Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013012.1 Kokia drynarioides strain JFW-HI SEQ_128030, 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: 96470
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Warning! 23 characters in sequence are not A, C, G, or T
Found at i:2433 original size:44 final size:44
Alignment explanation
Indices: 2370--2500 Score: 235
Period size: 44 Copynumber: 3.0 Consensus size: 44
2360 CAGTTGTACA
2370 TACACTGTAGTTTTACAATGGAAAAGAAATACAATGATTATACC
1 TACACTGTAGTTTTACAATGGAAAAGAAATACAATGATTATACC
2414 TACACTGTAGTTTTACAATGGAAAAGAAATACAATGATTATACC
1 TACACTGTAGTTTTACAATGGAAAAGAAATACAATGATTATACC
* **
2458 TACACTGTAATTTTACAATAAAAAAGAAATACAATGATTATAC
1 TACACTGTAGTTTTACAATGGAAAAGAAATACAATGATTATAC
2501 AATCTTCTTT
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
44 84 1.00
ACGTcount: A:0.46, C:0.13, G:0.11, T:0.30
Consensus pattern (44 bp):
TACACTGTAGTTTTACAATGGAAAAGAAATACAATGATTATACC
Found at i:2799 original size:14 final size:14
Alignment explanation
Indices: 2765--2800 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
2755 TACATATCTA
2765 TCCATATAAATATT
1 TCCATATAAATATT
*
2779 T-CATATAATTATT
1 TCCATATAAATATT
2792 TCCATATAA
1 TCCATATAA
2801 CCGATTCATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (14 bp):
TCCATATAAATATT
Found at i:2808 original size:27 final size:25
Alignment explanation
Indices: 2778--2837 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 25
2768 ATATAAATAT
**
2778 TTCATATAATTATTTCCATATAACCGA
1 TTCATATAACCATTT-CATATAACC-A
*
2805 TTCATATAGCCATTTCATATAACCA
1 TTCATATAACCATTTCATATAACCA
2830 TTCATATA
1 TTCATATA
2838 GTCATTTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
25 9 0.30
26 9 0.30
27 12 0.40
ACGTcount: A:0.37, C:0.20, G:0.03, T:0.40
Consensus pattern (25 bp):
TTCATATAACCATTTCATATAACCA
Found at i:2810 original size:13 final size:12
Alignment explanation
Indices: 2794--2837 Score: 61
Period size: 13 Copynumber: 3.5 Consensus size: 12
2784 TAATTATTTC
2794 CATATAACCGATT
1 CATATAACC-ATT
*
2807 CATATAGCCATTT
1 CATATAACCA-TT
2820 CATATAACCATT
1 CATATAACCATT
2832 CATATA
1 CATATA
2838 GTCATTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 9 0.32
13 19 0.68
ACGTcount: A:0.39, C:0.23, G:0.05, T:0.34
Consensus pattern (12 bp):
CATATAACCATT
Found at i:2838 original size:25 final size:27
Alignment explanation
Indices: 2789--2844 Score: 89
Period size: 25 Copynumber: 2.1 Consensus size: 27
2779 TCATATAATT
2789 ATTTCCATATAACCGATTCATATAGCC
1 ATTTCCATATAACCGATTCATATAGCC
*
2816 ATTT-CATATAACC-ATTCATATAGTC
1 ATTTCCATATAACCGATTCATATAGCC
2841 ATTT
1 ATTT
2845 TAAAGTGTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
25 15 0.54
26 9 0.32
27 4 0.14
ACGTcount: A:0.34, C:0.21, G:0.05, T:0.39
Consensus pattern (27 bp):
ATTTCCATATAACCGATTCATATAGCC
Found at i:2843 original size:12 final size:12
Alignment explanation
Indices: 2794--2843 Score: 55
Period size: 13 Copynumber: 4.0 Consensus size: 12
2784 TAATTATTTC
*
2794 CATATAACCGATT
1 CATATAGCC-ATT
2807 CATATAGCCATTT
1 CATATAGCCA-TT
*
2820 CATATAACCATT
1 CATATAGCCATT
*
2832 CATATAGTCATT
1 CATATAGCCATT
2844 TTAAAGTGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
12 13 0.41
13 19 0.59
ACGTcount: A:0.36, C:0.22, G:0.06, T:0.36
Consensus pattern (12 bp):
CATATAGCCATT
Found at i:11478 original size:43 final size:43
Alignment explanation
Indices: 11420--11509 Score: 117
Period size: 43 Copynumber: 2.1 Consensus size: 43
11410 ATTTTTTAAA
*
11420 AATATTTTCGAGGAAAACTATATGTTTGAGCATTATCTAGTTT
1 AATATTTTCGAGGAAAACTATATATTTGAGCATTATCTAGTTT
* ** * * *
11463 AATATTTTTGAGGAAAGTTATGTATTTGAGGATTGTCTAGTTT
1 AATATTTTCGAGGAAAACTATATATTTGAGCATTATCTAGTTT
11506 AATA
1 AATA
11510 ATACATTTTG
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.32, C:0.06, G:0.19, T:0.43
Consensus pattern (43 bp):
AATATTTTCGAGGAAAACTATATATTTGAGCATTATCTAGTTT
Found at i:14597 original size:12 final size:12
Alignment explanation
Indices: 14562--14600 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
14552 ATAAATACAA
*
14562 TATAAATCAACC
1 TATAAATCAGCC
* *
14574 TATTAATTAGCC
1 TATAAATCAGCC
14586 TATAAATCAGCC
1 TATAAATCAGCC
14598 TAT
1 TAT
14601 GATTCTGTAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.41, C:0.21, G:0.05, T:0.33
Consensus pattern (12 bp):
TATAAATCAGCC
Found at i:29813 original size:23 final size:23
Alignment explanation
Indices: 29769--29855 Score: 95
Period size: 23 Copynumber: 3.8 Consensus size: 23
29759 TTAATGTTCA
**
29769 CGAACATGTTCATTTAAC-TTAAT
1 CGAACATGTTCA-CGAACATTAAT
*
29792 CGAGCATGTTCACGAACATTAAT
1 CGAACATGTTCACGAACATTAAT
* *
29815 TGAACATGTTCACGAACATTAAA
1 CGAACATGTTCACGAACATTAAT
* *
29838 CGAATATGTTCAGGAACA
1 CGAACATGTTCACGAACA
29856 ATGTTAATGA
Statistics
Matches: 54, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
22 3 0.06
23 51 0.94
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (23 bp):
CGAACATGTTCACGAACATTAAT
Found at i:31981 original size:16 final size:16
Alignment explanation
Indices: 31960--31990 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
31950 TTTTAAAATT
31960 GGACTTAGACGACTAA
1 GGACTTAGACGACTAA
31976 GGACTTAGACGACTA
1 GGACTTAGACGACTA
31991 GGAAGCTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.19, G:0.26, T:0.19
Consensus pattern (16 bp):
GGACTTAGACGACTAA
Found at i:34478 original size:3 final size:3
Alignment explanation
Indices: 34456--34554 Score: 83
Period size: 3 Copynumber: 33.0 Consensus size: 3
34446 CATGATGTTT
* ** *
34456 ATG ATG AT- ATTG ATG CTG ATG ATG ATG ATG ACA AAG ATG ATG ATG
1 ATG ATG ATG A-TG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
** * * * * *
34501 ATG ATG ATG ATG ATG ACA ATG ATA ATG AAG TTG ATG AAG ACG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
34549 ATG ATG
1 ATG ATG
34555 GCAGTGAAGA
Statistics
Matches: 74, Mismatches: 20, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
2 1 0.01
3 72 0.97
4 1 0.01
ACGTcount: A:0.37, C:0.04, G:0.29, T:0.29
Consensus pattern (3 bp):
ATG
Found at i:40245 original size:19 final size:19
Alignment explanation
Indices: 40224--40294 Score: 61
Period size: 20 Copynumber: 3.6 Consensus size: 19
40214 TTACTATAAA
40224 TTTTAAGATTATACCAAAAT
1 TTTTAAGATT-TACCAAAAT
* *
40244 TTTTAAGATTTACCTATAT
1 TTTTAAGATTTACCAAAAT
* * *
40263 TTCTAAAGTTTTACCACAAT
1 TT-TTAAGATTTACCAAAAT
*
40283 TTCTAAAGATTT
1 TT-TTAAGATTT
40295 CCATGCTGTC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
19 9 0.21
20 33 0.79
ACGTcount: A:0.37, C:0.13, G:0.06, T:0.45
Consensus pattern (19 bp):
TTTTAAGATTTACCAAAAT
Found at i:40377 original size:20 final size:20
Alignment explanation
Indices: 40352--40389 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
40342 AGTGAAATCT
40352 TTAGAAATAATGATAAAGAC
1 TTAGAAATAATGATAAAGAC
* *
40372 TTAGAAATGATGGTAAAG
1 TTAGAAATAATGATAAAG
40390 CCTTTGAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.03, G:0.21, T:0.26
Consensus pattern (20 bp):
TTAGAAATAATGATAAAGAC
Found at i:40398 original size:20 final size:20
Alignment explanation
Indices: 40350--40398 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
40340 ACAGTGAAAT
40350 CTTTAGAAATAATGATAAAGA
1 CTTT-GAAATAATGATAAAGA
* * * *
40371 CTTAGAAATGATGGTAAAGC
1 CTTTGAAATAATGATAAAGA
40391 CTTTGAAA
1 CTTTGAAA
40399 CATTAGTAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 20 0.87
21 3 0.13
ACGTcount: A:0.45, C:0.08, G:0.18, T:0.29
Consensus pattern (20 bp):
CTTTGAAATAATGATAAAGA
Found at i:41195 original size:23 final size:22
Alignment explanation
Indices: 41169--41230 Score: 61
Period size: 25 Copynumber: 2.7 Consensus size: 22
41159 CAACATTTAA
*
41169 TTAATTTTTTAAAAATATATTTT
1 TTAATATTTTAAAAATAT-TTTT
* *
41192 TTAAAAGATTATAAAAATATTTTT
1 TT--AATATTTTAAAAATATTTTT
*
41216 TTAATATTTAAAAAA
1 TTAATATTTTAAAAA
41231 AAAATTAAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
22 10 0.32
23 2 0.06
24 6 0.19
25 13 0.42
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
TTAATATTTTAAAAATATTTTT
Found at i:41886 original size:29 final size:30
Alignment explanation
Indices: 41823--41883 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
41813 TAATAAACGT
*
41823 AAATTTAACATAATAATTTTAATAATATAA
1 AAATTGAACATAATAATTTTAATAATATAA
* * *
41853 CAATTGAACTTAA-AATTTTAA-AATTTAA
1 AAATTGAACATAATAATTTTAATAATATAA
41881 AAA
1 AAA
41884 ATTAAGCACG
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
28 8 0.31
29 8 0.31
30 10 0.38
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.38
Consensus pattern (30 bp):
AAATTGAACATAATAATTTTAATAATATAA
Found at i:43925 original size:3 final size:3
Alignment explanation
Indices: 43917--43944 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
43907 TAGTTTTGTT
43917 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
43945 GGAGGAGGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:45543 original size:18 final size:17
Alignment explanation
Indices: 45516--45554 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
45506 TCAACTATAA
**
45516 AAAAATAATATTTTAAT
1 AAAAATAATAAATTAAT
45533 AAAAATAAATAAATTAAT
1 AAAAAT-AATAAATTAAT
45551 AAAA
1 AAAA
45555 TCAATAATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAAATAATAAATTAAT
Found at i:45544 original size:21 final size:18
Alignment explanation
Indices: 45512--45563 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 18
45502 GGTATCAACT
45512 ATAAAA-AAATAATATTTTA
1 ATAAAATAAATAATA--TTA
45531 ATAAAAATAAATAA-ATTA
1 AT-AAAATAAATAATATTA
*
45549 ATAAAATCAATAATA
1 ATAAAATAAATAATA
45564 GCCCGAACTC
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 10 0.34
18 6 0.21
19 2 0.07
20 5 0.17
21 6 0.21
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (18 bp):
ATAAAATAAATAATATTA
Found at i:49015 original size:16 final size:16
Alignment explanation
Indices: 48996--49046 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
48986 TATGAAATTT
* * *
48996 AATTTTATAATATATC
1 AATTATATAAAATATA
49012 AATTATATAAAATATA
1 AATTATATAAAATATA
*
49028 AATTATATATAATTATA
1 AATTATATA-AAATATA
49045 AA
1 AA
49047 ATGATAATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
16 22 0.73
17 8 0.27
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
AATTATATAAAATATA
Found at i:65172 original size:24 final size:24
Alignment explanation
Indices: 65145--65190 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
65135 GCTGTTTAAG
*
65145 ATTAGATTAAAATTA-AATTAATCA
1 ATTA-ATTAAAATAATAATTAATCA
65169 ATTAATTAAAATAATAATTAAT
1 ATTAATTAAAATAATAATTAAT
65191 ATTATGTGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (24 bp):
ATTAATTAAAATAATAATTAATCA
Found at i:65175 original size:17 final size:16
Alignment explanation
Indices: 65155--65190 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
65145 ATTAGATTAA
*
65155 AATTAAATTAATCAATT
1 AATTAAAATAAT-AATT
65172 AATTAAAATAATAATT
1 AATTAAAATAATAATT
65188 AAT
1 AAT
65191 ATTATGTGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (16 bp):
AATTAAAATAATAATT
Found at i:65502 original size:57 final size:58
Alignment explanation
Indices: 65390--65499 Score: 149
Period size: 57 Copynumber: 1.9 Consensus size: 58
65380 GAAATAAATA
*
65390 AAATAGAAATATATCAATAATCTAAAAATAATATTAATATAATATTCTAATATATTTG
1 AAATAGAAATATATAAATAATCTAAAAATAATATTAATATAATATTCTAATATATTTG
*
65448 AAATA-AAATATATAAATAAAT-TAATAA-AATATATAA-ATAA-ATTCTAATATAT
1 AAATAGAAATATATAAAT-AATCTAAAAATAATAT-TAATATAATATTCTAATATAT
65500 ATTAGAATAT
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
55 12 0.25
56 9 0.19
57 19 0.40
58 8 0.17
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (58 bp):
AAATAGAAATATATAAATAATCTAAAAATAATATTAATATAATATTCTAATATATTTG
Found at i:65513 original size:14 final size:15
Alignment explanation
Indices: 65494--65539 Score: 58
Period size: 16 Copynumber: 3.1 Consensus size: 15
65484 ATAAATTCTA
65494 ATATATAT-TAGAAT
1 ATATATATATAGAAT
65508 ATATATATAATAGAAT
1 ATATATAT-ATAGAAT
* *
65524 ATATAAATATATAAT
1 ATATATATATAGAAT
65539 A
1 A
65540 GAATTAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 8 0.29
15 7 0.25
16 13 0.46
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (15 bp):
ATATATATATAGAAT
Found at i:65513 original size:16 final size:16
Alignment explanation
Indices: 65494--65533 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
65484 ATAAATTCTA
65494 ATATATATTAGAATAT
1 ATATATATTAGAATAT
*
65510 ATATATAATAGAATAT
1 ATATATATTAGAATAT
*
65526 ATAAATAT
1 ATATATAT
65534 ATAATAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (16 bp):
ATATATATTAGAATAT
Found at i:67158 original size:57 final size:59
Alignment explanation
Indices: 67097--67266 Score: 191
Period size: 57 Copynumber: 2.9 Consensus size: 59
67087 TTAATCAAAC
* *
67097 ATTTGGTATTTAAATTTGACATTTTTTTCTAATTTGGTACTTAAA-TTTTTTG-ACCCA
1 ATTTGGTATTTAAACTTGACATTTTTTTCTAATTTGGTACCTAAACTTTTTTGAACCCA
* * * * * *
67154 ATTTGATACTTGAACTTGACATTTTTTCCTATTTTGATACCTAAACTTTTTTTGAACCCA
1 ATTTGGTATTTAAACTTGACATTTTTTTCTAATTTGGTACCTAAAC-TTTTTTGAACCCA
* * * **
67214 ATTTAGTATCTAAACTTGATATTTTTTTCCTAATTTGGTACCTATGCTTTTTT
1 ATTTGGTATTTAAACTTGACATTTTTTT-CTAATTTGGTACCTAAACTTTTTT
67267 TTAGATTCAA
Statistics
Matches: 90, Mismatches: 19, Indels: 5
0.79 0.17 0.04
Matches are distributed among these distances:
57 37 0.41
59 7 0.08
60 32 0.36
61 14 0.16
ACGTcount: A:0.25, C:0.14, G:0.09, T:0.51
Consensus pattern (59 bp):
ATTTGGTATTTAAACTTGACATTTTTTTCTAATTTGGTACCTAAACTTTTTTGAACCCA
Found at i:67459 original size:22 final size:24
Alignment explanation
Indices: 67434--67494 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 24
67424 AAAAATTGAC
*
67434 TATTTTACTTTT-TTT-TTATATA
1 TATTTTAATTTTATTTGTTATATA
67456 TATTTTTGAATTTTATTTGTTATATA
1 TA-TTTT-AATTTTATTTGTTATATA
67482 T-TTTTAGATTTTA
1 TATTTTA-ATTTTA
67495 AAAAACTACT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 5 0.15
24 15 0.45
25 3 0.09
26 8 0.24
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.69
Consensus pattern (24 bp):
TATTTTAATTTTATTTGTTATATA
Found at i:69679 original size:103 final size:103
Alignment explanation
Indices: 69536--69743 Score: 344
Period size: 103 Copynumber: 2.0 Consensus size: 103
69526 AATGAGTGAT
* * * * *
69536 TTGATACTTAAGAGTGTTCATTACGATCCAACTCTCTTTCTTTGAAATTTGTCTAGTGCATAAAA
1 TTGACACTTAAGAGTGTCCATTACGATCCAACTCTCTTTCTTTGAAACTTGCCTAGTGCACAAAA
* *
69601 TTTTCAACATTTGTTACGTGGATGAGACTTTGGCTATA
66 TTTTCAACATTTGTTACGTGCATGAGACTTTAGCTATA
69639 TTGACACTTAAGAGTGTCCATTACGATCCAACTCTCTTTCTTTGAAACTTGCCTAGTGCACAAAA
1 TTGACACTTAAGAGTGTCCATTACGATCCAACTCTCTTTCTTTGAAACTTGCCTAGTGCACAAAA
*
69704 TTTTCAACATTTGTTACGTGCATGAGACTTTAGCTGTA
66 TTTTCAACATTTGTTACGTGCATGAGACTTTAGCTATA
69742 TT
1 TT
69744 AACAAGAATT
Statistics
Matches: 97, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
103 97 1.00
ACGTcount: A:0.27, C:0.18, G:0.16, T:0.39
Consensus pattern (103 bp):
TTGACACTTAAGAGTGTCCATTACGATCCAACTCTCTTTCTTTGAAACTTGCCTAGTGCACAAAA
TTTTCAACATTTGTTACGTGCATGAGACTTTAGCTATA
Found at i:70705 original size:6 final size:6
Alignment explanation
Indices: 70694--70726 Score: 57
Period size: 6 Copynumber: 5.3 Consensus size: 6
70684 TTATAACATG
70694 ATAATT ATAATT ATAATT ATAATTT ATAATT AT
1 ATAATT ATAATT ATAATT ATAA-TT ATAATT AT
70727 TAGAAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
ATAATT
Found at i:82197 original size:2 final size:2
Alignment explanation
Indices: 82190--82220 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
82180 GAGGGAGATG
82190 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
82221 TCCAAAGAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:84666 original size:41 final size:42
Alignment explanation
Indices: 84608--84716 Score: 127
Period size: 41 Copynumber: 2.6 Consensus size: 42
84598 CTGCCATCTC
*
84608 AGTGCACAA-TCGAATAAACAGAAGTAAAT-ATACTGGCACAT
1 AGTGCATAATTCG-ATAAACAGAAGTAAATCATACTGGCACAT
*
84649 AGTGCATAATTCGATAAATC-GAAGT-AATCATATTGGCACAT
1 AGTGCATAATTCGATAAA-CAGAAGTAAATCATACTGGCACAT
* * *
84690 AGTGCATCATTAGATAAATAGAAGTAA
1 AGTGCATAATTCGATAAACAGAAGTAA
84717 TCTGCACTCA
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
40 3 0.05
41 50 0.86
42 5 0.09
ACGTcount: A:0.44, C:0.14, G:0.17, T:0.25
Consensus pattern (42 bp):
AGTGCATAATTCGATAAACAGAAGTAAATCATACTGGCACAT
Found at i:84717 original size:41 final size:41
Alignment explanation
Indices: 84621--84718 Score: 135
Period size: 41 Copynumber: 2.4 Consensus size: 41
84611 GCACAATCGA
* *
84621 ATAAACAGAAGTAAAT-ATACTGGCACATAGTGCATAATTCG
1 ATAAATAGAAGT-AATCATACTGGCACATAGTGCATAATTAG
* * *
84662 ATAAATCGAAGTAATCATATTGGCACATAGTGCATCATTAG
1 ATAAATAGAAGTAATCATACTGGCACATAGTGCATAATTAG
84703 ATAAATAGAAGTAATC
1 ATAAATAGAAGTAATC
84719 TGCACTCAGC
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
40 3 0.06
41 47 0.94
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (41 bp):
ATAAATAGAAGTAATCATACTGGCACATAGTGCATAATTAG
Found at i:88771 original size:20 final size:20
Alignment explanation
Indices: 88743--88780 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
88733 TGTAAAAAAT
*
88743 AAAAAAAAATTAAATTCTTG
1 AAAAAAAAACTAAATTCTTG
*
88763 AAAATAAAACTAAATTCT
1 AAAAAAAAACTAAATTCT
88781 AAATTTGTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.61, C:0.08, G:0.03, T:0.29
Consensus pattern (20 bp):
AAAAAAAAACTAAATTCTTG
Done.