Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01004644.1 Kokia drynarioides strain JFW-HI SEQ_118174, 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: 74377
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 35 characters in sequence are not A, C, G, or T
Found at i:1464 original size:45 final size:45
Alignment explanation
Indices: 1334--1470 Score: 166
Period size: 45 Copynumber: 3.0 Consensus size: 45
1324 GGGAGGAATA
* * * ** **
1334 GAGTATCGCGATGACTCGTCAAACTCAACCTGATATCCTTCCCTT
1 GAGTATTGCGGTGGCTCGTCAAACTCAGGCTGATATCCTTGGCTT
* * *
1379 GAGTATTGCGGTGGCTCGTTAAATTTAGGCTGATATCCTTGGCTT
1 GAGTATTGCGGTGGCTCGTCAAACTCAGGCTGATATCCTTGGCTT
* *
1424 GAGTATTGCTGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTT
1 GAGTATTGCGGTGGCTCGTCAAACTCAGGCTGATATCCTTGGCTT
1469 GA
1 GA
1471 TAAGCTATGC
Statistics
Matches: 78, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 78 1.00
ACGTcount: A:0.20, C:0.22, G:0.25, T:0.33
Consensus pattern (45 bp):
GAGTATTGCGGTGGCTCGTCAAACTCAGGCTGATATCCTTGGCTT
Found at i:3364 original size:16 final size:16
Alignment explanation
Indices: 3343--3391 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
3333 TGGTGGAGAT
3343 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
3359 ATTATTTTTAT-ATT-
1 ATTATTTTGATAATTA
*
3373 A-TATTTTGGTAATTA
1 ATTATTTTGATAATTA
3388 ATTA
1 ATTA
3392 GCTAGATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
13 7 0.26
14 4 0.15
15 4 0.15
16 12 0.44
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:3676 original size:20 final size:21
Alignment explanation
Indices: 3651--3693 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
3641 TACTTACTAC
3651 TATTAAC-AACAAAATAAAAT
1 TATTAACTAACAAAATAAAAT
* *
3671 TATTAACTAGCAAAATTAAAT
1 TATTAACTAACAAAATAAAAT
3692 TA
1 TA
3694 AAGTAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.58, C:0.09, G:0.02, T:0.30
Consensus pattern (21 bp):
TATTAACTAACAAAATAAAAT
Found at i:4086 original size:4 final size:4
Alignment explanation
Indices: 4079--4117 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
4069 TTCCTTCTTC
*
4079 TTCT TTCT TTCT TTCT TTCTT TTTT TTCT TTCT TT-T TTC
1 TTCT TTCT TTCT TTCT TTC-T TTCT TTCT TTCT TTCT TTC
4118 CTTCAATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
3 3 0.10
4 25 0.81
5 3 0.10
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (4 bp):
TTCT
Found at i:4094 original size:25 final size:25
Alignment explanation
Indices: 4057--4117 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
4047 CTTTTTCCCG
*
4057 TTCTTCTCCTTCTTCCTTCTTCTTCT
1 TTCTT-TCTTTCTTCCTTCTTCTTCT
* * *
4083 TTCTTTCTTTCTTTCTTTTTTTTCT
1 TTCTTTCTTTCTTCCTTCTTCTTCT
4108 TTCTTT-TTTC
1 TTCTTTCTTTC
4118 CTTCAATTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 4 0.13
25 22 0.71
26 5 0.16
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (25 bp):
TTCTTTCTTTCTTCCTTCTTCTTCT
Found at i:4096 original size:12 final size:11
Alignment explanation
Indices: 4076--4117 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
4066 TTCTTCCTTC
*
4076 TTCTTCTTTCT
1 TTCTTTTTTCT
4087 TTCTTTCTTTC-
1 TTCTTT-TTTCT
4098 TT-TTTTTTCT
1 TTCTTTTTTCT
4108 TTCTTTTTTC
1 TTCTTTTTTC
4118 CTTCAATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
9 4 0.15
10 5 0.19
11 14 0.52
12 4 0.15
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (11 bp):
TTCTTTTTTCT
Found at i:4392 original size:10 final size:11
Alignment explanation
Indices: 4367--4393 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
4357 GTCAGATATT
4367 TTTTTATCGTA
1 TTTTTATCGTA
4378 TTTTTATCGTA
1 TTTTTATCGTA
4389 TTTTT
1 TTTTT
4394 CTGGAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.15, C:0.07, G:0.07, T:0.70
Consensus pattern (11 bp):
TTTTTATCGTA
Found at i:9882 original size:21 final size:21
Alignment explanation
Indices: 9845--9884 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
9835 TGTATATTAG
*
9845 GCTTTCTTGAAAGTAAAGTTC
1 GCTTTCTGGAAAGTAAAGTTC
9866 GCTTTCTGGCAAA-TAAAGT
1 GCTTTCTGG-AAAGTAAAGT
9885 GATCTAAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (21 bp):
GCTTTCTGGAAAGTAAAGTTC
Found at i:22030 original size:3 final size:3
Alignment explanation
Indices: 22024--22053 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
22014 ATTACAGTAT
*
22024 TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
22054 CTGTTATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:23678 original size:2 final size:2
Alignment explanation
Indices: 23673--23710 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
23663 TAAAATCATA
23673 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
23711 TCTAGACAAA
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:24899 original size:18 final size:21
Alignment explanation
Indices: 24878--24924 Score: 73
Period size: 18 Copynumber: 2.4 Consensus size: 21
24868 AATTTTTTAT
24878 TTAATTATG-AATTAAA-AG-
1 TTAATTATGTAATTAAAGAGA
24896 TTAATTATGTAATTAAAGAGA
1 TTAATTATGTAATTAAAGAGA
24917 TTAATTAT
1 TTAATTAT
24925 CGTCTTCTAC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.35
19 7 0.27
20 2 0.08
21 8 0.31
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.43
Consensus pattern (21 bp):
TTAATTATGTAATTAAAGAGA
Found at i:30951 original size:25 final size:22
Alignment explanation
Indices: 30898--30961 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 22
30888 TTAAAAAATT
*
30898 TAAAAATTGTTCAAAAATAAAAA
1 TAAAAATTATT-AAAAATAAAAA
30921 TAAAAATTATTAGAAAATAAATAAA
1 TAAAAATTATTA-AAAAT-AA-AAA
*
30946 TTAAAATTATTAAAAA
1 TAAAAATTATTAAAAA
30962 GCATAAAAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
22 1 0.03
23 15 0.42
24 6 0.17
25 14 0.39
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.30
Consensus pattern (22 bp):
TAAAAATTATTAAAAATAAAAA
Found at i:39820 original size:17 final size:18
Alignment explanation
Indices: 39798--39844 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
39788 AACAATATAT
*
39798 AAAATGTAAATAATTC-A
1 AAAATGTAAAAAATTCTA
*
39815 AAAATGAAAAAAAATTCTA
1 AAAATG-TAAAAAATTCTA
39834 AAAAT-TAAAAA
1 AAAATGTAAAAA
39845 GCCATATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 11 0.44
18 8 0.32
19 6 0.24
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.23
Consensus pattern (18 bp):
AAAATGTAAAAAATTCTA
Found at i:39843 original size:18 final size:18
Alignment explanation
Indices: 39809--39844 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
39799 AAATGTAAAT
39809 AATTCAAAAATGAAAAAA
1 AATTCAAAAATGAAAAAA
*
39827 AATTCTAAAAATTAAAAA
1 AATTC-AAAAATGAAAAA
39845 GCCATATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.69, C:0.06, G:0.03, T:0.22
Consensus pattern (18 bp):
AATTCAAAAATGAAAAAA
Found at i:40817 original size:22 final size:22
Alignment explanation
Indices: 40790--40832 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
40780 TTATAATTTT
40790 TATAATATTTTATAAA-AAAAAG
1 TATAAT-TTTTATAAATAAAAAG
*
40812 TATAATTTTTTTAAATAAAAA
1 TATAATTTTTATAAATAAAAA
40833 CAAACAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (22 bp):
TATAATTTTTATAAATAAAAAG
Found at i:41118 original size:23 final size:23
Alignment explanation
Indices: 41092--41161 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
41082 TTTATTTAAC
41092 TTAATCGAACATGTTCACGAACA
1 TTAATCGAACATGTTCACGAACA
* * * * *
41115 TTAAACAAACATGTTCATGTATA
1 TTAATCGAACATGTTCACGAACA
* *
41138 TATAATTGAACATGTTCACAAACA
1 T-TAATCGAACATGTTCACGAACA
41162 ATGTTAAAAA
Statistics
Matches: 34, Mismatches: 12, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
23 19 0.56
24 15 0.44
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.30
Consensus pattern (23 bp):
TTAATCGAACATGTTCACGAACA
Found at i:41283 original size:12 final size:12
Alignment explanation
Indices: 41250--41283 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
41240 ATCATTAATA
41250 AATAAACGAGTC
1 AATAAACGAGTC
*
41262 -ATAAATGAGTC
1 AATAAACGAGTC
41273 AATAAACGAGT
1 AATAAACGAGT
41284 TTTTAAACGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.50, C:0.12, G:0.18, T:0.21
Consensus pattern (12 bp):
AATAAACGAGTC
Found at i:41445 original size:26 final size:26
Alignment explanation
Indices: 41409--41461 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 26
41399 ATGAATATAA
41409 ATGAACGTTATACGAACAGTTCACGG
1 ATGAACGTTATACGAACAGTTCACGG
*
41435 ATGAACGTTATACGAGCAGTTCACGG
1 ATGAACGTTATACGAACAGTTCACGG
41461 A
1 A
41462 CAGTTCATCG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.34, C:0.19, G:0.25, T:0.23
Consensus pattern (26 bp):
ATGAACGTTATACGAACAGTTCACGG
Found at i:44188 original size:2 final size:2
Alignment explanation
Indices: 44181--44207 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
44171 TTGAGGGCTC
44181 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
44208 CACCCATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:47055 original size:29 final size:28
Alignment explanation
Indices: 46992--47070 Score: 86
Period size: 29 Copynumber: 2.7 Consensus size: 28
46982 ATATGTGAAC
* *
46992 TTTGATTTAATATGTAATATTATACATAAAT
1 TTTGATTT--TATGCAATTTTA-ACATAAAT
*
47023 TTTGATTTTGTGCAATTTTAACATGAAAT
1 TTTGATTTTATGCAATTTTAACAT-AAAT
*
47052 TTTGATTTTATTCAATTTT
1 TTTGATTTTATGCAATTTT
47071 TATAAATCAC
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
28 4 0.10
29 30 0.71
31 8 0.19
ACGTcount: A:0.33, C:0.05, G:0.09, T:0.53
Consensus pattern (28 bp):
TTTGATTTTATGCAATTTTAACATAAAT
Found at i:47285 original size:29 final size:30
Alignment explanation
Indices: 47253--47310 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
47243 TTAGGTGTAT
* *
47253 AATTGTACA-AAATCAAAGTTTATGTATCA
1 AATTGCACATAAATCAAAGTTCATGTATCA
*
47282 AATTGCACATTAAATTAAAGTTCATGTAT
1 AATTGCACA-TAAATCAAAGTTCATGTAT
47311 AGATTTGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 8 0.33
31 16 0.67
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.36
Consensus pattern (30 bp):
AATTGCACATAAATCAAAGTTCATGTATCA
Found at i:48467 original size:16 final size:17
Alignment explanation
Indices: 48446--48484 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
48436 ATTAGCTAGT
48446 ACTTAAATAAAT-TTTA
1 ACTTAAATAAATATTTA
* *
48462 ACTTAAATCAATATTTC
1 ACTTAAATAAATATTTA
48479 ACTTAA
1 ACTTAA
48485 CGTAAGACCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (17 bp):
ACTTAAATAAATATTTA
Found at i:49851 original size:41 final size:41
Alignment explanation
Indices: 49804--49894 Score: 164
Period size: 41 Copynumber: 2.2 Consensus size: 41
49794 CGCAAAAAGT
*
49804 AGAGCAATAGCGGCACTTATGGGCAAGCGCGGCTAAAGGTC
1 AGAGCAATAGCGGCACTTATGGGCAAGCGCCGCTAAAGGTC
*
49845 AGAGCAATAGCGGCGCTTATGGGCAAGCGCCGCTAAAGGTC
1 AGAGCAATAGCGGCACTTATGGGCAAGCGCCGCTAAAGGTC
49886 AGAGCAATA
1 AGAGCAATA
49895 TCATTAGGAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.31, C:0.22, G:0.33, T:0.14
Consensus pattern (41 bp):
AGAGCAATAGCGGCACTTATGGGCAAGCGCCGCTAAAGGTC
Found at i:50343 original size:43 final size:43
Alignment explanation
Indices: 50252--50345 Score: 143
Period size: 43 Copynumber: 2.2 Consensus size: 43
50242 ATGTTAGTGA
* *
50252 CGTTTGTGAGAAAAATGCCGCTAAAGATCATGTTCTTTACCGG
1 CGTTTGTGAGAAAAACGCCGCTAAAGATCATGTTCTTTACCAG
* * *
50295 TGTTTGTGGGAAAAACGCCGCTAAAGATCATGTTCTTTAGCAG
1 CGTTTGTGAGAAAAACGCCGCTAAAGATCATGTTCTTTACCAG
50338 CGTTTGTG
1 CGTTTGTG
50346 TTTTTGATAG
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.32
Consensus pattern (43 bp):
CGTTTGTGAGAAAAACGCCGCTAAAGATCATGTTCTTTACCAG
Found at i:53938 original size:96 final size:96
Alignment explanation
Indices: 53764--53955 Score: 255
Period size: 96 Copynumber: 2.0 Consensus size: 96
53754 ATTTTGGGAA
* ** *
53764 AAGGATATTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCA
1 AAGGATATTCGATTATCTCAATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
*
53829 GAATCGAAGAT-AAAGAAACATTGCCTCGATT
66 GAATCGAAGATAAAAG-AACATTACCTCGATT
* * *
53860 AAGGGTATTCGATTATTTCAATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAA-ATTTTA
1 AAGGATATTCGATTATCTCAATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
*
53924 GAAACTCGAA-ATAAAAGAATATTACCTCGATT
66 G-AA-TCGAAGATAAAAGAACATTACCTCGATT
53956 TTAAAGTCTT
Statistics
Matches: 84, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
95 6 0.07
96 69 0.82
97 9 0.11
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCAATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
GAATCGAAGATAAAAGAACATTACCTCGATT
Found at i:54216 original size:28 final size:28
Alignment explanation
Indices: 54174--54236 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
54164 AAAATGAGGC
** *
54174 TTTTCGGATACTCGGGGATGAAATGGTAA
1 TTTT-GGATACTCGGGGACAAAATGATAA
* *
54203 TTTTGGATTCTCGGGGGCAAAATGATAA
1 TTTTGGATACTCGGGGACAAAATGATAA
54231 TTTTGG
1 TTTTGG
54237 GAAAATTCGG
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 25 0.86
29 4 0.14
ACGTcount: A:0.25, C:0.10, G:0.30, T:0.35
Consensus pattern (28 bp):
TTTTGGATACTCGGGGACAAAATGATAA
Found at i:54374 original size:30 final size:30
Alignment explanation
Indices: 54338--54589 Score: 280
Period size: 30 Copynumber: 8.5 Consensus size: 30
54328 GCCCGAGGGC
*
54338 AAAATGGTAATTTTTGGAAGTTTTAGGGT-A
1 AAAATGG-AATTTTTGGAAGTTTTGGGGTAA
* * *
54368 AAAATGGAACTTTTGGAA-ATTTGGGGTCA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTAA
*
54397 AAAATGGAATTTTTGGAAGTTTTGGGGTTA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTAA
* * *
54427 AAAATGAAATTTTTGAAAG-TTCGAGGGT-A
1 AAAATGGAATTTTTGGAAGTTTTG-GGGTAA
* * *
54456 AAAATGGAATTTTTGAAAGTTTCGGGATAA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTAA
* * * * * *
54486 AAAATGAAATTTTTTGAAGCTTCGGTGTCA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTAA
*
54516 AAAATGGAATTTTTGGAAGTTTTGAGGTAA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTAA
*
54546 AAAATGGAATTTTTGGAAGTTTGGGGGT-A
1 AAAATGGAATTTTTGGAAGTTTTGGGGTAA
54575 AAAATGGAATTTTTG
1 AAAATGGAATTTTTG
54590 AATAGTTTAG
Statistics
Matches: 190, Mismatches: 27, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
28 7 0.04
29 69 0.36
30 114 0.60
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (30 bp):
AAAATGGAATTTTTGGAAGTTTTGGGGTAA
Found at i:54441 original size:59 final size:58
Alignment explanation
Indices: 54338--54589 Score: 292
Period size: 59 Copynumber: 4.3 Consensus size: 58
54328 GCCCGAGGGC
* * * *
54338 AAAATGGTAATTTTTGGAAGTTTTAGGGT-AAAAATGGAACTTTTGGAAATTTGGGGTCA
1 AAAATGG-AATTTTTGGAAGTTTTGGGGTAAAAAATGAAATTTTTGGAAATTCGGGGT-A
*
54397 AAAATGGAATTTTTGGAAGTTTTGGGGTTAAAAATGAAATTTTT-GAAAGTTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTAAAAAATGAAATTTTTGGAAA-TTCG-GGGTA
* * * * * *
54456 AAAATGGAATTTTTGAAAGTTTCGGGATAAAAAATGAAATTTTTTGAAGCTTCGGTGTCA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTAAAAAATGAAATTTTTGGAA-ATTCGGGGT-A
* * * *
54516 AAAATGGAATTTTTGGAAGTTTTGAGGTAAAAAATGGAATTTTTGGAAGTTTGGGGGTA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTAAAAAATGAAATTTTTGGAA-ATTCGGGGTA
54575 AAAATGGAATTTTTG
1 AAAATGGAATTTTTG
54590 AATAGTTTAG
Statistics
Matches: 168, Mismatches: 19, Indels: 12
0.84 0.10 0.06
Matches are distributed among these distances:
58 24 0.14
59 83 0.49
60 61 0.36
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (58 bp):
AAAATGGAATTTTTGGAAGTTTTGGGGTAAAAAATGAAATTTTTGGAAATTCGGGGTA
Found at i:56382 original size:13 final size:13
Alignment explanation
Indices: 56364--56388 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
56354 TGGGCCTGAT
56364 TTGTAATTGGACC
1 TTGTAATTGGACC
56377 TTGTAATTGGAC
1 TTGTAATTGGAC
56389 ATTATTTAAA
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:0.12, G:0.24, T:0.40
Consensus pattern (13 bp):
TTGTAATTGGACC
Found at i:56418 original size:17 final size:17
Alignment explanation
Indices: 56392--56461 Score: 106
Period size: 17 Copynumber: 4.2 Consensus size: 17
56382 ATTGGACATT
56392 ATTT-AAATAAATTTAA
1 ATTTAAAATAAATTTAA
*
56408 ATTTCAAATAAATTTAA
1 ATTTAAAATAAATTTAA
*
56425 ATTTAAAATAAACTTAA
1 ATTTAAAATAAATTTAA
*
56442 TTTTAAAATAAATTTAA
1 ATTTAAAATAAATTTAA
56459 ATT
1 ATT
56462 CTGTTGGACC
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
16 4 0.08
17 44 0.92
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (17 bp):
ATTTAAAATAAATTTAA
Found at i:56433 original size:7 final size:6
Alignment explanation
Indices: 56399--56461 Score: 53
Period size: 6 Copynumber: 11.0 Consensus size: 6
56389 ATTATTTAAA
* * *
56399 TAAATT TAAATT TCAAA-- TAAATT TAAATT TAAA-A TAAACT TAATTT
1 TAAATT TAAATT T-AAATT TAAATT TAAATT TAAATT TAAATT TAAATT
*
56445 TAAA-A TAAATT TAAATT
1 TAAATT TAAATT TAAATT
56462 CTGTTGGACC
Statistics
Matches: 45, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
4 3 0.07
5 9 0.20
6 30 0.67
7 3 0.07
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (6 bp):
TAAATT
Found at i:58727 original size:22 final size:20
Alignment explanation
Indices: 58699--58789 Score: 50
Period size: 22 Copynumber: 4.5 Consensus size: 20
58689 TAAATTTTAT
58699 TAATTATAATTATTTAAGTGTA
1 TAATTATAATTATTTAA-T-TA
*
58721 TAATTATCACAATT-TTT-ATTT
1 TAATTAT---AATTATTTAATTA
*
58742 TAATATATAA--ATTTTA-T-
1 TAAT-TATAATTATTTAATTA
58759 TAATTATAATTATTTAAGTGTA
1 TAATTATAATTATTTAA-T-TA
58781 TAATTATAA
1 TAATTATAA
58790 ATATATAAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 24
0.68 0.02 0.30
Matches are distributed among these distances:
16 5 0.09
17 4 0.07
18 9 0.16
19 3 0.05
21 6 0.11
22 20 0.36
23 1 0.02
24 3 0.05
25 4 0.07
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.52
Consensus pattern (20 bp):
TAATTATAATTATTTAATTA
Found at i:59324 original size:16 final size:16
Alignment explanation
Indices: 59311--59351 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
59301 AGTTATTTCG
*
59311 AATTTAAATTATTTAT
1 AATTTAAATTATTTAA
* *
59327 AATTTGAATTATTTTA
1 AATTTAAATTATTTAA
59343 AATTTAAAT
1 AATTTAAAT
59352 CATTCGAGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (16 bp):
AATTTAAATTATTTAA
Found at i:59925 original size:23 final size:23
Alignment explanation
Indices: 59882--59926 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
59872 AATAATTTTA
*
59882 ATGTATTTAATATTCTTAAAATG
1 ATGTATTTAATATTCTAAAAATG
*
59905 ATGTATTTACCTATT-TAAAAAT
1 ATGTATTTA-ATATTCTAAAAAT
59927 TTTTTTTACT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (23 bp):
ATGTATTTAATATTCTAAAAATG
Found at i:60387 original size:6 final size:6
Alignment explanation
Indices: 60376--60408 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
60366 CGTTAGTTCA
*
60376 ACAAAT ACAAAT ACAAAT ATAAAT ACAAAT ACA
1 ACAAAT ACAAAT ACAAAT ACAAAT ACAAAT ACA
60409 TTGATTTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.67, C:0.15, G:0.00, T:0.18
Consensus pattern (6 bp):
ACAAAT
Found at i:61070 original size:22 final size:22
Alignment explanation
Indices: 61045--61087 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
61035 TTAGTAATAA
* *
61045 TTTTATCTTTAAAGTGTTTTTT
1 TTTTATCTTAAAAGTGCTTTTT
61067 TTTTATCTTAAAAGTGCTTTT
1 TTTTATCTTAAAAGTGCTTTT
61088 AAAAAATAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.07, G:0.09, T:0.63
Consensus pattern (22 bp):
TTTTATCTTAAAAGTGCTTTTT
Found at i:61254 original size:17 final size:18
Alignment explanation
Indices: 61228--61270 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 18
61218 AATTGTAATT
61228 TTTATAATAGTTT-TATTA
1 TTTATAATAGTTTATA-TA
61246 TTT-TAATAGTTTATATA
1 TTTATAATAGTTTATATA
61263 TTTATAAT
1 TTTATAAT
61271 TTTTAGAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (18 bp):
TTTATAATAGTTTATATA
Found at i:61275 original size:17 final size:17
Alignment explanation
Indices: 61228--61275 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
61218 AATTGTAATT
61228 TTTATAATAGTTTTATTA
1 TTTATAATA-TTTTATTA
*
61246 TTT-TAATAGTTTATATA
1 TTTATAATATTTTAT-TA
61263 TTTATAAT-TTTTA
1 TTTATAATATTTTA
61276 GAATGTTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 5 0.19
17 14 0.54
18 7 0.27
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.62
Consensus pattern (17 bp):
TTTATAATATTTTATTA
Found at i:65683 original size:21 final size:22
Alignment explanation
Indices: 65648--65690 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
65638 AATATTATTT
65648 ATTAATTAATTTAATTAAATAA
1 ATTAATTAATTTAATTAAATAA
*
65670 ATTAATT-TTTTAATTAAATAA
1 ATTAATTAATTTAATTAAATAA
65691 TTTTTTCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
ATTAATTAATTTAATTAAATAA
Found at i:65687 original size:17 final size:17
Alignment explanation
Indices: 65651--65706 Score: 60
Period size: 17 Copynumber: 3.2 Consensus size: 17
65641 ATTATTTATT
* *
65651 AATTAATTTAATTAAATA
1 AATTAATTT-TTTAATTA
65669 AATTAATTTTTTAATTA
1 AATTAATTTTTTAATTA
*
65686 AA-TAATTTTTTCAATTC
1 AATTAATTTTTT-AATTA
65703 AATT
1 AATT
65707 CTTTTTTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 9 0.27
17 14 0.42
18 10 0.30
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.52
Consensus pattern (17 bp):
AATTAATTTTTTAATTA
Found at i:70703 original size:69 final size:68
Alignment explanation
Indices: 70498--70705 Score: 192
Period size: 69 Copynumber: 3.0 Consensus size: 68
70488 GCCTTATATA
* * **
70498 CTTCTTTCTCCATTAAATCAATAACCC-CTTTATCTGTGGCCACCACATCACAAAAGGT-TGTAT
1 CTTCTTGCTCCATTAAATCAAT-ACCCACTTTATCCGTGGCC-CCACATCACAAGTGGTGT-TAT
70561 CATGTT
63 CATGTT
* * * * * * *
70567 CTTTTTGC-CTCATTGATTCAATTCACACTTTATCCCTAGACCCCACATCACAAGT-G-GTTATG
1 CTTCTTGCTC-CATTAAATCAATACCCACTTTATCCGT-GGCCCCACATCACAAGTGGTGTTAT-
70629 ACATGTT
63 -CATGTT
* *
70636 CTTCTTGCTCCATTAAAACAATACCCACTTTATCCGTGGCCTTCACATCACAAGTGGTGTTATCA
1 CTTCTTGCTCCATTAAATCAATACCCACTTTATCCGTGGCC-CCACATCACAAGTGGTGTTATCA
70701 TGTT
65 TGTT
70705 C
1 C
70706 CATCATTGAC
Statistics
Matches: 109, Mismatches: 20, Indels: 20
0.73 0.13 0.13
Matches are distributed among these distances:
67 3 0.03
68 8 0.07
69 88 0.81
70 5 0.05
71 5 0.05
ACGTcount: A:0.25, C:0.28, G:0.12, T:0.35
Consensus pattern (68 bp):
CTTCTTGCTCCATTAAATCAATACCCACTTTATCCGTGGCCCCACATCACAAGTGGTGTTATCAT
GTT
Done.