Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015022.1 Kokia drynarioides strain JFW-HI SEQ_130066, 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: 42874
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Warning! 517 characters in sequence are not A, C, G, or T
Found at i:1330 original size:139 final size:139
Alignment explanation
Indices: 1166--1428 Score: 472
Period size: 139 Copynumber: 1.9 Consensus size: 139
1156 CTTTTTCTGT
*
1166 TTTTATTTTGCAAAACACTCTTACTTAGATTCACCTTTCTCATCAACAACACAATGGAGCAAACA
1 TTTTATTTTACAAAACACTCTTACTTAGATTCACCTTTCTCATCAACAACACAATGGAGCAAACA
*
1231 AAGTGCTGCTGACGCACTCAGTAATTCCAAGCAGTGGAGTTGCAATTTTTTCTTCTTTTTCTGTT
66 AAGTGCTGCTGACGCACTCAGTAATTCCAAGCAGTGGAGTGGCAATTTTTTCTTCTTTTTCTGTT
1296 TTTCTTTTA
131 TTTCTTTTA
* * *
1305 TTTTCTTTTACAAAACACTCTTACTTAGATTCATCTTTCTCATCAACAACACGATGGAGCAAACA
1 TTTTATTTTACAAAACACTCTTACTTAGATTCACCTTTCTCATCAACAACACAATGGAGCAAACA
*
1370 AAGTGCTGCTGACGTACTCAGTAATTCCAAGCAGTGGAGTGGCAATTTTTTCTTCTTTT
66 AAGTGCTGCTGACGCACTCAGTAATTCCAAGCAGTGGAGTGGCAATTTTTTCTTCTTTT
1429 ATTTGTATTT
Statistics
Matches: 118, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
139 118 1.00
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (139 bp):
TTTTATTTTACAAAACACTCTTACTTAGATTCACCTTTCTCATCAACAACACAATGGAGCAAACA
AAGTGCTGCTGACGCACTCAGTAATTCCAAGCAGTGGAGTGGCAATTTTTTCTTCTTTTTCTGTT
TTTCTTTTA
Found at i:3670 original size:22 final size:22
Alignment explanation
Indices: 3645--3688 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3635 TAGTAGCAAC
*
3645 ATAACAGCGAAATGACAACAAA
1 ATAACAGCAAAATGACAACAAA
*
3667 ATAACATCAAAATGACAACAAA
1 ATAACAGCAAAATGACAACAAA
3689 CAATAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.61, C:0.18, G:0.09, T:0.11
Consensus pattern (22 bp):
ATAACAGCAAAATGACAACAAA
Found at i:3688 original size:11 final size:11
Alignment explanation
Indices: 3654--3688 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
3644 CATAACAGCG
3654 AAATGACAACA
1 AAATGACAACA
* *
3665 AAATAACATCA
1 AAATGACAACA
3676 AAATGACAACA
1 AAATGACAACA
3687 AA
1 AA
3689 CAATAATAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.66, C:0.17, G:0.06, T:0.11
Consensus pattern (11 bp):
AAATGACAACA
Found at i:5176 original size:16 final size:16
Alignment explanation
Indices: 5152--5184 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5142 TTATAACGTG
5152 ACATAATTATATTCATT
1 ACATAATTATATT-ATT
5169 ACAT-ATTATATTATT
1 ACATAATTATATTATT
5184 A
1 A
5185 AAAATAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 8 0.50
17 4 0.25
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (16 bp):
ACATAATTATATTATT
Found at i:7344 original size:14 final size:14
Alignment explanation
Indices: 7325--7363 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
7315 CTTCAGATCC
7325 CACGTACTTCAAAG
1 CACGTACTTCAAAG
7339 CACGTACTTCAAAG
1 CACGTACTTCAAAG
*
7353 CAAGTACTTCA
1 CACGTACTTCA
7364 TTCTCTGATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (14 bp):
CACGTACTTCAAAG
Found at i:10949 original size:58 final size:55
Alignment explanation
Indices: 10826--10983 Score: 156
Period size: 58 Copynumber: 2.7 Consensus size: 55
10816 TACTAAATCA
* * * * *
10826 TGAACTTGACATTTTTTACTAATTTGATATCCAAATTTTTTTTTGTCCAATTTGGTAT
1 TGAACTTGACATTTTTT-TTAATTTGGTA-CCTAA-TTTTTTTTGTCCAATTTGATAC
* * *
10884 TCAAACTTGACATTTTTTTGTAAGTTGGTACTTAAGTTTTTTTTGTCCAATTTGATAAC
1 T-GAACTTGACATTTTTTT-TAATTTGGTACCTAA-TTTTTTTTGTCCAATTTGAT-AC
10943 TGAACTTGAC-TCTTTTTCTTAATTTGGTACCTAATTTTTTT
1 TGAACTTGACAT-TTTTT-TTAATTTGGTACCTAATTTTTTT
10984 ATATATTAAT
Statistics
Matches: 83, Mismatches: 12, Indels: 11
0.78 0.11 0.10
Matches are distributed among these distances:
57 8 0.10
58 49 0.59
59 26 0.31
ACGTcount: A:0.24, C:0.13, G:0.11, T:0.52
Consensus pattern (55 bp):
TGAACTTGACATTTTTTTTAATTTGGTACCTAATTTTTTTTGTCCAATTTGATAC
Found at i:11225 original size:60 final size:60
Alignment explanation
Indices: 11143--11316 Score: 226
Period size: 60 Copynumber: 2.9 Consensus size: 60
11133 TTAAATCTAA
* * * * *
11143 AAAAAAAAGCTTAGGTACAAAATTAAGAAAAAATATCAAATTCAAGTACCAAATTGGGTC
1 AAAAAAAAGTTTAGGTACAAAATTAAGAAAAAGTGTCAAGTTCAAGTATCAAATTGGGTC
** *
11203 CCAAAAAAGTTTAGGTACAAAATTAGGAAAAAGTGTCAAGTTC-AGATATCAAATTGGGTC
1 AAAAAAAAGTTTAGGTACAAAATTAAGAAAAAGTGTCAAGTTCAAG-TATCAAATTGGGTC
* *
11263 AAAAAAAATTTTAAGTATC-AAATTAAGAAAAAGTGTCAAGTTCAAGTATCAAAT
1 AAAAAAAAGTTTAGGTA-CAAAATTAAGAAAAAGTGTCAAGTTCAAGTATCAAAT
11317 GTTATATTAA
Statistics
Matches: 98, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
59 2 0.02
60 93 0.95
61 3 0.03
ACGTcount: A:0.50, C:0.10, G:0.15, T:0.25
Consensus pattern (60 bp):
AAAAAAAAGTTTAGGTACAAAATTAAGAAAAAGTGTCAAGTTCAAGTATCAAATTGGGTC
Found at i:14693 original size:13 final size:14
Alignment explanation
Indices: 14677--14731 Score: 67
Period size: 14 Copynumber: 4.0 Consensus size: 14
14667 CTCGAAAAAA
*
14677 AGTCAATGGTCAA-
1 AGTCAACGGTCAAC
*
14690 AGTCAACGATCAAC
1 AGTCAACGGTCAAC
*
14704 ATTCAACGGTCAAC
1 AGTCAACGGTCAAC
*
14718 AGTCAACGATCAAC
1 AGTCAACGGTCAAC
14732 GGGTCAGTCA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
13 11 0.31
14 24 0.69
ACGTcount: A:0.40, C:0.25, G:0.16, T:0.18
Consensus pattern (14 bp):
AGTCAACGGTCAAC
Found at i:14727 original size:28 final size:27
Alignment explanation
Indices: 14679--14731 Score: 88
Period size: 28 Copynumber: 1.9 Consensus size: 27
14669 CGAAAAAAAG
*
14679 TCAATGGTCAAAGTCAACGATCAACAT
1 TCAACGGTCAAAGTCAACGATCAACAT
14706 TCAACGGTCAACAGTCAACGATCAAC
1 TCAACGGTCAA-AGTCAACGATCAAC
14732 GGGTCAGTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
27 10 0.42
28 14 0.58
ACGTcount: A:0.40, C:0.26, G:0.15, T:0.19
Consensus pattern (27 bp):
TCAACGGTCAAAGTCAACGATCAACAT
Found at i:14764 original size:18 final size:18
Alignment explanation
Indices: 14741--14775 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
14731 CGGGTCAGTC
14741 AATGATCGATCAATGGTA
1 AATGATCGATCAATGGTA
*
14759 AATGATCGGTCAATGGT
1 AATGATCGATCAATGGT
14776 TAACGGTCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.29
Consensus pattern (18 bp):
AATGATCGATCAATGGTA
Found at i:14825 original size:29 final size:29
Alignment explanation
Indices: 14793--14858 Score: 105
Period size: 29 Copynumber: 2.3 Consensus size: 29
14783 CAGTCGACGA
*
14793 TCAACGGTCGATTAACGATCGTTCAATAG
1 TCAACGGTCGATTAACGATCGTTCAACAG
* *
14822 TCAACAGTCGATTAACGATCGTTCAACGG
1 TCAACGGTCGATTAACGATCGTTCAACAG
14851 TCAACGGT
1 TCAACGGT
14859 TGGTCAAATC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (29 bp):
TCAACGGTCGATTAACGATCGTTCAACAG
Found at i:14912 original size:17 final size:16
Alignment explanation
Indices: 14882--14920 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
14872 ATTGGTTTAA
*
14882 GGTTTGGTTTGGGCTT
1 GGTTTGGTTCGGGCTT
14898 GGTTTGGTTGCGGGCTT
1 GGTTTGGTT-CGGGCTT
14915 GGTTTG
1 GGTTTG
14921 ATTTGGGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 9 0.43
17 12 0.57
ACGTcount: A:0.00, C:0.08, G:0.46, T:0.46
Consensus pattern (16 bp):
GGTTTGGTTCGGGCTT
Found at i:27643 original size:9 final size:10
Alignment explanation
Indices: 27626--27652 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
27616 TTTTAAAAAT
27626 AATTTTTTTG
1 AATTTTTTTG
27636 AATTTTTTTG
1 AATTTTTTTG
27646 AATTTTT
1 AATTTTT
27653 ACATTGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.70
Consensus pattern (10 bp):
AATTTTTTTG
Found at i:28019 original size:23 final size:24
Alignment explanation
Indices: 27980--28026 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
27970 AATATTTTTG
27980 AATAAAAGTAAAGTTGAACAAATT
1 AATAAAAGTAAAGTTGAACAAATT
* *
28004 AATAAAA-TCAAGTTGAAGAAATT
1 AATAAAAGTAAAGTTGAACAAATT
28027 GCTAATAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.57, C:0.04, G:0.13, T:0.26
Consensus pattern (24 bp):
AATAAAAGTAAAGTTGAACAAATT
Found at i:28464 original size:15 final size:16
Alignment explanation
Indices: 28439--28468 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
28429 AAATGTTTCT
28439 CAAACATTAATAATAA
1 CAAACATTAATAATAA
28455 CAAA-ATTAATAATA
1 CAAACATTAATAATA
28469 CAATGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.63, C:0.10, G:0.00, T:0.27
Consensus pattern (16 bp):
CAAACATTAATAATAA
Found at i:28852 original size:2 final size:2
Alignment explanation
Indices: 28845--28882 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
28835 TTACAAAGAA
28845 AT AT AT AT AT AT 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 AT AT AT AT AT AT
28883 GAGGGTTTCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29349 original size:30 final size:31
Alignment explanation
Indices: 29315--29387 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 31
29305 ATTATATTTA
*
29315 ACAAAACAGTCAC-AATACTT-T-GAAAATGTG
1 ACAAAACAGTCACTAA-AATTATCGAAAA-GTG
29345 ACAAAACAGTCACTAAAATTATCGAAAAGTG
1 ACAAAACAGTCACTAAAATTATCGAAAAGTG
29376 ACAAAACAGTCA
1 ACAAAACAGTCA
29388 TATTGGCTTC
Statistics
Matches: 39, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
30 16 0.41
31 18 0.46
32 5 0.13
ACGTcount: A:0.51, C:0.18, G:0.12, T:0.19
Consensus pattern (31 bp):
ACAAAACAGTCACTAAAATTATCGAAAAGTG
Found at i:38609 original size:847 final size:837
Alignment explanation
Indices: 36976--38659 Score: 3260
Period size: 847 Copynumber: 2.0 Consensus size: 837
36966 CAAGTTCAAT
36976 TACTAACTAGGAAAAAAAAGTCCAACCCCCAATGTCAGAGTAATTGCCAAATTTCAAGCCAAAAA
1 TACTAACTAGGAAAAAAAAGTCCAACCCCCAATGTCAGAGTAATTGCCAAATTTCAAGCCAAAAA
37041 AGTGATTAAACCTTCTTAAAAATGATCTAATTTTTGGCACTAAAAATTTAGAAATCAATCTTTTT
66 AGTGATTAAACCTTCTTAAAAATGATCTAATTTTTGGCACTAAAAATTTAGAAATCAATCTTTTT
37106 TATCCCTATTTGCATGAATCTGGTTTAAGTACGGTGTATTTAACAATATCATGAAGCATTTTTAT
131 TATCCCTATTTGCATGAATCTGGTTTAAGTACGGTGTATTTAACAATATCATGAAGCATTTTTAT
37171 TTGACACAAAATGTTGAAACCATGTAGGTTTATAAACAAAGCATCATTGGGTGAGTCAGTCACAT
196 TTGACACAAAATGTTGAAACCATGTAGGTTTATAAACAAAGCATCATTGGGTGAGTCAGTCACAT
37236 CGACCGAGGTTGAGGAAACAAAGACATTCATAGGCCTCCTCCCCATATTTGCAAGCACCATTATG
261 CGACCGAGGTTGAGGAAACAAAGACATTCATAGGCCTCCTCCCCATATTTGCAAGCACCATTATG
37301 ATGAACTGCTGCTTAGCTCAGCTGACAACATTCTCGGTGCAACAAGGGAACATCATGAACAGATC
326 ATGAACTGCTGCTTAGCTCAGCTGACAACATTCTCGGTGCAACAAGGGAACATCATGAACAGATC
37366 ACTTAGCAGTTTCAAGATTCCCACTCAATCGTTATCAGTATTCCCCTTATCCATCATGCTGGCTT
391 ACTTAGCAGTTTCAAGATTCCCACTCAATCGTTATCAGTATTCCCCTTATCCATCATGCTGGCTT
37431 CTATACCTATATACGAATATTTTGTACGCATGTTCAGATCAAGGAACAACAACAATCCTAGCATG
456 CTATACCTATATACGAATATTTTGTACGCATGTTCAGATCAAGGAACAACAACAATCCTAGCATG
37496 CTCAACATGTTCCAACCATTGAGGCGGATCGGACTGGGGTTGGCCCTCGCATCGGGGTCGATGGC
521 CTCAACATGTTCCAACCATTGAGGCGGATCGGACTGGGGTTGGCCCTCGCATCGGGGTCGATGGC
*
37561 TGCCGCTGCTGTAGTCGAAGCTAAGAGGCGTGGGGCAGCAAACGACGATGTCGTCTTGTCTGTTT
586 TGCCGCTGCTGTAGTCGAAGCTAAGAGGCGTGAGGCAGCAAACGACGATGTCGTCTTGTCTGTTT
37626 TCTGGCTCGGGTGGCAATACTTGCTGCTCGGCGTATCGGACATGCTAACGCTCGGGGGAATGCTT
651 TCTGGCTCGGGTGGCAATACTTGCTGCTCGGCGTATCGGACATGCTAACGCTCGGGGGAATGCTT
37691 GAATTTTTCTACTCGGAGGCTCCGGATACCATGCGAAGTATGAGCACTGCGTTGTCTTGGTGCTC
716 GAATTTTTCTACTCGGAGGCTCCGGATACCATGCGAAGTATGAGCACTGCGTTGTCTTGGTGCTC
37756 GACGGCAATGGGGTACTTCATCAGCTCGGTGTTGGTTACGATAAGCAACTCGGTGAG
781 GACGGCAATGGGGTACTTCATCAGCTCGGTGTTGGTTACGATAAGCAACTCGGTGAG
37813 NNNNNNNNNNTACTAACTAGGAAAAAAAAGTCCAACCCCCAATGTCAGAGTAATTGCCAAATTTC
1 ----------TACTAACTAGGAAAAAAAAGTCCAACCCCCAATGTCAGAGTAATTGCCAAATTTC
37878 AAGCCAAAAAAGTGATTAAACCTTCTTAAAAATGATCTAATTTTTGGCACTAAAAATTTAGAAAT
56 AAGCCAAAAAAGTGATTAAACCTTCTTAAAAATGATCTAATTTTTGGCACTAAAAATTTAGAAAT
37943 CAATCTTTTTTATCCCTATTTGCATGAATCTGGTTTAAGTACGGTGTATTTAACAATATCATGAA
121 CAATCTTTTTTATCCCTATTTGCATGAATCTGGTTTAAGTACGGTGTATTTAACAATATCATGAA
38008 GCATTTTTATTTGACACAAAATGTTGAAACCATGTAGGTTTATAAACAAAGCATCATTGGGTGAG
186 GCATTTTTATTTGACACAAAATGTTGAAACCATGTAGGTTTATAAACAAAGCATCATTGGGTGAG
38073 TCAGTCACATCGACCGAGGTTGAGGAAACAAAGACATTCATAGGCCTCCTCCCCATATTTGCAAG
251 TCAGTCACATCGACCGAGGTTGAGGAAACAAAGACATTCATAGGCCTCCTCCCCATATTTGCAAG
38138 CACCATTATGATGAACTGCTGCTTAGCTCAGCTGACAACATTCTCGGTGCAACAAGGGAACATCA
316 CACCATTATGATGAACTGCTGCTTAGCTCAGCTGACAACATTCTCGGTGCAACAAGGGAACATCA
38203 TGAACAGATCACTTAGCAGTTTCAAGATTCCCACTCAATCGTTATCAGTATTCCCCTTATCCATC
381 TGAACAGATCACTTAGCAGTTTCAAGATTCCCACTCAATCGTTATCAGTATTCCCCTTATCCATC
38268 ATGCTGGCTTCTATACCTATATACGAATATTTTGTACGCATGTTCAGATCAAGGAACAACAACAA
446 ATGCTGGCTTCTATACCTATATACGAATATTTTGTACGCATGTTCAGATCAAGGAACAACAACAA
38333 TCCTAGCATGCTCAACATGTTCCAACCATTGAGGCGGATCGGACTGGGGTTGGCCCTCGCATCGG
511 TCCTAGCATGCTCAACATGTTCCAACCATTGAGGCGGATCGGACTGGGGTTGGCCCTCGCATCGG
*
38398 GGTCGATGGCTGCCGCTGCTGTAGTCGAAGCTAAGAGGCGTGAGGCAGCGAACGACGATGTCGTC
576 GGTCGATGGCTGCCGCTGCTGTAGTCGAAGCTAAGAGGCGTGAGGCAGCAAACGACGATGTCGTC
38463 TTGTCTGTTTTCTGGCTCGGGTGGCAATACTTGCTGCTCGGCGTATCGGACATGCTAACGCTCGG
641 TTGTCTGTTTTCTGGCTCGGGTGGCAATACTTGCTGCTCGGCGTATCGGACATGCTAACGCTCGG
38528 GGGAATGCTTGAATTTTTCTACTCGGAGGCTCCGGATACCATGCGAAGTATGAGCACTGCGTTGT
706 GGGAATGCTTGAATTTTTCTACTCGGAGGCTCCGGATACCATGCGAAGTATGAGCACTGCGTTGT
38593 CTTGGTGCTCGACGGCAATGGGGTACTTCATCAGCTCGGTGTTGGTTACGATAAGCAACTCGGTG
771 CTTGGTGCTCGACGGCAATGGGGTACTTCATCAGCTCGGTGTTGGTTACGATAAGCAACTCGGTG
38658 AG
836 AG
38660 CGGACATTTT
Statistics
Matches: 835, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
847 835 1.00
ACGTcount: A:0.28, C:0.22, G:0.22, T:0.28
Consensus pattern (837 bp):
TACTAACTAGGAAAAAAAAGTCCAACCCCCAATGTCAGAGTAATTGCCAAATTTCAAGCCAAAAA
AGTGATTAAACCTTCTTAAAAATGATCTAATTTTTGGCACTAAAAATTTAGAAATCAATCTTTTT
TATCCCTATTTGCATGAATCTGGTTTAAGTACGGTGTATTTAACAATATCATGAAGCATTTTTAT
TTGACACAAAATGTTGAAACCATGTAGGTTTATAAACAAAGCATCATTGGGTGAGTCAGTCACAT
CGACCGAGGTTGAGGAAACAAAGACATTCATAGGCCTCCTCCCCATATTTGCAAGCACCATTATG
ATGAACTGCTGCTTAGCTCAGCTGACAACATTCTCGGTGCAACAAGGGAACATCATGAACAGATC
ACTTAGCAGTTTCAAGATTCCCACTCAATCGTTATCAGTATTCCCCTTATCCATCATGCTGGCTT
CTATACCTATATACGAATATTTTGTACGCATGTTCAGATCAAGGAACAACAACAATCCTAGCATG
CTCAACATGTTCCAACCATTGAGGCGGATCGGACTGGGGTTGGCCCTCGCATCGGGGTCGATGGC
TGCCGCTGCTGTAGTCGAAGCTAAGAGGCGTGAGGCAGCAAACGACGATGTCGTCTTGTCTGTTT
TCTGGCTCGGGTGGCAATACTTGCTGCTCGGCGTATCGGACATGCTAACGCTCGGGGGAATGCTT
GAATTTTTCTACTCGGAGGCTCCGGATACCATGCGAAGTATGAGCACTGCGTTGTCTTGGTGCTC
GACGGCAATGGGGTACTTCATCAGCTCGGTGTTGGTTACGATAAGCAACTCGGTGAG
Found at i:40241 original size:18 final size:20
Alignment explanation
Indices: 40213--40251 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
40203 CGTAAAACGG
40213 ATATGTATAA-TATAAAAAA
1 ATATGTATAATTATAAAAAA
40232 ATAT-TATAATTATAAAAAA
1 ATATGTATAATTATAAAAAA
40251 A
1 A
40252 AATATTACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (20 bp):
ATATGTATAATTATAAAAAA
Done.