Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011068.1 Kokia drynarioides strain JFW-HI SEQ_126040, 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: 14053
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Found at i:1486 original size:6 final size:6
Alignment explanation
Indices: 1477--1546 Score: 65
Period size: 6 Copynumber: 11.8 Consensus size: 6
1467 GATTTATTTC
* * *
1477 TAAATT TAAATT T-ATTT TAAATT TAAATT TAAA-T TCATTT TAAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT T-AAATT
*
1524 TAAATT T-AGTT TAAATT TGAAAT
1 TAAATT TAAATT TAAATT T-AAAT
1547 AATTTTAAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
5 11 0.22
6 32 0.63
7 8 0.16
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.51
Consensus pattern (6 bp):
TAAATT
Found at i:1497 original size:11 final size:11
Alignment explanation
Indices: 1481--1541 Score: 58
Period size: 11 Copynumber: 5.8 Consensus size: 11
1471 TATTTCTAAA
1481 TTTAAATTTAT
1 TTTAAATTTAT
*
1492 TTTAAATTTAAA
1 TTTAAATTT-AT
*
1504 TTTAAATTCAT
1 TTTAAATTTAT
1515 TTTAAA---A-
1 TTTAAATTTAT
*
1522 TTTAAATTTAG
1 TTTAAATTTAT
1533 TTTAAATTT
1 TTTAAATTT
1542 GAAATAATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
7 6 0.14
8 1 0.02
10 1 0.02
11 25 0.60
12 9 0.21
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (11 bp):
TTTAAATTTAT
Found at i:1503 original size:23 final size:24
Alignment explanation
Indices: 1477--1531 Score: 94
Period size: 23 Copynumber: 2.3 Consensus size: 24
1467 GATTTATTTC
*
1477 TAAATTTAAATTTATTTT-AAATT
1 TAAATTTAAATTCATTTTAAAATT
1500 TAAATTTAAATTCATTTTAAAATT
1 TAAATTTAAATTCATTTTAAAATT
1524 TAAATTTA
1 TAAATTTA
1532 GTTTAAATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 17 0.57
24 13 0.43
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (24 bp):
TAAATTTAAATTCATTTTAAAATT
Found at i:1509 original size:29 final size:28
Alignment explanation
Indices: 1453--1555 Score: 75
Period size: 29 Copynumber: 3.6 Consensus size: 28
1443 TTTTTTTGAG
* *
1453 TTTAAATTATTTTAGATTTATTTCTAAA
1 TTTAAATTATTTTAAATTTAATTCTAAA
1481 TTTAAATTTATTTTAAATTTAAATT-TAAA
1 TTTAAA-TTATTTTAAATTT-AATTCTAAA
* ** * *
1510 TTCATTTTAAAATTTAAATTTAGTT-TAAA
1 TTTAAATT--ATTTTAAATTTAATTCTAAA
*
1539 TTTGAAATAATTTTAAA
1 TTT-AAATTATTTTAAA
1556 ACATAAACTT
Statistics
Matches: 58, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
28 15 0.26
29 28 0.48
30 15 0.26
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (28 bp):
TTTAAATTATTTTAAATTTAATTCTAAA
Found at i:1518 original size:17 final size:17
Alignment explanation
Indices: 1453--1555 Score: 75
Period size: 17 Copynumber: 6.0 Consensus size: 17
1443 TTTTTTTGAG
*
1453 TTTAAATT-ATTTTAGA
1 TTTAAATTAATTTTAAA
** *
1469 TTTATTTCTAAATTTAAA
1 TTTAAAT-TAATTTTAAA
** *
1487 TTTATTTTAAATTTAAA
1 TTTAAATTAATTTTAAA
*
1504 TTTAAATTCATTTTAAAA
1 TTTAAATTAATTTT-AAA
* *
1522 TTTAAATTTAGTTTAAA
1 TTTAAATTAATTTTAAA
1539 TTTGAAA-TAATTTTAAA
1 TTT-AAATTAATTTTAAA
1556 ACATAAACTT
Statistics
Matches: 71, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
16 5 0.07
17 35 0.49
18 31 0.44
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTAAATTAATTTTAAA
Found at i:1524 original size:18 final size:18
Alignment explanation
Indices: 1501--1556 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 18
1491 TTTTAAATTT
*
1501 AAATTTAAATTCATTTTA
1 AAATTTAAATTAATTTTA
* *
1519 AAATTTAAATTTAGTTT-
1 AAATTTAAATTAATTTTA
1536 AAATTTGAAA-TAATTTTA
1 AAATTT-AAATTAATTTTA
1554 AAA
1 AAA
1557 CATAAACTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
17 11 0.34
18 21 0.66
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (18 bp):
AAATTTAAATTAATTTTA
Found at i:2810 original size:29 final size:29
Alignment explanation
Indices: 2737--3081 Score: 322
Period size: 29 Copynumber: 11.8 Consensus size: 29
2727 TCCCTGAACA
* *
2737 TCCAAAAATTTCATTTTTGACCCTAAAACT
1 TCCAAAAATTACATTTTT-ACCCTCAAACT
2767 TCCAAAAATTACATTTTTACCCTCAAACT
1 TCCAAAAATTACATTTTTACCCTCAAACT
* * * *
2796 TCCAAAAATTCCATTTTGACCTTAAAACT
1 TCCAAAAATTACATTTTTACCCTCAAACT
***
2825 TTTGAAAATTACATTTTTACCCT-AAACT
1 TCCAAAAATTACATTTTTACCCTCAAACT
*
2853 TCCAAAAATTCCATTTTTAACCC-CAAAACT
1 TCCAAAAATTACATTTTT-ACCCTC-AAACT
* * * **
2883 TCCAAAGATTACATCTATACCCTTGAACT
1 TCCAAAAATTACATTTTTACCCTCAAACT
* * * * *
2912 TCTAAAAAATCCATTTTGACCCTAAAACT
1 TCCAAAAATTACATTTTTACCCTCAAACT
2941 TCCAAAAATTACATTTTTACCCTCAAACT
1 TCCAAAAATTACATTTTTACCCTCAAACT
* * * *
2970 TTCAAAAATTGCATTTTTGACCATAAAACT
1 TCCAAAAATTACATTTTT-ACCCTCAAACT
* * *
3000 TTCAAAAATTACATTTTTACCC-CTGACCT
1 TCCAAAAATTACATTTTTACCCTC-AAACT
*
3029 TCC-AAAATTCCATTTTTGA-CCTCGAAACT
1 TCCAAAAATTACATTTTT-ACCCTC-AAACT
* *
3058 TTCAAAAATTACATCTTTACCCTC
1 TCCAAAAATTACATTTTTACCCTC
3082 GGATGTCAAA
Statistics
Matches: 252, Mismatches: 53, Indels: 20
0.78 0.16 0.06
Matches are distributed among these distances:
28 34 0.13
29 140 0.56
30 78 0.31
ACGTcount: A:0.37, C:0.25, G:0.03, T:0.35
Consensus pattern (29 bp):
TCCAAAAATTACATTTTTACCCTCAAACT
Found at i:2836 original size:58 final size:59
Alignment explanation
Indices: 2737--3165 Score: 428
Period size: 58 Copynumber: 7.3 Consensus size: 59
2727 TCCCTGAACA
* *
2737 TCCAAAAATTTCATTTTTGACCCTAAAACTTCCAAAAATTACATTTTTACCCTCAAACT
1 TCCAAAAATTCCATTTTTGACCCTAAAACTTTCAAAAATTACATTTTTACCCTCAAACT
* **
2796 TCCAAAAATTCCA-TTTTGACCTTAAAACTTTTGAAAATTACATTTTTACCCT-AAACT
1 TCCAAAAATTCCATTTTTGACCCTAAAACTTTCAAAAATTACATTTTTACCCTCAAACT
* * * * * * **
2853 TCCAAAAATTCCATTTTTAACCCCAAAACTTCCAAAGATTACATCTATACCCTTGAACT
1 TCCAAAAATTCCATTTTTGACCCTAAAACTTTCAAAAATTACATTTTTACCCTCAAACT
* * *
2912 TCTAAAAAATCCA-TTTTGACCCTAAAACTTCCAAAAATTACATTTTTACCCTCAAACT
1 TCCAAAAATTCCATTTTTGACCCTAAAACTTTCAAAAATTACATTTTTACCCTCAAACT
* * * * *
2970 TTCAAAAATTGCATTTTTGACCATAAAACTTTCAAAAATTACATTTTTACCC-CTGACCT
1 TCCAAAAATTCCATTTTTGACCCTAAAACTTTCAAAAATTACATTTTTACCCTC-AAACT
* * **
3029 TCC-AAAATTCCATTTTTGA-CCTCGAAACTTTCAAAAATTACATCTTTACCCTCGGA-T
1 TCCAAAAATTCCATTTTTGACCCT-AAAACTTTCAAAAATTACATTTTTACCCTCAAACT
* * * * ** ** *
3086 GTCAAAAAACTCAATTTTTAACCCCGAAACTTTTGAAAATTACCA-TTTTACCC-CTGAA-T
1 -TCCAAAAATTCCATTTTTGACCCTAAAACTTTCAAAAATTA-CATTTTTACCCTC-AAACT
3145 ATCCAAAAATTCCATTTTTGA
1 -TCCAAAAATTCCATTTTTGA
3166 TCTCGATTTT
Statistics
Matches: 306, Mismatches: 53, Indels: 22
0.80 0.14 0.06
Matches are distributed among these distances:
57 21 0.07
58 158 0.52
59 123 0.40
60 4 0.01
ACGTcount: A:0.37, C:0.24, G:0.04, T:0.35
Consensus pattern (59 bp):
TCCAAAAATTCCATTTTTGACCCTAAAACTTTCAAAAATTACATTTTTACCCTCAAACT
Found at i:3094 original size:117 final size:115
Alignment explanation
Indices: 2739--3162 Score: 439
Period size: 117 Copynumber: 3.6 Consensus size: 115
2729 CCTGAACATC
* * *
2739 CAAAAATTTCATTTTTGACCCTAAAACTTCCAAAAATTACATTTTTA-CCCTCAAACTTCCAAAA
1 CAAAAA-TTCATTTTTAACCCCAAAACTTCCAAAAATTACATTTTTACCCCT-GAACTTCCAAAA
* **
2803 ATTCCATTTTGACCTTAAAACTTTTGAAAATTACATTTTTACCCT-AAACTT
64 ATTCCATTTTGACCTCAAAACTTTCAAAAATTACATTTTTACCCTCAAACTT
* * * * *
2854 CCAAAAATTCCATTTTTAACCCCAAAACTTCCAAAGATTACATCTATACCCTTGAACTTCTAAAA
1 -CAAAAATT-CATTTTTAACCCCAAAACTTCCAAAAATTACATTTTTACCCCTGAACTTCCAAAA
* *
2919 AATCCATTTTGACC-CTAAAACTTCCAAAAATTACATTTTTACCCTCAAACTTT
64 ATTCCATTTTGACCTC-AAAACTTTCAAAAATTACATTTTTACCCTCAAAC-TT
* ** * *
2972 CAAAAATTGCATTTTTGACCATAAAACTTTCAAAAATTACATTTTTACCCCTGACCTTCC-AAAA
1 CAAAAATT-CATTTTTAACCCCAAAACTTCCAAAAATTACATTTTTACCCCTGAACTTCCAAAAA
* * **
3036 TTCCATTTTTGACCTCGAAACTTTCAAAAATTACATCTTTACCCTCGGA-TGT
65 TTCCA-TTTTGACCTCAAAACTTTCAAAAATTACATTTTTACCCTCAAACT-T
* * ***
3088 CAAAAAACTCAATTTTTAACCCCGAAACTTTTGAAAATTACCA-TTTTACCCCTGAA-TATCCAA
1 C-AAAAATTC-ATTTTTAACCCCAAAACTTCCAAAAATTA-CATTTTTACCCCTGAACT-TCCAA
3151 AAATTCCATTTT
62 AAATTCCATTTT
3163 TGATCTCGAT
Statistics
Matches: 257, Mismatches: 38, Indels: 25
0.80 0.12 0.08
Matches are distributed among these distances:
115 3 0.01
116 100 0.39
117 140 0.54
118 14 0.05
ACGTcount: A:0.37, C:0.25, G:0.04, T:0.35
Consensus pattern (115 bp):
CAAAAATTCATTTTTAACCCCAAAACTTCCAAAAATTACATTTTTACCCCTGAACTTCCAAAAAT
TCCATTTTGACCTCAAAACTTTCAAAAATTACATTTTTACCCTCAAACTT
Found at i:10673 original size:153 final size:153
Alignment explanation
Indices: 10395--10724 Score: 543
Period size: 153 Copynumber: 2.2 Consensus size: 153
10385 ATAAAATGGT
*
10395 TAGCTTCCTGATTAGATACTGAGAGGTGGACCAAATTCGTCTTCCTAATGAGATACAGAGAAGCG
1 TAGCTTCCTGATGAGATACTGAGAGGTGGACCAAATTCGTCTTCCTAATGAGATACAGAGAAGCG
*
10460 AATTGATACAAGTGAGACGATCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCGAGGCTC
66 AATTGAAACAAGTGAGACGATCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCGAGGCTC
10525 AATGCAAGCAAATCTTCGAACCC
131 AATGCAAGCAAATCTTCGAACCC
* *
10548 TAGCTTCCTGATGAGATACTGAGAGGTGGATCAAATTCGTCTTCCTGATGAGATACAGAGAAGCG
1 TAGCTTCCTGATGAGATACTGAGAGGTGGACCAAATTCGTCTTCCTAATGAGATACAGAGAAGCG
** * * * *
10613 AATTGAAACAAGTGAGGTGGTCATCTTCTTGATGAGATACATAGAAGTATACTAACTCGAGGCTC
66 AATTGAAACAAGTGAGACGATCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCGAGGCTC
*
10678 AATGCGAGCAAATCTTCGAACCC
131 AATGCAAGCAAATCTTCGAACCC
* *
10701 CAGCTTCCTGATGAGAGACTGAGA
1 TAGCTTCCTGATGAGATACTGAGA
10725 AGCAGGTCAA
Statistics
Matches: 164, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
153 164 1.00
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.24
Consensus pattern (153 bp):
TAGCTTCCTGATGAGATACTGAGAGGTGGACCAAATTCGTCTTCCTAATGAGATACAGAGAAGCG
AATTGAAACAAGTGAGACGATCATCTTCCTGATGAGATACAGAGAAGTATACCAACTCGAGGCTC
AATGCAAGCAAATCTTCGAACCC
Found at i:10897 original size:201 final size:200
Alignment explanation
Indices: 10548--11063 Score: 807
Period size: 201 Copynumber: 2.6 Consensus size: 200
10538 CTTCGAACCC
* *
10548 TAGCTTCCTGATGAGATACTGAGAGGTGGATCAAATTCGTCTTCCTGATGAGATACAGAGAAGCG
1 TAGCTTCCTGATGAGATATTGAGAGGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCG
* *
10613 AATTGAAACAAGTGAGGTGGTCATCTTCTTGATGAGATACATAGAAGTATACTAACTCGAGGCTC
66 AATTGAAACAAGTGAGGCGGTCATCTTCTTGATGAGATACA-AGAAGTATACCAACTCGAGGCTC
10678 AATGCGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGAGACTGAGAAGCAGGTCAAAGCAATAA
130 AATGCGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGAGACTGAGAAGCAGGTCAAAGCAATAA
10743 AATGGT
195 AATGGT
* *
10749 TAGTTTCCTGATGAGATATTGAGAGGTGGACCAAATTCGTCTTCCTGATGAGATATAGAGAAGCG
1 TAGCTTCCTGATGAGATATTGAGAGGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCG
10814 AATTGAAACAAGTGAGGCGGTCATCTTCTTGATGAGATACAGAGAAGTATACCAACTCGAGGCTC
66 AATTGAAACAAGTGAGGCGGTCATCTTCTTGATGAGATACA-AGAAGTATACCAACTCGAGGCTC
* * *
10879 AATGCGAGCAAATCTTCGAACCCCAGCTTCTTGATGAGATACTGAGAAGCAGGTCGAAGCAATAA
130 AATGCGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGAGACTGAGAAGCAGGTCAAAGCAATAA
*
10944 AGTGGT
195 AATGGT
* * * * * *
10950 TAGCTTCCTGATGAGATATGGAGAAGCGAACCAAATTCGTCTTCCTGATGAGGTACAGGGAAGCG
1 TAGCTTCCTGATGAGATATTGAGAGGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCG
* * * * * *
11015 GATTGAAACAAGCGATGCGATCATCTTCCTGATAAGATACTAAGAAGTA
66 AATTGAAACAAGTGAGGCGGTCATCTTCTTGATGAGATAC-AAGAAGTA
11064 ACAAATCAAC
Statistics
Matches: 289, Mismatches: 25, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
201 288 1.00
202 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.24
Consensus pattern (200 bp):
TAGCTTCCTGATGAGATATTGAGAGGTGGACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCG
AATTGAAACAAGTGAGGCGGTCATCTTCTTGATGAGATACAAGAAGTATACCAACTCGAGGCTCA
ATGCGAGCAAATCTTCGAACCCCAGCTTCCTGATGAGAGACTGAGAAGCAGGTCAAAGCAATAAA
ATGGT
Found at i:11423 original size:6 final size:6
Alignment explanation
Indices: 11410--11487 Score: 81
Period size: 6 Copynumber: 13.3 Consensus size: 6
11400 TTTTAGATTT
* * *
11410 ATTT-A ATTTAA ATTTAA ATTT-A CTTTAA ATTTAA ATTTAA ATTCAT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* *
11456 TTTTAA ATTTAA ATTT-A GTTTAA ATTTGAA AT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA AT
11488 AATTTTAAAA
Statistics
Matches: 59, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
5 12 0.20
6 43 0.73
7 4 0.07
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (6 bp):
ATTTAA
Found at i:11424 original size:11 final size:11
Alignment explanation
Indices: 11401--11482 Score: 59
Period size: 11 Copynumber: 7.8 Consensus size: 11
11391 TTTAAATAAT
*
11401 TTTAGATTT-A
1 TTTAAATTTAA
11411 TTT-AATTTAAA
1 TTTAAATTT-AA
*
11422 TTTAAATTTAC
1 TTTAAATTTAA
11433 TTTAAATTTAAA
1 TTTAAATTT-AA
*
11445 TTTAAA-TTCA
1 TTTAAATTTAA
*
11455 TTT---TTAAA
1 TTTAAATTTAA
*
11463 TTTAAATTTAG
1 TTTAAATTTAA
11474 TTTAAATTT
1 TTTAAATTT
11483 GAAATAATTT
Statistics
Matches: 56, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
8 5 0.09
9 4 0.07
10 7 0.12
11 28 0.50
12 12 0.21
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.56
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:11493 original size:35 final size:35
Alignment explanation
Indices: 11422--11493 Score: 85
Period size: 35 Copynumber: 2.1 Consensus size: 35
11412 TTAATTTAAA
* *
11422 TTTAAATTTACTTTAAATTTAAATTTAAATTCATT
1 TTTAAATTTAATTTAAATTTAAATTTAAATTAATT
*
11457 TTTAAATTTAAATTT-AGTTTAAATTTGAAA-TAATT
1 TTTAAATTT-AATTTAAATTTAAATTT-AAATTAATT
11492 TT
1 TT
11494 AAAACATAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
35 25 0.78
36 7 0.22
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (35 bp):
TTTAAATTTAATTTAAATTTAAATTTAAATTAATT
Found at i:11494 original size:17 final size:17
Alignment explanation
Indices: 11410--11496 Score: 77
Period size: 17 Copynumber: 5.1 Consensus size: 17
11400 TTTTAGATTT
* *
11410 ATTTAATTTAAATTTAA
1 ATTTAAATTAATTTTAA
** *
11427 ATTTACTTTAAATTTAA
1 ATTTAAATTAATTTTAA
*
11444 ATTTAAATTCATTTTTAA
1 ATTTAAATT-AATTTTAA
* *
11462 ATTTAAATTTAGTTTAA
1 ATTTAAATTAATTTTAA
11479 ATTTGAAA-TAATTTTAA
1 ATTT-AAATTAATTTTAA
11496 A
1 A
11497 ACATAAACTT
Statistics
Matches: 58, Mismatches: 10, Indels: 4
0.81 0.14 0.06
Matches are distributed among these distances:
17 40 0.69
18 18 0.31
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (17 bp):
ATTTAAATTAATTTTAA
Found at i:13275 original size:29 final size:29
Alignment explanation
Indices: 13243--13687 Score: 377
Period size: 29 Copynumber: 15.2 Consensus size: 29
13233 AAAAATTATG
* *
13243 TTTTGACCTTCGAACTTCCAAAAATTCCA
1 TTTTTACCCTCGAACTTCCAAAAATTCCA
**
13272 TTTTTGA-CCTCGAAACTTCCAAAAATTAAA
1 TTTTT-ACCCTCG-AACTTCCAAAAATTCCA
* * *
13302 TTTTTACCCCCAAACTTCAAAAAATTCCA
1 TTTTTACCCTCGAACTTCCAAAAATTCCA
* * *
13331 TTTTGA-CCTTGAAACTTCCAAAAATTACA
1 TTTTTACCCTCG-AACTTCCAAAAATTCCA
13360 TTTTTACCCTCGAACTTCCAAAAATTCCA
1 TTTTTACCCTCGAACTTCCAAAAATTCCA
* *
13389 TTTTTAACCC-CAAAACTTCCAAAAATTACA
1 TTTTT-ACCCTC-GAACTTCCAAAAATTCCA
* *
13419 TTTCTACCCACGAACTTCCAAAAATTCCA
1 TTTTTACCCTCGAACTTCCAAAAATTCCA
** *** *
13448 TTTTTAACCCTAAAACTTTTGAAAATTACA
1 TTTTT-ACCCTCGAACTTCCAAAAATTCCA
13478 TTTTTACCCTCGAACTTCCAAAAATTCCA
1 TTTTTACCCTCGAACTTCCAAAAATTCCA
* * *
13507 -TTTTAACCTTGAAACTTCCAAAAATTACA
1 TTTTTACCCTCG-AACTTCCAAAAATTCCA
* *
13536 TCTTTACCCTTGAACTTCCAAAAA-TCCTA
1 TTTTTACCCTCGAACTTCCAAAAATTCC-A
* *** *
13565 TTTTTGACCC-CAAAACTTTTGAAAATTACA
1 TTTTT-ACCCTC-GAACTTCCAAAAATTCCA
* * *
13595 TTTTTACTCACGAACTTCCAAAAACTCCA
1 TTTTTACCCTCGAACTTCCAAAAATTCCA
*
13624 TTTTTTA-CCTCGAAACTTTCAAAAATTACCA
1 -TTTTTACCCTCG-AACTTCCAAAAATT-CCA
* *
13655 -TTTTACCCCCGAA-TGTCCAAAAATTCCG
1 TTTTTACCCTCGAACT-TCCAAAAATTCCA
13683 TTTTT
1 TTTTT
13688 TATCTCAATT
Statistics
Matches: 330, Mismatches: 64, Indels: 44
0.75 0.15 0.10
Matches are distributed among these distances:
28 16 0.05
29 183 0.55
30 126 0.38
31 5 0.02
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.34
Consensus pattern (29 bp):
TTTTTACCCTCGAACTTCCAAAAATTCCA
Found at i:13526 original size:176 final size:176
Alignment explanation
Indices: 13253--13686 Score: 615
Period size: 176 Copynumber: 2.5 Consensus size: 176
13243 TTTTGACCTT
* * * *
13253 CGAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTCCAAAAATTAAATTTTTACCCCCAAACT
1 CGAACTTCCAAAAATTCCATTTTTAACCTCGAAACTTTCAAAAATTACATTTTTACCCCCGAACT
* * *
13318 TCAAAAAATTCCATTTTGACCTTGAAACTTCCAAAAATTACATTTTTACCCTCGAACTTCCAAAA
66 TCCAAAAATTCCATTTTAACCTTGAAACTTCCAAAAATTACATCTTTACCCTCGAACTTCCAAAA
13383 ATTCC-ATTTTTAACCCCAAAACTTCCAAAAATTACATTTCTACCCA
131 A-TCCTATTTTTAACCCCAAAACTTCCAAAAATTACATTTCTACCCA
* ** *
13429 CGAACTTCCAAAAATTCCATTTTTAACC-CTAAAACTTTTGAAAATTACATTTTTACCCTCGAAC
1 CGAACTTCCAAAAATTCCATTTTTAACCTC-GAAACTTTCAAAAATTACATTTTTACCCCCGAAC
*
13493 TTCCAAAAATTCCATTTTAACCTTGAAACTTCCAAAAATTACATCTTTACCCTTGAACTTCCAAA
65 TTCCAAAAATTCCATTTTAACCTTGAAACTTCCAAAAATTACATCTTTACCCTCGAACTTCCAAA
* *** * *
13558 AATCCTATTTTTGACCCCAAAACTTTTGAAAATTACATTTTTACTCA
130 AATCCTATTTTTAACCCCAAAACTTCCAAAAATTACATTTCTACCCA
* *
13605 CGAACTTCCAAAAACTCCATTTTTTACCTCGAAACTTTCAAAAATTACCA-TTTTACCCCCGAA-
1 CGAACTTCCAAAAATTCCATTTTTAACCTCGAAACTTTCAAAAATTA-CATTTTTACCCCCGAAC
*
13668 TGTCCAAAAATTCCGTTTT
65 T-TCCAAAAATTCCATTTT
13687 TTATCTCAAT
Statistics
Matches: 228, Mismatches: 25, Indels: 10
0.87 0.10 0.04
Matches are distributed among these distances:
175 5 0.02
176 220 0.96
177 3 0.01
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (176 bp):
CGAACTTCCAAAAATTCCATTTTTAACCTCGAAACTTTCAAAAATTACATTTTTACCCCCGAACT
TCCAAAAATTCCATTTTAACCTTGAAACTTCCAAAAATTACATCTTTACCCTCGAACTTCCAAAA
ATCCTATTTTTAACCCCAAAACTTCCAAAAATTACATTTCTACCCA
Found at i:13689 original size:59 final size:59
Alignment explanation
Indices: 13232--13687 Score: 519
Period size: 59 Copynumber: 7.8 Consensus size: 59
13222 CCTAAATTGT
** * * *
13232 CAAAAATTATGTTTTGACCTTCGAACTTCCAAAAATTCCATTTTTGACCTCGAAACTTC
1 CAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCTCGAAACTTC
* * * * * *
13291 CAAAAATTAAATTTTTACCCCCAAACTTCAAAAAATTCCA-TTTTGACCTTGAAACTTC
1 CAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCTCGAAACTTC
* *
13349 CAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCCCAAAACTTC
1 CAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCTCGAAACTTC
* * * *
13408 CAAAAATTACATTTCTACCCACGAACTTCCAAAAATTCCATTTTTAACC-CTAAAACTTT
1 CAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCTC-GAAACTTC
** *
13467 TGAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCA-TTTTAACCTTGAAACTTC
1 CAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCTCGAAACTTC
* * * * * *
13525 CAAAAATTACATCTTTACCCTTGAACTTCCAAAAA-TCCTATTTTTGACCCCAAAACTTT
1 CAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCC-ATTTTTAACCTCGAAACTTC
** * * * * *
13584 TGAAAATTACATTTTTACTCACGAACTTCCAAAAACTCCATTTTTTACCTCGAAACTTT
1 CAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCTCGAAACTTC
* *
13643 CAAAAATTACCA-TTTTACCCCCGAA-TGTCCAAAAATTCCGTTTTT
1 CAAAAATTA-CATTTTTACCCTCGAACT-TCCAAAAATTCCATTTTT
13688 TATCTCAATT
Statistics
Matches: 339, Mismatches: 50, Indels: 16
0.84 0.12 0.04
Matches are distributed among these distances:
57 3 0.01
58 101 0.30
59 230 0.68
60 5 0.01
ACGTcount: A:0.36, C:0.26, G:0.04, T:0.34
Consensus pattern (59 bp):
CAAAAATTACATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTAACCTCGAAACTTC
Done.