Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 114 of 135
Found at i:34089470 original size:14 final size:14
Alignment explanation
Indices: 34089451--34089481 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
34089441 GATAACTATT
34089451 ATGGATCCATACGA
1 ATGGATCCATACGA
34089465 ATGGATCCATACGA
1 ATGGATCCATACGA
34089479 ATG
1 ATG
34089482 AGCAAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.23
Consensus pattern (14 bp):
ATGGATCCATACGA
Found at i:34092289 original size:28 final size:28
Alignment explanation
Indices: 34092249--34092304 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
34092239 TGAGAAGTTA
*
34092249 TTCCAATTATTAATGAACACATGAACTG
1 TTCCAATTATTAATAAACACATGAACTG
34092277 TTCCAATTATTAATAAACACATGAACTG
1 TTCCAATTATTAATAAACACATGAACTG
34092305 CTGATTTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.41, C:0.18, G:0.09, T:0.32
Consensus pattern (28 bp):
TTCCAATTATTAATAAACACATGAACTG
Found at i:34098147 original size:17 final size:17
Alignment explanation
Indices: 34098125--34098170 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 17
34098115 ATTTAAAGAG
34098125 TAATTAATTTAAAATTT
1 TAATTAATTTAAAATTT
34098142 TAATTAA--TAAAA-TT
1 TAATTAATTTAAAATTT
* *
34098156 TATTTAATTAAAAAT
1 TAATTAATTTAAAAT
34098171 ATATTTTCGT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
14 8 0.33
15 5 0.21
16 4 0.17
17 7 0.29
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TAATTAATTTAAAATTT
Found at i:34098167 original size:15 final size:16
Alignment explanation
Indices: 34098125--34098168 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
34098115 ATTTAAAGAG
34098125 TAATTAATTTAAAATTT
1 TAATTAA-TTAAAATTT
34098142 TAATTAA-TAAAA-TT
1 TAATTAATTAAAATTT
*
34098156 TATTTAATTAAAA
1 TAATTAATTAAAA
34098169 ATATATTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 8 0.32
15 10 0.40
17 7 0.28
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TAATTAATTAAAATTT
Found at i:34098314 original size:15 final size:15
Alignment explanation
Indices: 34098294--34098339 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
34098284 ACAAAATAAT
34098294 AACGTAAATGATTAA
1 AACGTAAATGATTAA
*
34098309 AACGTAACAT--TTCA
1 AACGTAA-ATGATTAA
*
34098323 AACATAAATGATTAA
1 AACGTAAATGATTAA
34098338 AA
1 AA
34098340 TATAATTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
13 2 0.08
14 9 0.36
15 12 0.48
16 2 0.08
ACGTcount: A:0.54, C:0.11, G:0.09, T:0.26
Consensus pattern (15 bp):
AACGTAAATGATTAA
Found at i:34105593 original size:31 final size:31
Alignment explanation
Indices: 34105555--34105623 Score: 138
Period size: 31 Copynumber: 2.2 Consensus size: 31
34105545 ATGTTTAAAA
34105555 TGTTACGTTTTAGTCACTTATGTTAGTATTT
1 TGTTACGTTTTAGTCACTTATGTTAGTATTT
34105586 TGTTACGTTTTAGTCACTTATGTTAGTATTT
1 TGTTACGTTTTAGTCACTTATGTTAGTATTT
34105617 TGTTACG
1 TGTTACG
34105624 AAGTGGTCAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.19, C:0.10, G:0.17, T:0.54
Consensus pattern (31 bp):
TGTTACGTTTTAGTCACTTATGTTAGTATTT
Found at i:34105633 original size:31 final size:31
Alignment explanation
Indices: 34105565--34105634 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
34105555 TGTTACGTTT
***
34105565 TAGTCACTTATGTTAGTATTTTGTTACGTTT
1 TAGTCACTTATGTTAGTATTTTGTTACGAAG
34105596 TAGTCACTTATGTTAGTATTTTGTTACGAAG
1 TAGTCACTTATGTTAGTATTTTGTTACGAAG
*
34105627 TGGTCACT
1 TAGTCACT
34105635 GTGCCGTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.21, C:0.11, G:0.19, T:0.49
Consensus pattern (31 bp):
TAGTCACTTATGTTAGTATTTTGTTACGAAG
Found at i:34110132 original size:30 final size:31
Alignment explanation
Indices: 34110057--34110132 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 31
34110047 TTGGTTCAAT
* * * *
34110057 TTGGTACTCAAACTTGACTCTTTTTCCTAAT
1 TTGGTACTTAAACTTAACACTTTTTCCTAAG
* * *
34110088 TTGATACATAAACTTAACACTTTTT-TTAAG
1 TTGGTACTTAAACTTAACACTTTTTCCTAAG
34110118 TTGGTACTTAAACTT
1 TTGGTACTTAAACTT
34110133 TTTGGGGTCC
Statistics
Matches: 36, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
30 16 0.44
31 20 0.56
ACGTcount: A:0.29, C:0.17, G:0.09, T:0.45
Consensus pattern (31 bp):
TTGGTACTTAAACTTAACACTTTTTCCTAAG
Found at i:34110497 original size:22 final size:22
Alignment explanation
Indices: 34110469--34110510 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
34110459 AAATTGAGTC
*
34110469 AAAAAAT-TTAAATATCAAATTA
1 AAAAAATATCAAAT-TCAAATTA
34110491 AAAAAATATCAAATTCAAAT
1 AAAAAATATCAAATTCAAAT
34110511 ATCAAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (22 bp):
AAAAAATATCAAATTCAAATTA
Found at i:34111228 original size:2 final size:2
Alignment explanation
Indices: 34111223--34111258 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
34111213 TTGCCACACA
34111223 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
34111259 TAATCCCCAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:34112043 original size:5 final size:6
Alignment explanation
Indices: 34112025--34112052 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
34112015 TATTAAAATT
34112025 AAGAAA AAGAAA AAGAAA AAGAAA AAGA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGA
34112053 GAGAGATGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:34117471 original size:16 final size:17
Alignment explanation
Indices: 34117450--34117481 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
34117440 ATTTTGTACA
34117450 TATTATTG-TAATATTG
1 TATTATTGTTAATATTG
34117466 TATTATTGTTAATATT
1 TATTATTGTTAATATT
34117482 ATATGTAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.59
Consensus pattern (17 bp):
TATTATTGTTAATATTG
Found at i:34124089 original size:2 final size:2
Alignment explanation
Indices: 34124084--34124132 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
34124074 ATTTATAGTA
34124084 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
34124126 AT AT AT A
1 AT AT AT A
34124133 ATAGTATGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:34124385 original size:33 final size:33
Alignment explanation
Indices: 34124348--34124422 Score: 84
Period size: 32 Copynumber: 2.3 Consensus size: 33
34124338 TATATTCAAA
* *
34124348 AAAATTAATAAATTAAAAA-CTATATAAAT-TTTT
1 AAAA-TAATAAACTAAAAATC-AAATAAATATTTT
*
34124381 AAAATATTAAACTAAAAATCAAATAAATATTTT
1 AAAATAATAAACTAAAAATCAAATAAATATTTT
34124414 AAAA-AATAA
1 AAAATAATAA
34124423 TATGGATAGG
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
32 23 0.64
33 13 0.36
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (33 bp):
AAAATAATAAACTAAAAATCAAATAAATATTTT
Found at i:34125940 original size:24 final size:24
Alignment explanation
Indices: 34125912--34125962 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
34125902 AATTTGACTC
*
34125912 AAACAAATAAACAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAACTG
* *
34125936 AAACAATTAACCAGAGTTTAACTG
1 AAACAAATAAACAGAGTTTAACTG
34125960 AAA
1 AAA
34125963 GATTATTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.53, C:0.12, G:0.12, T:0.24
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAACTG
Found at i:34127918 original size:24 final size:24
Alignment explanation
Indices: 34127884--34127940 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
34127874 AATAAGAGTT
*
34127884 TAACTCAAACAAATAAACAAAGTA
1 TAACTGAAACAAATAAACAAAGTA
* * * *
34127908 TAATTGAAACAATTAAACAGAGTT
1 TAACTGAAACAAATAAACAAAGTA
34127932 TAACTGAAA
1 TAACTGAAA
34127941 GATTATTTCT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.56, C:0.12, G:0.09, T:0.23
Consensus pattern (24 bp):
TAACTGAAACAAATAAACAAAGTA
Found at i:34129872 original size:30 final size:30
Alignment explanation
Indices: 34129838--34129898 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
34129828 TTTTACCCTT
34129838 ACTCTTTTATTTAGAGCAAATT-AGCTCTCA
1 ACTCTTTTATTTAGAGCAAATTGA-CTCTCA
*
34129868 ACTCTTTTATTTGGAGCAAATTGACTCTCA
1 ACTCTTTTATTTAGAGCAAATTGACTCTCA
34129898 A
1 A
34129899 TATTTGAGGC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 28 0.97
31 1 0.03
ACGTcount: A:0.30, C:0.20, G:0.11, T:0.39
Consensus pattern (30 bp):
ACTCTTTTATTTAGAGCAAATTGACTCTCA
Found at i:34132085 original size:18 final size:18
Alignment explanation
Indices: 34132062--34132098 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
34132052 ACAATTCATA
34132062 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
34132080 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
34132098 T
1 T
34132099 TGATTACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:34132429 original size:17 final size:18
Alignment explanation
Indices: 34132395--34132430 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
34132385 TGAATTTCTA
34132395 TCCAATTTATACCCTAAT
1 TCCAATTTATACCCTAAT
*
34132413 TCCAATTTA-ATCCTAAT
1 TCCAATTTATACCCTAAT
34132430 T
1 T
34132431 AACTCATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCAATTTATACCCTAAT
Found at i:34133246 original size:31 final size:31
Alignment explanation
Indices: 34133208--34133271 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
34133198 TTTTAGTCCC
34133208 TCTTTCTTTCTTTTAATCTATAATTAGGCTT
1 TCTTTCTTTCTTTTAATCTATAATTAGGCTT
* *
34133239 TCTTTCTTTCTTTTACTCTATAATTAGGTTT
1 TCTTTCTTTCTTTTAATCTATAATTAGGCTT
34133270 TC
1 TC
34133272 ACCCCTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.17, C:0.17, G:0.06, T:0.59
Consensus pattern (31 bp):
TCTTTCTTTCTTTTAATCTATAATTAGGCTT
Found at i:34133717 original size:17 final size:18
Alignment explanation
Indices: 34133679--34133718 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
34133669 ATGAAATTAG
*
34133679 AATTTGATTGAGAAAATT
1 AATTTAATTGAGAAAATT
34133697 -ATTTAATT-AGAAAATT
1 AATTTAATTGAGAAAATT
34133713 AATTTA
1 AATTTA
34133719 GTTAATTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.47, C:0.00, G:0.10, T:0.42
Consensus pattern (18 bp):
AATTTAATTGAGAAAATT
Found at i:34137838 original size:15 final size:16
Alignment explanation
Indices: 34137815--34137853 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
34137805 TTATATTTTC
*
34137815 ATAAATAAAA-ATTAA
1 ATAAATAAAAGATAAA
*
34137830 ATAATTAAAAGATAAA
1 ATAAATAAAAGATAAA
34137846 ATAAATAA
1 ATAAATAA
34137854 GCATCACGTC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (16 bp):
ATAAATAAAAGATAAA
Found at i:34140379 original size:20 final size:20
Alignment explanation
Indices: 34140354--34140391 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
34140344 ATTTTTTAAA
34140354 ATTTTAAAAAATATATTTAT
1 ATTTTAAAAAATATATTTAT
34140374 ATTTTAAAAAATATATTT
1 ATTTTAAAAAATATATTT
34140392 TAATTACCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTTTAAAAAATATATTTAT
Found at i:34141413 original size:21 final size:20
Alignment explanation
Indices: 34141389--34141427 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
34141379 TCATGGAATC
*
34141389 AAGTATATAATTATTATGTCA
1 AAGTATATAACTA-TATGTCA
*
34141410 AAGTTTATAACTATATGT
1 AAGTATATAACTATATGT
34141428 TTTAGAATTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.41, C:0.05, G:0.10, T:0.44
Consensus pattern (20 bp):
AAGTATATAACTATATGTCA
Found at i:34144500 original size:15 final size:13
Alignment explanation
Indices: 34144480--34144514 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
34144470 TTCGAGCGCC
*
34144480 TGTGTGTTCAAGG
1 TGTGTGTGCAAGG
34144493 TGTGTGTGCAAGG
1 TGTGTGTGCAAGG
34144506 TGTGTGTGC
1 TGTGTGTGC
34144515 GTTGTCAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.11, C:0.09, G:0.43, T:0.37
Consensus pattern (13 bp):
TGTGTGTGCAAGG
Found at i:34147660 original size:15 final size:15
Alignment explanation
Indices: 34147626--34147676 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
34147616 GACATAATTT
*
34147626 AAAATAAAAATTA-A
1 AAAATAAATATTATA
*
34147640 AGAAATAAATATTGTA
1 A-AAATAAATATTATA
*
34147656 AAAATAGATATTATA
1 AAAATAAATATTATA
34147671 AAAATA
1 AAAATA
34147677 TCGATATTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
14 1 0.03
15 28 0.90
16 2 0.06
ACGTcount: A:0.67, C:0.00, G:0.06, T:0.27
Consensus pattern (15 bp):
AAAATAAATATTATA
Found at i:34155404 original size:16 final size:16
Alignment explanation
Indices: 34155385--34155431 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
34155375 TTAAATAAGA
* *
34155385 TTGTAATGGAGTAAAG
1 TTGTAATGAAATAAAG
* *
34155401 TTGTCATGAAATAGAG
1 TTGTAATGAAATAAAG
34155417 TTGTAATGAAATAAA
1 TTGTAATGAAATAAA
34155432 ACTGTAATTA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.43, C:0.02, G:0.23, T:0.32
Consensus pattern (16 bp):
TTGTAATGAAATAAAG
Found at i:34155505 original size:44 final size:46
Alignment explanation
Indices: 34155420--34155513 Score: 122
Period size: 44 Copynumber: 2.1 Consensus size: 46
34155410 AATAGAGTTG
*
34155420 TAATGAAATAAAACTGTAATTAGTAATTCAATTGTTTGGTTGAATA
1 TAATGAAATAAAACTATAATTAGTAATTCAATTGTTTGGTTGAATA
* * *
34155466 TAATGAAATAGAACTATAA-TAGT-ATTC-TTGTGTTTGGTTGAATG
1 TAATGAAATAAAACTATAATTAGTAATTCAAT-TGTTTGGTTGAATA
34155510 TAAT
1 TAAT
34155514 AAAAATTGTA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
43 1 0.02
44 21 0.49
45 4 0.09
46 17 0.40
ACGTcount: A:0.38, C:0.04, G:0.17, T:0.40
Consensus pattern (46 bp):
TAATGAAATAAAACTATAATTAGTAATTCAATTGTTTGGTTGAATA
Found at i:34155744 original size:2 final size:2
Alignment explanation
Indices: 34155696--34155727 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
34155686 TATTCATTTG
34155696 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
34155728 TATTTTAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34155980 original size:61 final size:61
Alignment explanation
Indices: 34155845--34156020 Score: 162
Period size: 61 Copynumber: 2.9 Consensus size: 61
34155835 TTTTTGAAAC
* * * * *
34155845 TTTT-AGAATTATAA-CAAAATTGATAAATTTTATAAACGTCGAGGGCTAAATTTATAGAAT
1 TTTTAAGAATTAGAATCAAAA-TGATAAATTTTGTAAACATTGAGGGATAAATTTATAGAAT
* * *
34155905 TTTTAAGAATTAGAA-CTAAAATGACAAATTTTGTAAACATTGAGGGATAAATTTGTTGAAT
1 TTTTAAGAATTAGAATC-AAAATGATAAATTTTGTAAACATTGAGGGATAAATTTATAGAAT
* * * * * *
34155966 TTTTTAG-ATCTAGAATCAAATTGATAAAATATGTAAATATTGAAGGACTAAATTT
1 TTTTAAGAAT-TAGAATCAAAATGATAAATTTTGTAAACATTGAGGGA-TAAATTT
34156021 TTTATCAGGC
Statistics
Matches: 96, Mismatches: 15, Indels: 8
0.81 0.13 0.07
Matches are distributed among these distances:
60 6 0.06
61 78 0.81
62 12 0.12
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.37
Consensus pattern (61 bp):
TTTTAAGAATTAGAATCAAAATGATAAATTTTGTAAACATTGAGGGATAAATTTATAGAAT
Found at i:34156142 original size:20 final size:21
Alignment explanation
Indices: 34156111--34156149 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
34156101 TTTAATTTCG
*
34156111 AAAAATTAAATAATTAAATTA
1 AAAAATTAAATAACTAAATTA
34156132 AAAAATT-AATAACTAAAT
1 AAAAATTAAATAACTAAAT
34156150 AACTAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (21 bp):
AAAAATTAAATAACTAAATTA
Found at i:34164023 original size:28 final size:28
Alignment explanation
Indices: 34163992--34164051 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 28
34163982 AAATGCGACT
* *
34163992 TTTTGGA-TACCCGGGGGTAAAATGGTAA
1 TTTTGGACT-CCCGAGGGCAAAATGGTAA
*
34164020 TTTT-GACTCTCGAGGGCAAAATGGTAA
1 TTTTGGACTCCCGAGGGCAAAATGGTAA
34164047 TTTTG
1 TTTTG
34164052 AGAAAATTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
27 22 0.81
28 5 0.19
ACGTcount: A:0.27, C:0.12, G:0.28, T:0.33
Consensus pattern (28 bp):
TTTTGGACTCCCGAGGGCAAAATGGTAA
Found at i:34164157 original size:29 final size:29
Alignment explanation
Indices: 34164125--34164228 Score: 77
Period size: 29 Copynumber: 3.6 Consensus size: 29
34164115 AATTGAGATC
*
34164125 AAAAACGGAATTTTTGGACATCCGGGTGT
1 AAAAACGGAATTTTTGGACATTCGGGTGT
* * * *
34164154 -AAAATGGTAATTTTTGAAAATTTTGGGAT-T
1 AAAAACGG-AATTTTTGGACA-TTCGGG-TGT
* * *
34164184 AAAAATGGAGTTTTTGGACATTCGGGGGT
1 AAAAACGGAATTTTTGGACATTCGGGTGT
* *
34164213 AAAATCGTAATTTTTG
1 AAAAACGGAATTTTTG
34164229 AAAGTTTTAG
Statistics
Matches: 56, Mismatches: 14, Indels: 10
0.70 0.17 0.12
Matches are distributed among these distances:
28 6 0.11
29 28 0.50
30 14 0.25
31 8 0.14
ACGTcount: A:0.33, C:0.07, G:0.25, T:0.36
Consensus pattern (29 bp):
AAAAACGGAATTTTTGGACATTCGGGTGT
Found at i:34164247 original size:59 final size:59
Alignment explanation
Indices: 34164037--34164261 Score: 210
Period size: 59 Copynumber: 3.8 Consensus size: 59
34164027 TCTCGAGGGC
* * * * * *
34164037 AAAATGGTAATTTTGAGAAAATTTAT-GG-TTAAAAATGGCA-TTTTAGACATCCGAGGGT
1 AAAATCGTAATTTT-TGAAAATTT-TGGGATCAAAAATGGAATTTTTGGACATCCGGGGGT
* * * *
34164095 AAAA-CGGTAATTTTTAGAAAA-ATTGAGATCAAAAACGGAATTTTTGGACATCCGGGTGT
1 AAAATC-GTAATTTTT-GAAAATTTTGGGATCAAAAATGGAATTTTTGGACATCCGGGGGT
* * * *
34164154 AAAATGGTAATTTTTGAAAATTTTGGGATTAAAAATGGAGTTTTTGGACATTCGGGGGT
1 AAAATCGTAATTTTTGAAAATTTTGGGATCAAAAATGGAATTTTTGGACATCCGGGGGT
* *
34164213 AAAATCGTAATTTTTGAAAGTTTTAGGG-TCAAAAAATGTAATTTTTGGA
1 AAAATCGTAATTTTTGAAAATTTT-GGGATC-AAAAATGGAATTTTTGGA
34164262 AGTTTCGAGT
Statistics
Matches: 135, Mismatches: 23, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
56 1 0.01
57 2 0.01
58 31 0.23
59 82 0.61
60 19 0.14
ACGTcount: A:0.37, C:0.06, G:0.23, T:0.34
Consensus pattern (59 bp):
AAAATCGTAATTTTTGAAAATTTTGGGATCAAAAATGGAATTTTTGGACATCCGGGGGT
Found at i:34164277 original size:89 final size:88
Alignment explanation
Indices: 34164184--34164350 Score: 212
Period size: 89 Copynumber: 1.9 Consensus size: 88
34164174 TTTTGGGATT
* * *
34164184 AAAAATGGAGTTTTTGGACA-TTCGGGGGT-AAAATCGTAATTTTTGAAAGTTTTAGGGTCAAAA
1 AAAAATGGAATTTTT-GAAAGTTCAGGGGTAAAAAT-GTAATTTTTGAAAGTTTTAGGGT-AAAA
*
34164247 AATGTAATTTTTGGAAGTTTCGAGTC
63 AATGAAATTTTTGGAAGTTTCGAGTC
* * * **
34164273 AAAAATGGAATTTTTTAAAGTTTAGGGGTAAAAATGTAATTTTTGGAAGTTTTAGGGTTTAAAAT
1 AAAAATGGAATTTTTGAAAGTTCAGGGGTAAAAATGTAATTTTTGAAAGTTTTAGGGTAAAAAAT
34164338 GAAATTTTTGGAA
66 GAAATTTTTGGAA
34164351 TTTTGGGAGG
Statistics
Matches: 67, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
88 19 0.28
89 43 0.64
90 5 0.07
ACGTcount: A:0.35, C:0.04, G:0.23, T:0.38
Consensus pattern (88 bp):
AAAAATGGAATTTTTGAAAGTTCAGGGGTAAAAATGTAATTTTTGAAAGTTTTAGGGTAAAAAAT
GAAATTTTTGGAAGTTTCGAGTC
Found at i:34164329 original size:30 final size:30
Alignment explanation
Indices: 34164208--34164385 Score: 143
Period size: 30 Copynumber: 5.9 Consensus size: 30
34164198 TGGACATTCG
*
34164208 GGGGT-AAAATCGTAATTTTTGAAAGTTTTA
1 GGGGTAAAAAT-GTAATTTTTGGAAGTTTTA
34164238 -GGGTCAAAAAATGTAATTTTTGGAAG-TTT-
1 GGGGT--AAAAATGTAATTTTTGGAAGTTTTA
* * * **
34164267 CGAGTCAAAAATGGAATTTTTTAAAG-TTTA
1 GGGGT-AAAAATGTAATTTTTGGAAGTTTTA
34164297 GGGGTAAAAATGTAATTTTTGGAAGTTTTA
1 GGGGTAAAAATGTAATTTTTGGAAGTTTTA
* * * *
34164327 GGGTTTAAAATGAAATTTTTGGAA-TTTTG
1 GGGGTAAAAATGTAATTTTTGGAAGTTTTA
* * *
34164356 GGAGGTCAAAATATAATTTATGGACAGTTT
1 GG-GGTAAAAATGTAATTTTTGGA-AGTTT
34164386 AGAGACTTTT
Statistics
Matches: 119, Mismatches: 20, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
29 47 0.39
30 50 0.42
31 14 0.12
32 8 0.07
ACGTcount: A:0.35, C:0.03, G:0.23, T:0.39
Consensus pattern (30 bp):
GGGGTAAAAATGTAATTTTTGGAAGTTTTA
Found at i:34164354 original size:29 final size:29
Alignment explanation
Indices: 34164154--34164354 Score: 138
Period size: 29 Copynumber: 6.8 Consensus size: 29
34164144 ATCCGGGTGT
*
34164154 AAAATGGTAATTTTTGAAAATTTT-GGGATTA
1 AAAAT-GTAATTTTTG-GAATTTTAGGG-TTA
* * ** *
34164185 AAAATGGAGTTTTTGGACA-TTCGGGGGT-
1 AAAATGTAATTTTTGGA-ATTTTAGGGTTA
* *
34164213 AAAATCGTAATTTTTGAAAGTTTTAGGGTCAA
1 AAAAT-GTAATTTTTGGAA-TTTTAGGGT-TA
* * * *
34164245 AAAATGTAATTTTTGGAAGTTTCGAGTCA
1 AAAATGTAATTTTTGGAATTTTAGGGTTA
* ** * *
34164274 AAAATGGAATTTTTTAAAGTTTAGGGGTA
1 AAAATGTAATTTTTGGAATTTTAGGGTTA
*
34164303 AAAATGTAATTTTTGGAAGTTTTAGGGTTT
1 AAAATGTAATTTTTGGAA-TTTTAGGGTTA
*
34164333 AAAATGAAATTTTTGGAATTTT
1 AAAATGTAATTTTTGGAATTTT
34164355 GGGAGGTCAA
Statistics
Matches: 131, Mismatches: 31, Indels: 18
0.73 0.17 0.10
Matches are distributed among these distances:
28 6 0.05
29 55 0.42
30 48 0.37
31 17 0.13
32 5 0.04
ACGTcount: A:0.35, C:0.03, G:0.22, T:0.40
Consensus pattern (29 bp):
AAAATGTAATTTTTGGAATTTTAGGGTTA
Found at i:34165434 original size:18 final size:17
Alignment explanation
Indices: 34165411--34165444 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
34165401 TTTATTATTA
34165411 ATTAATATTATTATAATT
1 ATTAATATTATT-TAATT
34165429 ATTAATATTATTTAAT
1 ATTAATATTATTTAAT
34165445 AACAGCATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTAATATTATTTAATT
Found at i:34165774 original size:30 final size:30
Alignment explanation
Indices: 34165740--34165796 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
34165730 GAAAGCCATG
*
34165740 AGAGAAACACACAAGGGTTTTTTTTTTTTT
1 AGAGAAACACACAAGGGGTTTTTTTTTTTT
34165770 AGAGAAACACACAAGGGGTTTTTTTTT
1 AGAGAAACACACAAGGGGTTTTTTTTT
34165797 AGGAGAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.32, C:0.11, G:0.19, T:0.39
Consensus pattern (30 bp):
AGAGAAACACACAAGGGGTTTTTTTTTTTT
Found at i:34176891 original size:54 final size:54
Alignment explanation
Indices: 34176817--34176924 Score: 216
Period size: 54 Copynumber: 2.0 Consensus size: 54
34176807 ATATTTTGCC
34176817 AAGTGACTCTTTTGTTCACAGGAATTAATCCTGTTCAATTCCCTGCATATTTTT
1 AAGTGACTCTTTTGTTCACAGGAATTAATCCTGTTCAATTCCCTGCATATTTTT
34176871 AAGTGACTCTTTTGTTCACAGGAATTAATCCTGTTCAATTCCCTGCATATTTTT
1 AAGTGACTCTTTTGTTCACAGGAATTAATCCTGTTCAATTCCCTGCATATTTTT
34176925 TAGCAATACA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 54 1.00
ACGTcount: A:0.24, C:0.20, G:0.13, T:0.43
Consensus pattern (54 bp):
AAGTGACTCTTTTGTTCACAGGAATTAATCCTGTTCAATTCCCTGCATATTTTT
Found at i:34186324 original size:23 final size:23
Alignment explanation
Indices: 34186298--34186423 Score: 182
Period size: 23 Copynumber: 5.5 Consensus size: 23
34186288 TTACCGTTCA
* * *
34186298 GCACTGTGTGTGCTTATTGTTTC
1 GCACTTTGTGTGCCTACTGTTTC
*
34186321 GCACTTTGTGTGCTTACTGTTTC
1 GCACTTTGTGTGCCTACTGTTTC
34186344 GCACTTTGTGTGCCTACTGTTTC
1 GCACTTTGTGTGCCTACTGTTTC
34186367 GCACTTTGTGTGCCTACTGTTTC
1 GCACTTTGTGTGCCTACTGTTTC
* *
34186390 GCACTTCGTGTGCCTACTGATT-
1 GCACTTTGTGTGCCTACTGTTTC
*
34186412 GCACTGTGTGTG
1 GCACTTTGTGTG
34186424 TTTACTATTT
Statistics
Matches: 96, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
22 10 0.10
23 86 0.90
ACGTcount: A:0.10, C:0.23, G:0.25, T:0.43
Consensus pattern (23 bp):
GCACTTTGTGTGCCTACTGTTTC
Found at i:34192553 original size:23 final size:23
Alignment explanation
Indices: 34192527--34192641 Score: 135
Period size: 23 Copynumber: 4.9 Consensus size: 23
34192517 TTACCGTTCA
*
34192527 GCACTGTGTGTGCTTACTGTTTC
1 GCACTTTGTGTGCTTACTGTTTC
*
34192550 GCACTTTGTGTGCCTACTGTTTC
1 GCACTTTGTGTGCTTACTGTTTC
* *
34192573 GCACTTTGTGTGCCTACTGATT-
1 GCACTTTGTGTGCTTACTGTTTC
*
34192595 GCACTATGTGTGCTTACTGTTTCCCC
1 GCACTTTGTGTGCTTACTGTTT---C
34192621 AGCAC-TTGTGTGCTTACTGTT
1 -GCACTTTGTGTGCTTACTGTT
34192642 AAGTACTTCG
Statistics
Matches: 80, Mismatches: 7, Indels: 7
0.85 0.07 0.07
Matches are distributed among these distances:
22 19 0.24
23 42 0.52
26 15 0.19
27 4 0.05
ACGTcount: A:0.11, C:0.24, G:0.23, T:0.42
Consensus pattern (23 bp):
GCACTTTGTGTGCTTACTGTTTC
Found at i:34192613 original size:45 final size:46
Alignment explanation
Indices: 34192527--34192617 Score: 130
Period size: 45 Copynumber: 2.0 Consensus size: 46
34192517 TTACCGTTCA
* * *
34192527 GCACTGTGTGTGCTTACTGTTTCGCACTTTGTGTGCCTACTGTTTC
1 GCACTGTGTGTGCCTACTGATTCGCACTATGTGTGCCTACTGTTTC
* *
34192573 GCACTTTGTGTGCCTACTGATT-GCACTATGTGTGCTTACTGTTTC
1 GCACTGTGTGTGCCTACTGATTCGCACTATGTGTGCCTACTGTTTC
34192618 CCCAGCACTT
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
45 21 0.52
46 19 0.47
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.43
Consensus pattern (46 bp):
GCACTGTGTGTGCCTACTGATTCGCACTATGTGTGCCTACTGTTTC
Found at i:34202682 original size:20 final size:20
Alignment explanation
Indices: 34202657--34202698 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
34202647 TTTTTCAAAA
34202657 AAAGTCAACGATCAACGGTC
1 AAAGTCAACGATCAACGGTC
* *
34202677 AAAGTCAACGGTCAATGGTC
1 AAAGTCAACGATCAACGGTC
34202697 AA
1 AA
34202699 CGGTCAATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.17
Consensus pattern (20 bp):
AAAGTCAACGATCAACGGTC
Found at i:34202717 original size:21 final size:21
Alignment explanation
Indices: 34202693--34202740 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
34202683 AACGGTCAAT
34202693 GGTCAACGGTCAATCAACACC
1 GGTCAACGGTCAATCAACACC
** *
34202714 GGTCAACGGTCGGTCAACATC
1 GGTCAACGGTCAATCAACACC
34202735 GGTCAA
1 GGTCAA
34202741 TGGTTTGACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.29, C:0.29, G:0.25, T:0.17
Consensus pattern (21 bp):
GGTCAACGGTCAATCAACACC
Found at i:34202724 original size:7 final size:7
Alignment explanation
Indices: 34202660--34202705 Score: 58
Period size: 7 Copynumber: 6.7 Consensus size: 7
34202650 TTCAAAAAAA
34202660 GTCAACG
1 GTCAACG
*
34202667 ATCAACG
1 GTCAACG
*
34202674 GTCAA-A
1 GTCAACG
34202680 GTCAACG
1 GTCAACG
*
34202687 GTCAATG
1 GTCAACG
34202694 GTCAACG
1 GTCAACG
34202701 GTCAA
1 GTCAA
34202706 TCAACACCGG
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
6 5 0.16
7 27 0.84
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.17
Consensus pattern (7 bp):
GTCAACG
Found at i:34202795 original size:15 final size:15
Alignment explanation
Indices: 34202777--34202806 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
34202767 TGGTTCATTT
34202777 GGTTTGGTTCAAATG
1 GGTTTGGTTCAAATG
*
34202792 GGTTTGGTTTAAATG
1 GGTTTGGTTCAAATG
34202807 AATGTGGGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.03, G:0.33, T:0.43
Consensus pattern (15 bp):
GGTTTGGTTCAAATG
Found at i:34222503 original size:23 final size:23
Alignment explanation
Indices: 34222470--34222515 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
34222460 GGATTAATTT
* *
34222470 CTAATTTATTATATGATAAAAAA
1 CTAATTAATTAAATGATAAAAAA
34222493 CTAATTAATTAAATGATAAAAAA
1 CTAATTAATTAAATGATAAAAAA
34222516 ATTAATGTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (23 bp):
CTAATTAATTAAATGATAAAAAA
Found at i:34230286 original size:25 final size:25
Alignment explanation
Indices: 34230258--34230305 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
34230248 AAATAAATGT
*
34230258 CTCTAAAATAGTAACAAAATTAAAC
1 CTCTAAAATAATAACAAAATTAAAC
34230283 CTCTAAAATAATAACAAAATTAA
1 CTCTAAAATAATAACAAAATTAA
34230306 CAATAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.58, C:0.15, G:0.02, T:0.25
Consensus pattern (25 bp):
CTCTAAAATAATAACAAAATTAAAC
Found at i:34236983 original size:18 final size:20
Alignment explanation
Indices: 34236941--34236990 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 20
34236931 TAAGTTCACG
* *
34236941 TCTATCGATACAATTCTATT
1 TCTATCGATACAATGCTACT
34236961 TCTATCGATACAA-GC-ACT
1 TCTATCGATACAATGCTACT
*
34236979 TCTATCCATACA
1 TCTATCGATACA
34236991 TCTTGTGAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 13 0.48
19 1 0.04
20 13 0.48
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.36
Consensus pattern (20 bp):
TCTATCGATACAATGCTACT
Found at i:34241463 original size:16 final size:17
Alignment explanation
Indices: 34241424--34241463 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
34241414 GGAATAAAGC
*
34241424 TGTAATGAAATAACGGT
1 TGTAATAAAATAACGGT
*
34241441 CGTAATAAAATAA-GGT
1 TGTAATAAAATAACGGT
34241457 TGTAATA
1 TGTAATA
34241464 GTAATTTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (17 bp):
TGTAATAAAATAACGGT
Found at i:34241667 original size:20 final size:20
Alignment explanation
Indices: 34241642--34241730 Score: 69
Period size: 20 Copynumber: 4.6 Consensus size: 20
34241632 ATTATTAAAT
34241642 ATAATTTAATAAAATAATAA
1 ATAATTTAATAAAATAATAA
* * **
34241662 ATAATTTAATTATATTTTAA
1 ATAATTTAATAAAATAATAA
* **
34241682 CATAA-TTATTATTA-AAT-A
1 -ATAATTTAATAAAATAATAA
*
34241700 A-AATTTAATAAAATAATAT
1 ATAATTTAATAAAATAATAA
34241719 ATAATTTAATAA
1 ATAATTTAATAA
34241731 TATTATTAAT
Statistics
Matches: 51, Mismatches: 13, Indels: 10
0.69 0.18 0.14
Matches are distributed among these distances:
16 2 0.04
17 7 0.14
18 4 0.08
19 2 0.04
20 32 0.63
21 4 0.08
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (20 bp):
ATAATTTAATAAAATAATAA
Found at i:34241680 original size:57 final size:57
Alignment explanation
Indices: 34241613--34241771 Score: 230
Period size: 57 Copynumber: 2.8 Consensus size: 57
34241603 GATTATTGTT
*
34241613 ATTAAATTTTAATA-AGATTATTATTAAATATAATTTAATAAAATAATAAATAATTTA
1 ATTATATTTTAATATA-ATTATTATTAAATATAATTTAATAAAATAATAAATAATTTA
* * *
34241670 ATTATATTTTAACATAATTATTATTAAATAAAATTTAATAAAATAATATATAATTTA
1 ATTATATTTTAATATAATTATTATTAAATATAATTTAATAAAATAATAAATAATTTA
* *
34241727 ATAATATTATTAATATAATTATTATTAAAATATAAATTAATAAAA
1 ATTATATT-TTAATATAATTATTATT-AAATATAATTTAATAAAA
34241772 ATCATAATAT
Statistics
Matches: 91, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
57 58 0.64
58 17 0.19
59 16 0.18
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.44
Consensus pattern (57 bp):
ATTATATTTTAATATAATTATTATTAAATATAATTTAATAAAATAATAAATAATTTA
Found at i:34250578 original size:21 final size:21
Alignment explanation
Indices: 34250516--34250578 Score: 56
Period size: 24 Copynumber: 2.9 Consensus size: 21
34250506 CTCATGCAGC
* *
34250516 TCAGTCATCAACCCCTTCTGG
1 TCAGTCATCAAACCCTGCTGG
*
34250537 TC-GTTCGTCAAATACCGCTGCTGG
1 TCAG-TCATC-AA-ACC-CTGCTGG
34250561 TCAGTCATCAAACCCTGC
1 TCAGTCATCAAACCCTGC
34250579 ATCATTTCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
20 1 0.03
21 10 0.30
22 5 0.15
23 4 0.12
24 12 0.36
25 1 0.03
ACGTcount: A:0.21, C:0.35, G:0.17, T:0.27
Consensus pattern (21 bp):
TCAGTCATCAAACCCTGCTGG
Found at i:34253511 original size:17 final size:17
Alignment explanation
Indices: 34253489--34253531 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
34253479 AGAAGAATAA
* *
34253489 AAGAAGAAATGGAGAAG
1 AAGAAGAAACGAAGAAG
34253506 AAGAAGAAACGAAGAAG
1 AAGAAGAAACGAAGAAG
*
34253523 AGGAAGAAA
1 AAGAAGAAA
34253532 ATAACAGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.63, C:0.02, G:0.33, T:0.02
Consensus pattern (17 bp):
AAGAAGAAACGAAGAAG
Found at i:34255455 original size:18 final size:18
Alignment explanation
Indices: 34255418--34255459 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
34255408 ATAACTGATA
**
34255418 TGGAGGATACATTTGAGG
1 TGGAGGATACATCAGAGG
*
34255436 TGGAGGATACATCAGCGG
1 TGGAGGATACATCAGAGG
34255454 TGGAGG
1 TGGAGG
34255460 TGGGTGATAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.26, C:0.10, G:0.43, T:0.21
Consensus pattern (18 bp):
TGGAGGATACATCAGAGG
Found at i:34256425 original size:19 final size:18
Alignment explanation
Indices: 34256401--34256443 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
34256391 TGTACAATAT
*
34256401 AATTAAATAATATGAATTA
1 AATTAAATAAAAT-AATTA
*
34256420 AATTAAATAAAATAATTT
1 AATTAAATAAAATAATTA
34256438 AATTAA
1 AATTAA
34256444 CTATTTACCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (18 bp):
AATTAAATAAAATAATTA
Found at i:34261842 original size:32 final size:31
Alignment explanation
Indices: 34261800--34261893 Score: 85
Period size: 32 Copynumber: 3.1 Consensus size: 31
34261790 ATATTAGGAT
*
34261800 TTAGGGCAAGTATCATTAATTTAAAATTAACA
1 TTAGGACAAGT-TCATTAATTTAAAATTAACA
34261832 TTAGGACAAG-T-A-TAA---AAAA-TAATCA
1 TTAGGACAAGTTCATTAATTTAAAATTAA-CA
*
34261857 TTAATGACAAGTGTCATTAATTTAAAATTAACA
1 TT-AGGACAAGT-TCATTAATTTAAAATTAACA
34261890 TTAG
1 TTAG
34261894 CATTTAGGGC
Statistics
Matches: 49, Mismatches: 3, Indels: 20
0.68 0.04 0.28
Matches are distributed among these distances:
24 3 0.06
25 8 0.16
26 7 0.14
28 4 0.08
29 2 0.04
30 4 0.08
32 10 0.20
33 8 0.16
34 3 0.06
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.33
Consensus pattern (31 bp):
TTAGGACAAGTTCATTAATTTAAAATTAACA
Found at i:34262367 original size:7 final size:7
Alignment explanation
Indices: 34262351--34262383 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
34262341 CTCCAAAGCT
*
34262351 TCGAAGG
1 TCGAACG
34262358 TCGAACG
1 TCGAACG
34262365 TCGAACG
1 TCGAACG
34262372 TCGAACG
1 TCGAACG
34262379 TCGAA
1 TCGAA
34262384 GTGCTTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.30, C:0.24, G:0.30, T:0.15
Consensus pattern (7 bp):
TCGAACG
Found at i:34269381 original size:5 final size:5
Alignment explanation
Indices: 34269371--34269399 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
34269361 AATCATCCCT
34269371 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
34269400 TTCTCTACCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:34273953 original size:8 final size:8
Alignment explanation
Indices: 34273922--34273954 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
34273912 TTAAATTATA
*
34273922 TTTTAATA
1 TTTTAATT
34273930 TTTTAATT
1 TTTTAATT
34273938 TTTTAATT
1 TTTTAATT
34273946 TTTTAATT
1 TTTTAATT
34273954 T
1 T
34273955 ATAATTTAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (8 bp):
TTTTAATT
Found at i:34275614 original size:27 final size:27
Alignment explanation
Indices: 34275584--34275751 Score: 119
Period size: 27 Copynumber: 6.2 Consensus size: 27
34275574 TCGAATTTAA
* *
34275584 TTTTTTTTAATTTGTTATTTAAATTTC
1 TTTTTTTTAATTTGATATTTAAATTTG
* *
34275611 TTTTTGGTTTAATATGATACTTAAATTTG
1 TTTTT--TTTAATTTGATATTTAAATTTG
* * *
34275640 ATATTTTTAATTTGGTATTTAAATTTGG
1 TTTTTTTTAATTTGATATTTAAATTT-G
* *
34275668 TATTTTTTAAGTT-AGTATTTAAATTT-
1 TTTTTTTTAATTTGA-TATTTAAATTTG
** * * * *
34275694 TTTAAGTTCAATTTGGTACTTGAATTTG
1 TTT-TTTTTAATTTGATATTTAAATTTG
*
34275722 ATTTTTTTAATTTGATATTT-AATTT-
1 TTTTTTTTAATTTGATATTTAAATTTG
34275747 TTTTT
1 TTTTT
34275752 AATTTTATTT
Statistics
Matches: 105, Mismatches: 29, Indels: 16
0.70 0.19 0.11
Matches are distributed among these distances:
25 4 0.04
26 7 0.07
27 50 0.48
28 23 0.22
29 21 0.20
ACGTcount: A:0.26, C:0.02, G:0.10, T:0.61
Consensus pattern (27 bp):
TTTTTTTTAATTTGATATTTAAATTTG
Found at i:34275653 original size:14 final size:14
Alignment explanation
Indices: 34275634--34275674 Score: 57
Period size: 13 Copynumber: 3.0 Consensus size: 14
34275624 ATGATACTTA
*
34275634 AATTTGATATTTTT
1 AATTTGGTATTTTT
*
34275648 AATTTGGTA-TTTA
1 AATTTGGTATTTTT
34275661 AATTTGGTATTTTT
1 AATTTGGTATTTTT
34275675 TAAGTTAGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.61
Consensus pattern (14 bp):
AATTTGGTATTTTT
Found at i:34275685 original size:28 final size:27
Alignment explanation
Indices: 34275631--34275693 Score: 90
Period size: 28 Copynumber: 2.3 Consensus size: 27
34275621 AATATGATAC
* *
34275631 TTAAATTTGATATTTTTAATTTGGTAT
1 TTAAATTTGATATTTTTAAGTTAGTAT
*
34275658 TTAAATTTGGTATTTTTTAAGTTAGTAT
1 TTAAATTTGATA-TTTTTAAGTTAGTAT
34275686 TTAAATTT
1 TTAAATTT
34275694 TTTAAGTTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
27 11 0.34
28 21 0.66
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (27 bp):
TTAAATTTGATATTTTTAAGTTAGTAT
Found at i:34275741 original size:21 final size:21
Alignment explanation
Indices: 34275713--34275756 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
34275703 AATTTGGTAC
*
34275713 TTGAATTTGA-TTTTTTTAAT
1 TTGAATTTAATTTTTTTTAAT
34275733 TTGATATTTAATTTTTTTTAAT
1 TTGA-ATTTAATTTTTTTTAAT
34275755 TT
1 TT
34275757 TATTTCTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.19
21 5 0.24
22 12 0.57
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (21 bp):
TTGAATTTAATTTTTTTTAAT
Found at i:34275753 original size:55 final size:55
Alignment explanation
Indices: 34275648--34275750 Score: 138
Period size: 54 Copynumber: 1.9 Consensus size: 55
34275638 TGATATTTTT
* *
34275648 AATTTGGTATTTAAATTTGGTATTTTTTAAGTTAGTATTTAAATTTTTTAAGTTC
1 AATTTGGTACTTAAATTTGATATTTTTTAAGTTAGTATTTAAATTTTTTAAGTTC
* * *
34275703 AATTTGGTACTTGAATTTGAT-TTTTTTAA-TTTGATATTTAATTTTTTT
1 AATTTGGTACTTAAATTTGATATTTTTTAAGTTAG-TATTTAAATTTTTT
34275751 TAATTTTATT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
53 3 0.07
54 21 0.50
55 18 0.43
ACGTcount: A:0.27, C:0.02, G:0.12, T:0.59
Consensus pattern (55 bp):
AATTTGGTACTTAAATTTGATATTTTTTAAGTTAGTATTTAAATTTTTTAAGTTC
Found at i:34276018 original size:20 final size:19
Alignment explanation
Indices: 34275993--34276031 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
34275983 CAAATTAAGA
34275993 AAATGTTAAATTCAAGTATT
1 AAATGTTAAATT-AAGTATT
*
34276013 AAATGTTATATTAAGTATT
1 AAATGTTAAATTAAGTATT
34276032 TTTTAATCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.44
Consensus pattern (19 bp):
AAATGTTAAATTAAGTATT
Found at i:34278806 original size:27 final size:27
Alignment explanation
Indices: 34278747--34278812 Score: 96
Period size: 27 Copynumber: 2.4 Consensus size: 27
34278737 GAATAATTCG
* *
34278747 ATAATCAAATTATAATTTTTTAATTAA
1 ATAATTAAATAATAATTTTTTAATTAA
34278774 ATAATTAAATAATAATTTTTTAATTAA
1 ATAATTAAATAATAATTTTTTAATTAA
* *
34278801 GTAATTAGATAA
1 ATAATTAAATAA
34278813 AAGATTTCCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (27 bp):
ATAATTAAATAATAATTTTTTAATTAA
Found at i:34279010 original size:5 final size:5
Alignment explanation
Indices: 34279000--34279035 Score: 63
Period size: 5 Copynumber: 7.2 Consensus size: 5
34278990 CAAAACCTGC
*
34279000 GGATG GGATG GGATG GGATG GGATG GGATG GAATG G
1 GGATG GGATG GGATG GGATG GGATG GGATG GGATG G
34279036 CGGTGGGTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.22, C:0.00, G:0.58, T:0.19
Consensus pattern (5 bp):
GGATG
Found at i:34280017 original size:26 final size:27
Alignment explanation
Indices: 34279966--34280024 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 27
34279956 AATATTTATA
*
34279966 TTATATTATTTTAATATTTAATAA-TT
1 TTATATTATTTTAATATTGAATAATTT
* *
34279992 TTATATTTTTTTATTTATTGAA-AATTT
1 TTATATTATTTTA-ATATTGAATAATTT
34280019 TTATAT
1 TTATAT
34280025 AATTATCTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 14 0.50
27 14 0.50
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (27 bp):
TTATATTATTTTAATATTGAATAATTT
Found at i:34280120 original size:2 final size:2
Alignment explanation
Indices: 34280113--34280145 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
34280103 AAATTACATA
34280113 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
34280146 AGTATTATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:34280402 original size:114 final size:114
Alignment explanation
Indices: 34280202--34280408 Score: 274
Period size: 114 Copynumber: 1.8 Consensus size: 114
34280192 GAATTCGAGC
* * *** * * *
34280202 CCGACCCATATTTTAAATGGGCCTATTTTTTTTGTTCAAGCTCATTTTCAGGTCTAATATTTTTG
1 CCGACCCATATTTTAAACGGGCCTAATTTTTTTACCCAACCTCATTTTCAGGCCTAATATTTTTA
*
34280267 TTCAAACCCTCTTAAAATTCGGATGAACCTTTGTGCTAGAACGGATAAT
66 CTCAAACCCTCTTAAAATTCGGATGAACCTTTGTGCTAGAACGGATAAT
*
34280316 CCGACCCATATTTTAAACGGGCTTAATTTTTTTACCCAAACCT-ATTTTC-GGACCTAATATTTT
1 CCGACCCATATTTTAAACGGGCCTAATTTTTTTACCC-AACCTCATTTTCAGG-CCTAATATTTT
* *
34280379 TACTCAAACTCTCTTAAATTTCGGATGAAC
64 TACTCAAACCCTCTTAAAATTCGGATGAAC
34280409 TTTTAGACCT
Statistics
Matches: 79, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
113 2 0.03
114 73 0.92
115 4 0.05
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.39
Consensus pattern (114 bp):
CCGACCCATATTTTAAACGGGCCTAATTTTTTTACCCAACCTCATTTTCAGGCCTAATATTTTTA
CTCAAACCCTCTTAAAATTCGGATGAACCTTTGTGCTAGAACGGATAAT
Found at i:34286944 original size:30 final size:31
Alignment explanation
Indices: 34286903--34286971 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 31
34286893 ATTACGTTTA
*
34286903 ACAAAACAGTCACTCAACTT-T-GAAAATGTG
1 ACAAAACAGTCACTAAACTTATCGAAAA-GTG
* *
34286933 ACAAAATAGTCACTAAAGTTATCGAAAAGTG
1 ACAAAACAGTCACTAAACTTATCGAAAAGTG
34286964 ACAAAACA
1 ACAAAACA
34286972 ATCCTCTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 17 0.52
31 11 0.33
32 5 0.15
ACGTcount: A:0.49, C:0.17, G:0.13, T:0.20
Consensus pattern (31 bp):
ACAAAACAGTCACTAAACTTATCGAAAAGTG
Found at i:34287916 original size:31 final size:31
Alignment explanation
Indices: 34287875--34287988 Score: 77
Period size: 31 Copynumber: 3.4 Consensus size: 31
34287865 TCTGTTAATC
34287875 AATGACTATTTTATCACTTTTCAAAAACGTT
1 AATGACTATTTTATCACTTTTCAAAAACGTT
* * * **
34287906 AATGATTATTTTGTTAAGCTCAT-AACAGAATCTGTT
1 AATGACTATTTT-ATCA-CTTTTCAA-A-AA-C-GTT
34287942 AATCAATGACTATTTTATCACTTTTCAAAAACGTT
1 -A---ATGACTATTTTATCACTTTTCAAAAACGTT
*
34287977 AATGATTATTTT
1 AATGACTATTTT
34287989 GTTAATTTTT
Statistics
Matches: 61, Mismatches: 11, Indels: 22
0.65 0.12 0.23
Matches are distributed among these distances:
31 21 0.34
32 4 0.07
33 4 0.07
34 3 0.05
35 4 0.07
36 4 0.07
37 3 0.05
38 4 0.07
39 4 0.07
40 10 0.16
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (31 bp):
AATGACTATTTTATCACTTTTCAAAAACGTT
Found at i:34287964 original size:71 final size:71
Alignment explanation
Indices: 34287848--34287993 Score: 283
Period size: 71 Copynumber: 2.1 Consensus size: 71
34287838 AACAACCCCT
*
34287848 TTAAGCTCGTAACAGAATCTGTTAATCAATGACTATTTTATCACTTTTCAAAAACGTTAATGATT
1 TTAAGCTCATAACAGAATCTGTTAATCAATGACTATTTTATCACTTTTCAAAAACGTTAATGATT
34287913 ATTTTG
66 ATTTTG
34287919 TTAAGCTCATAACAGAATCTGTTAATCAATGACTATTTTATCACTTTTCAAAAACGTTAATGATT
1 TTAAGCTCATAACAGAATCTGTTAATCAATGACTATTTTATCACTTTTCAAAAACGTTAATGATT
34287984 ATTTTG
66 ATTTTG
34287990 TTAA
1 TTAA
34287994 TTTTTCAAAG
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 74 1.00
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.41
Consensus pattern (71 bp):
TTAAGCTCATAACAGAATCTGTTAATCAATGACTATTTTATCACTTTTCAAAAACGTTAATGATT
ATTTTG
Found at i:34287979 original size:35 final size:35
Alignment explanation
Indices: 34287868--34287979 Score: 93
Period size: 35 Copynumber: 3.2 Consensus size: 35
34287858 AACAGAATCT
34287868 GTTAATCAATGACTATTTTATCACTTTTCAAAAAC
1 GTTAATCAATGACTATTTTATCACTTTTCAAAAAC
* * * * * * ** * *
34287903 GTTAAT-GATTA-TTTTGTTAAGCTCATAACAGAATC
1 GTTAATCAATGACTATT-TT-ATCACTTTTCAAAAAC
34287938 TGTTAATCAATGACTATTTTATCACTTTTCAAAAAC
1 -GTTAATCAATGACTATTTTATCACTTTTCAAAAAC
34287974 GTTAAT
1 GTTAAT
34287980 GATTATTTTG
Statistics
Matches: 52, Mismatches: 20, Indels: 10
0.63 0.24 0.12
Matches are distributed among these distances:
33 3 0.06
34 5 0.10
35 21 0.40
36 15 0.29
37 5 0.10
38 3 0.06
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (35 bp):
GTTAATCAATGACTATTTTATCACTTTTCAAAAAC
Found at i:34291746 original size:49 final size:49
Alignment explanation
Indices: 34291690--34291788 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 49
34291680 TCTATAATAG
*
34291690 TAGCGCATGCCATTATTGAAGTCAGTGGTTTAATGCTTTCTTCCAGTTT
1 TAGCGCATGCCATTATTGAAGTCAGTGGCTTAATGCTTTCTTCCAGTTT
34291739 TAGCGCATGCCATTATTGAAGTCAGTGGCTTAATGCTTTCTTCCAGTTT
1 TAGCGCATGCCATTATTGAAGTCAGTGGCTTAATGCTTTCTTCCAGTTT
34291788 T
1 T
34291789 CTTGTATTAA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.40
Consensus pattern (49 bp):
TAGCGCATGCCATTATTGAAGTCAGTGGCTTAATGCTTTCTTCCAGTTT
Found at i:34297085 original size:30 final size:31
Alignment explanation
Indices: 34297051--34297116 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 31
34297041 CCTATGATTT
* *
34297051 AATTTAACTACTAAACTTTACT-TTTT-ATTA
1 AATTTAACAAC-AAACTTTAATATTTTAATTA
* *
34297081 AATTTTACAACCAACTTTAATATTTTAATTA
1 AATTTAACAACAAACTTTAATATTTTAATTA
34297112 AATTT
1 AATTT
34297117 CACCACCCAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 8 0.27
30 13 0.43
31 9 0.30
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.48
Consensus pattern (31 bp):
AATTTAACAACAAACTTTAATATTTTAATTA
Found at i:34303128 original size:16 final size:15
Alignment explanation
Indices: 34303090--34303129 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
34303080 ATAAGCCTTC
34303090 GGTTTCAAAACAAAT
1 GGTTTCAAAACAAAT
*
34303105 GGTTTCAAAACAAGT
1 GGTTTCAAAACAAAT
34303120 GGTTTTCAAA
1 GG-TTTCAAA
34303130 TCAATGCTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.30
Consensus pattern (15 bp):
GGTTTCAAAACAAAT
Found at i:34303315 original size:58 final size:59
Alignment explanation
Indices: 34303253--34303367 Score: 160
Period size: 59 Copynumber: 2.0 Consensus size: 59
34303243 GATATTTGAC
* * * *
34303253 ATAATTAATTAATTTT-TTATATTAGAATTTATCATATCCACAATGTAGGTGAAAAATA
1 ATAATTAATTAATTTTATAATATTAGAATTTACCATATCCACAATGAACGTGAAAAATA
* * *
34303311 ATAATTATTTGATTTTATAATATTAGAATTTACCATATCCATAATGAACGTGAAAAA
1 ATAATTAATTAATTTTATAATATTAGAATTTACCATATCCACAATGAACGTGAAAAA
34303368 AAAAATATTT
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
58 14 0.29
59 35 0.71
ACGTcount: A:0.43, C:0.08, G:0.09, T:0.40
Consensus pattern (59 bp):
ATAATTAATTAATTTTATAATATTAGAATTTACCATATCCACAATGAACGTGAAAAATA
Found at i:34306294 original size:44 final size:44
Alignment explanation
Indices: 34306223--34306308 Score: 145
Period size: 44 Copynumber: 2.0 Consensus size: 44
34306213 ATACCAAAAT
* *
34306223 ATAACAATATAATAAAATACTAGCATAGAAATTAACAATAATAA
1 ATAACAATATAATAAAAGACTAACATAGAAATTAACAATAATAA
*
34306267 ATAACAATATAATAAAAGACTAACATAGGAATTAACAATAAT
1 ATAACAATATAATAAAAGACTAACATAGAAATTAACAATAAT
34306309 CTCAAATATA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.60, C:0.09, G:0.06, T:0.24
Consensus pattern (44 bp):
ATAACAATATAATAAAAGACTAACATAGAAATTAACAATAATAA
Found at i:34309657 original size:23 final size:23
Alignment explanation
Indices: 34309631--34309757 Score: 148
Period size: 23 Copynumber: 5.4 Consensus size: 23
34309621 AGTGCTGGGC
34309631 AACAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
* * *
34309654 AACAGAGAGTACACAAAGTACTA
1 AACAGAGAGCACACACAGTGCTA
* *
34309677 ATCAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
*
34309700 ATCAGAGAGCACACACAGTGCTAA
1 AACAGAGAGCACACACAGTGCT-A
* *
34309724 TAACAGCGAGCACGAGAC-GTGCTA
1 -AACAGAGAGCAC-ACACAGTGCTA
34309748 AACAGAGAGC
1 AACAGAGAGC
34309758 GCGCTAGTGT
Statistics
Matches: 90, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
23 70 0.78
24 2 0.02
25 15 0.17
26 3 0.03
ACGTcount: A:0.43, C:0.23, G:0.23, T:0.11
Consensus pattern (23 bp):
AACAGAGAGCACACACAGTGCTA
Found at i:34309706 original size:69 final size:66
Alignment explanation
Indices: 34309584--34309723 Score: 192
Period size: 69 Copynumber: 2.0 Consensus size: 66
34309574 TATACGGAAC
*
34309584 AAACAGAGAGTACCAAAGTACTAACAAAGAGCACATAAGTGCTGGGCAACAGAGAGCACACACAG
1 AAACAGAGAGTACCAAAGTACTAACAAAGAGCACAAAAGTGCT--G-AACAGAGAGCACACACAG
34309649 TGCT
63 TGCT
*
34309653 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT-AATCAGAGAGCACACACA
1 AAACAGAGAGTAC-CAAAGTACTAA-CAAAGAGCACA-AAAGTGCTGAA-CAGAGAGCACACACA
34309717 GTGCT
62 GTGCT
34309722 AA
1 AA
34309724 TAACAGCGAG
Statistics
Matches: 65, Mismatches: 2, Indels: 8
0.87 0.03 0.11
Matches are distributed among these distances:
68 2 0.03
69 35 0.54
70 11 0.17
71 10 0.15
72 7 0.11
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.12
Consensus pattern (66 bp):
AAACAGAGAGTACCAAAGTACTAACAAAGAGCACAAAAGTGCTGAACAGAGAGCACACACAGTGC
T
Found at i:34315418 original size:17 final size:17
Alignment explanation
Indices: 34315396--34315438 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
34315386 CTAATGGCTG
34315396 TTCTCTTTCCAGCACTT
1 TTCTCTTTCCAGCACTT
34315413 TTCTCTTTCCAGCACTT
1 TTCTCTTTCCAGCACTT
34315430 TTCTCTTTC
1 TTCTCTTTC
34315439 GAACGAATCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.09, C:0.35, G:0.05, T:0.51
Consensus pattern (17 bp):
TTCTCTTTCCAGCACTT
Found at i:34317029 original size:23 final size:23
Alignment explanation
Indices: 34317003--34317129 Score: 139
Period size: 23 Copynumber: 5.4 Consensus size: 23
34316993 AGTGCTGGGC
34317003 AACAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
* * *
34317026 AACAGAGAGTACACAAAGTACTA
1 AACAGAGAGCACACACAGTGCTA
* *
34317049 ATCAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
* *
34317072 ATCAGAGAGCACACACAATGCTAA
1 AACAGAGAGCACACACAGTGCT-A
* *
34317096 TAATAGAGAGCACGAGAC-GTGCTA
1 -AACAGAGAGCAC-ACACAGTGCTA
34317120 AACAGAGAGC
1 AACAGAGAGC
34317130 GCGCTAGTGT
Statistics
Matches: 88, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
23 69 0.78
24 2 0.02
25 14 0.16
26 3 0.03
ACGTcount: A:0.45, C:0.21, G:0.22, T:0.12
Consensus pattern (23 bp):
AACAGAGAGCACACACAGTGCTA
Found at i:34317055 original size:46 final size:49
Alignment explanation
Indices: 34317005--34317129 Score: 161
Period size: 46 Copynumber: 2.6 Consensus size: 49
34316995 TGCTGGGCAA
* *
34317005 CAGAGAGCACACACAGTGCTAAACAGAGAGTACACA-AA-G-TACTAAT
1 CAGAGAGCACACACAGTGCTAAACAGAGAGCACACACAATGCTAATAAT
* *
34317051 CAGAGAGCACACAAAGTGCTAATCAGAGAGCACACACAATGCTAATAAT
1 CAGAGAGCACACACAGTGCTAAACAGAGAGCACACACAATGCTAATAAT
*
34317100 -AGAGAGCACGAGAC-GTGCTAAACAGAGAGC
1 CAGAGAGCAC-ACACAGTGCTAAACAGAGAGC
34317130 GCGCTAGTGT
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
46 33 0.49
47 2 0.03
48 25 0.37
49 8 0.12
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (49 bp):
CAGAGAGCACACACAGTGCTAAACAGAGAGCACACACAATGCTAATAAT
Found at i:34317078 original size:69 final size:66
Alignment explanation
Indices: 34316956--34317095 Score: 183
Period size: 69 Copynumber: 2.0 Consensus size: 66
34316946 TATACGGAAC
* *
34316956 AAACAGAGAGTACCAAAGTACTAACAAAGAGCACATAAGTGCTGGGCAACAGAGAGCACACACAG
1 AAACAGAGAGTACCAAAGTACTAACAAAGAGCACAAAAGTGCT--G-AACAGAGAGCACACACAA
34317021 TGCT
63 TGCT
*
34317025 AAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT-AATCAGAGAGCACACACA
1 AAACAGAGAGTAC-CAAAGTACTAA-CAAAGAGCACA-AAAGTGCTGAA-CAGAGAGCACACACA
34317089 ATGCT
62 ATGCT
34317094 AA
1 AA
34317096 TAATAGAGAG
Statistics
Matches: 64, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
68 2 0.03
69 34 0.53
70 11 0.17
71 10 0.16
72 7 0.11
ACGTcount: A:0.46, C:0.21, G:0.21, T:0.12
Consensus pattern (66 bp):
AAACAGAGAGTACCAAAGTACTAACAAAGAGCACAAAAGTGCTGAACAGAGAGCACACACAATGC
T
Found at i:34320437 original size:10 final size:10
Alignment explanation
Indices: 34320422--34320450 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
34320412 GAAGGACCAA
34320422 GCCAGACTCC
1 GCCAGACTCC
34320432 GCCAGACTCC
1 GCCAGACTCC
34320442 GCCAGACTC
1 GCCAGACTC
34320451 TAGAGGTGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.21, C:0.48, G:0.21, T:0.10
Consensus pattern (10 bp):
GCCAGACTCC
Found at i:34323727 original size:26 final size:28
Alignment explanation
Indices: 34323668--34323723 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 28
34323658 TTCCCGCAAC
*
34323668 AAAT-TTGGATATATTATTAATTTTTTT
1 AAATATTGGATATATTATTAATATTTTT
*
34323695 GAATATTGGATAT-TT-TT-ATATTTTT
1 AAATATTGGATATATTATTAATATTTTT
34323720 AAAT
1 AAAT
34323724 TATTTATTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
25 10 0.40
26 2 0.08
27 5 0.20
28 8 0.32
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (28 bp):
AAATATTGGATATATTATTAATATTTTT
Found at i:34342907 original size:5 final size:5
Alignment explanation
Indices: 34342897--34342938 Score: 84
Period size: 5 Copynumber: 8.4 Consensus size: 5
34342887 AGGACTTGGG
34342897 GCCAT GCCAT GCCAT GCCAT GCCAT GCCAT GCCAT GCCAT GC
1 GCCAT GCCAT GCCAT GCCAT GCCAT GCCAT GCCAT GCCAT GC
34342939 AATCGACTGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.19, C:0.40, G:0.21, T:0.19
Consensus pattern (5 bp):
GCCAT
Found at i:34345816 original size:21 final size:21
Alignment explanation
Indices: 34345792--34345887 Score: 90
Period size: 21 Copynumber: 4.6 Consensus size: 21
34345782 TTTACTCTTG
34345792 AATCGATTGTTTTCTTATTTC
1 AATCGATTGTTTTCTTATTTC
34345813 AATCGATTGTTTTCTT-TGGTT-
1 AATCGATTGTTTTCTTAT--TTC
* * *
34345834 AATTGCTTTTTTTCTTATTTC
1 AATCGATTGTTTTCTTATTTC
* * *
34345855 AATTGATTG-TTTCTTCTTTT
1 AATCGATTGTTTTCTTATTTC
*
34345875 TATCGATTGTTTT
1 AATCGATTGTTTT
34345888 GATATCTGAT
Statistics
Matches: 61, Mismatches: 9, Indels: 10
0.76 0.11 0.12
Matches are distributed among these distances:
20 19 0.31
21 39 0.64
22 3 0.05
ACGTcount: A:0.16, C:0.11, G:0.11, T:0.61
Consensus pattern (21 bp):
AATCGATTGTTTTCTTATTTC
Found at i:34347389 original size:21 final size:21
Alignment explanation
Indices: 34347365--34347448 Score: 107
Period size: 21 Copynumber: 4.0 Consensus size: 21
34347355 CTCATGAATC
34347365 GATTGTTTTCTTATTTCAATT
1 GATTGTTTTCTTATTTCAATT
* * * *
34347386 GATTATTTTCCTATTCCAATA
1 GATTGTTTTCTTATTTCAATT
*
34347407 GATTGTTTCCTTATTTCAATT
1 GATTGTTTTCTTATTTCAATT
*
34347428 GATTG-TTTCTTATTTTAATT
1 GATTGTTTTCTTATTTCAATT
34347448 G
1 G
34347449 CTTATTTCGA
Statistics
Matches: 52, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
20 14 0.27
21 38 0.73
ACGTcount: A:0.21, C:0.12, G:0.10, T:0.57
Consensus pattern (21 bp):
GATTGTTTTCTTATTTCAATT
Found at i:34347586 original size:21 final size:20
Alignment explanation
Indices: 34347557--34347605 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
34347547 CTCTTGAATC
* *
34347557 GATTATTTTCCTATTTCAATT
1 GATTGTTTTCCTA-TTCAATA
* *
34347578 GATTGTTTTTCTATTCCATA
1 GATTGTTTTCCTATTCAATA
34347598 GATTGTTT
1 GATTGTTT
34347606 CTTTTTTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.20, C:0.12, G:0.10, T:0.57
Consensus pattern (20 bp):
GATTGTTTTCCTATTCAATA
Found at i:34347716 original size:170 final size:171
Alignment explanation
Indices: 34347386--34347701 Score: 467
Period size: 170 Copynumber: 1.9 Consensus size: 171
34347376 TATTTCAATT
* *
34347386 GATTATTTTCCTATTCCAATAGATTGTTTCCTTATTTCAATTGATTGTTTCTTATTTTAATTGCT
1 GATTATTTTCCTATTCCAATAGATTGTTTCCTTATTTCAATAGATTGTTTCTTATTTTAATTGAT
* *
34347451 TATTTCGATACTCGGTGATACCTCAACAAAATTTCAGAGGGATGAAAGTCAAAGTTTTACATTAA
66 TATTTCGATACTCGATGATACCTCAACAAAATTTCAGAAGGATGAAAGTCAAAGTTTTACATTAA
*
34347516 AAAAGCTTAGATTAAAAAAGAAATTATTTTACTCTTGAATC
131 AAAAACTTAGATTAAAAAAGAAATTATTTTACTCTTGAATC
* * * * *
34347557 GATTATTTTCCTATTTCAATTGATTGTTT--TTCTATTCCATAGATTGTTTCTTTTTTTAATTGA
1 GATTATTTTCCTATTCCAATAGATTGTTTCCTTAT-TTCAATAGATTGTTTCTTATTTTAATTGA
* * * *
34347620 TTATTTCGATTC-CGAATGATATCTCAATAAAATTTCAGAAGGATGAAATTCAAAGTTTTACATT
65 TTATTTCGATACTCG-ATGATACCTCAACAAAATTTCAGAAGGATGAAAGTCAAAGTTTTACATT
34347684 AAAAAAACTTAGATTAAA
129 AAAAAAACTTAGATTAAA
34347702 TTATTAATTA
Statistics
Matches: 129, Mismatches: 14, Indels: 5
0.87 0.09 0.03
Matches are distributed among these distances:
169 5 0.04
170 97 0.75
171 27 0.21
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (171 bp):
GATTATTTTCCTATTCCAATAGATTGTTTCCTTATTTCAATAGATTGTTTCTTATTTTAATTGAT
TATTTCGATACTCGATGATACCTCAACAAAATTTCAGAAGGATGAAAGTCAAAGTTTTACATTAA
AAAAACTTAGATTAAAAAAGAAATTATTTTACTCTTGAATC
Found at i:34348811 original size:20 final size:20
Alignment explanation
Indices: 34348786--34348824 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
34348776 AACTAATTAG
34348786 GAATCAGTTGTAATTAGTTT
1 GAATCAGTTGTAATTAGTTT
34348806 GAATCAGTTGTAATTAGTT
1 GAATCAGTTGTAATTAGTT
34348825 AGGTGGTTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.05, G:0.21, T:0.44
Consensus pattern (20 bp):
GAATCAGTTGTAATTAGTTT
Found at i:34356270 original size:3 final size:3
Alignment explanation
Indices: 34356262--34356292 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
34356252 AATTTAAATT
34356262 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
34356293 GAAATGCCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:34358323 original size:23 final size:27
Alignment explanation
Indices: 34358274--34358326 Score: 69
Period size: 25 Copynumber: 2.1 Consensus size: 27
34358264 AAGAAATTCA
34358274 ATTTATATAAAAAAAATCTATAGTAAT
1 ATTTATATAAAAAAAATCTATAGTAAT
*
34358301 ATTT-TAT-AAAATAATCTA-A-TAAT
1 ATTTATATAAAAAAAATCTATAGTAAT
34358324 ATT
1 ATT
34358327 AAAATAATGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 7 0.28
24 1 0.04
25 10 0.40
26 3 0.12
27 4 0.16
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (27 bp):
ATTTATATAAAAAAAATCTATAGTAAT
Found at i:34359669 original size:30 final size:30
Alignment explanation
Indices: 34359633--34359689 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
34359623 ATTTATTGTT
*
34359633 AATATTTTAATAT-ATGAAATATTAATTTTA
1 AATATTTTAAAATAAT-AAATATTAATTTTA
*
34359663 AATATTTTAAAATAATTAATATTAATT
1 AATATTTTAAAATAATAAATATTAATT
34359690 ATTTATAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 22 0.92
31 2 0.08
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (30 bp):
AATATTTTAAAATAATAAATATTAATTTTA
Found at i:34359687 original size:24 final size:24
Alignment explanation
Indices: 34359649--34359700 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
34359639 TTAATATATG
*
34359649 AAATATTAATTTTAAATATTT-TA
1 AAATATTAATATTAAATATTTATA
*
34359672 AAATAATTAATATTAATTATTTATA
1 AAAT-ATTAATATTAAATATTTATA
34359697 AAAT
1 AAAT
34359701 CTAATTAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 4 0.16
24 15 0.60
25 6 0.24
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
AAATATTAATATTAAATATTTATA
Found at i:34363449 original size:13 final size:13
Alignment explanation
Indices: 34363418--34363460 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
34363408 ATGGATAGAC
* *
34363418 AATAAATACAACA
1 AATAAATAAAATA
*
34363431 ATTAAATAAAATA
1 AATAAATAAAATA
34363444 AATAAATAAAATTA
1 AATAAATAAAA-TA
34363458 AAT
1 AAT
34363461 TTAAAAAGCA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
13 20 0.80
14 5 0.20
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.26
Consensus pattern (13 bp):
AATAAATAAAATA
Found at i:34382978 original size:23 final size:24
Alignment explanation
Indices: 34382952--34383043 Score: 95
Period size: 23 Copynumber: 4.0 Consensus size: 24
34382942 TAGCGCGCTC
34382952 ATTG-TTCAGCATTGTGTGTGCTT
1 ATTGATTCAGCATTGTGTGTGCTT
*
34382975 ATTGATTC-GCATTGTGTGTACTT
1 ATTGATTCAGCATTGTGTGTGCTT
* *
34382998 ACTGATTCA-CACTGTGTGTGC-T
1 ATTGATTCAGCATTGTGTGTGCTT
* * *
34383020 ACTGATT-TGCACTGTGTGTGCTT
1 ATTGATTCAGCATTGTGTGTGCTT
34383043 A
1 A
34383044 CTGTTTCCCC
Statistics
Matches: 60, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
22 20 0.33
23 37 0.62
24 3 0.05
ACGTcount: A:0.16, C:0.16, G:0.24, T:0.43
Consensus pattern (24 bp):
ATTGATTCAGCATTGTGTGTGCTT
Found at i:34393003 original size:18 final size:19
Alignment explanation
Indices: 34392952--34393006 Score: 55
Period size: 17 Copynumber: 3.1 Consensus size: 19
34392942 TGCAAAAATA
34392952 ATACATATGA-TAATATAC
1 ATACATATGATTAATATAC
*
34392970 AAACA-ATG-TT-ATATATC
1 ATACATATGATTAATATA-C
*
34392987 GTACATATGATTAATATAC
1 ATACATATGATTAATATAC
34393006 A
1 A
34393007 CAGGGTTATG
Statistics
Matches: 28, Mismatches: 4, Indels: 9
0.68 0.10 0.22
Matches are distributed among these distances:
16 5 0.18
17 8 0.29
18 7 0.25
19 3 0.11
20 5 0.18
ACGTcount: A:0.47, C:0.11, G:0.07, T:0.35
Consensus pattern (19 bp):
ATACATATGATTAATATAC
Found at i:34393117 original size:46 final size:46
Alignment explanation
Indices: 34393031--34393120 Score: 110
Period size: 46 Copynumber: 2.0 Consensus size: 46
34393021 AATGTTATAG
** *
34393031 TACATATGATAATTTACAAAAAATAATGCAGAAATGTACATAAAAA
1 TACATATGATAATGCACAAAAAATAATGCAGAAATATACATAAAAA
* * *
34393077 TACATATGATAATGCACAAACAATATTGTA-AAATAATACATAAA
1 TACATATGATAATGCACAAAAAATAATGCAGAAAT-ATACATAAA
34393121 GATATACACA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
45 4 0.11
46 33 0.89
ACGTcount: A:0.56, C:0.10, G:0.08, T:0.27
Consensus pattern (46 bp):
TACATATGATAATGCACAAAAAATAATGCAGAAATATACATAAAAA
Found at i:34397436 original size:24 final size:22
Alignment explanation
Indices: 34397408--34397454 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 22
34397398 AAAAATGAGG
34397408 AAAACCTAAGTTTTTTTACAATGA
1 AAAACCTAAG--TTTTTACAATGA
*
34397432 AAAACCTGAGTTTTTACAATGA
1 AAAACCTAAGTTTTTACAATGA
34397454 A
1 A
34397455 TAAAGTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 13 0.59
24 9 0.41
ACGTcount: A:0.43, C:0.13, G:0.11, T:0.34
Consensus pattern (22 bp):
AAAACCTAAGTTTTTACAATGA
Found at i:34398409 original size:3 final size:3
Alignment explanation
Indices: 34398401--34398434 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
34398391 AATTTCGAAG
*
34398401 TAA TAA TAA TAA TAA TAA TAA TAG TAAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA
34398435 ACTAAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.93
4 2 0.07
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:34399518 original size:7 final size:7
Alignment explanation
Indices: 34399495--34399541 Score: 53
Period size: 7 Copynumber: 7.0 Consensus size: 7
34399485 TTTCAAAAAA
34399495 GTCAACG
1 GTCAACG
* *
34399502 ATCAA-A
1 GTCAACG
34399508 GTCAACG
1 GTCAACG
34399515 GTCAAC-
1 GTCAACG
34399521 GTCAACG
1 GTCAACG
*
34399528 GTTAACG
1 GTCAACG
34399535 GTCAACG
1 GTCAACG
34399542 CCCGATCAAC
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
6 10 0.31
7 22 0.69
ACGTcount: A:0.34, C:0.26, G:0.23, T:0.17
Consensus pattern (7 bp):
GTCAACG
Found at i:34399520 original size:20 final size:20
Alignment explanation
Indices: 34399495--34399541 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
34399485 TTTCAAAAAA
34399495 GTCAACGATCAA-AGTCAACG
1 GTCAACG-TCAACAGTCAACG
* *
34399515 GTCAACGTCAACGGTTAACG
1 GTCAACGTCAACAGTCAACG
34399535 GTCAACG
1 GTCAACG
34399542 CCCGATCAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 4 0.17
20 20 0.83
ACGTcount: A:0.34, C:0.26, G:0.23, T:0.17
Consensus pattern (20 bp):
GTCAACGTCAACAGTCAACG
Found at i:34399528 original size:13 final size:13
Alignment explanation
Indices: 34399495--34399541 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
34399485 TTTCAAAAAA
* *
34399495 GTCAACGATCAAA
1 GTCAACGGTCAAC
34399508 GTCAACGGTCAAC
1 GTCAACGGTCAAC
*
34399521 GTCAACGGTTAAC
1 GTCAACGGTCAAC
34399534 GGTCAACG
1 -GTCAACG
34399542 CCCGATCAAC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
13 23 0.77
14 7 0.23
ACGTcount: A:0.34, C:0.26, G:0.23, T:0.17
Consensus pattern (13 bp):
GTCAACGGTCAAC
Found at i:34403264 original size:20 final size:20
Alignment explanation
Indices: 34403227--34403266 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
34403217 GCCATGGACA
34403227 CAGGAGTCGTGCCAGAATAG
1 CAGGAGTCGTGCCAGAATAG
34403247 CAGGAGTCGTGCCAGAATAG
1 CAGGAGTCGTGCCAGAATAG
34403267 ACTTCTATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.20, G:0.35, T:0.15
Consensus pattern (20 bp):
CAGGAGTCGTGCCAGAATAG
Found at i:34410888 original size:14 final size:14
Alignment explanation
Indices: 34410869--34410916 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
34410859 TAAGTAAAAG
34410869 ATAATATAAAATTT
1 ATAATATAAAATTT
34410883 ATAATATATAACATTT
1 ATAATATA-AA-ATTT
* *
34410899 ATAAAAAAAAATTAT
1 ATAATATAAAATT-T
34410914 ATA
1 ATA
34410917 TTATCTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
14 11 0.38
15 8 0.28
16 10 0.34
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (14 bp):
ATAATATAAAATTT
Found at i:34421009 original size:27 final size:27
Alignment explanation
Indices: 34420944--34421010 Score: 66
Period size: 29 Copynumber: 2.4 Consensus size: 27
34420934 TAAATTAATC
* *
34420944 ATTTTGAAATTTATTCATTATATTTTT
1 ATTTTAAAATTTAATCATTATATTTTT
34420971 ATTATTAAAAATTTAATC-TTACT-TTTTAT
1 ATT-TT-AAAATTTAATCATTA-TATTTT-T
34421000 ATTTTAAAATT
1 ATTTTAAAATT
34421011 CAAGTTCAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
27 9 0.26
28 11 0.32
29 14 0.41
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.58
Consensus pattern (27 bp):
ATTTTAAAATTTAATCATTATATTTTT
Found at i:34424568 original size:3 final size:3
Alignment explanation
Indices: 34424560--34424591 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
34424550 CATCGGTCAC
34424560 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
34424592 GAGTTGGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:34433575 original size:34 final size:34
Alignment explanation
Indices: 34433536--34433637 Score: 143
Period size: 34 Copynumber: 3.0 Consensus size: 34
34433526 TATCGAATCT
*
34433536 TAGTTCAATTGATTTCGATATTGATATTAATATA
1 TAGTTCAATTGATTTCGATATTGATATCAATATA
* * *
34433570 TAGTTCAATTGATTTTGATGTTGTTATCAATATA
1 TAGTTCAATTGATTTCGATATTGATATCAATATA
*
34433604 TAGTTCAATTGATTTCGATGTT-ATTATCAATATA
1 TAGTTCAATTGATTTCGATATTGA-TATCAATATA
34433638 GGAAAACGTA
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
34 61 1.00
ACGTcount: A:0.32, C:0.07, G:0.13, T:0.48
Consensus pattern (34 bp):
TAGTTCAATTGATTTCGATATTGATATCAATATA
Found at i:34440334 original size:292 final size:286
Alignment explanation
Indices: 34439940--34440518 Score: 851
Period size: 292 Copynumber: 2.0 Consensus size: 286
34439930 AATATATTTT
* *
34439940 ATTTTATGATTTTATATCTCATACAATCGTTAAAAAGGTAAAATTTTCAATTCATAAAAGTATTT
1 ATTTTATGATTTTATATCTCATACAATCGTTAAAAAGGAAAAATTTTAAATTCATAAAAGTATTT
* *
34440005 TGTTTTATGATTTTGTTTAGCATATAGATAAACAAATACGTATAGTTTTATTTTTT-GCTTGGTA
66 TGTTTTATAATTTTGTTTAGCATATAGATAAAC-AA-A--TATAGTTTTATTTTTTCACTTGGTA
* *
34440069 TTATTTATTATTTTTACATTGTATAATCTGAGAAAAAATTATATGAAATA-AGAATTTTTTCTTT
127 TTATTTATTATTTTTACATTATATAATCTGAGAAAAAATTATATGAAATAGAG-A--TATT-TTT
* * *
34440133 TTCAATAATTTTATTTCACATCAATAATTTTATTTT-AGATTTTAGAATTTTTATTTAAATTT-A
188 TT-AATAATTTTATATCACATCAATAATTTTATTTTGA-ATTTCAAAATTTTTATTTAAATTTGA
*
34440196 TTTTTTTTCAAGATGAAAATATTAAAAATCAGGATG
251 TTTTTTTTCAAGATAAAAATATTAAAAATCAGGATG
* * *
34440232 ATTTTATGATTTTGTATCTCATACAATTGTTAAAAAGGAAAAATTTTAAATTTATAAAAGTATTT
1 ATTTTATGATTTTATATCTCATACAATCGTTAAAAAGGAAAAATTTTAAATTCATAAAAGTATTT
*
34440297 TGTTTTATAATTTTGTTTAGCATATAGATAAACAAATATAGTTTTGTTTTTTCACTTGGTATTAT
66 TGTTTTATAATTTTGTTTAGCATATAGATAAACAAATATAGTTTTATTTTTTCACTTGGTATTAT
* * * *
34440362 TTATTATTTTTACATTATATGATTTGAGAAAAAATTATATGAAGTAGAGATATTTTTTTAATAGT
131 TTATTATTTTTACATTATATAATCTGAGAAAAAATTATATGAAATAGAGATATTTTTTTAATAAT
**
34440427 TTTATATCACATCAATAATTTTATTTTGAATTTCAAAATTTTTATTTTCATTTGATTTTTTTTCA
196 TTTATATCACATCAATAATTTTATTTTGAATTTCAAAATTTTTATTTAAATTTGATTTTTTTTCA
*
34440492 AGATAAAAATGTTAAAAATCAGGATG
261 AGATAAAAATATTAAAAATCAGGATG
34440518 A
1 A
34440519 AAATTTTGAC
Statistics
Matches: 262, Mismatches: 21, Indels: 14
0.88 0.07 0.05
Matches are distributed among these distances:
285 51 0.19
286 42 0.16
287 3 0.01
288 15 0.06
289 54 0.21
290 3 0.01
291 2 0.01
292 92 0.35
ACGTcount: A:0.36, C:0.06, G:0.10, T:0.48
Consensus pattern (286 bp):
ATTTTATGATTTTATATCTCATACAATCGTTAAAAAGGAAAAATTTTAAATTCATAAAAGTATTT
TGTTTTATAATTTTGTTTAGCATATAGATAAACAAATATAGTTTTATTTTTTCACTTGGTATTAT
TTATTATTTTTACATTATATAATCTGAGAAAAAATTATATGAAATAGAGATATTTTTTTAATAAT
TTTATATCACATCAATAATTTTATTTTGAATTTCAAAATTTTTATTTAAATTTGATTTTTTTTCA
AGATAAAAATATTAAAAATCAGGATG
Found at i:34441618 original size:27 final size:27
Alignment explanation
Indices: 34441425--34441672 Score: 250
Period size: 27 Copynumber: 9.3 Consensus size: 27
34441415 TTCTGCCTTC
* * * * *
34441425 GGCACTCCTTCTTCCACCCCTGCCTTT
1 GGCACTCCGTCTTCGACACCGGCGTTT
* * * *
34441452 GGCACTCCTTCTTCCACCCCGGCCTTT
1 GGCACTCCGTCTTCGACACCGGCGTTT
* * * * *
34441479 GGAACTCCTTCTTCCACTCCGGCTTTT
1 GGCACTCCGTCTTCGACACCGGCGTTT
* *
34441506 GGGACT-C--CTTCGACACCGGCATTT
1 GGCACTCCGTCTTCGACACCGGCGTTT
34441530 GGCACTCCGTCTTCGACACCGGCGTTT
1 GGCACTCCGTCTTCGACACCGGCGTTT
* *
34441557 GGCACTCCGTCTTTGACACCTGCGTTT
1 GGCACTCCGTCTTCGACACCGGCGTTT
*
34441584 GGCACTCCGTCTTCGACACCTGCGTTT
1 GGCACTCCGTCTTCGACACCGGCGTTT
**
34441611 GGGGCTCCGTCTTCGACACCGGCGTTT
1 GGCACTCCGTCTTCGACACCGGCGTTT
* * *
34441638 GGAACTCCGTCCTCGACACCGGCTTTT
1 GGCACTCCGTCTTCGACACCGGCGTTT
*
34441665 GGAACTCC
1 GGCACTCC
34441673 ATCAACGCCG
Statistics
Matches: 198, Mismatches: 20, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
24 19 0.10
25 1 0.01
26 1 0.01
27 177 0.89
ACGTcount: A:0.11, C:0.38, G:0.21, T:0.29
Consensus pattern (27 bp):
GGCACTCCGTCTTCGACACCGGCGTTT
Found at i:34455603 original size:22 final size:21
Alignment explanation
Indices: 34455577--34455629 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
34455567 AATATATATT
*
34455577 AATATAAACAATATTTTAGATC
1 AATATAAA-AATATATTAGATC
*
34455599 AATATGATAAATATATTAGATC
1 AATAT-AAAAATATATTAGATC
34455621 AAT-TAAAAA
1 AATATAAAAA
34455630 ATTTATATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 4 0.15
21 1 0.04
22 20 0.74
23 2 0.07
ACGTcount: A:0.55, C:0.06, G:0.06, T:0.34
Consensus pattern (21 bp):
AATATAAAAATATATTAGATC
Found at i:34456010 original size:23 final size:23
Alignment explanation
Indices: 34455983--34456031 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
34455973 GTATTAAGAG
34455983 TTAGATTCTATTTTATCTTTTTA
1 TTAGATTCTATTTTATCTTTTTA
*
34456006 TTAGATTGTATTTTATCTTTTTA
1 TTAGATTCTATTTTATCTTTTTA
34456029 TTA
1 TTA
34456032 AAAAATAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.22, C:0.06, G:0.06, T:0.65
Consensus pattern (23 bp):
TTAGATTCTATTTTATCTTTTTA
Found at i:34462783 original size:22 final size:22
Alignment explanation
Indices: 34462749--34462792 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
34462739 AATATTTATT
*
34462749 AATATAGATAATATTTTAGATC
1 AATATAGATAATATATTAGATC
34462771 AATAT-GATAAATATATTAGATC
1 AATATAGAT-AATATATTAGATC
34462793 GATTAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.48, C:0.05, G:0.09, T:0.39
Consensus pattern (22 bp):
AATATAGATAATATATTAGATC
Found at i:34463716 original size:23 final size:23
Alignment explanation
Indices: 34463658--34463766 Score: 130
Period size: 23 Copynumber: 4.7 Consensus size: 23
34463648 ATTAACATTA
* *
34463658 TTCGTGAACGTGTTCAATTATATG
1 TTCGTGAACATGTTCGATTA-ATG
*
34463682 TTCATGAACATGTTCGATTAATG
1 TTCGTGAACATGTTCGATTAATG
*
34463705 TTCGTGACCATGTTCGATTAATG
1 TTCGTGAACATGTTCGATTAATG
*
34463728 TTCGTGACCATGTTCGATTAA-G
1 TTCGTGAACATGTTCGATTAATG
**
34463750 TTAAATGAACATGTTCG
1 TT-CGTGAACATGTTCG
34463767 TGAACATTAA
Statistics
Matches: 76, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
22 3 0.04
23 56 0.74
24 17 0.22
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.39
Consensus pattern (23 bp):
TTCGTGAACATGTTCGATTAATG
Found at i:34463719 original size:12 final size:12
Alignment explanation
Indices: 34463702--34463743 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
34463692 TGTTCGATTA
34463702 ATGTTCGTGACC
1 ATGTTCGTGACC
*
34463714 ATGTTCGATTA--
1 ATGTTCG-TGACC
34463725 ATGTTCGTGACC
1 ATGTTCGTGACC
34463737 ATGTTCG
1 ATGTTCG
34463744 ATTAAGTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
10 2 0.08
11 7 0.28
12 14 0.56
13 2 0.08
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (12 bp):
ATGTTCGTGACC
Done.