTTAGAATT
*
126010 CATAAAGAGGGTCTTAGAATT
1 CATAAAGAGGGCCTTAGAATT
126031 CA
1 CA
126033 AACTAGATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (21 bp):
CATAAAGAGGGCCTTAGAATT
Left flanking sequence: Indices 125489 -- 125988
GGGGAGATTCCCCTTTCGATTGGAGTTCTACGGTGGGAAAGAAAGTAAGGAGTTAGAGCTCGGAA
GTGAGAACTAGCTTATAGGAGCGAAGCCACTCGACCTACGGGAGAGGAATGAGTACTCTCTCTCC
TCATTCAAAGAAGATAGAGGAATTCCCCAGGACTGCTATAACTATAGGGGGAGAAGTGAGAACTA
GCTAGACCATATTGACTTTTATATAGGCTCGACCTTCAAAGAGGGAGTAAAAACTGACTTATAGG
GGTTGCCAGTCATAGCTATAGGAAGAGGGAATCCAACTATCGCAATTCAATCATAGGGCTAAACT
GTGCTTGATTAGTACCGGCTTTCGTTGAACTGAACAAGCGAAATGAGAATGTCAGTCTAGTGCTA
AAAAGGGCGAATAGCAATCGGGCTAAATGCATGGCTTCTACTCCTAATTCTACCTTGAAAGGGCT
TCGTTTCGGCCTATGGAATCTCAGTTCTGTAAAAGTCTTTGAGAG
Right flanking sequence: Indices 126033 -- 126532
AACTAGATATCGGATGAAAGTGGTATGACAACCTCAAACCCCGGTCCCATGGGGAGAGTTTTCTA
TTTGAGTTTCGGAAAAGAAAGGAGAAAGGACTTTTGAAGCTTGCTGACTAGGGTTGGAAGCTAAA
TTCAGTCTTATAATAACATAAGAAAGTCGTGGAGTGCATAAGCCCCTTTAGAGATAGGGGCTACT
TTCTTGTGGTAGTCATTGCGAATGAGCAAGTAGGGGGCGGCAACTAAAGAGGTAGCGAGACTGAC
CGCAATTGCAGGAATAGGTTGACTTTCTTTCATTTTGGTTATGGAAAGTGAAAGTTCTTTCGTTT
AGTACGAGATCGCTTCACACCTCGCGGTGCTTACACCTCTCGCCTATCGAAGTTCTGTTCAAAAA
CCTCGTCCGAGAACTTGTATAGAGAAGGATTTCCCGCGGCGCAGCAGTTCTTCCATACCAACTTA
GCTGCCCGGCGCTGCTATTGGCATAACAACCGGTACACCATAGGT
Found at i:127664 original size:18 final size:18
Alignment explanation
Indices: 127643--127685 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
127633 CAACCTTGTT
127643 GACTATGACAACAG-TCGC
1 GACTATGA-AACAGATCGC
127661 GACTAT-AAACAGACTCGC
1 GACTATGAAACAGA-TCGC
127679 GACTATG
1 GACTATG
127686 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 127143 -- 127642
TACCGTCTAGCCGTTGGTACTCCGCATCTTCACGGAGAATTCAATTTCACCGGGTCCATGTCGGA
GACAGCGGGGCAGTCGTTACACCATTCGTGCAGGTCGCTACTTATGCGACAAGGAATTTCGCTAC
CTTAGGACAGTTAGAGTTACTGCCGCCGTTTACCGGGGCTTCCATTCAAAGCTTATAACACTTCT
CCTTCCGACTTTCCAGCACCGGGCAGGTGTCAGACTCTATACATCGTGTTACCACTTAGCAGAGT
CCTGTGTTTTTAATAAACAGTCGCTACCCCCTGGTATGTGCCGCTTTCCTAATCAAAAGATAGGA
GAGCACCCCTTCTCCCGAAGTTACGGGGTCATTTTGCCGAGTTCCTTCGACATGGTTCTCTCAAG
CGCCCTAGTATACTCTACTTGTTCACCTGTGTCGGTTTGGGGTACGGTCAGTTCACCGGGAGGAT
CGCCCTCCCAATTCGAAGTTTTTTCCTGGAAGTTTCAACCTTGTT
Right flanking sequence: Indices 127686 -- 128185
GCAGGGCGGTACGCTCTGCTCTCTCGCGACCCCTACTCTAATCAAAAGACTAAAGGCCCCTACTG
AAGATTCAAAGGGCGAGCACTTAAATGAGAAAGGCTTGTAGACTCGTGACGCTGAACGAGACATT
CGAAAACTAAAGCGCACACTAGAAAGTGCTTCGAAAGGTGTCAGCAGGTGCGCGGAGCCGGAGCC
CGGCATGTTCGCCCGCTGGGCCGAGTGTTCGCCCACTTCAGAGTCTTCGCCTTTAGATAACAAAA
AGTGTCCGCCCCTTAGGTCGCCAAACTACGACGAGAGTTTCGCCTTTTGAAGCGCCAGTCGCGTA
GGGCGACCGGGCCAGGCCGAGTCAGAAAGGCTTTGATGACTCAAGGTTCATATTAGGGAAAGGAG
AGTGAGGGGAAGAGGGGGCAGCCCTCGGCCCGATCATCCAATTCGCTCCAACAGACAGGCATGGT
TCTGTAGTCAAAGCAACTTCGTCACTTTCGTGTACCCATCGGACG
Found at i:138664 original size:27 final size:27
Alignment explanation
Indices: 138626--138677 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
138616 ACTTGTCAAT
*
138626 AAACAATTCTATGTTCAATTTGACTAC
1 AAACAATTCTATGTTCAACTTGACTAC
*
138653 AAACAATTCTATGTTCCACTTGACT
1 AAACAATTCTATGTTCAACTTGACT
138678 CCTACCCATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.35, C:0.21, G:0.08, T:0.37
Consensus pattern (27 bp):
AAACAATTCTATGTTCAACTTGACTAC
Left flanking sequence: Indices 138126 -- 138625
AATGATCACTGGCCGGAACGATCTATGATAGCTATTAACTAGTGCCATGGAGTCAGTCAGTCTAA
ACTCTATAGCTCAACAGTCTAGTGCAGCTAATGTACGAAGGAAGCAAGAAGTCAGCTAAAAAGTA
TGAGAATCTCCACTGTTCAATCAACAACAACAGGGAGGGATGCCCCCGAGGGCATCCCGATCGAT
TCAATCAACAAAGCAAGTGTTGTGAGCCCACCGGCGAGTGAGGGCTAAACGGTATTTATAGATTG
AAACTAGAAAACCTTAATTCCTGAACTAGCCTCATGAACAAGCCAGTCTCAACTTTCCTGTTCAA
CTTTCTAGTGCGTCTATCTAAGGATAGATCTCGGTATCTGTGGAGAGGAAAAGAATGAATCCTAC
TAATGCGTCAAAATCTAAAAAACATTTATCTGTATTCCCCTTTCTTTATAGGTCTCGTGTTCCCC
CTATTGAACGAAATGCAAAAACCACATACCCACAAACTTGTCAAT
Right flanking sequence: Indices 138678 -- 139177
CCTACCCATACCGTGTTCAATTTGTATAGTTCCCATACCGTGTTCAATTGTACAACTACCAATTC
AATCTTGAGATTTAGTAAGAATAGCAGACGGTATACTAGTCAGGACTCTTCTTTTCTACGAACAA
GTCAGTACTCGCACTATTGGGAGAACATGCGTCAAAGAAGGTCGTTTTCTTTTCCGTCCTCGCAC
TATTGTACGAATTTATCCCTGTACCTAAAAAAGTCTTTATTTCACGCTGGAGCATTTGTAAGCGA
CGGGATCTTAGCAGCTTCTTCCCGAGTTGCATTAGCTAAAGTGGATCTACGATCACGGGAACTAA
TCAATCGGTCTGTTCTGCCCCATAAGCATCTGGATGGTCTACGATCAGTGCTATTCGTACACCCT
ATGCCTGATTTCGCAACTTCAACCCTTTCCCGCTGTAACTGCGCCTTATTGGCTTCTTTTCAGGC
TTGAACAAGCAAGTACGCAAACAGCCTTCGGTTCCTAACAAGCTA
Found at i:143663 original size:28 final size:28
Alignment explanation
Indices: 143623--143678 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
143613 ATCCATAGCT
143623 AAATGGTTCAACATTTGAAGTTCTTTCC
1 AAATGGTTCAACATTTGAAGTTCTTTCC
143651 AAATGGTTCAACATTTGAAGTTCTTTCC
1 AAATGGTTCAACATTTGAAGTTCTTTCC
143679 TTGGTCTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (28 bp):
AAATGGTTCAACATTTGAAGTTCTTTCC
Left flanking sequence: Indices 143123 -- 143622
CTTGAAAATGACATCTTCGTGAAATAGAGAAAGCCGCCCCGTCTCCAACTGAGGTCTTCTCGCCC
GCTGCCAGGAAGATTCGATCCCAACGACCGCCTCGCAAGACCTCTGTACTTTTTTCTTGCCTTTC
CTTATTTTCATTTCAGGAAATCCACTTCTTTACTAGAGAGAACTCGATTTGAAGCTTTCATTCCT
CTTCGGGTGGTTTGCTTTCTCTTTATTTAGCTATTGAGCAAAAAGAGTTCGCTACCTTTCTGCGT
CAATCTTGTTTTCGGGGGGTTCGTAAGCTGCAAGAAAGGAGAGAGAGGCAGGCTATCTCTTTTTT
GAAGTCAGTGCTTGTATTTGGTCGTCCAGTTCTTCCGGGAGGAAAGGGGCATTCTTCACTCCTTC
GCGACGCCTCTATGTACTACATAAGGGGCGGACTAAGGGCCCATTGGTTCTACCTTCTTTTCTTT
GTCGGCGACAAGGGATCTCTCAACCCCCGCTAAGCATCCATAGCT
Right flanking sequence: Indices 143679 -- 144178
TTGGTCTTCATTCAGTGAAAGGAGTGAAGCTTTCCGCAGCTGGAAAGCGGAGACCCACGAAGGCG
AGATGATCCCAAAGCGAGAATGAAGCTAGAGCCATTACTTGACCAAGAACGTGAGAGGATTGAAC
ACACCTTCCCCGGACCGGGTGGATACACTTTTTGACCCTTCCCAGGATTGAACTACGGGATCGAT
CTCTTATTTACCAAGATATGAAAGCCACGAGCCACTTTCTTTCGATGTGCTGTCATGATCACATT
CTCAGTTTCGTACGAGATTCCCAGTTTAGCTTACGGGGTCAAAGTCTTCTTTGGACTTTTCCAAT
TCTATTTCTTTTTCATCAATCGGGGCGAGAGGGAGCTGCTTCGAGGAGGCGACACCCACTAGTTT
TGTCCGGATCAAACTCTCCCCAAAGCAGGTAGGTGAGAAGGGCTCGGCTCCATGCAGGTCTTTCA
CCAACGGCTGGCACTGAATTAGCGCGATGCGAAAGAGTCCGGGCT
Found at i:156348 original size:15 final size:15
Alignment explanation
Indices: 156308--156354 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
156298 AGAAAGGTGA
156308 AAGAGCTACAGAA-G
1 AAGAGCTACAGAAGG
* *
156322 CAG-GCAACAGAAGG
1 AAGAGCTACAGAAGG
*
156336 AAGAGCTACAGAAGC
1 AAGAGCTACAGAAGG
156351 AAGA
1 AAGA
156355 CTAAGAACTA
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
13 8 0.31
14 5 0.19
15 13 0.50
ACGTcount: A:0.49, C:0.17, G:0.30, T:0.04
Consensus pattern (15 bp):
AAGAGCTACAGAAGG
Left flanking sequence: Indices 155808 -- 156307
CTATCCTTTATCTTTCTCCTATGATTCCCAATATCCGTGGGATTTCCTCTAAAGCCTTTCTCTTT
AGTGACTCAAACAAAGAACCTTAGCGGATGGATGAAAGAAGTAACTGAAAGCAAGGATAATATCT
TCTTTATCCCATCTAGGTATAGGGATAGATTGAATATTCCAGCGGTTGGTTGAAAAGATATACAA
TAATAAGAAGAGACTGATTGATATAGCATCTCACTAACTTAATCTCATGACTTTAGAATATCACT
TTGTGAAAGTGCTCTCGATATGCCACCAAGAAGCCATTAGTGCAAGCTGGTATTTAGCTCGCTCC
TTAGATAAGCTATAGCTCCCTCTTTCTCGGTCAACCAAAAACAATGTAAAATGTATTAAATACCT
ATTCTTTGTTCTAATCAGCAAGCGGTATACGACAGCTTCGATAGCATCCTCTCCTCTTTCTGCTC
CAAATCCCTAGTTTAGAATGCAACGAATGAAGCGAAGAAAGGTGA
Right flanking sequence: Indices 156355 -- 156854
CTAAGAACTAGCTCGGCTTAAGGATTAGCTAGCTAGGAGTCTTTCTGTATATTCGAGACTTTATC
CCTCGGTTCTAAGTGCAAGGCTTCCTTAGCTGCGGTAACCCTGCTATGCAGGAATTCTTACAGTT
ATCTCAAATCTAAGCTTGGAACGACGAACCGGGAACAAGCTTCCTTCGTTTTCGCTTACCTGCTT
AACCGTTAGTTGTTAAGGATTAGCAGCACCGTCTACTAGCTAGAGCTGTGAAACCTGAGAGAGCC
GGGTGGGAACTCAAGACTAAGGCAGTAAGAAAGAGCTAGGATTAGTAGTTTGAGTTGGTTAGGCG
GGATGGGATCGAAGAGACTGTACCGAGAACCGGCTAACTGCCATGAAAGCAGAGAGAGCTACTGA
GCAACGGAGGACAGAGCGAGAAAGATCTTGAACTCTTAAGCTTCATCCCTGTATGCATATTCCTA
TACCAAAAGCAAGATAAGCGATGAATATTTACTGGATATAAGATA
Found at i:171212 original size:24 final size:21
Alignment explanation
Indices: 171185--171228 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
171175 TATGAAAGCT
171185 TTCCTATTCAAGACCTACTACCAA
1 TTCCT-TTCAAG--CTACTACCAA
*
171209 TTCCTTTGAAGCTACTACCA
1 TTCCTTTCAAGCTACTACCA
171229 CTACCGAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 9 0.47
23 5 0.26
24 5 0.26
ACGTcount: A:0.30, C:0.32, G:0.07, T:0.32
Consensus pattern (21 bp):
TTCCTTTCAAGCTACTACCAA
Left flanking sequence: Indices 170685 -- 171184
CCATGATAGTCTAGATCCGGTTTAGCGCTTGATAGTTACACTTTTTTTTGTTGGCATCCGATGAC
GTCGACACGCTGGGCTGGGTGAAAAAAGATATTCCGAGAAAGTAGGTTTAATACAATAATATCGT
AGTATAAAGAGTGATGCATCAACAGGTCAGACAGACCGACCTTCCTCCTGCCCACTGGCCTTCTT
CTGGCTTACGAAACTTGCTAGTGAAACTATAGCTATCCGGGAATCCGCAACTAGAACTACAAAGC
AAAGGGATTACTTGTCCCCAACAAAAGGTGCAAAGCTTGGTTGGGCCAGTTCCTGCTTAAACTCC
AAACCCCATAGCCCTTCCTGTTATGGCACGCCCTCTATTGCCAGGACGAGACTGAAACTGCCATA
TGCACGGGCGAAGAAAAGCCTATATCTGGGTCTGCGTCAACAAGTTATGATTCCTTTACTGAAGA
ATTCAAGCTCTTCAACATGGGTTTAGTTCATACATTATGAAAGCT
Right flanking sequence: Indices 171229 -- 171728
CTACCGAAGCTTGCTTCTTTTGGTTACCGGTTGGGGGTTTGAAACCAGAGAAAGAAGATCCGGTT
GGGTATACCATCTCGATACAGAGTGAAATTAATTACCAGCTTTCATACCAAGGAGTCTTTTCCCG
TATAACTTCCTTACTCTTTCAGTATTCATACGCACCTGCATCCGCAGCTAATTCTTAAAAGTAGT
TGCTTAGTTATTTTATACGCACGAGGCTCGAGGTTGAGTTCTACACCGATCCCTTCACATTTGAA
TGAGCGGCTCTTTATGCTTTAGTAAGAAGGATTAGTCTCGCCCTGAGGCGTACCCCGCTTGAAGA
ATGCTCTTTGAGGGTTTTAAGAATAGCAATTATAGGGGAAACTAATTCATTGATGGAGCCGAAGC
CCTAGTTTCTTGATGATAGGAATTGCCGTTTTCTTCTTTCAATCCCACCGTATCTGCTGAGCCTA
TCGGAGTTGCCTATGTGAGGTTCCTTCCGATCTCTGGACTCTTTC
Found at i:242791 original size:19 final size:19
Alignment explanation
Indices: 242767--242807 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
242757 CGAAATGACT
242767 TCTTAAGTGAAGAGTAACC
1 TCTTAAGTGAAGAGTAACC
242786 TCTTAAGTGAAGAGTAACC
1 TCTTAAGTGAAGAGTAACC
242805 TCT
1 TCT
242808 AAATCCCTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (19 bp):
TCTTAAGTGAAGAGTAACC
Left flanking sequence: Indices 242267 -- 242766
AGTTAGACAGTCAAATCCGGTACTTGTATCGGGCGCACCTTCACCTTTAATTAAGTGAGTGGAGA
CATGTCTGCCCCTCTCGCTATCGGTGGATAAAACTGACGGTCTGATCTCTTCTCCGCCTCCTTAG
CCAACCAAGCAACTCGACGTTGTCGCCACCTGTAAGAAAGATAAGGCCAAAAACTGGACTAAACA
ACTCTGCTATCGCTCCCGGCGCGGGATCTTCCAAGTGAGCCTCATCTAGACTATGTTAATTATTT
CCGCTACTCCTTTTGAAAGACAAGAGTGCTCACCTTTCCTTTCTACTTTCATACCTCAACGAAAG
AACTAGGGCTCTTAGATCAACTACACCCAGGGGCGAGACAGGAAAGAGAGGAACTGCACCAACAA
CTAGATTCTAAAAGATGGAAGGTCGCTAAGCCTGATTACAGCACGAGTGAGGAATGAAGCTGATT
GCCCATTTCAAACCTCGGGCTAAACTGCTGACTGACGAAATGACT
Right flanking sequence: Indices 242808 -- 243307
AAATCCCTCCAACACCAGCTTATTCAACACGACTGGGGAGGAGCTACTGAACTCCTACTGGCTTA
ATGGCATTCCTACTGTCACTAACGGACTAGAAGCATGACTTCTTAGCTGGCTTACTACTTCCGGG
ACTATCGCACATGACAGGAGCTGGTTTGCTAGCTTATTATTGGACTGATTTCCGGGTACACAAGT
TCGGGCTTGCAATGGAGCTGGCTATACTTGTTATGAAATGGGGGAGGAGGGAACTAGGCCTACTA
AACTCTACCTCCACTACGGTATAGCTTCAACTGGATTCCCCACTATACACTACGAGAAGGGTATT
GGCCTTTCCCGAAACAAAGGCACTTGCTGGCATGAAAACTTCCGCTCGTACATACTTTTCTTTCC
GTTTCAACTTCAACCGCTATCTATAACATCTAAAAAGCTGCTAAAGCCCTACTCGCCTCAATTAC
ATCGAGCCTAGCTTTACGGGTCAAAACCAACCCCATTAGGGGCTA
Found at i:247658 original size:19 final size:20
Alignment explanation
Indices: 247634--247679 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 20
247624 CCTTTCTATT
247634 TATAATAG-A-AGAAGTCTAA
1 TATAATAGTATAGAAGTCT-A
247653 TATAATTAGTATAGAAGTCTA
1 TATAA-TAGTATAGAAGTCTA
247674 TATAAT
1 TATAAT
247680 TAGCCAAATC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 5 0.21
20 4 0.17
21 7 0.29
22 8 0.33
ACGTcount: A:0.48, C:0.04, G:0.13, T:0.35
Consensus pattern (20 bp):
TATAATAGTATAGAAGTCTA
Left flanking sequence: Indices 247134 -- 247633
TTCCTATCGATTTCCGATGGATAACAATCCATCTTTCTCGCTTTCGCTCTTTCTCCCAATCAGTC
GCGAGGGTTCCGGGCATGAGAACGCAAGTGCCGGAATCAAACAAAAGGTCCGAACGTCCGAGGAC
GAAAGAGAAAATGCTCCGCGGGGAAGTCGTTTCCATCTAGGATAGCGTATTCGTGCCGGTTAGAC
GTCGGCCATGAAATCCATCACTATACCGAGCAAATCATGGGCATTCACATCTCGGTCAAAGGGAA
CTGTGCGCGATTCTCTCGTGAATCGCCTTCAGCAAGGTATGGCATTCAGGGTCTTAACCCAGGGA
TAAATCTTTCTTCATAGATACAAGACATTCGTTGCTGATCTAAAAAAGATCTTCTCCCGTGGGCG
TTAGCGGACGTTTTTCATTTTTCACTCGGTCCTGACTTCCCAAAGCAAAGGTTTTTTTTAGGTTT
ACTTTGGAAAGGCGCTAAACAGGCCTATAGGTTCGCCTTTCTATT
Right flanking sequence: Indices 247680 -- 248179
TAGCCAAATCGTCTGAAGCATGAACAGAATCGCCTTTGTTCCGAAGGCCTAGCGAGTTAAGCGAG
TTCCTTTTTTCTTTTTTCAAAGGCAGTCCTTTTCTTTCCCCGGACCGATGACTCGCTTGTTCAGT
ACTGCTAACTCTTATTGGAGGATTCCGTCCCCTCGGGACTACCAGTAGCTTCGGTTGTTGAATCT
CGTGCAAGTTAGGTTGTGGTTGTATTGGCTGCAAGCGGAACGTAGGCGCTTTAGGTGTGTGTTGG
CCATGCACTCTCGCGTCGTGTAATGTCGTATGTATGATAGAGGTGGTGTGGTGATTGACCTCAAT
GCTAATGGTTATCCCCAAGGTTCAACGAATGAATGAAGCTATGCTATGATCGTACCCGGATAGAG
ATGATAGTCTTCCTCTGATGTATCCAAGCCGGCCATAATAGAATCGATAGGCGAAGCAGCCAATA
GCAGTCTGTTCTCGCCTATCGATAGATAGCAGGTTGCTTCCAAGC
Done.