Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 93 of 135
Found at i:31402789 original size:36 final size:36
Alignment explanation
Indices: 31402741--31402813 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
31402731 TAAGAAATAG
* *
31402741 TGATTAATTAAAGGTAGAAGTTTTAATTTTTTTTTC
1 TGATTAACTAAAGGTAGAAGTTTTAATATTTTTTTC
31402777 TGATTAACTAAAGGTAGAAGTTTTAATATTTTTTTC
1 TGATTAACTAAAGGTAGAAGTTTTAATATTTTTTTC
31402813 T
1 T
31402814 TTAACATTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.32, C:0.04, G:0.14, T:0.51
Consensus pattern (36 bp):
TGATTAACTAAAGGTAGAAGTTTTAATATTTTTTTC
Found at i:31406947 original size:26 final size:26
Alignment explanation
Indices: 31406914--31407019 Score: 142
Period size: 26 Copynumber: 4.1 Consensus size: 26
31406904 TCTTAAACTT
* *
31406914 TAAACATAATTTAGTAAATACAAACA
1 TAAACATAATTAATTAAATACAAACA
*
31406940 TAAACATAATTAATGAAATACAAACA
1 TAAACATAATTAATTAAATACAAACA
*
31406966 -AAGACATAATTAATTAAATAAAAACA
1 TAA-ACATAATTAATTAAATACAAACA
* *
31406992 TAAATATAATTAATTAAATACAAGCA
1 TAAACATAATTAATTAAATACAAACA
31407018 TA
1 TA
31407020 CGTCGAGTTT
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
25 2 0.03
26 66 0.94
27 2 0.03
ACGTcount: A:0.60, C:0.09, G:0.04, T:0.26
Consensus pattern (26 bp):
TAAACATAATTAATTAAATACAAACA
Found at i:31407003 original size:22 final size:20
Alignment explanation
Indices: 31406969--31407009 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
31406959 ACAAACAAAG
31406969 ACATAATTAATTAAATAAAA
1 ACATAATTAATTAAATAAAA
*
31406989 ACATAAATATAATTAATTAAA
1 ACAT-AAT-TAATTAAATAAA
31407010 TACAAGCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 3 0.17
22 11 0.61
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (20 bp):
ACATAATTAATTAAATAAAA
Found at i:31407535 original size:18 final size:19
Alignment explanation
Indices: 31407494--31407535 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
31407484 GAGTTGAGGT
* *
31407494 TCGGGCTTAAGCTCGAGCG
1 TCGGGCTCAAACTCGAGCG
31407513 T-GGGCTCAAACTCGAGC-
1 TCGGGCTCAAACTCGAGCG
31407530 TCGGGC
1 TCGGGC
31407536 GGATGAGAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 1 0.05
18 18 0.90
19 1 0.05
ACGTcount: A:0.17, C:0.29, G:0.36, T:0.19
Consensus pattern (19 bp):
TCGGGCTCAAACTCGAGCG
Found at i:31409347 original size:17 final size:17
Alignment explanation
Indices: 31409325--31409357 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
31409315 TATTTTAAAA
31409325 TATTTT-AATAAAATTAT
1 TATTTTCAA-AAAATTAT
31409342 TATTTTCAAAAAATTA
1 TATTTTCAAAAAATTA
31409358 AAAAGTCATC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (17 bp):
TATTTTCAAAAAATTAT
Found at i:31427796 original size:24 final size:24
Alignment explanation
Indices: 31427735--31427797 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
31427725 AATCTAGACT
* *
31427735 AATAAGAGTTTGACTCAAACAAATA
1 AATAA-AGTTTAATTCAAACAAATA
* *
31427760 AACAGAGTTTAATTCAAACAAATA
1 AATAAAGTTTAATTCAAACAAATA
31427784 AATAAAGTTTAATT
1 AATAAAGTTTAATT
31427798 GAAAGATTAT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
24 29 0.91
25 3 0.09
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.29
Consensus pattern (24 bp):
AATAAAGTTTAATTCAAACAAATA
Found at i:31431741 original size:18 final size:17
Alignment explanation
Indices: 31431703--31431750 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
31431693 TGAAATGATT
*
31431703 AAATAAAAAAGG-AGGG
1 AAATAAAAAAGGAAGGA
*
31431719 TAATAATAAAAGGAAGGA
1 AAATAA-AAAAGGAAGGA
31431737 AAATAGAAAAAGGA
1 AAATA-AAAAAGGA
31431751 GAAAAAAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 5 0.19
17 6 0.23
18 14 0.54
19 1 0.04
ACGTcount: A:0.65, C:0.00, G:0.25, T:0.10
Consensus pattern (17 bp):
AAATAAAAAAGGAAGGA
Found at i:31433577 original size:12 final size:12
Alignment explanation
Indices: 31433557--31433589 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
31433547 CTGCAGGGTT
*
31433557 CACAGGGGCTGA
1 CACACGGGCTGA
31433569 CACACGGGCTGA
1 CACACGGGCTGA
31433581 CACACGGGC
1 CACACGGGC
31433590 AGGCACATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.24, C:0.33, G:0.36, T:0.06
Consensus pattern (12 bp):
CACACGGGCTGA
Found at i:31437749 original size:3 final size:3
Alignment explanation
Indices: 31437741--31437775 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
31437731 ATTCGATCTT
31437741 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
31437776 TTAAAAGATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:31438730 original size:25 final size:24
Alignment explanation
Indices: 31438696--31438746 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
31438686 ATATATTTTT
31438696 TAAAATTTATTTTCAAT-TTGTTAG
1 TAAAATTTATTTT-AATGTTGTTAG
*
31438720 TAAATATTTATTTTAATGTTTTTAG
1 TAAA-ATTTATTTTAATGTTGTTAG
31438745 TA
1 TA
31438747 TTTTTAATGC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.57
Consensus pattern (24 bp):
TAAAATTTATTTTAATGTTGTTAG
Found at i:31439091 original size:16 final size:16
Alignment explanation
Indices: 31439067--31439113 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
31439057 GGGGAATGTG
*
31439067 TAAAAAAACAT-AAATA
1 TAAATAAACATGAAA-A
31439083 TAAATAAACATGAAAA
1 TAAATAAACATGAAAA
*
31439099 TAAATAAAGATGAAA
1 TAAATAAACATGAAA
31439114 TAAGAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
16 25 0.89
17 3 0.11
ACGTcount: A:0.70, C:0.04, G:0.06, T:0.19
Consensus pattern (16 bp):
TAAATAAACATGAAAA
Found at i:31439921 original size:148 final size:148
Alignment explanation
Indices: 31439671--31440029 Score: 548
Period size: 147 Copynumber: 2.4 Consensus size: 148
31439661 CAAAATCAAA
31439671 TTTTTTTTAAACAAAATCACTACTTTTCTTAAAAATAAAAGTTTTTATTTCGAAAT-GTTAAAAA
1 TTTTTTTTAAA-AAAATCACTACTTTTCTTAAAAATAAAAGTTTTTATTTCGAAATAGTTAAAAA
* *
31439735 AAATCAAATTTTGTTTAAAAATTTAAACTTTTCTCTTTAAAATGACT-AAAAACATATTTTTATT
65 AAATCAAACTTTGTTTAAAAATTTAAACTTTTCCCTTTAAAATGACTAAAAAACATATTTTTATT
* *
31439799 TTT-AAAATCTAAATTTTC
130 TTTAAAAATCAAAACTTTC
* *
31439817 TTTTTTTCTTAAAAAAATCACTACTTTTCTTAAAAATCAAAGTTTTTATTTTGAAATAGTTAAAA
1 -TTTTTT-TTAAAAAAATCACTACTTTTCTTAAAAATAAAAGTTTTTATTTCGAAATAGTTAAAA
* *
31439882 AAAATCAAACTTTGTTTAAAAATTTAAACTTTTCCCTTTAAAATTACTAAAAAAACCTATTTTTA
64 AAAATCAAACTTTGTTTAAAAATTTAAACTTTTCCCTTTAAAATGACT-AAAAAACATATTTTTA
31439947 TTTTTAAAAATCAAAACTTTC
128 TTTTTAAAAATCAAAACTTTC
* * *
31439968 --TTTTTAAAAAAAATCACTGCTTTTCTTAAAAATAAAAATTTTTATTTCGAAATAGTTAAAAA
1 TTTTTTTTAAAAAAATCACTACTTTTCTTAAAAATAAAAGTTTTTATTTCGAAATAGTTAAAAA
31440030 CTTTAAACTT
Statistics
Matches: 194, Mismatches: 13, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
147 101 0.52
148 61 0.31
150 19 0.10
151 13 0.07
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.43
Consensus pattern (148 bp):
TTTTTTTTAAAAAAATCACTACTTTTCTTAAAAATAAAAGTTTTTATTTCGAAATAGTTAAAAAA
AATCAAACTTTGTTTAAAAATTTAAACTTTTCCCTTTAAAATGACTAAAAAACATATTTTTATTT
TTAAAAATCAAAACTTTC
Found at i:31440275 original size:51 final size:51
Alignment explanation
Indices: 31440219--31440320 Score: 116
Period size: 52 Copynumber: 2.0 Consensus size: 51
31440209 TACTTTTCTT
* * *
31440219 AAAAATAAAAACTTTTAT-TTCGAAATAATTAAAAAATCAAAATTTTATTTA
1 AAAAATAAAAACTTTT-TCTTCAAAATAACTAAAAAAACAAAATTTTATTTA
** * *
31440270 AAAAATTTAAACTTTTTCCTTTAAAATAACTAAAAAAACAAATTTTTATTT
1 AAAAATAAAAACTTTTT-CTTCAAAATAACTAAAAAAACAAAATTTTATTT
31440321 TTAAAAATTT
Statistics
Matches: 42, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
50 1 0.02
51 14 0.33
52 27 0.64
ACGTcount: A:0.52, C:0.08, G:0.01, T:0.39
Consensus pattern (51 bp):
AAAAATAAAAACTTTTTCTTCAAAATAACTAAAAAAACAAAATTTTATTTA
Found at i:31443645 original size:14 final size:14
Alignment explanation
Indices: 31443626--31443663 Score: 67
Period size: 14 Copynumber: 2.6 Consensus size: 14
31443616 TCAATAAAGT
31443626 ATTATTTTTATTAA
1 ATTATTTTTATTAA
31443640 ATTATTTTTATTAA
1 ATTATTTTTATTAA
31443654 ATTATATTTT
1 ATTAT-TTTT
31443664 GAATTGAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 19 0.83
15 4 0.17
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
ATTATTTTTATTAA
Found at i:31443691 original size:33 final size:34
Alignment explanation
Indices: 31443635--31443713 Score: 94
Period size: 33 Copynumber: 2.4 Consensus size: 34
31443625 TATTATTTTT
*
31443635 ATTAAA-TT-ATTTTTATTAAATTATATTT-TGA
1 ATTAAATTTAATTTTTATCAAATTATATTTGTGA
* *
31443666 ATTGAACTTTAATTTTTA-CAAATTATATTTGTGT
1 ATT-AAATTTAATTTTTATCAAATTATATTTGTGA
31443700 ATTAAATTTAATTT
1 ATTAAATTTAATTT
31443714 CCTTTTAGTT
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
31 3 0.08
32 2 0.05
33 23 0.57
34 12 0.30
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.56
Consensus pattern (34 bp):
ATTAAATTTAATTTTTATCAAATTATATTTGTGA
Found at i:31445258 original size:21 final size:21
Alignment explanation
Indices: 31445234--31445283 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
31445224 GATCAAATTA
*
31445234 ATTTATATTTTATATATCATT
1 ATTTAAATTTTATATATCATT
31445255 ATTTAAATTTTAT-T-T-ATT
1 ATTTAAATTTTATATATCATT
31445273 A-TTAAATTTTA
1 ATTTAAATTTTA
31445284 AATTTTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 10 0.36
18 4 0.14
19 1 0.04
20 1 0.04
21 12 0.43
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (21 bp):
ATTTAAATTTTATATATCATT
Found at i:31445430 original size:3 final size:3
Alignment explanation
Indices: 31445422--31445446 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
31445412 TTTTTAATTG
31445422 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
31445447 TAATACATCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:31446557 original size:28 final size:29
Alignment explanation
Indices: 31446521--31446576 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
31446511 TTCTTTAAAC
31446521 TATCTTTGTAGTTTCATTTTTCATTTTTT
1 TATCTTTGTAGTTTCATTTTTCATTTTTT
* * *
31446550 TATC-TTGTATTTTTATTTTTTATTTTT
1 TATCTTTGTAGTTTCATTTTTCATTTTT
31446577 ATAAAATTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 20 0.83
29 4 0.17
ACGTcount: A:0.14, C:0.07, G:0.05, T:0.73
Consensus pattern (29 bp):
TATCTTTGTAGTTTCATTTTTCATTTTTT
Found at i:31459470 original size:4 final size:4
Alignment explanation
Indices: 31459461--31459540 Score: 81
Period size: 4 Copynumber: 20.2 Consensus size: 4
31459451 GCCATGCTTG
* * * *
31459461 GTAT GTAT GTAT GTAT GTAT GTAT GTTT GTAC GTAC GTAT GT-T TTAT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT
* * * *
31459508 GTAT GTAT GTAT GTGT GTGT GTGT GCAT GTAT G
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT G
31459541 ATGCATGATA
Statistics
Matches: 65, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
3 2 0.03
4 63 0.97
ACGTcount: A:0.19, C:0.04, G:0.29, T:0.49
Consensus pattern (4 bp):
GTAT
Found at i:31477431 original size:123 final size:124
Alignment explanation
Indices: 31477213--31477452 Score: 322
Period size: 123 Copynumber: 1.9 Consensus size: 124
31477203 GGACGTTTTG
* * *
31477213 AAGAGAATATTCTATCGCATGAATTATACGAAAATTACACCCAACACGTTAGGGCATGGTATTTC
1 AAGAGAATATTCTACCGCATGAATTATACGAAAATCACACCCAACACGTTAGGACATGGTATTTC
* * *
31477278 GAGGTCTTTACATGAAAGGACGTCGCCTCGTTTTATTTTAAAATCATTTGTAATCTTTA
66 GAGGTCTTTACACGAAAGGACATCGCCTCGTTTTACTTTAAAATCATTTGTAATCTTTA
* * * *
31477337 AAGAGGATATTCTACCGTATGAATTATACGAAAATCACA-CCAGCACGTTAGGACATGGTTTTTC
1 AAGAGAATATTCTACCGCATGAATTATACGAAAATCACACCCAACACGTTAGGACATGGTATTTC
* * * * *
31477401 TAGGT-TTTCACACGAAAGGATATTGCCTCGTTTTGCTTTAAAATCTTTTGTA
66 GAGGTCTTT-ACACGAAAGGACATCGCCTCGTTTTACTTTAAAATCATTTGTA
31477453 TATAAAGATA
Statistics
Matches: 100, Mismatches: 15, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
122 3 0.03
123 62 0.62
124 35 0.35
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Consensus pattern (124 bp):
AAGAGAATATTCTACCGCATGAATTATACGAAAATCACACCCAACACGTTAGGACATGGTATTTC
GAGGTCTTTACACGAAAGGACATCGCCTCGTTTTACTTTAAAATCATTTGTAATCTTTA
Found at i:31478114 original size:29 final size:29
Alignment explanation
Indices: 31478082--31478448 Score: 313
Period size: 29 Copynumber: 12.4 Consensus size: 29
31478072 AAAAGTAAAG
* *
31478082 TTTTTGGATGTTCGGGGGT-AAAATGGTAA
1 TTTTTGGAAGTTTGGGGGTAAAAAT-GTAA
** * * *
31478111 TTTTTAAAAGTTTTGGGGTTAAAATGTAC
1 TTTTTGGAAGTTTGGGGGTAAAAATGTAA
* * *
31478140 TTTTTGAAAGTTTGGGGGCAAAACTGTAA
1 TTTTTGGAAGTTTGGGGGTAAAAATGTAA
** ** *
31478169 TTTTTGGAAGTTTTAGGGCCAAAATGGAA
1 TTTTTGGAAGTTTGGGGGTAAAAATGTAA
* * * * *
31478198 TTTTTTGAAGTTCGAGGTTAAAAAATGGAA
1 TTTTTGGAAGTTTGGGGGT-AAAAATGTAA
*
31478228 TTTTTGGAAGTTTAGGGGTAAAAATGTAA
1 TTTTTGGAAGTTTGGGGGTAAAAATGTAA
* ** * *
31478257 TGTTTGGAAGTTTTAGGGTTAAAATGGAA
1 TTTTTGGAAGTTTGGGGGTAAAAATGTAA
* * * *
31478286 ATTTTGAAAGTTTGAGGGTAAAAATGTAG
1 TTTTTGGAAGTTTGGGGGTAAAAATGTAA
* *
31478315 TTTTTGGAAGTTTTGGGGTTAAAAATGGAA
1 TTTTTGGAAG-TTTGGGGGTAAAAATGTAA
*
31478345 TTTTTGGAAGTTTGAGGGTAAAAAATGTAA
1 TTTTTGGAAGTTTGGGGGT-AAAAATGTAA
** *
31478375 TTTTTGGAAGTTTTAAGGTTAAAAATGTAA
1 TTTTTGGAAG-TTTGGGGGTAAAAATGTAA
* * *
31478405 TTTTAGAGAAGTTTGAGGGTTAAAATGTAA
1 TTTTTG-GAAGTTTGGGGGTAAAAATGTAA
31478435 TTTTTGGATAGTTT
1 TTTTTGGA-AGTTT
31478449 AGGGACTTAT
Statistics
Matches: 273, Mismatches: 58, Indels: 13
0.79 0.17 0.04
Matches are distributed among these distances:
29 149 0.55
30 113 0.41
31 11 0.04
ACGTcount: A:0.32, C:0.02, G:0.27, T:0.39
Consensus pattern (29 bp):
TTTTTGGAAGTTTGGGGGTAAAAATGTAA
Found at i:31478136 original size:30 final size:29
Alignment explanation
Indices: 31478082--31478448 Score: 305
Period size: 30 Copynumber: 12.4 Consensus size: 29
31478072 AAAAGTAAAG
* * *
31478082 TTTTTGGATG-TTCGGGGGTAAAATGGTAA
1 TTTTTGGAAGTTTTGGGGTTAAAAT-GTAA
** *
31478111 TTTTTAAAAGTTTTGGGGTTAAAATGTAC
1 TTTTTGGAAGTTTTGGGGTTAAAATGTAA
* **
31478140 TTTTTGAAAG-TTTGGGGGCAAAACTGTAA
1 TTTTTGGAAGTTTTGGGGTTAAAA-TGTAA
* ** *
31478169 TTTTTGGAAGTTTTAGGGCCAAAATGGAA
1 TTTTTGGAAGTTTTGGGGTTAAAATGTAA
* * * *
31478198 TTTTTTGAAG-TTCGAGGTTAAAAAATGGAA
1 TTTTTGGAAGTTTTGGGGTT--AAAATGTAA
* *
31478228 TTTTTGGAAGTTTAGGGGTAAAAATGTAA
1 TTTTTGGAAGTTTTGGGGTTAAAATGTAA
* * *
31478257 TGTTTGGAAGTTTTAGGGTTAAAATGGAA
1 TTTTTGGAAGTTTTGGGGTTAAAATGTAA
* * * *
31478286 ATTTTGAAAG-TTTGAGGGTAAAAATGTAG
1 TTTTTGGAAGTTTTG-GGGTTAAAATGTAA
*
31478315 TTTTTGGAAGTTTTGGGGTTAAAAATGGAA
1 TTTTTGGAAGTTTTGGGGTT-AAAATGTAA
*
31478345 TTTTTGGAAG-TTTGAGGGTAAAAAATGTAA
1 TTTTTGGAAGTTTTG-GGGT-TAAAATGTAA
**
31478375 TTTTTGGAAGTTTTAAGGTTAAAAATGTAA
1 TTTTTGGAAGTTTTGGGGTT-AAAATGTAA
*
31478405 TTTTAGAGAAG-TTTGAGGGTTAAAATGTAA
1 TTTTTG-GAAGTTTTG-GGGTTAAAATGTAA
31478435 TTTTTGGATAGTTT
1 TTTTTGGA-AGTTT
31478449 AGGGACTTAT
Statistics
Matches: 270, Mismatches: 51, Indels: 32
0.76 0.14 0.09
Matches are distributed among these distances:
28 18 0.07
29 113 0.42
30 120 0.44
31 19 0.07
ACGTcount: A:0.32, C:0.02, G:0.27, T:0.39
Consensus pattern (29 bp):
TTTTTGGAAGTTTTGGGGTTAAAATGTAA
Found at i:31478236 original size:59 final size:59
Alignment explanation
Indices: 31478101--31478448 Score: 357
Period size: 58 Copynumber: 5.9 Consensus size: 59
31478091 GTTCGGGGGT
** * * * * **
31478101 AAAATGGTAATTTTTAAAAGTTTTG-GGGTTAAAATGTACTTTTTGAAAG-TTTGGGGGCA
1 AAAATGG-AATTTTTGGAAG-TTTGAGGGTAAAAATGTAATTTTTGGAAGTTTTGAGGTTA
* * * ** * * *
31478160 AAACTGTAATTTTTGGAAGTTTTAGGGCCAAAATGGAATTTTTTGAAG-TTCGAGGTTAA
1 AAAATGGAATTTTTGGAAGTTTGAGGGTAAAAATGTAATTTTTGGAAGTTTTGAGGTT-A
*
31478219 AAAATGGAATTTTTGGAAGTTT-AGGGGTAAAAATGTAATGTTTGGAAGTTTT-AGGGTT-
1 AAAATGGAATTTTTGGAAGTTTGA-GGGTAAAAATGTAATTTTTGGAAGTTTTGA-GGTTA
* * * *
31478277 AAAATGGAAATTTTGAAAGTTTGAGGGTAAAAATGTAGTTTTTGGAAGTTTTGGGGTTA
1 AAAATGGAATTTTTGGAAGTTTGAGGGTAAAAATGTAATTTTTGGAAGTTTTGAGGTTA
*
31478336 AAAATGGAATTTTTGGAAGTTTGAGGGTAAAAAATGTAATTTTTGGAAGTTTTAAGGTTA
1 AAAATGGAATTTTTGGAAGTTTGAGGGT-AAAAATGTAATTTTTGGAAGTTTTGAGGTTA
* * *
31478396 AAAATGTAATTTTAGAGAAGTTTGAGGGTTAAAATGTAATTTTTGGATAGTTT
1 AAAATGGAATTTTTG-GAAGTTTGAGGGTAAAAATGTAATTTTTGGA-AGTTT
31478449 AGGGACTTAT
Statistics
Matches: 242, Mismatches: 36, Indels: 20
0.81 0.12 0.07
Matches are distributed among these distances:
57 3 0.01
58 84 0.35
59 73 0.30
60 64 0.26
61 18 0.07
ACGTcount: A:0.34, C:0.02, G:0.26, T:0.39
Consensus pattern (59 bp):
AAAATGGAATTTTTGGAAGTTTGAGGGTAAAAATGTAATTTTTGGAAGTTTTGAGGTTA
Found at i:31478239 original size:88 final size:87
Alignment explanation
Indices: 31478101--31478453 Score: 361
Period size: 88 Copynumber: 4.0 Consensus size: 87
31478091 GTTCGGGGGT
** * * * * *
31478101 AAAATGGTAATTTTTAAAAGTTTTGGGGTT-AAAATGTACTTTTTGAAAGTTTGGGGGCAAAACT
1 AAAATGG-AATTTTTTGAAG-TTTGAGGTTAAAAATGTAATTTTTGGAAGTTTGGGGGTAAAAAT
**
31478165 GTAATTTTTGGAAGTTTTAGGGCC
64 GTAATTTTTGGAAGTTTTAGGGAA
* * *
31478189 AAAATGGAATTTTTTGAAGTTCGAGGTTAAAAAATGGAATTTTTGGAAGTTTAGGGGTAAAAATG
1 AAAATGGAATTTTTTGAAGTTTGAGGTT-AAAAATGTAATTTTTGGAAGTTTGGGGGTAAAAATG
* **
31478254 TAATGTTTGGAAGTTTTAGGGTT
65 TAATTTTTGGAAGTTTTAGGGAA
* * * *
31478277 AAAATGGAA-ATTTTGAAAGTTTGAGGGTAAAAATGTAGTTTTTGGAAGTTTTGGGGTTAAAAAT
1 AAAATGGAATTTTTTG-AAGTTTGAGGTTAAAAATGTAATTTTTGGAAG-TTTGGGGGTAAAAAT
* *
31478341 GGAATTTTTGGAAGTTTGAGGGTAA
64 GTAATTTTTGGAAGTTTTAGGG-AA
* * * * * *
31478366 AAAATGTAATTTTTGGAAGTTTTAAGGTTAAAAATGTAATTTTAGAGAAGTTTGAGGGTTAAAAT
1 AAAATGGAATTTTTTGAAG-TTTGAGGTTAAAAATGTAATTTTTG-GAAGTTTGGGGGTAAAAAT
31478431 GTAATTTTTGGATAG-TTTAGGGA
64 GTAATTTTTGGA-AGTTTTAGGGA
31478454 CTTATAGAGC
Statistics
Matches: 219, Mismatches: 37, Indels: 17
0.80 0.14 0.06
Matches are distributed among these distances:
86 7 0.03
87 33 0.15
88 107 0.49
89 12 0.05
90 54 0.25
91 6 0.03
ACGTcount: A:0.34, C:0.02, G:0.26, T:0.38
Consensus pattern (87 bp):
AAAATGGAATTTTTTGAAGTTTGAGGTTAAAAATGTAATTTTTGGAAGTTTGGGGGTAAAAATGT
AATTTTTGGAAGTTTTAGGGAA
Found at i:31479593 original size:34 final size:34
Alignment explanation
Indices: 31479520--31479584 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
31479510 TGACCTTTCG
31479520 ATTT-TTTATTACTAAAAATTATTATAAAAAAAT
1 ATTTATTTATTACTAAAAATTATTATAAAAAAAT
** *
31479553 ATTTATTTATTACTATTAATTATTATTAAAAA
1 ATTTATTTATTACTAAAAATTATTATAAAAAA
31479585 TTTATTATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 4 0.14
34 24 0.86
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (34 bp):
ATTTATTTATTACTAAAAATTATTATAAAAAAAT
Found at i:31480315 original size:6 final size:6
Alignment explanation
Indices: 31480306--31480394 Score: 80
Period size: 6 Copynumber: 14.8 Consensus size: 6
31480296 TTAATATTAT
* *
31480306 TTTAAA TTT-AA -TTAAA TTTAAA TTTAAA -GTAAA TTTAAA TTGGTGAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT--TAAA
31480353 TTTAAA TTTAAGA --TAAA TTTAAA TTTAAAA TTTAAA CTTTAA
1 TTTAAA TTTAA-A TTTAAA TTTAAA TTT-AAA TTTAAA -TTTAA
31480395 TTAAAATTAA
Statistics
Matches: 69, Mismatches: 4, Indels: 19
0.75 0.04 0.21
Matches are distributed among these distances:
4 3 0.04
5 11 0.16
6 38 0.55
7 12 0.17
8 5 0.07
ACGTcount: A:0.48, C:0.01, G:0.06, T:0.45
Consensus pattern (6 bp):
TTTAAA
Found at i:31480324 original size:17 final size:17
Alignment explanation
Indices: 31480306--31480381 Score: 81
Period size: 17 Copynumber: 4.7 Consensus size: 17
31480296 TTAATATTAT
*
31480306 TTTAAATTT-AATTAAA
1 TTTAAATTTAAAGTAAA
31480322 TTTAAATTTAAAGTAAA
1 TTTAAATTTAAAGTAAA
* *
31480339 TTTAAA-TT--GGTGAA
1 TTTAAATTTAAAGTAAA
31480353 TTTAAATTT-AAGATAAA
1 TTTAAATTTAAAG-TAAA
31480370 TTTAAATTTAAA
1 TTTAAATTTAAA
31480382 ATTTAAACTT
Statistics
Matches: 50, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
14 10 0.20
15 2 0.04
16 12 0.24
17 24 0.48
18 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.45
Consensus pattern (17 bp):
TTTAAATTTAAAGTAAA
Found at i:31483518 original size:20 final size:20
Alignment explanation
Indices: 31483493--31483653 Score: 279
Period size: 20 Copynumber: 8.1 Consensus size: 20
31483483 GTGCATTCTA
*
31483493 TGTATCAGGCTTCGTGCCGG
1 TGTATCAGGCTTTGTGCCGG
31483513 TGTATCAGGCTTTGTGCCGG
1 TGTATCAGGCTTTGTGCCGG
*
31483533 TGTATCAGGCTTTGTGTCGG
1 TGTATCAGGCTTTGTGCCGG
31483553 TGTATCAGGCTTT-TGCCGG
1 TGTATCAGGCTTTGTGCCGG
31483572 TGTATCAGGCTTTGTGCCGG
1 TGTATCAGGCTTTGTGCCGG
31483592 TGTATCAGGCTTTGTGCCGG
1 TGTATCAGGCTTTGTGCCGG
*
31483612 TGTATCAGGCTTTATGCCGG
1 TGTATCAGGCTTTGTGCCGG
*
31483632 TGTATCAAGCTTTGTGCCGG
1 TGTATCAGGCTTTGTGCCGG
31483652 TG
1 TG
31483654 ATTCAGGAAC
Statistics
Matches: 134, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
19 18 0.13
20 116 0.87
ACGTcount: A:0.11, C:0.20, G:0.34, T:0.35
Consensus pattern (20 bp):
TGTATCAGGCTTTGTGCCGG
Found at i:31483624 original size:79 final size:80
Alignment explanation
Indices: 31483493--31483653 Score: 279
Period size: 79 Copynumber: 2.0 Consensus size: 80
31483483 GTGCATTCTA
* *
31483493 TGTATCAGGCTTCGTGCCGGTGTATCAGGCTTTGTGCCGGTGTATCAGGCTTTGTGTCGGTGTAT
1 TGTATCAGGCTTCGTGCCGGTGTATCAGGCTTTGTGCCGGTGTATCAGGCTTTATGCCGGTGTAT
*
31483558 CAGGCTTT-TGCCGG
66 CAAGCTTTGTGCCGG
*
31483572 TGTATCAGGCTTTGTGCCGGTGTATCAGGCTTTGTGCCGGTGTATCAGGCTTTATGCCGGTGTAT
1 TGTATCAGGCTTCGTGCCGGTGTATCAGGCTTTGTGCCGGTGTATCAGGCTTTATGCCGGTGTAT
31483637 CAAGCTTTGTGCCGG
66 CAAGCTTTGTGCCGG
31483652 TG
1 TG
31483654 ATTCAGGAAC
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
79 69 0.90
80 8 0.10
ACGTcount: A:0.11, C:0.20, G:0.34, T:0.35
Consensus pattern (80 bp):
TGTATCAGGCTTCGTGCCGGTGTATCAGGCTTTGTGCCGGTGTATCAGGCTTTATGCCGGTGTAT
CAAGCTTTGTGCCGG
Found at i:31490201 original size:20 final size:20
Alignment explanation
Indices: 31490073--31490194 Score: 172
Period size: 20 Copynumber: 6.1 Consensus size: 20
31490063 GTGCATTCTA
* *
31490073 TGTATCAGGCTTTATGCCAG
1 TGTATCAGGCTTTGTGCCGG
*
31490093 TGTATCAGGCTTCGTGCCGG
1 TGTATCAGGCTTTGTGCCGG
**
31490113 TGTATCAGGCTTCATGCCGG
1 TGTATCAGGCTTTGTGCCGG
*
31490133 TGTATTAGGCTTTGTGCCGG
1 TGTATCAGGCTTTGTGCCGG
* *
31490153 TGTATCTGGCATTGTGCCGG
1 TGTATCAGGCTTTGTGCCGG
31490173 TGTATCAGGCTTTGTGCCGG
1 TGTATCAGGCTTTGTGCCGG
31490193 TG
1 TG
31490195 ATTCAGGATT
Statistics
Matches: 90, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 90 1.00
ACGTcount: A:0.12, C:0.20, G:0.33, T:0.34
Consensus pattern (20 bp):
TGTATCAGGCTTTGTGCCGG
Found at i:31497689 original size:24 final size:24
Alignment explanation
Indices: 31497662--31497713 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
31497652 GCTTACCCTC
* *
31497662 ATCCAGGTGCTGCTTCTTCTTTTT
1 ATCCAGGTGCCGCTTCCTCTTTTT
** *
31497686 ATCCTTGTGCCGTTTCCTCTTTTT
1 ATCCAGGTGCCGCTTCCTCTTTTT
31497710 ATCC
1 ATCC
31497714 GTCGTACCAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.08, C:0.29, G:0.13, T:0.50
Consensus pattern (24 bp):
ATCCAGGTGCCGCTTCCTCTTTTT
Found at i:31505757 original size:13 final size:14
Alignment explanation
Indices: 31505739--31505768 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
31505729 GTCAGCGCAA
31505739 TCAGA-GTTAAATG
1 TCAGAGGTTAAATG
31505752 TCAGAGGTTAAATG
1 TCAGAGGTTAAATG
31505766 TCA
1 TCA
31505769 ATGTACTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.31
14 11 0.69
ACGTcount: A:0.37, C:0.10, G:0.23, T:0.30
Consensus pattern (14 bp):
TCAGAGGTTAAATG
Found at i:31524550 original size:25 final size:25
Alignment explanation
Indices: 31524516--31524566 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
31524506 GGTCCTTCCT
31524516 TGTGGCCACATTAAGTTTGCGATAA
1 TGTGGCCACATTAAGTTTGCGATAA
*
31524541 TGTGGCCACATTAAGTTTGTGATAA
1 TGTGGCCACATTAAGTTTGCGATAA
31524566 T
1 T
31524567 TCATACAGAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (25 bp):
TGTGGCCACATTAAGTTTGCGATAA
Found at i:31533197 original size:17 final size:17
Alignment explanation
Indices: 31533175--31533216 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
31533165 GATTAACATT
31533175 AAGAAAATAAAAAAAGA
1 AAGAAAATAAAAAAAGA
* **
31533192 AAGAAATTCGAAAAAGA
1 AAGAAAATAAAAAAAGA
31533209 AA-AAAATA
1 AAGAAAATA
31533217 TACATCATAT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
16 4 0.20
17 16 0.80
ACGTcount: A:0.76, C:0.02, G:0.12, T:0.10
Consensus pattern (17 bp):
AAGAAAATAAAAAAAGA
Found at i:31548939 original size:29 final size:29
Alignment explanation
Indices: 31548891--31548974 Score: 98
Period size: 30 Copynumber: 2.9 Consensus size: 29
31548881 AGGTTTTAGG
*
31548891 TTCTTTAAAAGTTG-AAAAAAAATTTAAA
1 TTCTTTAAAAATTGAAAAAAAAATTTAAA
*
31548919 TTCTTTAAAAATTAGAAAAAAAAATTTAGA
1 TTCTTTAAAAATT-GAAAAAAAAATTTAAA
* * * *
31548949 TCCTTTAAAAGTTTATAAAAAAATTT
1 TTCTTTAAAAATTGAAAAAAAAATTT
31548975 TGGACCCTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
28 12 0.25
29 12 0.25
30 24 0.50
ACGTcount: A:0.52, C:0.05, G:0.06, T:0.37
Consensus pattern (29 bp):
TTCTTTAAAAATTGAAAAAAAAATTTAAA
Found at i:31548985 original size:29 final size:29
Alignment explanation
Indices: 31548935--31549019 Score: 86
Period size: 29 Copynumber: 2.9 Consensus size: 29
31548925 AAAAATTAGA
* * * *
31548935 AAAAAAAATTTAGATCCTTTAAAAGTTTAT
1 AAAAAAATTTTGGACCCCTTAAAAGTTT-T
31548965 AAAAAAATTTTGGA-CCCTTAAAAG--TT
1 AAAAAAATTTTGGACCCCTTAAAAGTTTT
31548991 AAAAAAATTTTAGAGACCCCTTAAAAGTT
1 AAAAAAATTTT-G-GACCCCTTAAAAGTT
31549020 GGTAATTTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
26 12 0.26
27 2 0.04
28 2 0.04
29 19 0.40
30 12 0.26
ACGTcount: A:0.48, C:0.11, G:0.09, T:0.32
Consensus pattern (29 bp):
AAAAAAATTTTGGACCCCTTAAAAGTTTT
Found at i:31548993 original size:26 final size:29
Alignment explanation
Indices: 31548964--31549019 Score: 91
Period size: 26 Copynumber: 2.0 Consensus size: 29
31548954 TAAAAGTTTA
31548964 TAAAAAAATTTT-G-GA-CCCTTAAAAGT
1 TAAAAAAATTTTAGAGACCCCTTAAAAGT
31548990 TAAAAAAATTTTAGAGACCCCTTAAAAGT
1 TAAAAAAATTTTAGAGACCCCTTAAAAGT
31549019 T
1 T
31549020 GGTAATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
26 12 0.44
27 1 0.04
28 2 0.07
29 12 0.44
ACGTcount: A:0.46, C:0.12, G:0.11, T:0.30
Consensus pattern (29 bp):
TAAAAAAATTTTAGAGACCCCTTAAAAGT
Found at i:31549320 original size:2 final size:2
Alignment explanation
Indices: 31549313--31549359 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
31549303 CCTTATAAAC
31549313 AT AT 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 AT AT
31549355 AT AT A
1 AT AT A
31549360 GTTAATTTGT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:31550628 original size:96 final size:96
Alignment explanation
Indices: 31550454--31550645 Score: 246
Period size: 96 Copynumber: 2.0 Consensus size: 96
31550444 AACCTTGGAA
* * * *
31550454 AAGGATATTCGATTATCTCGATTTGAAGAAAAGTCGCGCTTAGTAACTTAAGGCACAAATTTTCA
1 AAGGATATTCGATTATCTCGACTTGAAGAAAAATCGCACCTAGTAACTTAAGGCACAAATTTTCA
* *
31550519 AAACCAGAGAT-AAAGAAACATTGCCTTGATT
66 AAACCAGAAATAAAAG-AACATTGCCTCGATT
* * *
31550550 AAGGGTATTCGATTAT-TCCGACTTGAAGAAAAATCGCACCTAGTAAGTTAAGGGACAAATTTTC
1 AAGGATATTCGATTATCT-CGACTTGAAGAAAAATCGCACCTAGTAACTTAAGGCACAAATTTTC
*
31550614 AAAACTC-GAAATAAAAGAATATTGCCTCGATT
65 AAAAC-CAGAAATAAAAGAACATTGCCTCGATT
31550646 TTAAATGTTT
Statistics
Matches: 83, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
95 1 0.01
96 77 0.93
97 5 0.06
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.28
Consensus pattern (96 bp):
AAGGATATTCGATTATCTCGACTTGAAGAAAAATCGCACCTAGTAACTTAAGGCACAAATTTTCA
AAACCAGAAATAAAAGAACATTGCCTCGATT
Found at i:31550962 original size:29 final size:29
Alignment explanation
Indices: 31550920--31551240 Score: 300
Period size: 30 Copynumber: 10.8 Consensus size: 29
31550910 TTAATTTTGG
*
31550920 AAAATGGTAATTTTTGGACA-TCCGAGGGT
1 AAAATGGTAATTTTTGGA-AGTTCGAGGGT
* *
31550949 AAAATGGTAATTTTTGGACACTTCG-GAGGC
1 AAAATGGTAATTTTTGGA-AGTTCGAG-GGT
* *
31550979 AAAATGGTAA-TTTTGGACACTTCGAGGGA
1 AAAATGGTAATTTTTGGA-AGTTCGAGGGT
*
31551008 AAAATGGTAATTTTTGGAAGTTC-AAGGT
1 AAAATGGTAATTTTTGGAAGTTCGAGGGT
31551036 CAAAAATGGTAATTTTTGGAAGTTCGAGGGT
1 --AAAATGGTAATTTTTGGAAGTTCGAGGGT
*
31551067 AAAATGGTAATTTTTGGAAGTTC-AAGGT
1 AAAATGGTAATTTTTGGAAGTTCGAGGGT
31551095 CAAAAATGGTAATTTTTGGAAGTTCGAGGGTT
1 --AAAATGGTAATTTTTGGAAGTTCGAGGG-T
*
31551127 AAAAT-GTAATTTTTGGAAAGCTCGAGGGT
1 AAAATGGTAATTTTTGG-AAGTTCGAGGGT
* * **
31551156 CAAAAT-ATAATTTTTGAAAAGTTTAAGGGT
1 -AAAATGGTAATTTTTG-GAAGTTCGAGGGT
* *
31551186 CAAAAT-GTAATTTTTGAAAAGTTTGAGGGT
1 -AAAATGGTAATTTTTG-GAAGTTCGAGGGT
*
31551216 CAAAAT-GTAATTTTTGAAGAGTTCG
1 -AAAATGGTAATTTTTGGA-AGTTCG
31551241 GGAGTTAAAA
Statistics
Matches: 259, Mismatches: 18, Indels: 29
0.85 0.06 0.09
Matches are distributed among these distances:
28 7 0.03
29 88 0.34
30 156 0.60
31 7 0.03
32 1 0.00
ACGTcount: A:0.35, C:0.07, G:0.25, T:0.33
Consensus pattern (29 bp):
AAAATGGTAATTTTTGGAAGTTCGAGGGT
Found at i:31550966 original size:46 final size:45
Alignment explanation
Indices: 31550875--31550962 Score: 108
Period size: 45 Copynumber: 2.0 Consensus size: 45
31550865 GCTCGAGAGC
* *
31550875 AAAATGGTAATTTTGGACACTTCAGGGGAAAAATATTAATTTTGG
1 AAAATGGTAATTTTGGACACTCCAGGGGAAAAATAGTAATTTTGG
* *
31550920 AAAATGGTAATTTTTGGACA-TCC-GAGGGTAAAATGGTAATTTT
1 AAAATGGTAA-TTTTGGACACTCCAG-GGGAAAAATAGTAATTTT
31550963 TGGACACTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
44 1 0.03
45 27 0.73
46 9 0.24
ACGTcount: A:0.36, C:0.07, G:0.23, T:0.34
Consensus pattern (45 bp):
AAAATGGTAATTTTGGACACTCCAGGGGAAAAATAGTAATTTTGG
Found at i:31551012 original size:59 final size:59
Alignment explanation
Indices: 31550920--31551240 Score: 329
Period size: 59 Copynumber: 5.4 Consensus size: 59
31550910 TTAATTTTGG
* * *
31550920 AAAATGGTAATTTTTGGACA-TCCGAGGGTAAAATGGTAATTTTTGGACACTTCGGAGG-C-
1 AAAATGGTAATTTTTGGA-AGTTCGAGGGTAAAATGGTAATTTTTGGA-AGTTC-AAGGTCA
* *
31550979 AAAATGGTAA-TTTTGGACACTTCGAGGGAAAAATGGTAATTTTTGGAAGTTCAAGGTCA
1 AAAATGGTAATTTTTGGA-AGTTCGAGGGTAAAATGGTAATTTTTGGAAGTTCAAGGTCA
31551038 AAAATGGTAATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGTTCAAGGTCA
1 AAAATGGTAATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGTTCAAGGTCA
* *
31551097 AAAATGGTAATTTTTGGAAGTTCGAGGGTTAAAAT-GTAATTTTTGGAAAGCTCGAGGGTC-
1 AAAATGGTAATTTTTGGAAGTTCGAGGG-TAAAATGGTAATTTTTGG-AAGTTC-AAGGTCA
* * ** * * *
31551157 AAAAT-ATAATTTTTGAAAAGTTTAAGGGTCAAAAT-GTAATTTTTGAAAAGTTTGAGGGTC-
1 AAAATGGTAATTTTTG-GAAGTTCGAGGGT-AAAATGGTAATTTTTG-GAAG-TTCAAGGTCA
*
31551217 AAAAT-GTAATTTTTGAAGAGTTCG
1 AAAATGGTAATTTTTGGA-AGTTCG
31551241 GGAGTTAAAA
Statistics
Matches: 232, Mismatches: 18, Indels: 23
0.85 0.07 0.08
Matches are distributed among these distances:
57 3 0.01
58 14 0.06
59 135 0.58
60 74 0.32
61 6 0.03
ACGTcount: A:0.35, C:0.07, G:0.25, T:0.33
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGAAGTTCGAGGGTAAAATGGTAATTTTTGGAAGTTCAAGGTCA
Found at i:31551977 original size:31 final size:30
Alignment explanation
Indices: 31551896--31551990 Score: 81
Period size: 32 Copynumber: 3.2 Consensus size: 30
31551886 ATAAGTGAAA
*
31551896 AAAAAATCTTTTTACTCTTTT-CTTCTTTTT
1 AAAAAATCTTTTT-CTATTTTCCTTCTTTTT
*
31551926 AAAACAA-CTTTTTTTATTTTCCTTCCTTTTTT
1 AAAA-AATCTTTTTCTATTTTCCTT-C-TTTTT
* * *
31551958 AAAAAATCCTTTTCT-TTTTCATT-TCTTT
1 AAAAAATCTTTTTCTATTTTCCTTCTTTTT
31551986 AAAAA
1 AAAAA
31551991 CTGTTTTGAT
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
28 9 0.17
29 5 0.09
30 13 0.24
31 12 0.22
32 15 0.28
ACGTcount: A:0.27, C:0.17, G:0.00, T:0.56
Consensus pattern (30 bp):
AAAAAATCTTTTTCTATTTTCCTTCTTTTT
Found at i:31552069 original size:20 final size:22
Alignment explanation
Indices: 31552034--31552077 Score: 74
Period size: 20 Copynumber: 2.1 Consensus size: 22
31552024 TTCATCTTAT
31552034 TGCTTGGAAGAAACCCCAGATC
1 TGCTTGGAAGAAACCCCAGATC
31552056 TGCTTGG-A-AAACCCCAGATC
1 TGCTTGGAAGAAACCCCAGATC
31552076 TG
1 TG
31552078 GGTTTTATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 14 0.64
21 1 0.05
22 7 0.32
ACGTcount: A:0.30, C:0.27, G:0.23, T:0.20
Consensus pattern (22 bp):
TGCTTGGAAGAAACCCCAGATC
Found at i:31552303 original size:3 final size:3
Alignment explanation
Indices: 31552285--31552360 Score: 125
Period size: 3 Copynumber: 25.0 Consensus size: 3
31552275 TTTTATTTCT
* *
31552285 TTA TTA CTA ATA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
31552333 TTA TTA TTA TTA TTA TTA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA
31552361 AGACTAAAAA
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
3 66 0.96
4 3 0.04
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:31553106 original size:17 final size:17
Alignment explanation
Indices: 31553098--31553160 Score: 90
Period size: 17 Copynumber: 3.7 Consensus size: 17
31553088 AAATAAATTT
* *
31553098 TAAATTTAAACTTATAA
1 TAAATTTAAATTTAAAA
31553115 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* *
31553132 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
31553149 TAAATTTAAATT
1 TAAATTTAAATT
31553161 CTGTTGGGCT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:31553145 original size:23 final size:23
Alignment explanation
Indices: 31553093--31553147 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
31553083 TATTTAAATA
*
31553093 AATTTTAAATTTAAACTTATAAT
1 AATTTTAAATTTAAACATATAAT
*
31553116 AAATTTAAATTTAAA-ATA-AACTT
1 AATTTTAAATTTAAACATATAA--T
31553139 AATTTTAAA
1 AATTTTAAA
31553148 ATAAATTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 2 0.07
22 2 0.07
23 23 0.85
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.44
Consensus pattern (23 bp):
AATTTTAAATTTAAACATATAAT
Found at i:31553836 original size:201 final size:201
Alignment explanation
Indices: 31553479--31554320 Score: 1400
Period size: 201 Copynumber: 4.2 Consensus size: 201
31553469 ATTTAGTCTT
* * * * *
31553479 CTTCTCAGTATCTCATCAGGAAGATGACCGCATCGA-TTGTTTCAATTCGCTTCTCTATATCTCA
1 CTTCTCTGTATCTCATCAGGAAGATGACTGCCTC-ACTTGTTTCAATCCGCTTCTCTGTATCTCA
*
31553543 TCAGGAAGACGAATTTGGTCCACTTCTCATTATCTCATCAGGAAGCTAACCATTTTATTGCTTCG
65 TCAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCG
31553608 ACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGCCTTGAGT
130 ACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGCCTTGAGT
*
31553673 TAGTATA
195 TGGTATA
*
31553680 CTTCTCTGTATTTCATCAGGAAGATGACTGCCTCACTTGTTTCAATCCGCTTCTCTGTATCTCAT
1 CTTCTCTGTATCTCATCAGGAAGATGACTGCCTCACTTGTTTCAATCCGCTTCTCTGTATCTCAT
* *
31553745 CAGGAAGACGAATTTGGTCCACTTCTTAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGG
66 CAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGA
* * *
31553810 CCTGCTTCTCAGTATCTTATCAGGAAGTTGGGGTTCGAAGATTTGCTCGCATTGAGCCTTAAGTT
131 CCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGCCTTGAGTT
31553875 GGTATA
196 GGTATA
*
31553881 CTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATCCGCTTCTCTGTATCTCAT
1 CTTCTCTGTATCTCATCAGGAAGATGACTGCCTCACTTGTTTCAATCCGCTTCTCTGTATCTCAT
*
31553946 CAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTACTTCGA
66 CAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGA
* * *
31554011 CCTACTTCTCAGTATCTCATTAGGAAGTTGGGGTTCGAAGATTTGCTCGCATTGAGCCTTGAGTT
131 CCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGCCTTGAGTT
31554076 GGTATA
196 GGTATA
* *
31554082 CTTCTCTATATCTCATCAGGAAGATGATTGCCTCACTTGTTTCAATCCGCTTCTCTGTATCTCAT
1 CTTCTCTGTATCTCATCAGGAAGATGACTGCCTCACTTGTTTCAATCCGCTTCTCTGTATCTCAT
* * *
31554147 CAGGAAGACAAATTTGGTCCACTTCTCAGTATCTCATCAAGAAGCTAACCATTTTATTGCTTCAA
66 CAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGA
* * *
31554212 CCTGCTTCTCAATATCTCATCAGGAAGCTGGGGTTCGAAGAGTTGCTCGCATTGAGCCATGAGTT
131 CCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGCCTTGAGTT
31554277 GGTATA
196 GGTATA
* *
31554283 CTTCTCTGTATCTCCTCAAGAAGATGA-TCGCCTCACTT
1 CTTCTCTGTATCTCATCAGGAAGATGACT-GCCTCACTT
31554321 TTTGTGGATA
Statistics
Matches: 601, Mismatches: 38, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
200 2 0.00
201 599 1.00
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.34
Consensus pattern (201 bp):
CTTCTCTGTATCTCATCAGGAAGATGACTGCCTCACTTGTTTCAATCCGCTTCTCTGTATCTCAT
CAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATCAGGAAGCTAACCATTTTATTGCTTCGA
CCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCGCATTGAGCCTTGAGTT
GGTATA
Found at i:31566214 original size:87 final size:85
Alignment explanation
Indices: 31566115--31566424 Score: 269
Period size: 88 Copynumber: 3.5 Consensus size: 85
31566105 TGCTCAGGGC
*
31566115 AAAATGGTAA-TTTTGGACACTTCGAGGGTAAAATGGTAATTTTTGGACATCCGAGGGTAAAATG
1 AAAATGGTAATTTTTGGA-AGTTC-AGGGTAAAATGGTAATTTTTGGACATCCGAGGGTAAAATG
31566179 GTAATTTTTGGACA-TCCGAAGG-T
64 GTAA-TTTTGGA-AGTCCG-AGGCT
* * * **
31566202 AAAATAGTAATTTTTGGAAGTTCAAGGTCAAAAATGG-AATTTTTGGATATTTGAGGGTAAAATG
1 AAAATGGTAATTTTTGGAAGTTCAGGGT--AAAATGGTAATTTTTGGACATCCGAGGGTAAAATG
*
31566266 GTAATTTTGGAATGTTCGAGGTCT
64 GTAATTTTGGAA-GTCCGAGG-CT
* **
31566290 AAAATGGTAATTTTTGGAAGTTCAGGGGTAAAATGGTAATTTTTGGAAAATTTG-GGGTCAAAAA
1 AAAATGGTAATTTTTGGAAGTTCA-GGGTAAAATGGTAATTTTTGG-ACATCCGAGGGT--AAAA
* *
31566354 TGG-AATTTTTGGAAGTTCAAGAG-T
62 TGGTAA-TTTTGGAAGTCCGAG-GCT
* *
31566378 CAAAAT-GTTATTTTTGGAAGCTCGAGGGTCAAAAT-GTAATTTTTGGA
1 -AAAATGGTAATTTTTGGAAGTTC-AGGGT-AAAATGGTAATTTTTGGA
31566425 AAGCTCGGGG
Statistics
Matches: 193, Mismatches: 13, Indels: 34
0.80 0.05 0.14
Matches are distributed among these distances:
85 1 0.01
86 14 0.07
87 52 0.27
88 82 0.42
89 28 0.15
90 16 0.08
ACGTcount: A:0.34, C:0.06, G:0.26, T:0.34
Consensus pattern (85 bp):
AAAATGGTAATTTTTGGAAGTTCAGGGTAAAATGGTAATTTTTGGACATCCGAGGGTAAAATGGT
AATTTTGGAAGTCCGAGGCT
Found at i:31566431 original size:30 final size:31
Alignment explanation
Indices: 31566110--31566512 Score: 318
Period size: 29 Copynumber: 13.7 Consensus size: 31
31566100 TTGGATGCTC
* *
31566110 AGGG-CAAAATGGTAA-TTTTGGACACTTCG
1 AGGGTCAAAATGGTAATTTTTGGAAAGTTCG
* *
31566139 AGGGT-AAAATGGTAATTTTTGGACA-TCCG
1 AGGGTCAAAATGGTAATTTTTGGAAAGTTCG
* *
31566168 AGGGT-AAAATGGTAATTTTTGGACA-TCCG
1 AGGGTCAAAATGGTAATTTTTGGAAAGTTCG
* *
31566197 AAGGT-AAAATAGTAATTTTTGG-AAGTTC-
1 AGGGTCAAAATGGTAATTTTTGGAAAGTTCG
* * *
31566225 AAGGTCAAAAATGG-AATTTTTGGATA-TTTG
1 AGGGTC-AAAATGGTAATTTTTGGAAAGTTCG
*
31566255 AGGGT-AAAATGGTAA-TTTTGGAATGTTCG
1 AGGGTCAAAATGGTAATTTTTGGAAAGTTCG
31566284 A-GGTCTAAAATGGTAATTTTTGG-AAGTTC-
1 AGGGTC-AAAATGGTAATTTTTGGAAAGTTCG
* *
31566313 AGGGGT-AAAATGGTAATTTTTGGAAAATTTG
1 A-GGGTCAAAATGGTAATTTTTGGAAAGTTCG
*
31566344 -GGGTCAAAAATGG-AATTTTTGG-AAGTTCA
1 AGGGTC-AAAATGGTAATTTTTGGAAAGTTCG
* * *
31566373 AGAGTCAAAAT-GTTATTTTTGG-AAGCTCG
1 AGGGTCAAAATGGTAATTTTTGGAAAGTTCG
*
31566402 AGGGTCAAAAT-GTAATTTTTGGAAAGCTCG
1 AGGGTCAAAATGGTAATTTTTGGAAAGTTCG
* * * * **
31566432 GGGGTTAAAAT-ATAATTTTTGAAAAGTTTA
1 AGGGTCAAAATGGTAATTTTTGGAAAGTTCG
** *
31566462 AGGGTCAAAAT-GTAATTTTTAAAAAGTTTG
1 AGGGTCAAAATGGTAATTTTTGGAAAGTTCG
* *
31566492 AGGGTTAAAAT-ATAATTTTTG
1 AGGGTCAAAATGGTAATTTTTG
31566513 AAGAGTTTGG
Statistics
Matches: 314, Mismatches: 39, Indels: 41
0.80 0.10 0.10
Matches are distributed among these distances:
28 24 0.08
29 149 0.47
30 125 0.40
31 16 0.05
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.34
Consensus pattern (31 bp):
AGGGTCAAAATGGTAATTTTTGGAAAGTTCG
Found at i:31566473 original size:60 final size:60
Alignment explanation
Indices: 31566167--31566549 Score: 231
Period size: 60 Copynumber: 6.5 Consensus size: 60
31566157 TTGGACATCC
* * *
31566167 GAGGGT-AAAATGGTAATTTTTGGACA-TCCGAA-GG-TAAAATAGTAATTTTTG-GAAG-TT
1 GAGGGTCAAAAT-GTAATTTTTGGAAAGTTC-AAGGGTTAAAATA-TAATTTTTGAAAAGTTT
* * * * ** * * * *
31566224 CAAGGTCAAAAATGGAATTTTTGGATA-TTTGAGGG-TAAAATGGTAA-TTTTGGAATGTTC
1 GAGGGTC-AAAATGTAATTTTTGGAAAGTTCAAGGGTTAAAAT-ATAATTTTTGAAAAGTTT
* *
31566283 GA-GGTCTAAAATGGTAATTTTTGG-AAGTTC-AGGGGTAAAATGGTAATTTTTGGAAAA-TTT
1 GAGGGTC-AAAAT-GTAATTTTTGGAAAGTTCAAGGGTTAAAAT-ATAATTTTT-GAAAAGTTT
* * * * * * * *
31566343 G-GGGTCAAAAATGGAATTTTTGG-AAGTTCAAGAGTCAAAATGTTATTTTTG-GAAGCTC
1 GAGGGTC-AAAATGTAATTTTTGGAAAGTTCAAGGGTTAAAATATAATTTTTGAAAAGTTT
* **
31566401 GAGGGTCAAAATGTAATTTTTGGAAAGCTCGGGGGTTAAAATATAATTTTTGAAAAGTTT
1 GAGGGTCAAAATGTAATTTTTGGAAAGTTCAAGGGTTAAAATATAATTTTTGAAAAGTTT
* ** ** *
31566461 AAGGGTCAAAATGTAATTTTTAAAAAGTTTGAGGGTTAAAATATAATTTTTGAAGAGTTT
1 GAGGGTCAAAATGTAATTTTTGGAAAGTTCAAGGGTTAAAATATAATTTTTGAAAAGTTT
* * * * *
31566521 GGGGGTTAAAATATGATTTTTGAAAAGTT
1 GAGGGTCAAAATGTAATTTTTGGAAAGTT
31566550 TAGGGGCCTT
Statistics
Matches: 257, Mismatches: 52, Indels: 31
0.76 0.15 0.09
Matches are distributed among these distances:
57 12 0.05
58 58 0.23
59 80 0.31
60 104 0.40
61 3 0.01
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (60 bp):
GAGGGTCAAAATGTAATTTTTGGAAAGTTCAAGGGTTAAAATATAATTTTTGAAAAGTTT
Found at i:31566520 original size:30 final size:30
Alignment explanation
Indices: 31566401--31566554 Score: 184
Period size: 30 Copynumber: 5.2 Consensus size: 30
31566391 TTGGAAGCTC
* * * * *
31566401 GAGGGTCAAAATGTAATTTTTGGAAAGCTC
1 GAGGGTTAAAATATAATTTTTGAAAAGTTT
*
31566431 GGGGGTTAAAATATAATTTTTGAAAAGTTT
1 GAGGGTTAAAATATAATTTTTGAAAAGTTT
* * * *
31566461 AAGGGTCAAAATGTAATTTTTAAAAAGTTT
1 GAGGGTTAAAATATAATTTTTGAAAAGTTT
*
31566491 GAGGGTTAAAATATAATTTTTGAAGAGTTT
1 GAGGGTTAAAATATAATTTTTGAAAAGTTT
* *
31566521 GGGGGTTAAAATATGATTTTTGAAAAGTTT
1 GAGGGTTAAAATATAATTTTTGAAAAGTTT
31566551 -AGGG
1 GAGGG
31566555 GCCTTTTGGG
Statistics
Matches: 104, Mismatches: 20, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
29 3 0.03
30 101 0.97
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (30 bp):
GAGGGTTAAAATATAATTTTTGAAAAGTTT
Found at i:31568381 original size:17 final size:17
Alignment explanation
Indices: 31568359--31568429 Score: 67
Period size: 17 Copynumber: 4.2 Consensus size: 17
31568349 ATTGGACATT
31568359 ATTT-AAATAAATTTTAA
1 ATTTAAAATAAA-TTTAA
*
31568376 ATTTAAACTTATAA--TAA
1 ATTTAAA-ATA-AATTTAA
*
31568393 ATTTAAAATAAACTTAA
1 ATTTAAAATAAATTTAA
*
31568410 TTTTAAAATAAATTTAA
1 ATTTAAAATAAATTTAA
31568427 ATT
1 ATT
31568430 CTGTTGGGCT
Statistics
Matches: 44, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
15 2 0.05
16 2 0.05
17 34 0.77
18 2 0.05
19 2 0.05
20 2 0.05
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTTAAAATAAATTTAA
Found at i:31568395 original size:24 final size:22
Alignment explanation
Indices: 31568364--31568408 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
31568354 ACATTATTTA
*
31568364 AATAAATTTTAAATTTAAACTTAT
1 AATAAA-TTTAAA-ATAAACTTAT
31568388 AATAAATTTAAAATAAACTTA
1 AATAAATTTAAAATAAACTTA
31568409 ATTTTAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 8 0.40
23 6 0.30
24 6 0.30
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (22 bp):
AATAAATTTAAAATAAACTTAT
Found at i:31568404 original size:28 final size:28
Alignment explanation
Indices: 31568373--31568427 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
31568363 AAATAAATTT
* *
31568373 TAAATTTAAACTTATAATAAATTTAAAA
1 TAAACTTAAACTTAAAATAAATTTAAAA
**
31568401 TAAACTTAATTTTAAAATAAATTTAAA
1 TAAACTTAAACTTAAAATAAATTTAAA
31568428 TTCTGTTGGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (28 bp):
TAAACTTAAACTTAAAATAAATTTAAAA
Found at i:31569506 original size:6 final size:6
Alignment explanation
Indices: 31569495--31569553 Score: 88
Period size: 6 Copynumber: 10.3 Consensus size: 6
31569485 CATTTTAAGA
*
31569495 TTTCTT TTTCTT TTTC-- -TTCTT TTTCTT TTTCTT TTTCTT TGTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
31569540 TTTCTT TTTCTT TT
1 TTTCTT TTTCTT TT
31569554 GCCCAGCACA
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
3 3 0.06
6 45 0.94
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.81
Consensus pattern (6 bp):
TTTCTT
Found at i:31570614 original size:30 final size:30
Alignment explanation
Indices: 31570580--31570645 Score: 116
Period size: 30 Copynumber: 2.2 Consensus size: 30
31570570 AAATTAATTT
31570580 TTTTGTTTACCCTAAATC-TTAAACCTTTTA
1 TTTTGTTTACCCTAAATCATT-AACCTTTTA
31570610 TTTTGTTTACCCTAAATCATTAACCTTTTA
1 TTTTGTTTACCCTAAATCATTAACCTTTTA
31570640 TTTTGT
1 TTTTGT
31570646 ATTCTAATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
30 33 0.94
31 2 0.06
ACGTcount: A:0.24, C:0.18, G:0.05, T:0.53
Consensus pattern (30 bp):
TTTTGTTTACCCTAAATCATTAACCTTTTA
Found at i:31570795 original size:24 final size:24
Alignment explanation
Indices: 31570767--31570821 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
31570757 TCTTTTTAGA
*
31570767 ATATTTAGT-ATTTATTAGTATAAT
1 ATATTT-GTCATTTATTAGCATAAT
*
31570791 ATATTTTTCATTTATTAGCATAAT
1 ATATTTGTCATTTATTAGCATAAT
*
31570815 TTATTTG
1 ATATTTG
31570822 ACATAGGAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 1 0.04
24 25 0.96
ACGTcount: A:0.33, C:0.04, G:0.07, T:0.56
Consensus pattern (24 bp):
ATATTTGTCATTTATTAGCATAAT
Found at i:31579598 original size:21 final size:21
Alignment explanation
Indices: 31579580--31579620 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
31579570 TTGGTAGATG
31579580 TGTCACTTGTATCGATAGAAC
1 TGTCACTTGTATCGATAGAAC
*
31579601 TGTCACTTGTATCGGTAGAA
1 TGTCACTTGTATCGATAGAA
31579621 GTCTGCACTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (21 bp):
TGTCACTTGTATCGATAGAAC
Found at i:31587587 original size:17 final size:17
Alignment explanation
Indices: 31587565--31587597 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
31587555 TAATTCTTTA
31587565 AAACTATCGAA-CTTACT
1 AAACTAT-GAAGCTTACT
31587582 AAACTATGAAGCTTAC
1 AAACTATGAAGCTTAC
31587598 CAAAGATGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.42, C:0.21, G:0.09, T:0.27
Consensus pattern (17 bp):
AAACTATGAAGCTTACT
Found at i:31588135 original size:21 final size:21
Alignment explanation
Indices: 31588120--31588191 Score: 94
Period size: 21 Copynumber: 3.4 Consensus size: 21
31588110 GGAGTTTTTA
31588120 GTATCGGTAGAAGAGTCACTT
1 GTATCGGTAGAAGAGTCACTT
*
31588141 GTATCGGTAGAACTA-TCACTT
1 GTATCGGTAGAA-GAGTCACTT
*
31588162 GTATCGGTAGAACTA-TCACTT
1 GTATCGGTAGAA-GAGTCACTT
31588183 GTATCGGTA
1 GTATCGGTA
31588192 AAAGTCTGCA
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
21 48 0.98
22 1 0.02
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.32
Consensus pattern (21 bp):
GTATCGGTAGAAGAGTCACTT
Found at i:31588959 original size:58 final size:60
Alignment explanation
Indices: 31588888--31589048 Score: 238
Period size: 58 Copynumber: 2.7 Consensus size: 60
31588878 TTAATATAAC
*
31588888 ATTTGGTACCTGAACTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTT-ATCC-A
1 ATTTGGTACCTGAACTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTTGAACCAA
* * *
31588946 ATTTGGTATCTGAACTTGACACTTTTTTCTAATTTAGTACCTAAACTTTTTTTGAACCAA
1 ATTTGGTACCTGAACTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTTGAACCAA
* * *
31589006 ATTTGGTACCTGAACTTGCCATTTTTTCCT-ATGTGGTACCTAA
1 ATTTGGTACCTGAACTTGACACTTTTTCCTAATTTGGTACCTAA
31589049 GTGATAAAGA
Statistics
Matches: 91, Mismatches: 10, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
58 50 0.55
59 14 0.15
60 27 0.30
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.44
Consensus pattern (60 bp):
ATTTGGTACCTGAACTTGACACTTTTTCCTAATTTGGTACCTAAACTTTTTTTGAACCAA
Found at i:31595714 original size:7 final size:7
Alignment explanation
Indices: 31595704--31595737 Score: 68
Period size: 7 Copynumber: 4.9 Consensus size: 7
31595694 GAAAGAATAA
31595704 AGAAGAG
1 AGAAGAG
31595711 AGAAGAG
1 AGAAGAG
31595718 AGAAGAG
1 AGAAGAG
31595725 AGAAGAG
1 AGAAGAG
31595732 AGAAGA
1 AGAAGA
31595738 AAAGAATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (7 bp):
AGAAGAG
Found at i:31596063 original size:16 final size:16
Alignment explanation
Indices: 31596042--31596081 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
31596032 CGTTTGGTTC
31596042 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
31596058 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
31596074 GCTGTAAT
1 GCTGTAAT
31596082 CAGTAATTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.35, C:0.07, G:0.30, T:0.28
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:31596318 original size:58 final size:55
Alignment explanation
Indices: 31596251--31596396 Score: 177
Period size: 58 Copynumber: 2.5 Consensus size: 55
31596241 AATTTTAATG
*
31596251 ATTATTATTAAATATAATTGAATAAAAATAT-TAATTTATTTAATTATATTTTAACATA
1 ATTATTATTAAATATAATT-AATAAAAATATGTAATTTA-ATAA-TAT-TTTTAACATA
*
31596309 ATTATTATTAAATATAATTTAATAAAATAATATGTAATTTAATAATATTTTTAATATA
1 ATTATTATTAAATATAA-TTAAT-AAA-AATATGTAATTTAATAATATTTTTAACATA
*
31596367 ATTATTATTAAAATATGAATTAGTAAAAAT
1 ATTATTATT-AAATAT-AATTAATAAAAAT
31596397 TATAATATAT
Statistics
Matches: 79, Mismatches: 3, Indels: 13
0.83 0.03 0.14
Matches are distributed among these distances:
57 3 0.04
58 41 0.52
59 18 0.23
60 10 0.13
61 7 0.09
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.47
Consensus pattern (55 bp):
ATTATTATTAAATATAATTAATAAAAATATGTAATTTAATAATATTTTTAACATA
Found at i:31600007 original size:57 final size:58
Alignment explanation
Indices: 31599939--31600065 Score: 154
Period size: 58 Copynumber: 2.2 Consensus size: 58
31599929 TATTTTAATG
* * *
31599939 ATTATTATTAAATATAATGTAA-AAAA-AAT-T-TAATTTATTTAATTATATTTTAACATA
1 ATTATTATTAAATACAATGTAATAAAATAATATACAATTTA-ATAA-TAT-TTTTAACATA
* *
31599996 ATTATTATTAAATACAATTTAATAAAATAATATACAATTTAATAATATTTTTAATATA
1 ATTATTATTAAATACAATGTAATAAAATAATATACAATTTAATAATATTTTTAACATA
31600054 ATTATTATTAAA
1 ATTATTATTAAA
31600066 ATATGAATTA
Statistics
Matches: 61, Mismatches: 5, Indels: 7
0.84 0.07 0.10
Matches are distributed among these distances:
57 20 0.33
58 25 0.41
59 6 0.10
60 4 0.07
61 6 0.10
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.46
Consensus pattern (58 bp):
ATTATTATTAAATACAATGTAATAAAATAATATACAATTTAATAATATTTTTAACATA
Found at i:31603953 original size:8 final size:8
Alignment explanation
Indices: 31603940--31603967 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
31603930 TCTTATTTCT
31603940 TTTTTTTA
1 TTTTTTTA
31603948 TTTTTTTA
1 TTTTTTTA
31603956 TTTTTTTA
1 TTTTTTTA
31603964 TTTT
1 TTTT
31603968 ATAATACACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.11, C:0.00, G:0.00, T:0.89
Consensus pattern (8 bp):
TTTTTTTA
Found at i:31604741 original size:18 final size:19
Alignment explanation
Indices: 31604707--31604757 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
31604697 ATGACAAAAA
*
31604707 TAATAAAAATCAATAAATGT
1 TAATAAAAAT-ATTAAATGT
* *
31604727 T-ATAAAATTATTAAATTT
1 TAATAAAAATATTAAATGT
31604745 TAATAAAAATATT
1 TAATAAAAATATT
31604758 TAAAAATTAG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 8 0.31
19 17 0.65
20 1 0.04
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (19 bp):
TAATAAAAATATTAAATGT
Found at i:31604782 original size:29 final size:28
Alignment explanation
Indices: 31604746--31604867 Score: 115
Period size: 29 Copynumber: 4.3 Consensus size: 28
31604736 ATTAAATTTT
* *
31604746 AATA-AAAATATTTAAAAATTAGAAAAAA
1 AATATAAAATATATAAAAATTA-TAAAAA
* *
31604774 AATATAAAATATAGAAAAATTATAAAAT
1 AATATAAAATATATAAAAATTATAAAAA
** *
31604802 TTTATAAAATCATAAAAAAATTATAAAAA
1 AATATAAAAT-ATATAAAAATTATAAAAA
31604831 AATATAAAA-ATAT-AAAATTCATTAAAAA
1 AATATAAAATATATAAAAATT-A-TAAAAA
*
31604859 ATTATAAAA
1 AATATAAAA
31604868 ATTATCGTAT
Statistics
Matches: 78, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
26 6 0.08
27 4 0.05
28 30 0.38
29 38 0.49
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.29
Consensus pattern (28 bp):
AATATAAAATATATAAAAATTATAAAAA
Found at i:31604819 original size:47 final size:46
Alignment explanation
Indices: 31604746--31604868 Score: 133
Period size: 47 Copynumber: 2.6 Consensus size: 46
31604736 ATTAAATTTT
* *
31604746 AATA-AAAATATTTAAAAATTAGAAAAAAAATAT-AAAATATAGAAA
1 AATATAAAAT-TTTAAAAATTATAAAAAAAATATAAAAAAATAGAAA
* * *
31604791 AATTATAAAATTTTATAAAATCATAAAAAAATTATAAAAAAATATAAA
1 AA-TATAAAATTTTA-AAAATTATAAAAAAAATATAAAAAAATAGAAA
31604839 AATATAAAATTCATTAAAAAATTATAAAAA
1 AATATAAAATT--TT-AAAAATTATAAAAA
31604869 TTATCGTATC
Statistics
Matches: 65, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
45 2 0.03
46 6 0.09
47 30 0.46
48 12 0.18
49 14 0.22
50 1 0.02
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (46 bp):
AATATAAAATTTTAAAAATTATAAAAAAAATATAAAAAAATAGAAA
Found at i:31604821 original size:58 final size:59
Alignment explanation
Indices: 31604730--31604844 Score: 155
Period size: 58 Copynumber: 2.0 Consensus size: 59
31604720 TAAATGTTAT
* **
31604730 AAAATTATTAAATTTTAATAAAAATATTTAAAAATTAGAAAAAAAATAT-AAAATATAGA
1 AAAATTATAAAATTTTAATAAAAATATAAAAAAATTA-AAAAAAAATATAAAAATATAGA
*
31604789 AAAATTATAAAATTTT-AT-AAAATCATAAAAAAATTATAAAAAAATATAAAAATATA
1 AAAATTATAAAATTTTAATAAAAAT-ATAAAAAAATTAAAAAAAAATATAAAAATATA
31604845 AAATTCATTA
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
57 15 0.30
58 20 0.40
59 15 0.30
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.31
Consensus pattern (59 bp):
AAAATTATAAAATTTTAATAAAAATATAAAAAAATTAAAAAAAAATATAAAAATATAGA
Found at i:31604827 original size:11 final size:11
Alignment explanation
Indices: 31604807--31604840 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
31604797 AAAATTTTAT
*
31604807 AAAATCATAAA
1 AAAATTATAAA
31604818 AAAATTATAAA
1 AAAATTATAAA
31604829 AAAA-TATAAA
1 AAAATTATAAA
31604839 AA
1 AA
31604841 TATAAAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 8 0.36
11 14 0.64
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (11 bp):
AAAATTATAAA
Found at i:31604862 original size:8 final size:9
Alignment explanation
Indices: 31604702--31604872 Score: 71
Period size: 10 Copynumber: 18.0 Consensus size: 9
31604692 GACATATGAC
*
31604702 AAAAATAAT
1 AAAAATTAT
*
31604711 AAAAATCAAT
1 AAAAAT-TAT
**
31604721 AAATGTTAT
1 AAAAATTAT
31604730 -AAAATTATT
1 AAAAATTA-T
**
31604739 AAATTTTAAT
1 AAAAATT-AT
*
31604749 AAAAATATTT
1 AAAAAT-TAT
*
31604759 AAAAATTAG
1 AAAAATTAT
**
31604768 AAAAAAAAT
1 AAAAATTAT
*
31604777 ATAAAATATAG
1 A-AAAAT-TAT
31604788 AAAAATTAT
1 AAAAATTAT
*
31604797 -AAAATTTT
1 AAAAATTAT
*
31604805 ATAAAATCATAA
1 A-AAAAT--TAT
31604817 AAAAATTAT
1 AAAAATTAT
*
31604826 AAAAAAATAT
1 -AAAAATTAT
31604836 AAAAA-TAT
1 AAAAATTAT
31604844 -AAAATTCATT
1 AAAAATT-A-T
31604854 AAAAAATTAT
1 -AAAAATTAT
31604864 AAAAATTAT
1 AAAAATTAT
31604873 CGTATCTCAT
Statistics
Matches: 121, Mismatches: 24, Indels: 34
0.68 0.13 0.19
Matches are distributed among these distances:
7 4 0.03
8 16 0.13
9 36 0.30
10 47 0.39
11 10 0.08
12 8 0.07
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:31604866 original size:10 final size:10
Alignment explanation
Indices: 31604747--31604872 Score: 67
Period size: 9 Copynumber: 13.2 Consensus size: 10
31604737 TTAAATTTTA
31604747 ATAAAAATATT
1 ATAAAAA-ATT
31604758 -T-AAAAATT
1 ATAAAAAATT
* *
31604766 AGAAAAAA-A
1 ATAAAAAATT
*
31604775 ATATAAAA-T
1 ATAAAAAATT
31604784 ATAGAAAAATT
1 ATA-AAAAATT
31604795 AT--AAAATT
1 ATAAAAAATT
* * *
31604803 TTATAAAATC
1 ATAAAAAATT
31604813 ATAAAAAAATT
1 AT-AAAAAATT
*
31604824 ATAAAAAAAT
1 ATAAAAAATT
31604834 AT-AAAAA-T
1 ATAAAAAATT
31604842 AT--AAAATT
1 ATAAAAAATT
31604850 CATTAAAAAATT
1 -A-TAAAAAATT
31604862 AT-AAAAATT
1 ATAAAAAATT
31604871 AT
1 AT
31604873 CGTATCTCAT
Statistics
Matches: 91, Mismatches: 12, Indels: 26
0.71 0.09 0.20
Matches are distributed among these distances:
7 4 0.04
8 14 0.15
9 28 0.31
10 27 0.30
11 12 0.13
12 6 0.07
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (10 bp):
ATAAAAAATT
Found at i:31606652 original size:17 final size:20
Alignment explanation
Indices: 31606617--31606654 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
31606607 TAGAAAAATC
31606617 TTATTATGTATAAATTATAA
1 TTATTATGTATAAATTATAA
31606637 TTATTA-GT-TAAATATATA
1 TTATTATGTATAAAT-TATA
31606655 GTTTTCAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 5 0.29
19 6 0.35
20 6 0.35
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (20 bp):
TTATTATGTATAAATTATAA
Found at i:31608100 original size:21 final size:21
Alignment explanation
Indices: 31608060--31608108 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
31608050 AAATTAAAAA
31608060 ATTTATATTTATATTATTTTT
1 ATTTATATTTATATTATTTTT
31608081 ATTTAATATTTAATATT-TTTTT
1 ATTT-ATATTT-ATATTATTTTT
*
31608103 ACTTAT
1 ATTTAT
31608109 TGAAATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 6 0.24
22 14 0.56
23 5 0.20
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (21 bp):
ATTTATATTTATATTATTTTT
Found at i:31608395 original size:34 final size:35
Alignment explanation
Indices: 31608357--31608423 Score: 111
Period size: 35 Copynumber: 1.9 Consensus size: 35
31608347 ATTCATGTTG
31608357 TCTCAAG-TTTTATATG-TTTTAGATCTGCAAGTCT
1 TCTCAAGTTTTTATATGTTTTTA-ATCTGCAAGTCT
31608391 TCTCAAGTTTTTATATGTTTTTAATCTGCAAGT
1 TCTCAAGTTTTTATATGTTTTTAATCTGCAAGT
31608424 TTTATTAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
34 7 0.23
35 19 0.61
36 5 0.16
ACGTcount: A:0.24, C:0.13, G:0.13, T:0.49
Consensus pattern (35 bp):
TCTCAAGTTTTTATATGTTTTTAATCTGCAAGTCT
Found at i:31608597 original size:15 final size:16
Alignment explanation
Indices: 31608564--31608600 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
31608554 TTTCACTTTG
31608564 TGTGATAGTGGGTGTA
1 TGTGATAGTGGGTGTA
*
31608580 TGTGTTAGTGGG-GTA
1 TGTGATAGTGGGTGTA
31608595 TGTGAT
1 TGTGAT
31608601 GGGTAGTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.16, C:0.00, G:0.43, T:0.41
Consensus pattern (16 bp):
TGTGATAGTGGGTGTA
Found at i:31610041 original size:23 final size:23
Alignment explanation
Indices: 31610015--31610073 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
31610005 TTTATTTAAT
*
31610015 TTAATCGAACATATTTATGAACA
1 TTAATCGAACATATTCATGAACA
* **
31610038 TTAAACGAACACGTTCATGAACA
1 TTAATCGAACATATTCATGAACA
*
31610061 TATAATTGAACAT
1 T-TAATCGAACAT
31610074 GTACTCACGA
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
23 20 0.71
24 8 0.29
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (23 bp):
TTAATCGAACATATTCATGAACA
Found at i:31620911 original size:32 final size:32
Alignment explanation
Indices: 31620875--31620935 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
31620865 TTATTCTACT
* *
31620875 AATTGTATTTGTGCGAGTTGAATGATTATGCG
1 AATTGTATTTGTACGAGCTGAATGATTATGCG
31620907 AATTGTATTTGTACGAGCTGAATGATTAT
1 AATTGTATTTGTACGAGCTGAATGATTAT
31620936 ATGAACTATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.28, C:0.07, G:0.25, T:0.41
Consensus pattern (32 bp):
AATTGTATTTGTACGAGCTGAATGATTATGCG
Found at i:31621021 original size:32 final size:32
Alignment explanation
Indices: 31620977--31621038 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
31620967 TACTAACTCT
*
31620977 ATCTGTGCGAGTTGAATAATTATGTGAACTTC
1 ATCTGTGCGAGTTGAATAATTATGCGAACTTC
* *
31621009 ATCTGTGTGAGTTGAATGATTATGCGAACT
1 ATCTGTGCGAGTTGAATAATTATGCGAACT
31621039 GTATGTACGC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.27, C:0.11, G:0.24, T:0.37
Consensus pattern (32 bp):
ATCTGTGCGAGTTGAATAATTATGCGAACTTC
Found at i:31626480 original size:14 final size:14
Alignment explanation
Indices: 31626461--31626490 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
31626451 ATGCTGTTAT
31626461 CATGAAGCCCACTG
1 CATGAAGCCCACTG
*
31626475 CATGAAGCCTACTG
1 CATGAAGCCCACTG
31626489 CA
1 CA
31626491 GTGACATTGT
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:0.30, C:0.33, G:0.20, T:0.17
Consensus pattern (14 bp):
CATGAAGCCCACTG
Found at i:31661624 original size:21 final size:21
Alignment explanation
Indices: 31661600--31661653 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
31661590 CCTGTGCTAG
* *
31661600 TTCTATCGATAGAAGT-ATAAC
1 TTCTACCGATACAAGTCAT-AC
31661621 TTCTACCGATACAAGTCATAC
1 TTCTACCGATACAAGTCATAC
*
31661642 TTCTACTGATAC
1 TTCTACCGATAC
31661654 TAAAAGTCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 27 0.93
22 2 0.07
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.33
Consensus pattern (21 bp):
TTCTACCGATACAAGTCATAC
Found at i:31662385 original size:36 final size:36
Alignment explanation
Indices: 31662337--31662689 Score: 571
Period size: 36 Copynumber: 9.8 Consensus size: 36
31662327 GTTGTGAAAT
* *
31662337 TAAATATATGGGTATGTTATTCATGCCATGAGACAG
1 TAAATATGTGGGTATGTTATTCATGCCATGTGACAG
*
31662373 TAAATATGTGGGTATGTTATTCATCCCATGTGACAG
1 TAAATATGTGGGTATGTTATTCATGCCATGTGACAG
* * *
31662409 TAAATATGTAGGTATGTTATTCATGCCATGAGATAG
1 TAAATATGTGGGTATGTTATTCATGCCATGTGACAG
31662445 TAAATATGTGGGTATGTTATTCATGCCATGTGACAG
1 TAAATATGTGGGTATGTTATTCATGCCATGTGACAG
* *
31662481 TAAATATGTGGGTATGTTATTCATTCCATGAGACAG
1 TAAATATGTGGGTATGTTATTCATGCCATGTGACAG
*
31662517 TAAATATGTGGGTCTGTTATTCATGCCATGTGACAG
1 TAAATATGTGGGTATGTTATTCATGCCATGTGACAG
* *
31662553 TATATATGTGGGTATGTTATTCATGCCATGAGACAG
1 TAAATATGTGGGTATGTTATTCATGCCATGTGACAG
*
31662589 TAAATATGTGGGTATGTTACTCATGCCATGTGACAG
1 TAAATATGTGGGTATGTTATTCATGCCATGTGACAG
*
31662625 TAAATATGTGGGTATGTTATTCATGCCATGTGACTG
1 TAAATATGTGGGTATGTTATTCATGCCATGTGACAG
* *
31662661 TGAATATGTGAGTATGTTATTCATGCCAT
1 TAAATATGTGGGTATGTTATTCATGCCAT
31662690 ATGATTGTGA
Statistics
Matches: 292, Mismatches: 25, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 292 1.00
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.36
Consensus pattern (36 bp):
TAAATATGTGGGTATGTTATTCATGCCATGTGACAG
Found at i:31670837 original size:30 final size:28
Alignment explanation
Indices: 31670797--31670985 Score: 162
Period size: 30 Copynumber: 6.3 Consensus size: 28
31670787 TAAATCATTT
*
31670797 TTTAACCCCCAAAGTTTTTAAAAATTCAAA
1 TTTAA-CCCCAAA-TTTTCAAAAATTCAAA
* *
31670827 TTTAAGCCCCAGATTTTCTAAAAATTGAAA
1 TTTAA-CCCCAAATTTTC-AAAAATTCAAA
* * *
31670857 TTTCACCCCCAAATGTTCCAAAAATTCATA
1 TTT-AACCCCAAAT-TTTCAAAAATTCAAA
*
31670887 TTTAATCCCCAAAGTTTTCAAAAATTTAAA
1 TTTAA-CCCCAAA-TTTTCAAAAATTCAAA
* **
31670917 TTTGATCCTTAAATTTTCCAAAAATTCAAA
1 TTT-AACCCCAAATTTT-CAAAAATTCAAA
* *
31670947 TTTAACCCCTAAAGTTTTCAAAAAATAAAA
1 TTTAACCCC-AAA-TTTTCAAAAATTCAAA
31670977 TTTAACCCC
1 TTTAACCCC
31670986 GTTTTAATGT
Statistics
Matches: 128, Mismatches: 22, Indels: 18
0.76 0.13 0.11
Matches are distributed among these distances:
29 12 0.09
30 106 0.83
31 10 0.08
ACGTcount: A:0.41, C:0.21, G:0.04, T:0.34
Consensus pattern (28 bp):
TTTAACCCCAAATTTTCAAAAATTCAAA
Found at i:31670880 original size:60 final size:59
Alignment explanation
Indices: 31670816--31670985 Score: 198
Period size: 60 Copynumber: 2.8 Consensus size: 59
31670806 CAAAGTTTTT
*
31670816 AAAAATTCAAATTTAAGCCCCAGA-TTTTCTAAAAATTGAAATTTCACCCCCAAATGTTCC
1 AAAAATTCAAATTTAA-CCCCAAAGTTTTC-AAAAATTGAAATTTCACCCCCAAATGTTCC
* * * * ** *
31670876 AAAAATTCATATTTAATCCCCAAAGTTTTCAAAAATTTAAATTTGATCCTTAAATTTTCC
1 AAAAATTCAAATTTAA-CCCCAAAGTTTTCAAAAATTGAAATTTCACCCCCAAATGTTCC
* * *
31670936 AAAAATTCAAATTTAACCCCTAAAGTTTTCAAAAAATAAAATTTAACCCC
1 AAAAATTCAAATTTAACCCC-AAAGTTTTCAAAAATTGAAATTTCACCCC
31670986 GTTTTAATGT
Statistics
Matches: 93, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
59 4 0.04
60 84 0.90
61 5 0.05
ACGTcount: A:0.43, C:0.20, G:0.04, T:0.33
Consensus pattern (59 bp):
AAAAATTCAAATTTAACCCCAAAGTTTTCAAAAATTGAAATTTCACCCCCAAATGTTCC
Found at i:31670980 original size:90 final size:89
Alignment explanation
Indices: 31670797--31670985 Score: 209
Period size: 90 Copynumber: 2.1 Consensus size: 89
31670787 TAAATCATTT
* * * * *
31670797 TTTAACCCCCAAAGTTTTTAAAAATTCAAATTTAAGCCCCAGATTTTCTAAAAATTGAAATTTCA
1 TTTAA-CCCCAAAGTTTTCAAAAATTCAAATTTAAGCCCCAAATTTTCCAAAAATTCAAATTTAA
* * *
31670862 CCCCCAAATGTTCCAAAAATTCATA
65 CCCCCAAATGTTCCAAAAAATAAAA
* * * **
31670887 TTTAATCCCCAAAGTTTTCAAAAATTTAAATTTGATCCTTAAATTTTCCAAAAATTCAAATTTAA
1 TTTAA-CCCCAAAGTTTTCAAAAATTCAAATTTAAGCCCCAAATTTTCCAAAAATTCAAATTTAA
* *
31670952 CCCCTAAA-GTTTTCAAAAAATAAAA
65 CCCCCAAATG-TTCCAAAAAATAAAA
31670977 TTTAACCCC
1 TTTAACCCC
31670986 GTTTTAATGT
Statistics
Matches: 82, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
89 5 0.06
90 77 0.94
ACGTcount: A:0.41, C:0.21, G:0.04, T:0.34
Consensus pattern (89 bp):
TTTAACCCCAAAGTTTTCAAAAATTCAAATTTAAGCCCCAAATTTTCCAAAAATTCAAATTTAAC
CCCCAAATGTTCCAAAAAATAAAA
Found at i:31680008 original size:14 final size:15
Alignment explanation
Indices: 31679984--31680014 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
31679974 GAGTTGTTTG
31679984 AAAGCATAAAAATAA
1 AAAGCATAAAAATAA
31679999 AAAG-ATAAAAATAA
1 AAAGCATAAAAATAA
31680013 AA
1 AA
31680015 TAAATTAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.75
15 4 0.25
ACGTcount: A:0.77, C:0.03, G:0.06, T:0.13
Consensus pattern (15 bp):
AAAGCATAAAAATAA
Found at i:31683623 original size:50 final size:50
Alignment explanation
Indices: 31683512--31683660 Score: 149
Period size: 50 Copynumber: 2.9 Consensus size: 50
31683502 AACTAATGGA
* * *
31683512 TTACTAAATGCATGACT-TGATTTAATGATGCAAACTTCAACTAACATGGGAG
1 TTACTTAATGCATGA-TATGATTT-ATGATGCAAA-TTTAACTAACATGGAAG
* * * * *
31683564 TTACATAATGCATGATAGGATTTATGATGCATATTTAACTAACATGTAAT
1 TTACTTAATGCATGATATGATTTATGATGCAAATTTAACTAACATGGAAG
* *
31683614 TTACTTAATGCATG-TCATTATTTATGATGCAAACTTAACTAATCATG
1 TTACTTAATGCATGAT-ATGATTTATGATGCAAATTTAACTAA-CATG
31683661 AGAGTTAACG
Statistics
Matches: 81, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
49 1 0.01
50 48 0.59
51 14 0.17
52 18 0.22
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.36
Consensus pattern (50 bp):
TTACTTAATGCATGATATGATTTATGATGCAAATTTAACTAACATGGAAG
Found at i:31683894 original size:17 final size:17
Alignment explanation
Indices: 31683863--31683895 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
31683853 CAAACACATA
31683863 TTAAACTAAAATAAAAC
1 TTAAACTAAAATAAAAC
31683880 TTAAA-TAAAATTAAAA
1 TTAAACTAAAA-TAAAA
31683896 AGTCCTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (17 bp):
TTAAACTAAAATAAAAC
Found at i:31685231 original size:21 final size:21
Alignment explanation
Indices: 31685190--31685243 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
31685180 CTGCTTGATC
31685190 ACTTTCTTCTTT-TTCAATCTT
1 ACTTTCTT-TTTCTTCAATCTT
**
31685211 ACTTTCTTTTTCTTCTCTCTT
1 ACTTTCTTTTTCTTCAATCTT
* *
31685232 GCTCTCTTTTTC
1 ACTTTCTTTTTC
31685244 AATTTTCTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 3 0.11
21 25 0.89
ACGTcount: A:0.07, C:0.28, G:0.02, T:0.63
Consensus pattern (21 bp):
ACTTTCTTTTTCTTCAATCTT
Found at i:31685443 original size:16 final size:15
Alignment explanation
Indices: 31685424--31685457 Score: 59
Period size: 16 Copynumber: 2.2 Consensus size: 15
31685414 TCTCTCTCTC
31685424 TTTTCTCAATTTCTGT
1 TTTTCTCAATTTCT-T
31685440 TTTTCTCAATTTCTT
1 TTTTCTCAATTTCTT
31685455 TTT
1 TTT
31685458 CTCTACACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.12, C:0.18, G:0.03, T:0.68
Consensus pattern (15 bp):
TTTTCTCAATTTCTT
Found at i:31687130 original size:50 final size:50
Alignment explanation
Indices: 31687052--31687174 Score: 149
Period size: 50 Copynumber: 2.4 Consensus size: 50
31687042 TTGATTTAAA
*
31687052 GATGCAAACTTTAACTAACATGGGAGTTACATAATGCATGAT-AGGATTTAT
1 GATGCAAA-TTTAACTAACATGGAAGTTACATAATGCATG-TCAGGATTTAT
* * * **
31687103 GATGCATATTTAACTAACATGTAAGTTACTTAATGCATGTCATTATTTAT
1 GATGCAAATTTAACTAACATGGAAGTTACATAATGCATGTCAGGATTTAT
*
31687153 GATGCAAACTTAACTAATCATG
1 GATGCAAATTTAACTAA-CATG
31687175 AGAGTCAATG
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
49 1 0.02
50 50 0.81
51 11 0.18
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (50 bp):
GATGCAAATTTAACTAACATGGAAGTTACATAATGCATGTCAGGATTTAT
Found at i:31687396 original size:17 final size:17
Alignment explanation
Indices: 31687376--31687408 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
31687366 CAAATACTTA
31687376 TTAAATTAAAA-TAAAAC
1 TTAAA-TAAAATTAAAAC
31687393 TTAAATAAAATTAAAA
1 TTAAATAAAATTAAAA
31687409 AGTCCTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (17 bp):
TTAAATAAAATTAAAAC
Found at i:31688305 original size:23 final size:21
Alignment explanation
Indices: 31688269--31688346 Score: 57
Period size: 23 Copynumber: 3.4 Consensus size: 21
31688259 TGTTTATGCA
* *
31688269 TGCAAGTCAAAGTGACACTACAG
1 TGCAAGTGATAGTGACACT-C-G
*
31688292 TGCAAGTGATAGTGGCACTCTGG
1 TGCAAGTGATAGTGACACTC--G
* *
31688315 TGCAAGAGCTAGTGACACTTCG
1 TGCAAGTGATAGTGACAC-TCG
31688337 ATGCAAGTGA
1 -TGCAAGTGA
31688347 CAGTAGCACA
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
22 2 0.05
23 39 0.91
24 2 0.05
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.22
Consensus pattern (21 bp):
TGCAAGTGATAGTGACACTCG
Found at i:31703241 original size:13 final size:14
Alignment explanation
Indices: 31703212--31703241 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
31703202 TTCAGTACAT
31703212 TGACATTTAACCTC
1 TGACATTTAACCTC
31703226 TGACATTTAA-CTC
1 TGACATTTAACCTC
31703239 TGA
1 TGA
31703242 TTGCATTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (14 bp):
TGACATTTAACCTC
Found at i:31712193 original size:19 final size:18
Alignment explanation
Indices: 31712161--31712207 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 18
31712151 CAGTCATTTG
*
31712161 AAAAAGAAACAAAATGAGA
1 AAAAAGAAACAAAA-GAAA
31712180 AAAAAGAAGA-AAAAGAAA
1 AAAAAGAA-ACAAAAGAAA
31712198 AAGAAAGAAA
1 AA-AAAGAAA
31712208 TTTTTGATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 6 0.24
19 18 0.72
20 1 0.04
ACGTcount: A:0.79, C:0.02, G:0.17, T:0.02
Consensus pattern (18 bp):
AAAAAGAAACAAAAGAAA
Found at i:31715451 original size:18 final size:18
Alignment explanation
Indices: 31715430--31715465 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
31715420 AAGAAGATAC
*
31715430 AGAAGAGGATCCAGTGGA
1 AGAAGAAGATCCAGTGGA
*
31715448 AGAAGAAGATCCTGTGGA
1 AGAAGAAGATCCAGTGGA
31715466 GATTGAAGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.39, C:0.11, G:0.36, T:0.14
Consensus pattern (18 bp):
AGAAGAAGATCCAGTGGA
Found at i:31719655 original size:22 final size:22
Alignment explanation
Indices: 31719599--31719642 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
31719589 AACCTGCTCT
* *
31719599 GATGTCACGACATCTAACCTTC
1 GATGTCGCGACATCCAACCTTC
31719621 GATGTCGCGACATCCAACCTTC
1 GATGTCGCGACATCCAACCTTC
31719643 AGTGTCTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.25, C:0.34, G:0.16, T:0.25
Consensus pattern (22 bp):
GATGTCGCGACATCCAACCTTC
Found at i:31720190 original size:199 final size:199
Alignment explanation
Indices: 31719850--31720246 Score: 785
Period size: 199 Copynumber: 2.0 Consensus size: 199
31719840 TTGACCCTCT
*
31719850 ATTGTAACCAAACTTTAGCGAAAGCCTATAAATAACTTGAATAACTCCAAAGGAGTGCAATTATA
1 ATTGTAACCAAACTTTAGCGAAAGCCTATAAATAACTTGAATAACTCCAAAGGAGTCCAATTATA
31719915 TTAAAGTAAAGTTCTAAAATTTGTGATCGAGTTGAGTAGCTTAGTGCATTAATGTGACATCCCTT
66 TTAAAGTAAAGTTCTAAAATTTGTGATCGAGTTGAGTAGCTTAGTGCATTAATGTGACATCCCTT
31719980 ACTCGTGACAAATCGATTTATTCTGGGTAAGGGGTGTTACATTAGATCCTGGCCTCCTACCTCTT
131 ACTCGTGACAAATCGATTTATTCTGGGTAAGGGGTGTTACATTAGATCCTGGCCTCCTACCTCTT
31720045 AGTG
196 AGTG
31720049 ATTGTAACCAAACTTTAGCGAAAGCCTATAAATAACTTGAATAACTCCAAAGGAGTCCAATTATA
1 ATTGTAACCAAACTTTAGCGAAAGCCTATAAATAACTTGAATAACTCCAAAGGAGTCCAATTATA
31720114 TTAAAGTAAAGTTCTAAAATTTGTGATCGAGTTGAGTAGCTTAGTGCATTAATGTGACATCCCTT
66 TTAAAGTAAAGTTCTAAAATTTGTGATCGAGTTGAGTAGCTTAGTGCATTAATGTGACATCCCTT
31720179 ACTCGTGACAAATCGATTTATTCTGGGTAAGGGGTGTTACATTAGATCCTGGCCTCCTACCTCTT
131 ACTCGTGACAAATCGATTTATTCTGGGTAAGGGGTGTTACATTAGATCCTGGCCTCCTACCTCTT
31720244 AGT
196 AGT
31720247 AGGGTTGGCA
Statistics
Matches: 197, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
199 197 1.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (199 bp):
ATTGTAACCAAACTTTAGCGAAAGCCTATAAATAACTTGAATAACTCCAAAGGAGTCCAATTATA
TTAAAGTAAAGTTCTAAAATTTGTGATCGAGTTGAGTAGCTTAGTGCATTAATGTGACATCCCTT
ACTCGTGACAAATCGATTTATTCTGGGTAAGGGGTGTTACATTAGATCCTGGCCTCCTACCTCTT
AGTG
Found at i:31723624 original size:26 final size:26
Alignment explanation
Indices: 31723588--31723641 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
31723578 AATAGGGAGT
*
31723588 AAAATAAGCATCATGACCTTTGGGTC
1 AAAATAAGCATCATGACCTTTAGGTC
*
31723614 AAAATGAGCATCATGACCTTTAGGTC
1 AAAATAAGCATCATGACCTTTAGGTC
31723640 AA
1 AA
31723642 CAGGGAGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.26
Consensus pattern (26 bp):
AAAATAAGCATCATGACCTTTAGGTC
Found at i:31728501 original size:36 final size:37
Alignment explanation
Indices: 31728450--31728546 Score: 160
Period size: 37 Copynumber: 2.6 Consensus size: 37
31728440 TGGTAACAGG
*
31728450 CATGACCTTTAGGTCAACAGGGAGT-AAAATGAGCAT
1 CATGACCTTTGGGTCAACAGGGAGTAAAAATGAGCAT
*
31728486 CATGACCTTTGGGTCAACAAGGAGTAAAAATGAGCAT
1 CATGACCTTTGGGTCAACAGGGAGTAAAAATGAGCAT
*
31728523 CATGGCCTTTGGGTCAACAGGGAG
1 CATGACCTTTGGGTCAACAGGGAG
31728547 CAAATCGAAT
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
36 23 0.41
37 33 0.59
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.22
Consensus pattern (37 bp):
CATGACCTTTGGGTCAACAGGGAGTAAAAATGAGCAT
Found at i:31729293 original size:21 final size:21
Alignment explanation
Indices: 31729264--31729315 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
31729254 TGGATTTTTA
31729264 GTATCGGTAGAAG-CATGACAT
1 GTATCGGTAGAAGTCAT-ACAT
* *
31729285 GTTTCGGTAGAAGTCATACTT
1 GTATCGGTAGAAGTCATACAT
31729306 GTATCGGTAG
1 GTATCGGTAG
31729316 TATTGTCTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 24 0.89
22 3 0.11
ACGTcount: A:0.27, C:0.13, G:0.29, T:0.31
Consensus pattern (21 bp):
GTATCGGTAGAAGTCATACAT
Found at i:31746117 original size:13 final size:13
Alignment explanation
Indices: 31746099--31746131 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
31746089 ATTGTGAATG
31746099 AGAAAAAGAGAAA
1 AGAAAAAGAGAAA
31746112 AGAAAAA-AGAAA
1 AGAAAAAGAGAAA
31746124 A-AAAAAGA
1 AGAAAAAGA
31746132 AATATTGCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.26
12 7 0.37
13 7 0.37
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (13 bp):
AGAAAAAGAGAAA
Found at i:31773781 original size:24 final size:24
Alignment explanation
Indices: 31773748--31773798 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
31773738 CCAAACAAAA
* *
31773748 TTAGCACTTATGAGCCTAGGAAGG
1 TTAGCACTTACGAGCCCAGGAAGG
* *
31773772 TTAGCTCTTACGAGCCCAGTAAGG
1 TTAGCACTTACGAGCCCAGGAAGG
31773796 TTA
1 TTA
31773799 ACCAGTATAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.27
Consensus pattern (24 bp):
TTAGCACTTACGAGCCCAGGAAGG
Found at i:31776269 original size:24 final size:24
Alignment explanation
Indices: 31776210--31776272 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
31776200 CCAAATAGAA
*
31776210 TTAGCTCTTACAAGCCAAAAAAGG
1 TTAGCTCTTACGAGCCAAAAAAGG
* * * *
31776234 TTAGCTTTTACGAGCCCAGAGAGG
1 TTAGCTCTTACGAGCCAAAAAAGG
31776258 TTAGCTCTTACGAGC
1 TTAGCTCTTACGAGC
31776273 TCGAAAAGGT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.25
Consensus pattern (24 bp):
TTAGCTCTTACGAGCCAAAAAAGG
Found at i:31776282 original size:24 final size:23
Alignment explanation
Indices: 31776210--31776284 Score: 78
Period size: 24 Copynumber: 3.1 Consensus size: 23
31776200 CCAAATAGAA
*
31776210 TTAGCTCTTACAAGCCAAAAAAGG
1 TTAGCTCTTACGAGCC-AAAAAGG
* * *
31776234 TTAGCTTTTACGAGCCCAGAGAGG
1 TTAGCTCTTACGAG-CCAAAAAGG
*
31776258 TTAGCTCTTACGAGCTCGAAAAGG
1 TTAGCTCTTACGAGC-CAAAAAGG
31776282 TTA
1 TTA
31776285 ACTAGTATAC
Statistics
Matches: 41, Mismatches: 8, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
23 1 0.02
24 38 0.93
25 2 0.05
ACGTcount: A:0.32, C:0.20, G:0.23, T:0.25
Consensus pattern (23 bp):
TTAGCTCTTACGAGCCAAAAAGG
Found at i:31777888 original size:25 final size:24
Alignment explanation
Indices: 31777822--31777897 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
31777812 GTATACTGGT
*
31777822 TAACCTTTCTGGGCTCGTAAGAAC
1 TAACCTTTCTGGGCTCGTAAGAGC
*
31777846 TAACCTTCCTGGGCTCGTAAGAGC
1 TAACCTTTCTGGGCTCGTAAGAGC
** *
31777870 TAATTTTGTCTGGGCTCGTATGAGC
1 TAACCTT-TCTGGGCTCGTAAGAGC
31777895 TAA
1 TAA
31777898 ATTCTGGAAG
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
24 27 0.60
25 18 0.40
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (24 bp):
TAACCTTTCTGGGCTCGTAAGAGC
Found at i:31778522 original size:21 final size:23
Alignment explanation
Indices: 31778474--31778527 Score: 76
Period size: 21 Copynumber: 2.4 Consensus size: 23
31778464 TGATACTAAA
*
31778474 GTATCGGTAGTTCTGATCATAGTT
1 GTATCGGTAGTTCTGA-CATACTT
31778498 GTATCGGTAGTT-TGA-ATACTT
1 GTATCGGTAGTTCTGACATACTT
31778519 GTATCGGTA
1 GTATCGGTA
31778528 AAAGTTATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 14 0.48
23 3 0.10
24 12 0.41
ACGTcount: A:0.22, C:0.11, G:0.26, T:0.41
Consensus pattern (23 bp):
GTATCGGTAGTTCTGACATACTT
Found at i:31783592 original size:19 final size:19
Alignment explanation
Indices: 31783568--31783610 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
31783558 AACACATTTG
31783568 ATATTCACATCAACGTCAC
1 ATATTCACATCAACGTCAC
* **
31783587 ATATTCATATCAATTTCAC
1 ATATTCACATCAACGTCAC
31783606 ATATT
1 ATATT
31783611 TTCATATCTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.37, C:0.23, G:0.02, T:0.37
Consensus pattern (19 bp):
ATATTCACATCAACGTCAC
Found at i:31783867 original size:45 final size:45
Alignment explanation
Indices: 31783800--31783921 Score: 163
Period size: 45 Copynumber: 2.7 Consensus size: 45
31783790 ACCACTCCGA
* * *
31783800 GTTGCCCGACAATGATGGCTCACTTATATTGAATTGCTACCTCGG
1 GTTGCCCGACAACGATAGCTCACTTATATTGAATTGCTACCCCGG
* * * *
31783845 GTTGCCCGGCAACGATAACTCACTTATGTTAAATTGCTACCCCGG
1 GTTGCCCGACAACGATAGCTCACTTATATTGAATTGCTACCCCGG
* *
31783890 GTTACTCGACAACGATAGCTCACTTATATTGA
1 GTTGCCCGACAACGATAGCTCACTTATATTGA
31783922 TATGCAGTTA
Statistics
Matches: 64, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 64 1.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (45 bp):
GTTGCCCGACAACGATAGCTCACTTATATTGAATTGCTACCCCGG
Found at i:31791386 original size:19 final size:19
Alignment explanation
Indices: 31791362--31791460 Score: 103
Period size: 19 Copynumber: 5.3 Consensus size: 19
31791352 AACACATTTG
* * *
31791362 ATATTCACGTCAATTTTAC
1 ATATTCACATCAACTTCAC
*
31791381 ATATTCACATCAACGTCAC
1 ATATTCACATCAACTTCAC
*
31791400 ATATTCACATCAACATCAC
1 ATATTCACATCAACTTCAC
* *
31791419 ATATTCACAACAATTTCAC
1 ATATTCACATCAACTTCAC
*
31791438 ATATTC-CA-CAAATTTCAC
1 ATATTCACATC-AACTTCAC
31791456 ATATT
1 ATATT
31791461 TTCATATCTC
Statistics
Matches: 71, Mismatches: 8, Indels: 3
0.87 0.10 0.04
Matches are distributed among these distances:
17 1 0.01
18 15 0.21
19 55 0.77
ACGTcount: A:0.38, C:0.26, G:0.02, T:0.33
Consensus pattern (19 bp):
ATATTCACATCAACTTCAC
Found at i:31791752 original size:45 final size:45
Alignment explanation
Indices: 31791701--31791855 Score: 159
Period size: 45 Copynumber: 3.4 Consensus size: 45
31791691 GAAAATGATG
* *
31791701 GCTCACTTATATTAAAATGCTACCCCGAGTTACCCGACAACGATA
1 GCTCACTTATATTAAAATGCTACCCCGGGTTACACGACAACGATA
* * * * * * * *
31791746 GCTCACTTATGTCAAATTGTTACCTCGGGTTACATGGCAATGATA
1 GCTCACTTATATTAAAATGCTACCCCGGGTTACACGACAACGATA
* * * *
31791791 GCTCACTTATATTGAATTGCTACCCCGGGTTGCAC-AGCGACGATA
1 GCTCACTTATATTAAAATGCTACCCCGGGTTACACGA-CAACGATA
*
31791836 GCTCACTTATATTGAAATGC
1 GCTCACTTATATTAAAATGC
31791856 AGTTAAACTG
Statistics
Matches: 88, Mismatches: 21, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
45 88 1.00
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (45 bp):
GCTCACTTATATTAAAATGCTACCCCGGGTTACACGACAACGATA
Found at i:31792700 original size:60 final size:60
Alignment explanation
Indices: 31792626--31792869 Score: 359
Period size: 60 Copynumber: 4.1 Consensus size: 60
31792616 GAGACTACAT
* * * *
31792626 TAGATTCCACACACAACATTTATTTCATTTAAGAACACTTGGACAACTTAAAGAATAGTC
1 TAGATCCCAAACACAACATTTATTTCATTTAAGAACACTTGAACAACTTAAAGTATAGTC
* * * *
31792686 TAAATCCCAAACACAATATTTATTTCATATAAGAACACCTGAACAACTTAAAGTATAGTC
1 TAGATCCCAAACACAACATTTATTTCATTTAAGAACACTTGAACAACTTAAAGTATAGTC
*
31792746 TAGATCCC--ACAC-ACTATTTATTTCATTTAAGAACACTTGAACAACTTAAAGTATATTC
1 TAGATCCCAAACACAAC-ATTTATTTCATTTAAGAACACTTGAACAACTTAAAGTATAGTC
* *
31792804 TAGATCCCAAAAACAATATTTATTTCATTTAAGAACACTTGAACAACTTAAAGTATAGTC
1 TAGATCCCAAACACAACATTTATTTCATTTAAGAACACTTGAACAACTTAAAGTATAGTC
31792864 TAGATC
1 TAGATC
31792870 TCACACCTTT
Statistics
Matches: 164, Mismatches: 16, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
57 1 0.01
58 52 0.32
60 110 0.67
61 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.08, T:0.31
Consensus pattern (60 bp):
TAGATCCCAAACACAACATTTATTTCATTTAAGAACACTTGAACAACTTAAAGTATAGTC
Found at i:31792793 original size:118 final size:118
Alignment explanation
Indices: 31792626--31792875 Score: 394
Period size: 118 Copynumber: 2.1 Consensus size: 118
31792616 GAGACTACAT
*
31792626 TAGATTCCACACACAACATTTATTTCATTTAAGAACACTTGGACAACTTAAAGAATAGTCTAAAT
1 TAGA-TCC-CACACAACATTTATTTCATTTAAGAACACTTGAACAACTTAAAGAATAGTCTAAAT
*
31792691 CCCAAACACAATATTTATTTCATATAAGAACACCTGAACAACTTAAAGTATAGTC
64 CCCAAAAACAATATTTATTTCATATAAGAACACCTGAACAACTTAAAGTATAGTC
* * *
31792746 TAGATCCCACAC-ACTATTTATTTCATTTAAGAACACTTGAACAACTTAAAGTATATTCTAGATC
1 TAGATCCCACACAAC-ATTTATTTCATTTAAGAACACTTGAACAACTTAAAGAATAGTCTAAATC
* *
31792810 CCAAAAACAATATTTATTTCATTTAAGAACACTTGAACAACTTAAAGTATAGTC
65 CCAAAAACAATATTTATTTCATATAAGAACACCTGAACAACTTAAAGTATAGTC
*
31792864 TAGATCTCACAC
1 TAGATCCCACAC
31792876 CTTTAATACC
Statistics
Matches: 121, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
117 2 0.02
118 112 0.93
119 3 0.02
120 4 0.03
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (118 bp):
TAGATCCCACACAACATTTATTTCATTTAAGAACACTTGAACAACTTAAAGAATAGTCTAAATCC
CAAAAACAATATTTATTTCATATAAGAACACCTGAACAACTTAAAGTATAGTC
Found at i:31806844 original size:84 final size:83
Alignment explanation
Indices: 31806669--31806844 Score: 205
Period size: 83 Copynumber: 2.1 Consensus size: 83
31806659 CTTTTATTGC
* * * ** *
31806669 TTCTT-TTACCTCATAAGATTAATGTTTAAGATATTTCTCGTAAAGGTAAAGGAGGGTTTAGAAA
1 TTCTTGTTACATCATAAGATTAATGTTTAAGATATTTATCATAAACATAAAGGAGGGTTCAGAAA
31806733 TATTTCATGCTAACCCTT
66 TATTTCATGCTAACCCTT
* * *
31806751 TTCTTGTTACATCATGAGATTAGTGTTTAGGATATTTATCATAAACATAAA-GAGGGTTCAGAAA
1 TTCTTGTTACATCATAAGATTAATGTTTAAGATATTTATCATAAACATAAAGGAGGGTTCAGAAA
* *
31806815 TCTATTTCTTGCTAAGCCTT
66 --TATTTCATGCTAACCCTT
31806835 TTGC-TGTTAC
1 TT-CTTGTTAC
31806845 TTTTACTTCA
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
82 17 0.22
83 37 0.47
84 24 0.30
85 1 0.01
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.40
Consensus pattern (83 bp):
TTCTTGTTACATCATAAGATTAATGTTTAAGATATTTATCATAAACATAAAGGAGGGTTCAGAAA
TATTTCATGCTAACCCTT
Found at i:31831565 original size:16 final size:16
Alignment explanation
Indices: 31831544--31831577 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
31831534 ATCAAAACGA
*
31831544 AATAATTTTACCTTTT
1 AATAATTTTAACTTTT
31831560 AATAATTTTAACTTTT
1 AATAATTTTAACTTTT
31831576 AA
1 AA
31831578 CTTTAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (16 bp):
AATAATTTTAACTTTT
Found at i:31832514 original size:5 final size:5
Alignment explanation
Indices: 31832504--31832535 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
31832494 TCAATCAATC
*
31832504 GTGCG GTGCG GTGCG GTGCG GTGAG GTGCG GT
1 GTGCG GTGCG GTGCG GTGCG GTGCG GTGCG GT
31832536 TGAATCTACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.03, C:0.16, G:0.59, T:0.22
Consensus pattern (5 bp):
GTGCG
Found at i:31832963 original size:47 final size:47
Alignment explanation
Indices: 31832909--31833003 Score: 190
Period size: 47 Copynumber: 2.0 Consensus size: 47
31832899 GAGAGAGAAA
31832909 ATAAAGAGGGTGATTGTAAAGGTAATTGTAAACTGAAATAGCATAAT
1 ATAAAGAGGGTGATTGTAAAGGTAATTGTAAACTGAAATAGCATAAT
31832956 ATAAAGAGGGTGATTGTAAAGGTAATTGTAAACTGAAATAGCATAAT
1 ATAAAGAGGGTGATTGTAAAGGTAATTGTAAACTGAAATAGCATAAT
31833003 A
1 A
31833004 AATGGATGTA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.45, C:0.04, G:0.23, T:0.27
Consensus pattern (47 bp):
ATAAAGAGGGTGATTGTAAAGGTAATTGTAAACTGAAATAGCATAAT
Found at i:31834564 original size:18 final size:18
Alignment explanation
Indices: 31834523--31834566 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
31834513 TTATTTGCCA
*
31834523 ATTAATCTATATCTAAAT
1 ATTAAACTATATCTAAAT
* **
31834541 AGTAAACTATATCTATTT
1 ATTAAACTATATCTAAAT
31834559 ATTAAACT
1 ATTAAACT
31834567 CCCAGCATCC
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.43, C:0.11, G:0.02, T:0.43
Consensus pattern (18 bp):
ATTAAACTATATCTAAAT
Done.