Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009437.1 Kokia drynarioides strain JFW-HI SEQ_124144, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 49626
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:605 original size:2 final size:2
Alignment explanation
Indices: 600--625 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
590 AAAAAAAAAA
600 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
626 TAAATGTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1808 original size:30 final size:30
Alignment explanation
Indices: 1772--2204 Score: 442
Period size: 29 Copynumber: 14.7 Consensus size: 30
1762 TTTACCACTG
**
1772 AACTTCCAAAAATTCCATTTTTAACCTTGA
1 AACTTCCAAAAATTCCATTTTTAACCCCGA
*
1802 AACTTCCAAAAATTCCATTTTT-ACCCCCA
1 AACTTCCAAAAATTCCATTTTTAACCCCGA
*
1831 AACTTCCAAGAATTCCATTTTT-ACCCCGA
1 AACTTCCAAAAATTCCATTTTTAACCCCGA
* **
1860 AACTTCCAAAAATTCCAATTTT-ACCCTTA
1 AACTTCCAAAAATTCCATTTTTAACCCCGA
** *
1889 AACTTCCAAAAATTCCATTTTCGACCTCGA
1 AACTTCCAAAAATTCCATTTTTAACCCCGA
* * **
1919 AACTTCCAAAAATTCCATTTTTGATCCTAA
1 AACTTCCAAAAATTCCATTTTTAACCCCGA
*
1949 AACTTCCAAAAATTCCATTTTTATCCCCG-
1 AACTTCCAAAAATTCCATTTTTAACCCCGA
**
1978 AACTTCCAAAAATTCCATTTTCGACCCCGA
1 AACTTCCAAAAATTCCATTTTTAACCCCGA
* **
2008 AACTTCCAAAAAATCCATTTTT-ACCCTTA
1 AACTTCCAAAAATTCCATTTTTAACCCCGA
* *
2037 AACTTCCAAAAATTCCATTTTTGACCCCAA
1 AACTTCCAAAAATTCCATTTTTAACCCCGA
* * **
2067 AACTTCCAAAAATTCTATTTTTAGCCCTAA
1 AACTTCCAAAAATTCCATTTTTAACCCCGA
*
2097 AACTTCCAAAAATTCCATTTTT-TCCCTCG-
1 AACTTCCAAAAATTCCATTTTTAACCC-CGA
* * * *
2126 AACCTCC-AAAATTTCATTTTTGACCTCGA
1 AACTTCCAAAAATTCCATTTTTAACCCCGA
*
2155 AACTTTC-AAAATTACCATTTTGT--CCCCG-
1 AACTTCCAAAAATT-CCATTTT-TAACCCCGA
*
2183 AA-TGTCCAAAAACTCCATTTTT
1 AACT-TCCAAAAATTCCATTTTT
2205 CGACTTCAAA
Statistics
Matches: 341, Mismatches: 52, Indels: 23
0.82 0.12 0.06
Matches are distributed among these distances:
27 2 0.01
28 26 0.08
29 159 0.47
30 153 0.45
31 1 0.00
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (30 bp):
AACTTCCAAAAATTCCATTTTTAACCCCGA
Found at i:1835 original size:59 final size:59
Alignment explanation
Indices: 1753--2299 Score: 458
Period size: 59 Copynumber: 9.3 Consensus size: 59
1743 ACTATTCAAG
* * **
1753 AATTACATTTTTACCACTGAACTTCCAAAAATTCCATTTTTAACCTTGAAACTTCCAAA
1 AATTCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTAACCTTGAAACTTCCAAA
* **
1812 AATTCCATTTTTACCCCCAAACTTCCAAGAATTCCATTTTT-ACCCCGAAACTTCCAAA
1 AATTCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTAACCTTGAAACTTCCAAA
* ** ** *
1870 AATTCCAATTTTACCCTTAAACTTCCAAAAATTCCATTTTCGACCTCGAAACTTCCAAA
1 AATTCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTAACCTTGAAACTTCCAAA
* ** * **
1929 AATTCCATTTTTGATCCTAAAACTTCCAAAAATTCCATTTTTATCCCCG-AACTTCCAAA
1 AATTCCATTTTT-ACCCCCAAACTTCCAAAAATTCCATTTTTAACCTTGAAACTTCCAAA
* * * *
1988 AATTCCATTTTCGACCCCGAAACTTCCAAAAAATCCATTTTTACCCTT-AAACTTCCAAA
1 AATTCCATTTT-TACCCCCAAACTTCCAAAAATTCCATTTTTAACCTTGAAACTTCCAAA
* * * * *
2047 AATTCCATTTTTGACCCCAAAACTTCCAAAAATTCTATTTTTAGCCCTAAAACTTCCAAA
1 AATTCCATTTTT-ACCCCCAAACTTCCAAAAATTCCATTTTTAACCTTGAAACTTCCAAA
* * * * * * * *
2107 AATTCCATTTTTTCCCTCGAACCTCC-AAAATTTCATTTTTGACCTCGAAACTTTC-AA
1 AATTCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTAACCTTGAAACTTCCAAA
* * * *
2164 AATTACCATTTTGT--CCCCGAA-TGTCCAAAAACTCCATTTTTCGA-CTTCAAAAC-TCTC-AA
1 AATT-CCATTTT-TACCCCCAAACT-TCCAAAAATTCCATTTTT-AACCTT-GAAACTTC-CAAA
* * * * * *
2223 AATTACC-CTTTTACCCCTAAA-TGTCTAAAAATTCCATTTTTAACCCT-AAATTTTCCCAA
1 AATT-CCATTTTTACCCCCAAACT-TCCAAAAATTCCATTTTTAACCTTGAAA-CTTCCAAA
2282 AATTACCA-TTTTACCCCC
1 AATT-CCATTTTTACCCCC
2300 GGGTATCCAA
Statistics
Matches: 405, Mismatches: 63, Indels: 40
0.80 0.12 0.08
Matches are distributed among these distances:
57 19 0.05
58 99 0.24
59 234 0.58
60 53 0.13
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.34
Consensus pattern (59 bp):
AATTCCATTTTTACCCCCAAACTTCCAAAAATTCCATTTTTAACCTTGAAACTTCCAAA
Found at i:2254 original size:29 final size:30
Alignment explanation
Indices: 2221--2298 Score: 88
Period size: 29 Copynumber: 2.6 Consensus size: 30
2211 CAAAACTCTC
* *
2221 AAAATTACCCTTTTACCCCTAAA-TGTCTA
1 AAAATTACCATTTTACCCCTAAATTGTCCA
* * *
2250 AAAATT-CCATTTTTAACCCTAAATTTTCCC
1 AAAATTACCA-TTTTACCCCTAAATTGTCCA
2280 AAAATTACCATTTTACCCC
1 AAAATTACCATTTTACCCC
2299 CGGGTATCCA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
28 2 0.05
29 18 0.45
30 17 0.43
31 3 0.08
ACGTcount: A:0.35, C:0.28, G:0.01, T:0.36
Consensus pattern (30 bp):
AAAATTACCATTTTACCCCTAAATTGTCCA
Found at i:3775 original size:28 final size:29
Alignment explanation
Indices: 3711--3765 Score: 78
Period size: 27 Copynumber: 2.0 Consensus size: 29
3701 ATTCAAAAGT
*
3711 AATTTTTAAATAAATATTATTTTCACTTC
1 AATTCTTAAATAAATATTATTTTCACTTC
*
3740 AATTCTTAAA-AAAT-TTTTTTTCACTT
1 AATTCTTAAATAAATATTATTTTCACTT
3766 GAGTCTCTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 11 0.46
28 4 0.17
29 9 0.38
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.53
Consensus pattern (29 bp):
AATTCTTAAATAAATATTATTTTCACTTC
Found at i:5625 original size:59 final size:61
Alignment explanation
Indices: 5555--5671 Score: 157
Period size: 62 Copynumber: 1.9 Consensus size: 61
5545 TCACTTTAAT
* * * *
5555 ATTAAATTAATATAATACTTA-T-CAAGATAAATATTAGATTAAATTTAATATTAAAAATA
1 ATTAAATTAATAGAATACTTACTACAAAATAAACATTAAATTAAATTTAATATTAAAAATA
* *
5614 ATTAAATTAATAGAATATTTATCTACAAAATAAACATTAAATTTAATTTAATATTAAA
1 ATTAAATTAATAGAATACTTA-CTACAAAATAAACATTAAATTAAATTTAATATTAAA
5672 TAATCACTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
59 19 0.39
61 1 0.02
62 29 0.59
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (61 bp):
ATTAAATTAATAGAATACTTACTACAAAATAAACATTAAATTAAATTTAATATTAAAAATA
Found at i:5749 original size:17 final size:18
Alignment explanation
Indices: 5727--5762 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5717 TTAAATCAAA
*
5727 TTTTTATAA-ATGTTTAT
1 TTTTTAAAATATGTTTAT
5744 TTTTTAAAATATGTTTAT
1 TTTTTAAAATATGTTTAT
5762 T
1 T
5763 ATATTATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.64
Consensus pattern (18 bp):
TTTTTAAAATATGTTTAT
Found at i:6005 original size:23 final size:24
Alignment explanation
Indices: 5979--6023 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
5969 TATTGCCTCG
5979 ATTTT-AAAGTTTTTATGAAAAAA
1 ATTTTGAAAGTTTTTATGAAAAAA
* *
6002 ATTTTGAAATTTTTTTTGAAAA
1 ATTTTGAAAGTTTTTATGAAAA
6024 CAAACATGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (24 bp):
ATTTTGAAAGTTTTTATGAAAAAA
Found at i:6248 original size:29 final size:28
Alignment explanation
Indices: 6220--6619 Score: 136
Period size: 30 Copynumber: 13.6 Consensus size: 28
6210 GATACCCGAG
*
6220 GGGCAAAATGGTAATTTTGGATTTTCGA
1 GGGCAAAATGGTAATTTTGGAATTTCGA
*
6248 GGGCAAAATGGTAATTTTGGGAAAATTCGA
1 GGGCAAAATGGTAATTTT-GG-AATTTCGA
** * * * *
6278 GGTTAAAAAGGAAATTTTCAGAAATTCGA
1 GGGCAAAATGGTAATTTT-GGAATTTCGA
* * *
6307 GGGTAAAATGGTAATTTCGAGAGTTTCGA
1 GGGCAAAATGGTAATTTTG-GAATTTCGA
* *
6336 GGTTG-AAAATGG-AGTTTTTGGACTTTCGA
1 GG--GCAAAATGGTA-ATTTTGGAATTTCGA
*
6365 GGGCAAAATGGTAATTTTTGAAAGTTTC-A
1 GGGCAAAATGGTAA-TTTTGGAA-TTTCGA
* * ** *
6394 GGGTTAAAAATGGAAATTTTGGAGCTTCGG
1 GGG--CAAAATGGTAATTTTGGAATTTCGA
* *
6424 GGGTAAATATGG-AATTTATGGAAGTTTTGA
1 GGGCAAA-ATGGTAATTT-TGGAA-TTTCGA
** * *
6454 GGTTAGAAATGG-AGTTCTTGGAAGTTTTGA
1 GGGCA-AAATGGTAATT-TTGGAA-TTTCGA
** *
6484 GGTTAGAAATGG-AATTCTTGGAAGTTTTGA
1 GGGCA-AAATGGTAATT-TTGGAA-TTTCGA
* * * * *
6514 GGTCAAAAATAGAAATTTTAGAAGTTCGA
1 GGGC-AAAATGGTAATTTTGGAATTTCGA
* * *
6543 GGGTGAAAATGG-AATTTTTGAAAGTTT-TA
1 GGG-CAAAATGGTAA-TTTTGGAA-TTTCGA
*
6572 GGGTCAAAAATGG-AATTTTTGGAAGTTCGA
1 GGG-C-AAAATGGTAA-TTTTGGAATTTCGA
*
6602 GGGTAAAAATGG-AATTTT
1 GGG-CAAAATGGTAATTTT
6620 TAGAAGTTTG
Statistics
Matches: 295, Mismatches: 52, Indels: 50
0.74 0.13 0.13
Matches are distributed among these distances:
27 1 0.00
28 39 0.13
29 100 0.34
30 137 0.46
31 18 0.06
ACGTcount: A:0.34, C:0.05, G:0.28, T:0.33
Consensus pattern (28 bp):
GGGCAAAATGGTAATTTTGGAATTTCGA
Found at i:6416 original size:59 final size:57
Alignment explanation
Indices: 6224--6653 Score: 328
Period size: 59 Copynumber: 7.3 Consensus size: 57
6214 CCCGAGGGGC
* * * * * *
6224 AAAATGGTAATTTTGGATTTTCGAGGGCAAAATGGTAATTTTGGGAAAATTCGAGGTTA
1 AAAATGGAAATTTTGGAATTTCGAGGGTAAAATGG-AATTTT-TGAAAGTTTGAGGTTA
* * * * *
6283 AAAA-GGAAATTTTCAGAAATTCGAGGGTAAAATGGTAA-TTTCGAGAGTTTCGAGGTTG
1 AAAATGGAAATTTT-GGAATTTCGAGGGTAAAATGG-AATTTTTGAAAGTTT-GAGGTTA
** * * *
6341 AAAATGGAGTTTTTGGACTTTCGAGGGCAAAATGGTAATTTTTGAAAGTTTCAGGGTTA
1 AAAATGGAAATTTTGGAATTTCGAGGGTAAAATGG-AATTTTTGAAAGTTTGA-GGTTA
** * * *
6400 AAAATGGAAATTTTGGAGCTTCGGGGGTAAATATGGAATTTATGGAAGTTTTGAGGTTA
1 AAAATGGAAATTTTGGAATTTCGAGGGTAAA-ATGGAATTTTTGAAAG-TTTGAGGTTA
* * * * * * *
6459 GAAATGG-AGTTCTTGGAAGTTTTGAGGTTAGAAATGGAATTCTTGGAAGTTTTGAGGTCA
1 AAAATGGAAATT-TTGGAA-TTTCGAGGGTA-AAATGGAATTTTTGAAAG-TTTGAGGTTA
* * * * *
6519 AAAATAGAAATTTTAGAAGTTCGAGGGTGAAAATGGAATTTTTGAAAGTTTTAGGGTCA
1 AAAATGGAAATTTTGGAATTTCGAGGGT-AAAATGGAATTTTTGAAAGTTTGA-GGTTA
* * * *
6578 AAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTT-AGAAGTTTGGGGGTA
1 AAAATGGAAATTTTGGAATTTCGAGGGT-AAAATGGAATTTTTGA-AAGTTTGAGGTTA
**
6636 AAAATGGATTTTTTGGAA
1 AAAATGGAAATTTTGGAA
6654 GGTTTAAGGA
Statistics
Matches: 299, Mismatches: 58, Indels: 29
0.77 0.15 0.08
Matches are distributed among these distances:
57 5 0.02
58 70 0.23
59 169 0.57
60 50 0.17
61 5 0.02
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.33
Consensus pattern (57 bp):
AAAATGGAAATTTTGGAATTTCGAGGGTAAAATGGAATTTTTGAAAGTTTGAGGTTA
Found at i:6466 original size:30 final size:30
Alignment explanation
Indices: 6328--6654 Score: 247
Period size: 30 Copynumber: 11.1 Consensus size: 30
6318 TAATTTCGAG
* * *
6328 AGTTTCGAGGTTGAAAATGGAGTTTTTGG-
1 AGTTTTGAGGTTAAAAATGGAATTTTTGGA
* * ** *
6357 ACTTTCGAGG-GCAAAATGGTAATTTTTGAA
1 AGTTTTGAGGTTAAAAATGG-AATTTTTGGA
* *
6387 AG-TTTCAGGGTTAAAAATGGAAATTTTGG-
1 AGTTTTGA-GGTTAAAAATGGAATTTTTGGA
* * * * * *
6416 AGCTTCGGGGGTAAATATGGAATTTATGGA
1 AGTTTTGAGGTTAAAAATGGAATTTTTGGA
* * *
6446 AGTTTTGAGGTTAGAAATGGAGTTCTTGGA
1 AGTTTTGAGGTTAAAAATGGAATTTTTGGA
* *
6476 AGTTTTGAGGTTAGAAATGGAATTCTTGGA
1 AGTTTTGAGGTTAAAAATGGAATTTTTGGA
* * * *
6506 AGTTTTGAGGTCAAAAATAGAAATTTTAGA
1 AGTTTTGAGGTTAAAAATGGAATTTTTGGA
* * * *
6536 AG-TTCGAGGGTGAAAATGGAATTTTTGAA
1 AGTTTTGAGGTTAAAAATGGAATTTTTGGA
*
6565 AGTTTT-AGGGTCAAAAATGGAATTTTTGGA
1 AGTTTTGA-GGTTAAAAATGGAATTTTTGGA
* * *
6595 AG-TTCGAGGGTAAAAATGGAATTTTTAGA
1 AGTTTTGAGGTTAAAAATGGAATTTTTGGA
* * *
6624 AG-TTTGGGGGTAAAAATGGATTTTTTGGA
1 AGTTTTGAGGTTAAAAATGGAATTTTTGGA
6653 AG
1 AG
6655 GTTTAAGGAC
Statistics
Matches: 233, Mismatches: 56, Indels: 18
0.76 0.18 0.06
Matches are distributed among these distances:
28 7 0.03
29 108 0.46
30 111 0.48
31 7 0.03
ACGTcount: A:0.32, C:0.04, G:0.29, T:0.34
Consensus pattern (30 bp):
AGTTTTGAGGTTAAAAATGGAATTTTTGGA
Found at i:6620 original size:29 final size:29
Alignment explanation
Indices: 6224--6654 Score: 270
Period size: 29 Copynumber: 14.7 Consensus size: 29
6214 CCCGAGGGGC
** *
6224 AAAATGGTAA-TTTTGGATTTTCGAGGG-C
1 AAAATGG-AATTTTTGGAAGTTCGAGGGTA
* * *
6252 AAAATGGTAATTTTGGGAAAATTCGAGGTTA
1 AAAATGG-AATTTTTGG-AAGTTCGAGGGTA
** *
6283 AAAA-GGAAATTTTCAGAAATTCGAGGGT-
1 AAAATGG-AATTTTTGGAAGTTCGAGGGTA
* * *
6311 AAAATGGTAA--TTTCGAGAGTTTCGAGGTTG
1 AAAATGG-AATTTTTGGA-AG-TTCGAGGGTA
* ** *
6341 AAAATGGAGTTTTTGGACTTTCGAGGG-C
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
*
6369 AAAATGGTAATTTTTGAAAGTTTC-AGGGTTA
1 AAAATGG-AATTTTTGGAAG-TTCGAGGG-TA
* *
6400 AAAATGGAAATTTTGG-AGCTTCGGGGGTA
1 AAAATGGAATTTTTGGAAG-TTCGAGGGTA
* * * *
6429 AATATGGAATTTATGGAAGTTTTGAGGTTA
1 AAAATGGAATTTTTGGAAG-TTCGAGGGTA
* * * * *
6459 GAAATGGAGTTCTTGGAAGTTTTGAGGTTA
1 AAAATGGAATTTTTGGAAG-TTCGAGGGTA
* * *
6489 GAAATGGAATTCTTGGAAGTTTTGA-GGTCA
1 AAAATGGAATTTTTGGAAG-TTCGAGGGT-A
* * * *
6519 AAAATAGAAATTTTAGAAGTTCGAGGGTG
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
* **
6548 AAAATGGAATTTTTGAAAGTTTTAGGGTCA
1 AAAATGGAATTTTTGGAAGTTCGAGGGT-A
6578 AAAATGGAATTTTTGGAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
* * *
6607 AAAATGGAATTTTTAGAAGTTTGGGGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
*
6636 AAAATGGATTTTTTGGAAG
1 AAAATGGAATTTTTGGAAG
6655 GTTTAAGGAC
Statistics
Matches: 320, Mismatches: 65, Indels: 35
0.76 0.15 0.08
Matches are distributed among these distances:
27 4 0.01
28 22 0.07
29 140 0.44
30 138 0.43
31 16 0.05
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.33
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTCGAGGGTA
Found at i:8539 original size:17 final size:17
Alignment explanation
Indices: 8513--8559 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
8503 ACATTAATTT
*
8513 AAATAGATTTAAACTTA
1 AAATAAATTTAAACTTA
**
8530 AAATAAATTTAATTTTA
1 AAATAAATTTAAACTTA
8547 AAATAAATTTAAA
1 AAATAAATTTAAA
8560 TTCTCTTGGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (17 bp):
AAATAAATTTAAACTTA
Found at i:9632 original size:194 final size:197
Alignment explanation
Indices: 9301--9887 Score: 739
Period size: 194 Copynumber: 2.9 Consensus size: 197
9291 TAATTTGGTC
* * ** * *
9301 TACTTCTCAGTATCTCCTTGGGAAGATGATCGCCCCGTTTGTTTCAATCTGCTTCTCTGTACCTC
1 TACTTCTCTGTATCTCATCAGGAAGATGATCGCCTCATTTGTTTCAATCTGCTTCTCTGTACCTC
* * *
9366 ATCAAGAAGACGAATTTGGTTCACTTCTCAGTGTCTCATCAGGAAGCTAACCTTTTTATTGCTTC
66 ATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTTATTGCTTC
* * * * * * * *
9431 ACCCTGCTTCTCAATATCTTATCAGGAAGCTGGGGTTCAAAGACTTGCTCGCTTTGA-GT-T-GA
131 GCCCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCAAAGATTTGCTCACATCGACGTGTCGA
9493 TA
196 TA
* * *
9495 TACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATCTGCTTCTCTTTACCTC
1 TACTTCTCTGTATCTCATCAGGAAGATGATCGCCTCATTTGTTTCAATCTGCTTCTCTGTACCTC
* *
9560 ATCAGGAAGACGAATTTGGTCCACTTCTTAGTATCTCATCAGGAAGCTAACCTTTTTATTGCTTT
66 ATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTTATTGCTTC
* ** *
9625 GCCCTGCTTCTCAGTGTCTCATCAGGAAGCTAGGGTTTGAAGATTTACTCACATCGAGCGTGGAC
131 GCCCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCAAAGATTTGCTCACATCGA-CGT-G--
*
9690 TCGATT
192 TCGATA
* * * * * *
9696 TGGTCTTCTTCTCAGTATCTCATCAGGGAGATGATCGCATCATTTGTTTCAATTTGCTTTTCCGT
1 T--ACTTC-TCT--GTATCTCATCAGGAAGATGATCGCCTCATTTGTTTCAATCTGCTTCTCTGT
* * *
9761 ATCTCATCAGGAATATGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTTATT
61 ACCTCATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTTATT
*
9826 GCTTCGCCCTGCTTCTCAGTGTCTCATCAAGAAGCTGGGGTTCAAAGATTTGCTCACATCGA
126 GCTTCGCCCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCAAAGATTTGCTCACATCGA
9888 GCATGGGTTT
Statistics
Matches: 335, Mismatches: 46, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
194 161 0.48
196 2 0.01
200 1 0.00
201 4 0.01
203 4 0.01
204 3 0.01
206 160 0.48
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (197 bp):
TACTTCTCTGTATCTCATCAGGAAGATGATCGCCTCATTTGTTTCAATCTGCTTCTCTGTACCTC
ATCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTTATTGCTTC
GCCCTGCTTCTCAGTGTCTCATCAGGAAGCTGGGGTTCAAAGATTTGCTCACATCGACGTGTCGA
TA
Found at i:9876 original size:206 final size:206
Alignment explanation
Indices: 9497--9935 Score: 644
Period size: 206 Copynumber: 2.1 Consensus size: 206
9487 AGTTGATATA
* * * *
9497 CTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATCTGCTTCTCTTTACCTCAT
1 CTTCTCAGTATCTCATCAGGAAGATGATCGCATCACTTGTTTCAATCTGCTTCTCTGTACCTCAT
* *
9562 CAGGAAGACGAATTTGGTCCACTTCTTAGTATCTCATCAGGAAGCTAACCTTTTTATTGCTTTGC
66 CAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTTATTGCTTCGC
* * ** * *
9627 CCTGCTTCTCAGTGTCTCATCAGGAAGCTAGGGTTTGAAGATTTACTCACATCGAGCGTGGACTC
131 CCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCAAAGATTTGCTCACATCGAGCGTGGGCTC
9692 GATTTGGTCTT
196 GATTTGGTCTT
* * * * * *
9703 CTTCTCAGTATCTCATCAGGGAGATGATCGCATCATTTGTTTCAATTTGCTTTTCCGTATCTCAT
1 CTTCTCAGTATCTCATCAGGAAGATGATCGCATCACTTGTTTCAATCTGCTTCTCTGTACCTCAT
* *
9768 CAGGAATATGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTTATTGCTTCGC
66 CAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTTATTGCTTCGC
* * * * *
9833 CCTGCTTCTCAGTGTCTCATCAAGAAGCTGGGGTTCAAAGATTTGCTCACATCGAGCATGGGTTT
131 CCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCAAAGATTTGCTCACATCGAGCGTGGGCTC
9898 GATTTGGTCTT
196 GATTTGGTCTT
*
9909 CTTCTCAGTATCTCATCAGAAAGATGA
1 CTTCTCAGTATCTCATCAGGAAGATGA
9936 CCGCGTCGTT
Statistics
Matches: 208, Mismatches: 25, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
206 208 1.00
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.36
Consensus pattern (206 bp):
CTTCTCAGTATCTCATCAGGAAGATGATCGCATCACTTGTTTCAATCTGCTTCTCTGTACCTCAT
CAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTTATTGCTTCGC
CCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCAAAGATTTGCTCACATCGAGCGTGGGCTC
GATTTGGTCTT
Found at i:10792 original size:46 final size:46
Alignment explanation
Indices: 10703--10792 Score: 121
Period size: 46 Copynumber: 2.0 Consensus size: 46
10693 CTTGGTTCCA
* * *
10703 AGACGCCCTTTGCGGGTTTTCATCCTGAACCCTTTTTTTTTTTTCG
1 AGACGCCCTTTGCGGGTTTTCATCCTCAACCCTCTTTTGTTTTTCG
10749 AGACGCCCTTTGCGGGTTTTCAT-CTCAATTCCC-CTTTTGTTTTT
1 AGACGCCCTTTGCGGGTTTTCATCCTCAA--CCCTCTTTTGTTTTT
10793 AGGTGAAGTA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
45 4 0.10
46 32 0.82
47 3 0.08
ACGTcount: A:0.11, C:0.27, G:0.17, T:0.46
Consensus pattern (46 bp):
AGACGCCCTTTGCGGGTTTTCATCCTCAACCCTCTTTTGTTTTTCG
Found at i:21828 original size:29 final size:28
Alignment explanation
Indices: 21789--22010 Score: 257
Period size: 29 Copynumber: 7.7 Consensus size: 28
21779 TTTGGAGTCA
*
21789 AAAATGGAATTTTTGGAAGTTTCGTGGTC
1 AAAATGGAATTTTTGGAAG-TTCGGGGTC
*
21818 AAAATGGAATTTTTGGAAGTTCAGGGGTG
1 AAAATGGAATTTTTGGAAGTTC-GGGGTC
**
21847 AAAATGGAATTTTTGGAAGTTTTAGGGTC
1 AAAATGGAATTTTTGGAAG-TTCGGGGTC
*
21876 AAAATGGAATTTTTGGAAATTCGGGGAT-
1 AAAATGGAATTTTTGGAAGTTCGGGG-TC
*
21904 AAAATGGAATTTTTGGAAGTTTCGAGGTC
1 AAAATGGAATTTTTGGAAG-TTCGGGGTC
* * *
21933 AAAAATGGAATTTTTGGGAGTTCAAGGGTA
1 -AAAATGGAATTTTTGGAAGTTC-GGGGTC
* *
21963 AAAATGGAATTTTTTGAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTCG-GGGTC
*
21992 AAAATGGAATTTTTTGAAG
1 AAAATGGAATTTTTGGAAG
22011 GTTTAGGGAC
Statistics
Matches: 168, Mismatches: 17, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
28 27 0.16
29 118 0.70
30 23 0.14
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.34
Consensus pattern (28 bp):
AAAATGGAATTTTTGGAAGTTCGGGGTC
Found at i:23277 original size:17 final size:17
Alignment explanation
Indices: 23252--23331 Score: 106
Period size: 17 Copynumber: 4.7 Consensus size: 17
23242 TAAATAGATT
* *
23252 TAAACTTAAATTTATAA
1 TAAATTTAAATTTAAAA
* *
23269 TAAATTTAAATTTTAAG
1 TAAATTTAAATTTAAAA
*
23286 TAAATTTAAACTTAAAA
1 TAAATTTAAATTTAAAA
*
23303 TAAATTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
23320 TAAATTTAAATT
1 TAAATTTAAATT
23332 ATGTTGGGCC
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 53 1.00
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:23278 original size:6 final size:6
Alignment explanation
Indices: 23249--23331 Score: 59
Period size: 6 Copynumber: 14.5 Consensus size: 6
23239 ATTTAAATAG
* * *
23249 ATTTAA ACTTAA ATTTATA A--TAA ATTTAA ATTTTA A-GTAA ATTTAA
1 ATTTAA ATTTAA ATTTA-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* * * *
23295 ACTTAA A-ATAA ATTTAA TTTTAA A-ATAA ATTTAA ATT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATT
23332 ATGTTGGGCC
Statistics
Matches: 58, Mismatches: 13, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
4 2 0.03
5 13 0.22
6 41 0.71
7 2 0.03
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (6 bp):
ATTTAA
Found at i:23318 original size:12 final size:12
Alignment explanation
Indices: 23249--23331 Score: 59
Period size: 11 Copynumber: 7.2 Consensus size: 12
23239 ATTTAAATAG
*
23249 ATTTAAACTTAA
1 ATTTAAATTTAA
23261 ATTTATAA--TAA
1 ATTTA-AATTTAA
*
23272 ATTTAAATTTTA
1 ATTTAAATTTAA
*
23284 A-GTAAATTTAA
1 ATTTAAATTTAA
* *
23295 ACTTAAA-ATAA
1 ATTTAAATTTAA
*
23306 ATTTAATTTTAA
1 ATTTAAATTTAA
*
23318 A-ATAAATTTAA
1 ATTTAAATTTAA
23329 ATT
1 ATT
23332 ATGTTGGGCC
Statistics
Matches: 54, Mismatches: 11, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
10 2 0.04
11 34 0.63
12 16 0.30
13 2 0.04
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (12 bp):
ATTTAAATTTAA
Found at i:25830 original size:3 final size:3
Alignment explanation
Indices: 25822--25856 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
25812 CTTTTCTCCC
25822 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
25857 AAGTTGAGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:34593 original size:28 final size:32
Alignment explanation
Indices: 34519--34579 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
34509 CTTTCAATGT
*
34519 TAGATTACTTTGAATCTTACTTAATCTTTATC
1 TAGATTACTTTGAATCTTACTTAATCTCTATC
34551 TAGATTACTTTGAATCTTACTTAATCTCT
1 TAGATTACTTTGAATCTTACTTAATCTCT
34580 GTTTATTCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.28, C:0.16, G:0.07, T:0.49
Consensus pattern (32 bp):
TAGATTACTTTGAATCTTACTTAATCTCTATC
Found at i:39602 original size:84 final size:84
Alignment explanation
Indices: 39461--39624 Score: 258
Period size: 84 Copynumber: 2.0 Consensus size: 84
39451 CATCTAGCCG
* *
39461 AAGGTTATCAAATATTCCTCCAAGGTTTATGAAGCTTAGAATTCGCACTTAATTCTTCTCACCCG
1 AAGGTTATCAAATATTCCTCCAAGGTTCATGAAGCTTAGAATTCGCACTTAATTCTTCTCACCCA
*
39526 AGTATTCATTAATTCCTCC
66 AGTATTCATCAATTCCTCC
* * *
39545 AAGGTTATCAAATATTCCTTCAAGGTTCATGAGGCTTAGAA-TCTGCGCTTAATTCTTCTCACCC
1 AAGGTTATCAAATATTCCTCCAAGGTTCATGAAGCTTAGAATTC-GCACTTAATTCTTCTCACCC
39609 AAGTATTCATCAATTC
65 AAGTATTCATCAATTC
39625 TCTGAATTAC
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
83 2 0.03
84 71 0.97
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.35
Consensus pattern (84 bp):
AAGGTTATCAAATATTCCTCCAAGGTTCATGAAGCTTAGAATTCGCACTTAATTCTTCTCACCCA
AGTATTCATCAATTCCTCC
Found at i:39939 original size:16 final size:16
Alignment explanation
Indices: 39918--39952 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
39908 CTATTTTCTA
*
39918 TTTCTTTTAATTTTGT
1 TTTCTTTTAATTTTAT
*
39934 TTTCTTTTATTTTTAT
1 TTTCTTTTAATTTTAT
39950 TTT
1 TTT
39953 GTTCCAGATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.11, C:0.06, G:0.03, T:0.80
Consensus pattern (16 bp):
TTTCTTTTAATTTTAT
Found at i:39951 original size:21 final size:22
Alignment explanation
Indices: 39911--39955 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
39901 TCCACTCCTA
*
39911 TTTTCTATTTCTTTTAATTTTG
1 TTTTCTATTTATTTTAATTTTG
*
39933 TTTTCT-TTTATTTTTATTTTG
1 TTTTCTATTTATTTTAATTTTG
39954 TT
1 TT
39956 CCAGATCACG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.11, C:0.07, G:0.04, T:0.78
Consensus pattern (22 bp):
TTTTCTATTTATTTTAATTTTG
Found at i:41495 original size:21 final size:21
Alignment explanation
Indices: 41471--41512 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
41461 GAATTTCAGC
*
41471 AGCAATCTATAGATTTTCAAA
1 AGCAAACTATAGATTTTCAAA
*
41492 AGCAAACTGTAGATTTTCAAA
1 AGCAAACTATAGATTTTCAAA
41513 GGAAAATTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.31
Consensus pattern (21 bp):
AGCAAACTATAGATTTTCAAA
Found at i:42714 original size:13 final size:13
Alignment explanation
Indices: 42693--42730 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
42683 AACCCAAATT
42693 TTTATTTTTATTT-
1 TTTA-TTTTATTTA
42706 TTCTATTTTATTTA
1 TT-TATTTTATTTA
42720 TTTATTTTATT
1 TTTATTTTATT
42731 ATATGTCCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 19 0.83
14 4 0.17
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTATTTTATTTA
Found at i:43629 original size:99 final size:102
Alignment explanation
Indices: 43466--43649 Score: 218
Period size: 99 Copynumber: 1.8 Consensus size: 102
43456 GTGTGTTAGA
* * * * *
43466 CTGAGTAACCGGGGTAGAGTGCTTAGTTTTCATTTCATTTCGTGTCAAAAGGGCTACCACATTC-
1 CTGAGTAACCGAGATAGAGTGCTTAGGTGTCATTTCATTTCGCGTCAAAAGGGCTACCACATTCT
43530 T-AA-AAAAAAAGAAAAAAATTTGAGAGCATGTTGGG
66 TAAAGAAAAAAAGAAAAAAATTTGAGAGCATGTTGGG
* * *
43565 CTGAGTAATCGAGATAGAGTGCTTGGGTGTCATTTCATTTCGCGTCAAAA-GG-T-CCGATGTAT
1 CTGAGTAACCGAGATAGAGTGCTTAGGTGTCATTTCATTTCGCGTCAAAAGGGCTACC-A--CAT
43627 TCTTAAAGGAAAAAAAGAAAAAA
63 TCTTAAA-GAAAAAAAGAAAAAA
43650 TTGACAAGAT
Statistics
Matches: 70, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
96 2 0.03
97 2 0.03
98 2 0.03
99 47 0.67
100 1 0.01
101 2 0.03
103 14 0.20
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (102 bp):
CTGAGTAACCGAGATAGAGTGCTTAGGTGTCATTTCATTTCGCGTCAAAAGGGCTACCACATTCT
TAAAGAAAAAAAGAAAAAAATTTGAGAGCATGTTGGG
Found at i:44997 original size:16 final size:16
Alignment explanation
Indices: 44976--45019 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
44966 TTCGACACTC
44976 TTAATTTTTATTTCTT
1 TTAATTTTTATTTCTT
*
44992 TTAA-TTCTACTTTCTT
1 TTAATTTTTA-TTTCTT
45008 TT-ATTTTTATTT
1 TTAATTTTTATTT
45020 TTCCCTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
15 8 0.33
16 16 0.67
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (16 bp):
TTAATTTTTATTTCTT
Done.