Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1181
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: 83823
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:9772 original size:38 final size:40
Alignment explanation
Indices: 9708--9782 Score: 109
Period size: 38 Copynumber: 1.9 Consensus size: 40
9698 ATTTGATGTG
*
9708 TATCCGGGCTTAAAGACCCGCAGGCTTCGTTCTGGTAAAA
1 TATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGTAAAA
* *
9748 TATCCGGG-TTAAA-TCCTGCAGGCTTCGTGCTGGTA
1 TATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGTA
9783 TTATATTCGG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
38 19 0.59
39 5 0.16
40 8 0.25
ACGTcount: A:0.21, C:0.24, G:0.27, T:0.28
Consensus pattern (40 bp):
TATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGTAAAA
Found at i:9882 original size:43 final size:43
Alignment explanation
Indices: 9802--9886 Score: 134
Period size: 43 Copynumber: 2.0 Consensus size: 43
9792 GGCCTATTTC
* **
9802 GTGTATTCGGGCCTTTGTGCCTAGCAAGCTTCGTGCCGGTGAT
1 GTGTATTCGGGCCTTTGTGCCTAGCAAGCGTAATGCCGGTGAT
*
9845 GTGTATTCGGGCCTTTGTGCCTAGCAGGCGTAATGCCGGTGA
1 GTGTATTCGGGCCTTTGTGCCTAGCAAGCGTAATGCCGGTGA
9887 AATGATATGT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.13, C:0.22, G:0.34, T:0.31
Consensus pattern (43 bp):
GTGTATTCGGGCCTTTGTGCCTAGCAAGCGTAATGCCGGTGAT
Found at i:15943 original size:40 final size:39
Alignment explanation
Indices: 15906--16139 Score: 353
Period size: 40 Copynumber: 5.9 Consensus size: 39
15896 GGATATAGCT
* * *
15906 ACTCGCTCAAATGCCTTCGGGACATAGCCCGGTTATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTT-TGGTA
*
15946 ACTCGCACCAATGCCTTCGGGACTTAGCCCGGATTTGGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG-TTTGGTA
15986 ACTCAG-ACAAATGCCTTCGGGACTTAGCCCGGATTTGGTA
1 ACTC-GCACAAATGCCTTCGGGACTTAGCCCGG-TTTGGTA
16026 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATTTGGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG-TTTGGTA
*
16066 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTTTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG-TTTGGTA
*
16106 ACTCACACAAATGCCTTCGGGACTTAGCCCGGTT
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTT
16140 ATCATCCGAA
Statistics
Matches: 183, Mismatches: 8, Indels: 7
0.92 0.04 0.04
Matches are distributed among these distances:
39 3 0.02
40 177 0.97
41 3 0.02
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.25
Consensus pattern (39 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGTTTGGTA
Found at i:17800 original size:68 final size:68
Alignment explanation
Indices: 17725--17863 Score: 269
Period size: 68 Copynumber: 2.0 Consensus size: 68
17715 ATTTACTAAA
*
17725 TCGAAACTTAAATCTTTCACACATTCATAATCACATATTTTAGACAATAAATATCATATTCAAAT
1 TCGAAACTTAAAACTTTCACACATTCATAATCACATATTTTAGACAATAAATATCATATTCAAAT
17790 AAT
66 AAT
17793 TCGAAACTTAAAACTTTCACACATTCATAATCACATATTTTAGACAATAAATATCATATTCAAAT
1 TCGAAACTTAAAACTTTCACACATTCATAATCACATATTTTAGACAATAAATATCATATTCAAAT
17858 AAT
66 AAT
17861 TCG
1 TCG
17864 GTGACTCAGT
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 70 1.00
ACGTcount: A:0.44, C:0.18, G:0.04, T:0.35
Consensus pattern (68 bp):
TCGAAACTTAAAACTTTCACACATTCATAATCACATATTTTAGACAATAAATATCATATTCAAAT
AAT
Found at i:19719 original size:25 final size:25
Alignment explanation
Indices: 19691--19738 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
19681 GCAGTACAGT
19691 CTATCTATAGCAGTTTCAGTTTATG
1 CTATCTATAGCAGTTTCAGTTTATG
19716 CTATCTATAGCAGTTTCAGTTTA
1 CTATCTATAGCAGTTTCAGTTTA
19739 AAACACATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.25, C:0.17, G:0.15, T:0.44
Consensus pattern (25 bp):
CTATCTATAGCAGTTTCAGTTTATG
Found at i:22724 original size:21 final size:21
Alignment explanation
Indices: 22700--22739 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
22690 GGGTAGGATT
* *
22700 CTGTATATTTTTTCTGTATAC
1 CTGTATATATTATCTGTATAC
*
22721 CTGTTTATATTATCTGTAT
1 CTGTATATATTATCTGTAT
22740 TTGAAAAGGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.20, C:0.12, G:0.10, T:0.57
Consensus pattern (21 bp):
CTGTATATATTATCTGTATAC
Found at i:24674 original size:12 final size:12
Alignment explanation
Indices: 24657--24683 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
24647 ATACTTAATT
24657 AATATAATATGA
1 AATATAATATGA
24669 AATATAATATGA
1 AATATAATATGA
24681 AAT
1 AAT
24684 CTTATTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.07, T:0.33
Consensus pattern (12 bp):
AATATAATATGA
Found at i:24821 original size:16 final size:17
Alignment explanation
Indices: 24789--24823 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
24779 TTAAGATAAG
*
24789 TATTAAATTTAATTAAA
1 TATTAAATCTAATTAAA
24806 TATTAAATCT-ATTAAA
1 TATTAAATCTAATTAAA
24822 TA
1 TA
24824 ATATTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (17 bp):
TATTAAATCTAATTAAA
Found at i:27875 original size:41 final size:41
Alignment explanation
Indices: 27818--27899 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
27808 AATGGATAAG
* *
27818 AGTATGCGGGTAGACTTTAGCATGGCTACTGGAGAGAAGGT
1 AGTATGCGGATAGACTTTAGCATGGCTACTAGAGAGAAGGT
27859 AGTATGCGGATAGACTTTAGCATGGCTACTAGAGAGAAGGT
1 AGTATGCGGATAGACTTTAGCATGGCTACTAGAGAGAAGGT
27900 CTTATCGCAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.29, C:0.12, G:0.34, T:0.24
Consensus pattern (41 bp):
AGTATGCGGATAGACTTTAGCATGGCTACTAGAGAGAAGGT
Found at i:33442 original size:46 final size:46
Alignment explanation
Indices: 33392--33567 Score: 182
Period size: 46 Copynumber: 3.8 Consensus size: 46
33382 TGTTTGGGCA
*
33392 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCCAATG
* * *
33438 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCCAA-T--G
* *
33483 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCCAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCCAATG
* **
33531 -CACGAGCTCGTTGAGTTGAGTCCGAGTTTGCTTATGG
1 TC-CGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
33568 GCGGCTTACA
Statistics
Matches: 110, Mismatches: 10, Indels: 20
0.79 0.07 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 4 0.04
46 62 0.56
47 28 0.25
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCCAATG
Found at i:33547 original size:93 final size:93
Alignment explanation
Indices: 33388--33558 Score: 290
Period size: 93 Copynumber: 1.8 Consensus size: 93
33378 AGGATGTTTG
* *
33388 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCCAACGTCCGAACTCGTTGAG
33453 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* *
33481 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCCAACG-CACGAGCTCGTTGA
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCCAACGTC-CGAACTCGTTGA
33545 GTTGAGTCCGAGTT
65 GTTGAGTCCGAGTT
33559 TGCTTATGGG
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
92 1 0.01
93 72 0.99
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCCAACGTCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:35026 original size:40 final size:40
Alignment explanation
Indices: 34933--35189 Score: 333
Period size: 40 Copynumber: 6.5 Consensus size: 40
34923 AAGCCAAGTA
* * *
34933 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTC-AATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
34971 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
35011 CCTTCGGGACTTAGCCCGGATATAGTAGCTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
35051 CCTTCGGGACTTAGCCCGGATGTAATAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
35091 CCTTCGGGACTTAGCCCGGATGTAATAACTTGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
35131 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
35171 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
35190 TTATCATCCG
Statistics
Matches: 197, Mismatches: 18, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
38 12 0.06
39 17 0.09
40 168 0.85
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:40088 original size:26 final size:26
Alignment explanation
Indices: 40052--40161 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
40042 TGATACAAAT
40052 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
40078 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* * *
40104 TGACAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
40130 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
40156 TGATAA
1 TGATAA
40162 GAATTTCATG
Statistics
Matches: 80, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 80 1.00
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.35
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:47745 original size:38 final size:38
Alignment explanation
Indices: 47702--47779 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
47692 AATATTAGAG
47702 TCAGATTAACAGAACATATATACCGAATCCTACCCCCA
1 TCAGATTAACAGAACATATATACCGAATCCTACCCCCA
* *
47740 TCAGATTAACAGAACATATATACTGAATCCTACCCTCA
1 TCAGATTAACAGAACATATATACCGAATCCTACCCCCA
47778 TC
1 TC
47780 CTCTACACAC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.38, C:0.29, G:0.08, T:0.24
Consensus pattern (38 bp):
TCAGATTAACAGAACATATATACCGAATCCTACCCCCA
Found at i:50672 original size:14 final size:11
Alignment explanation
Indices: 50636--50675 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
50626 ATTCTTGTCT
*
50636 ATAAATATATA
1 ATAATTATATA
50647 ATAATTATATA
1 ATAATTATATA
*
50658 ATAATTATAAA
1 ATAATTATATA
50669 ATAATTA
1 ATAATTA
50676 AAATGTACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
ATAATTATATA
Found at i:51606 original size:20 final size:18
Alignment explanation
Indices: 51570--51609 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 18
51560 ACTTGTGATG
51570 TTAATATGCTTAATTTAA
1 TTAATATGCTTAATTTAA
51588 TTAATATGGCTTAAATTTAA
1 TTAATAT-GCTT-AATTTAA
51608 TT
1 TT
51610 CGTGTTAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 7 0.35
19 4 0.20
20 9 0.45
ACGTcount: A:0.38, C:0.05, G:0.07, T:0.50
Consensus pattern (18 bp):
TTAATATGCTTAATTTAA
Found at i:53376 original size:10 final size:10
Alignment explanation
Indices: 53363--53445 Score: 70
Period size: 10 Copynumber: 8.6 Consensus size: 10
53353 TCGTAAAAAA
53363 TATAAAATTT
1 TATAAAATTT
53373 TATAAAATTT
1 TATAAAATTT
*
53383 TATAAAAATTG
1 TAT-AAAATTT
53394 TA-AAAA-TT
1 TATAAAATTT
*
53402 TATAAAA-TA
1 TATAAAATTT
53411 TATAGAAA---
1 TATA-AAATTT
*
53419 TATAAAATAAT
1 TATAAAAT-TT
53430 TATAAAATTT
1 TATAAAATTT
53440 TATAAA
1 TATAAA
53446 TTCGTAAGAA
Statistics
Matches: 62, Mismatches: 4, Indels: 14
0.77 0.05 0.17
Matches are distributed among these distances:
7 3 0.05
8 7 0.11
9 13 0.21
10 23 0.37
11 16 0.26
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (10 bp):
TATAAAATTT
Found at i:53378 original size:19 final size:19
Alignment explanation
Indices: 53373--53445 Score: 62
Period size: 19 Copynumber: 3.8 Consensus size: 19
53363 TATAAAATTT
*
53373 TATAAAATTTTATAAAAAT
1 TATAAAATTTTATAAAAAA
* * *
53392 TGTAAAAATTTATAAAATA
1 TATAAAATTTTATAAAAAA
53411 TATAGAAA---TATAAAATAA
1 TATA-AAATTTTATAAAA-AA
53429 TTATAAAATTTTATAAA
1 -TATAAAATTTTATAAA
53446 TTCGTAAGAA
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
17 7 0.17
18 4 0.10
19 22 0.52
20 3 0.07
21 6 0.14
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (19 bp):
TATAAAATTTTATAAAAAA
Found at i:53388 original size:29 final size:29
Alignment explanation
Indices: 53356--53445 Score: 103
Period size: 29 Copynumber: 3.1 Consensus size: 29
53346 ATAAAAATCG
53356 TAAAAAATATAAAATTTTATAAAATTTTA
1 TAAAAAATATAAAATTTTATAAAATTTTA
* * * *
53385 TAAAAATTGTAAAAATTTATAAAA-TATA
1 TAAAAAATATAAAATTTTATAAAATTTTA
* *
53413 T-AGAAATATAAAATAATTATAAAATTTTA
1 TAAAAAATATAAAAT-TTTATAAAATTTTA
53442 TAAA
1 TAAA
53446 TTCGTAAGAA
Statistics
Matches: 47, Mismatches: 11, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
27 9 0.19
28 12 0.26
29 25 0.53
30 1 0.02
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (29 bp):
TAAAAAATATAAAATTTTATAAAATTTTA
Found at i:53399 original size:57 final size:57
Alignment explanation
Indices: 53338--53484 Score: 149
Period size: 57 Copynumber: 2.5 Consensus size: 57
53328 AAAATTAGAA
* * *
53338 AAAAAAATATAAAAATCGTA-AAAAATATAAAAT-TTTATAAAATTTTATAAAAATT-GT
1 AAAAAATTATAAAAAT-ATATAAAAATATAAAATAATTATAAAATTTTAT--AAATTCGT
* *
53395 AAAAATTTAT-AAAATATATAGAAATATAAAATAATTATAAAATTTTATAAATTCGT
1 AAAAAATTATAAAAATATATAAAAATATAAAATAATTATAAAATTTTATAAATTCGT
* *
53451 AAGAAAATTATAAAAAAATTTAAAGAAATATAAA
1 AA-AAAATTATAAAAATATAT-AA-AAATATAAA
53485 TTTCTTAAAA
Statistics
Matches: 74, Mismatches: 9, Indels: 11
0.79 0.10 0.12
Matches are distributed among these distances:
55 7 0.09
56 21 0.28
57 29 0.39
58 7 0.09
59 1 0.01
60 9 0.12
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.33
Consensus pattern (57 bp):
AAAAAATTATAAAAATATATAAAAATATAAAATAATTATAAAATTTTATAAATTCGT
Found at i:53460 original size:29 final size:27
Alignment explanation
Indices: 53372--53465 Score: 91
Period size: 29 Copynumber: 3.3 Consensus size: 27
53362 ATATAAAATT
*
53372 TTATAAAATTTTATAAAAATTGTAAAAAT
1 TTATAAAATTTTAT--AAATTGTAAAAAA
* * *
53401 TTATAAAA-TATATAGAAATATAAAATAA
1 TTATAAAATTTTATA-AATTGTAAAA-AA
53429 TTATAAAATTTTATAAATTCGTAAGAAAA
1 TTATAAAATTTTATAAATT-GTAA-AAAA
53458 TTATAAAA
1 TTATAAAA
53466 AAATTTAAAG
Statistics
Matches: 53, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
26 1 0.02
27 8 0.15
28 16 0.30
29 26 0.49
30 2 0.04
ACGTcount: A:0.57, C:0.01, G:0.04, T:0.37
Consensus pattern (27 bp):
TTATAAAATTTTATAAATTGTAAAAAA
Found at i:58207 original size:34 final size:34
Alignment explanation
Indices: 58169--58245 Score: 86
Period size: 34 Copynumber: 2.3 Consensus size: 34
58159 TGAACACTTA
* *
58169 ATAAGCATGACT-TTTGCTACTGA-GTTGATCTATT
1 ATAAGCAT-ACTATTTACTACT-ATGTTGAACTATT
* *
58203 ATAAGCATATTATTTACTACTATGTTGAACTGTT
1 ATAAGCATACTATTTACTACTATGTTGAACTATT
58237 ATAAGCATA
1 ATAAGCATA
58246 TTGATTGCTA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
33 3 0.08
34 34 0.92
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.40
Consensus pattern (34 bp):
ATAAGCATACTATTTACTACTATGTTGAACTATT
Found at i:58257 original size:34 final size:34
Alignment explanation
Indices: 58181--58258 Score: 97
Period size: 34 Copynumber: 2.3 Consensus size: 34
58171 AAGCATGACT
*
58181 TTTGCTACTGAGTTGATCTATTATAAGCATATTA
1 TTTGCTACTGAGTTGAACTATTATAAGCATATTA
* *
58215 TTTACTACT-ATGTTGAACTGTTATAAGCATATTGA
1 TTTGCTACTGA-GTTGAACTATTATAAGCATATT-A
58250 -TTGCTACTG
1 TTTGCTACTG
58259 TATTGTTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
33 1 0.03
34 35 0.95
35 1 0.03
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.44
Consensus pattern (34 bp):
TTTGCTACTGAGTTGAACTATTATAAGCATATTA
Found at i:59316 original size:23 final size:20
Alignment explanation
Indices: 59278--59327 Score: 55
Period size: 23 Copynumber: 2.3 Consensus size: 20
59268 TCCACTCAGG
59278 ATTTTTTTAAAAATAAATTAA
1 ATTTTTTTAAAAATAAA-TAA
*
59299 ATTTTCTTCTAAATATAAATAA
1 ATTTT-TT-TAAAAATAAATAA
59321 ATATTTT
1 AT-TTTT
59328 AAATTAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 5 0.20
22 8 0.32
23 12 0.48
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTTTTTTAAAAATAAATAA
Found at i:61603 original size:28 final size:27
Alignment explanation
Indices: 61523--61605 Score: 89
Period size: 28 Copynumber: 3.0 Consensus size: 27
61513 CGTGTGTATC
61523 CTATTTTTCAAATTTTATAGTCTTGCCA
1 CTATTTTTCAAATTTTATAGT-TTGCCA
* *
61551 CTATTTTTCATATTTTATTATTTTGTCC-
1 CTATTTTTCAAATTTTA-TAGTTTG-CCA
61579 CTAATTTTT-AAATTTTATAGCTTTGCC
1 CT-ATTTTTCAAATTTTATAG-TTTGCC
61606 TTTATTTTCA
Statistics
Matches: 47, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
27 4 0.09
28 32 0.68
29 11 0.23
ACGTcount: A:0.23, C:0.16, G:0.06, T:0.55
Consensus pattern (27 bp):
CTATTTTTCAAATTTTATAGTTTGCCA
Found at i:65162 original size:11 final size:11
Alignment explanation
Indices: 65146--65170 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
65136 TGACTATGCC
65146 ATTACAAGCCT
1 ATTACAAGCCT
65157 ATTACAAGCCT
1 ATTACAAGCCT
65168 ATT
1 ATT
65171 CTACAGGTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.24, G:0.08, T:0.32
Consensus pattern (11 bp):
ATTACAAGCCT
Found at i:67864 original size:15 final size:15
Alignment explanation
Indices: 67844--67877 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
67834 GGTATTATAA
67844 AATTAAGAAAAAATC
1 AATTAAGAAAAAATC
*
67859 AATTAATAAAAAATC
1 AATTAAGAAAAAATC
67874 AATT
1 AATT
67878 GAACTGGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (15 bp):
AATTAAGAAAAAATC
Found at i:68299 original size:18 final size:18
Alignment explanation
Indices: 68261--68299 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
68251 AATTATAGAA
*
68261 ATAAAAAACATATAAATT
1 ATAAAAAACATATAAAAT
68279 ATAAAAAA-ATATAATAAT
1 ATAAAAAACATATAA-AAT
68297 ATA
1 ATA
68300 TAATACAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (18 bp):
ATAAAAAACATATAAAAT
Found at i:68630 original size:17 final size:17
Alignment explanation
Indices: 68601--68633 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
68591 AAAAACAATA
68601 ATTATATTTTTATAAAT
1 ATTATATTTTTATAAAT
68618 ATTAT-TTTATTATAAA
1 ATTATATTT-TTATAAA
68634 ATTTAGACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTATATTTTTATAAAT
Found at i:72702 original size:58 final size:58
Alignment explanation
Indices: 72637--72773 Score: 141
Period size: 58 Copynumber: 2.4 Consensus size: 58
72627 TTAATTCATA
*** ** * *
72637 TAATAATAATTATATTAAGAATGTTATTAAAATATATATTA-TTTTATTAAATTTTATT
1 TAATAATAATTATATTAA-AATAAGATTAAAATATATATTATTTTTAGCAAAATATATT
* * * *
72695 TAATAATAAATATTTTAAAATAAGATTAAATTATTTATTATTTTTAGCAAAATATATT
1 TAATAATAATTATATTAAAATAAGATTAAAATATATATTATTTTTAGCAAAATATATT
* *
72753 TAACAATAATTTTATTAAAAT
1 TAATAATAATTATATTAAAAT
72774 TTAATAATAA
Statistics
Matches: 63, Mismatches: 15, Indels: 2
0.79 0.19 0.03
Matches are distributed among these distances:
57 17 0.27
58 46 0.73
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.48
Consensus pattern (58 bp):
TAATAATAATTATATTAAAATAAGATTAAAATATATATTATTTTTAGCAAAATATATT
Found at i:72937 original size:44 final size:46
Alignment explanation
Indices: 72868--72960 Score: 111
Period size: 44 Copynumber: 2.1 Consensus size: 46
72858 TATAACATCT
* * *
72868 ATTCCATTCGACCAAACACAAGAATT-CT-ATTATAGTTCTATTCC
1 ATTCCATTCAACCAAACACAAGAATTACTGATTACAGCTCTATTCC
* *
72912 ATTCCATTCAACCAAACA-ATTGAATTATTGATTACAGCTCTATTCC
1 ATTCCATTCAACCAAACACA-AGAATTACTGATTACAGCTCTATTCC
72958 ATT
1 ATT
72961 ATAGTGAACC
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
43 1 0.02
44 22 0.54
45 1 0.02
46 17 0.41
ACGTcount: A:0.34, C:0.24, G:0.06, T:0.35
Consensus pattern (46 bp):
ATTCCATTCAACCAAACACAAGAATTACTGATTACAGCTCTATTCC
Found at i:76466 original size:39 final size:40
Alignment explanation
Indices: 76408--76588 Score: 107
Period size: 40 Copynumber: 4.6 Consensus size: 40
76398 AATCAAGCAT
* * *
76408 CTTCGGGT-TT-AGCCGGATATAACCACTCGCA-CAAGGC
1 CTTCGGGTCTTAACCCGGATATAACCACTAGCATAAAGGC
*** *
76445 CTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAATGC
1 CTTCGGGTCTTAACCCGGATATAACCACTAGCATAAAGGC
* * ** * * *
76485 CTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC
1 CTTCGGGTCTTAACCCGGATATAACCACTAGCATAAAGGC
* ** * ** * * *
76525 CTTCGGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAAGC
1 CTTCGGGTCTTAACCCGGATATAACCAC-TAGCATAAAGGC
* *
76566 CTTCGGGACTTAGCCCGGATATA
1 CTTCGGGTCTTAACCCGGATATA
76589 GTCGCTTAGC
Statistics
Matches: 119, Mismatches: 21, Indels: 4
0.83 0.15 0.03
Matches are distributed among these distances:
37 8 0.07
38 2 0.02
39 16 0.13
40 63 0.53
41 30 0.25
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (40 bp):
CTTCGGGTCTTAACCCGGATATAACCACTAGCATAAAGGC
Found at i:76490 original size:40 final size:41
Alignment explanation
Indices: 76443--76626 Score: 252
Period size: 40 Copynumber: 4.6 Consensus size: 41
76433 CTCGCACAAG
* * * * *
76443 GCCTTCGGGTCTTAACCCGGATATGGTCAC-TAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTTAGCACAAAT
76483 GCCTTCGGGACTTAGCCCGGATATAGTCGC-TAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTTAGCACAAAT
* * *
76523 GCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGCTTAGCACAAAT
76564 GCCTTCGGGACTTAGCCCGGATATAGTCGCTTAGCACAAA-
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTTAGCACAAAT
76604 -CCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
76627 CATTCGAGTA
Statistics
Matches: 131, Mismatches: 10, Indels: 7
0.89 0.07 0.05
Matches are distributed among these distances:
39 26 0.20
40 59 0.45
41 43 0.33
42 3 0.02
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (41 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTTAGCACAAAT
Found at i:76577 original size:81 final size:80
Alignment explanation
Indices: 76444--76624 Score: 242
Period size: 81 Copynumber: 2.3 Consensus size: 80
76434 TCGCACAAGG
* * * * * * *
76444 CCTTCGGGTCTTAACCCGGATATGGTCAC-TAGCATAAATGCCTTCGGGACTTAGCCCGGATATA
1 CCTTCGGGACTTAGCCCGGATGTAGTCGCTTAGCACAAAAGCCTTCGGGACTTAGCCCGGATATA
76508 GTCGC-TAGCACAAA
66 GTCGCTTAGCACAAA
*
76522 TGCCTTC-GGATCTTAGTCCGGATGTAGTCGCTTAGCACAAAAGCCTTCGGGACTTAGCCCGGAT
1 --CCTTCGGGA-CTTAGCCCGGATGTAGTCGCTTAGCACAAAAGCCTTCGGGACTTAGCCCGGAT
76586 ATAGTCGCTTAGCACAAA
63 ATAGTCGCTTAGCACAAA
76604 CCTTCGGGACTTAGCCCGGAT
1 CCTTCGGGACTTAGCCCGGAT
76625 ATCATTCGAG
Statistics
Matches: 88, Mismatches: 9, Indels: 8
0.84 0.09 0.08
Matches are distributed among these distances:
79 2 0.02
80 36 0.41
81 41 0.47
82 9 0.10
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (80 bp):
CCTTCGGGACTTAGCCCGGATGTAGTCGCTTAGCACAAAAGCCTTCGGGACTTAGCCCGGATATA
GTCGCTTAGCACAAA
Found at i:83710 original size:19 final size:19
Alignment explanation
Indices: 83686--83727 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
83676 ATCAAGGTTC
83686 ATTTAAAT-AATTTATCACT
1 ATTTAAATCAATTTAT-ACT
*
83705 ATTTAATTCAATTTATACT
1 ATTTAAATCAATTTATACT
83724 ATTT
1 ATTT
83728 TTAGTGATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (19 bp):
ATTTAAATCAATTTATACT
Done.