Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013590.1 Corchorus olitorius cultivar O-4 contig13623, 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: 141966
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:3785 original size:6 final size:6
Alignment explanation
Indices: 3776--3845 Score: 54
Period size: 6 Copynumber: 11.2 Consensus size: 6
3766 TTCATTGGCC
* *
3776 TCATCT TCATCT TCATCT TCATCT TCTTCACT TCCATCG TCA-CTT TCATCT
1 TCATCT TCATCT TCATCT TCATCT TCAT--CT T-CATCT TCATC-T TCATCT
*
3827 TCATCC TCA-CTT TCATCT T
1 TCATCT TCATC-T TCATCT T
3846 TTTGGTCACT
Statistics
Matches: 51, Mismatches: 6, Indels: 14
0.72 0.08 0.20
Matches are distributed among these distances:
5 2 0.04
6 40 0.78
7 4 0.08
8 3 0.06
9 2 0.04
ACGTcount: A:0.16, C:0.36, G:0.01, T:0.47
Consensus pattern (6 bp):
TCATCT
Found at i:3855 original size:18 final size:18
Alignment explanation
Indices: 3781--3845 Score: 69
Period size: 18 Copynumber: 3.4 Consensus size: 18
3771 TGGCCTCATC
*
3781 TTCATCTTCATCTTCATCTT
1 TTCATCTTCATCGTCA-C-T
3801 CTTCA-CTTCCATCGTCACT
1 -TTCATCTT-CATCGTCACT
*
3820 TTCATCTTCATCCTCACT
1 TTCATCTTCATCGTCACT
3838 TTCATCTT
1 TTCATCTT
3846 TTTGGTCACT
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
18 21 0.52
19 4 0.10
20 4 0.10
21 11 0.28
ACGTcount: A:0.15, C:0.35, G:0.02, T:0.48
Consensus pattern (18 bp):
TTCATCTTCATCGTCACT
Found at i:8428 original size:24 final size:24
Alignment explanation
Indices: 8401--8516 Score: 162
Period size: 24 Copynumber: 4.8 Consensus size: 24
8391 TCACATGGCA
* *
8401 ACATAGTGGTCATGAGATTTGGCC
1 ACATAGTGGTCGTGAGATTCGGCC
*
8425 ACATAGTGGTCATGAGATTCGGCC
1 ACATAGTGGTCGTGAGATTCGGCC
*
8449 ACATAGTGGTTGTGAGATTCGGCC
1 ACATAGTGGTCGTGAGATTCGGCC
*
8473 ACATAGTGTGGCCGTGA-ATTCGGCC
1 ACATA--GTGGTCGTGAGATTCGGCC
8498 ACATAGTGGTCGTGAGATT
1 ACATAGTGGTCGTGAGATT
8517 AGACCAATGC
Statistics
Matches: 83, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
23 9 0.11
24 53 0.64
25 13 0.16
26 8 0.10
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.28
Consensus pattern (24 bp):
ACATAGTGGTCGTGAGATTCGGCC
Found at i:10029 original size:32 final size:31
Alignment explanation
Indices: 9988--10092 Score: 122
Period size: 32 Copynumber: 3.3 Consensus size: 31
9978 GGCAATTGGG
* *
9988 CGGGTTCGGGTTTTTTCAGGTTCGGGTATTTT
1 CGGGTTCGGGTTATGTC-GGTTCGGGTATTTT
*
10020 CGGGTTCGGGTTAAGTCGGGTTCGGGTATTTT
1 CGGGTTCGGGTTATGTC-GGTTCGGGTATTTT
* *
10052 CGGGCTT-AGGTTATGTCGGATTTGGGTATTTT
1 CGGG-TTCGGGTTATGTCGG-TTCGGGTATTTT
10084 CGGGTTCGG
1 CGGGTTCGG
10093 TCTTGGGTAG
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
31 4 0.06
32 56 0.90
33 2 0.03
ACGTcount: A:0.09, C:0.12, G:0.38, T:0.41
Consensus pattern (31 bp):
CGGGTTCGGGTTATGTCGGTTCGGGTATTTT
Found at i:10054 original size:16 final size:16
Alignment explanation
Indices: 9988--10092 Score: 97
Period size: 16 Copynumber: 6.6 Consensus size: 16
9978 GGCAATTGGG
*
9988 CGGGTTCGGGTTTTTT
1 CGGGTTCGGGTATTTT
*
10004 CAGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
**
10020 CGGGTTCGGGT-TAAGT
1 CGGGTTCGGGTAT-TTT
10036 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
* * *
10052 CGGGCTTAGGTTA-TGT
1 CGGG-TTCGGGTATTTT
* *
10068 CGGATTTGGGTATTTT
1 CGGGTTCGGGTATTTT
10084 CGGGTTCGG
1 CGGGTTCGG
10093 TCTTGGGTAG
Statistics
Matches: 69, Mismatches: 16, Indels: 8
0.74 0.17 0.09
Matches are distributed among these distances:
15 7 0.10
16 55 0.80
17 7 0.10
ACGTcount: A:0.09, C:0.12, G:0.38, T:0.41
Consensus pattern (16 bp):
CGGGTTCGGGTATTTT
Found at i:10111 original size:6 final size:6
Alignment explanation
Indices: 10102--10160 Score: 86
Period size: 6 Copynumber: 10.2 Consensus size: 6
10092 GTCTTGGGTA
*
10102 GGGCTC GGGCTC GGGCTC GGG-TC GGGTTC GGGCTC GGGCTC GGG-TC
1 GGGCTC GGGCTC GGGCTC GGGCTC GGGCTC GGGCTC GGGCTC GGGCTC
*
10148 GGGTTC GGGCTC G
1 GGGCTC GGGCTC G
10161 AGTTTGATTT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
5 10 0.20
6 39 0.80
ACGTcount: A:0.00, C:0.27, G:0.53, T:0.20
Consensus pattern (6 bp):
GGGCTC
Found at i:10115 original size:23 final size:23
Alignment explanation
Indices: 10106--10160 Score: 110
Period size: 23 Copynumber: 2.4 Consensus size: 23
10096 TGGGTAGGGC
10106 TCGGGCTCGGGCTCGGGTCGGGT
1 TCGGGCTCGGGCTCGGGTCGGGT
10129 TCGGGCTCGGGCTCGGGTCGGGT
1 TCGGGCTCGGGCTCGGGTCGGGT
10152 TCGGGCTCG
1 TCGGGCTCG
10161 AGTTTGATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.00, C:0.27, G:0.51, T:0.22
Consensus pattern (23 bp):
TCGGGCTCGGGCTCGGGTCGGGT
Found at i:10126 original size:17 final size:18
Alignment explanation
Indices: 10102--10160 Score: 86
Period size: 17 Copynumber: 3.4 Consensus size: 18
10092 GTCTTGGGTA
10102 GGGCTCGGGCTCGGGCTC
1 GGGCTCGGGCTCGGGCTC
*
10120 GGG-TCGGGTTCGGGCTC
1 GGGCTCGGGCTCGGGCTC
*
10137 GGGCTCGGG-TCGGGTTC
1 GGGCTCGGGCTCGGGCTC
10154 GGGCTCG
1 GGGCTCG
10161 AGTTTGATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
17 30 0.79
18 8 0.21
ACGTcount: A:0.00, C:0.27, G:0.53, T:0.20
Consensus pattern (18 bp):
GGGCTCGGGCTCGGGCTC
Found at i:10660 original size:9 final size:9
Alignment explanation
Indices: 10646--10671 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
10636 TCAAAGTCTT
10646 AAATTAAAC
1 AAATTAAAC
10655 AAATTAAAC
1 AAATTAAAC
10664 AAATTAAA
1 AAATTAAA
10672 AGCTGATAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (9 bp):
AAATTAAAC
Found at i:10924 original size:12 final size:13
Alignment explanation
Indices: 10899--10928 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
10889 TGCTTTAAGT
10899 TATATAAGTTATA
1 TATATAAGTTATA
10912 TATATAA-TTATA
1 TATATAAGTTATA
10924 TATAT
1 TATAT
10929 TTAGTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (13 bp):
TATATAAGTTATA
Found at i:12586 original size:21 final size:21
Alignment explanation
Indices: 12562--12604 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
12552 TGGACCTTCA
* *
12562 GTCCCATGTCCACCTCCAATT
1 GTCCCAAGTCCAACTCCAATT
12583 GTCCCAAGTCCAACTCCAATT
1 GTCCCAAGTCCAACTCCAATT
12604 G
1 G
12605 GGATAGGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.23, C:0.40, G:0.12, T:0.26
Consensus pattern (21 bp):
GTCCCAAGTCCAACTCCAATT
Found at i:13592 original size:11 final size:11
Alignment explanation
Indices: 13576--13601 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
13566 CTTTGCCTAA
13576 AAAACTAGAAG
1 AAAACTAGAAG
13587 AAAACTAGAAG
1 AAAACTAGAAG
13598 AAAA
1 AAAA
13602 GAAATTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:14231 original size:19 final size:18
Alignment explanation
Indices: 14198--14233 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
14188 TTGAAATAAT
14198 TCTTCAAAAATCTTCAAG
1 TCTTCAAAAATCTTCAAG
*
14216 TCTTCAAATTATCTTCAA
1 TCTTCAAA-AATCTTCAA
14234 ATGGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.36, C:0.22, G:0.03, T:0.39
Consensus pattern (18 bp):
TCTTCAAAAATCTTCAAG
Found at i:16487 original size:33 final size:33
Alignment explanation
Indices: 16426--16496 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
16416 ATGGCTCAGC
* *
16426 TGGCCGGGCATTTGGCGCAGAGGATAGCGC-GG
1 TGGCCGGGAATGTGGCGCAGAGGATAGCGCTGG
*
16458 ATGGCCGGGAATGTGGCGCGGATGG-TAGCGCTGG
1 -TGGCCGGGAATGTGGCGCAGA-GGATAGCGCTGG
16492 TGGCC
1 TGGCC
16497 AGGCGGATGG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
33 29 0.88
34 4 0.12
ACGTcount: A:0.14, C:0.21, G:0.48, T:0.17
Consensus pattern (33 bp):
TGGCCGGGAATGTGGCGCAGAGGATAGCGCTGG
Found at i:19411 original size:22 final size:19
Alignment explanation
Indices: 19376--19422 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 19
19366 GATTGTTTTT
*
19376 TCAAAAAAAAAACGCAACAC
1 TCAAAAAAAAAACGCAA-AA
19396 TCAAAAATTAAAAACGCAAAA
1 TCAAAAA--AAAAACGCAAAA
19417 TCAAAA
1 TCAAAA
19423 TCTGTTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 7 0.29
21 7 0.29
22 10 0.42
ACGTcount: A:0.66, C:0.19, G:0.04, T:0.11
Consensus pattern (19 bp):
TCAAAAAAAAAACGCAAAA
Found at i:31018 original size:16 final size:16
Alignment explanation
Indices: 30999--31034 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
30989 TCGGGCTGCC
* *
30999 TCGGGTTCGGGTATTT
1 TCGGGCTCGGGTAATT
31015 TCGGGCTCGGGTAATT
1 TCGGGCTCGGGTAATT
31031 TCGG
1 TCGG
31035 ATTCTGGTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.08, C:0.17, G:0.39, T:0.36
Consensus pattern (16 bp):
TCGGGCTCGGGTAATT
Found at i:31589 original size:21 final size:20
Alignment explanation
Indices: 31552--31590 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
31542 AGTTGTTTAT
*
31552 AGCTTTAAAGAAGAAAAATA
1 AGCTTTAAAGAAAAAAAATA
*
31572 AGCTTTACCAGAAAAAAAA
1 AGCTTTA-AAGAAAAAAAA
31591 ACGAAGAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 7 0.44
21 9 0.56
ACGTcount: A:0.59, C:0.10, G:0.13, T:0.18
Consensus pattern (20 bp):
AGCTTTAAAGAAAAAAAATA
Found at i:44149 original size:16 final size:15
Alignment explanation
Indices: 44111--44154 Score: 63
Period size: 16 Copynumber: 2.9 Consensus size: 15
44101 AAGACCTTGC
44111 AAAAATAAAAA-AAT
1 AAAAATAAAAAGAAT
44125 AAAAATAAAAAGAAGT
1 AAAAATAAAAAGAA-T
*
44141 AAAAGTAAAAAGAA
1 AAAAATAAAAAGAA
44155 AACCTTTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 11 0.41
15 2 0.07
16 14 0.52
ACGTcount: A:0.80, C:0.00, G:0.09, T:0.11
Consensus pattern (15 bp):
AAAAATAAAAAGAAT
Found at i:46732 original size:2 final size:2
Alignment explanation
Indices: 46725--46754 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
46715 AGTAACTCTC
46725 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
46755 TATTTTTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53070 original size:29 final size:30
Alignment explanation
Indices: 53012--53072 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
53002 GTTCTAATTA
* *
53012 ATGTATACATATAAATTATTCAATTTTATT
1 ATGTATAAATATAAATTATTCAATTATATT
*
53042 ATGTATAAATAT-AATTATTTAATTATATT
1 ATGTATAAATATAAATTATTCAATTATATT
53071 AT
1 AT
53073 ATTATTTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (30 bp):
ATGTATAAATATAAATTATTCAATTATATT
Found at i:54904 original size:21 final size:21
Alignment explanation
Indices: 54878--54921 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
54868 TCAAATTGAA
54878 AAGTAGATGGAATACTAGTCC
1 AAGTAGATGGAATACTAGTCC
54899 AAGTAGATGGAATACTAGTCC
1 AAGTAGATGGAATACTAGTCC
54920 AA
1 AA
54922 ACTTGTTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.23
Consensus pattern (21 bp):
AAGTAGATGGAATACTAGTCC
Found at i:63051 original size:3 final size:3
Alignment explanation
Indices: 63043--63088 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
63033 AATAATTACC
63043 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
63089 ATTAAACCTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:63296 original size:11 final size:11
Alignment explanation
Indices: 63253--63290 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
63243 TTCCTGTATA
*
63253 AAATAAATTAT
1 AAATTAATTAT
63264 CAAA-TAATTAT
1 -AAATTAATTAT
63275 AAATTAATTAT
1 AAATTAATTAT
63286 AAATT
1 AAATT
63291 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:64510 original size:14 final size:14
Alignment explanation
Indices: 64491--64520 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
64481 ACAAATTATT
64491 AAAAAATAACCAAC
1 AAAAAATAACCAAC
*
64505 AAAAAATACCCAAC
1 AAAAAATAACCAAC
64519 AA
1 AA
64521 TGGATTTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.70, C:0.23, G:0.00, T:0.07
Consensus pattern (14 bp):
AAAAAATAACCAAC
Found at i:65737 original size:19 final size:19
Alignment explanation
Indices: 65712--65755 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
65702 GGTTGGGTTA
65712 GTTTTGCTATCAAAACTAG
1 GTTTTGCTATCAAAACTAG
* *
65731 TTTTTGCTGTCAAAACTAG
1 GTTTTGCTATCAAAACTAG
65750 GTTTTG
1 GTTTTG
65756 ACACAAATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.25, C:0.14, G:0.18, T:0.43
Consensus pattern (19 bp):
GTTTTGCTATCAAAACTAG
Found at i:66221 original size:54 final size:55
Alignment explanation
Indices: 66138--66251 Score: 160
Period size: 54 Copynumber: 2.1 Consensus size: 55
66128 GCCGTGCACC
* *
66138 TTTTTCTTTCCGTTTTTTTTTCCTGGTTTTGCTTCACTCATCGAAGGAAATTTCT
1 TTTTTCTTTCCGTTTTTTTTCCCTAGTTTTGCTTCACTCATCGAAGGAAATTTCT
* * *
66193 TTTTTC-TT-CGTTTTTTTTCCCCTAGTTTTGCTTTACTCATGGAAGGAGATTTCT
1 TTTTTCTTTCCGTTTTTTTT-CCCTAGTTTTGCTTCACTCATCGAAGGAAATTTCT
66247 TTTTT
1 TTTTT
66252 TTTTTTTCTT
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
53 10 0.19
54 37 0.70
55 6 0.11
ACGTcount: A:0.12, C:0.18, G:0.13, T:0.56
Consensus pattern (55 bp):
TTTTTCTTTCCGTTTTTTTTCCCTAGTTTTGCTTCACTCATCGAAGGAAATTTCT
Found at i:66284 original size:56 final size:56
Alignment explanation
Indices: 66150--66301 Score: 170
Period size: 54 Copynumber: 2.8 Consensus size: 56
66140 TTTCTTTCCG
* * * *
66150 TTTTTT-TTTCCTGGTTTTGCTTCACTCATCGAAGGAAATTTCTTTTTTCTTCGTT
1 TTTTTTCTTTTCTGGTTTTGCTTTACTCATGGAAGGAGATTTCTTTTTTCTTCGTT
** * *
66205 TTTTTTC--CCCTAGTTTTGCTTTACTCATGGAAGGAGATTTCTTTTTT-TT-TTT
1 TTTTTTCTTTTCTGGTTTTGCTTTACTCATGGAAGGAGATTTCTTTTTTCTTCGTT
*
66257 TTCTTTTCTTTTCTGGTTTTTGCTTTACTCATGGGAGGAGATTTC
1 TT-TTTTCTTTTCTGG-TTTTGCTTTACTCATGGAAGGAGATTTC
66302 CATACCAGAG
Statistics
Matches: 82, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
52 4 0.05
53 7 0.09
54 35 0.43
55 9 0.11
56 27 0.33
ACGTcount: A:0.12, C:0.16, G:0.15, T:0.56
Consensus pattern (56 bp):
TTTTTTCTTTTCTGGTTTTGCTTTACTCATGGAAGGAGATTTCTTTTTTCTTCGTT
Found at i:70364 original size:70 final size:70
Alignment explanation
Indices: 70279--70492 Score: 419
Period size: 70 Copynumber: 3.1 Consensus size: 70
70269 TGGCCTGCGC
*
70279 TTGCGCTGCAGTCATCTTCTTATTAGGGCTGTATTTTTTGTAGTTGTTTAAGTCGGTTAGTAAGA
1 TTGCGCTGCAATCATCTTCTTATTAGGGCTGTATTTTTTGTAGTTGTTTAAGTCGGTTAGTAAGA
70344 AGATA
66 AGATA
70349 TTGCGCTGCAATCATCTTCTTATTAGGGCTGTATTTTTTGTAGTTGTTTAAGTCGGTTAGTAAGA
1 TTGCGCTGCAATCATCTTCTTATTAGGGCTGTATTTTTTGTAGTTGTTTAAGTCGGTTAGTAAGA
70414 AGATA
66 AGATA
70419 TTGCGCTGCAATCATCTTCTTATTAGGGCTGTATTTTTTGTAGTTGTTTAAGTCGGTTAGTAAGA
1 TTGCGCTGCAATCATCTTCTTATTAGGGCTGTATTTTTTGTAGTTGTTTAAGTCGGTTAGTAAGA
70484 AGATA
66 AGATA
70489 TTGC
1 TTGC
70493 ATTGTATGTG
Statistics
Matches: 143, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 143 1.00
ACGTcount: A:0.22, C:0.12, G:0.23, T:0.43
Consensus pattern (70 bp):
TTGCGCTGCAATCATCTTCTTATTAGGGCTGTATTTTTTGTAGTTGTTTAAGTCGGTTAGTAAGA
AGATA
Found at i:70650 original size:42 final size:42
Alignment explanation
Indices: 70599--70689 Score: 166
Period size: 42 Copynumber: 2.2 Consensus size: 42
70589 AGTGCATTAC
*
70599 CTAA-ATTCTACTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACTCCATCTCTAGATAATTCATCAAAATAAAG
70640 CTAATATTCTACTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTACTCCATCTCTAGATAATTCATCAAAATAAAG
70682 CTAATATT
1 CTAATATT
70690 AATTGTTGCT
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 4 0.08
42 44 0.92
ACGTcount: A:0.40, C:0.21, G:0.05, T:0.34
Consensus pattern (42 bp):
CTAATATTCTACTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:72550 original size:16 final size:16
Alignment explanation
Indices: 72529--72577 Score: 89
Period size: 16 Copynumber: 3.1 Consensus size: 16
72519 TTATTTTATT
*
72529 GTTATTATTAATTGTA
1 GTTATTAATAATTGTA
72545 GTTATTAATAATTGTA
1 GTTATTAATAATTGTA
72561 GTTATTAATAATTGTA
1 GTTATTAATAATTGTA
72577 G
1 G
72578 AGGAGAGGGG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (16 bp):
GTTATTAATAATTGTA
Found at i:73845 original size:21 final size:22
Alignment explanation
Indices: 73809--73853 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
73799 ATACCGAAAA
73809 TTATTAAATAAATAATTAATAT
1 TTATTAAATAAATAATTAATAT
* *
73831 TTATTTAAT-AATAATTATTAT
1 TTATTAAATAAATAATTAATAT
73852 TT
1 TT
73854 CCCATGTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TTATTAAATAAATAATTAATAT
Found at i:75097 original size:21 final size:22
Alignment explanation
Indices: 75057--75098 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
75047 CGCAAAAAAT
75057 AAGCTCCATGCTTATTTTCTCA
1 AAGCTCCATGCTTATTTTCTCA
*
75079 AAGCTCCTTGCTT-TTTTCTC
1 AAGCTCCATGCTTATTTTCTC
75099 TGAAATCTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.17, C:0.29, G:0.10, T:0.45
Consensus pattern (22 bp):
AAGCTCCATGCTTATTTTCTCA
Found at i:75252 original size:51 final size:51
Alignment explanation
Indices: 75151--75257 Score: 119
Period size: 51 Copynumber: 2.1 Consensus size: 51
75141 TGTTCTTCAA
* * ***
75151 TATTTCCTTGTTTCAATCTTGTCTCCGAACAAAAGAACACTTTTTTCGTGT
1 TATTTCCTTATTTCAATCTTGTCTCCGAACAAAAGAACACTGTACACGTGT
* **
75202 TATTTCCTTATTTCAATCTTGTCTCCGGACATCCA-AACACTGTACACGTGT
1 TATTTCCTTATTTCAATCTTGTCTCCGAACA-AAAGAACACTGTACACGTGT
75253 T-TTTC
1 TATTTC
75258 TCTTCAGCAA
Statistics
Matches: 47, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
50 4 0.09
51 42 0.89
52 1 0.02
ACGTcount: A:0.22, C:0.24, G:0.11, T:0.42
Consensus pattern (51 bp):
TATTTCCTTATTTCAATCTTGTCTCCGAACAAAAGAACACTGTACACGTGT
Found at i:85681 original size:39 final size:38
Alignment explanation
Indices: 85638--86093 Score: 431
Period size: 39 Copynumber: 11.6 Consensus size: 38
85628 TTTCCAAATT
* *
85638 GGGAAAGATCCCACCAAGTTTTTCAAGATTTCAAAATTA
1 GGGAAAGATCCCATCAAGTTTTTCAAGATTTC-AATTTA
85677 GGGAAAGATCCCATCAA-TTTCTTCAAGATTTTCAATTTA
1 GGGAAAGATCCCATCAAGTTT-TTCAAGA-TTTCAATTTA
* *
85716 GGGAAAGATCCCACCAAGTTTTTCAAGATTTCAAAATTA
1 GGGAAAGATCCCATCAAGTTTTTCAAGATTTC-AATTTA
85755 GGGAAAGATCCCATC-AGTTTCTTCAAGATTTTCAATTTA
1 GGGAAAGATCCCATCAAGTTT-TTCAAGA-TTTCAATTTA
* * *
85794 GGGAAAGATCCCACCTAGTTTTTCAAGATTTCAAAATTA
1 GGGAAAGATCCCATCAAGTTTTTCAAGATTTC-AATTTA
*
85833 GGGAAAGCTCCCATC-AGTTTCTTCAAGATTTTCAATTTA
1 GGGAAAGATCCCATCAAGTTT-TTCAAGA-TTTCAATTTA
* * * *
85872 GGGAAAGATCCCATCTAGTATTT-AAGCTTTTTAATTTA
1 GGGAAAGATCCCATCAAGTTTTTCAAG-ATTTCAATTTA
* * * **
85910 GGGAAAGATCCCTTCAAATAGTTTTCAAAAGTTTTTATTTA
1 GGGAAAGATCCCATCAAGT--TTTTCAAGA-TTTCAATTTA
* *
85951 GGGAAAGATCCCATCTAGTCTTCTTCAA-ATTTTTTAAATTTA
1 GGGAAAGATCCCATCAAGT-TT-TTCAAGA---TTTCAATTTA
* * *
85993 GGGAAAGATCCCGTCGAG-TTTTCAAGTTTTCAATTTA
1 GGGAAAGATCCCATCAAGTTTTTCAAGATTTCAATTTA
** *
86030 GGGAAAGATCCCATTTAGTCTTTTTCAAGTTTTCAA-TTA
1 GGGAAAGATCCCATCAAG--TTTTTCAAGATTTCAATTTA
*
86069 GGGGAAAGATCCCATCCAAGATTTT
1 -GGGAAAGATCCCAT-CAAGTTTTT
86094 AAAATTAAGT
Statistics
Matches: 353, Mismatches: 39, Indels: 50
0.80 0.09 0.11
Matches are distributed among these distances:
37 24 0.07
38 49 0.14
39 161 0.46
40 61 0.17
41 34 0.10
42 24 0.07
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (38 bp):
GGGAAAGATCCCATCAAGTTTTTCAAGATTTCAATTTA
Found at i:85709 original size:78 final size:78
Alignment explanation
Indices: 85613--86084 Score: 539
Period size: 78 Copynumber: 6.0 Consensus size: 78
85603 AATCAAAGGG
* * *
85613 AATTTCCTTCAAAATTTTCCAAATT-GGGAAAGATCCCACCAAGTTTTTCAAGATTTCAAAATTA
1 AATTT-CTTCAAGATTTT-CAATTTAGGGAAAGATCCCACCTAGTTTTTCAAGATTTCAAAATTA
85677 GGGAAAGATCCCATC
64 GGGAAAGATCCCATC
*
85692 AATTTCTTCAAGATTTTCAATTTAGGGAAAGATCCCACCAAGTTTTTCAAGATTTCAAAATTAGG
1 AATTTCTTCAAGATTTTCAATTTAGGGAAAGATCCCACCTAGTTTTTCAAGATTTCAAAATTAGG
85757 GAAAGATCCCATC
66 GAAAGATCCCATC
*
85770 AGTTTCTTCAAGATTTTCAATTTAGGGAAAGATCCCACCTAGTTTTTCAAGATTTCAAAATTAGG
1 AATTTCTTCAAGATTTTCAATTTAGGGAAAGATCCCACCTAGTTTTTCAAGATTTCAAAATTAGG
*
85835 GAAAGCTCCCATC
66 GAAAGATCCCATC
* * * * ** *
85848 AGTTTCTTCAAGATTTTCAATTTAGGGAAAGATCCCATCTAGTATTT-AAGCTTTTTAATTTAGG
1 AATTTCTTCAAGATTTTCAATTTAGGGAAAGATCCCACCTAGTTTTTCAAGATTTCAAAATTAGG
*
85912 GAAAGATCCCTTC
66 GAAAGATCCCATC
* * * *
85925 AAATAGTT-TTCAAAAGTTTT-TATTTAGGGAAAGATCCCATCTAGTCTTCTTCAA-ATTTTTTA
1 -AAT--TTCTTCAAGA-TTTTCAATTTAGGGAAAGATCCCACCTAGT-TT-TTCAAGA--TTTCA
* *
85987 AATTTAGGGAAAGATCCCGTC
58 AAATTAGGGAAAGATCCCATC
* * ** *
86008 GAGTT-TTCAAG-TTTTCAATTTAGGGAAAGATCCCATTTAGTCTTTTTCAAGTTTTC--AATTA
1 AATTTCTTCAAGATTTTCAATTTAGGGAAAGATCCCACCTAG--TTTTTCAAGATTTCAAAATTA
86069 GGGGAAAGATCCCATC
64 -GGGAAAGATCCCATC
86085 CAAGATTTTA
Statistics
Matches: 349, Mismatches: 29, Indels: 32
0.85 0.07 0.08
Matches are distributed among these distances:
76 4 0.01
77 43 0.12
78 194 0.56
79 62 0.18
80 16 0.05
81 3 0.01
82 3 0.01
83 24 0.07
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (78 bp):
AATTTCTTCAAGATTTTCAATTTAGGGAAAGATCCCACCTAGTTTTTCAAGATTTCAAAATTAGG
GAAAGATCCCATC
Found at i:94013 original size:18 final size:17
Alignment explanation
Indices: 93980--94014 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
93970 ATTAACAAAG
*
93980 TTGTTAATATACAATTT
1 TTGTTAATAAACAATTT
93997 TTGTTAATAGAACAATTT
1 TTGTTAATA-AACAATTT
94015 GGTGAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.37, C:0.06, G:0.09, T:0.49
Consensus pattern (17 bp):
TTGTTAATAAACAATTT
Found at i:96350 original size:51 final size:51
Alignment explanation
Indices: 96248--96350 Score: 138
Period size: 51 Copynumber: 2.0 Consensus size: 51
96238 CATTCTTCAA
* **
96248 TATTTCCTTGTTTCAATCTTGTCTCCGGACAAAAGAACACTCTTTTAGTGT
1 TATTTCCTTGTTTCAATCTTGTCTCCGGACAAAAGAACACTCGTACAGTGT
*
96299 TATTTTCTTGTTTCAATCTTGTCTCCGGACATAAA-AACACT-GTACACGTGT
1 TATTTCCTTGTTTCAATCTTGTCTCCGGACA-AAAGAACACTCGTACA-GTGT
96350 T
1 T
96351 TCTCTCTCAG
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
50 2 0.04
51 41 0.89
52 3 0.07
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (51 bp):
TATTTCCTTGTTTCAATCTTGTCTCCGGACAAAAGAACACTCGTACAGTGT
Found at i:97103 original size:16 final size:17
Alignment explanation
Indices: 97077--97108 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
97067 TATAGTTTAG
97077 TTTTGCTTTATAATTGC
1 TTTTGCTTTATAATTGC
97094 TTTT-CTTTATAATTG
1 TTTTGCTTTATAATTG
97109 GTACTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.19, C:0.09, G:0.09, T:0.62
Consensus pattern (17 bp):
TTTTGCTTTATAATTGC
Found at i:98265 original size:18 final size:19
Alignment explanation
Indices: 98233--98268 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
98223 TAACTACTAA
*
98233 TAATAAATAATACTAATAT
1 TAATAAATAACACTAATAT
98252 TAAT-AATAACACTAATA
1 TAATAAATAACACTAATA
98269 ATTATTATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.58, C:0.08, G:0.00, T:0.33
Consensus pattern (19 bp):
TAATAAATAACACTAATAT
Found at i:98578 original size:24 final size:24
Alignment explanation
Indices: 98545--98592 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
98535 AGTCAAAAAT
98545 TTAGAAAGTTAGAAATGATTTGAG
1 TTAGAAAGTTAGAAATGATTTGAG
*
98569 TTAGAGAGTTAGAAATGATTTGAG
1 TTAGAAAGTTAGAAATGATTTGAG
98593 AGAATTTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.27, T:0.33
Consensus pattern (24 bp):
TTAGAAAGTTAGAAATGATTTGAG
Found at i:99422 original size:24 final size:24
Alignment explanation
Indices: 99389--99436 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
99379 AGTTAAAAAT
99389 TTAGAAAGTTAGAAATGATTTGAG
1 TTAGAAAGTTAGAAATGATTTGAG
*
99413 TTAGAGAGTTAGAAATGATTTGAG
1 TTAGAAAGTTAGAAATGATTTGAG
99437 AGAATTTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.00, G:0.27, T:0.33
Consensus pattern (24 bp):
TTAGAAAGTTAGAAATGATTTGAG
Found at i:101095 original size:99 final size:100
Alignment explanation
Indices: 100919--101115 Score: 333
Period size: 99 Copynumber: 2.0 Consensus size: 100
100909 CATGACAAGT
*
100919 AGGAGTCGAATTGATGAATATTGTTAATGCAAGTGACTCACAACACAAAATAAGCAAACTCGTCG
1 AGGAGTCGAATCGATGAATATTGTTAATGCAAGTGACTCACAACACAAAATAAGCAAACTCGTCG
*
100984 GTAGCACTTTTAATAAAGAGAGTTGAAATAGATAG
66 GTAGCACTTTTAATAAAGAAAGTTGAAATAGATAG
* * *
101019 AGGA-TCGAATCGATGAATGTTGTTAATGCAAGTGACTCACTATACAAAATAAGCAAACTCGTCG
1 AGGAGTCGAATCGATGAATATTGTTAATGCAAGTGACTCACAACACAAAATAAGCAAACTCGTCG
*
101083 GTAGCACTTTTAATAGAGAAAGTTGAAATAGAT
66 GTAGCACTTTTAATAAAGAAAGTTGAAATAGAT
101116 TGCTGTAATA
Statistics
Matches: 91, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
99 87 0.96
100 4 0.04
ACGTcount: A:0.40, C:0.13, G:0.21, T:0.26
Consensus pattern (100 bp):
AGGAGTCGAATCGATGAATATTGTTAATGCAAGTGACTCACAACACAAAATAAGCAAACTCGTCG
GTAGCACTTTTAATAAAGAAAGTTGAAATAGATAG
Found at i:103750 original size:41 final size:41
Alignment explanation
Indices: 103704--103785 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
103694 ACTAAAAACA
103704 TACTTCCTTTCCAATGGTAGAAATAAATCAATTAGGATATG
1 TACTTCCTTTCCAATGGTAGAAATAAATCAATTAGGATATG
103745 TACTTCCTTTCCAATGGTAGAAATAAATCAATTAGGATATG
1 TACTTCCTTTCCAATGGTAGAAATAAATCAATTAGGATATG
103786 GATCATCGAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.34
Consensus pattern (41 bp):
TACTTCCTTTCCAATGGTAGAAATAAATCAATTAGGATATG
Found at i:107951 original size:20 final size:20
Alignment explanation
Indices: 107923--107975 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
107913 CTTCTGTCTT
107923 TGCCGCAACTATGTAATCTC
1 TGCCGCAACTATGTAATCTC
*
107943 TGTCGCAACTATGTAATCTC
1 TGCCGCAACTATGTAATCTC
*
107963 TGCCGCAGCTATG
1 TGCCGCAACTATG
107976 ACACTTCGAC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (20 bp):
TGCCGCAACTATGTAATCTC
Found at i:109036 original size:12 final size:12
Alignment explanation
Indices: 109021--109046 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
109011 CTTCATCAAG
109021 AAGTTCAAATCA
1 AAGTTCAAATCA
109033 AAGTTCAAATCA
1 AAGTTCAAATCA
109045 AA
1 AA
109047 TGTGAATCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.15, G:0.08, T:0.23
Consensus pattern (12 bp):
AAGTTCAAATCA
Found at i:111209 original size:68 final size:67
Alignment explanation
Indices: 111077--111515 Score: 389
Period size: 67 Copynumber: 6.7 Consensus size: 67
111067 GATTTTAGAT
* * * *
111077 GTACAGCGTAAGATGGTTTGTTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTTATTAAG
1 GTACACCGGAAGATGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAAG
111142 GA
66 GA
* * *
111144 GTACACCCGAAGACGGTTTGCTAGAAAGAATTTTCAAAATGTTGATTGGAAGACAATCTCGTTAA
1 GTACACCGGAAGATGGTTTGCTAGAAAGAATTTTC-AAATGTTGATTGGAAGACAATCTCATTAA
111209 GGA
65 GGA
* * * * *
111212 GTAAACCGGAATACGGTTTGCTAGAAAGAATTTTCCAATATTGATTGGAAGACAATCTCATTAAG
1 GTACACCGGAAGATGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAAG
111277 GA
66 GA
* * * * * * * *
111279 ATACATCGGAAGATGGTTTGCTAGAAAGAATTTTCAGATGTTGATTAGAAAACGATCTCGTCAAG
1 GTACACCGGAAGATGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAAG
*
111344 AA
66 GA
* * * * * * * * *
111346 GTACACCAGAAGATGGTTT-CT--CAAGAGTTTT-AAGAAGATGATCGGAAGACGATCTTATCAA
1 GTACACCGGAAGATGGTTTGCTAGAAAGAATTTTCAA-ATGTTGATTGGAAGACAATCTCATTAA
*
111407 GAA
65 GGA
* * * * ** *
111410 GTACACCAGAAGATGGTTT-CT-CAAA-AATTTTCAGAA-GTTGATCGGAAGACGATCTTGTCAA
1 GTACACCGGAAGATGGTTTGCTAGAAAGAATTTTCA-AATGTTGATTGGAAGACAATCTCATTAA
*
111471 GAA
65 GGA
* *
111474 GTACACCGAAAGATGGTTT-CT-CAAA-AATTTTCAGAA-GTTGAT
1 GTACACCGGAAGATGGTTTGCTAGAAAGAATTTTCA-AATGTTGAT
111516 CGAAAGACGA
Statistics
Matches: 321, Mismatches: 46, Indels: 13
0.84 0.12 0.03
Matches are distributed among these distances:
63 1 0.00
64 123 0.38
65 4 0.01
66 3 0.01
67 128 0.40
68 62 0.19
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.28
Consensus pattern (67 bp):
GTACACCGGAAGATGGTTTGCTAGAAAGAATTTTCAAATGTTGATTGGAAGACAATCTCATTAAG
GA
Found at i:111411 original size:64 final size:64
Alignment explanation
Indices: 111105--111729 Score: 576
Period size: 64 Copynumber: 9.6 Consensus size: 64
111095 TGTTAGAAAG
* * * * * * * *
111105 AATTTTCA-AATGTTGATTGGAAGACAATCTTATTAAGGAGTACACCCGAAGACGGTTTGCTAGA
1 AATTTTCAGAA-GTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTT-CT-CA
111169 AA
63 AA
* * * * * * * * * * *
111171 GAATTTTCAAAATGTTGATTGGAAGACAATCTCGTTAAGGAGTAAACCGGAATACGGTTTGCTAG
1 -AATTTTCAGAA-GTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTT-CT-C
111236 AAA
62 AAA
* * ** * * *
111239 GAATTTTCCA-ATA-TTGATTGGAAGACAATCTCATTAAGGAA-TACATCGGAAGATGGTTTGCT
1 -AATTTT-CAGA-AGTTGATCGGAAGACGATCTTGTCAA-GAAGTACACCAGAAGATGGTTT-CT
*
111301 AGAAA
61 -CAAA
* ** * * *
111306 GAATTTTCAGATGTTGATTAGAAAACGATCTCGTCAAGAAGTACACCAGAAGATGGTTTCTCAAG
1 -AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
* * * *
111371 AGTTTTAAGAAGATGATCGGAAGACGATCTTATCAAGAAGTACACCAGAAGATGGTTTCTCAAA
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
111435 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACC-GAAAGATGGTTTCTCAAA
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAG-AAGATGGTTTCTCAAA
* ** *
111499 AATTTTCAGAAGTTGATCGAAAGACGATCTTGTCAAGAAAAACACCAGAAGATGGTTTCTCAAC
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
* * *
111563 CATTTTCAGAAGTTGATCGGAAGACGATTTTGTCAAGAAGTACGCCAGAAGATGGTTTCTCAAA
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
* * * * * * *
111627 AAATTTCAGAAGTTGATCAGAACACGATCTTGTTAAAAAGTAGACCAGAAGATAGTTTCTCGAAA
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTC-AAA
** * *
111692 AGGTTTCAGAAGTTGATCGGAAAACGATCTTGTTAAGA
1 AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGA
111730 GATGCACCGG
Statistics
Matches: 487, Mismatches: 61, Indels: 22
0.85 0.11 0.04
Matches are distributed among these distances:
63 1 0.00
64 278 0.57
65 39 0.08
66 7 0.01
67 96 0.20
68 63 0.13
69 3 0.01
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (64 bp):
AATTTTCAGAAGTTGATCGGAAGACGATCTTGTCAAGAAGTACACCAGAAGATGGTTTCTCAAA
Found at i:112082 original size:27 final size:27
Alignment explanation
Indices: 112052--112104 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
112042 GGAGACGGCT
*
112052 CTTTTAATATT-AGATTGGAAGACAATC
1 CTTTTAAGATTGA-ATTGGAAGACAATC
112079 CTTTTAAGATTGAATTGGAAGACAAT
1 CTTTTAAGATTGAATTGGAAGACAAT
112105 TAAAAGAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 23 0.96
28 1 0.04
ACGTcount: A:0.38, C:0.09, G:0.17, T:0.36
Consensus pattern (27 bp):
CTTTTAAGATTGAATTGGAAGACAATC
Found at i:112127 original size:77 final size:77
Alignment explanation
Indices: 112000--112154 Score: 238
Period size: 77 Copynumber: 2.0 Consensus size: 77
111990 CAGGAGACGG
*** * **
112000 TCCTTTTAAGATCGAATTGAAAGACAATTAGTGGGATGTGCGGGAGACGGCTCTTTTAATATTAG
1 TCCTTTTAAGATCGAATTGAAAGACAATTAAAAGAATAAGCGGGAGACGGCTCTTTTAATATTAG
112065 ATTGGAAGACAA
66 ATTGGAAGACAA
* *
112077 TCCTTTTAAGATTGAATTGGAAGACAATTAAAAGAATAAGCGGGAGACGGCTCTTTTAATATTAG
1 TCCTTTTAAGATCGAATTGAAAGACAATTAAAAGAATAAGCGGGAGACGGCTCTTTTAATATTAG
112142 ATTGGAAGACAA
66 ATTGGAAGACAA
112154 T
1 T
112155 TCGAAGAAGT
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
77 70 1.00
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (77 bp):
TCCTTTTAAGATCGAATTGAAAGACAATTAAAAGAATAAGCGGGAGACGGCTCTTTTAATATTAG
ATTGGAAGACAA
Found at i:112480 original size:27 final size:27
Alignment explanation
Indices: 112450--112523 Score: 123
Period size: 27 Copynumber: 2.7 Consensus size: 27
112440 TAGGGTCATC
112450 CAGGGGCATTTTGGTCATTTGC-CAGTT
1 CAGGGGCATTTTGGTCATTTGCACA-TT
*
112477 CAGGGGCATTTTAGTCATTTGCACATT
1 CAGGGGCATTTTGGTCATTTGCACATT
112504 CAGGGGCATTTTGGTCATTT
1 CAGGGGCATTTTGGTCATTT
112524 TAAGTTCACT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
27 42 0.95
28 2 0.05
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.38
Consensus pattern (27 bp):
CAGGGGCATTTTGGTCATTTGCACATT
Found at i:116949 original size:72 final size:72
Alignment explanation
Indices: 116860--117218 Score: 558
Period size: 72 Copynumber: 5.0 Consensus size: 72
116850 AGGTATTAGC
* * **
116860 AAGGATTGTGCGAAGGACTGCC-AATGTGGGAACTGCCTCGACTACAATCGCAATGAGGAAGATA
1 AAGGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAAGAAGAGG
***
116924 ATCGCAT
66 ATCATGT
116931 AAGGATTTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAAGAAGAG
1 AAGGA-TTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAAGAAGAG
116996 GATCATGT
65 GATCATGT
* * * * * *
117004 AAGAATTATGCGAAGGACTGCCAATTGTGGGAACTACCTCGGCTACAATCGCAATGAAGGAGATG
1 AAGGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAAGAAGAGG
117069 ATCATGT
66 ATCATGT
*
117076 AAGGATTGTGTGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAAGAAGAGG
1 AAGGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAAGAAGAGG
117141 ATCATGT
66 ATCATGT
*
117148 AAGGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAAGAATAGG
1 AAGGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAAGAAGAGG
*
117213 ACCATG
66 ATCATG
117219 GGATGGGCTG
Statistics
Matches: 263, Mismatches: 23, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
71 5 0.02
72 212 0.81
73 46 0.17
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.20
Consensus pattern (72 bp):
AAGGATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAAGAAGAGG
ATCATGT
Found at i:117634 original size:35 final size:35
Alignment explanation
Indices: 117589--117656 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
117579 ATGACATGGC
*
117589 CCCCAAGTGTTGAATGATAAAGGGGTCGTTGGAGT
1 CCCCAAGTGTTGAATGATAAAGGGGTCGCTGGAGT
* *
117624 CCCCACGTGTTGAATGATGAAGGGGTCGCTGGA
1 CCCCAAGTGTTGAATGATAAAGGGGTCGCTGGA
117657 ATTCGCAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.24
Consensus pattern (35 bp):
CCCCAAGTGTTGAATGATAAAGGGGTCGCTGGAGT
Found at i:137123 original size:42 final size:43
Alignment explanation
Indices: 137064--137153 Score: 137
Period size: 46 Copynumber: 2.0 Consensus size: 43
137054 ATGGTAGATA
*
137064 ACAGAATTATGTAACACAATT-GCAAAGTAGTTAGTCCAAATT
1 ACAGAATCATGTAACACAATTAGCAAAGTAGTTAGTCCAAATT
137106 ACAGAATCATGTAACACAATTAGCAGCAAAGTAGTTAGTCCAAATT
1 ACAGAATCATGTAACACAATT---AGCAAAGTAGTTAGTCCAAATT
137152 AC
1 AC
137154 TTAGCATCTC
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
42 20 0.47
46 23 0.53
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (43 bp):
ACAGAATCATGTAACACAATTAGCAAAGTAGTTAGTCCAAATT
Found at i:138865 original size:18 final size:19
Alignment explanation
Indices: 138842--138881 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
138832 TTCTTGAAAT
138842 AATTCTTC-AATGATCTTC
1 AATTCTTCAAATGATCTTC
*
138860 AATTCTTCAAATTATCTTC
1 AATTCTTCAAATGATCTTC
138879 AAT
1 AAT
138882 AAATCTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.33, C:0.20, G:0.03, T:0.45
Consensus pattern (19 bp):
AATTCTTCAAATGATCTTC
Found at i:140333 original size:2 final size:2
Alignment explanation
Indices: 140320--140363 Score: 61
Period size: 2 Copynumber: 20.5 Consensus size: 2
140310 CTACTATTAT
140320 TA TA TGA TA TA TA TA TA TA TA TA TA TA TGA TA TA TGA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA T-A TA TA T-A TA TA TA
140363 T
1 T
140364 GATGTGTTCA
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
2 33 0.85
3 6 0.15
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (2 bp):
TA
Done.