Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012147.1 Kokia drynarioides strain JFW-HI SEQ_127146, 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: 100269
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 44 characters in sequence are not A, C, G, or T
Found at i:275 original size:56 final size:56
Alignment explanation
Indices: 189--302 Score: 176
Period size: 56 Copynumber: 2.0 Consensus size: 56
179 TTTAGTTATT
* *
189 TTTGCTGGGGTGTTTTTGTTAGCTTTTTAAGCCATGATTGAA-CTTGTATGGGCTGC
1 TTTGCCGGGGTGTTTTTGTTAGCTTTTTAAGCCAGGATT-AAGCTTGTATGGGCTGC
* *
245 TTTGCCGGGGTGTTTTTGTTAGTTTTTTAAGCCAGGATTAAGCTTGTATGGGTTGC
1 TTTGCCGGGGTGTTTTTGTTAGCTTTTTAAGCCAGGATTAAGCTTGTATGGGCTGC
301 TT
1 TT
303 ATAACAATCC
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
55 2 0.04
56 51 0.96
ACGTcount: A:0.14, C:0.11, G:0.29, T:0.46
Consensus pattern (56 bp):
TTTGCCGGGGTGTTTTTGTTAGCTTTTTAAGCCAGGATTAAGCTTGTATGGGCTGC
Found at i:4104 original size:18 final size:18
Alignment explanation
Indices: 4081--4123 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
4071 CAAGGTCACG
4081 ATCAATAGCGTCACTACC
1 ATCAATAGCGTCACTACC
4099 ATCAATAGCGTCACTACC
1 ATCAATAGCGTCACTACC
4117 ATCAATA
1 ATCAATA
4124 TCATCATTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.37, C:0.30, G:0.09, T:0.23
Consensus pattern (18 bp):
ATCAATAGCGTCACTACC
Found at i:14504 original size:6 final size:6
Alignment explanation
Indices: 14493--14520 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
14483 GTAAAACATA
14493 ATAATT ATAATT ATAATT ATAATT ATAA
1 ATAATT ATAATT ATAATT ATAATT ATAA
14521 AAAATCACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (6 bp):
ATAATT
Found at i:19330 original size:21 final size:21
Alignment explanation
Indices: 19297--19346 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
19287 TGTCCCACGG
* *
19297 CCTCAACCAGAAACAGTACCA
1 CCTCTACCCGAAACAGTACCA
*
19318 CCTTTACCCGAAACAGTACCA
1 CCTCTACCCGAAACAGTACCA
19339 CCTCTACC
1 CCTCTACC
19347 AGTGCCTCGG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.34, C:0.42, G:0.08, T:0.16
Consensus pattern (21 bp):
CCTCTACCCGAAACAGTACCA
Found at i:21260 original size:39 final size:39
Alignment explanation
Indices: 21139--21566 Score: 416
Period size: 39 Copynumber: 11.0 Consensus size: 39
21129 AATTGTACGA
* *
21139 TGTTTACAGTGTCACTGCCTA-ATCA-TAATAATAT-AGCAG
1 TGTTTACAGTGTCACTGCC-AGTTCAGT-ATAGTATCA-CAG
* * * * * *
21178 TGGTCACAGTATCACTGCCAGTTTAGTGTAGTATCTCAG
1 TGTTTACAGTGTCACTGCCAGTTCAGTATAGTATCACAG
* * *
21217 TGTTTACAGTGTCATTGCCACTTCAGTATAGCT-TCACAA
1 TGTTTACAGTGTCACTGCCAGTTCAGTATAG-TATCACAG
*
21256 TGTTTACAGTGTCATTGCCAGTTCAGTATAGTATCACAG
1 TGTTTACAGTGTCACTGCCAGTTCAGTATAGTATCACAG
* * * * ***
21295 TGTTTATAGTGTCAATGCCAATTCAATATAGTATTGTAG
1 TGTTTACAGTGTCACTGCCAGTTCAGTATAGTATCACAG
* * *
21334 TGTTTACAGTGTCATTACCAATTCAGTATAGTATCA-AG
1 TGTTTACAGTGTCACTGCCAGTTCAGTATAGTATCACAG
* * * **
21372 TGTTTACAGTGTCACTGGCAGTTCAATAAAGTATCGTAG
1 TGTTTACAGTGTCACTGCCAGTTCAGTATAGTATCACAG
* **
21411 TGTTTACAGTGTCACTGCCAATTCAGTATAGTATTGCAG
1 TGTTTACAGTGTCACTGCCAGTTCAGTATAGTATCACAG
* * * *
21450 TGTTTACAGTGTCACTACCAGTTCAGTATGGTATAATAG
1 TGTTTACAGTGTCACTGCCAGTTCAGTATAGTATCACAG
* **
21489 TGTTTACAGTGTCACTGCCAGTTCAGTAAAGTATCGTAG
1 TGTTTACAGTGTCACTGCCAGTTCAGTATAGTATCACAG
* * * *
21528 TGTTTACAGTGTCACTACTAATTCAGTATAATATCACAG
1 TGTTTACAGTGTCACTGCCAGTTCAGTATAGTATCACAG
21567 CATTTATGGT
Statistics
Matches: 320, Mismatches: 63, Indels: 12
0.81 0.16 0.03
Matches are distributed among these distances:
38 33 0.10
39 285 0.89
40 2 0.01
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (39 bp):
TGTTTACAGTGTCACTGCCAGTTCAGTATAGTATCACAG
Found at i:21553 original size:194 final size:194
Alignment explanation
Indices: 21207--21563 Score: 511
Period size: 194 Copynumber: 1.8 Consensus size: 194
21197 AGTTTAGTGT
* * *
21207 AGTATCTCAGTGTTTACAGTGTCATTGCCACTTCAGTATAGCTTCACAATGTTTACAGTGTCATT
1 AGTATCTCAGTGTTTACAGTGTCACTGCCAATTCAGTATAGCTTCACAATGTTTACAGTGTCACT
* * * * *
21272 GCCAGTTCAGTATAGTATCACAGTGTTTATAGTGTCAATGCCAATTCAATATAGTATTGTAGTGT
66 ACCAGTTCAGTATAGTATAACAGTGTTTACAGTGTCAATGCCAATTCAATAAAGTATCGTAGTGT
* *
21337 TTACAGTGTCATTACCAATTCAGTATAGTATCAAGTGTTTACAGTGTCACTGGCAGTTCAATAA
131 TTACAGTGTCACTACCAATTCAGTATAATATCAAGTGTTTACAGTGTCACTGGCAGTTCAATAA
** *
21401 AGTATCGT-AGTGTTTACAGTGTCACTGCCAATTCAGTATAG-TATTGCAGTGTTTACAGTGTCA
1 AGTATC-TCAGTGTTTACAGTGTCACTGCCAATTCAGTATAGCT-TCACAATGTTTACAGTGTCA
* * * * *
21464 CTACCAGTTCAGTATGGTATAATAGTGTTTACAGTGTCACTGCCAGTTCAGTAAAGTATCGTAGT
64 CTACCAGTTCAGTATAGTATAACAGTGTTTACAGTGTCAATGCCAATTCAATAAAGTATCGTAGT
*
21529 GTTTACAGTGTCACTACTAATTCAGTATAATATCA
129 GTTTACAGTGTCACTACCAATTCAGTATAATATCA
21564 CAGCATTTAT
Statistics
Matches: 142, Mismatches: 19, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
193 1 0.01
194 140 0.99
195 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (194 bp):
AGTATCTCAGTGTTTACAGTGTCACTGCCAATTCAGTATAGCTTCACAATGTTTACAGTGTCACT
ACCAGTTCAGTATAGTATAACAGTGTTTACAGTGTCAATGCCAATTCAATAAAGTATCGTAGTGT
TTACAGTGTCACTACCAATTCAGTATAATATCAAGTGTTTACAGTGTCACTGGCAGTTCAATAA
Found at i:21788 original size:73 final size:72
Alignment explanation
Indices: 21682--21864 Score: 213
Period size: 72 Copynumber: 2.5 Consensus size: 72
21672 CTCACCCACG
* * * *
21682 CCCGTGTGTCCAACCCATGTAACTCACTATTTCTGGTTTCAACAAGTAAACTAGCCACACGGTCT
1 CCCGTGTGCCCAAACCGTGTAACTCACTATTTCTGGTTTCAACAAATAAAC-AGCCACACGGTCT
**
21747 AGCACATG
65 AGCACACA
* ** * * ** *
21755 TCCGTGTGCTTAAACCGTGTAACTCACTGTTTCTGCTTTCTTCAAATAATCAGCCACACGGTCTA
1 CCCGTGTGCCCAAACCGTGTAACTCACTATTTCTGGTTTCAACAAATAAACAGCCACACGGTCTA
21820 GCACACA
66 GCACACA
* *
21827 CCCGTGTGCCCAGACTGTGTAACTCACTATTTCTGGTT
1 CCCGTGTGCCCAAACCGTGTAACTCACTATTTCTGGTT
21865 ATATGACACA
Statistics
Matches: 89, Mismatches: 21, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
72 50 0.56
73 39 0.44
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.30
Consensus pattern (72 bp):
CCCGTGTGCCCAAACCGTGTAACTCACTATTTCTGGTTTCAACAAATAAACAGCCACACGGTCTA
GCACACA
Found at i:22489 original size:14 final size:14
Alignment explanation
Indices: 22470--22496 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
22460 AACTAAACAT
22470 AATAAATAAATAAA
1 AATAAATAAATAAA
22484 AATAAATAAATAA
1 AATAAATAAATAA
22497 TAAAAGAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
AATAAATAAATAAA
Found at i:22736 original size:32 final size:32
Alignment explanation
Indices: 22695--22786 Score: 157
Period size: 32 Copynumber: 2.9 Consensus size: 32
22685 CTCTCCAAAG
*
22695 TCCAAATCTCCCAAAAACAGTGGTAAGTGCTC
1 TCCAAATCTCCCAAAAATAGTGGTAAGTGCTC
*
22727 TCCAAATCTCCCAAAAATAATGGTAAGTGCTC
1 TCCAAATCTCCCAAAAATAGTGGTAAGTGCTC
*
22759 TCCATATCTCCCAAAAATAGTGGTAAGT
1 TCCAAATCTCCCAAAAATAGTGGTAAGT
22787 TTCTTCTTTA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 56 1.00
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.25
Consensus pattern (32 bp):
TCCAAATCTCCCAAAAATAGTGGTAAGTGCTC
Found at i:24416 original size:15 final size:16
Alignment explanation
Indices: 24396--24475 Score: 56
Period size: 15 Copynumber: 4.8 Consensus size: 16
24386 AATGTCCGTA
24396 TAATTTTT-TATTTGT
1 TAATTTTTATATTTGT
* * *
24411 TAATTTTATCTTTTAATTT
1 TAATTTT-TATATT--TGT
* *
24430 TAATAATTTTATTTTTTT
1 TAAT--TTTTATATTTGT
24448 TAATTTTT-TATTTGT
1 TAATTTTTATATTTGT
24463 TAATTTTTATATT
1 TAATTTTTATATT
24476 ACATTTATTT
Statistics
Matches: 53, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
15 20 0.38
16 9 0.17
17 3 0.06
18 7 0.13
19 6 0.11
20 5 0.09
21 3 0.06
ACGTcount: A:0.25, C:0.01, G:0.03, T:0.71
Consensus pattern (16 bp):
TAATTTTTATATTTGT
Found at i:24487 original size:39 final size:38
Alignment explanation
Indices: 24402--24488 Score: 90
Period size: 39 Copynumber: 2.3 Consensus size: 38
24392 CGTATAATTT
**
24402 TTTATTTGTTAATTTTATCTTTTAATTTTAATAATTTTA
1 TTTATTT-TTAATTTTATCTTTTAATTTTAATAATTACA
*
24441 TTT-TTTTTAATTTTTTAT-TTGTTAATTTTTAT-ATTACA
1 TTTATTTTTAA--TTTTATCTT-TTAATTTTAATAATTACA
24479 TTTATTTTTA
1 TTTATTTTTA
24489 TTATCATGAT
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
37 4 0.10
38 12 0.29
39 25 0.61
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.70
Consensus pattern (38 bp):
TTTATTTTTAATTTTATCTTTTAATTTTAATAATTACA
Found at i:27170 original size:19 final size:19
Alignment explanation
Indices: 27139--27181 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
27129 GGGTAAATAG
27139 TTAA-TTAAATTAT-TTAAT
1 TTAATTTAAATTATATT-AT
*
27157 TTAATTTAATTTATATTAT
1 TTAATTTAAATTATATTAT
27176 TTAATT
1 TTAATT
27182 ATATTGTACA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 4 0.18
19 16 0.73
20 2 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
TTAATTTAAATTATATTAT
Found at i:27177 original size:14 final size:13
Alignment explanation
Indices: 27139--27186 Score: 57
Period size: 13 Copynumber: 3.8 Consensus size: 13
27129 GGGTAAATAG
*
27139 TTAATTAAATTAT
1 TTAATTATATTAT
27152 TTAATT-TA--AT
1 TTAATTATATTAT
27162 TTAATTTATATTAT
1 TTAA-TTATATTAT
27176 TTAATTATATT
1 TTAATTATATT
27187 GTACATTTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
10 6 0.20
11 2 0.07
12 3 0.10
13 13 0.43
14 6 0.20
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TTAATTATATTAT
Found at i:35010 original size:17 final size:18
Alignment explanation
Indices: 34979--35012 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
34969 AATTTAATTT
34979 TAATTAAATTATTTAAAA
1 TAATTAAATTATTTAAAA
*
34997 TAATT-AATTTTTTAAA
1 TAATTAAATTATTTAAA
35013 TCATAAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATTAAATTATTTAAAA
Found at i:35689 original size:17 final size:18
Alignment explanation
Indices: 35658--35691 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
35648 AATTTAATTT
35658 TAATTAAATTATTTAAAA
1 TAATTAAATTATTTAAAA
*
35676 TAATT-AATTTTTTAAA
1 TAATTAAATTATTTAAA
35692 TCATAAACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATTAAATTATTTAAAA
Found at i:38391 original size:25 final size:23
Alignment explanation
Indices: 38325--38391 Score: 66
Period size: 25 Copynumber: 2.8 Consensus size: 23
38315 CTCAAAAATT
*
38325 AAAAA-TAAAAAAATTATAATTTC
1 AAAAATTAAAAAAA-TAAAATTTC
38348 AAAAATTATAAAAAA-AAAACTTCTC
1 AAAAATTA-AAAAAATAAAA-TT-TC
*
38373 AAAATTTAAAAAAATAAAA
1 AAAAATTAAAAAAATAAAA
38392 AAGAATTTCT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
23 8 0.22
24 10 0.27
25 19 0.51
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (23 bp):
AAAAATTAAAAAAATAAAATTTC
Found at i:46908 original size:7 final size:7
Alignment explanation
Indices: 46882--46926 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
46872 TCATGTTCAC
*
46882 ATTTAAT
1 ATTTTAT
*
46889 ATTTCAT
1 ATTTTAT
46896 -TTTTAT
1 ATTTTAT
*
46902 ATGTTAT
1 ATTTTAT
46909 ATTTTAT
1 ATTTTAT
46916 ATTTTAT
1 ATTTTAT
46923 ATTT
1 ATTT
46927 ACATAATTTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
6 5 0.15
7 28 0.85
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (7 bp):
ATTTTAT
Found at i:46927 original size:27 final size:29
Alignment explanation
Indices: 46868--46927 Score: 70
Period size: 27 Copynumber: 2.1 Consensus size: 29
46858 TTTGATTTTC
*
46868 TTTATCATGTTCACATTTAATATTTCATT
1 TTTATCATGTTCACATTTAATATTTCATA
* * *
46897 TTTAT-ATGTT-ATATTTTATATTTTATA
1 TTTATCATGTTCACATTTAATATTTCATA
46924 TTTA
1 TTTA
46928 CATAATTTGG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 17 0.63
28 5 0.19
29 5 0.19
ACGTcount: A:0.28, C:0.07, G:0.03, T:0.62
Consensus pattern (29 bp):
TTTATCATGTTCACATTTAATATTTCATA
Found at i:49685 original size:7 final size:7
Alignment explanation
Indices: 49673--49699 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
49663 AGAAATGAAA
49673 GGAGGGC
1 GGAGGGC
49680 GGAGGGC
1 GGAGGGC
49687 GGAGGGC
1 GGAGGGC
49694 GGAGGG
1 GGAGGG
49700 TGGGGGAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.11, G:0.74, T:0.00
Consensus pattern (7 bp):
GGAGGGC
Found at i:50238 original size:31 final size:31
Alignment explanation
Indices: 50200--50258 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
50190 GAGATGAAAA
50200 CTCGGACGCGAATCTTTTGTCTAAGCTTCAT
1 CTCGGACGCGAATCTTTTGTCTAAGCTTCAT
50231 CTCGGACGCGAATCTTTTGTCTAAGCTT
1 CTCGGACGCGAATCTTTTGTCTAAGCTT
50259 AGTCTATCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.19, C:0.25, G:0.20, T:0.36
Consensus pattern (31 bp):
CTCGGACGCGAATCTTTTGTCTAAGCTTCAT
Found at i:50597 original size:18 final size:19
Alignment explanation
Indices: 50568--50612 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
50558 AGGTTTGTAG
50568 TTAAATAATTCA-ATT-TTT
1 TTAAA-AATTCAGATTATTT
50586 TGTAAAAATTCAGATTATTT
1 T-TAAAAATTCAGATTATTT
50606 TTAAAAA
1 TTAAAAA
50613 AAATAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
18 7 0.29
19 13 0.54
20 4 0.17
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (19 bp):
TTAAAAATTCAGATTATTT
Found at i:59583 original size:96 final size:96
Alignment explanation
Indices: 59411--59585 Score: 239
Period size: 96 Copynumber: 1.8 Consensus size: 96
59401 TTTGATTATC
* * * *
59411 TCGATTTGAAGAAAAATTGCACCTAGTAACTTAAGGCGCAAATTTTCAGAATCGAAGATAAGGAA
1 TCGATTTAAAAAAAAATTGCACCTAGTAACTTAAGACGCAAATTTTCAGAATCGAAGATAAAGAA
*
59476 ACATTGTCTCGATTAAGGGTATTCGACTATT
66 ACATTGCCTCGATTAAGGGTATTCGACTATT
*
59507 TCGATTTAAAAAAAAATTGCACCTAGTAAGTTAAGACGCAAATTTTC-GAAACTCGAA-ATAAA-
1 TCGATTTAAAAAAAAATTGCACCTAGTAACTTAAGACGCAAATTTTCAG-AA-TCGAAGATAAAG
*
59569 AGAATATTGCCTCGATT
64 A-AACATTGCCTCGATT
59586 TTAAAGCTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
95 2 0.03
96 62 0.90
97 5 0.07
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (96 bp):
TCGATTTAAAAAAAAATTGCACCTAGTAACTTAAGACGCAAATTTTCAGAATCGAAGATAAAGAA
ACATTGCCTCGATTAAGGGTATTCGACTATT
Found at i:59896 original size:29 final size:28
Alignment explanation
Indices: 59853--59941 Score: 74
Period size: 30 Copynumber: 3.1 Consensus size: 28
59843 TTTGGGGTTT
*
59853 AAAATGGAA-TTTTAGACATTCGAGAGT-
1 AAAACGGAATTTTTAGACATTCGAGA-TA
* * *
59880 AAAACGATAATTTTTAGGAAAATCGAGATAA
1 AAAACG-GAATTTTTA-GACATTCGAGAT-A
*
59911 AAAACGGAATTTTTGGACATTCGAGGATA
1 AAAACGGAATTTTTAGACATTCGA-GATA
59940 AA
1 AA
59942 TTGGTAATTT
Statistics
Matches: 48, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
27 5 0.10
28 2 0.04
29 16 0.33
30 19 0.40
31 6 0.12
ACGTcount: A:0.45, C:0.08, G:0.20, T:0.27
Consensus pattern (28 bp):
AAAACGGAATTTTTAGACATTCGAGATA
Found at i:60005 original size:58 final size:58
Alignment explanation
Indices: 59910--60164 Score: 200
Period size: 58 Copynumber: 4.3 Consensus size: 58
59900 AATCGAGATA
* * * * *
59910 AAAAACGGAATTTTTGGACATTCGAGGAT-AAATTGGTAATTTTTAAGGGTTTCGGGGTC
1 AAAAATGGAATTTTTGGACA-TCGGGGGTAAAAAT-GTAATTTTTAAGAGTTTCGGGGTC
* * * * **
59969 -AAAATGGAGTTTTTGGACATTTGGGGG-AAAAATGGTAAATTTTGAA-AGTTTTGATGTC
1 AAAAATGGAATTTTTGGACA-TCGGGGGTAAAAAT-GT-AATTTTTAAGAGTTTCGGGGTC
* * * *
60027 AAAAATGGATTTTTTGGATGATCGGGGGTAAAAATGTAATTTTT-GGAAGTTTTGGGGTC
1 AAAAATGGAATTTTTGGA-CATCGGGGGTAAAAATGTAATTTTTAAG-AGTTTCGGGGTC
* * * *
60086 -AAAATGGAATTTTAGGA-AGTTCGGGGGTAAAAAATGTAATTTTCAAAAGTTTCTGGGTC
1 AAAAATGGAATTTTTGGACA--TCGGGGGT-AAAAATGTAATTTTTAAGAGTTTCGGGGTC
60145 AAAAATGGAATTTTTGGACA
1 AAAAATGGAATTTTTGGACA
60165 GTTTAGGAAC
Statistics
Matches: 157, Mismatches: 26, Indels: 24
0.76 0.13 0.12
Matches are distributed among these distances:
56 1 0.01
58 66 0.42
59 66 0.42
60 23 0.15
61 1 0.01
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.35
Consensus pattern (58 bp):
AAAAATGGAATTTTTGGACATCGGGGGTAAAAATGTAATTTTTAAGAGTTTCGGGGTC
Found at i:60041 original size:59 final size:58
Alignment explanation
Indices: 59910--60164 Score: 211
Period size: 59 Copynumber: 4.3 Consensus size: 58
59900 AATCGAGATA
* * * * * * *
59910 AAAAACGGAATTTTTGGACATTCGAGGAT-AAATTGGT-AATTTTTAAGGGTTTCGGGGTC
1 AAAAATGGAATTTTTGGACATTCGGGGGTAAAAAT-GTAAATTTTGAA-AGTTT-TGGGTC
* * *
59969 -AAAATGGAGTTTTTGGACATTTGGGGG-AAAAATGGTAAATTTTGAAAGTTTTGATGTC
1 AAAAATGGAATTTTTGGACATTCGGGGGTAAAAAT-GTAAATTTTGAAAGTTTTG-GGTC
* * * *
60027 AAAAATGGATTTTTTGGATGA-TCGGGGGTAAAAATGTAATTTTTGGAAGTTTTGGGGTC
1 AAAAATGGAATTTTTGGA-CATTCGGGGGTAAAAATGTAAATTTTGAAAGTTTT-GGGTC
* *
60086 -AAAATGGAATTTTAGGA-AGTTCGGGGGTAAAAAATGT-AATTTTCAAAAGTTTCTGGGTC
1 AAAAATGGAATTTTTGGACA-TTCGGGGGT-AAAAATGTAAATTTT-GAAAGTTT-TGGGTC
60145 AAAAATGGAATTTTTGGACA
1 AAAAATGGAATTTTTGGACA
60165 GTTTAGGAAC
Statistics
Matches: 160, Mismatches: 22, Indels: 26
0.77 0.11 0.12
Matches are distributed among these distances:
56 1 0.01
57 1 0.01
58 64 0.40
59 68 0.43
60 25 0.16
61 1 0.01
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.35
Consensus pattern (58 bp):
AAAAATGGAATTTTTGGACATTCGGGGGTAAAAATGTAAATTTTGAAAGTTTTGGGTC
Found at i:60060 original size:29 final size:29
Alignment explanation
Indices: 59963--60167 Score: 128
Period size: 29 Copynumber: 6.9 Consensus size: 29
59953 TAAGGGTTTC
* * *
59963 GGGGTCAAAATGGAGTTTTTGGACA-TTTG
1 GGGGTAAAAATGGAATTTTTGGA-AGTTCG
* * **
59992 GGGG-AAAAATGGTAAATTTTGAAAGTTTT
1 GGGGTAAAAATGG-AATTTTTGGAAGTTCG
** * * *
60021 GATGTCAAAAATGGATTTTTTGGATGATCG
1 GGGGT-AAAAATGGAATTTTTGGAAGTTCG
* **
60051 GGGGTAAAAATGTAATTTTTGGAAGTTTT
1 GGGGTAAAAATGGAATTTTTGGAAGTTCG
* *
60080 GGGGTCAAAATGGAATTTTAGGAAGTTCG
1 GGGGTAAAAATGGAATTTTTGGAAGTTCG
* ***
60109 GGGGTAAAAAATGTAATTTTCAAAAGTTTC-
1 GGGGT-AAAAATGGAATTTTTGGAAG-TTCG
*
60139 TGGGTCAAAAATGGAATTTTTGGACAGTT
1 GGGGT-AAAAATGGAATTTTTGGA-AGTT
60168 TAGGAACCTT
Statistics
Matches: 131, Mismatches: 38, Indels: 13
0.72 0.21 0.07
Matches are distributed among these distances:
28 8 0.06
29 63 0.48
30 47 0.36
31 13 0.10
ACGTcount: A:0.32, C:0.05, G:0.28, T:0.35
Consensus pattern (29 bp):
GGGGTAAAAATGGAATTTTTGGAAGTTCG
Found at i:60136 original size:30 final size:28
Alignment explanation
Indices: 60048--60158 Score: 89
Period size: 30 Copynumber: 3.8 Consensus size: 28
60038 TTTTGGATGA
* *
60048 TCGGGGGTAAAAATGTAATTTTTGGAAGT
1 TCGGGGGTAAAAATGGAA-TTTTAGAAGT
** *
60077 TTTGGGGTCAAAATGGAATTTTAGGAAGT
1 TCGGGGGTAAAAATGGAATTTTA-GAAGT
* *
60106 TCGGGGGTAAAAAATGTAATTTTCAAAAGTT
1 TCGGGGGT-AAAAATGGAATTTT-AGAAG-T
*
60137 TC-TGGGTCAAAAATGGAATTTT
1 TCGGGGGT-AAAAATGGAATTTT
60159 TGGACAGTTT
Statistics
Matches: 65, Mismatches: 13, Indels: 7
0.76 0.15 0.08
Matches are distributed among these distances:
28 4 0.06
29 25 0.38
30 32 0.49
31 4 0.06
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.34
Consensus pattern (28 bp):
TCGGGGGTAAAAATGGAATTTTAGAAGT
Found at i:62033 original size:27 final size:29
Alignment explanation
Indices: 61988--62045 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 29
61978 AATCATTCCG
*
61988 AATTTAAACTAAATTTAAATTTAAAA-CC
1 AATTTAAACTAAATATAAATTTAAAATCC
*
62016 AATTTAACCT-AATATAAATTTAAAATCC
1 AATTTAAACTAAATATAAATTTAAAATCC
62044 AA
1 AA
62046 AGTTGACCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 14 0.52
28 13 0.48
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.34
Consensus pattern (29 bp):
AATTTAAACTAAATATAAATTTAAAATCC
Found at i:62706 original size:205 final size:205
Alignment explanation
Indices: 62348--62954 Score: 780
Period size: 205 Copynumber: 3.0 Consensus size: 205
62338 GTCTAGTTTC
* *** ** *
62348 ATTGATTTGGCCTTCTTCTCAGTATCTTATCAAGAAGATGACAATATCACTTGTTTTGATCCACT
1 ATTGATTTGGTCTTCTTCTCAGTATCTTATCAAGAAGATGACCGCATCACTTGTTTCAATCCGCT
* * * *
62413 TCTCTGTGTTTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATTTCAACAGGAAGCTAACCA
66 TCTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCA
* * *
62478 -TTTATTGTTTCGACCTACTTCTCAATATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACA
131 TTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACA
**
62542 TTGAGTGT-G
196 TTGAGCCTCG
* *
62551 AGTTTGATTTGGTCTTCTTCTCAATATCTTATCAAGAAGATGACCGCATCGCTTGTTTCAATCCG
1 A--TTGATTTGGTCTTCTTCTCAGTATCTTATCAAGAAGATGACCGCATCACTTGTTTCAATCCG
* * *
62616 CTTCTCTATATCTCATTAGGAAGACGAA-TTGGTTCACTTCTCAGTATCTCATCAGGAAGTTAAC
64 CTTCTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAAC
* * *
62680 CATTTTATTGCTTCGACTTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCAAAGATTTGCTCG
129 CATTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCA
62745 CATTGAGCCTCG
194 CATTGAGCCTCG
* * * * * * *
62757 A--G--TTGGTATTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTTACTTGTTTCAATCCGTT
1 ATTGATTTGGTCTTCTTCTCAGTATCTTATCAAGAAGATGACCGCATCACTTGTTTCAATCCGCT
* * *
62818 TCTCTGTACCTCACCAGGAAGACGAATTTGGTTCACTTCTTAGTATCTCATCAGGAAGCTAACC-
66 TCTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCA
* * * * *
62882 TTTTATTGCTTCGCCCTGCTTCTCAGTATCTCATTAGGAAGCTGAGATTCGAAGATTTGCTCATA
131 TTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACA
*
62947 TCGAGCCT
196 TTGAGCCT
62955 TGAGGTGGTA
Statistics
Matches: 351, Mismatches: 48, Indels: 13
0.85 0.12 0.03
Matches are distributed among these distances:
200 136 0.39
201 35 0.10
202 1 0.00
203 1 0.00
204 35 0.10
205 141 0.40
206 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (205 bp):
ATTGATTTGGTCTTCTTCTCAGTATCTTATCAAGAAGATGACCGCATCACTTGTTTCAATCCGCT
TCTCTGTATCTCATCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCA
TTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACA
TTGAGCCTCG
Found at i:62890 original size:200 final size:199
Alignment explanation
Indices: 62360--62989 Score: 740
Period size: 200 Copynumber: 3.1 Consensus size: 199
62350 TGATTTGGCC
* * * *** ** * * ***
62360 TTCTTCTCAGTATCTTATCAAGAAGATGACAATATCACTTGTTTTGATCCACTTCTCTGTGTTTC
1 TTCTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTATACCTC
* * * * *
62425 ATCAGGAAGACGAATTTGGTTCACTTCTCAGTATTTCAACAGGAAGCTAACCATTTATTGTTTCG
66 ACCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCG
* * **
62490 ACCTACTTCTCAATATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATTGAGTGTGAGTT
131 ACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATTGAGCCTGA---
*
62555 TGATTTGGTC
193 -G--TTGGTA
** * * * *
62565 TTCTTCTCAATATCTTATCAAGAAGATGACCGCATCGCTTGTTTCAATCCGCTTCTCTATATCTC
1 TTCTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTATACCTC
** *
62630 ATTAGGAAGACGAA-TTGGTTCACTTCTCAGTATCTCATCAGGAAGTTAACCATTTTATTGCTTC
66 ACCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACC-TTTTATTGCTTC
* * *
62694 GACTTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCAAAGATTTGCTCGCATTGAGCCTCGAG
130 GACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATTGAGCCT-GAG
62759 TTGGTA
194 TTGGTA
* * * *
62765 TTCTTCTCTGTATCTCATCAGGAAGATGACCGCCTTACTTGTTTCAATCCGTTTCTCTGTACCTC
1 TTCTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTATACCTC
*
62830 ACCAGGAAGACGAATTTGGTTCACTTCTTAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCG
66 ACCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCG
* * * * * * *
62895 CCCTGCTTCTCAGTATCTCATTAGGAAGCTGAGATTCGAAGATTTGCTCATATCGAGCCTTGAGG
131 ACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATTGAGCC-TGAGT
62960 TGGTA
195 TGGTA
*
62965 TACTTCTCTGTATCTCATCAGGAAG
1 TTCTTCTCTGTATCTCATCAGGAAG
62990 CTAACCATTT
Statistics
Matches: 371, Mismatches: 50, Indels: 13
0.85 0.12 0.03
Matches are distributed among these distances:
200 167 0.45
201 36 0.10
202 1 0.00
204 34 0.09
205 131 0.35
206 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.19, T:0.36
Consensus pattern (199 bp):
TTCTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTCTATACCTC
ACCAGGAAGACGAATTTGGTTCACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCG
ACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATTGAGCCTGAGTT
GGTA
Found at i:63069 original size:115 final size:114
Alignment explanation
Indices: 62852--63058 Score: 337
Period size: 115 Copynumber: 1.8 Consensus size: 114
62842 AATTTGGTTC
* **
62852 ACTTCTTAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGCCCTGCTTCTCAGTATCTCATT
1 ACTTCTTAGTATCTCATCAGGAAGCTAACCTTTTATTACTTCAACCTGCTTCTCAGTATCTCATT
62917 AGGAAGCTGAGATTCGAAGATTTGCTCATATCGAGCCTTGAGGTGGTAT
66 AGGAAGCTGAGATTCGAAGATTTGCTCATATCGAGCCTTGAGGTGGTAT
*
62966 ACTTCTCT-GTATCTCATCAGGAAGCTAACCATTTTATTACTTCAACCTGCTTCTCAGTATCTTA
1 ACTTCT-TAGTATCTCATCAGGAAGCTAACC-TTTTATTACTTCAACCTGCTTCTCAGTATCTCA
63030 TTAGGAAGCT-AGAGTTCGAAGATTTGCTC
64 TTAGGAAGCTGAGA-TTCGAAGATTTGCTC
63059 GCTTTGAGCC
Statistics
Matches: 86, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
114 31 0.36
115 55 0.64
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (114 bp):
ACTTCTTAGTATCTCATCAGGAAGCTAACCTTTTATTACTTCAACCTGCTTCTCAGTATCTCATT
AGGAAGCTGAGATTCGAAGATTTGCTCATATCGAGCCTTGAGGTGGTAT
Found at i:78401 original size:28 final size:29
Alignment explanation
Indices: 78365--78425 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
78355 AAAATGAGAC
78365 TTTTCGGATACTCGGGGGAAAAATGGTAA
1 TTTTCGGATACTCGGGGGAAAAATGGTAA
** * *
78394 TTTT-GGATTTTTGGGGGCAAAATGGTAA
1 TTTTCGGATACTCGGGGGAAAAATGGTAA
78422 TTTT
1 TTTT
78426 AGGAAAGTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 24 0.86
29 4 0.14
ACGTcount: A:0.26, C:0.07, G:0.30, T:0.38
Consensus pattern (29 bp):
TTTTCGGATACTCGGGGGAAAAATGGTAA
Found at i:78559 original size:29 final size:29
Alignment explanation
Indices: 78527--78728 Score: 201
Period size: 29 Copynumber: 6.8 Consensus size: 29
78517 AGGTTCGAGT
* * *
78527 GTAAAAATGGGATTTTTGGGAGTTTGGGG
1 GTAAAAATGGAATTTTTGGAAGTTTAGGG
*
78556 GTAAAAATGAAATTTTTGGAAGTTTAGGG
1 GTAAAAATGGAATTTTTGGAAGTTTAGGG
* *
78585 ATAAATATGGAATTTTTGGAAGTTTTA-GG
1 GTAAAAATGGAATTTTTGGAAG-TTTAGGG
* *
78614 GTCAAAAATGGAATTTTTGGAAG-TTCGTTG
1 GT-AAAAATGGAATTTTTGGAAGTTTAG-GG
*
78644 GTAAAAAGGGAATTTTTGGAAGTTTTAGGG
1 GTAAAAATGGAATTTTTGGAAG-TTTAGGG
** * * *
78674 CCAAAAATGGAATCTTTGGAAGTTTCGAG
1 GTAAAAATGGAATTTTTGGAAGTTTAGGG
*
78703 ATCAAAAATGGAATTTTTGGACAGTT
1 GT-AAAAATGGAATTTTTGGA-AGTT
78729 CAGGTACTTC
Statistics
Matches: 142, Mismatches: 23, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
28 2 0.01
29 71 0.50
30 62 0.44
31 7 0.05
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (29 bp):
GTAAAAATGGAATTTTTGGAAGTTTAGGG
Found at i:78614 original size:30 final size:29
Alignment explanation
Indices: 78527--78728 Score: 205
Period size: 30 Copynumber: 6.8 Consensus size: 29
78517 AGGTTCGAGT
* * **
78527 GTAAAAATGGGATTTTTGGGAGTTTGGGG
1 GTAAAAATGGAATTTTTGGAAGTTTTAGG
*
78556 GTAAAAATGAAATTTTTGGAAG-TTTAGG
1 GTAAAAATGGAATTTTTGGAAGTTTTAGG
*
78584 GATAAATATGGAATTTTTGGAAGTTTTAGG
1 G-TAAAAATGGAATTTTTGGAAGTTTTAGG
78614 GTCAAAAATGGAATTTTTGGAAGTTCGTT--G
1 GT-AAAAATGGAATTTTTGGAAGTT--TTAGG
*
78644 GTAAAAAGGGAATTTTTGGAAGTTTTAGG
1 GTAAAAATGGAATTTTTGGAAGTTTTAGG
* * *
78673 GCCAAAAATGGAATCTTTGGAAG-TTTCGAG
1 G-TAAAAATGGAATTTTTGGAAGTTTTAG-G
*
78703 ATCAAAAATGGAATTTTTGGACAGTT
1 GT-AAAAATGGAATTTTTGGA-AGTT
78729 CAGGTACTTC
Statistics
Matches: 145, Mismatches: 16, Indels: 21
0.80 0.09 0.12
Matches are distributed among these distances:
27 2 0.01
28 5 0.03
29 66 0.46
30 67 0.46
31 2 0.01
32 3 0.02
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (29 bp):
GTAAAAATGGAATTTTTGGAAGTTTTAGG
Found at i:78630 original size:59 final size:58
Alignment explanation
Indices: 78528--78728 Score: 235
Period size: 59 Copynumber: 3.4 Consensus size: 58
78518 GGTTCGAGTG
* * ** *
78528 TAAAAATGGGATTTTTGGGAGTTTGGGGGT-AAAAATGAAATTTTTGGAAGTTTAGGGA
1 TAAAAATGGAATTTTTGGAAGTTTTAGGGTCAAAAATGGAATTTTTGGAAGTTT-GGGA
* *
78586 TAAATATGGAATTTTTGGAAGTTTTAGGGTCAAAAATGGAATTTTTGGAAGTTCGTTGG-
1 TAAAAATGGAATTTTTGGAAGTTTTAGGGTCAAAAATGGAATTTTTGGAAGTT--TGGGA
* * * *
78645 TAAAAAGGGAATTTTTGGAAGTTTTAGGGCCAAAAATGGAATCTTTGGAAGTTTCGAGA
1 TAAAAATGGAATTTTTGGAAGTTTTAGGGTCAAAAATGGAATTTTTGGAAGTTT-GGGA
78704 TCAAAAATGGAATTTTTGGACAGTT
1 T-AAAAATGGAATTTTTGGA-AGTT
78729 CAGGTACTTC
Statistics
Matches: 122, Mismatches: 14, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
57 1 0.01
58 26 0.21
59 71 0.58
60 19 0.16
61 5 0.04
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (58 bp):
TAAAAATGGAATTTTTGGAAGTTTTAGGGTCAAAAATGGAATTTTTGGAAGTTTGGGA
Found at i:84016 original size:82 final size:82
Alignment explanation
Indices: 83917--84068 Score: 241
Period size: 82 Copynumber: 1.9 Consensus size: 82
83907 TATTATTAAA
* * * * * *
83917 TAATATTTATAGACTCGACCATTGGAGAACGGTGTTCTGAAACCGCTATTTCCAACACCATTGGA
1 TAATATTTACAAACTCGACCATCGGAGAACGGTGTTCTGAAACCGCCATTTCCAACACCACTAGA
83982 ACCTGGGTCATTACAAT
66 ACCTGGGTCATTACAAT
*
83999 TAATATTTACAAACTCGACCATCGGAGAACGGTGTTCTGAAACCGCCATTTCCGACACCACTAGA
1 TAATATTTACAAACTCGACCATCGGAGAACGGTGTTCTGAAACCGCCATTTCCAACACCACTAGA
84064 ACCTG
66 ACCTG
84069 CATCGTTACA
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
82 63 1.00
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (82 bp):
TAATATTTACAAACTCGACCATCGGAGAACGGTGTTCTGAAACCGCCATTTCCAACACCACTAGA
ACCTGGGTCATTACAAT
Found at i:84332 original size:20 final size:20
Alignment explanation
Indices: 84309--84348 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
84299 TCTAGTACTT
84309 ATATTTGAGTTTATTAACCC
1 ATATTTGAGTTTATTAACCC
84329 ATATTTGAGTTTATTAACCC
1 ATATTTGAGTTTATTAACCC
84349 TTCTTGATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.45
Consensus pattern (20 bp):
ATATTTGAGTTTATTAACCC
Found at i:88044 original size:19 final size:19
Alignment explanation
Indices: 88003--88044 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
87993 GGTTTTAATT
*
88003 TTTTTTAATTTTAATTACT
1 TTTTTTAATTTTAATTACA
88022 TTTTTTAATTTTAAATT-CA
1 TTTTTTAATTTT-AATTACA
88041 TTTT
1 TTTT
88045 CTGACGTGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTTTAATTTTAATTACA
Found at i:90565 original size:107 final size:107
Alignment explanation
Indices: 90379--90593 Score: 421
Period size: 107 Copynumber: 2.0 Consensus size: 107
90369 GTAGGCACTA
90379 TACTAAAAAGAGCATATATGATCAGAATATATAAACATGAAAACATAATGAAAAATACAATACAA
1 TACTAAAAAGAGCATATATGATCAGAATATATAAACATGAAAACATAATGAAAAATACAATACAA
*
90444 ACATTCGAAATAGCTAATTTGTCTTTGCCATCATTACCCCTT
66 ACATTCGAAATAGCTAATTTGTCTCTGCCATCATTACCCCTT
90486 TACTAAAAAGAGCATATATGATCAGAATATATAAACATGAAAACATAATGAAAAATACAATACAA
1 TACTAAAAAGAGCATATATGATCAGAATATATAAACATGAAAACATAATGAAAAATACAATACAA
90551 ACATTCGAAATAGCTAATTTGTCTCTGCCATCATTACCCCTT
66 ACATTCGAAATAGCTAATTTGTCTCTGCCATCATTACCCCTT
90593 T
1 T
90594 TACAGCCCTT
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
107 107 1.00
ACGTcount: A:0.46, C:0.17, G:0.09, T:0.28
Consensus pattern (107 bp):
TACTAAAAAGAGCATATATGATCAGAATATATAAACATGAAAACATAATGAAAAATACAATACAA
ACATTCGAAATAGCTAATTTGTCTCTGCCATCATTACCCCTT
Found at i:95096 original size:24 final size:24
Alignment explanation
Indices: 95064--95356 Score: 253
Period size: 24 Copynumber: 12.2 Consensus size: 24
95054 TTAGACTATA
**
95064 TAAACGTATATAAGCTGACGAGCG
1 TAAACGTATGCAAGCTGACGAGCG
* *
95088 TAAACGTATACAAGCTGATGAGCG
1 TAAACGTATGCAAGCTGACGAGCG
* * * **
95112 AAAACGTGTGCAAGCTGATGAGTA
1 TAAACGTATGCAAGCTGACGAGCG
** * * *
95136 TAAACGTATATAAGCTGATGCGTG
1 TAAACGTATGCAAGCTGACGAGCG
* *
95160 TAAACGTGTGCAAGCTGCCGAGCG
1 TAAACGTATGCAAGCTGACGAGCG
** *
95184 TAAACGTATATAAGCTGACGAGTG
1 TAAACGTATGCAAGCTGACGAGCG
*
95208 TAAACGTGTGCAAGCTGACGAGCG
1 TAAACGTATGCAAGCTGACGAGCG
* * * *
95232 TAAACGTGTGTAAGCTAACAAGCG
1 TAAACGTATGCAAGCTGACGAGCG
** *
95256 TAAACGCGTGCAAGCTAACGAGCG
1 TAAACGTATGCAAGCTGACGAGCG
** * *
95280 TAAACGCGTGCAAGGTAACGAGCG
1 TAAACGTATGCAAGCTGACGAGCG
*
95304 TAAACGTATGCATGCTGACGAGCG
1 TAAACGTATGCAAGCTGACGAGCG
* ** * *
95328 TAAAGGTATATAAGCTGACAAGCA
1 TAAACGTATGCAAGCTGACGAGCG
95352 TAAAC
1 TAAAC
95357 ATGTGAAGGT
Statistics
Matches: 221, Mismatches: 48, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 221 1.00
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.20
Consensus pattern (24 bp):
TAAACGTATGCAAGCTGACGAGCG
Found at i:95356 original size:48 final size:48
Alignment explanation
Indices: 95075--95361 Score: 313
Period size: 48 Copynumber: 6.0 Consensus size: 48
95065 AAACGTATAT
* * *
95075 AAGCTGACGAGCGTAAACGTATACAAGCTGATGAGCGAAAACGTGTGC
1 AAGCTGACGAGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGC
* ** * * *
95123 AAGCTGATGAGTATAAACGTATATAAGCTGATGCGTGTAAACGTGTGC
1 AAGCTGACGAGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGC
* *
95171 AAGCTGCCGAGCGTAAACGTATATAAGCTGACGAGTGTAAACGTGTGC
1 AAGCTGACGAGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGC
* * * * *
95219 AAGCTGACGAGCGTAAACGTGTGTAAGCTAACAAGCGTAAACGCGTGC
1 AAGCTGACGAGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGC
* ** ** * * *
95267 AAGCTAACGAGCGTAAACGCGTGCAAGGTAACGAGCGTAAACGTATGC
1 AAGCTGACGAGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGC
* * * * *
95315 ATGCTGACGAGCGTAAAGGTATATAAGCTGACAAGCATAAACATGTG
1 AAGCTGACGAGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTG
95362 AAGGTTGTTA
Statistics
Matches: 199, Mismatches: 40, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
48 199 1.00
ACGTcount: A:0.34, C:0.18, G:0.28, T:0.20
Consensus pattern (48 bp):
AAGCTGACGAGCGTAAACGTATATAAGCTGACGAGCGTAAACGTGTGC
Found at i:95461 original size:27 final size:28
Alignment explanation
Indices: 95423--95483 Score: 115
Period size: 27 Copynumber: 2.2 Consensus size: 28
95413 TAATTATAAG
95423 TACTTAAATAAATTGAGGAAGTTGATT-
1 TACTTAAATAAATTGAGGAAGTTGATTA
95450 TACTTAAATAAATTGAGGAAGTTGATTA
1 TACTTAAATAAATTGAGGAAGTTGATTA
95478 TACTTA
1 TACTTA
95484 CCTTATAGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 27 0.82
28 6 0.18
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.38
Consensus pattern (28 bp):
TACTTAAATAAATTGAGGAAGTTGATTA
Found at i:96099 original size:21 final size:21
Alignment explanation
Indices: 96075--96123 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
96065 GGATTGTTTT
*
96075 GGTAGAACCTATACTTATATC
1 GGTAGAACCTACACTTATATC
* * *
96096 GGTAGAAGCTCCACTTCTATC
1 GGTAGAACCTACACTTATATC
96117 GGTAGAA
1 GGTAGAA
96124 AACTGCAGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (21 bp):
GGTAGAACCTACACTTATATC
Done.