Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015054.1 Kokia drynarioides strain JFW-HI SEQ_130098, 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: 570327
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 497 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:4575 original size:50 final size:50
Alignment explanation
Indices: 4516--4618 Score: 197
Period size: 50 Copynumber: 2.1 Consensus size: 50
4506 TTAATAAACA
*
4516 TGAAGGTAGTGAGACATATTTTGTTTGAATGAGAGTCACGTGGTATAATC
1 TGAAGGTAGTGAGACATATTTTGTTTGAATGAGAGTCACGTGGTACAATC
4566 TGAAGGTAGTGAGACATATTTTGTTTGAATGAGAGTCACGTGGTACAATC
1 TGAAGGTAGTGAGACATATTTTGTTTGAATGAGAGTCACGTGGTACAATC
4616 TGA
1 TGA
4619 TTGACGCCAT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.30, C:0.09, G:0.28, T:0.33
Consensus pattern (50 bp):
TGAAGGTAGTGAGACATATTTTGTTTGAATGAGAGTCACGTGGTACAATC
Found at i:13796 original size:57 final size:57
Alignment explanation
Indices: 13727--13842 Score: 232
Period size: 57 Copynumber: 2.0 Consensus size: 57
13717 GGGAGAATGG
13727 TAATGCGTGTGAGGCTGGTTTGACAGAGCAGCGACAACTTTCCATTCTTTGCAGTGC
1 TAATGCGTGTGAGGCTGGTTTGACAGAGCAGCGACAACTTTCCATTCTTTGCAGTGC
13784 TAATGCGTGTGAGGCTGGTTTGACAGAGCAGCGACAACTTTCCATTCTTTGCAGTGC
1 TAATGCGTGTGAGGCTGGTTTGACAGAGCAGCGACAACTTTCCATTCTTTGCAGTGC
13841 TA
1 TA
13843 GGATAGCAAG
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
57 59 1.00
ACGTcount: A:0.22, C:0.21, G:0.28, T:0.30
Consensus pattern (57 bp):
TAATGCGTGTGAGGCTGGTTTGACAGAGCAGCGACAACTTTCCATTCTTTGCAGTGC
Found at i:18119 original size:22 final size:21
Alignment explanation
Indices: 18094--18145 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
18084 TATTACCAGT
*
18094 AAATTTAATAAAATAATTTTAA
1 AAATTTAAT-AAATAATTCTAA
*
18116 AAATATTAATAAATAGTTCTAA
1 AAAT-TTAATAAATAATTCTAA
*
18138 AATTTTAA
1 AAATTTAA
18146 ATTCAAAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
21 4 0.15
22 17 0.65
23 5 0.19
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (21 bp):
AAATTTAATAAATAATTCTAA
Found at i:22925 original size:4 final size:4
Alignment explanation
Indices: 22916--22941 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
22906 GTTTCGCCCT
22916 TACA TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TACA TA
22942 TATATATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:28293 original size:207 final size:207
Alignment explanation
Indices: 27938--28352 Score: 776
Period size: 207 Copynumber: 2.0 Consensus size: 207
27928 CAACAAAATC
*
27938 ACCGAAAAAAAGCTTAAAAAGGGATCAGCATATGCCAATAGCAGCTGCAATAGTGATATCTATAT
1 ACCGAAAAAAAGCTCAAAAAGGGATCAGCATATGCCAATAGCAGCTGCAATAGTGATATCTATAT
*
28003 TACTAAACCACCCTACCATGCTAATAGCAGCGAAAGGACATTTGTGACACAAAAGCACTAACAGC
66 TACTAAACCACCCTACCATGCAAATAGCAGCGAAAGGACATTTGTGACACAAAAGCACTAACAGC
28068 AGCCAAGTTCTCAGTCTAGTATTATATCTGATTCTAAAAGGATTGAACAAATGCGAGTACAAACT
131 AGCCAAGTTCTCAGTCTAGTATTATATCTGATTCTAAAAGGATTGAACAAATGCGAGTACAAACT
28133 ATGCTACCAAAA
196 ATGCTACCAAAA
* *
28145 ACCGAAATAAAGCTCAAAAAGGGATCATCATATGCCAATAGCAGCTGCAATAGTGATATCTATAT
1 ACCGAAAAAAAGCTCAAAAAGGGATCAGCATATGCCAATAGCAGCTGCAATAGTGATATCTATAT
*
28210 TACTAAACCACCCTACCATGCAAATAGCAGCGAAATGACATTTGTGACACAAAAGCACTAACAGC
66 TACTAAACCACCCTACCATGCAAATAGCAGCGAAAGGACATTTGTGACACAAAAGCACTAACAGC
*
28275 AGCCAAGTTCTCAGTCTAGTATTATATCTGATTCTAAAAGGATTGAACAAATGTGAGTACAAACT
131 AGCCAAGTTCTCAGTCTAGTATTATATCTGATTCTAAAAGGATTGAACAAATGCGAGTACAAACT
28340 ATGCTACCAAAA
196 ATGCTACCAAAA
28352 A
1 A
28353 AAATTTGCCT
Statistics
Matches: 202, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
207 202 1.00
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.23
Consensus pattern (207 bp):
ACCGAAAAAAAGCTCAAAAAGGGATCAGCATATGCCAATAGCAGCTGCAATAGTGATATCTATAT
TACTAAACCACCCTACCATGCAAATAGCAGCGAAAGGACATTTGTGACACAAAAGCACTAACAGC
AGCCAAGTTCTCAGTCTAGTATTATATCTGATTCTAAAAGGATTGAACAAATGCGAGTACAAACT
ATGCTACCAAAA
Found at i:32033 original size:17 final size:17
Alignment explanation
Indices: 32013--32067 Score: 64
Period size: 14 Copynumber: 3.5 Consensus size: 17
32003 ATTTTCTTTT
32013 AATTAATTAAAAAATTC
1 AATTAATTAAAAAATTC
*
32030 AATTAATT---AAATTT
1 AATTAATTAAAAAATTC
*
32044 ATTTAATTAAAAAA-TC
1 AATTAATTAAAAAATTC
32060 AATTAATT
1 AATTAATT
32068 TACCTGGTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
14 12 0.39
16 8 0.26
17 11 0.35
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTAATTAAAAAATTC
Found at i:32062 original size:30 final size:31
Alignment explanation
Indices: 32010--32067 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
32000 AACATTTTCT
32010 TTTAATTAATTAAAAAATTCAATTAATTAAA
1 TTTAATTAATTAAAAAATTCAATTAATTAAA
*
32041 TTTATTTAATTAAAAAA-TCAATTAATT
1 TTTAATTAATTAAAAAATTCAATTAATT
32068 TACCTGGTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 10 0.38
31 16 0.62
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (31 bp):
TTTAATTAATTAAAAAATTCAATTAATTAAA
Found at i:39456 original size:31 final size:29
Alignment explanation
Indices: 39395--39460 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 29
39385 ATAACGTAAA
*
39395 TGACTAAAACGTAACATTTCAAACATAAG
1 TGACTAAAACGTAACATTTCAAACAAAAG
*
39424 TGACTAAAATGTAACATGAGTT-AAACAAAAG
1 TGACTAAAACGTAACAT---TTCAAACAAAAG
39455 TGACTA
1 TGACTA
39461 TTTTGATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 16 0.50
31 14 0.44
32 2 0.06
ACGTcount: A:0.48, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
TGACTAAAACGTAACATTTCAAACAAAAG
Found at i:39534 original size:18 final size:18
Alignment explanation
Indices: 39513--39563 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
39503 TAAAAATAAT
39513 TATTAAATAACAAATTAA
1 TATTAAATAACAAATTAA
* *
39531 TATTAATATTA-ATATTAA
1 TATTAA-ATAACAAATTAA
39549 TATTAAATGAACAAA
1 TATTAAAT-AACAAA
39564 AAAATCCTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
17 2 0.08
18 19 0.73
19 5 0.19
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (18 bp):
TATTAAATAACAAATTAA
Found at i:39537 original size:6 final size:6
Alignment explanation
Indices: 39526--39554 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
39516 TAAATAACAA
39526 ATTAAT ATTAAT ATTAAT ATTAAT ATTAA
1 ATTAAT ATTAAT ATTAAT ATTAAT ATTAA
39555 ATGAACAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
ATTAAT
Found at i:46245 original size:16 final size:16
Alignment explanation
Indices: 46224--46274 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
46214 AACAAATACC
46224 TATTTTCATAATTAAT
1 TATTTTCATAATTAAT
**
46240 TATTTTC-T-CGT-AT
1 TATTTTCATAATTAAT
*
46253 TATTTTCACAATTAAT
1 TATTTTCATAATTAAT
46269 TATTTT
1 TATTTT
46275 TTATTATTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 6
0.71 0.13 0.16
Matches are distributed among these distances:
13 9 0.33
14 1 0.04
15 2 0.07
16 15 0.56
ACGTcount: A:0.29, C:0.10, G:0.02, T:0.59
Consensus pattern (16 bp):
TATTTTCATAATTAAT
Found at i:56208 original size:18 final size:18
Alignment explanation
Indices: 56187--56229 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
56177 TAATCACTTT
*
56187 AATTAAT-ATAATTGTTTA
1 AATTAATCATAATCG-TTA
*
56205 AATTAATCATTATCGTTA
1 AATTAATCATAATCGTTA
56223 AATTAAT
1 AATTAAT
56230 TCATTAATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 17 0.77
19 5 0.23
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.47
Consensus pattern (18 bp):
AATTAATCATAATCGTTA
Found at i:56725 original size:22 final size:24
Alignment explanation
Indices: 56683--56726 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
56673 TTAAAATTAA
*
56683 AAAATATTAAATTGTATATAAAAT
1 AAAATATTAAATTATATATAAAAT
56707 AAAAT-TTAAA-TATATATAAA
1 AAAATATTAAATTATATATAAA
56727 TGCATCATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 9 0.47
23 5 0.26
24 5 0.26
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (24 bp):
AAAATATTAAATTATATATAAAAT
Found at i:60563 original size:24 final size:23
Alignment explanation
Indices: 60515--60564 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
60505 GATTTGGTCA
60515 AATTAATTTTTTTATTATTAAATT
1 AATTAATTTTTTTATTATT-AATT
*
60539 AATTAATTTAATTTTTTTATT-ATT
1 AATTAATTT--TTTTATTATTAATT
60563 AA
1 AA
60565 ACAAATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
24 14 0.61
26 9 0.39
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
AATTAATTTTTTTATTATTAATT
Found at i:60571 original size:29 final size:29
Alignment explanation
Indices: 60517--60573 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
60507 TTTGGTCAAA
**
60517 TTAATTTTTTTATTATTAAATTAATTAAT
1 TTAATTTTTTTATTATTAAACAAATTAAT
60546 TTAATTTTTTTATTATTAAACAAATTAA
1 TTAATTTTTTTATTATTAAACAAATTAA
60574 ATAATATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (29 bp):
TTAATTTTTTTATTATTAAACAAATTAAT
Found at i:71217 original size:66 final size:66
Alignment explanation
Indices: 71135--71268 Score: 259
Period size: 66 Copynumber: 2.0 Consensus size: 66
71125 GAACTAAGAG
*
71135 TATGCTATAGTTTCAGTCATAAACAGAGATAGAAATGAAAAGGAGAAAAAAGAACATGAAGTCAC
1 TATGCTATAGTTTCAGTCATAAACAGAGATAGAAACGAAAAGGAGAAAAAAGAACATGAAGTCAC
71200 C
66 C
71201 TATGCTATAGTTTCAGTCATAAACAGAGATAGAAACGAAAAGGAGAAAAAAGAACATGAAGTCAC
1 TATGCTATAGTTTCAGTCATAAACAGAGATAGAAACGAAAAGGAGAAAAAAGAACATGAAGTCAC
71266 C
66 C
71267 TA
1 TA
71269 AAAGGATGTG
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.49, C:0.13, G:0.19, T:0.19
Consensus pattern (66 bp):
TATGCTATAGTTTCAGTCATAAACAGAGATAGAAACGAAAAGGAGAAAAAAGAACATGAAGTCAC
C
Found at i:75169 original size:62 final size:62
Alignment explanation
Indices: 75084--75214 Score: 244
Period size: 62 Copynumber: 2.1 Consensus size: 62
75074 GTGGAAAAAC
* *
75084 CAAATTTAACTTGTTCAAATTTTCCATGCTTCCCATCCTTGTCATTGAGAGGAAAATTTCTT
1 CAAACTTAACTTGTTCAAATTTTCCATGCCTCCCATCCTTGTCATTGAGAGGAAAATTTCTT
75146 CAAACTTAACTTGTTCAAATTTTCCATGCCTCCCATCCTTGTCATTGAGAGGAAAATTTCTT
1 CAAACTTAACTTGTTCAAATTTTCCATGCCTCCCATCCTTGTCATTGAGAGGAAAATTTCTT
75208 CAAACTT
1 CAAACTT
75215 GCTGTTATTA
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 67 1.00
ACGTcount: A:0.28, C:0.23, G:0.11, T:0.38
Consensus pattern (62 bp):
CAAACTTAACTTGTTCAAATTTTCCATGCCTCCCATCCTTGTCATTGAGAGGAAAATTTCTT
Found at i:88965 original size:29 final size:29
Alignment explanation
Indices: 88932--88988 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
88922 TTTGTAACGA
*
88932 TTAGGCCATTATATAACCATTTTAAAAGG
1 TTAGGCCATTATATAACAATTTTAAAAGG
88961 TTAGGCCATTATATAACAATTTTAAAAG
1 TTAGGCCATTATATAACAATTTTAAAAG
88989 ATTTGACTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (29 bp):
TTAGGCCATTATATAACAATTTTAAAAGG
Found at i:90600 original size:4 final size:4
Alignment explanation
Indices: 90578--90677 Score: 71
Period size: 4 Copynumber: 25.0 Consensus size: 4
90568 ACACATTACT
* * * * * *
90578 TTTC TTTC CTTC -TTA TTTC TTTC CTTC -TTA TTTC TTTCC TCTC CTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC TTT-C TTTC TTTC
* * *
90625 -TTC TTTC TTTCC TCTC ATTC TTCC TTTC TTTC TTTC TTTCC TTTC TTTC
1 TTTC TTTC TTT-C TTTC TTTC TTTC TTTC TTTC TTTC TTT-C TTTC TTTC
90674 TTTC
1 TTTC
90678 CCGTTTATTT
Statistics
Matches: 75, Mismatches: 15, Indels: 12
0.74 0.15 0.12
Matches are distributed among these distances:
3 7 0.09
4 58 0.77
5 10 0.13
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.65
Consensus pattern (4 bp):
TTTC
Found at i:90624 original size:20 final size:20
Alignment explanation
Indices: 90599--90678 Score: 90
Period size: 20 Copynumber: 3.9 Consensus size: 20
90589 CTTATTTCTT
*
90599 TCCTTCTTATTTCTTTCCTC
1 TCCTTCTTCTTTCTTTCCTC
90619 TCCTTCTTCTTTCTTTCCTC
1 TCCTTCTTCTTTCTTTCCTC
* *
90639 TCATTCTTCCTTTCTTT-CTT
1 TCCTTCTT-CTTTCTTTCCTC
*
90659 TCTTTCCTTTCTTTCTTTCC
1 TCCTT-C-TTCTTTCTTTCC
90679 CGTTTATTTG
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
20 32 0.62
21 17 0.33
22 3 0.06
ACGTcount: A:0.03, C:0.35, G:0.00, T:0.62
Consensus pattern (20 bp):
TCCTTCTTCTTTCTTTCCTC
Found at i:90651 original size:17 final size:15
Alignment explanation
Indices: 90581--90675 Score: 55
Period size: 17 Copynumber: 5.7 Consensus size: 15
90571 CATTACTTTT
* *
90581 CTTTCCTTCTTATTT
1 CTTTCCTTCTTCTTC
90596 CTTTCCTTCTTATTTCTTTC
1 CTTTCCTTC----TTC-TTC
* *
90616 CTCTCCTTCTTCTTT
1 CTTTCCTTCTTCTTC
90631 CTTTCCTCTCATTCTTC
1 CTTTCCT-TC-TTCTTC
*
90648 CTTTCTTTCTTTCTTTC
1 CTTTCCTTC-TTC-TTC
*
90665 CTTTCTTTCTT
1 CTTTCCTTCTT
90676 TCCCGTTTAT
Statistics
Matches: 64, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
15 17 0.27
16 12 0.19
17 23 0.36
19 2 0.03
20 10 0.16
ACGTcount: A:0.03, C:0.33, G:0.00, T:0.64
Consensus pattern (15 bp):
CTTTCCTTCTTCTTC
Found at i:90676 original size:17 final size:17
Alignment explanation
Indices: 90578--90677 Score: 88
Period size: 15 Copynumber: 6.2 Consensus size: 17
90568 ACACATTACT
*
90578 TTTCTTTCC-TTC-TTA
1 TTTCTTTCCTTTCTTTC
*
90593 TTTCTTTCC-TTC-TTA
1 TTTCTTTCCTTTCTTTC
* *
90608 TTTCTTTCCTCTCCTTC
1 TTTCTTTCCTTTCTTTC
*
90625 -TTCTTT-CTTTCCTCTC
1 TTTCTTTCCTTT-CTTTC
*
90641 ATTC-TTCCTTTCTTTC
1 TTTCTTTCCTTTCTTTC
90657 TTTCTTTCCTTTCTTTC
1 TTTCTTTCCTTTCTTTC
90674 TTTC
1 TTTC
90678 CCGTTTATTT
Statistics
Matches: 72, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
15 27 0.38
16 20 0.28
17 25 0.35
ACGTcount: A:0.03, C:0.32, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTCTTTCCTTTCTTTC
Found at i:93219 original size:25 final size:26
Alignment explanation
Indices: 93166--93219 Score: 67
Period size: 25 Copynumber: 2.1 Consensus size: 26
93156 CTAATTTTTA
*
93166 AAAAATAAAAACTATTTTCTCAAAAT
1 AAAAATAAAAACTATTTTCTAAAAAT
*
93192 AAAAATAAATA-TATTTTC-AAAAACT
1 AAAAATAAAAACTATTTTCTAAAAA-T
93217 AAA
1 AAA
93220 CCATAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 4 0.16
25 11 0.44
26 10 0.40
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (26 bp):
AAAAATAAAAACTATTTTCTAAAAAT
Found at i:110386 original size:18 final size:18
Alignment explanation
Indices: 110363--110405 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
110353 GAATAAATTT
110363 TTAATTAAATAATTTT-AA
1 TTAATTAAA-AATTTTAAA
*
110381 TTAATTGAAAATTTTAAA
1 TTAATTAAAAATTTTAAA
110399 TTAATTA
1 TTAATTA
110406 CAACTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
TTAATTAAAAATTTTAAA
Found at i:112467 original size:10 final size:11
Alignment explanation
Indices: 112451--112482 Score: 57
Period size: 10 Copynumber: 3.0 Consensus size: 11
112441 TTCATATTTT
112451 ATAATATATTA
1 ATAATATATTA
112462 AT-ATATATTA
1 ATAATATATTA
112472 ATAATATATTA
1 ATAATATATTA
112483 CAATTCTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
ATAATATATTA
Found at i:115330 original size:19 final size:19
Alignment explanation
Indices: 115308--115354 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
115298 GTAAACTATC
*
115308 AAAATAATTA-TCCAAATAT
1 AAAATAATTACT-CAAATAG
*
115327 AAAATTAAATACTCAAATAG
1 AAAA-TAATTACTCAAATAG
115347 AAAATAAT
1 AAAATAAT
115355 ACAACCCAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 7 0.30
20 15 0.65
21 1 0.04
ACGTcount: A:0.62, C:0.09, G:0.02, T:0.28
Consensus pattern (19 bp):
AAAATAATTACTCAAATAG
Found at i:122333 original size:11 final size:11
Alignment explanation
Indices: 122317--122341 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
122307 TAAATTGAGT
122317 CACTGATATAC
1 CACTGATATAC
122328 CACTGATATAC
1 CACTGATATAC
122339 CAC
1 CAC
122342 CTTTGAGGAT
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:0.32, G:0.08, T:0.24
Consensus pattern (11 bp):
CACTGATATAC
Found at i:131050 original size:20 final size:20
Alignment explanation
Indices: 131008--131061 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
130998 TCAAGGAATA
* *
131008 AAAATAATAATAATTTTCTT
1 AAAATAAAAATAATTTACTT
131028 AAAATAAAAATCAATTTAC-T
1 AAAATAAAAAT-AATTTACTT
*
131048 AAATTAAAATATAA
1 AAAATAAAA-ATAA
131062 GAATTACGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 21 0.72
21 8 0.28
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (20 bp):
AAAATAAAAATAATTTACTT
Found at i:140775 original size:19 final size:19
Alignment explanation
Indices: 140721--140788 Score: 57
Period size: 19 Copynumber: 3.5 Consensus size: 19
140711 AATATTCATA
**
140721 TTATTATTTAAATTTAAA-T
1 TTATTA-TTAAAAATAAATT
***
140740 TTATTATTAATGCTAAATT
1 TTATTATTAAAAATAAATT
140759 TTATTATTAAAAATAAAATT
1 TTATTATTAAAAAT-AAATT
*
140779 TTAATATTAA
1 TTATTATTAA
140789 TAATTTTATT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
18 8 0.20
19 18 0.45
20 14 0.35
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (19 bp):
TTATTATTAAAAATAAATT
Found at i:140818 original size:26 final size:28
Alignment explanation
Indices: 140782--140838 Score: 82
Period size: 26 Copynumber: 2.1 Consensus size: 28
140772 TAAAATTTTA
*
140782 ATATTAATAATTT-TATTATT-TTAATT
1 ATATTAATAATTTATATTATTATTAAAT
*
140808 ATATTAATAATTTATTTTATTATTAAAT
1 ATATTAATAATTTATATTATTATTAAAT
140836 ATA
1 ATA
140839 ATTATGCATG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
26 13 0.48
27 6 0.22
28 8 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (28 bp):
ATATTAATAATTTATATTATTATTAAAT
Found at i:143294 original size:29 final size:27
Alignment explanation
Indices: 143231--143297 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
143221 TTTGAGCCCC
143231 AAATTTTTTTTAAAACTTTTATAGGTT
1 AAATTTTTTTTAAAACTTTTATAGGTT
* *
143258 AAACTTTTTTTATCAACTTTTA-AGAGTTT
1 AAATTTTTTTTA-AAACTTTTATAG-G-TT
*
143287 CAATTTTTTTT
1 AAATTTTTTTT
143298 TAGTTGTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 13 0.39
28 9 0.27
29 11 0.33
ACGTcount: A:0.30, C:0.07, G:0.06, T:0.57
Consensus pattern (27 bp):
AAATTTTTTTTAAAACTTTTATAGGTT
Found at i:155332 original size:25 final size:25
Alignment explanation
Indices: 155296--155344 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
155286 AAAATTCAAA
*
155296 TTTTCAAGTTAA-TCAAATTAAGTTT
1 TTTTCAAATTAACTCAAA-TAAGTTT
155321 TTTTCAAATTAACTCAAATAAGTT
1 TTTTCAAATTAACTCAAATAAGTT
155345 ATTCGATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (25 bp):
TTTTCAAATTAACTCAAATAAGTTT
Found at i:163449 original size:12 final size:12
Alignment explanation
Indices: 163434--163463 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
163424 CAACGTGTCA
163434 ACTATGGATTCC
1 ACTATGGATTCC
*
163446 ACTATGGATTTC
1 ACTATGGATTCC
163458 ACTATG
1 ACTATG
163464 TTCGTACTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.37
Consensus pattern (12 bp):
ACTATGGATTCC
Found at i:166929 original size:14 final size:14
Alignment explanation
Indices: 166912--166974 Score: 56
Period size: 14 Copynumber: 4.2 Consensus size: 14
166902 TTTTTATTTT
166912 TATATAAAAATAAA
1 TATATAAAAATAAA
166926 TATA-AAAAATATAA
1 TATATAAAAATA-AA
166940 TATATCAAATGCAATAAA
1 TATAT-AAA---AATAAA
* *
166958 AATATTAAAATAAA
1 TATATAAAAATAAA
166972 TAT
1 TAT
166975 TTATTCTTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
13 7 0.17
14 18 0.45
16 3 0.08
17 2 0.05
18 6 0.15
19 4 0.10
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.30
Consensus pattern (14 bp):
TATATAAAAATAAA
Found at i:178243 original size:19 final size:19
Alignment explanation
Indices: 178207--178245 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
178197 TGAGTTCGAG
**
178207 GTTTGAGTTTGAGGTTCAA
1 GTTTGAGTTCAAGGTTCAA
*
178226 GTTTGAGTTCAAGTTTCAA
1 GTTTGAGTTCAAGGTTCAA
178245 G
1 G
178246 ATTCAAGTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.23, C:0.08, G:0.28, T:0.41
Consensus pattern (19 bp):
GTTTGAGTTCAAGGTTCAA
Found at i:178252 original size:14 final size:13
Alignment explanation
Indices: 178220--178259 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
178210 TGAGTTTGAG
*
178220 GTTCAAGTTT-GA
1 GTTCAAGTTTCAA
178232 GTTCAAGTTTCAA
1 GTTCAAGTTTCAA
178245 GATTCAAGTTTCAA
1 G-TTCAAGTTTCAA
178259 G
1 G
178260 GTTTGAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 10 0.40
13 2 0.08
14 13 0.52
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (13 bp):
GTTCAAGTTTCAA
Found at i:187631 original size:17 final size:18
Alignment explanation
Indices: 187601--187642 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
187591 TATAGAATTG
187601 TTAAAAA-TAAAAAATCA
1 TTAAAAATTAAAAAATCA
* *
187618 -TAAAAATTACAAAATTA
1 TTAAAAATTAAAAAATCA
187635 TTAAAAAT
1 TTAAAAAT
187643 AGGCAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 6 0.29
17 8 0.38
18 7 0.33
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.29
Consensus pattern (18 bp):
TTAAAAATTAAAAAATCA
Found at i:189688 original size:55 final size:54
Alignment explanation
Indices: 189537--189695 Score: 282
Period size: 54 Copynumber: 2.9 Consensus size: 54
189527 ATGAAAATTT
189537 TGGTTTGAAATTTCAAATGAAATTACAGTATCTAAAACTTGATGGGACTCGTTA
1 TGGTTTGAAATTTCAAATGAAATTACAGTATCTAAAACTTGATGGGACTCGTTA
189591 TGGTTTGAAATTTCAAATGAAATTACAGTATCTAAAACTTGATGGGACTCGTTA
1 TGGTTTGAAATTTCAAATGAAATTACAGTATCTAAAACTTGATGGGACTCGTTA
* * *
189645 TGGTTTGAAATTATCAAATGAAATTACATTATCTAAAATTTGATGGAACTC
1 TGGTTTGAAATT-TCAAATGAAATTACAGTATCTAAAACTTGATGGGACTC
189696 TATTTTAACA
Statistics
Matches: 101, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
54 66 0.65
55 35 0.35
ACGTcount: A:0.36, C:0.11, G:0.17, T:0.36
Consensus pattern (54 bp):
TGGTTTGAAATTTCAAATGAAATTACAGTATCTAAAACTTGATGGGACTCGTTA
Found at i:195153 original size:3 final size:3
Alignment explanation
Indices: 195140--195172 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
195130 GAATCCCAGG
195140 TAT TAAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TA
195173 AAATAGGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:196591 original size:22 final size:21
Alignment explanation
Indices: 196538--196580 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
196528 TCATAACTTT
*
196538 AATTTAAATA-TT-TTTTATA
1 AATTTAATTATTTCTTTTATA
196557 AATTTAATTTATTTCTTTTATA
1 AATTTAA-TTATTTCTTTTATA
196579 AA
1 AA
196581 ATTCTAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 7 0.35
20 2 0.10
21 2 0.10
22 9 0.45
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
AATTTAATTATTTCTTTTATA
Found at i:200844 original size:23 final size:23
Alignment explanation
Indices: 200809--200863 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
200799 CATATGGTAG
* * *
200809 AAGCGTTCTACAAGGCAGAGGAA
1 AAGCGTGCCACAAGGCAGAGAAA
*
200832 AAGCGTGCCACAAGGTAGAGAAA
1 AAGCGTGCCACAAGGCAGAGAAA
200855 AAGCGTGCC
1 AAGCGTGCC
200864 GCAAAGACAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.38, C:0.20, G:0.31, T:0.11
Consensus pattern (23 bp):
AAGCGTGCCACAAGGCAGAGAAA
Found at i:201324 original size:10 final size:10
Alignment explanation
Indices: 201271--201324 Score: 53
Period size: 10 Copynumber: 5.7 Consensus size: 10
201261 GTTTATAAAA
201271 TTTTAA-AAT
1 TTTTAATAAT
*
201280 TTTTAACAAT
1 TTTTAATAAT
201290 TTTTAAT-AT
1 TTTTAATAAT
*
201299 TTATT-GTAA-
1 TT-TTAATAAT
201308 TTTTAATAAT
1 TTTTAATAAT
201318 TTTTAAT
1 TTTTAAT
201325 TTGTTTTGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
8 2 0.05
9 16 0.43
10 19 0.51
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (10 bp):
TTTTAATAAT
Found at i:201336 original size:19 final size:17
Alignment explanation
Indices: 201314--201358 Score: 63
Period size: 19 Copynumber: 2.5 Consensus size: 17
201304 GTAATTTTAA
201314 TAATTTTTAATTTGTTTT
1 TAATTTTTAATTT-TTTT
201332 GTAATTTTGTAATTTTTTT
1 -TAATTTT-TAATTTTTTT
201351 TAATTTTT
1 TAATTTTT
201359 TTCATTTAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 1 0.04
18 7 0.28
19 11 0.44
20 6 0.24
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.71
Consensus pattern (17 bp):
TAATTTTTAATTTTTTT
Found at i:201349 original size:28 final size:28
Alignment explanation
Indices: 201280--201348 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
201270 ATTTTAAAAT
*
201280 TTTTAACAATTTTTAATATTTATTGTAA
1 TTTTAATAATTTTTAATATTTATTGTAA
*
201308 TTTTAATAATTTTTAAT-TTGTTTTGTAA
1 TTTTAATAATTTTTAATATT-TATTGTAA
*
201336 TTTT-GTAATTTTT
1 TTTTAATAATTTTT
201349 TTTAATTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 10 0.27
28 27 0.73
ACGTcount: A:0.29, C:0.01, G:0.06, T:0.64
Consensus pattern (28 bp):
TTTTAATAATTTTTAATATTTATTGTAA
Found at i:202383 original size:12 final size:12
Alignment explanation
Indices: 202368--202392 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
202358 AATAACCCGA
202368 AAAATATGCACT
1 AAAATATGCACT
202380 AAAATATGCACT
1 AAAATATGCACT
202392 A
1 A
202393 GTGCAATTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.16, G:0.08, T:0.24
Consensus pattern (12 bp):
AAAATATGCACT
Found at i:204552 original size:46 final size:47
Alignment explanation
Indices: 204492--204609 Score: 141
Period size: 46 Copynumber: 2.6 Consensus size: 47
204482 CGCGCTTATT
* * *
204492 ATTCAGCACTGTGTGTGCTTATTGTTCAGTACTGTGTGTGCTTACTG
1 ATTCAGCACTGTGTGTGCTTACTGTTCAGCACTGTGTGTGCCTACTG
* ** *
204539 ATTC-GCATTGTGTGTGCTTACTGTTTTGCATTGTGTGTGCCTACTG
1 ATTCAGCACTGTGTGTGCTTACTGTTCAGCACTGTGTGTGCCTACTG
**
204585 ATTCA-CACTGCATGTGCTTACTGTT
1 ATTCAGCACTGTGTGTGCTTACTGTT
204610 TCCCCAACAC
Statistics
Matches: 60, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
46 56 0.93
47 4 0.07
ACGTcount: A:0.14, C:0.19, G:0.24, T:0.43
Consensus pattern (47 bp):
ATTCAGCACTGTGTGTGCTTACTGTTCAGCACTGTGTGTGCCTACTG
Found at i:204559 original size:23 final size:23
Alignment explanation
Indices: 204492--204607 Score: 117
Period size: 23 Copynumber: 5.0 Consensus size: 23
204482 CGCGCTTATT
*
204492 ATTCAGCACTGTGTGTGCTTATTG
1 ATTC-GCACTGTGTGTGCTTACTG
*
204516 -TTCAGTACTGTGTGTGCTTACTG
1 ATTC-GCACTGTGTGTGCTTACTG
*
204539 ATTCGCATTGTGTGTGCTTACTG
1 ATTCGCACTGTGTGTGCTTACTG
* * * *
204562 TTTTGCATTGTGTGTGCCTACTG
1 ATTCGCACTGTGTGTGCTTACTG
* **
204585 ATTCACACTGCATGTGCTTACTG
1 ATTCGCACTGTGTGTGCTTACTG
204608 TTTCCCCAAC
Statistics
Matches: 77, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
23 74 0.96
24 3 0.04
ACGTcount: A:0.15, C:0.19, G:0.24, T:0.42
Consensus pattern (23 bp):
ATTCGCACTGTGTGTGCTTACTG
Found at i:205682 original size:2 final size:2
Alignment explanation
Indices: 205675--205710 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
205665 TTTTCACTTA
205675 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
205711 TACAATATTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:206371 original size:22 final size:22
Alignment explanation
Indices: 206345--206386 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
206335 GACAAATAAA
206345 TAAT-AAGATTATTATTAAATTT
1 TAATAAAG-TTATTATTAAATTT
206367 TAATAAAGTTATTATTAAAT
1 TAATAAAGTTATTATTAAAT
206387 ATAATTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (22 bp):
TAATAAAGTTATTATTAAATTT
Found at i:206476 original size:38 final size:37
Alignment explanation
Indices: 206407--206478 Score: 99
Period size: 38 Copynumber: 1.9 Consensus size: 37
206397 AATAATAAAT
* * *
206407 AATTTAATCATATTTTAACATAATTATTATTAAATAC
1 AATTTAATAACATTTTAACATAATTACTATTAAATAC
*
206444 AATTTAATAACATTCTTAATATAATTACTATTAAA
1 AATTTAATAACATT-TTAACATAATTACTATTAAA
206479 ATATGAATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 12 0.40
38 18 0.60
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.44
Consensus pattern (37 bp):
AATTTAATAACATTTTAACATAATTACTATTAAATAC
Found at i:209596 original size:6 final size:6
Alignment explanation
Indices: 209585--209614 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
209575 GACATGTAAA
209585 AGTTGG AGTTGG AGTTGG AGTTGG AGTTGG
1 AGTTGG AGTTGG AGTTGG AGTTGG AGTTGG
209615 GAATGGCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.50, T:0.33
Consensus pattern (6 bp):
AGTTGG
Found at i:219461 original size:4 final size:4
Alignment explanation
Indices: 219452--219498 Score: 94
Period size: 4 Copynumber: 11.8 Consensus size: 4
219442 ATAAAGTTAT
219452 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
219499 TATGTATATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.51, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:224754 original size:15 final size:15
Alignment explanation
Indices: 224734--224764 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
224724 ACATTAGATT
224734 AAAATTTTATAAAAG
1 AAAATTTTATAAAAG
*
224749 AAAATTTTATACAAG
1 AAAATTTTATAAAAG
224764 A
1 A
224765 TGATGGGTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.32
Consensus pattern (15 bp):
AAAATTTTATAAAAG
Found at i:227056 original size:22 final size:23
Alignment explanation
Indices: 227030--227083 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 23
227020 GATTTAAAAA
227030 TTTAAATTTAAT-GAT-TAATAT
1 TTTAAATTTAATAGATGTAATAT
227051 TATT-AATTT-ATAGATGTAATAT
1 T-TTAAATTTAATAGATGTAATAT
*
227073 TTTAAAATTAA
1 TTTAAATTTAA
227084 AAAAAAATCA
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
20 2 0.07
21 11 0.41
22 13 0.48
23 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (23 bp):
TTTAAATTTAATAGATGTAATAT
Found at i:227058 original size:21 final size:21
Alignment explanation
Indices: 227029--227077 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
227019 AGATTTAAAA
*
227029 ATTTAAATTTA-ATGAT-TAAT
1 ATTTTAATTTATA-GATGTAAT
227049 ATTATTAATTTATAGATGTAAT
1 ATT-TTAATTTATAGATGTAAT
227071 ATTTTAA
1 ATTTTAA
227078 AATTAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 3 0.12
21 14 0.56
22 8 0.32
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (21 bp):
ATTTTAATTTATAGATGTAAT
Found at i:229114 original size:75 final size:78
Alignment explanation
Indices: 228968--229281 Score: 454
Period size: 78 Copynumber: 4.1 Consensus size: 78
228958 GAAACATTGT
* * * *
228968 CATCATCCTTGGACTTAGTAGACTTGGGTGTGTCACCAGCGTCCTCATTTTTGGATTTGTTGCCT
1 CATCATCCTTGGATTTGGTAGACTTGGGTGTATCACCAGTGTCCTCATTTTTGGATTTGTTGCCT
229033 ACTTTTGAAGCGA
66 ACTTTTGAAGCGA
* *
229046 CATCCTCCTTGGATTTGGTAGACTTGGGTGTGTCACCAGTGT-C-C-TTTTTGGATTTGTTGCCT
1 CATCATCCTTGGATTTGGTAGACTTGGGTGTATCACCAGTGTCCTCATTTTTGGATTTGTTGCCT
* *
229108 ATTTTTGAAGCGG
66 ACTTTTGAAGCGA
* * *
229121 CAACATCCTTGGATTTGGTAGACTTGGGTCTATCACCAGTGTCCTCATTTTTGGATTTGTTTCCT
1 CATCATCCTTGGATTTGGTAGACTTGGGTGTATCACCAGTGTCCTCATTTTTGGATTTGTTGCCT
*
229186 ATTTTTGAAGCGA
66 ACTTTTGAAGCGA
* * * *
229199 CACCATCCTTGGATTTGATAGACTTGGGTGTATCACTAGTGTCCTCATTTTTGGATTTATTGCCT
1 CATCATCCTTGGATTTGGTAGACTTGGGTGTATCACCAGTGTCCTCATTTTTGGATTTGTTGCCT
*
229264 ACTTTTGAAGCGC
66 ACTTTTGAAGCGA
229277 CATCA
1 CATCA
229282 ACTGATCTAC
Statistics
Matches: 212, Mismatches: 21, Indels: 6
0.89 0.09 0.03
Matches are distributed among these distances:
75 67 0.32
76 2 0.01
77 2 0.01
78 141 0.67
ACGTcount: A:0.18, C:0.20, G:0.22, T:0.39
Consensus pattern (78 bp):
CATCATCCTTGGATTTGGTAGACTTGGGTGTATCACCAGTGTCCTCATTTTTGGATTTGTTGCCT
ACTTTTGAAGCGA
Found at i:235684 original size:112 final size:111
Alignment explanation
Indices: 235483--235925 Score: 595
Period size: 112 Copynumber: 4.0 Consensus size: 111
235473 GCATATAGAC
** * ** **
235483 AAAAAACTCGTGCACGTTTAGATAGACACTCACTTAAATGCAGCTCACATGATTCCCTTTAGGAG
1 AAAAAACTCACGCACGTGTAGATAGACACTCACTTAAATGCAAATCATGTGATTCCCTTTAGGAG
* * *
235548 GAATCAAGACTGTTACGCCACAATTCCCTTTAGAAGGAATCAAGAAA
66 GAATCAAGACCGTTACGCCGCAATTCCCTTTAGGAGGAATCAAG-AA
* ** *
235595 AAAAAACTCACACACGTGTAGATAGA-AGCTCACTTAAATATAAATCATGTGATTCACTTTAGGA
1 AAAAAACTCACGCACGTGTAGATAGACA-CTCACTTAAATGCAAATCATGTGATTCCCTTTAGGA
* *
235659 GGAATCGAGACCGTTACGTCGCAATTCCCTTTAGGAGGAATCAAGACA
65 GGAATCAAGACCGTTACGCCGCAATTCCCTTTAGGAGGAATCAAGA-A
* * *
235707 AAAAAACTCACGCACGTGAAGATAGACACTCACTTAAATGCAAGTCATGCGATTCCCTTTAGGAG
1 AAAAAACTCACGCACGTGTAGATAGACACTCACTTAAATGCAAATCATGTGATTCCCTTTAGGAG
**
235772 GAATCAAGATTGTT-CGCCGCAATTCCCTTTAGGAGGAATCAAG-A
66 GAATCAAGACCGTTACGCCGCAATTCCCTTTAGGAGGAATCAAGAA
* *
235816 CAAAAACTCGCGCACGTGTAGATAGACACTCACTTAAATGCAAATCATGTGATTCCCTTTAGGAG
1 AAAAAACTCACGCACGTGTAGATAGACACTCACTTAAATGCAAATCATGTGATTCCCTTTAGGAG
* * * *
235881 GAATCAAGATCATTTCGCCGCAATTCCCTTTAGGATGAATCAAGA
66 GAATCAAGACCGTTACGCCGCAATTCCCTTTAGGAGGAATCAAGA
235926 CCGTTGCGCT
Statistics
Matches: 291, Mismatches: 35, Indels: 11
0.86 0.10 0.03
Matches are distributed among these distances:
109 73 0.25
110 28 0.10
111 30 0.10
112 159 0.55
113 1 0.00
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.24
Consensus pattern (111 bp):
AAAAAACTCACGCACGTGTAGATAGACACTCACTTAAATGCAAATCATGTGATTCCCTTTAGGAG
GAATCAAGACCGTTACGCCGCAATTCCCTTTAGGAGGAATCAAGAA
Found at i:235880 original size:221 final size:222
Alignment explanation
Indices: 235479--235926 Score: 634
Period size: 221 Copynumber: 2.0 Consensus size: 222
235469 CACCGCATAT
** ** *
235479 AGACAAAAAACTCGTGCACGTTTAGATAGACACTCACTTAAATGCAGCTCACATGATTCCCTTTA
1 AGACAAAAAACTCACGCACGTGAAGATAGACACTCACTTAAATGCAGCTCACACGATTCCCTTTA
235544 GGAGGAATCAAGACTGTTACGCCACAATTCCCTTTAGAAGGAATCAAGAAAAAAAAACTCACACA
66 GGAGGAATCAAGACTGTTACGCCACAATTCCCTTTAGAAGGAATCAAG-AAAAAAAACTCACACA
* * *
235609 CGTGTAGATAGAAGCTCACTTAAATATAAATCATGTGATTCACTTTAGGAGGAATCGAGACCGTT
130 CGTGTAGATAGAAGCTCACTTAAATACAAATCATGTGATTCACTTTAGGAGGAATCAAGACCATT
*
235674 ACGTCGCAATTCCCTTTAGGAGGAATCA
195 ACGCCGCAATTCCCTTTAGGAGGAATCA
**
235702 AGACAAAAAAACTCACGCACGTGAAGATAGACACTCACTTAAATGCAAG-TCATGCGATTCCCTT
1 AGAC-AAAAAACTCACGCACGTGAAGATAGACACTCACTTAAATGC-AGCTCACACGATTCCCTT
* * * * * *
235766 TAGGAGGAATCAAGATTGTT-CGCCGCAATTCCCTTTAGGAGGAATCAAG-ACAAAAACTCGCGC
64 TAGGAGGAATCAAGACTGTTACGCCACAATTCCCTTTAGAAGGAATCAAGAAAAAAAACTCACAC
* * *
235829 ACGTGTAGATAGACA-CTCACTTAAATGCAAATCATGTGATTCCCTTTAGGAGGAATCAAGATCA
129 ACGTGTAGATAGA-AGCTCACTTAAATACAAATCATGTGATTCACTTTAGGAGGAATCAAGACCA
* *
235893 TTTCGCCGCAATTCCCTTTAGGATGAATCA
193 TTACGCCGCAATTCCCTTTAGGAGGAATCA
235923 AGAC
1 AGAC
235927 CGTTGCGCTG
Statistics
Matches: 200, Mismatches: 22, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
221 98 0.49
222 1 0.00
223 31 0.16
224 68 0.34
225 2 0.01
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.24
Consensus pattern (222 bp):
AGACAAAAAACTCACGCACGTGAAGATAGACACTCACTTAAATGCAGCTCACACGATTCCCTTTA
GGAGGAATCAAGACTGTTACGCCACAATTCCCTTTAGAAGGAATCAAGAAAAAAAACTCACACAC
GTGTAGATAGAAGCTCACTTAAATACAAATCATGTGATTCACTTTAGGAGGAATCAAGACCATTA
CGCCGCAATTCCCTTTAGGAGGAATCA
Found at i:235965 original size:36 final size:36
Alignment explanation
Indices: 235867--235971 Score: 138
Period size: 36 Copynumber: 2.9 Consensus size: 36
235857 AAATCATGTG
* * *
235867 ATTCCCTTTAGGAGGAATCAAGATCATTTCGCCGCA
1 ATTCCCTTTAGGAGGAATCAAGACCGTTGCGCCGCA
* *
235903 ATTCCCTTTAGGATGAATCAAGACCGTTGCGCTGCA
1 ATTCCCTTTAGGAGGAATCAAGACCGTTGCGCCGCA
* * *
235939 ATTCCCTTTAGGAGGAACCAAAACCGTTACGCC
1 ATTCCCTTTAGGAGGAATCAAGACCGTTGCGCC
235972 ACATATAGAT
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 59 1.00
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.26
Consensus pattern (36 bp):
ATTCCCTTTAGGAGGAATCAAGACCGTTGCGCCGCA
Found at i:236087 original size:36 final size:36
Alignment explanation
Indices: 236047--236127 Score: 117
Period size: 36 Copynumber: 2.2 Consensus size: 36
236037 TCCTCCTTAA
* ** *
236047 GAGGAATCAAGATCGTTATGCGGCGATTCCCTTTAG
1 GAGGAATCAAGACCGTTACACAGCGATTCCCTTTAG
*
236083 GAGGAATCAAGACCGTTACACAGTGATTCCCTTTAG
1 GAGGAATCAAGACCGTTACACAGCGATTCCCTTTAG
236119 GAGGAATCA
1 GAGGAATCA
236128 GGACTGAACA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.25
Consensus pattern (36 bp):
GAGGAATCAAGACCGTTACACAGCGATTCCCTTTAG
Found at i:239674 original size:19 final size:19
Alignment explanation
Indices: 239629--239674 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
239619 ACTTCTTAAA
239629 TTTTTTAATGTGATCGAGT
1 TTTTTTAATGTGATCGAGT
*
239648 TTTCTTAAT-TGAT-GAGAT
1 TTTTTTAATGTGATCGAG-T
239666 TTATTTTAA
1 TT-TTTTAA
239675 AAATATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 3 0.13
18 7 0.30
19 13 0.57
ACGTcount: A:0.26, C:0.04, G:0.15, T:0.54
Consensus pattern (19 bp):
TTTTTTAATGTGATCGAGT
Found at i:245927 original size:2 final size:2
Alignment explanation
Indices: 245920--245961 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
245910 TAAGGGCTTA
245920 AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
245961 A
1 A
245962 ATGGATGGAG
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:258294 original size:31 final size:30
Alignment explanation
Indices: 258246--258331 Score: 84
Period size: 30 Copynumber: 2.9 Consensus size: 30
258236 AATATGGGAG
*
258246 CTTTGA-TTTGATGCAATTGTACACATGAAA
1 CTTTGATTTTGATTCAATTGTACACAT-AAA
* * *
258276 CTTTGATTTTGATTCAATTCTAAAAATAAA
1 CTTTGATTTTGATTCAATTGTACACATAAA
** * *
258306 CTTCAATTTTGGTTCAACTGTACACA
1 CTTTGATTTTGATTCAATTGTACACA
258332 ATAGAAAATC
Statistics
Matches: 44, Mismatches: 11, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
30 28 0.64
31 16 0.36
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.40
Consensus pattern (30 bp):
CTTTGATTTTGATTCAATTGTACACATAAA
Found at i:259823 original size:235 final size:237
Alignment explanation
Indices: 259397--259872 Score: 823
Period size: 235 Copynumber: 2.0 Consensus size: 237
259387 ACATTTAAAA
*
259397 TTACATCTTTTTCGAAGAAAGAATAGAGAATTTTTATCTGTGTGCATCCCTAATATATTGATTGT
1 TTACATCTTTTTCGAAGAAAGAATAGAGAATTTTCATCTGTGTGCATCCCTAATATATTGATTGT
259462 TTTTTTGGAGTGCCCAAATTTAGTAATTGTGCAGTCTGCCTTTTATAGAGTTTTATTTAGCATAA
66 TTTTTTGGAGTGCCCAAATTTAGTAATTGTGCAGTCTGCCTTTTATAGAGTTTTATTTAGCATAA
* * * **
259527 TATCTCGACTAATAGAACATTCAGAGCAATGATAGTAGACTGCTCTCTTGAAGGTTTCAGTGTTG
131 TATCTCGACTAATAGAACATTCAGAACAATGAAAATAGACTGAGCTCTTGAAGGTTTCAGTGTTG
259592 GATTTGAGTGGTTAGATTGGTCAATTAATTGTCGT-AGGTATT
196 GATTTGAGTGGTTAGATTGGTCAATTAATTGTC-TAAGGTATT
* *
259634 TTACATTTTTTTGGAAGAAAGAATAGAGAATTTTCATCTGTGTGCATCCCTAATATATTGA-T-T
1 TTACATCTTTTTCGAAGAAAGAATAGAGAATTTTCATCTGTGTGCATCCCTAATATATTGATTGT
* *
259697 TTTTTTGGAGTGCCCAAATTTAGTAATTGTGGAGTCTGCCTTTTATAGTGTTTTATTTAGCATAA
66 TTTTTTGGAGTGCCCAAATTTAGTAATTGTGCAGTCTGCCTTTTATAGAGTTTTATTTAGCATAA
*
259762 TATCTCGACTAATAGAACATTCAGAACAATGAAAATAGACTTAGCTCTTGAAGGTTTCAGTGTTG
131 TATCTCGACTAATAGAACATTCAGAACAATGAAAATAGACTGAGCTCTTGAAGGTTTCAGTGTTG
259827 GATTTGAGTGGTTAGATTGGTCAATTAATTGTCTAAGGTATT
196 GATTTGAGTGGTTAGATTGGTCAATTAATTGTCTAAGGTATT
259869 TTAC
1 TTAC
259873 TTTGATGAGA
Statistics
Matches: 227, Mismatches: 11, Indels: 4
0.94 0.05 0.02
Matches are distributed among these distances:
234 1 0.00
235 167 0.74
236 1 0.00
237 58 0.26
ACGTcount: A:0.28, C:0.12, G:0.20, T:0.40
Consensus pattern (237 bp):
TTACATCTTTTTCGAAGAAAGAATAGAGAATTTTCATCTGTGTGCATCCCTAATATATTGATTGT
TTTTTTGGAGTGCCCAAATTTAGTAATTGTGCAGTCTGCCTTTTATAGAGTTTTATTTAGCATAA
TATCTCGACTAATAGAACATTCAGAACAATGAAAATAGACTGAGCTCTTGAAGGTTTCAGTGTTG
GATTTGAGTGGTTAGATTGGTCAATTAATTGTCTAAGGTATT
Found at i:271643 original size:3 final size:3
Alignment explanation
Indices: 271635--271662 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
271625 TGTGGTCAAA
271635 TGG TGG TGG TGG TGG TGG TGG TGG TGG T
1 TGG TGG TGG TGG TGG TGG TGG TGG TGG T
271663 CTGAATGGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.64, T:0.36
Consensus pattern (3 bp):
TGG
Found at i:272555 original size:26 final size:26
Alignment explanation
Indices: 272507--272556 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
272497 AATTTATAAA
* *
272507 TAAATATTAGTAATTTTATTTAAATG
1 TAAATATTAGTAAATATATTTAAATG
272533 TAAATATTA-TAAATATATATTAAA
1 TAAATATTAGTAAATATAT-TTAAA
272557 AACACTCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (26 bp):
TAAATATTAGTAAATATATTTAAATG
Found at i:273966 original size:42 final size:42
Alignment explanation
Indices: 273919--274004 Score: 111
Period size: 42 Copynumber: 2.0 Consensus size: 42
273909 AAAGCGCAAC
** *
273919 CAACTGGACGTACTTTCTACACAGTTGGC-AGAAAAGCTCGTT
1 CAACTGGACAAACTTTCCACACAGTTGGCAAG-AAAGCTCGTT
* *
273961 CAACTGGGCAAACTTTCCACACAGTTGTCAAGAAAGCTCGTT
1 CAACTGGACAAACTTTCCACACAGTTGGCAAGAAAGCTCGTT
274003 CA
1 CA
274005 GCTGAACGAG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
42 36 0.95
43 2 0.05
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (42 bp):
CAACTGGACAAACTTTCCACACAGTTGGCAAGAAAGCTCGTT
Found at i:276740 original size:17 final size:17
Alignment explanation
Indices: 276705--276738 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
276695 TAATTAATTT
*
276705 TAAAAATAATTATAAAA
1 TAAAAATAACTATAAAA
276722 TAAAAATACACTATAAA
1 TAAAAATA-ACTATAAA
276739 TATACCAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (17 bp):
TAAAAATAACTATAAAA
Found at i:278313 original size:104 final size:104
Alignment explanation
Indices: 278128--278333 Score: 403
Period size: 104 Copynumber: 2.0 Consensus size: 104
278118 CAATATTCTT
278128 ATTGAGTTCTCTGGAAACATGATGAATCGACCAATGTACCATCTTAATTAATAACAATCGGATTC
1 ATTGAGTTCTCTGGAAACATGATGAATCGACCAATGTACCATCTTAATTAATAACAATCGGATTC
*
278193 TTTCGATCAAAGCTAAATTCGAACCCTTTAAAGACTTTA
66 TTTCGATCAAAACTAAATTCGAACCCTTTAAAGACTTTA
278232 ATTGAGTTCTCTGGAAACATGATGAATCGACCAATGTACCATCTTAATTAATAACAATCGGATTC
1 ATTGAGTTCTCTGGAAACATGATGAATCGACCAATGTACCATCTTAATTAATAACAATCGGATTC
278297 TTTCGATCAAAACTAAATTCGAACCCTTTAAAGACTT
66 TTTCGATCAAAACTAAATTCGAACCCTTTAAAGACTT
278334 GCTTTGTAGA
Statistics
Matches: 101, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
104 101 1.00
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.32
Consensus pattern (104 bp):
ATTGAGTTCTCTGGAAACATGATGAATCGACCAATGTACCATCTTAATTAATAACAATCGGATTC
TTTCGATCAAAACTAAATTCGAACCCTTTAAAGACTTTA
Found at i:279241 original size:15 final size:16
Alignment explanation
Indices: 279208--279242 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
279198 TTTATTTATT
279208 TAATTTTAAAATATTAA
1 TAATTTTAAAATA-TAA
279225 TAATTTTAAAATA-AA
1 TAATTTTAAAATATAA
279240 TAA
1 TAA
279243 ATAAATAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
17 13 0.72
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TAATTTTAAAATATAA
Found at i:285468 original size:31 final size:32
Alignment explanation
Indices: 285433--285492 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
285423 TTTTTTTTAG
285433 TTAAACTTGA-TTCTCAAACTTTT-AAAAAGAA
1 TTAAACTTGACTT-TCAAACTTTTGAAAAAGAA
* *
285464 TTAAATTTGACTTTCAATCTTTTGAAAAA
1 TTAAACTTGACTTTCAAACTTTTGAAAAA
285493 ATGTCGTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 18 0.72
32 7 0.28
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.40
Consensus pattern (32 bp):
TTAAACTTGACTTTCAAACTTTTGAAAAAGAA
Found at i:286532 original size:41 final size:41
Alignment explanation
Indices: 286485--286577 Score: 141
Period size: 41 Copynumber: 2.2 Consensus size: 41
286475 TATGTACATA
* *
286485 ACTTATTTATGTGTCCATGCTATGTATCATAAAAATAATAT
1 ACTTATTTACGCGTCCATGCTATGTATCATAAAAATAATAT
*
286526 ACTTATTTACGCGTCTATGCTATGTATCATAAAAATAATAT
1 ACTTATTTACGCGTCCATGCTATGTATCATAAAAATAATAT
*
286567 ATTTAATTTAC
1 ACTT-ATTTAC
286578 TTATTAAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
41 41 0.87
42 6 0.13
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.42
Consensus pattern (41 bp):
ACTTATTTACGCGTCCATGCTATGTATCATAAAAATAATAT
Found at i:288258 original size:3 final size:3
Alignment explanation
Indices: 288250--288279 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
288240 AGAGAGGCTG
288250 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
288280 TCCTATTGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:289176 original size:3 final size:3
Alignment explanation
Indices: 289168--289212 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
289158 AATTCACATG
289168 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
289213 TATATATATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:289952 original size:2 final size:2
Alignment explanation
Indices: 289945--289979 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
289935 GATAAACCCG
289945 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
289980 TTCATAGGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:292107 original size:5 final size:5
Alignment explanation
Indices: 292097--292121 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
292087 TATCTGCTAA
292097 TTAAT TTAAT TTAAT TTAAT TTAAT
1 TTAAT TTAAT TTAAT TTAAT TTAAT
292122 CAGTCCTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTAAT
Found at i:292949 original size:2 final size:2
Alignment explanation
Indices: 292942--292979 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
292932 GATTCTGATC
292942 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
292980 TGACACAATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:299353 original size:39 final size:39
Alignment explanation
Indices: 299310--299398 Score: 169
Period size: 39 Copynumber: 2.3 Consensus size: 39
299300 AAGCTTTTTT
299310 ATGTTGGAAATGAGGGAAGCTCACAATAGAATCATGTGG
1 ATGTTGGAAATGAGGGAAGCTCACAATAGAATCATGTGG
299349 ATGTTGGAAATGAGGGAAGCTCACAATAGAATCATGTGG
1 ATGTTGGAAATGAGGGAAGCTCACAATAGAATCATGTGG
299388 ATGTTTGGAAA
1 ATG-TTGGAAA
299399 ATATAAATTA
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 42 0.86
40 7 0.14
ACGTcount: A:0.36, C:0.09, G:0.30, T:0.25
Consensus pattern (39 bp):
ATGTTGGAAATGAGGGAAGCTCACAATAGAATCATGTGG
Found at i:308737 original size:80 final size:80
Alignment explanation
Indices: 308596--308745 Score: 228
Period size: 80 Copynumber: 1.9 Consensus size: 80
308586 ATAAACCGAT
* ** * * * *
308596 AATCCTGGCACCCAGTGCCTGGCAGATAAACCGTGAAAGTGAGCCCAACTCTAGTCGGTTAAATT
1 AATCCTGGCACCCAGTGCCTAGCAGATAAACCGCAAAAATGAGCCCAACTCTAATCAGTTAAACT
308661 GACAAATATTCGTTA
66 GACAAATATTCGTTA
*
308676 AATCCTGGCACCCAGTGCCTAGCGGATAAACCGCAAAAATGAGCCCAACTCTAATCAGTTAAACT
1 AATCCTGGCACCCAGTGCCTAGCAGATAAACCGCAAAAATGAGCCCAACTCTAATCAGTTAAACT
308741 GACAA
66 GACAA
308746 CATGAATAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
80 62 1.00
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (80 bp):
AATCCTGGCACCCAGTGCCTAGCAGATAAACCGCAAAAATGAGCCCAACTCTAATCAGTTAAACT
GACAAATATTCGTTA
Found at i:312191 original size:39 final size:38
Alignment explanation
Indices: 312142--312216 Score: 96
Period size: 39 Copynumber: 1.9 Consensus size: 38
312132 CAACCGTGAG
*
312142 AATTTTCAGCATCAAAATACCTAAAATTTCAGACATTAT
1 AATTTGCAGCATCAAAATACCTAAAATTTCAG-CATTAT
** * *
312181 AATTTGCAGCATTTAAATGCCTAAAGTTTCAGCATT
1 AATTTGCAGCATCAAAATACCTAAAATTTCAGCATT
312217 CAAACCACAT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
38 4 0.13
39 27 0.87
ACGTcount: A:0.39, C:0.17, G:0.09, T:0.35
Consensus pattern (38 bp):
AATTTGCAGCATCAAAATACCTAAAATTTCAGCATTAT
Found at i:313575 original size:62 final size:60
Alignment explanation
Indices: 313471--313626 Score: 224
Period size: 62 Copynumber: 2.5 Consensus size: 60
313461 ATTATTTTAA
* * *
313471 TATTAAATTAATATGATACTTATC-AAGATAAATATTAGATTAAGTTTAATATTAAATGT
1 TATTAAATTAATAGGATATTTATCTAAGATAAATATTAGATTAAATTTAATATTAAATGT
*
313530 TATTAAATTAATAGGATATTTATCTTGTAGATAAATATTAGATTAAATTTAATATTAAATGT
1 TATTAAATTAATAGGATATTTATC-T-AAGATAAATATTAGATTAAATTTAATATTAAATGT
*
313592 TATTAAATTAATAGAATATTTATCTACAAGATAAA
1 TATTAAATTAATAGGATATTTATCT--AAGATAAA
313627 CGTTGAACTA
Statistics
Matches: 86, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
59 22 0.26
61 1 0.01
62 63 0.73
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.42
Consensus pattern (60 bp):
TATTAAATTAATAGGATATTTATCTAAGATAAATATTAGATTAAATTTAATATTAAATGT
Found at i:313639 original size:62 final size:62
Alignment explanation
Indices: 313471--313644 Score: 196
Period size: 62 Copynumber: 2.9 Consensus size: 62
313461 ATTATTTTAA
* * * *
313471 TATTAAATTAATATG-ATACTTA--T-CAAGATAAATATTAGATTAAGTTTAATATTAAATGT
1 TATTAAATTAATA-GAATATTTATCTACAAGATAAACATTAGACTAAATTTAATATTAAATGT
* *** * *
313530 TATTAAATTAATAGGATATTTATCTTGTAGATAAATATTAGATTAAATTTAATATTAAATGT
1 TATTAAATTAATAGAATATTTATCTACAAGATAAACATTAGACTAAATTTAATATTAAATGT
*
313592 TATTAAATTAATAGAATATTTATCTACAAGATAAACGTT-GAACTAAATTTAAT
1 TATTAAATTAATAGAATATTTATCTACAAGATAAACATTAG-ACTAAATTTAAT
313645 TATCTTAATA
Statistics
Matches: 99, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
58 1 0.01
59 19 0.19
61 2 0.02
62 77 0.78
ACGTcount: A:0.45, C:0.04, G:0.09, T:0.42
Consensus pattern (62 bp):
TATTAAATTAATAGAATATTTATCTACAAGATAAACATTAGACTAAATTTAATATTAAATGT
Found at i:313696 original size:32 final size:32
Alignment explanation
Indices: 313655--313728 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
313645 TATCTTAATA
313655 TTAAATTAATAAAATATTATTCAAA-TAATTAT
1 TTAAATTAATAAAATATTATT-AAATTAATTAT
* **
313687 TTAATTTAATTTAATATTATTAAATTAATTAT
1 TTAAATTAATAAAATATTATTAAATTAATTAT
313719 TTAAAATTAA
1 TT-AAATTAA
313729 ATTAATTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 3 0.08
32 27 0.75
33 6 0.17
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (32 bp):
TTAAATTAATAAAATATTATTAAATTAATTAT
Found at i:313727 original size:19 final size:19
Alignment explanation
Indices: 313705--313742 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
313695 ATTTAATATT
313705 ATTAAATTAATTATTTAAA
1 ATTAAATTAATTATTTAAA
313724 ATTAAATTAATTATTTAAA
1 ATTAAATTAATTATTTAAA
313743 TTTGCATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTAAATTAATTATTTAAA
Found at i:313735 original size:51 final size:50
Alignment explanation
Indices: 313680--313807 Score: 127
Period size: 51 Copynumber: 2.5 Consensus size: 50
313670 ATTATTCAAA
* *
313680 TAATTATTTAATTTAATTTAATATTATTAA-ATTAATTATTTAAAATTAAA-T
1 TAATTATTTAATTTAATTTAATATTAATAAGA-TAAATA-TT-AAATTAAATT
*
313731 TAATTATTTAAATTTGCATATTAA-ATTAATAAGATAAATATTAAATTAAATT
1 TAATTATTT-AATTT-AAT-TTAATATTAATAAGATAAATATTAAATTAAATT
* * *
313783 TAATTATTAAATTTGATCTAATATT
1 TAATTATTTAATTTAATTTAATATT
313808 TATTTTCATT
Statistics
Matches: 65, Mismatches: 6, Indels: 13
0.77 0.07 0.15
Matches are distributed among these distances:
49 3 0.05
50 5 0.08
51 22 0.34
52 16 0.25
53 14 0.22
54 5 0.08
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (50 bp):
TAATTATTTAATTTAATTTAATATTAATAAGATAAATATTAAATTAAATT
Found at i:313742 original size:32 final size:31
Alignment explanation
Indices: 313670--313744 Score: 82
Period size: 32 Copynumber: 2.4 Consensus size: 31
313660 TTAATAAAAT
* * *
313670 ATTATTCAAA-TAATTATTTAATTTAATTTA
1 ATTATTTAAATTAATTATTTAAATTAAATTA
313700 A-TATTATTAAATTAATTATTTAAAATTAAATTA
1 ATTA-T-TTAAATTAATTATTT-AAATTAAATTA
313733 ATTATTTAAATT
1 ATTATTTAAATT
313745 TGCATATTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
29 2 0.05
30 2 0.05
31 4 0.11
32 16 0.43
33 11 0.30
34 2 0.05
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (31 bp):
ATTATTTAAATTAATTATTTAAATTAAATTA
Found at i:313833 original size:21 final size:23
Alignment explanation
Indices: 313765--313833 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 23
313755 ATTAATAAGA
*
313765 TAAATATTAAATTAAATTTAATTAT
1 TAAAT-TTGAATTAAATTTAATT-T
313790 TAAATTTG-ATCTAATATTT-ATTT
1 TAAATTTGAAT-TAA-ATTTAATTT
*
313813 T-CA-TTGAATTAAATTTAATTT
1 TAAATTTGAATTAAATTTAATTT
313834 AATATTAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
20 4 0.11
21 10 0.26
22 3 0.08
23 4 0.11
24 8 0.21
25 9 0.24
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (23 bp):
TAAATTTGAATTAAATTTAATTT
Found at i:333796 original size:27 final size:29
Alignment explanation
Indices: 333729--333796 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 29
333719 ATAACACAAT
* * *
333729 AAATTATACATGAATTTTGATTTAATATGC
1 AAATTATACATGAACTTTAATTT-AGATGC
333759 AAATGTATACATGAACTTTAATTT-GATGC
1 AAAT-TATACATGAACTTTAATTTAGATGC
333788 -AATTATACA
1 AAATTATACA
333797 CATCAAACTC
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 6 0.18
28 3 0.09
29 4 0.12
30 4 0.12
31 17 0.50
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.40
Consensus pattern (29 bp):
AAATTATACATGAACTTTAATTTAGATGC
Found at i:342616 original size:21 final size:21
Alignment explanation
Indices: 342592--342640 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
342582 GAAATACGAG
342592 TAAAAATTCTTTTAAAA-AAAA
1 TAAAAATTC-TTTAAAATAAAA
* *
342613 TAAAATTTCTTTAAAATAAAC
1 TAAAAATTCTTTAAAATAAAA
342634 TAAAAAT
1 TAAAAAT
342641 ATTCATTCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.59, C:0.06, G:0.00, T:0.35
Consensus pattern (21 bp):
TAAAAATTCTTTAAAATAAAA
Found at i:354214 original size:29 final size:29
Alignment explanation
Indices: 354152--354218 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
354142 ATATTTATTT
*
354152 TTTAAATAAAAAAATAAAATTAATTATAA
1 TTTAAATAAAAAAATAAAATTAATTACAA
* *
354181 ATTAAATAAAAAAATAACATTGAATT-CAA
1 TTTAAATAAAAAAATAAAATT-AATTACAA
354210 TTTAAATAA
1 TTTAAATAA
354219 TCGAAATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 29 0.88
30 4 0.12
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (29 bp):
TTTAAATAAAAAAATAAAATTAATTACAA
Found at i:354282 original size:3 final size:3
Alignment explanation
Indices: 354274--354301 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
354264 ATTCCAACCC
354274 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
354302 GATGATGGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:356202 original size:12 final size:12
Alignment explanation
Indices: 356185--356210 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
356175 GCGTGTAAGG
356185 CATGAACTCAAA
1 CATGAACTCAAA
356197 CATGAACTCAAA
1 CATGAACTCAAA
356209 CA
1 CA
356211 GGGTTACAAG
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:0.50, C:0.27, G:0.08, T:0.15
Consensus pattern (12 bp):
CATGAACTCAAA
Found at i:363129 original size:5 final size:5
Alignment explanation
Indices: 363119--363150 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
363109 AACGCATAAA
363119 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AA
363151 TAATGAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:375331 original size:19 final size:20
Alignment explanation
Indices: 375287--375331 Score: 51
Period size: 19 Copynumber: 2.3 Consensus size: 20
375277 AGATGTAACC
375287 ACAGTGAAAAAGCAAGGAGAG
1 ACAG-GAAAAAGCAAGGAGAG
375308 A-AGGAAAAAG-AA-GAGAGG
1 ACAGGAAAAAGCAAGGAGA-G
375326 ACAGGA
1 ACAGGA
375332 TAGATCCAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
17 4 0.18
18 4 0.18
19 11 0.50
20 2 0.09
21 1 0.05
ACGTcount: A:0.56, C:0.07, G:0.36, T:0.02
Consensus pattern (20 bp):
ACAGGAAAAAGCAAGGAGAG
Found at i:378407 original size:237 final size:237
Alignment explanation
Indices: 377992--378465 Score: 921
Period size: 237 Copynumber: 2.0 Consensus size: 237
377982 CGGCAGCAGA
377992 TGGAAATGATGATGAAGCACCTTCAAAAACATCTTGCCTGCTGGGAAGAATAGATCCACACCTTC
1 TGGAAATGATGATGAAGCACCTTCAAAAACATCTTGCCTGCTGGGAAGAATAGATCCACACCTTC
*
378057 CTTCCCTAGATTTTGATGATTCAAGGAGAGAATGCTGTATATTAGTATTAGAAGTTCTATCCAAT
66 CTTCCCTAGATTTTGATGATTCAAGAAGAGAATGCTGTATATTAGTATTAGAAGTTCTATCCAAT
*
378122 CTTCCTAGCTCATGATTCATTCCAACTGAAGAAATTGCATGTCGCTTTGACAACTCTGAAATCTG
131 CTTCCTAGCTCATGACTCATTCCAACTGAAGAAATTGCATGTCGCTTTGACAACTCTGAAATCTG
378187 GCTCAACGCAAGCAGTCTCATACTATCATCAAGCAAACAAGG
196 GCTCAACGCAAGCAGTCTCATACTATCATCAAGCAAACAAGG
378229 TGGAAATGATGATGAAGCACCTTCAAAAACATCTTGCCTGCTGGGAAGAATAGATCCACACCTTC
1 TGGAAATGATGATGAAGCACCTTCAAAAACATCTTGCCTGCTGGGAAGAATAGATCCACACCTTC
378294 CTTCCCTAGATTTTGATGATTCAAGAAGAGAATGCTGTATATTAGTATTAGAAGTTCTATCCAAT
66 CTTCCCTAGATTTTGATGATTCAAGAAGAGAATGCTGTATATTAGTATTAGAAGTTCTATCCAAT
*
378359 CTTCCTAGCTCATGGCTCATTCCAACTGAAGAAATTGCATGTCGCTTTGACAACTCTGAAATCTG
131 CTTCCTAGCTCATGACTCATTCCAACTGAAGAAATTGCATGTCGCTTTGACAACTCTGAAATCTG
378424 GCTCAACGCAAGCAGTCTCATACTATCATCAAGCAAACAAGG
196 GCTCAACGCAAGCAGTCTCATACTATCATCAAGCAAACAAGG
378466 GCCCTCTTGT
Statistics
Matches: 234, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
237 234 1.00
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (237 bp):
TGGAAATGATGATGAAGCACCTTCAAAAACATCTTGCCTGCTGGGAAGAATAGATCCACACCTTC
CTTCCCTAGATTTTGATGATTCAAGAAGAGAATGCTGTATATTAGTATTAGAAGTTCTATCCAAT
CTTCCTAGCTCATGACTCATTCCAACTGAAGAAATTGCATGTCGCTTTGACAACTCTGAAATCTG
GCTCAACGCAAGCAGTCTCATACTATCATCAAGCAAACAAGG
Found at i:387181 original size:70 final size:70
Alignment explanation
Indices: 387068--387208 Score: 282
Period size: 70 Copynumber: 2.0 Consensus size: 70
387058 CCATGTGTCG
387068 TACATGAGTGTTTAAAGAAAAATGAGGAGTCCGAGTACTAGGATGTCAAGGAAGAACTTAATTAA
1 TACATGAGTGTTTAAAGAAAAATGAGGAGTCCGAGTACTAGGATGTCAAGGAAGAACTTAATTAA
387133 GATGT
66 GATGT
387138 TACATGAGTGTTTAAAGAAAAATGAGGAGTCCGAGTACTAGGATGTCAAGGAAGAACTTAATTAA
1 TACATGAGTGTTTAAAGAAAAATGAGGAGTCCGAGTACTAGGATGTCAAGGAAGAACTTAATTAA
387203 GATGT
66 GATGT
387208 T
1 T
387209 TAGTTGCATT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 71 1.00
ACGTcount: A:0.40, C:0.09, G:0.26, T:0.26
Consensus pattern (70 bp):
TACATGAGTGTTTAAAGAAAAATGAGGAGTCCGAGTACTAGGATGTCAAGGAAGAACTTAATTAA
GATGT
Found at i:387753 original size:24 final size:24
Alignment explanation
Indices: 387726--387784 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 24
387716 ATGACAATGA
387726 TGATGAGGAAGATGAAGCA-GCAGG
1 TGATGAGGAAGATGAAG-ATGCAGG
*
387750 TGAT---CAAGATGAAGATGCAGG
1 TGATGAGGAAGATGAAGATGCAGG
*
387771 TGAGGAGGAAGATG
1 TGATGAGGAAGATG
387785 GATCAGGTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 8
0.72 0.08 0.21
Matches are distributed among these distances:
20 1 0.04
21 17 0.61
24 10 0.36
ACGTcount: A:0.37, C:0.07, G:0.41, T:0.15
Consensus pattern (24 bp):
TGATGAGGAAGATGAAGATGCAGG
Found at i:387758 original size:21 final size:21
Alignment explanation
Indices: 387734--387773 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
387724 GATGATGAGG
387734 AAGATGAAGCA-GCAGGTGATC
1 AAGATGAAG-ATGCAGGTGATC
387755 AAGATGAAGATGCAGGTGA
1 AAGATGAAGATGCAGGTGA
387774 GGAGGAAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.40, C:0.10, G:0.35, T:0.15
Consensus pattern (21 bp):
AAGATGAAGATGCAGGTGATC
Found at i:387895 original size:3 final size:3
Alignment explanation
Indices: 387889--387922 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
387879 CGACAACGAA
*
387889 GAT GAT GAC GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
387923 GGGAGGAAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.32, C:0.03, G:0.35, T:0.29
Consensus pattern (3 bp):
GAT
Found at i:387948 original size:18 final size:18
Alignment explanation
Indices: 387925--387968 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
387915 TGATGATGGG
387925 GAGGAAG-GTGAAGAAGAA
1 GAGGAAGAG-GAAGAAGAA
*
387943 GAGGAAGAGGAGGAAGAA
1 GAGGAAGAGGAAGAAGAA
*
387961 GATGAAGA
1 GAGGAAGA
387969 AGAGGAAGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 22 0.96
19 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.45, T:0.05
Consensus pattern (18 bp):
GAGGAAGAGGAAGAAGAA
Found at i:387949 original size:9 final size:9
Alignment explanation
Indices: 387937--387977 Score: 64
Period size: 9 Copynumber: 4.6 Consensus size: 9
387927 GGAAGGTGAA
387937 GAAGAAGAG
1 GAAGAAGAG
*
387946 GAAGAGGAG
1 GAAGAAGAG
*
387955 GAAGAAGAT
1 GAAGAAGAG
387964 GAAGAAGAG
1 GAAGAAGAG
387973 GAAGA
1 GAAGA
387978 GCTTCAGCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.54, C:0.00, G:0.44, T:0.02
Consensus pattern (9 bp):
GAAGAAGAG
Found at i:389732 original size:9 final size:9
Alignment explanation
Indices: 389718--389765 Score: 51
Period size: 9 Copynumber: 5.1 Consensus size: 9
389708 CTAGATTTTT
389718 TTTTTATAA
1 TTTTTATAA
*
389727 TTTTTAAAA
1 TTTTTATAA
*
389736 TTTTTAAAA
1 TTTTTATAA
389745 TTTTTAATGAA
1 TTTTT-AT-AA
*
389756 ATTTTATAA
1 TTTTTATAA
389765 T
1 T
389766 ATACTCATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
9 24 0.73
10 3 0.09
11 6 0.18
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (9 bp):
TTTTTATAA
Found at i:389739 original size:8 final size:9
Alignment explanation
Indices: 389718--389751 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
389708 CTAGATTTTT
*
389718 TTTTTATAA
1 TTTTTAAAA
389727 TTTTTAAAA
1 TTTTTAAAA
389736 TTTTTAAAA
1 TTTTTAAAA
389745 TTTTTAA
1 TTTTTAA
389752 TGAAATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:389741 original size:18 final size:19
Alignment explanation
Indices: 389718--389765 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
389708 CTAGATTTTT
389718 TTTTTATAATTTTTAA-AA
1 TTTTTATAATTTTTAAGAA
*
389736 TTTTTAAAATTTTTAATGAA
1 TTTTTATAATTTTTAA-GAA
*
389756 ATTTTATAAT
1 TTTTTATAAT
389766 ATACTCATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 15 0.60
20 10 0.40
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
TTTTTATAATTTTTAAGAA
Found at i:402287 original size:20 final size:19
Alignment explanation
Indices: 402260--402298 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
402250 TCTAATATAC
402260 ATAAAAAATTAT-TTTTTAT
1 ATAAAAAA-TATGTTTTTAT
402279 ATAATAAAATATGTTTTTAT
1 ATAA-AAAATATGTTTTTAT
402299 GTATTTGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (19 bp):
ATAAAAAATATGTTTTTAT
Found at i:417787 original size:1 final size:1
Alignment explanation
Indices: 417739--417767 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
417729 TCACATTCAG
417739 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAA
417768 NNNNNNNNNN
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:418171 original size:5 final size:5
Alignment explanation
Indices: 418163--418187 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
418153 AACTAAACAT
418163 ACCGC ACCGC ACCGC ACCGC ACCGC
1 ACCGC ACCGC ACCGC ACCGC ACCGC
418188 CATTCCAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.60, G:0.20, T:0.00
Consensus pattern (5 bp):
ACCGC
Found at i:420352 original size:23 final size:23
Alignment explanation
Indices: 420319--420442 Score: 128
Period size: 23 Copynumber: 5.3 Consensus size: 23
420309 GCTGGGCAAT
420319 AGAGAGCACACACAGTGCTAAAC
1 AGAGAGCACACACAGTGCTAAAC
* * *
420342 AGAGAGTACACAAAGTACTAATA-
1 AGAGAGCACACACAGTGCTAA-AC
*
420365 AGAGAGCACACA-ATGTGCTAATC
1 AGAGAGCACACACA-GTGCTAAAC
420388 AGAGAGCACACACAGTGCTAATAAC
1 AGAGAGCACACACAGTGCT-A-AAC
*
420413 AGAGAGCACGAGAC-GTGCTAAAC
1 AGAGAGCAC-ACACAGTGCTAAAC
*
420436 ATAGAGC
1 AGAGAGC
420443 GCGCTAGTGT
Statistics
Matches: 85, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
22 1 0.01
23 61 0.72
24 4 0.05
25 16 0.19
26 3 0.04
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.13
Consensus pattern (23 bp):
AGAGAGCACACACAGTGCTAAAC
Found at i:420368 original size:69 final size:69
Alignment explanation
Indices: 420270--420418 Score: 191
Period size: 69 Copynumber: 2.1 Consensus size: 69
420260 TATACGGAAC
*
420270 AAACAGAGAGTACCAAAGTACTAAC-A-AGAGCACATAA-GTGCTGGGCAAT-AGAGAGCACACA
1 AAACAGAGAGTACCAAAGTACTAACAAGAGAGCACACAATGTGCT----AATCAGAGAGCACACA
420331 CAGTGCT-
62 CAGTGCTA
*
420338 AAACAGAGAGTACACAAAGTACTAATAAGAGAGCACACAATGTGCTAATCAGAGAGCACACACAG
1 AAACAGAGAGTAC-CAAAGTACTAACAAGAGAGCACACAATGTGCTAATCAGAGAGCACACACAG
420403 TGCTA
65 TGCTA
420408 ATAACAGAGAG
1 A-AACAGAGAG
420419 CACGAGACGT
Statistics
Matches: 72, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
68 16 0.22
69 30 0.42
70 2 0.03
71 19 0.26
72 5 0.07
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.13
Consensus pattern (69 bp):
AAACAGAGAGTACCAAAGTACTAACAAGAGAGCACACAATGTGCTAATCAGAGAGCACACACAGT
GCTA
Found at i:420391 original size:46 final size:48
Alignment explanation
Indices: 420319--420442 Score: 148
Period size: 46 Copynumber: 2.6 Consensus size: 48
420309 GCTGGGCAAT
*
420319 AGAGAGCACACACAGTGCTAAACAGAGAGTACACAAAGTACTAAT-A-
1 AGAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTACTAATAAC
* * *
420365 AGAGAGCACACA-ATGTGCTAATCAGAGAGCACACACAGTGCTAATAAC
1 AGAGAGCACACACA-GTGCTAAACAGAGAGCACACAAAGTACTAATAAC
* *
420413 AGAGAGCACGAGAC-GTGCTAAACATAGAGC
1 AGAGAGCAC-ACACAGTGCTAAACAGAGAGC
420443 GCGCTAGTGT
Statistics
Matches: 66, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
45 1 0.02
46 39 0.59
47 1 0.02
48 23 0.35
49 2 0.03
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.13
Consensus pattern (48 bp):
AGAGAGCACACACAGTGCTAAACAGAGAGCACACAAAGTACTAATAAC
Found at i:423495 original size:20 final size:19
Alignment explanation
Indices: 423450--423506 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 19
423440 ACATTCTTTT
423450 TAATATAATATAAAAGT-TAA
1 TAAT-TAATATAAAA-TATAA
423470 TAAATTAATATAAAATATAAA
1 T-AATTAATATAAAATAT-AA
*
423491 TAATT-ATATTAAATAT
1 TAATTAATATAAAATAT
423507 TGAATATTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
19 11 0.33
20 16 0.48
21 6 0.18
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (19 bp):
TAATTAATATAAAATATAA
Found at i:426334 original size:16 final size:16
Alignment explanation
Indices: 426288--426336 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
426278 AAATTTCAAT
426288 AAATAA-AAAGTATATA
1 AAATAATAAAGTAT-TA
* *
426304 AAATTATAAAATATTA
1 AAATAATAAAGTATTA
*
426320 AAATAATATAGTATTA
1 AAATAATAAAGTATTA
426336 A
1 A
426337 TTTTTTTAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 21 0.78
17 6 0.22
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (16 bp):
AAATAATAAAGTATTA
Found at i:436019 original size:15 final size:14
Alignment explanation
Indices: 435994--436030 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
435984 ATTTAATAAT
435994 TATTAAAAATAAAA
1 TATTAAAAATAAAA
436008 TATTATAAAATAAAA
1 TATTA-AAAATAAAA
*
436023 AATTAAAA
1 TATTAAAA
436031 TATCCAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
TATTAAAAATAAAA
Found at i:437390 original size:15 final size:15
Alignment explanation
Indices: 437354--437394 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
437344 AAATATATCT
*
437354 AATACT-TAAACT-A
1 AATACTATAAAATAA
437367 AATACTATAAAATAA
1 AATACTATAAAATAA
*
437382 AATATTATAAAAT
1 AATACTATAAAAT
437395 TAAGCTCCTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 6 0.25
14 5 0.21
15 13 0.54
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (15 bp):
AATACTATAAAATAA
Found at i:444926 original size:19 final size:19
Alignment explanation
Indices: 444875--444929 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 19
444865 AATTTATAAA
*
444875 TAATAACAAATAATAAATTT
1 TAATAA-AAATATTAAATTT
**
444895 TAGA-AAATTTATTAAATTT
1 TA-ATAAAAATATTAAATTT
444914 TAATAAAAATATTAAA
1 TAATAAAAATATTAAA
444930 AATAAAAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
18 1 0.04
19 22 0.79
20 4 0.14
21 1 0.04
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (19 bp):
TAATAAAAATATTAAATTT
Found at i:445230 original size:39 final size:38
Alignment explanation
Indices: 445145--445241 Score: 90
Period size: 39 Copynumber: 2.5 Consensus size: 38
445135 TTTTGGTACG
* *
445145 ATAATTTTTATAATTTTTTTTACGAAATTTATATTTTT
1 ATAATTTTTATAATTTTTCTTACGAAATTTATAATTTT
* *
445183 TTACATTTTGTATAA-TTTTCTTACG-ACTTTATAAAATTTT
1 ATA-ATTTT-TATAATTTTTCTTACGAAATTTAT--AATTTT
*
445223 ATAATTTTTTTATATTTTT
1 ATAATTTTTATA-ATTTTT
445242 ATATATTTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
38 11 0.23
39 20 0.43
40 16 0.34
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (38 bp):
ATAATTTTTATAATTTTTCTTACGAAATTTATAATTTT
Found at i:445250 original size:18 final size:17
Alignment explanation
Indices: 445219--445275 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 17
445209 CTTTATAAAA
445219 TTTTATAATTTTTTTATAT
1 TTTTAT-ATTTTTTTA-AT
*
445238 TTTTATATATTTTTACGA-
1 TTTTATATTTTTTTA--AT
445256 TTTTATATTTTTTTAAT
1 TTTTATATTTTTTTAAT
445273 TTT
1 TTT
445276 AATAAATTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
16 1 0.03
17 3 0.09
18 22 0.67
19 7 0.21
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (17 bp):
TTTTATATTTTTTTAAT
Found at i:445252 original size:10 final size:10
Alignment explanation
Indices: 445219--445252 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
445209 CTTTATAAAA
445219 TTTTATA-AT
1 TTTTATATAT
*
445228 TTTTTTATAT
1 TTTTATATAT
445238 TTTTATATAT
1 TTTTATATAT
445248 TTTTA
1 TTTTA
445253 CGATTTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 6 0.27
10 16 0.73
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTTATATAT
Found at i:445301 original size:35 final size:36
Alignment explanation
Indices: 445220--445303 Score: 89
Period size: 35 Copynumber: 2.4 Consensus size: 36
445210 TTTATAAAAT
* * * * *
445220 TTTATAATTTTTTTATATTTTTATATATTTTTACGA
1 TTTAAAATTTTTTTATATTTTAATAAATTTGTAAGA
* * *
445256 TTTTATATTTTTTTA-ATTTTAATAAATTTGTAATA
1 TTTAAAATTTTTTTATATTTTAATAAATTTGTAAGA
445291 TTTAAAATTTTTT
1 TTTAAAATTTTTT
445304 ATTAAAATTT
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
35 26 0.68
36 12 0.32
ACGTcount: A:0.31, C:0.01, G:0.02, T:0.65
Consensus pattern (36 bp):
TTTAAAATTTTTTTATATTTTAATAAATTTGTAAGA
Found at i:447650 original size:2 final size:2
Alignment explanation
Indices: 447643--447676 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
447633 TTCGAATGAA
447643 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
447677 TATTGTTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.