Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010270.1 Kokia drynarioides strain JFW-HI SEQ_125114, 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: 49224
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.33
Found at i:212 original size:58 final size:58
Alignment explanation
Indices: 121--656 Score: 448
Period size: 58 Copynumber: 9.2 Consensus size: 58
111 GTCCCTAAAC
* * * *
121 CTTCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCTCGAAT
1 CTTCCAAAAA-TACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAT
180 CTTCCAAAAATACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAT
1 CTTCCAAAAATACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAT
* *
238 CTTCCAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAAT
1 CTTCCAAAAATACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAT
*
296 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAAT
1 CTTCCAAAAA-TACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAT
* * ** * *
355 CTTTCAAAATTACTATTTTACCCCTAAACTTCCAAAAATCCCATTTTTAATCCCC-AAA
1 CTTCCAAAAATACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGA-CCCCGAAT
* * * * * ** ** *
413 CTCCCAAAAATCCCATTTTTGA-TCCCAAACCTTCCAAAAATTAC-TATTTT-ACCCTTAAA
1 CTTCCAAAAATACTA-TTTT-ACCCCCGAA-CTTCCAAAAATCCCAT-TTTTGACCCCGAAT
* * * * * * * * *
472 CTTCTAAAAATCCCATTTTTAACCCCGAACCTTCTTAAAATTACCA-TTTT-ACCCCTAAA
1 CTTCCAAAAATACTA-TTTTACCCCCGAA-CTTC-CAAAAATCCCATTTTTGACCCCGAAT
* ** * * *
531 CTTCCAACAAT-CTCATTTTTGA-CCTTGAATCTTCCAAAAATTACTATTTTT--CCTCGAAT
1 CTTCCAAAAATACT-A-TTTT-ACCCCCGAA-CTTCCAAAAA-TCCCATTTTTGACCCCGAAT
* * * **
590 -TTCCAAAAATTACCATTTTACCCTCGAACTTCCAAAAATCCTATTTTTGATTCCGAA-
1 CTTCCAAAAA-TACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAT
647 CATTCCAAAA
1 C-TTCCAAAA
657 CTACCATTCT
Statistics
Matches: 403, Mismatches: 53, Indels: 42
0.81 0.11 0.08
Matches are distributed among these distances:
56 9 0.02
57 11 0.03
58 189 0.47
59 165 0.41
60 29 0.07
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.33
Consensus pattern (58 bp):
CTTCCAAAAATACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAT
Found at i:335 original size:59 final size:59
Alignment explanation
Indices: 121--402 Score: 462
Period size: 58 Copynumber: 4.8 Consensus size: 59
111 GTCCCTAAAC
* * * *
121 CTTCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCTCGAAT
1 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAT
180 CTTCCAAAAA-TACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAT
1 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAT
*
238 CTTCC-AAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAAT
1 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAT
*
296 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAAT
1 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAT
* **
355 CTTTC-AAAATTACTATTTTACCCCTAAACTTCCAAAAATCCCATTTTT
1 CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTT
403 AATCCCCAAA
Statistics
Matches: 211, Mismatches: 10, Indels: 5
0.93 0.04 0.02
Matches are distributed among these distances:
57 4 0.02
58 142 0.67
59 65 0.31
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.33
Consensus pattern (59 bp):
CTTCCAAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAT
Found at i:344 original size:117 final size:116
Alignment explanation
Indices: 121--402 Score: 492
Period size: 117 Copynumber: 2.4 Consensus size: 116
111 GTCCCTAAAC
* *
121 CTTCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATCCCATTTTTGACCTCGAATCTTCCA
1 CTTCC-AAAATTACTATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCTCGAATCTTCCA
*
186 AAAATACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCGAAT
65 AAAATACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAAT
*
238 CTTCCAAAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCTCGAATCTTCCAA
1 CTTCCAAAATTACTATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCTCGAATCTTCCAA
303 AAATTACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAAT
66 AAA-TACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAAT
* *
355 CTTTCAAAATTACTATTTTACCCCTAAACTTCCAAAAATCCCATTTTT
1 CTTCCAAAATTACTATTTTACCCCCAAACTTCCAAAAATCCCATTTTT
403 AATCCCCAAA
Statistics
Matches: 157, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
116 60 0.38
117 97 0.62
ACGTcount: A:0.33, C:0.31, G:0.04, T:0.33
Consensus pattern (116 bp):
CTTCCAAAATTACTATTTTACCCCCAAACTTCCAAAAATCCCATTTTTGACCTCGAATCTTCCAA
AAATACTATTTTACCCCCGAACTTCCAAAAATCCCATTTTTGACCCCAAAT
Found at i:487 original size:59 final size:58
Alignment explanation
Indices: 406--580 Score: 208
Period size: 59 Copynumber: 3.0 Consensus size: 58
396 CATTTTTAAT
* *
406 CCCC-AAACTCCCAAAAATCCCATTTTTGATCCCAAACCTTCCAAAAATTACTATTTTA
1 CCCCTAAACTTCCAAAAATCCCATTTTTGA-CCCGAACCTTCCAAAAATTACTATTTTA
* * * ** *
464 CCCTTAAACTTCTAAAAATCCCATTTTTAACCCCGAACCTTCTTAAAATTACCATTTTA
1 CCCCTAAACTTCCAAAAATCCCATTTTTGA-CCCGAACCTTCCAAAAATTACTATTTTA
* * * *
523 CCCCTAAACTTCCAACAATCTCATTTTTGACCTTGAATCTTCCAAAAATTACTATTTT
1 CCCCTAAACTTCCAAAAATCCCATTTTTGACC-CGAACCTTCCAAAAATTACTATTTT
581 TCCTCGAATT
Statistics
Matches: 96, Mismatches: 19, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
58 5 0.05
59 91 0.95
ACGTcount: A:0.34, C:0.30, G:0.02, T:0.34
Consensus pattern (58 bp):
CCCCTAAACTTCCAAAAATCCCATTTTTGACCCGAACCTTCCAAAAATTACTATTTTA
Found at i:1631 original size:21 final size:21
Alignment explanation
Indices: 1593--1633 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1583 CATTTTGGAA
** *
1593 GGTGTGTTGTGACGTAGAGAC
1 GGTGTGTTGCAACATAGAGAC
1614 GGTGTGTTGCAACATAGAGA
1 GGTGTGTTGCAACATAGAGA
1634 GCAATCCACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.10, G:0.39, T:0.27
Consensus pattern (21 bp):
GGTGTGTTGCAACATAGAGAC
Found at i:1808 original size:21 final size:21
Alignment explanation
Indices: 1782--1829 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
1772 GAAACTTAAC
1782 GAAAACATTACTTATTTGCTA
1 GAAAACATTACTTATTTGCTA
1803 GAAAACATTACTTATTTGCTA
1 GAAAACATTACTTATTTGCTA
1824 GAAAAC
1 GAAAAC
1830 GAGCTCACTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.42, C:0.15, G:0.10, T:0.33
Consensus pattern (21 bp):
GAAAACATTACTTATTTGCTA
Found at i:2618 original size:17 final size:17
Alignment explanation
Indices: 2596--2633 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
2586 CAGGTAAAAA
*
2596 ATATTTATGTAAA-AATT
1 ATATTTAT-AAAATAATT
2613 ATATTTATAAAATAATT
1 ATATTTATAAAATAATT
2630 ATAT
1 ATAT
2634 AAAAATAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
ATATTTATAAAATAATT
Found at i:2641 original size:14 final size:14
Alignment explanation
Indices: 2592--2641 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
2582 GATGCAGGTA
* *
2592 AAAAATATTTATGT
1 AAAAATAATTATAT
2606 AAAAATTATATT-TAT
1 AAAAA-TA-ATTATAT
2621 -AAAATAATTATAT
1 AAAAATAATTATAT
2634 AAAAATAA
1 AAAAATAA
2642 AATAAAATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
12 3 0.10
13 5 0.17
14 16 0.53
15 4 0.13
16 2 0.07
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (14 bp):
AAAAATAATTATAT
Found at i:3197 original size:127 final size:126
Alignment explanation
Indices: 2941--3201 Score: 321
Period size: 127 Copynumber: 2.1 Consensus size: 126
2931 CTTTTGGGGA
* * * * *
2941 GACACTTTTCTAAGTGTTGGGACAGACTTGCTGACATACGCTTTAGCCAACTCTTTCTATAAGGG
1 GACACTTTCCTAAGTGTTAGGACACACTTGCTAACATACGCTTTAGCCAACTCTTTCTATAAAGG
* * * * * *
3006 TTCGGATATGCATGCCTAAGACAATGCTTAAATAAGAGTTGTCTTTGTCCAACATTATGCC
66 TTCGGAGATGCATGCCTAAGACAACGCTAAAAGAAGAGTCGGCTTTGTCCAACATTATGCC
* * * *
3067 GACACTTTCCTAAGTGTTAGGATACACTTG-TCAACATATGCTTTTGCCAACTCTTTTGTATAAA
1 GACACTTTCCTAAGTGTTAGGACACACTTGCT-AACATACGCTTTAGCCAACTC-TTTCTATAAA
*
3131 GGTT-GAGAGATGCATGCCTAA-AGCAACGCTAAAAGAAGAGTCGGCTTTGTCCAACATTATGGC
64 GGTTCG-GAGATGCATGCCTAAGA-CAACGCTAAAAGAAGAGTCGGCTTTGTCCAACATTATGCC
3194 GACACTTT
1 GACACTTT
3202 TGCGCTGACA
Statistics
Matches: 115, Mismatches: 16, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
125 1 0.01
126 46 0.40
127 68 0.59
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.31
Consensus pattern (126 bp):
GACACTTTCCTAAGTGTTAGGACACACTTGCTAACATACGCTTTAGCCAACTCTTTCTATAAAGG
TTCGGAGATGCATGCCTAAGACAACGCTAAAAGAAGAGTCGGCTTTGTCCAACATTATGCC
Found at i:3320 original size:140 final size:141
Alignment explanation
Indices: 3067--3331 Score: 363
Period size: 140 Copynumber: 1.9 Consensus size: 141
3057 ACATTATGCC
* * *
3067 GACACTTTCCTAAGTGTTAGGATACACTTGTCAACATATGCTTTTGCCAACTCTTTTGTATAAAG
1 GACACATTCCTAAGTGTTAGGATACACTTGTCAACATACGCTTTGGCCAACTCTTTTGTATAAAG
* *
3132 GTTGAGAGATGCATGCCTAAAGCAACGCTAAAAGAAGAGTCGGCTTTGTCCAACATTATGGCGAC
66 GTTGAGAGATGCATGCCTAAAGCAACACTAAAAGAAGAGTCGGCTTTGTCCAACACTATGGCGAC
3197 ACTTTTGCGCT
131 ACTTTTGCGCT
* * ** *
3208 GACACATTCCTAAGTGTTGGGATAGACTTG-CTGGCATACGCTTTGGCCAACTC-TTTGTATAAG
1 GACACATTCCTAAGTGTTAGGATACACTTGTC-AACATACGCTTTGGCCAACTCTTTTGTATAAA
* * * * * *
3271 GGTTGGGATATGCATGCCTAAGGCAACACTTAAATAAGAGTTGGCTTTGTCCAACACTATG
65 GGTTGAGAGATGCATGCCTAAAGCAACACTAAAAGAAGAGTCGGCTTTGTCCAACACTATG
3332 CCAACCTTTT
Statistics
Matches: 107, Mismatches: 16, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
140 63 0.59
141 44 0.41
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (141 bp):
GACACATTCCTAAGTGTTAGGATACACTTGTCAACATACGCTTTGGCCAACTCTTTTGTATAAAG
GTTGAGAGATGCATGCCTAAAGCAACACTAAAAGAAGAGTCGGCTTTGTCCAACACTATGGCGAC
ACTTTTGCGCT
Found at i:3394 original size:38 final size:37
Alignment explanation
Indices: 3332--3498 Score: 176
Period size: 38 Copynumber: 4.5 Consensus size: 37
3322 CAACACTATG
* * *
3332 CCAACCTTTTT-AAGGTTGTCTTAGAGAAGGTCTATC
1 CCAACCTTTTTAAAGGTTGTATTAGATAAGGTTTATC
* * *
3368 TCAACCTTTTTAAAAGGTTGTATTAGACAATGTTTATC
1 CCAACCTTTTT-AAAGGTTGTATTAGATAAGGTTTATC
* ***
3406 CCAACCTTTTTAAAAAGTTACCTTAGATAAGGTTTATC
1 CCAACCTTTTT-AAAGGTTGTATTAGATAAGGTTTATC
* *
3444 CCAACCTTTTT-AAGGTTGAATTAGATAAGGTATATC
1 CCAACCTTTTTAAAGGTTGTATTAGATAAGGTTTATC
*
3480 CCAACTTTTTTGAAAGGTT
1 CCAACCTTTTT-AAAGGTT
3499 ACCTTAAACA
Statistics
Matches: 109, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
36 40 0.37
38 69 0.63
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (37 bp):
CCAACCTTTTTAAAGGTTGTATTAGATAAGGTTTATC
Found at i:3410 original size:74 final size:73
Alignment explanation
Indices: 3332--3568 Score: 244
Period size: 74 Copynumber: 3.2 Consensus size: 73
3322 CAACACTATG
** * *
3332 CCAACCTTTTT-AAGGTTGTCTTAGAGAAGGTCTATCTCAACCTTTTTAAAAGGTTGTATTAGAC
1 CCAACCTTTTTAAAGGTTACCTTAGACAAGGTCTATCCCAACCTTTTT--AAGGTTGTATTAGAC
3396 AATGTTTATC
64 AATGTTTATC
* * * * *
3406 CCAACCTTTTTAAAAAGTTACCTTAGATAAGGTTTATCCCAACCTTTTTAAGGTTGAATTAGATA
1 CCAACCTTTTT-AAAGGTTACCTTAGACAAGGTCTATCCCAACCTTTTTAAGGTTGTATTAGACA
* *
3471 AGGTATATC
65 ATGTTTATC
* * * * * * *
3480 CCAACTTTTTTGAAAGGTTACCTTAAACAAGGCCTATCCCATCCTTTTTCAGATTGTCTTAGAC-
1 CCAACCTTTTT-AAAGGTTACCTTAGACAAGGTCTATCCCAACCTTTTTAAGGTTGTATTAGACA
3544 ATGATTTATC
65 ATG-TTTATC
*
3554 CTAACCTTTTTAAAG
1 CCAACCTTTTTAAAG
3569 ATACTTTAGA
Statistics
Matches: 133, Mismatches: 27, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
73 6 0.05
74 97 0.73
76 30 0.23
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (73 bp):
CCAACCTTTTTAAAGGTTACCTTAGACAAGGTCTATCCCAACCTTTTTAAGGTTGTATTAGACAA
TGTTTATC
Found at i:3518 original size:38 final size:37
Alignment explanation
Indices: 3332--3528 Score: 157
Period size: 38 Copynumber: 5.3 Consensus size: 37
3322 CAACACTATG
** * *
3332 CCAACCTTTTT-AAGGTTGTCTTAGAGAAGGTCTATC
1 CCAACCTTTTTAAAGGTTACCTTAGATAAGGTATATC
* *** * * *
3368 TCAACCTTTTTAAAAGGTTGTATTAGACAATGTTTATC
1 CCAACCTTTTT-AAAGGTTACCTTAGATAAGGTATATC
* *
3406 CCAACCTTTTTAAAAAGTTACCTTAGATAAGGTTTATC
1 CCAACCTTTTT-AAAGGTTACCTTAGATAAGGTATATC
*
3444 CCAACCTTTTT-AAGGTTGA-ATTAGATAAGGTATATC
1 CCAACCTTTTTAAAGGTT-ACCTTAGATAAGGTATATC
* * * **
3480 CCAACTTTTTTGAAAGGTTACCTTAAACAAGGCCTATC
1 CCAACCTTTTT-AAAGGTTACCTTAGATAAGGTATATC
*
3518 CCATCCTTTTT
1 CCAACCTTTTT
3529 CAGATTGTCT
Statistics
Matches: 132, Mismatches: 23, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
36 40 0.30
37 2 0.02
38 90 0.68
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.38
Consensus pattern (37 bp):
CCAACCTTTTTAAAGGTTACCTTAGATAAGGTATATC
Found at i:3588 original size:12 final size:12
Alignment explanation
Indices: 3571--3603 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
3561 TTTTAAAGAT
3571 ACTTTAGACGAG
1 ACTTTAGACGAG
3583 ACTTTAGACGAG
1 ACTTTAGACGAG
3595 ACTTTAGAC
1 ACTTTAGAC
3604 AAGTTTATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.27
Consensus pattern (12 bp):
ACTTTAGACGAG
Found at i:3714 original size:133 final size:133
Alignment explanation
Indices: 3476--3715 Score: 295
Period size: 133 Copynumber: 1.8 Consensus size: 133
3466 AGATAAGGTA
* * *
3476 TATCCCAACTTTTTTGAAAGGTTACCTTAAACAAGGCCTATCCCATCCTTTTTCAGATTGTCTTA
1 TATCCCAACTTTTTTGAAAGGTTACCTTAAACAAGGCCTATCCCAACCTTTTTAAGATTGACTTA
* * * *
3541 GACATGATTTATCCTAACCTTTTTAAAGATACTTTAGACGAGACTTTAGACGAGACTTTAGACAA
66 GACAAGATCTATCCCAACCTTTTTAAAGATACCTTAGACGAGACTTTAGACGAGACTTTAGACAA
3606 GTT
131 GTT
* * * * * *
3609 TATCCCAACTTTTTTTAAATGTTGCCTTAGACAAGGTCTA-CTCCAACCTTTTTAAGGTT-ACGT
1 TATCCCAACTTTTTTGAAAGGTTACCTTAAACAAGGCCTATC-CCAACCTTTTTAAGATTGAC-T
* * * *
3672 TAGACAAGGTCTATCCCAACCTTTTTAAGGTTGCCTTAGACGAG
64 TAGACAAGATCTATCCCAACCTTTTTAAAGATACCTTAGACGAG
3716 TCTATCTCAA
Statistics
Matches: 88, Mismatches: 17, Indels: 4
0.81 0.16 0.04
Matches are distributed among these distances:
132 2 0.02
133 86 0.98
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (133 bp):
TATCCCAACTTTTTTGAAAGGTTACCTTAAACAAGGCCTATCCCAACCTTTTTAAGATTGACTTA
GACAAGATCTATCCCAACCTTTTTAAAGATACCTTAGACGAGACTTTAGACGAGACTTTAGACAA
GTT
Found at i:3727 original size:35 final size:36
Alignment explanation
Indices: 3598--3734 Score: 154
Period size: 36 Copynumber: 3.8 Consensus size: 36
3588 AGACGAGACT
* * * *
3598 TTAGACAA-GTTTATCCCAACTTTTTTTAAATGTTGCC
1 TTAGACAAGGTCTATCTCAAC-CTTTTT-AAGGTTGCC
* *
3635 TTAGACAAGGTCTA-CTCCAACCTTTTTAAGGTTACG
1 TTAGACAAGGTCTATCT-CAACCTTTTTAAGGTTGCC
*
3671 TTAGACAAGGTCTATCCCAACCTTTTTAAGGTTGCC
1 TTAGACAAGGTCTATCTCAACCTTTTTAAGGTTGCC
*
3707 TTAGACGA-GTCTATCTCAACCTTTTTAA
1 TTAGACAAGGTCTATCTCAACCTTTTTAA
3735 TATTTTACAA
Statistics
Matches: 86, Mismatches: 11, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
35 19 0.22
36 44 0.51
37 15 0.17
38 8 0.09
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (36 bp):
TTAGACAAGGTCTATCTCAACCTTTTTAAGGTTGCC
Found at i:4925 original size:20 final size:21
Alignment explanation
Indices: 4900--4944 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
4890 ATACATATAT
4900 AAGAAATAAAAG-AA-AAAAGA
1 AAGAAA-AAAAGAAACAAAAGA
4920 AAG-AAAAAAGAAACAAAAGA
1 AAGAAAAAAAGAAACAAAAGA
4940 AAGAA
1 AAGAA
4945 GAACAAAAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 5 0.23
19 4 0.18
20 12 0.55
21 1 0.05
ACGTcount: A:0.80, C:0.02, G:0.16, T:0.02
Consensus pattern (21 bp):
AAGAAAAAAAGAAACAAAAGA
Found at i:4951 original size:15 final size:16
Alignment explanation
Indices: 4919--4953 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
4909 AAGAAAAAAG
4919 AAAGAAAAAAGAAACA
1 AAAGAAAAAAGAAACA
*
4935 AAAGAAAGAAG-AACA
1 AAAGAAAAAAGAAACA
4950 AAAG
1 AAAG
4954 CTCAAACGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.77, C:0.06, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAGAAAAAAGAAACA
Found at i:4953 original size:11 final size:11
Alignment explanation
Indices: 4908--4937 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
4898 ATAAGAAATA
4908 AAAGAAAAAAG
1 AAAGAAAAAAG
4919 AAAGAAAAAAG
1 AAAGAAAAAAG
*
4930 AAACAAAA
1 AAAGAAAA
4938 GAAAGAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.83, C:0.03, G:0.13, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAAG
Found at i:8668 original size:23 final size:23
Alignment explanation
Indices: 8609--8802 Score: 129
Period size: 23 Copynumber: 8.6 Consensus size: 23
8599 ACACTAGCGC
* **
8609 GCTCTCTGTTTAGAACTGTACGT
1 GCTCTCTGTTTAGCACTGTGTGT
* *
8632 GCCCTCTATTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
*
8655 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGTTTAGCACTGTGT-GT
8678 GCTCTCTGTTATTAGCACT-TCGTGT
1 GCTCTCTG-T-TTAGCACTGT-GTGT
* *
8703 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
* *
8726 G--CTC-----AGTACTTTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
* *
8742 ACTCTCTGTTTAGCACTTTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
* *
8765 GCTCTCTGTTACCCAGCACT-TATGT
1 GCTCTCTGTT---TAGCACTGTGTGT
8790 GCTCTCTGTTTAG
1 GCTCTCTGTTTAG
8803 TACTTCGGTA
Statistics
Matches: 138, Mismatches: 17, Indels: 33
0.73 0.09 0.18
Matches are distributed among these distances:
16 11 0.08
18 3 0.02
21 3 0.02
22 5 0.04
23 75 0.54
24 2 0.01
25 32 0.23
26 7 0.05
ACGTcount: A:0.13, C:0.25, G:0.21, T:0.42
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTGTGTGT
Found at i:8679 original size:46 final size:48
Alignment explanation
Indices: 8609--8719 Score: 131
Period size: 48 Copynumber: 2.4 Consensus size: 48
8599 ACACTAGCGC
*
8609 GCTCTCTGTTTAGAACTGTACGTGCCCTCT-AT-TTAGCACTGT-GTGT
1 GCTCTCTGTTTAGCACTGTACGTGCCCTCTGATATTAGCACT-TCGTGT
* * *
8655 GCTCTCTGTTTAGCAC-GTCTCGTGCTCTCTGTTATTAGCACTTCGTGT
1 GCTCTCTGTTTAGCACTGT-ACGTGCCCTCTGATATTAGCACTTCGTGT
*
8703 GCTCTCTGATTAGCACT
1 GCTCTCTGTTTAGCACT
8720 TTGTGTGCTC
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
45 2 0.04
46 24 0.44
47 2 0.04
48 27 0.49
ACGTcount: A:0.14, C:0.26, G:0.21, T:0.40
Consensus pattern (48 bp):
GCTCTCTGTTTAGCACTGTACGTGCCCTCTGATATTAGCACTTCGTGT
Found at i:8758 original size:39 final size:39
Alignment explanation
Indices: 8694--8768 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
8684 TGTTATTAGC
*
8694 ACTTCGTGTGCTCTCTGATTAGCACTTTGTGTGCTCAGT
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
* *
8733 ACTTTGTGTACTCTCTGTTTAGCACTTTGTGTGCTC
1 ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTC
8769 TCTGTTACCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (39 bp):
ACTTCGTGTACTCTCTGATTAGCACTTTGTGTGCTCAGT
Found at i:9233 original size:14 final size:14
Alignment explanation
Indices: 9214--9242 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
9204 CTTTACCGGC
9214 TTAACGCATTTATT
1 TTAACGCATTTATT
9228 TTAACGCATTTATT
1 TTAACGCATTTATT
9242 T
1 T
9243 GTACATGTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.14, G:0.07, T:0.52
Consensus pattern (14 bp):
TTAACGCATTTATT
Found at i:10535 original size:21 final size:22
Alignment explanation
Indices: 10497--10538 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
10487 AAAAAAATTA
**
10497 AAAAAATTCTAATTTTTTTAAT
1 AAAAAATTCTAAAATTTTTAAT
10519 AAAAAATTC-AAAATTTTTAA
1 AAAAAATTCTAAAATTTTTAA
10539 AACTAATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (22 bp):
AAAAAATTCTAAAATTTTTAAT
Found at i:13441 original size:21 final size:21
Alignment explanation
Indices: 13416--13468 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
13406 AGAGCTTTTA
13416 GTATCGGTAGAGGTGAAACTT
1 GTATCGGTAGAGGTGAAACTT
*
13437 GTATCGGTAAAGGTGAAACTT
1 GTATCGGTAGAGGTGAAACTT
* *
13458 ATATTGGTAGA
1 GTATCGGTAGA
13469 AGAGTCACTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.30
Consensus pattern (21 bp):
GTATCGGTAGAGGTGAAACTT
Found at i:15514 original size:37 final size:37
Alignment explanation
Indices: 15464--15920 Score: 310
Period size: 38 Copynumber: 12.3 Consensus size: 37
15454 TGTCAATTCT
* * *
15464 AACC-TTTTT-AAGGTTGTTTTAGACATGTTTATCCC
1 AACCTTTTTTAAAGGTTGTCTTAGACAGGTCTATCCC
* * *
15499 AACCTTTTTTAAAGGTTGTCTTAGATTAAGTCTATTCC
1 AACCTTTTTTAAAGGTTGTCTTAGA-CAGGTCTATCCC
* *
15537 AACCTTTTTTAAAGGTTGCCTTAGACAAGGTTTATCCC
1 AACCTTTTTTAAAGGTTGTCTTAGAC-AGGTCTATCCC
* * * ** * *
15575 AATCTTTTTAAAAGATTACCTTAGACGGGTCTATCCT
1 AACCTTTTTTAAAGGTTGTCTTAGACAGGTCTATCCC
* * * *
15612 AACCTTTTTTAAAAGTTGTCTTAGATAAGGTTTATTCC
1 AACCTTTTTTAAAGGTTGTCTTAGA-CAGGTCTATCCC
**
15650 AA-CTTTTTTAAAAGGTTG-CTTTAGACAATATCTATCCC
1 AACCTTTTTT-AAAGGTTGTC-TTAGAC-AGGTCTATCCC
* * *
15688 AACC--TTTTAAAGGTTGTTTTAGACATGTCTATCCT
1 AACCTTTTTTAAAGGTTGTCTTAGACAGGTCTATCCC
* * * * *
15723 AACCTTTTTCAAAAGGTTGTCTTAGATAAGATATATCCT
1 AACCTTTTT-TAAAGGTTGTCTTAGA-CAGGTCTATCCC
* * * * *
15762 AA-CTTTTTT-AAGGTTTTCTTAGACAAAGTTTAACTC
1 AACCTTTTTTAAAGGTTGTCTTAGAC-AGGTCTATCCC
* *
15798 AACCTTTTTT-AA-GTTGCCTTAGATAAGGTCTATCCC
1 AACCTTTTTTAAAGGTTGTCTTAGA-CAGGTCTATCCC
* * *
15834 AA-CTTTTTT-AAGGTTGTCTTAAACGGGTTTATCCC
1 AACCTTTTTTAAAGGTTGTCTTAGACAGGTCTATCCC
* * **
15869 CACTTTTTTTAAAAGGTT-TGCTTAGACAAGACCTATCCC
1 AACCTTTTTT-AAAGGTTGT-CTTAGAC-AGGTCTATCCC
15908 AACCTTTATTTAA
1 AACCTTT-TTTAA
15921 GGTCGGCCTT
Statistics
Matches: 325, Mismatches: 73, Indels: 44
0.74 0.17 0.10
Matches are distributed among these distances:
35 36 0.11
36 72 0.22
37 65 0.20
38 124 0.38
39 25 0.08
40 3 0.01
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (37 bp):
AACCTTTTTTAAAGGTTGTCTTAGACAGGTCTATCCC
Found at i:15730 original size:74 final size:74
Alignment explanation
Indices: 15464--15914 Score: 357
Period size: 75 Copynumber: 6.1 Consensus size: 74
15454 TGTCAATTCT
* * * *
15464 AACCTTTTTAAGGTTGTTTTAGACATGTTTATCCCAACCTTTTTT-AAAGGTTG-TCTTAGATTA
1 AACCTTTTAAAGGTTGTCTTAGACAGGTTTATCCCAACCTTTTTTAAAAGGTTGCT-TTAGA-CA
*
15527 AG-TCTATTCC
64 AGATCTATCCC
* * * * *
15537 AACCTTTTTTAAAGGTTGCCTTAGACAAGGTTTATCCCAATC-TTTTTAAAAGATTACCTTAGAC
1 AACC--TTTTAAAGGTTGTCTTAGAC-AGGTTTATCCCAACCTTTTTTAAAAGGTTGCTTTAGAC
* * *
15601 -GGGTCTATCCT
63 AAGATCTATCCC
* * *
15612 AACCTTTTTTAAAAGTTGTCTTAGATAAGGTTTATTCCAA-CTTTTTTAAAAGGTTGCTTTAGAC
1 AACC--TTTTAAAGGTTGTCTTAGA-CAGGTTTATCCCAACCTTTTTTAAAAGGTTGCTTTAGAC
*
15676 AATATCTATCCC
63 AAGATCTATCCC
* * * * * *
15688 AACCTTTTAAAGGTTGTTTTAGACATGTCTATCCTAACCTTTTTCAAAAGGTTG-TCTTAGATAA
1 AACCTTTTAAAGGTTGTCTTAGACAGGTTTATCCCAACCTTTTTTAAAAGGTTGCT-TTAGACAA
* *
15752 GATATATCCT
65 GATCTATCCC
* * * * * * * *
15762 AACTTTTTTAAGGTTTTCTTAGACAAAGTTTAACTCAACCTTTTTT--AA-GTTGCCTTAGATAA
1 AACCTTTTAAAGGTTGTCTTAGAC-AGGTTTATCCCAACCTTTTTTAAAAGGTTGCTTTAGACAA
*
15824 GGTCTATCCC
65 GATCTATCCC
* * * * * *
15834 AACTTTTTTAAGGTTGTCTTAAACGGGTTTATCCCCACTTTTTTTAAAAGGTTTGC-TTAGACAA
1 AACCTTTTAAAGGTTGTCTTAGACAGGTTTATCCCAACCTTTTTTAAAAGG-TTGCTTTAGACAA
*
15898 GACCTATCCC
65 GATCTATCCC
15908 AACCTTT
1 AACCTTT
15915 ATTTAAGGTC
Statistics
Matches: 300, Mismatches: 61, Indels: 33
0.76 0.15 0.08
Matches are distributed among these distances:
71 15 0.05
72 41 0.14
73 18 0.06
74 90 0.30
75 101 0.34
76 35 0.12
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.41
Consensus pattern (74 bp):
AACCTTTTAAAGGTTGTCTTAGACAGGTTTATCCCAACCTTTTTTAAAAGGTTGCTTTAGACAAG
ATCTATCCC
Found at i:21958 original size:23 final size:23
Alignment explanation
Indices: 21932--21976 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
21922 TTTTAAAAAG
21932 TTAAAATATAAATTTATTATTTA
1 TTAAAATATAAATTTATTATTTA
** *
21955 TTAATTTATAATTTTATTATTT
1 TTAAAATATAAATTTATTATTT
21977 TAAAGAGTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TTAAAATATAAATTTATTATTTA
Found at i:22685 original size:23 final size:23
Alignment explanation
Indices: 22655--22698 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
22645 ATCTCTCAAT
22655 TATATAGACTTTTTGATACTTAC
1 TATATAGACTTTTTGATACTTAC
22678 TATATAGACTTTTTGATACTT
1 TATATAGACTTTTTGATACTT
22699 GCTAACGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.50
Consensus pattern (23 bp):
TATATAGACTTTTTGATACTTAC
Found at i:33883 original size:23 final size:23
Alignment explanation
Indices: 33827--33883 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
33817 CCTCCATCAT
*
33827 TGCTGACTAGACCTTCTAGAAGC
1 TGCTGACTGGACCTTCTAGAAGC
*
33850 TGCTGATTGGACCTTCTAGAAGC
1 TGCTGACTGGACCTTCTAGAAGC
*
33873 TGTTGACTGGA
1 TGCTGACTGGA
33884 TGCCACGTCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (23 bp):
TGCTGACTGGACCTTCTAGAAGC
Found at i:34650 original size:10 final size:9
Alignment explanation
Indices: 34618--34688 Score: 61
Period size: 9 Copynumber: 7.4 Consensus size: 9
34608 AGCAACCATG
34618 TTTTCTTCTT
1 TTTTCTT-TT
34628 TTTCTCTTTT
1 TTT-TCTTTT
*
34638 TTTCCTTTT
1 TTTTCTTTT
***
34647 TTTTCGAACCT
1 TTTTC--TTTT
*
34658 TTTGCTTTT
1 TTTTCTTTT
34667 TTTTCTTTT
1 TTTTCTTTT
34676 TTTTCTTTT
1 TTTTCTTTT
34685 TTTT
1 TTTT
34689 GCTGTTTGTA
Statistics
Matches: 48, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
9 31 0.65
10 8 0.17
11 9 0.19
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.77
Consensus pattern (9 bp):
TTTTCTTTT
Found at i:35639 original size:18 final size:17
Alignment explanation
Indices: 35606--35668 Score: 60
Period size: 17 Copynumber: 3.6 Consensus size: 17
35596 TAAAATACCA
35606 AAAATAAAT-A-GAAAT
1 AAAATAAATAATGAAAT
35621 AAAATAAATAATCGAAAT
1 AAAATAAATAAT-GAAAT
*
35639 -AAATTAATAATGAAGTAT
1 AAAATAAATAATGAA--AT
35657 AAAATTAAATAA
1 AAAA-TAAATAA
35669 ATAAAACAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
15 9 0.23
16 4 0.10
17 10 0.26
18 7 0.18
19 3 0.08
20 6 0.15
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.25
Consensus pattern (17 bp):
AAAATAAATAATGAAAT
Found at i:47717 original size:13 final size:13
Alignment explanation
Indices: 47699--47723 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
47689 AAATGTGATA
47699 GATTTGATATTTG
1 GATTTGATATTTG
47712 GATTTGATATTT
1 GATTTGATATTT
47724 TTCGATAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.20, T:0.56
Consensus pattern (13 bp):
GATTTGATATTTG
Done.