Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 100 of 193
Found at i:32236117 original size:3 final size:3
Alignment explanation
Indices: 32236105--32236165 Score: 53
Period size: 3 Copynumber: 21.7 Consensus size: 3
32236095 CAAATTTCAA
*
32236105 TCT T-T TCT TCT TCT TCT TCT TCT T-T TTT TCT T-T T-T TCCT TC-
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T-CT TCT
32236146 TCT T-T TGCT TCT TCT TCT TC
1 TCT TCT T-CT TCT TCT TCT TC
32236166 CAGCAACTAG
Statistics
Matches: 50, Mismatches: 1, Indels: 14
0.77 0.02 0.22
Matches are distributed among these distances:
2 12 0.24
3 34 0.68
4 4 0.08
ACGTcount: A:0.00, C:0.28, G:0.02, T:0.70
Consensus pattern (3 bp):
TCT
Found at i:32240360 original size:48 final size:47
Alignment explanation
Indices: 32240307--32240423 Score: 128
Period size: 48 Copynumber: 2.4 Consensus size: 47
32240297 TTTTTTACAC
** *
32240307 ATTAATCGTATTAATCACATGAGTACTTAAGCATTTA-ACATAACACAT
1 ATTAATCACATTAATCACATGAATACTTAAGCATTTATACAT--CACAT
* * *
32240355 ATTAATCACATTAGTCACATGAATATTTCAGCATTTATTACATCACAT
1 ATTAATCACATTAATCACATGAATACTTAAGCATTTA-TACATCACAT
*
32240403 ATTAATCACATTTAGTCACAT
1 ATTAATCACA-TTAATCACAT
32240424 ATAATCACAT
Statistics
Matches: 60, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
48 46 0.77
49 10 0.17
50 4 0.07
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.36
Consensus pattern (47 bp):
ATTAATCACATTAATCACATGAATACTTAAGCATTTATACATCACAT
Found at i:32240380 original size:24 final size:26
Alignment explanation
Indices: 32240350--32240423 Score: 86
Period size: 24 Copynumber: 3.0 Consensus size: 26
32240340 TTTAACATAA
32240350 CACATATTAATCACA-TTAGTCACAT
1 CACATATTAATCACATTTAGTCACAT
* *
32240375 GA-ATATT--TCAGCATTTA-TTACAT
1 CACATATTAATCA-CATTTAGTCACAT
32240398 CACATATTAATCACATTTAGTCACAT
1 CACATATTAATCACATTTAGTCACAT
32240424 ATAATCACAT
Statistics
Matches: 39, Mismatches: 4, Indels: 11
0.72 0.07 0.20
Matches are distributed among these distances:
22 3 0.08
23 8 0.21
24 13 0.33
25 7 0.18
26 8 0.21
ACGTcount: A:0.38, C:0.20, G:0.05, T:0.36
Consensus pattern (26 bp):
CACATATTAATCACATTTAGTCACAT
Found at i:32240423 original size:10 final size:10
Alignment explanation
Indices: 32240396--32240498 Score: 75
Period size: 10 Copynumber: 9.8 Consensus size: 10
32240386 CATTTATTAC
32240396 ATCACATATTA
1 ATCACAT-TTA
32240407 ATCACATTTA
1 ATCACATTTA
* *
32240417 GTCACATATA
1 ATCACATTTA
32240427 ATCACATTAATA
1 ATCACATT--TA
*
32240439 TTTCAACATTT-
1 -ATC-ACATTTA
*
32240450 ATCACA-TCA
1 ATCACATTTA
32240459 CATCACATATTA
1 -ATCACAT-TTA
32240471 ATCACATTTA
1 ATCACATTTA
* *
32240481 GTCACATATA
1 ATCACATTTA
32240491 ATCACATT
1 ATCACATT
32240499 AATATTTCAA
Statistics
Matches: 72, Mismatches: 12, Indels: 17
0.71 0.12 0.17
Matches are distributed among these distances:
8 1 0.01
9 3 0.04
10 42 0.58
11 14 0.19
12 5 0.07
13 2 0.03
14 5 0.07
ACGTcount: A:0.41, C:0.21, G:0.02, T:0.36
Consensus pattern (10 bp):
ATCACATTTA
Found at i:32240464 original size:33 final size:34
Alignment explanation
Indices: 32240410--32240513 Score: 137
Period size: 31 Copynumber: 3.2 Consensus size: 34
32240400 CATATTAATC
32240410 ACATTTAGTCACATATAATCACATTAATATTTCA
1 ACATTTAGTCACATATAATCACATTAATATTTCA
* * *
32240444 ACATTTA-TCACATCA-CATCACA-TATTA-ATC-
1 ACATTTAGTCACAT-ATAATCACATTAATATTTCA
32240474 ACATTTAGTCACATATAATCACATTAATATTTCA
1 ACATTTAGTCACATATAATCACATTAATATTTCA
32240508 ACATTT
1 ACATTT
32240514 TTCACATCAC
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
30 8 0.14
31 14 0.24
32 8 0.14
33 14 0.24
34 14 0.24
ACGTcount: A:0.40, C:0.20, G:0.02, T:0.38
Consensus pattern (34 bp):
ACATTTAGTCACATATAATCACATTAATATTTCA
Found at i:32240477 original size:123 final size:123
Alignment explanation
Indices: 32240350--32240612 Score: 324
Period size: 123 Copynumber: 2.2 Consensus size: 123
32240340 TTTAACATAA
* *
32240350 CACATATTAATCACAT-TAGTCACATGAATATTTCAGCATTTATT-ACATCACATATTAATCACA
1 CACAT-TTAATCACATATAATCACATGAATATTTCAACATTT-TTCACATCACATATTAATCACA
* *
32240413 TTTAGTCACATATAATCACATTAATATTTCAACATTTATCACATCACATCACATATTAAT
64 TCTAGTCACATATAATCACATGAATATTTCAACATTTATCACATCACATCACATATTAAT
* *
32240473 CACATTTAGTCACATATAATCACATTAATATTTCAACATTTTTCACATCACATATTAATCACATC
1 CACATTTAATCACATATAATCACATGAATATTTCAACATTTTTCACATCACATATTAATCACATC
* * * * ** *
32240538 TAGTTATATGTAATCATATGAATATTTCAGTATTTATCGCATCACAT----T-TTAAT
66 TAGTCACATATAATCACATGAATATTTCAACATTTATCACATCACATCACATATTAAT
* *
32240591 CACATTTAGTCACATTTAATCA
1 CACATTTAATCACATATAATCA
32240613 TATAATCACA
Statistics
Matches: 124, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
118 26 0.21
119 1 0.01
122 11 0.09
123 86 0.69
ACGTcount: A:0.38, C:0.19, G:0.04, T:0.38
Consensus pattern (123 bp):
CACATTTAATCACATATAATCACATGAATATTTCAACATTTTTCACATCACATATTAATCACATC
TAGTCACATATAATCACATGAATATTTCAACATTTATCACATCACATCACATATTAAT
Found at i:32240488 original size:64 final size:60
Alignment explanation
Indices: 32240350--32240612 Score: 318
Period size: 59 Copynumber: 4.4 Consensus size: 60
32240340 TTTAACATAA
* * *
32240350 CACATATTAATCACAT-TAGTCACATGAATATTTCAGCATTTATT-ACATCACATATTAAT
1 CACAT-TTAGTCACATATAATCACATGAATATTTCAACATTTATTCACATCACATATTAAT
*
32240409 CACATTTAGTCACATATAATCACATTAATATTTCAACATTTATCACATCACATCACATATTAAT
1 CACATTTAGTCACATATAATCACATGAATATTTCAACATTTAT----TCACATCACATATTAAT
*
32240473 CACATTTAGTCACATATAATCACATTAATATTTCAACATTT-TTCACATCACATATTAAT
1 CACATTTAGTCACATATAATCACATGAATATTTCAACATTTATTCACATCACATATTAAT
* * * * * ** * *
32240532 CACATCTAGTTATATGTAATCATATGAATATTTCAGTATTTA-TCGCATCACATTTTAAT
1 CACATTTAGTCACATATAATCACATGAATATTTCAACATTTATTCACATCACATATTAAT
*
32240591 CACATTTAGTCACATTTAATCA
1 CACATTTAGTCACATATAATCA
32240613 TATAATCACA
Statistics
Matches: 179, Mismatches: 18, Indels: 14
0.85 0.09 0.07
Matches are distributed among these distances:
58 9 0.05
59 112 0.63
63 2 0.01
64 56 0.31
ACGTcount: A:0.38, C:0.19, G:0.04, T:0.38
Consensus pattern (60 bp):
CACATTTAGTCACATATAATCACATGAATATTTCAACATTTATTCACATCACATATTAAT
Found at i:32240495 original size:31 final size:31
Alignment explanation
Indices: 32240396--32240497 Score: 127
Period size: 31 Copynumber: 3.2 Consensus size: 31
32240386 CATTTATTAC
32240396 ATCACATATTAATCACATTTAGTCACATATA
1 ATCACATATTAATCACATTTAGTCACATATA
* * *
32240427 ATCACATTAATATTTCAACATTTA-TCACATCA-C
1 ATCACA-TATTA-ATC-ACATTTAGTCACAT-ATA
32240460 ATCACATATTAATCACATTTAGTCACATATA
1 ATCACATATTAATCACATTTAGTCACATATA
32240491 ATCACAT
1 ATCACAT
32240498 TAATATTTCA
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
30 8 0.14
31 21 0.36
32 8 0.14
33 14 0.24
34 8 0.14
ACGTcount: A:0.41, C:0.22, G:0.02, T:0.35
Consensus pattern (31 bp):
ATCACATATTAATCACATTTAGTCACATATA
Found at i:32240603 original size:10 final size:10
Alignment explanation
Indices: 32240578--32240624 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
32240568 TATTTATCGC
32240578 ATCACATTTTA
1 ATCACA-TTTA
32240589 ATCACATTTA
1 ATCACATTTA
*
32240599 GTCACATTTA
1 ATCACATTTA
*
32240609 AT--CATATA
1 ATCACATTTA
32240617 ATCACATT
1 ATCACATT
32240625 AAACACATGT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
8 7 0.23
10 17 0.57
11 6 0.20
ACGTcount: A:0.38, C:0.19, G:0.02, T:0.40
Consensus pattern (10 bp):
ATCACATTTA
Found at i:32241094 original size:36 final size:36
Alignment explanation
Indices: 32241042--32241228 Score: 248
Period size: 36 Copynumber: 5.2 Consensus size: 36
32241032 ATATATTCAG
* *
32241042 TGTCACATGGTATGAATAACATACCAACATTTTTAC
1 TGTCACATGGTATGAATAACATACCCACATATTTAC
* * *
32241078 TGTCTCATGGCATGAATAACATACCCACATATTTAT
1 TGTCACATGGTATGAATAACATACCCACATATTTAC
* * *
32241114 TATCACATGGTATGAATAATATATCCACATATTTAC
1 TGTCACATGGTATGAATAACATACCCACATATTTAC
* *
32241150 TGTCTCATGGTATGAATAACATACCCACACATTTAC
1 TGTCACATGGTATGAATAACATACCCACATATTTAC
** *
32241186 TGTCACATGACATGAATAACATGCCCACATATTTAC
1 TGTCACATGGTATGAATAACATACCCACATATTTAC
*
32241222 TTTCACA
1 TGTCACA
32241229 ATAATCATCA
Statistics
Matches: 129, Mismatches: 22, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 129 1.00
ACGTcount: A:0.35, C:0.22, G:0.10, T:0.33
Consensus pattern (36 bp):
TGTCACATGGTATGAATAACATACCCACATATTTAC
Found at i:32242146 original size:20 final size:20
Alignment explanation
Indices: 32242121--32242174 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
32242111 CTCCAGTGAG
* *
32242121 ACTTCTACCGGTAGAACTCA
1 ACTTCTACCGATACAACTCA
*
32242141 ACTTCTACCGATACAACTCC
1 ACTTCTACCGATACAACTCA
32242161 ACTTCTACCGATAC
1 ACTTCTACCGATAC
32242175 CTTGAAGACT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.30, C:0.35, G:0.09, T:0.26
Consensus pattern (20 bp):
ACTTCTACCGATACAACTCA
Found at i:32250279 original size:29 final size:29
Alignment explanation
Indices: 32250247--32250315 Score: 75
Period size: 29 Copynumber: 2.3 Consensus size: 29
32250237 TATAGAATTT
* * *
32250247 TTTATATATAAACAAATTTTATATCTATA
1 TTTATATATAAACAAATTATACATATATA
* * *
32250276 TTTATACATATACTAATTATACATATATA
1 TTTATATATAAACAAATTATACATATATA
32250305 TATTATATATA
1 T-TTATATATA
32250316 TTTCTGACTT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
29 24 0.75
30 8 0.25
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (29 bp):
TTTATATATAAACAAATTATACATATATA
Found at i:32250297 original size:15 final size:15
Alignment explanation
Indices: 32250272--32250316 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
32250262 ATTTTATATC
32250272 TATAT-TTATACATA
1 TATATATTATACATA
32250286 TACTA-ATTATACATA
1 TA-TATATTATACATA
*
32250301 TATATATTATATATA
1 TATATATTATACATA
32250316 T
1 T
32250317 TTCTGACTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 4 0.15
15 23 0.85
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (15 bp):
TATATATTATACATA
Found at i:32255652 original size:25 final size:25
Alignment explanation
Indices: 32255616--32255664 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
32255606 CTGGTTAAAC
*
32255616 TCTGTCTCGGCTCATAAGAGCTAAT
1 TCTGTCTAGGCTCATAAGAGCTAAT
* *
32255641 TCTGTCTAGGCTCGTATGAGCTAA
1 TCTGTCTAGGCTCATAAGAGCTAA
32255665 ATTTCTAGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (25 bp):
TCTGTCTAGGCTCATAAGAGCTAAT
Found at i:32256366 original size:21 final size:21
Alignment explanation
Indices: 32256319--32256367 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
32256309 GAGTTTTTTA
32256319 TATCGGTAGAAGCATTACATG
1 TATCGGTAGAAGCATTACATG
* *
32256340 TTTCGGTAGAAGTCA-TACTTG
1 TATCGGTAGAAG-CATTACATG
32256361 TATCGGT
1 TATCGGT
32256368 GGTACTGCCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 22 0.92
22 2 0.08
ACGTcount: A:0.27, C:0.14, G:0.24, T:0.35
Consensus pattern (21 bp):
TATCGGTAGAAGCATTACATG
Found at i:32278412 original size:18 final size:18
Alignment explanation
Indices: 32278371--32278404 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
32278361 ATGTACTAAC
32278371 AAAT-AAAATGCAATGAA
1 AAATAAAAATGCAATGAA
32278388 AAATAAAAATGCAATGA
1 AAATAAAAATGCAATGA
32278405 CAACTAAATG
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:0.65, C:0.06, G:0.12, T:0.18
Consensus pattern (18 bp):
AAATAAAAATGCAATGAA
Found at i:32292064 original size:14 final size:15
Alignment explanation
Indices: 32292045--32292077 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
32292035 TGAAGAACAT
32292045 AAAGGACCTG-AAGA
1 AAAGGACCTGAAAGA
32292059 AAAGGACCTGAAAGA
1 AAAGGACCTGAAAGA
32292074 AAAG
1 AAAG
32292078 AAAAATGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.55, C:0.12, G:0.27, T:0.06
Consensus pattern (15 bp):
AAAGGACCTGAAAGA
Found at i:32292527 original size:17 final size:18
Alignment explanation
Indices: 32292488--32292531 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
32292478 ATTCATAGCA
* *
32292488 TTTAGTTGTCATTGCATT
1 TTTATTTGTCACTGCATT
32292506 TTTATTTGTCACTGCA-T
1 TTTATTTGTCACTGCATT
32292523 TTTATTTGT
1 TTTATTTGT
32292532 TAGAACATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.16, C:0.11, G:0.14, T:0.59
Consensus pattern (18 bp):
TTTATTTGTCACTGCATT
Found at i:32304338 original size:30 final size:30
Alignment explanation
Indices: 32304302--32304358 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
32304292 AATTTTAAAT
32304302 AATTAATA-TTCAT-TACTTAAAAATATTTAA
1 AATTAATATTTCATATA-TT-AAAATATTTAA
32304332 AATTAATATTTCATATATTAAAATATT
1 AATTAATATTTCATATATTAAAATATT
32304359 AACAATAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
30 16 0.64
31 7 0.28
32 2 0.08
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (30 bp):
AATTAATATTTCATATATTAAAATATTTAA
Found at i:32305077 original size:13 final size:13
Alignment explanation
Indices: 32305059--32305117 Score: 93
Period size: 13 Copynumber: 4.6 Consensus size: 13
32305049 AATTATAATG
32305059 ATTGATTTGATTA
1 ATTGATTTGATTA
32305072 ATTGATTTGATTA
1 ATTGATTTGATTA
*
32305085 ATTGATTTGATCA
1 ATTGATTTGATTA
*
32305098 ATTGATTTTATTA
1 ATTGATTTGATTA
32305111 ATT-ATTT
1 ATTGATTT
32305118 ATTTAAAAGT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
12 4 0.09
13 39 0.91
ACGTcount: A:0.31, C:0.02, G:0.12, T:0.56
Consensus pattern (13 bp):
ATTGATTTGATTA
Found at i:32307815 original size:10 final size:10
Alignment explanation
Indices: 32307791--32307832 Score: 50
Period size: 10 Copynumber: 4.3 Consensus size: 10
32307781 TCCTTCTCTC
32307791 AACTCTATC-
1 AACTCTATCA
32307800 AACTCTATCA
1 AACTCTATCA
* *
32307810 AACTCTCTTA
1 AACTCTATCA
*
32307820 AACTCTCTCA
1 AACTCTATCA
32307830 AAC
1 AAC
32307833 CTTCTAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
9 9 0.31
10 20 0.69
ACGTcount: A:0.36, C:0.33, G:0.00, T:0.31
Consensus pattern (10 bp):
AACTCTATCA
Found at i:32308040 original size:16 final size:16
Alignment explanation
Indices: 32308003--32308041 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
32307993 GGTAATACAA
32308003 AAATTTAAATTTCGTT
1 AAATTTAAATTTCGTT
32308019 -AATTTAAATATTC-TT
1 AAATTTAAAT-TTCGTT
32308034 AAATTTAA
1 AAATTTAA
32308042 TTTAATTAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.49
Consensus pattern (16 bp):
AAATTTAAATTTCGTT
Found at i:32316074 original size:2 final size:2
Alignment explanation
Indices: 32316067--32316096 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
32316057 TTTGCCATTA
32316067 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
32316097 GAAATTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32331282 original size:2 final size:2
Alignment explanation
Indices: 32331275--32331317 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
32331265 CGTGATATTC
32331275 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
32331316 AT
1 AT
32331318 CAAATGAAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:32340597 original size:21 final size:22
Alignment explanation
Indices: 32340572--32340622 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 22
32340562 GATATACAAC
32340572 ATTTGAGAAAAATTTGAGCATT
1 ATTTGAGAAAAATTTGAGCATT
* * *
32340594 -TTTGA-AAAGATTTGATCCTT
1 ATTTGAGAAAAATTTGAGCATT
32340614 ATTTGAGAA
1 ATTTGAGAA
32340623 CTTTCGAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 12 0.50
21 10 0.42
22 2 0.08
ACGTcount: A:0.37, C:0.06, G:0.18, T:0.39
Consensus pattern (22 bp):
ATTTGAGAAAAATTTGAGCATT
Found at i:32341011 original size:22 final size:22
Alignment explanation
Indices: 32340958--32341021 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 22
32340948 CACACATTAG
* *
32340958 CTTTAGTTTAGCTTA-GTTTTCT
1 CTTTAGTTT-TCTTAGGTTTTAT
32340980 CTTTAGTTTTCTTAGGTTTTAT
1 CTTTAGTTTTCTTAGGTTTTAT
32341002 CTTTCA-TTTT-TTAGGGTTTT
1 CTTT-AGTTTTCTTA-GGTTTT
32341022 TTAGTTCTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
21 7 0.19
22 29 0.78
23 1 0.03
ACGTcount: A:0.12, C:0.11, G:0.14, T:0.62
Consensus pattern (22 bp):
CTTTAGTTTTCTTAGGTTTTAT
Found at i:32345032 original size:29 final size:29
Alignment explanation
Indices: 32344999--32345054 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
32344989 TGTCCACTTC
*
32344999 TCTCAAATCGGTACTTAAAGTTTTTTTTG
1 TCTCAAATCGGTACTTAAACTTTTTTTTG
* *
32345028 TCTCAAATTGGTACTTCAACTTTTTTT
1 TCTCAAATCGGTACTTAAACTTTTTTT
32345055 CCATCAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.23, C:0.16, G:0.11, T:0.50
Consensus pattern (29 bp):
TCTCAAATCGGTACTTAAACTTTTTTTTG
Found at i:32345179 original size:8 final size:8
Alignment explanation
Indices: 32345160--32345205 Score: 67
Period size: 8 Copynumber: 5.8 Consensus size: 8
32345150 TCATAATCTC
32345160 TTTTTCTA
1 TTTTTCTA
32345168 -TTTTCTA
1 TTTTTCTA
32345175 TTTTTCTA
1 TTTTTCTA
32345183 TTTTTCTA
1 TTTTTCTA
*
32345191 TTTTTTTCA
1 TTTTTCT-A
32345200 TTTTTC
1 TTTTTC
32345206 CTTTTCTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
7 7 0.21
8 21 0.62
9 6 0.18
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (8 bp):
TTTTTCTA
Found at i:32345215 original size:18 final size:18
Alignment explanation
Indices: 32345175--32345224 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
32345165 CTATTTTCTA
32345175 TTTTTCTATTTTT-CTATT
1 TTTTTC-ATTTTTCCTATT
32345193 TTTTTCATTTTTCCT-TT
1 TTTTTCATTTTTCCTATT
32345210 TCTTTT-ATTATTTCC
1 T-TTTTCATT-TTTCC
32345225 CATTCCCATC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
17 12 0.41
18 17 0.59
ACGTcount: A:0.10, C:0.16, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTCATTTTTCCTATT
Found at i:32348116 original size:28 final size:28
Alignment explanation
Indices: 32348075--32348191 Score: 104
Period size: 28 Copynumber: 4.4 Consensus size: 28
32348065 TCATAACACT
*
32348075 CTTTCAGAGTTCACCATTCATATATGTTC
1 CTTT-AGAGTTCACCATTCGTATATGTTC
*
32348104 CTTTAGAGTTCACCA-T--T-TCT-TTC
1 CTTTAGAGTTCACCATTCGTATATGTTC
* * * *
32348127 TTTTAGAGTTCGCAATTCGTA-ATGCT-
1 CTTTAGAGTTCACCATTCGTATATGTTC
*
32348153 CTTTAAGAGTTCGCCATTCGTATATGTTC
1 CTTT-AGAGTTCACCATTCGTATATGTTC
32348182 CTTTAGAGTT
1 CTTTAGAGTT
32348192 TGCTATTTCT
Statistics
Matches: 71, Mismatches: 9, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
23 15 0.21
24 3 0.04
25 1 0.01
26 5 0.07
27 18 0.25
28 21 0.30
29 8 0.11
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.44
Consensus pattern (28 bp):
CTTTAGAGTTCACCATTCGTATATGTTC
Found at i:32348163 original size:27 final size:27
Alignment explanation
Indices: 32348128--32348191 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 27
32348118 ATTTCTTTCT
32348128 TTTAGAGTTCGCAATTCGTA-ATGCTC
1 TTTAGAGTTCGCAATTCGTATATGCTC
* *
32348154 TTTAAGAGTTCGCCATTCGTATATGTTCC
1 TTT-AGAGTTCGCAATTCGTATATGCT-C
32348183 TTTAGAGTT
1 TTTAGAGTT
32348192 TGCTATTTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 3 0.09
27 16 0.48
28 10 0.30
29 4 0.12
ACGTcount: A:0.22, C:0.17, G:0.19, T:0.42
Consensus pattern (27 bp):
TTTAGAGTTCGCAATTCGTATATGCTC
Found at i:32348228 original size:78 final size:78
Alignment explanation
Indices: 32348039--32348230 Score: 233
Period size: 78 Copynumber: 2.5 Consensus size: 78
32348029 TTCGCCACGC
* * ** *
32348039 CTATTTGTTT-CTTCAGAGTTTGCCATTCATAACACTCTTTCAGAGTTCACCATTCATATATGTT
1 CTATTTCTTTCCTTCAGAGTTCGCCATTCATAATGCTCTTTAAGAGTTCACCATTCATATATGTT
32348103 CCTTTAGAGTTCA
66 CCTTTAGAGTTCA
* * * * * * *
32348116 CCATTTCTTTCTTTTAGAGTTCGCAATTCGTAATGCTCTTTAAGAGTTCGCCATTCGTATATGTT
1 CTATTTCTTTCCTTCAGAGTTCGCCATTCATAATGCTCTTTAAGAGTTCACCATTCATATATGTT
**
32348181 CCTTTAGAGTTTG
66 CCTTTAGAGTTCA
* *
32348194 CTATTTCTTTCCTTCAGGGTTCACCATTCATAATGCT
1 CTATTTCTTTCCTTCAGAGTTCGCCATTCATAATGCT
32348231 TTTTTTATAG
Statistics
Matches: 93, Mismatches: 21, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
77 8 0.09
78 85 0.91
ACGTcount: A:0.21, C:0.22, G:0.14, T:0.44
Consensus pattern (78 bp):
CTATTTCTTTCCTTCAGAGTTCGCCATTCATAATGCTCTTTAAGAGTTCACCATTCATATATGTT
CCTTTAGAGTTCA
Found at i:32348988 original size:12 final size:12
Alignment explanation
Indices: 32348971--32348995 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
32348961 AAGAGATAAA
32348971 ATTTAAACTCTT
1 ATTTAAACTCTT
32348983 ATTTAAACTCTT
1 ATTTAAACTCTT
32348995 A
1 A
32348996 GAAAATTTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.16, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTTAAACTCTT
Found at i:32349866 original size:17 final size:17
Alignment explanation
Indices: 32349846--32349931 Score: 111
Period size: 17 Copynumber: 5.1 Consensus size: 17
32349836 TAAACCTTAG
32349846 TTTATTTTAAATTTAAA
1 TTTATTTTAAATTTAAA
32349863 TTTATTTTAAATTTAAA
1 TTTATTTTAAATTTAAA
*
32349880 TTCA-TTTAGAATTTAAA
1 TTTATTTTA-AATTTAAA
* *
32349897 TTTATGTTAAATTTGAA
1 TTTATTTTAAATTTAAA
* *
32349914 TTTATTTTGAATTAAAA
1 TTTATTTTAAATTTAAA
32349931 T
1 T
32349932 GTTTAAACAA
Statistics
Matches: 59, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
16 4 0.07
17 52 0.88
18 3 0.05
ACGTcount: A:0.40, C:0.01, G:0.05, T:0.55
Consensus pattern (17 bp):
TTTATTTTAAATTTAAA
Found at i:32349893 original size:7 final size:6
Alignment explanation
Indices: 32349851--32349917 Score: 54
Period size: 6 Copynumber: 11.7 Consensus size: 6
32349841 CTTAGTTTAT
* *
32349851 TTTAAA TTTAAA TTT-AT TTTAAA TTTAAA -TT-CA TTTAGAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA-AA TTTAAA
*
32349897 TTT--A TGTTAAA TTTGAA TTTA
1 TTTAAA T-TTAAA TTTAAA TTTA
32349918 TTTTGAATTA
Statistics
Matches: 48, Mismatches: 6, Indels: 14
0.71 0.09 0.21
Matches are distributed among these distances:
4 3 0.06
5 10 0.21
6 28 0.58
7 7 0.15
ACGTcount: A:0.40, C:0.01, G:0.04, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:32351351 original size:10 final size:10
Alignment explanation
Indices: 32351336--32351364 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
32351326 ACCCATCGAC
32351336 CCGACCCGAT
1 CCGACCCGAT
32351346 CCGACCCGAT
1 CCGACCCGAT
32351356 CCGACCCGA
1 CCGACCCGA
32351365 ACCCGCTCTA
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:0.52, G:0.21, T:0.07
Consensus pattern (10 bp):
CCGACCCGAT
Found at i:32351454 original size:32 final size:33
Alignment explanation
Indices: 32351416--32351479 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
32351406 TGTGCGTTTG
* *
32351416 GTCCTTTCGCATTTTTTATTTGTTT-CAATTTA
1 GTCCTTTCGCATTTTTTAATTATTTACAATTTA
32351448 GTCCTTTCGCATTTTTTAATTATTTACAATTT
1 GTCCTTTCGCATTTTTTAATTATTTACAATTT
32351480 TACCCGGTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 23 0.79
33 6 0.21
ACGTcount: A:0.19, C:0.16, G:0.08, T:0.58
Consensus pattern (33 bp):
GTCCTTTCGCATTTTTTAATTATTTACAATTTA
Found at i:32351713 original size:161 final size:161
Alignment explanation
Indices: 32351508--32351873 Score: 562
Period size: 162 Copynumber: 2.3 Consensus size: 161
32351498 GGTTTTCAAT
* *
32351508 TTAGTCCTTT-ACTTTTGACTGCACCAGAGGCTGCCACGTGTCAC-TTTTGGCTTATTTATGTAT
1 TTAGTCCTTTGACTTTTGGCTACACCAGAGGCTGCCACGTGTCACTTTTTGGCTTATTTATGTAT
* *
32351571 CTAGTCCCTGTCA-TTTCTAATTTGTTTTAATTTAATCCTTAAATCAACTTTTATTTAATTACAC
66 CTAGTCCCTATCACTTT-TAATTTGTTTTAATTTAATCCTTAAATCAACTTTTATTTAATTACAA
32351635 AATTGGCCCAATG-ATTTTTCAAGATTTATAAA
130 AATTGGCCCAA-GAATTTTTCAAGATTTATAAA
*
32351667 TTAGTCCTTTGACTGTTTGGTTACACCAGAGGCTGCCACGTGTCACTTTTTGGCTTATTTATGTA
1 TTAGTCCTTTGACT-TTTGGCTACACCAGAGGCTGCCACGTGTCACTTTTTGGCTTATTTATGTA
* *
32351732 TCTAGTCTCTATCACTTTTAATTTGTTTTAATTTAATCCTTTAATCAACTTTTATTTAATTACAA
65 TCTAGTCCCTATCACTTTTAATTTGTTTTAATTTAATCCTTAAATCAACTTTTATTTAATTACAA
32351797 AATTGGCCCAAGAATTTTTCAAGATTTATAAA
130 AATTGGCCCAAGAATTTTTCAAGATTTATAAA
* * **
32351829 TTAGTCCTTTGACTTCTGGGTAC-CTGTGAGGCTGCCACGTGTCAC
1 TTAGTCCTTTGACTTTTGGCTACAC-CAGAGGCTGCCACGTGTCAC
32351874 CCTTTCTTGG
Statistics
Matches: 190, Mismatches: 11, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
159 10 0.05
160 4 0.02
161 54 0.28
162 119 0.63
163 3 0.02
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.43
Consensus pattern (161 bp):
TTAGTCCTTTGACTTTTGGCTACACCAGAGGCTGCCACGTGTCACTTTTTGGCTTATTTATGTAT
CTAGTCCCTATCACTTTTAATTTGTTTTAATTTAATCCTTAAATCAACTTTTATTTAATTACAAA
ATTGGCCCAAGAATTTTTCAAGATTTATAAA
Found at i:32351975 original size:29 final size:30
Alignment explanation
Indices: 32351943--32352150 Score: 115
Period size: 29 Copynumber: 7.2 Consensus size: 30
32351933 CCTAAACTTT
*
32351943 TCAAAATT-CCATTTTTAACCCCGGTTTCA
1 TCAAAATTACCATTTTTAACCCCGATTTCA
*
32351972 TCAAAACTTACCA-TTTT-ACCCCAAACTTTC-
1 TCAAAA-TTACCATTTTTAACCCC-GA-TTTCA
32352002 -CAAAATT-CCATTTTTAACCCCGATTGT-A
1 TCAAAATTACCATTTTTAACCCCGATT-TCA
* *
32352030 CCAAAATTACCA-TTTT-ACCCCTAAACTTTC-
1 TCAAAATTACCATTTTTAACCCC--GA-TTTCA
* * * *
32352060 -CAAAATT-CCATTTTTAGCCTCGGTTTTA
1 TCAAAATTACCATTTTTAACCCCGATTTCA
* *
32352088 CCAAAATTACCA-TTTTACCCCCGAACTTTC-
1 TCAAAATTACCATTTTTAACCCCG-A-TTTCA
*
32352118 -CAAAATTA-CATTTTTAGCCCCGATTTCA
1 TCAAAATTACCATTTTTAACCCCGATTTCA
*
32352146 CCAAA
1 TCAAA
32352151 GTTTCCAAAA
Statistics
Matches: 141, Mismatches: 14, Indels: 48
0.69 0.07 0.24
Matches are distributed among these distances:
27 12 0.09
28 19 0.13
29 81 0.57
30 17 0.12
31 12 0.09
ACGTcount: A:0.31, C:0.29, G:0.05, T:0.35
Consensus pattern (30 bp):
TCAAAATTACCATTTTTAACCCCGATTTCA
Found at i:32352006 original size:58 final size:58
Alignment explanation
Indices: 32351916--32352150 Score: 330
Period size: 58 Copynumber: 4.1 Consensus size: 58
32351906 GGACTGTTCG
* * * *
32351916 AAAATTACCATTTTGCCCCTAAACTTTTCAAAATTCCATTTTTAACCCCGGTTTCATC
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
32351974 AAAACTTACCATTTTACCCC-AAACTTTCCAAAATTCCATTTTTAACCCCGATTGT-ACC
1 AAAA-TTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATT-TCACC
* * * *
32352032 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAGCCTCGGTTTTACC
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
** * *
32352090 AAAATTACCATTTTACCCCCGAACTTTCCAAAATTACATTTTTAGCCCCGATTTCACC
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
32352148 AAA
1 AAA
32352151 GTTTCCAAAA
Statistics
Matches: 160, Mismatches: 13, Indels: 8
0.88 0.07 0.04
Matches are distributed among these distances:
57 16 0.10
58 129 0.81
59 15 0.09
ACGTcount: A:0.31, C:0.29, G:0.05, T:0.35
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACC
Found at i:32354662 original size:37 final size:37
Alignment explanation
Indices: 32354603--32354734 Score: 185
Period size: 37 Copynumber: 3.6 Consensus size: 37
32354593 CGGCACAAAA
*
32354603 CCTACTAGGCACATAGCCTGAAAACACCAGCACGAAG
1 CCTACTAGGCACAAAGCCTGAAAACACCAGCACGAAG
* * *
32354640 CCTAGTAGGCATAAAGCTTGAAAACACCAGCACGAAG
1 CCTACTAGGCACAAAGCCTGAAAACACCAGCACGAAG
* * *
32354677 CCTACTAGGCACAAAACCT-AAAAGCATCACCACGAAG
1 CCTACTAGGCACAAAGCCTGAAAA-CACCAGCACGAAG
32354714 CCTACTAGGCACAAAGCCTGA
1 CCTACTAGGCACAAAGCCTGA
32354735 TTGTTTAAAT
Statistics
Matches: 82, Mismatches: 11, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
36 4 0.05
37 77 0.94
38 1 0.01
ACGTcount: A:0.39, C:0.30, G:0.18, T:0.12
Consensus pattern (37 bp):
CCTACTAGGCACAAAGCCTGAAAACACCAGCACGAAG
Found at i:32363697 original size:20 final size:19
Alignment explanation
Indices: 32363668--32363753 Score: 82
Period size: 20 Copynumber: 4.3 Consensus size: 19
32363658 AAATCAAATT
* *
32363668 AAAATGATTTTAAACATGTC
1 AAAATAATTTT-AACAAGTC
32363688 AAAATAATTTTAACTAAGTC
1 AAAATAATTTTAAC-AAGTC
* **
32363708 AAAATCATTTTAACACTTC
1 AAAATAATTTTAACAAGTC
*
32363727 AAAATATTTTTCAAACAAGTC
1 AAAATAATTTT--AACAAGTC
32363748 AAAATA
1 AAAATA
32363754 GCTCCAGGCC
Statistics
Matches: 54, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
19 15 0.28
20 27 0.50
21 12 0.22
ACGTcount: A:0.49, C:0.13, G:0.05, T:0.34
Consensus pattern (19 bp):
AAAATAATTTTAACAAGTC
Found at i:32363718 original size:40 final size:39
Alignment explanation
Indices: 32363668--32363752 Score: 102
Period size: 40 Copynumber: 2.1 Consensus size: 39
32363658 AAATCAAATT
*
32363668 AAAATGATTTTAA-ACATGTCAAAATAATTTT-AACTAAGTC
1 AAAATCATTTTAACAC-T-TCAAAATAATTTTAAAC-AAGTC
*
32363708 AAAATCATTTTAACACTTCAAAATATTTTTCAAACAAGTC
1 AAAATCATTTTAACACTTCAAAATAATTTT-AAACAAGTC
32363748 AAAAT
1 AAAAT
32363753 AGCTCCAGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
39 12 0.30
40 23 0.57
41 5 0.12
ACGTcount: A:0.48, C:0.13, G:0.05, T:0.34
Consensus pattern (39 bp):
AAAATCATTTTAACACTTCAAAATAATTTTAAACAAGTC
Found at i:32365167 original size:21 final size:18
Alignment explanation
Indices: 32365129--32365167 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 18
32365119 ATCAATATTT
32365129 TAAATTTTAATTAATAAA
1 TAAATTTTAATTAATAAA
32365147 TAAATTATTATATTAAATAAA
1 TAAATT-TTA-ATT-AATAAA
32365168 AACAATACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 3 0.17
20 3 0.17
21 6 0.33
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAATTTTAATTAATAAA
Found at i:32369773 original size:18 final size:19
Alignment explanation
Indices: 32369750--32369785 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
32369740 ATCCAAACTT
32369750 TTAAATAT-TAATATAAAA
1 TTAAATATATAATATAAAA
*
32369768 TTAAATATATTATATAAA
1 TTAAATATATAATATAAA
32369786 TGTAAACATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TTAAATATATAATATAAAA
Found at i:32373184 original size:24 final size:24
Alignment explanation
Indices: 32373148--32373225 Score: 66
Period size: 24 Copynumber: 3.6 Consensus size: 24
32373138 AATAAAATAG
32373148 AAATAA-TAGTAATTATACATTTAA
1 AAATAATTA-TAATTATACATTTAA
32373172 AAATAATTATAATT-TA-A--T--
1 AAATAATTATAATTATACATTTAA
* *
32373190 AAA-AATGATAATTACACATTTAA
1 AAATAATTATAATTATACATTTAA
32373213 AAATAATTA-AATT
1 AAATAATTATAATT
32373226 TAAATTACAA
Statistics
Matches: 43, Mismatches: 3, Indels: 17
0.68 0.05 0.27
Matches are distributed among these distances:
17 9 0.21
18 4 0.09
19 1 0.02
20 1 0.02
21 1 0.02
22 1 0.02
23 9 0.21
24 15 0.35
25 2 0.05
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (24 bp):
AAATAATTATAATTATACATTTAA
Found at i:32373188 original size:17 final size:18
Alignment explanation
Indices: 32373157--32373202 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
32373147 GAAATAATAG
32373157 TAATTATACATTTAA-AAA
1 TAATTATA-ATTTAATAAA
32373175 TAATTATAATTTAATAAA
1 TAATTATAATTTAATAAA
*
32373193 -AATGATAATT
1 TAATTATAATT
32373203 ACACATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (18 bp):
TAATTATAATTTAATAAA
Found at i:32373190 original size:35 final size:37
Alignment explanation
Indices: 32373149--32373228 Score: 99
Period size: 41 Copynumber: 2.1 Consensus size: 37
32373139 ATAAAATAGA
*
32373149 AATAAT-AGTAATTATACATTTAAAAATAATTATAATTT
1 AATAATGA-TAATTACACATTTAAAAATAATTA-AATTT
32373187 AATAAAAATGATAATTACACATTTAAAAATAATTAAATTT
1 AAT---AATGATAATTACACATTTAAAAATAATTAAATTT
32373227 AA
1 AA
32373229 ATTACAATTG
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
38 3 0.08
40 7 0.19
41 26 0.70
42 1 0.03
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.38
Consensus pattern (37 bp):
AATAATGATAATTACACATTTAAAAATAATTAAATTT
Found at i:32373228 original size:16 final size:18
Alignment explanation
Indices: 32373157--32373229 Score: 53
Period size: 18 Copynumber: 3.9 Consensus size: 18
32373147 GAAATAATAG
*
32373157 TAATTATACATTTAAAAA
1 TAATTACACATTTAAAAA
*
32373175 TAATTATA-ATTTAATAAAAATGA
1 TAATTACACA-TT--T-AAAA--A
32373198 TAATTACACATTTAAAAA
1 TAATTACACATTTAAAAA
32373216 TAATTA-A-ATTTAAA
1 TAATTACACATTTAAA
32373230 TTACAATTGT
Statistics
Matches: 47, Mismatches: 1, Indels: 16
0.73 0.02 0.25
Matches are distributed among these distances:
16 7 0.15
17 2 0.04
18 17 0.36
20 5 0.11
21 5 0.11
23 10 0.21
24 1 0.02
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.38
Consensus pattern (18 bp):
TAATTACACATTTAAAAA
Found at i:32377064 original size:22 final size:22
Alignment explanation
Indices: 32377039--32377083 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
32377029 ATTATTTAAC
32377039 TAGTAGACGAAGTACAATATTA
1 TAGTAGACGAAGTACAATATTA
32377061 TAGTAGACGAAGTACAATATTA
1 TAGTAGACGAAGTACAATATTA
32377083 T
1 T
32377084 TTAACTACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.44, C:0.09, G:0.18, T:0.29
Consensus pattern (22 bp):
TAGTAGACGAAGTACAATATTA
Found at i:32378769 original size:42 final size:39
Alignment explanation
Indices: 32378685--32378849 Score: 143
Period size: 42 Copynumber: 4.0 Consensus size: 39
32378675 AAGCGCCGCT
***
32378685 ACGCCGCAAAAGGTAAAGCAATAGCGGCGCTTT-CCCATAA
1 ACGCCGCAAAAGGTAAAGCAATAGCGGCG-TTTATGGA-AA
32378725 ACGCCGCAAAAGGTAAAGAGCAATAGCGGCGTTTATAGGAAA
1 ACGCCGCAAAAGGT-AA-AGCAATAGCGGCGTTTAT-GGAAA
* *
32378767 ACGCCGTAAAAGGTAAACCAATAGCGGCGTTTATGAGAAA
1 ACGCCGCAAAAGGTAAAGCAATAGCGGCGTTTATG-GAAA
** * * * *
32378807 ACATCACAAAAGGTATAGAGCATTAGCGACATTTATGGGAAA
1 ACGCCGCAAAAGGTA-A-AGCAATAGCGGCGTTTAT-GGAAA
32378849 A
1 A
32378850 ACGTCGCTAA
Statistics
Matches: 104, Mismatches: 13, Indels: 14
0.79 0.10 0.11
Matches are distributed among these distances:
39 1 0.01
40 46 0.44
41 8 0.08
42 47 0.45
43 2 0.02
ACGTcount: A:0.40, C:0.19, G:0.24, T:0.17
Consensus pattern (39 bp):
ACGCCGCAAAAGGTAAAGCAATAGCGGCGTTTATGGAAA
Found at i:32378772 original size:90 final size:90
Alignment explanation
Indices: 32378602--32378772 Score: 236
Period size: 90 Copynumber: 1.9 Consensus size: 90
32378592 AAAATGCCAG
* *
32378602 AAAAGGTAAAGCAATAGCGGCACTTTACCATAAACGTCGTAAAAAGTAAAGAGAAATAACGACAT
1 AAAAGGTAAAGCAATAGCGGCACTTTACCATAAACGCCGCAAAAAGTAAAGAGAAATAACGACAT
*
32378667 TTATGGTAAAGCGCCGCTACGCCGC
66 TTATGGTAAAACGCCGCTACGCCGC
* * * * * * *
32378692 AAAAGGTAAAGCAATAGCGGCGCTTTCCCATAAACGCCGCAAAAGGTAAAGAGCAATAGCGGCGT
1 AAAAGGTAAAGCAATAGCGGCACTTTACCATAAACGCCGCAAAAAGTAAAGAGAAATAACGACAT
32378757 TTATAGG-AAAACGCCG
66 TTAT-GGTAAAACGCCG
32378773 TAAAAGGTAA
Statistics
Matches: 70, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
90 68 0.97
91 2 0.03
ACGTcount: A:0.40, C:0.20, G:0.23, T:0.16
Consensus pattern (90 bp):
AAAAGGTAAAGCAATAGCGGCACTTTACCATAAACGCCGCAAAAAGTAAAGAGAAATAACGACAT
TTATGGTAAAACGCCGCTACGCCGC
Found at i:32378807 original size:40 final size:39
Alignment explanation
Indices: 32378685--32378808 Score: 142
Period size: 40 Copynumber: 3.1 Consensus size: 39
32378675 AAGCGCCGCT
** *
32378685 ACGCCGCAAAAGGTAAAGCAATAGCGGCGCTTTCCCA-TAA
1 ACGCCGCAAAAGGTAAAGCAATAGCGGCG-TTT-ATAGAAA
32378725 ACGCCGCAAAAGGTAAAGAGCAATAGCGGCGTTTATAGGAAA
1 ACGCCGCAAAAGGT-AA-AGCAATAGCGGCGTTTATA-GAAA
* *
32378767 ACGCCGTAAAAGGTAAACCAATAGCGGCGTTTATGAGAAA
1 ACGCCGCAAAAGGTAAAGCAATAGCGGCGTTTAT-AGAAA
32378807 AC
1 AC
32378809 ATCACAAAAG
Statistics
Matches: 74, Mismatches: 5, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
40 38 0.51
41 8 0.11
42 28 0.38
ACGTcount: A:0.39, C:0.21, G:0.25, T:0.15
Consensus pattern (39 bp):
ACGCCGCAAAAGGTAAAGCAATAGCGGCGTTTATAGAAA
Found at i:32378818 original size:40 final size:41
Alignment explanation
Indices: 32378731--32378849 Score: 107
Period size: 40 Copynumber: 2.9 Consensus size: 41
32378721 ATAAACGCCG
* * *
32378731 CAAAAGGTAAAGAGCAATAGCGGCGTTTATAGGAAAACGCCG
1 CAAAAGGT-AAGACCAATAGCGGCGTTTATAGGAAAACACCA
* *
32378773 TAAAAGGTAA-ACCAATAGCGGCGTTTAT-GAGAAAACATCA
1 CAAAAGGTAAGACCAATAGCGGCGTTTATAG-GAAAACACCA
* * * * *
32378813 CAAAAGGTATAGAGCATTAGCGACATTTATGGGAAAA
1 CAAAAGGTA-AGACCAATAGCGGCGTTTATAGGAAAA
32378850 ACGTCGCTAA
Statistics
Matches: 63, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
39 1 0.02
40 32 0.51
41 3 0.05
42 26 0.41
43 1 0.02
ACGTcount: A:0.43, C:0.14, G:0.24, T:0.18
Consensus pattern (41 bp):
CAAAAGGTAAGACCAATAGCGGCGTTTATAGGAAAACACCA
Found at i:32378839 original size:172 final size:173
Alignment explanation
Indices: 32378514--32378844 Score: 389
Period size: 172 Copynumber: 1.9 Consensus size: 173
32378504 AGCAATAAAT
* ** * *
32378514 GCCGCAAAAGGTAAAGCAATAGCGGCATTTATAGGAAAAACATCGCAAAAAGTAAAGAGTAATAG
1 GCCGCAAAAGGTAAAGCAATAGCGGCACTTATACCAAAAACACCGCAAAAAGTAAAGAGCAATAG
* * * * * * **
32378579 CGGTGTTTATGGGAAAATGCCAGAAAAGGTAAAGCAATAGCGGCACTTTACCATAAACGTCGTAA
66 CGGCGTTTATAGGAAAACGCCAGAAAAGGTAAACCAATAGCGGCACTTTACCAAAAACATCACAA
32378644 AAAGTAAAGAGAAATAACGACATTTATGGTAAAGCGCCGCTAC
131 AAAGTAAAGAGAAATAACGACATTTATGGTAAAGCGCCGCTAC
* * * * *
32378687 GCCGCAAAAGGTAAAGCAATAGCGGCGCTT-TCCCATAAACGCCGCAAAAGGTAAAGAGCAATAG
1 GCCGCAAAAGGTAAAGCAATAGCGGCACTTATACCAAAAACACCGCAAAAAGTAAAGAGCAATAG
* **
32378751 CGGCGTTTATAGGAAAACGCC-GTAAAAGGTAAACCAATAGCGGC-GTTTATGAGAAAACATCAC
66 CGGCGTTTATAGGAAAACGCCAG-AAAAGGTAAACCAATAGCGGCACTTTACCA-AAAACATCAC
* * * * *
32378814 AAAAGGTATAGAGCATTAGCGACATTTATGG
129 AAAAAGTAAAGAGAAATAACGACATTTATGG
32378845 GAAAAACGTC
Statistics
Matches: 130, Mismatches: 26, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
171 6 0.05
172 96 0.74
173 28 0.22
ACGTcount: A:0.41, C:0.17, G:0.24, T:0.18
Consensus pattern (173 bp):
GCCGCAAAAGGTAAAGCAATAGCGGCACTTATACCAAAAACACCGCAAAAAGTAAAGAGCAATAG
CGGCGTTTATAGGAAAACGCCAGAAAAGGTAAACCAATAGCGGCACTTTACCAAAAACATCACAA
AAAGTAAAGAGAAATAACGACATTTATGGTAAAGCGCCGCTAC
Found at i:32379112 original size:12 final size:12
Alignment explanation
Indices: 32379095--32379119 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
32379085 TATCACTAAG
32379095 TGAAAAATTAAA
1 TGAAAAATTAAA
32379107 TGAAAAATTAAA
1 TGAAAAATTAAA
32379119 T
1 T
32379120 TAAATTAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (12 bp):
TGAAAAATTAAA
Found at i:32383469 original size:2 final size:2
Alignment explanation
Indices: 32383462--32383497 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
32383452 AAATACATAC
32383462 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
32383498 GCTTACATTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32384280 original size:34 final size:33
Alignment explanation
Indices: 32384242--32384335 Score: 94
Period size: 34 Copynumber: 3.0 Consensus size: 33
32384232 ATTCTACAAA
32384242 TAATTATTTAATTATTAAAAATAA-C------T
1 TAATTATTTAATTATTAAAAATAACCAAATATT
*
32384268 TAAATATTTAATTATTAAAAATAACCCAAATATT
1 TAATTATTTAATTATTAAAAATAA-CCAAATATT
* *
32384302 TAATTACTTAATTATTAAAAACAACTCAAATATT
1 TAATTATTTAATTATTAAAAATAAC-CAAATATT
32384336 CAGTTCAAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
26 23 0.42
28 1 0.02
33 1 0.02
34 30 0.55
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (33 bp):
TAATTATTTAATTATTAAAAATAACCAAATATT
Found at i:32384282 original size:26 final size:26
Alignment explanation
Indices: 32384246--32384312 Score: 107
Period size: 26 Copynumber: 2.5 Consensus size: 26
32384236 TACAAATAAT
**
32384246 TATTTAATTATTAAAAATAACTTAAA
1 TATTTAATTATTAAAAATAACCCAAA
32384272 TATTTAATTATTAAAAATAACCCAAA
1 TATTTAATTATTAAAAATAACCCAAA
32384298 TATTTAATTACTTAA
1 TATTTAATTA-TTAA
32384313 TTATTAAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
26 34 0.89
27 4 0.11
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (26 bp):
TATTTAATTATTAAAAATAACCCAAA
Found at i:32386138 original size:18 final size:18
Alignment explanation
Indices: 32386115--32386152 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
32386105 GACTTCAAGT
32386115 GATAGTTCGGTTAATCTA
1 GATAGTTCGGTTAATCTA
32386133 GATAGTTCGGTTAATCTA
1 GATAGTTCGGTTAATCTA
32386151 GA
1 GA
32386153 GGACATTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.11, G:0.24, T:0.37
Consensus pattern (18 bp):
GATAGTTCGGTTAATCTA
Found at i:32386852 original size:43 final size:43
Alignment explanation
Indices: 32386747--32386881 Score: 125
Period size: 43 Copynumber: 3.2 Consensus size: 43
32386737 TCTATTAATG
* * * *
32386747 TTAGCGGCGTTTGT-AGGAAAAGCGCCACTAAA-A-AATGTTCT
1 TTAGCGACGTTTGTGA-AAAAAGCGCCACTAAAGAGCACGTTCT
* * ** *
32386788 TTAGCGGCGTTTGTGAAAAAAGCGTCGTTAAAGGGCACGTTCT
1 TTAGCGACGTTTGTGAAAAAAGCGCCACTAAAGAGCACGTTCT
* *
32386831 TTAGCGACGTTTGTTG-AAAAAGTGCCACTAAAGATCACGTTCT
1 TTAGCGACGTTTG-TGAAAAAAGCGCCACTAAAGAGCACGTTCT
32386874 TTAGCGAC
1 TTAGCGAC
32386882 TTGTTGGAAA
Statistics
Matches: 76, Mismatches: 14, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
41 26 0.34
42 1 0.01
43 47 0.62
44 2 0.03
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (43 bp):
TTAGCGACGTTTGTGAAAAAAGCGCCACTAAAGAGCACGTTCT
Found at i:32386912 original size:39 final size:41
Alignment explanation
Indices: 32386823--32386922 Score: 132
Period size: 39 Copynumber: 2.4 Consensus size: 41
32386813 CGTTAAAGGG
*
32386823 CACGTTCTTTAGCGACGTTTGTTGAAAAAGTGCCACTAAAGAT
1 CACGTTCTTTAGCGAC--TTGTTGAAAAAGCGCCACTAAAGAT
* *
32386866 CACGTTCTTTAGCGACTTGTTG-GAAA-CGCCGCTAAAGAT
1 CACGTTCTTTAGCGACTTGTTGAAAAAGCGCCACTAAAGAT
*
32386905 CACGTTCTATAGCGACTT
1 CACGTTCTTTAGCGACTT
32386923 TTTTCCGCAT
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
39 28 0.53
40 3 0.06
41 6 0.11
43 16 0.30
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.30
Consensus pattern (41 bp):
CACGTTCTTTAGCGACTTGTTGAAAAAGCGCCACTAAAGAT
Found at i:32422520 original size:31 final size:30
Alignment explanation
Indices: 32422472--32422554 Score: 80
Period size: 29 Copynumber: 2.7 Consensus size: 30
32422462 ATATCAAAAT
* *
32422472 TATACATCAATTATGATTTAATGTGTAATAG
1 TATACATGAATT-TGATTTAATGTGCAATAG
**
32422503 TATACATGAACTTTGATTT--TGTGCAATTT
1 TATACATGAA-TTTGATTTAATGTGCAATAG
32422532 TATACATGAAATTTTGATTTAAT
1 TATACATG-AA-TTTGATTTAAT
32422555 CTAATTCTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
29 15 0.35
30 10 0.23
31 15 0.35
32 3 0.07
ACGTcount: A:0.35, C:0.07, G:0.12, T:0.46
Consensus pattern (30 bp):
TATACATGAATTTGATTTAATGTGCAATAG
Found at i:32422764 original size:29 final size:31
Alignment explanation
Indices: 32422731--32422791 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
32422721 TTTCACGTGC
*
32422731 ATAATTGCAC-T-AAATTAAAGTTCATATAT
1 ATAATTGCACATGAAATCAAAGTTCATATAT
*
32422760 ATAATTGCACATGAAATCAAAGTTCATGTAT
1 ATAATTGCACATGAAATCAAAGTTCATATAT
32422791 A
1 A
32422792 ATTTTGAGAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 10 0.36
30 1 0.04
31 17 0.61
ACGTcount: A:0.44, C:0.11, G:0.10, T:0.34
Consensus pattern (31 bp):
ATAATTGCACATGAAATCAAAGTTCATATAT
Found at i:32422792 original size:29 final size:28
Alignment explanation
Indices: 32422731--32422794 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
32422721 TTTCACGTGC
*
32422731 ATAATTGCACTAAATTAAAGTTCATATAT
1 ATAATTGCACTAAATCAAAGTTCA-ATAT
*
32422760 ATAATTGCACATGAAATCAAAGTTC-ATGT
1 ATAATTGCAC-T-AAATCAAAGTTCAATAT
32422789 ATAATT
1 ATAATT
32422795 TTGAGATTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 19 0.61
30 1 0.03
31 11 0.35
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.36
Consensus pattern (28 bp):
ATAATTGCACTAAATCAAAGTTCAATAT
Found at i:32424159 original size:23 final size:24
Alignment explanation
Indices: 32424108--32424159 Score: 56
Period size: 23 Copynumber: 2.2 Consensus size: 24
32424098 ATTAAATTTA
*
32424108 GAATTTTTATTTATATTTTAAAATC
1 GAATTTATATTTATATTTT-AAATC
*
32424133 --ATTTATATTTATATTTT-TATC
1 GAATTTATATTTATATTTTAAATC
32424154 GAATTT
1 GAATTT
32424160 TAAATAGTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
21 3 0.13
23 20 0.87
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.60
Consensus pattern (24 bp):
GAATTTATATTTATATTTTAAATC
Found at i:32437819 original size:61 final size:61
Alignment explanation
Indices: 32437766--32437879 Score: 151
Period size: 61 Copynumber: 1.9 Consensus size: 61
32437756 TGGGTAATTT
* **
32437766 AAAACGGTAATTTTGGACAC-TTCGAGGGCAAAATGGTAA-TTTTAGACACTTTGGGGGGGC
1 AAAACGGTAATTTTAGACACTTTCGAGGGCAAAATGGTAATTTTTAGACA-TTTGGGAAGGC
* * *
32437826 AAAATGGTAATTTTAGACACTTTGGGGGGCAAAATGGTAATTTTTAGACATTTG
1 AAAACGGTAATTTTAGACACTTTCGAGGGCAAAATGGTAATTTTTAGACATTTG
32437880 AGGGTAAAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
60 18 0.38
61 21 0.44
62 9 0.19
ACGTcount: A:0.32, C:0.11, G:0.27, T:0.31
Consensus pattern (61 bp):
AAAACGGTAATTTTAGACACTTTCGAGGGCAAAATGGTAATTTTTAGACATTTGGGAAGGC
Found at i:32437855 original size:30 final size:30
Alignment explanation
Indices: 32437766--32437898 Score: 173
Period size: 31 Copynumber: 4.5 Consensus size: 30
32437756 TGGGTAATTT
* * *
32437766 AAAACGGTAATTTTGGACAC-TTCGAGGGC
1 AAAATGGTAATTTTAGACACTTTGGAGGGC
*
32437795 AAAATGGTAATTTTAGACACTTTGGGGGGGC
1 AAAATGGTAATTTTAGACACTTT-GGAGGGC
*
32437826 AAAATGGTAATTTTAGACACTTTGGGGGGC
1 AAAATGGTAATTTTAGACACTTTGGAGGGC
*
32437856 AAAATGGTAATTTTTAGACA-TTT-GAGGGT
1 AAAATGGTAA-TTTTAGACACTTTGGAGGGC
32437885 AAAATGGTAATTTT
1 AAAATGGTAATTTT
32437899 TGGAAAGTTT
Statistics
Matches: 95, Mismatches: 6, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
28 4 0.04
29 32 0.34
30 22 0.23
31 37 0.39
ACGTcount: A:0.32, C:0.09, G:0.27, T:0.32
Consensus pattern (30 bp):
AAAATGGTAATTTTAGACACTTTGGAGGGC
Found at i:32437899 original size:29 final size:30
Alignment explanation
Indices: 32437765--32438163 Score: 187
Period size: 29 Copynumber: 13.5 Consensus size: 30
32437755 TTGGGTAATT
* * * *
32437765 TAAAACGGTAA-TTTTGGACACTTCGAGGG
1 TAAAATGGTAATTTTTAGACAGTTTGAGGG
* * *
32437794 CAAAATGGTAA-TTTTAGACACTTTGGGGGGG
1 TAAAATGGTAATTTTTAGACAGTTT--GAGGG
* * *
32437825 CAAAATGGTAA-TTTTAGACACTTTGGGGGG
1 TAAAATGGTAATTTTTAGACAGTTT-GAGGG
*
32437855 CAAAATGGTAATTTTTAGACA-TTTGAGGG
1 TAAAATGGTAATTTTTAGACAGTTTGAGGG
* * *
32437884 TAAAATGGTAATTTTTGGAAAGTTT-AGGT
1 TAAAATGGTAATTTTTAGACAGTTTGAGGG
* *
32437913 TAAAAT-GTGATTTTTGGA-AGTTT-AGTGG
1 TAAAATGGTAATTTTTAGACAGTTTGAG-GG
* *
32437941 TAAAAAT-GTAATTTTT-GATAAGTTCGAGGG
1 T-AAAATGGTAATTTTTAGA-CAGTTTGAGGG
** *
32437971 TAAAAAAT-GTGGTTTTTA-A-AGTTTAAGGG
1 T--AAAATGGTAATTTTTAGACAGTTTGAGGG
32438000 TAAAAAT-GTAATTTTTAGA-AGTTTGAGGG
1 T-AAAATGGTAATTTTTAGACAGTTTGAGGG
** * *
32438029 TAAAAAAGTAATTTTTGAGA-AGTTCG-GGA
1 TAAAATGGTAATTTTT-AGACAGTTTGAGGG
* *
32438058 TCAAAAAT-GTAA-TTTTAGAATAGTTTAAGGG
1 T--AAAATGGTAATTTTTAG-ACAGTTTGAGGG
** * * *
32438089 TTAAAAT-GTAGCTTTTGGAAAGTTAG-GGG
1 -TAAAATGGTAATTTTTAGACAGTTTGAGGG
* *
32438118 TAAAAAT-GTAATTTTTGGAAAGTTTGAGGG
1 T-AAAATGGTAATTTTTAGACAGTTTGAGGG
32438148 TCAAAAT-GTAATTTTT
1 T-AAAATGGTAATTTTT
32438164 GGAAAGTTCA
Statistics
Matches: 310, Mismatches: 37, Indels: 45
0.79 0.09 0.11
Matches are distributed among these distances:
27 7 0.02
28 36 0.12
29 125 0.40
30 77 0.25
31 64 0.21
32 1 0.00
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.36
Consensus pattern (30 bp):
TAAAATGGTAATTTTTAGACAGTTTGAGGG
Found at i:32437973 original size:30 final size:29
Alignment explanation
Indices: 32437856--32438171 Score: 281
Period size: 29 Copynumber: 10.7 Consensus size: 29
32437846 TTTGGGGGGC
*
32437856 AAAATGGTAATTTTTAGACA-TTTGAGGGT-
1 AAAAT-GTAATTTTT-GAAAGTTTGAGGGTA
*
32437885 AAAATGGTAATTTTTGGAAAGTTT-A-GGTT
1 AAAAT-GTAATTTTT-GAAAGTTTGAGGGTA
* *
32437914 AAAATGTGATTTTTGGAAGTTT-AGTGGTA
1 AAAATGTAATTTTTGAAAGTTTGAG-GGTA
*
32437943 AAAATGTAATTTTTGATAAGTTCGAGGGTAA
1 AAAATGTAATTTTTGA-AAGTTTGAGGGT-A
** *
32437974 AAAATGTGGTTTTT-AAAGTTTAAGGGTA
1 AAAATGTAATTTTTGAAAGTTTGAGGGTA
32438002 AAAATGTAATTTTT-AGAAGTTTGAGGGTA
1 AAAATGTAATTTTTGA-AAGTTTGAGGGTA
* * *
32438031 AAAAAGTAATTTTTGAGAAGTTCG-GGATCA
1 AAAATGTAATTTTTGA-AAGTTTGAGGGT-A
* * *
32438061 AAAATGTAATTTTAGAATAGTTTAAGGGTT
1 AAAATGTAATTTTTGAA-AGTTTGAGGGTA
* * *
32438091 AAAATGTAGCTTTTGGAAAGTTAG-GGGTA
1 AAAATGTA-ATTTTTGAAAGTTTGAGGGTA
*
32438120 AAAATGTAATTTTTGGAAAGTTTGAGGGTC
1 AAAATGTAATTTTT-GAAAGTTTGAGGGTA
32438150 AAAATGTAATTTTTGGAAAGTT
1 AAAATGTAATTTTT-GAAAGTT
32438172 CAGGGACCTT
Statistics
Matches: 239, Mismatches: 33, Indels: 29
0.79 0.11 0.10
Matches are distributed among these distances:
27 8 0.03
28 29 0.12
29 100 0.42
30 77 0.32
31 25 0.10
ACGTcount: A:0.36, C:0.02, G:0.24, T:0.37
Consensus pattern (29 bp):
AAAATGTAATTTTTGAAAGTTTGAGGGTA
Found at i:32438005 original size:59 final size:57
Alignment explanation
Indices: 32437880--32438176 Score: 261
Period size: 59 Copynumber: 5.1 Consensus size: 57
32437870 TAGACATTTG
* *
32437880 AGGGT-AAAATGGTAATTTTTGGAAAGTTT-A-GGT-TAAAATGTGATTTTTGGAAGTTT
1 AGGGTAAAAAT-GTAATTTTT-GAAAGTTTGAGGGTAAAAAATGTGATTTTTGAAAG-TT
* *
32437936 AGTGGTAAAAATGTAATTTTTGATAAGTTCGAGGGTAAAAAATGTGGTTTTT-AAAGTTT
1 AG-GGTAAAAATGTAATTTTTGA-AAGTTTGAGGGTAAAAAATGTGATTTTTGAAAG-TT
*
32437995 AAGGGTAAAAATGTAATTTTT-AGAAGTTTGAGGGTAAAAAA-GTAATTTTTGAGAAGTT
1 -AGGGTAAAAATGTAATTTTTGA-AAGTTTGAGGGTAAAAAATGTGATTTTTGA-AAGTT
* * * * * *
32438053 CGGGATCAAAAATGTAATTTTAGAATAGTTTAAGGGT-TAAAATGTAGCTTTTGGAAAGTT
1 AGGG-T-AAAAATGTAATTTTTGAA-AGTTTGAGGGTAAAAAATGT-GATTTTTGAAAGTT
* *
32438113 AGGGGTAAAAATGTAATTTTTGGAAAGTTTGAGGGT-CAAAATGTAATTTTTGGAAAGTT
1 A-GGGTAAAAATGTAATTTTT-GAAAGTTTGAGGGTAAAAAATGTGATTTTT-GAAAGTT
32438172 CAGGG
1 -AGGG
32438177 ACCTTTTGGG
Statistics
Matches: 200, Mismatches: 22, Indels: 35
0.78 0.09 0.14
Matches are distributed among these distances:
56 4 0.02
57 27 0.14
58 32 0.16
59 90 0.45
60 38 0.19
61 9 0.05
ACGTcount: A:0.36, C:0.02, G:0.26, T:0.36
Consensus pattern (57 bp):
AGGGTAAAAATGTAATTTTTGAAAGTTTGAGGGTAAAAAATGTGATTTTTGAAAGTT
Found at i:32440098 original size:17 final size:17
Alignment explanation
Indices: 32440076--32440110 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
32440066 CTTTAAAATT
32440076 TAAATTTAAATTCAAAA
1 TAAATTTAAATTCAAAA
*
32440093 TAAATTTAAATTTAAAA
1 TAAATTTAAATTCAAAA
32440110 T
1 T
32440111 TTAAAATTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (17 bp):
TAAATTTAAATTCAAAA
Found at i:32440098 original size:23 final size:24
Alignment explanation
Indices: 32440071--32440117 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
32440061 TTGCACTTTA
32440071 AAATTTAAATTT-AAATTCAAAAT
1 AAATTTAAATTTAAAATTCAAAAT
*
32440094 AAATTTAAATTTAAAATTTAAAAT
1 AAATTTAAATTTAAAATTCAAAAT
32440118 TGGGTTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (24 bp):
AAATTTAAATTTAAAATTCAAAAT
Found at i:32440118 original size:7 final size:6
Alignment explanation
Indices: 32440071--32440115 Score: 56
Period size: 6 Copynumber: 7.5 Consensus size: 6
32440061 TTGCACTTTA
* *
32440071 AAATTT AAATTT AAATTC AAA-AT AAATTT AAATTT AAAATTT AAA
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT -AAATTT AAA
32440116 ATTGGGTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
5 3 0.09
6 24 0.73
7 6 0.18
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (6 bp):
AAATTT
Found at i:32440867 original size:172 final size:172
Alignment explanation
Indices: 32440512--32440890 Score: 562
Period size: 172 Copynumber: 2.2 Consensus size: 172
32440502 AAGAAGACGA
* * * *
32440512 ATTTGGTCCACTTTTCTATATCTCATCAGGAAGACAACCACTTTATTGCTTCGACCTGCTTCTTA
1 ATTTGATCCGCTTCTCTATATCTCATCAGGAAGACAACCACTTTATTGCTTCGACCTGCTTCTCA
* * * * ** *
32440577 GTATCTTATCAGGAAGCTGCGATTCTAAGTTTAGCTCACATTGAGCTTGGTTTCATTGATTTGGT
66 GTATCTCATCAGAAAGCTGCGACTCGAAGTTTAGCTCACATCCAGCTTGGTTTCATTGACTTGGT
*
32440642 CTACTTCTCAGTATCTCATCAGGAAGATGACCGTATCACTTG
131 CTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTG
* * *
32440684 TTTTAATCCGCTTCTCTATATCTCATAAGGAAGACAACCACTTTATTGCTTCGACCTGCTTCTCA
1 ATTTGATCCGCTTCTCTATATCTCATCAGGAAGACAACCACTTTATTGCTTCGACCTGCTTCTCA
* * *
32440749 GTATCTCATCAGAAAGCTGGGGCTCGAAGTTTCGCTCACATCCAGCTTTGGTTTCATTGACTTGG
66 GTATCTCATCAGAAAGCTGCGACTCGAAGTTTAGCTCACATCCAGC-TTGGTTTCATTGACTTGG
* *
32440814 TCTACTTCTCAGTATCTCATCAGGAAGATGATCGCATTACTT-
130 TCTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTG
32440856 ATTTGATCCGCTTCTCTATATCTCATCAGGAAGAC
1 ATTTGATCCGCTTCTCTATATCTCATCAGGAAGAC
32440891 GTATTTGGTC
Statistics
Matches: 183, Mismatches: 23, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
172 127 0.69
173 56 0.31
ACGTcount: A:0.23, C:0.24, G:0.17, T:0.36
Consensus pattern (172 bp):
ATTTGATCCGCTTCTCTATATCTCATCAGGAAGACAACCACTTTATTGCTTCGACCTGCTTCTCA
GTATCTCATCAGAAAGCTGCGACTCGAAGTTTAGCTCACATCCAGCTTGGTTTCATTGACTTGGT
CTACTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTG
Found at i:32440907 original size:37 final size:37
Alignment explanation
Indices: 32440855--32440928 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
32440845 TCGCATTACT
*
32440855 TATTTGATCCGCTTCTCTATATCTCATCAGGAAGACG
1 TATTTGATCCACTTCTCTATATCTCATCAGGAAGACG
* *
32440892 TATTTGGTCCACTTCTCTGTATCTCATCAGGAAGACG
1 TATTTGATCCACTTCTCTATATCTCATCAGGAAGACG
32440929 ACCACTTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.23, C:0.24, G:0.18, T:0.35
Consensus pattern (37 bp):
TATTTGATCCACTTCTCTATATCTCATCAGGAAGACG
Found at i:32441079 original size:209 final size:209
Alignment explanation
Indices: 32440694--32441081 Score: 575
Period size: 209 Copynumber: 1.9 Consensus size: 209
32440684 TTTTAATCCG
*
32440694 CTTCTCTATATCTCATAAGGAAGACAACCACTTTATTGCTTCGACCTGCTTCTCAGTATCTCATC
1 CTTCTCTATATCTCATAAGGAAGACAACCACTTTATTGCTTCGACCTGCTTCTCAGTACCTCATC
32440759 AGAAAGCTGGGGCTCGAAGTTTCGCTCACATCCAGCTTTGGTTTCATTGACTTGGTCTACTTCTC
66 AGAAAGCTGGGGCTCGAAGTTTCGCTCACATCCAGCTTTGGTTTCATTGACTTGGTCTACTTCTC
* * *
32440824 AGTATCTCATCAGGAAGATGATCGCATTACTTATTTGATCCGCTTCTCTATATCTCATCAGGAAG
131 AGTATCTCATCAGGAAGATGACCACATCACTTATTTGATCCGCTTCTCTATATCTCATCAGGAAG
32440889 ACGTATTTGGTCCA
196 ACGTATTTGGTCCA
* * * *
32440903 CTTCTCTGTATCTCATCAGGAAGACGACCACTTTATTGCTTCGACTTGCTTC-CTAGTACCTCAT
1 CTTCTCTATATCTCATAAGGAAGACAACCACTTTATTGCTTCGACCTGCTTCTC-AGTACCTCAT
* * * **
32440967 CAGGAAGCTGGGGTTCGAAGTTTTGCTCACATTGAGCTTT-GTTTCATTGA-TTAGGTCTACTTC
65 CAGAAAGCTGGGGCTCGAAGTTTCGCTCACATCCAGCTTTGGTTTCATTGACTT-GGTCTACTTC
* * * *
32441030 TTAGTATTTCATCAGGAAGATGACCACATCACTTGTTTTGATTCGCTTCTCT
129 TCAGTATCTCATCAGGAAGATGACCACATCACTT-ATTTGATCCGCTTCTCT
32441082 GCCCCATGAT
Statistics
Matches: 159, Mismatches: 17, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
207 2 0.01
208 50 0.31
209 107 0.67
ACGTcount: A:0.22, C:0.24, G:0.18, T:0.36
Consensus pattern (209 bp):
CTTCTCTATATCTCATAAGGAAGACAACCACTTTATTGCTTCGACCTGCTTCTCAGTACCTCATC
AGAAAGCTGGGGCTCGAAGTTTCGCTCACATCCAGCTTTGGTTTCATTGACTTGGTCTACTTCTC
AGTATCTCATCAGGAAGATGACCACATCACTTATTTGATCCGCTTCTCTATATCTCATCAGGAAG
ACGTATTTGGTCCA
Found at i:32443495 original size:23 final size:23
Alignment explanation
Indices: 32443468--32443512 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
32443458 AATCAACTAG
32443468 CTTAGAATCTCTTGTTTCCCATA
1 CTTAGAATCTCTTGTTTCCCATA
32443491 CTTAGAATCTCTTGTTTCCCAT
1 CTTAGAATCTCTTGTTTCCCAT
32443513 TCTCCTTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.20, C:0.27, G:0.09, T:0.44
Consensus pattern (23 bp):
CTTAGAATCTCTTGTTTCCCATA
Found at i:32448633 original size:23 final size:24
Alignment explanation
Indices: 32448588--32448633 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
32448578 AATATGCGAA
* *
32448588 TATGCAATGCGAATAAAATGCATG
1 TATGCAATGCGAAGAAAAGGCATG
*
32448612 TATGTAATGC-AAGAAAAGGCAT
1 TATGCAATGCGAAGAAAAGGCAT
32448634 TGATTTTGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.43, C:0.11, G:0.22, T:0.24
Consensus pattern (24 bp):
TATGCAATGCGAAGAAAAGGCATG
Found at i:32452620 original size:29 final size:28
Alignment explanation
Indices: 32452578--32452826 Score: 148
Period size: 29 Copynumber: 8.4 Consensus size: 28
32452568 CTTCGAGGGC
*
32452578 AAATGGTAATTTTTTAGATGTTCGAGGTCAA
1 AAAT-GTAA-TTTTTAGAAGTTCGAGGT-AA
** *
32452609 AAATGTAATTTTGGGACA-TTTGAGGGT-A
1 AAATGTAATTTTTAGA-AGTTCGA-GGTAA
32452637 AAATGGTAATTTTTAGAAAGTTCGAGGTTAA
1 AAAT-GTAATTTTTAG-AAGTTCGAGG-TAA
* * *
32452668 AAATGTGATTTTTGGAAGTTTGAGGGT-A
1 AAATGTAATTTTTAGAAGTTCGA-GGTAA
*
32452696 AAATGTAATTTTTAAGAAGTTCGGGGTAAAA
1 AAATGTAATTTTT-AGAAGTTCGAGGT--AA
* * * * *
32452727 AAATATGATTTTTGGAAGTTTAGGGGTAA
1 AAATGTAATTTTTAGAAG-TTCGAGGTAA
*
32452756 AAATGTAATTTTTTA-AGAGTTCAAGGGT-A
1 AAATGTAA-TTTTTAGA-AGTTCGA-GGTAA
**
32452785 AAATGTAATTTTTAAGAAGTTCGAAATGAA
1 AAATGTAATTTTT-AGAAGTTCGAGGT-AA
*
32452815 AAATGCAATTTT
1 AAATGTAATTTT
32452827 GGAACAGTTT
Statistics
Matches: 170, Mismatches: 28, Indels: 41
0.71 0.12 0.17
Matches are distributed among these distances:
28 27 0.16
29 64 0.38
30 51 0.30
31 28 0.16
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (28 bp):
AAATGTAATTTTTAGAAGTTCGAGGTAA
Found at i:32452645 original size:59 final size:57
Alignment explanation
Indices: 32452578--32452797 Score: 225
Period size: 59 Copynumber: 3.7 Consensus size: 57
32452568 CTTCGAGGGC
* *
32452578 AAATGGTAATTTTTTAGATGTTCGAGGTCAAAAATGTAATTTTGGGACA-TTTGAGGGTA
1 AAAT-GTAATTTTTTAGAAGTTCGAGGT-AAAAATGTAATTTTTGGA-AGTTTGAGGGTA
*
32452637 AAATGGTAA-TTTTTAGAAAGTTCGAGGTTAAAAATGTGATTTTTGGAAGTTTGAGGGTA
1 AAAT-GTAATTTTTTAG-AAGTTCGAGG-TAAAAATGTAATTTTTGGAAGTTTGAGGGTA
* * * *
32452696 AAATGTAATTTTTAAGAAGTTCGGGGTAAAAAAATATGATTTTTGGAAGTTT-AGGGGTAA
1 AAATGTAATTTTTTAGAAGTTCGAGGT--AAAAATGTAATTTTTGGAAGTTTGA-GGGT-A
*
32452756 AAATGTAATTTTTTA-AGAGTTCAAGGGT-AAAATGTAATTTTT
1 AAATGTAATTTTTTAGA-AGTTCGA-GGTAAAAATGTAATTTTT
32452798 AAGAAGTTCG
Statistics
Matches: 140, Mismatches: 11, Indels: 21
0.81 0.06 0.12
Matches are distributed among these distances:
57 1 0.01
58 34 0.24
59 81 0.58
60 21 0.15
61 3 0.02
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.38
Consensus pattern (57 bp):
AAATGTAATTTTTTAGAAGTTCGAGGTAAAAATGTAATTTTTGGAAGTTTGAGGGTA
Found at i:32452817 original size:89 final size:89
Alignment explanation
Indices: 32452690--32452858 Score: 229
Period size: 89 Copynumber: 1.9 Consensus size: 89
32452680 TGGAAGTTTG
* * *
32452690 AGGGTAAAATGTAATTTTTAAGAAGTTCGGGGTAAA-AAAATATG-ATTTTTGG-A-AGTTTAGG
1 AGGGTAAAATGTAATTTTTAAGAAGTTC---G-AAATAAAAAATGCAATTTTGGAACAGTTTAAG
32452751 GGTAAAAATGTAATTTTTTAAGAGTTCA
62 GGTAAAAATGTAATTTTTTAAGAGTTCA
* *
32452779 AGGGTAAAATGTAATTTTTAAGAAGTTCGAAATGAAAAATGCAATTTTGGAACAGTTTAAGGGTC
1 AGGGTAAAATGTAATTTTTAAGAAGTTCGAAATAAAAAATGCAATTTTGGAACAGTTTAAGGGTA
32452844 AAAATGTAATTTTTT
66 AAAATGTAATTTTTT
32452859 GAAAAGTTTG
Statistics
Matches: 71, Mismatches: 5, Indels: 8
0.85 0.06 0.10
Matches are distributed among these distances:
85 3 0.04
86 7 0.10
87 7 0.10
88 1 0.01
89 53 0.75
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.36
Consensus pattern (89 bp):
AGGGTAAAATGTAATTTTTAAGAAGTTCGAAATAAAAAATGCAATTTTGGAACAGTTTAAGGGTA
AAAATGTAATTTTTTAAGAGTTCA
Found at i:32452879 original size:31 final size:29
Alignment explanation
Indices: 32452635--32452879 Score: 70
Period size: 30 Copynumber: 8.2 Consensus size: 29
32452625 CATTTGAGGG
*
32452635 TAAAATGGTAATTTTTAGAAAGTTCGAG-GT
1 TAAAAT-GTAATTTTTA-AAAGTTCAAGAGT
* ** ** *
32452665 TAAAAATGTGATTTTTGGAAGTTTGAG-GG
1 T-AAAATGTAATTTTTAAAAGTTCAAGAGT
* *
32452694 TAAAATGTAATTTTTAAGAAGTTC-GGGGT
1 TAAAATGTAATTTTTAA-AAGTTCAAGAGT
* * * ** * * *
32452723 AAAAAAATATGATTTTTGGAAGTTTAGGGGT
1 --TAAAATGTAATTTTTAAAAGTTCAAGAGT
* * *
32452754 AAAAATGTAATTTTTTAAGAGTTCAAG-GG
1 TAAAATGTAA-TTTTTAAAAGTTCAAGAGT
32452783 TAAAATGTAATTTTTAAGAAGTTCGAA-A-T
1 TAAAATGTAATTTTTAA-AAGTTC-AAGAGT
* * * * * *
32452812 GAAAAATGCAATTTTGGAACAGTTTAAGGGT
1 -TAAAATGTAATTTT-TAAAAGTTCAAGAGT
* **
32452843 CAAAATGTAATTTTTTGAAAAGTTTGAGAGT
1 TAAAATGTAA-TTTTT-AAAAGTTCAAGAGT
32452874 TAAAAT
1 TAAAAT
32452880 ATGATTTCTG
Statistics
Matches: 158, Mismatches: 41, Indels: 31
0.69 0.18 0.13
Matches are distributed among these distances:
28 21 0.13
29 41 0.26
30 51 0.32
31 45 0.28
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36
Consensus pattern (29 bp):
TAAAATGTAATTTTTAAAAGTTCAAGAGT
Found at i:32457430 original size:20 final size:19
Alignment explanation
Indices: 32457400--32457454 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 19
32457390 ATTAGTATGA
32457400 TTTATATTAAGTGTAAATAG-G
1 TTTA-ATTAAGT-TAAA-AGTG
32457421 TTTAATTAAGATTAAAAGTG
1 TTTAATTAAG-TTAAAAGTG
*
32457441 ATTAATTAAGTTAA
1 TTTAATTAAGTTAA
32457455 TTATGAAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
19 6 0.19
20 20 0.65
21 5 0.16
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.42
Consensus pattern (19 bp):
TTTAATTAAGTTAAAAGTG
Found at i:32472500 original size:176 final size:177
Alignment explanation
Indices: 32472206--32472563 Score: 648
Period size: 176 Copynumber: 2.0 Consensus size: 177
32472196 TAGATAACAA
32472206 TTATATTAAGATATTATTTAGAAAACTATATAATGAGCATTATATATAATTTGTATAATTTATTT
1 TTATATTAAGATATTATTTAGAAAACTATATAATGAGCATTATATATAATTTGTATAATTTATTT
32472271 AATTAATAATTATTTTTAAAAAAATTATATATTCTAAATAGAAATTTCATTTAAAATTAAATTTT
66 AATTAATAATTATTTTTAAAAAAATTATATATTCTAAATAGAAATTTCATTT-AAATTAAATTTT
32472336 GTAATATATTAAAATAAAATTG-TT-TAAATTATTTTACTTAAATTAT
130 GTAATATATTAAAATAAAATTGTTTATAAATTATTTTACTTAAATTAT
32472382 TTATATTAAGATATTATTTAGAAAACTATATAATGAGCATTATATATAATTTGTATAATTTATTT
1 TTATATTAAGATATTATTTAGAAAACTATATAATGAGCATTATATATAATTTGTATAATTTATTT
** *
32472447 AATTAATAATTATTTTTTTAAAAATTATATATTCTAAATAGAAATTTCATTTAAATTGAATTTTG
66 AATTAATAATTATTTTTAAAAAAATTATATATTCTAAATAGAAATTTCATTTAAATTAAATTTTG
32472512 TAATATATTAAAATAAAATTGTTTAAATAAATTATTTTACTTAAATTAT
131 TAATATATTAAAATAAAATTGTTT--ATAAATTATTTTACTTAAATTAT
32472561 TTA
1 TTA
32472564 AATTTTGTTT
Statistics
Matches: 175, Mismatches: 3, Indels: 5
0.96 0.02 0.03
Matches are distributed among these distances:
175 33 0.19
176 117 0.67
179 25 0.14
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.48
Consensus pattern (177 bp):
TTATATTAAGATATTATTTAGAAAACTATATAATGAGCATTATATATAATTTGTATAATTTATTT
AATTAATAATTATTTTTAAAAAAATTATATATTCTAAATAGAAATTTCATTTAAATTAAATTTTG
TAATATATTAAAATAAAATTGTTTATAAATTATTTTACTTAAATTAT
Found at i:32475792 original size:3 final size:3
Alignment explanation
Indices: 32475777--32475807 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
32475767 TGTGACCAGC
*
32475777 ATT ATT GTT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
32475808 CTCAGACAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:32478165 original size:2 final size:2
Alignment explanation
Indices: 32478158--32478185 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
32478148 ATGCAAAAAG
32478158 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
32478186 CCTTCATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32478858 original size:15 final size:15
Alignment explanation
Indices: 32478838--32478870 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
32478828 TTTAGGTTTA
*
32478838 TTAAATAATATATTT
1 TTAAATAATATATAT
32478853 TTAAATAATATATAT
1 TTAAATAATATATAT
32478868 TTA
1 TTA
32478871 GGTTTAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TTAAATAATATATAT
Found at i:32482402 original size:21 final size:20
Alignment explanation
Indices: 32482378--32482416 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
32482368 CAAAACAACA
32482378 TGAGAGAATACAAATAAAATG
1 TGAGAGAATACAAA-AAAATG
*
32482399 TGAGAGATTACAAAAAAA
1 TGAGAGAATACAAAAAAA
32482417 CATGAAAATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.59, C:0.05, G:0.18, T:0.18
Consensus pattern (20 bp):
TGAGAGAATACAAAAAAATG
Found at i:32482699 original size:19 final size:19
Alignment explanation
Indices: 32482670--32482740 Score: 54
Period size: 19 Copynumber: 3.6 Consensus size: 19
32482660 AGTATGATAG
*
32482670 TATACCGAAAATCTGAGGA
1 TATACCAAAAATCTGAGGA
*
32482689 TATACCAAAAAGTCTAAGAGA
1 TATACCAAAAA-TCTGAG-GA
* ** *
32482710 GTA-ACAAAAAATAAGAAGA
1 -TATACCAAAAATCTGAGGA
32482729 TATACCAAAAAT
1 TATACCAAAAAT
32482741 TTTGAAACTA
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
18 2 0.05
19 20 0.50
20 7 0.17
21 9 0.22
22 2 0.05
ACGTcount: A:0.55, C:0.13, G:0.14, T:0.18
Consensus pattern (19 bp):
TATACCAAAAATCTGAGGA
Found at i:32482857 original size:20 final size:20
Alignment explanation
Indices: 32482805--32482862 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
32482795 TGAAAATCAC
* *
32482805 GAGGAAATATTAAAAAATAT
1 GAGGAAATATCAAAAAAAAT
*
32482825 GAGTG-ATTA-CAAAAAAAAT
1 GAG-GAAATATCAAAAAAAAT
32482844 GAGGAAATATCAAAAAAAA
1 GAGGAAATATCAAAAAAAA
32482863 GTAAAATAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
18 1 0.03
19 14 0.45
20 15 0.48
21 1 0.03
ACGTcount: A:0.62, C:0.03, G:0.16, T:0.19
Consensus pattern (20 bp):
GAGGAAATATCAAAAAAAAT
Found at i:32482858 original size:19 final size:19
Alignment explanation
Indices: 32482805--32482861 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 19
32482795 TGAAAATCAC
*
32482805 GAGGAAATATTAAAAAATAT
1 GAGGAAATATCAAAAAA-AT
*
32482825 GAGTG-ATTA-CAAAAAAAAT
1 GAG-GAAATATC-AAAAAAAT
32482844 GAGGAAATATCAAAAAAA
1 GAGGAAATATCAAAAAAA
32482862 AGTAAAATAG
Statistics
Matches: 30, Mismatches: 3, Indels: 9
0.71 0.07 0.21
Matches are distributed among these distances:
18 1 0.03
19 15 0.50
20 13 0.43
21 1 0.03
ACGTcount: A:0.61, C:0.04, G:0.16, T:0.19
Consensus pattern (19 bp):
GAGGAAATATCAAAAAAAT
Found at i:32483603 original size:40 final size:40
Alignment explanation
Indices: 32483559--32483729 Score: 122
Period size: 40 Copynumber: 4.3 Consensus size: 40
32483549 AAAAATGAGA
*
32483559 AAATACCAAAAAATGAGAGAGATTACTAAAAAATGTAAGG
1 AAATACCAAAAAATGATAGAGATTACTAAAAAATGTAAGG
* * *
32483599 AAATATCAGAAAACATGATAGA-ATAAC-AAAAAATGTGA-G
1 AAATACCA-AAAA-ATGATAGAGATTACTAAAAAATGTAAGG
* *
32483638 AGAACACCAAAAAAT-A-AGGGCA-TACTAAAAAATGTAAGG
1 A-AATACCAAAAAATGATAGAG-ATTACTAAAAAATGTAAGG
* * ** * *
32483677 GAATGCCAAAAAACCACTAGAGAATACT-AAAAATGTGAGG
1 AAATACCAAAAAATGA-TAGAGATTACTAAAAAATGTAAGG
* *
32483717 GATTACCAAAAAA
1 AAATACCAAAAAA
32483730 ACATAAGGAT
Statistics
Matches: 103, Mismatches: 17, Indels: 22
0.73 0.12 0.15
Matches are distributed among these distances:
36 2 0.02
37 3 0.03
38 23 0.22
39 8 0.08
40 45 0.44
41 15 0.15
42 7 0.07
ACGTcount: A:0.56, C:0.11, G:0.17, T:0.16
Consensus pattern (40 bp):
AAATACCAAAAAATGATAGAGATTACTAAAAAATGTAAGG
Found at i:32483687 original size:20 final size:20
Alignment explanation
Indices: 32483560--32483689 Score: 74
Period size: 20 Copynumber: 6.6 Consensus size: 20
32483550 AAAATGAGAA
*
32483560 AATACCAAAAAATG-AGAGAG
1 AATACCAAAAAATGTA-AGGG
* * *
32483580 ATTACTAAAAAATGTAAGGA
1 AATACCAAAAAATGTAAGGG
*
32483600 AATATCAGAAAACATG-ATA--G
1 AATACCA-AAAA-ATGTA-AGGG
* * *
32483620 AATAACAAAAAATGTGAGAG
1 AATACCAAAAAATGTAAGGG
*
32483640 AACACCAAAAAA--TAAGGG
1 AATACCAAAAAATGTAAGGG
* *
32483658 CATACTAAAAAATGTAAGGG
1 AATACCAAAAAATGTAAGGG
*
32483678 AATGCCAAAAAA
1 AATACCAAAAAA
32483690 CCACTAGAGA
Statistics
Matches: 81, Mismatches: 20, Indels: 18
0.68 0.17 0.15
Matches are distributed among these distances:
18 17 0.21
19 4 0.05
20 50 0.62
21 6 0.07
22 4 0.05
ACGTcount: A:0.58, C:0.10, G:0.17, T:0.15
Consensus pattern (20 bp):
AATACCAAAAAATGTAAGGG
Found at i:32483690 original size:78 final size:78
Alignment explanation
Indices: 32483582--32483729 Score: 183
Period size: 78 Copynumber: 1.9 Consensus size: 78
32483572 TGAGAGAGAT
* * *
32483582 TACTAAAAAATGTAAGGAAATATCAGAAAA-CA-TGATAGAATAACAAAAAATGTGAGAGAACAC
1 TACTAAAAAATGTAAGGAAATACCAAAAAACCACT-AGAGAAT-ACAAAAAATGTGAGAGAACAC
32483645 CAAAAAATAAGGGCA
64 CAAAAAATAAGGGCA
* * * * **
32483660 TACTAAAAAATGTAAGGGAATGCCAAAAAACCACTAGAGAATACTAAAAATGTGAGGGATTACCA
1 TACTAAAAAATGTAAGGAAATACCAAAAAACCACTAGAGAATACAAAAAATGTGAGAGAACACCA
32483725 AAAAA
66 AAAAA
32483730 ACATAAGGAT
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
78 50 0.85
79 8 0.14
80 1 0.02
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.16
Consensus pattern (78 bp):
TACTAAAAAATGTAAGGAAATACCAAAAAACCACTAGAGAATACAAAAAATGTGAGAGAACACCA
AAAAATAAGGGCA
Found at i:32494356 original size:18 final size:19
Alignment explanation
Indices: 32494329--32494367 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
32494319 AATTTTGATT
*
32494329 TTTTATAAA-TATTTTAAA
1 TTTTAAAAATTATTTTAAA
*
32494347 TTTTAAAAATTATTTTGAA
1 TTTTAAAAATTATTTTAAA
32494366 TT
1 TT
32494368 ATTTTGTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (19 bp):
TTTTAAAAATTATTTTAAA
Found at i:32501382 original size:13 final size:13
Alignment explanation
Indices: 32501364--32501391 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
32501354 TTTCAACTCC
32501364 ATCATATTTAGTT
1 ATCATATTTAGTT
32501377 ATCATATTTAGTT
1 ATCATATTTAGTT
32501390 AT
1 AT
32501392 GACATAACTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.07, G:0.07, T:0.54
Consensus pattern (13 bp):
ATCATATTTAGTT
Found at i:32505169 original size:17 final size:16
Alignment explanation
Indices: 32505129--32505171 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
32505119 AGGAAAAAGT
*
32505129 AGTTACAAGAATATGAA
1 AGTTA-AAGAAGATGAA
32505146 AGATTAAAGAAGATGAAA
1 AG-TTAAAGAAGATG-AA
32505164 AGTTAAAG
1 AGTTAAAG
32505172 GTCAAGGGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.56, C:0.02, G:0.21, T:0.21
Consensus pattern (16 bp):
AGTTAAAGAAGATGAA
Found at i:32522698 original size:21 final size:22
Alignment explanation
Indices: 32522660--32522708 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
32522650 AAAAAATCTA
32522660 AATTTTTTAATTAAATAAATAT
1 AATTTTTTAATTAAATAAATAT
* *
32522682 AATTTTTTTA-TATATAAATAT
1 AATTTTTTAATTAAATAAATAT
*
32522703 GATTTT
1 AATTTT
32522709 ATCTTAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
AATTTTTTAATTAAATAAATAT
Found at i:32527206 original size:76 final size:75
Alignment explanation
Indices: 32527082--32527265 Score: 210
Period size: 76 Copynumber: 2.4 Consensus size: 75
32527072 CTGAGTTTAA
** * * *
32527082 CTCTTACGAGCCTAGACAGAATATCGCTCTTACAAACTAGTTAGAATATTGCTCTTACAATCTAG
1 CTCTTACGAGCC-AGACAGAATATCGCTCTTACAAACTAGACAGAATATCGCTCTTACAAGCCAG
*
32527147 ACAGAATATTG
65 ACAGAATATCG
*
32527158 CTCTTACGAGCCAGACAGAATATCG-TCCTTACAAGAC-AGACAGAAATATCGCTCTTACGAGCC
1 CTCTTACGAGCCAGACAGAATATCGCT-CTTACAA-ACTAGACAG-AATATCGCTCTTACAAGCC
32527221 AGACAGAATATCG
63 AGACAGAATATCG
* * *
32527234 CTCTTATGAGCCAAAATCAGAATAACGCTCTT
1 CTCTTACGAGCC-AGA-CAGAATATCGCTCTT
32527266 TCGACCCAAA
Statistics
Matches: 92, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
74 1 0.01
75 24 0.26
76 52 0.57
77 2 0.02
78 12 0.13
79 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.16, T:0.26
Consensus pattern (75 bp):
CTCTTACGAGCCAGACAGAATATCGCTCTTACAAACTAGACAGAATATCGCTCTTACAAGCCAGA
CAGAATATCG
Found at i:32527244 original size:25 final size:25
Alignment explanation
Indices: 32527082--32527302 Score: 183
Period size: 25 Copynumber: 8.6 Consensus size: 25
32527072 CTGAGTTTAA
32527082 CTCTTACGAGCCTAGACAGAATATCG
1 CTCTTACGAGCC-AGACAGAATATCG
* * * ** *
32527108 CTCTTACAAACTAGTTAGAATATTG
1 CTCTTACGAGCCAGACAGAATATCG
* * * *
32527133 CTCTTACAATCTAGACAGAATATTG
1 CTCTTACGAGCCAGACAGAATATCG
32527158 CTCTTACGAGCCAGACAGAATATCG
1 CTCTTACGAGCCAGACAGAATATCG
* *
32527183 -TCCTTACAAGACAGACAGAAATATCG
1 CT-CTTACGAGCCAGACAG-AATATCG
32527209 CTCTTACGAGCCAGACAGAATATCG
1 CTCTTACGAGCCAGACAGAATATCG
* * *
32527234 CTCTTATGAGCCAAAATCAGAATAACG
1 CTCTTACGAGCC-AGA-CAGAATATCG
* * * *
32527261 CTCTTTCGACCCAAAATCAGAATAACG
1 CTCTTACGAGCC-AGA-CAGAATATCG
* *
32527288 CTCTTTCAAGCCAGA
1 CTCTTACGAGCCAGA
32527303 ATCAAATTAC
Statistics
Matches: 164, Mismatches: 26, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
24 1 0.01
25 85 0.52
26 34 0.21
27 44 0.27
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.24
Consensus pattern (25 bp):
CTCTTACGAGCCAGACAGAATATCG
Found at i:32527305 original size:27 final size:27
Alignment explanation
Indices: 32527202--32527306 Score: 117
Period size: 27 Copynumber: 4.0 Consensus size: 27
32527192 GACAGACAGA
* * *
32527202 AATATCGCTCTTACGAGCC-AGA-CAG
1 AATAACGCTCTTTCGAGCCAAAATCAG
*
32527227 AATATCGCTCTTAT-GAGCCAAAATCAG
1 AATAACGCTCTT-TCGAGCCAAAATCAG
*
32527254 AATAACGCTCTTTCGACCCAAAATCAG
1 AATAACGCTCTTTCGAGCCAAAATCAG
* *
32527281 AATAACGCTCTTTCAAGCCAGAATCA
1 AATAACGCTCTTTCGAGCCAAAATCA
32527307 AATTACTCCT
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
25 17 0.25
26 3 0.04
27 49 0.71
ACGTcount: A:0.36, C:0.27, G:0.14, T:0.23
Consensus pattern (27 bp):
AATAACGCTCTTTCGAGCCAAAATCAG
Found at i:32527557 original size:46 final size:46
Alignment explanation
Indices: 32527501--32527592 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
32527491 GATCCAAATA
32527501 AAGAACCAAAGCTAACTGAAGCTTCCTTCAATGGATTCTTAGGGTT
1 AAGAACCAAAGCTAACTGAAGCTTCCTTCAATGGATTCTTAGGGTT
32527547 AAGAACCAAAGCTAACTGAAGCTTCCTTCAATGGATTCTTAGGGTT
1 AAGAACCAAAGCTAACTGAAGCTTCCTTCAATGGATTCTTAGGGTT
32527593 TTAGTTTGTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.28
Consensus pattern (46 bp):
AAGAACCAAAGCTAACTGAAGCTTCCTTCAATGGATTCTTAGGGTT
Found at i:32531209 original size:21 final size:21
Alignment explanation
Indices: 32531183--32531235 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
32531173 TATGTTCAAA
32531183 ACTATCGATACTTCAAATCGT
1 ACTATCGATACTTCAAATCGT
32531204 ACTATCGATACTTCAAATCGT
1 ACTATCGATACTTCAAATCGT
32531225 ACTATCGATAC
1 ACTATCGATAC
32531236 AACGCAAGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.34, C:0.25, G:0.09, T:0.32
Consensus pattern (21 bp):
ACTATCGATACTTCAAATCGT
Found at i:32531851 original size:25 final size:25
Alignment explanation
Indices: 32531810--32531889 Score: 99
Period size: 25 Copynumber: 3.2 Consensus size: 25
32531800 CTATCAAGCC
* *
32531810 CAGACAGATTAAT-GCTCTTTCGAGT
1 CAGACAGAAT-ATCGCTCTTACGAGT
32531835 CAGACAGAATATCGCTCTTACGAGT
1 CAGACAGAATATCGCTCTTACGAGT
* * *
32531860 CAGATAGAATATCACTCTTACGAGC
1 CAGACAGAATATCGCTCTTACGAGT
32531885 CAGAC
1 CAGAC
32531890 TTCAGAGCAT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
24 2 0.04
25 46 0.96
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.25
Consensus pattern (25 bp):
CAGACAGAATATCGCTCTTACGAGT
Found at i:32538818 original size:26 final size:25
Alignment explanation
Indices: 32538755--32538853 Score: 121
Period size: 25 Copynumber: 3.9 Consensus size: 25
32538745 TCGAGTCTTC
* *
32538755 CAGAATTTAGCTC-TACGAGCCCAGA
1 CAGAATATCGCTCTTACGAG-CCAGA
*
32538780 CAGATTAAT-GCTCTTACGAGCCAGA
1 CAGAAT-ATCGCTCTTACGAGCCAGA
*
32538805 CAGAAATATCGCTCTTACGAGCCAAA
1 CAG-AATATCGCTCTTACGAGCCAGA
32538831 CAGAATATCGCTCTTACGAGCCA
1 CAGAATATCGCTCTTACGAGCCA
32538854 AACTTTAGAG
Statistics
Matches: 66, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
25 39 0.59
26 27 0.41
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.21
Consensus pattern (25 bp):
CAGAATATCGCTCTTACGAGCCAGA
Found at i:32541145 original size:291 final size:291
Alignment explanation
Indices: 32540621--32541196 Score: 1107
Period size: 291 Copynumber: 2.0 Consensus size: 291
32540611 ATGTTACCAT
32540621 ACTATTTAACTATTTACACCAAAACAACTCATGTAACACAATCCTAATACATGCCAAATAAGTCA
1 ACTATTTAACTATTTACACCAAAACAACTCATGTAACACAATCCTAATACATGCCAAATAAGTCA
* *
32540686 AGTGATACGAAAGACTATCGAACGTGCTCCCGAGATAGTGTGATTCTTCTTGAGGATCCGATCTT
66 AGTGATACGAAAGACTACCGAACGAGCTCCCGAGATAGTGTGATTCTTCTTGAGGATCCGATCTT
* *
32540751 CCACCGTCAAACGAATTTACAAAATAATAAGTAGATACACAGGTAAGCTTACAAAGCTTAGTAAG
131 CCACCGCCAAACGAATTTACAAAACAATAAGTAGATACACAGGTAAGCTTACAAAGCTTAGTAAG
32540816 TTCGCAAGAACGATTAACTTACTGAATAACATATTCGGTTATAGAAAGAGTGATATGAACATCTT
196 TTCGCAAGAACGATTAACTTACTGAATAACATATTCGGTTATAGAAAGAGTGATATGAACATCTT
32540881 CGAAATCCCACGACATTGGCATCGAAATCCC
261 CGAAATCCCACGACATTGGCATCGAAATCCC
32540912 ACTATTTAACTATTTACACCAAAACAACTCATGTAACACAATCCTAATACATGCCAAATAAGTCA
1 ACTATTTAACTATTTACACCAAAACAACTCATGTAACACAATCCTAATACATGCCAAATAAGTCA
*
32540977 AGTGATACGAAAGACTACCGAACGAGCTCCCGAGATAGTGTGATTCTTCTTGAGGATTCGATCTT
66 AGTGATACGAAAGACTACCGAACGAGCTCCCGAGATAGTGTGATTCTTCTTGAGGATCCGATCTT
32541042 CCACCGCCAAACGAATTTACAAAACAATAAGTAGATACACAGGTAAGCTTACAAAGCTTAGTAAG
131 CCACCGCCAAACGAATTTACAAAACAATAAGTAGATACACAGGTAAGCTTACAAAGCTTAGTAAG
32541107 TTCGCAAGAACGATTAACTTACTGAATAACATATTCGGTTATAGAAAGAGTGATATGAACATCTT
196 TTCGCAAGAACGATTAACTTACTGAATAACATATTCGGTTATAGAAAGAGTGATATGAACATCTT
32541172 CGAAATCCCACGACATTGGCATCGA
261 CGAAATCCCACGACATTGGCATCGA
32541197 GTTAATCTCT
Statistics
Matches: 280, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
291 280 1.00
ACGTcount: A:0.38, C:0.21, G:0.16, T:0.25
Consensus pattern (291 bp):
ACTATTTAACTATTTACACCAAAACAACTCATGTAACACAATCCTAATACATGCCAAATAAGTCA
AGTGATACGAAAGACTACCGAACGAGCTCCCGAGATAGTGTGATTCTTCTTGAGGATCCGATCTT
CCACCGCCAAACGAATTTACAAAACAATAAGTAGATACACAGGTAAGCTTACAAAGCTTAGTAAG
TTCGCAAGAACGATTAACTTACTGAATAACATATTCGGTTATAGAAAGAGTGATATGAACATCTT
CGAAATCCCACGACATTGGCATCGAAATCCC
Found at i:32541265 original size:26 final size:26
Alignment explanation
Indices: 32541236--32541291 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
32541226 AGCTCATATA
* *
32541236 AGCCCAGACAGAGT-TTAGCTCTTACG
1 AGCCCAGACAAAATATT-GCTCTTACG
*
32541262 AGCCTAGACAAAATATTGCTCTTACG
1 AGCCCAGACAAAATATTGCTCTTACG
32541288 AGCC
1 AGCC
32541292 AATCAGAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 24 0.92
27 2 0.08
ACGTcount: A:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (26 bp):
AGCCCAGACAAAATATTGCTCTTACG
Found at i:32541343 original size:27 final size:27
Alignment explanation
Indices: 32541279--32541433 Score: 190
Period size: 27 Copynumber: 5.8 Consensus size: 27
32541269 ACAAAATATT
* *
32541279 GCTCTTACGAGCC--AATCAGAATATC
1 GCTCTTTCGAGCCAGAATCAGAATAAC
* * *
32541304 CCTCTTAT-GAGCCAAAATCAAAATAAC
1 GCTCTT-TCGAGCCAGAATCAGAATAAC
* * *
32541331 GCTTTTTCAAGCCAGAATCAGAATATC
1 GCTCTTTCGAGCCAGAATCAGAATAAC
*
32541358 GCTCTTTCGAGCCAGAATCAGAATAAT
1 GCTCTTTCGAGCCAGAATCAGAATAAC
*
32541385 GCTCTTTCGAGCCAGAATCAGAATAAT
1 GCTCTTTCGAGCCAGAATCAGAATAAC
32541412 GCTCTTTCGAGCCAGAATCAGA
1 GCTCTTTCGAGCCAGAATCAGA
32541434 TTACTCATTA
Statistics
Matches: 112, Mismatches: 14, Indels: 6
0.85 0.11 0.05
Matches are distributed among these distances:
25 10 0.09
26 1 0.01
27 101 0.90
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (27 bp):
GCTCTTTCGAGCCAGAATCAGAATAAC
Found at i:32543187 original size:27 final size:27
Alignment explanation
Indices: 32543146--32543212 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
32543136 TGTATGATCT
*
32543146 CGTGTTTATTATCCTTG-CAGACTACCC
1 CGTGTTTACTATCC-TGACAGACTACCC
* * *
32543173 TGTGTTTACTGTCCTGACGGACTACCC
1 CGTGTTTACTATCCTGACAGACTACCC
*
32543200 CGTGTTTAATATC
1 CGTGTTTACTATC
32543213 TTGGCGAACT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
26 2 0.06
27 30 0.94
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.37
Consensus pattern (27 bp):
CGTGTTTACTATCCTGACAGACTACCC
Found at i:32543223 original size:27 final size:27
Alignment explanation
Indices: 32543166--32543224 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 27
32543156 ATCCTTGCAG
* * * *
32543166 ACTACCCTGTGTTTACTGTCCTGACGG
1 ACTACCCCGTGTTTAATATCCTGACGA
* *
32543193 ACTACCCCGTGTTTAATATCTTGGCGA
1 ACTACCCCGTGTTTAATATCCTGACGA
32543220 ACTAC
1 ACTAC
32543225 ATTAGTTATC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.20, C:0.29, G:0.19, T:0.32
Consensus pattern (27 bp):
ACTACCCCGTGTTTAATATCCTGACGA
Found at i:32546418 original size:29 final size:29
Alignment explanation
Indices: 32546318--32546479 Score: 83
Period size: 29 Copynumber: 5.5 Consensus size: 29
32546308 GTTTAAGGGT
* *
32546318 AAAATGGTAATTTTTGGTGTAATCGAGGTTA
1 AAAATGG-AA-TTTTGGTGAAATCGGGGTTA
32546349 AAAATAGG-ATTTT-G-GAAAGTTCAGGGG-T-
1 AAAAT-GGAATTTTGGTGAAA--TC-GGGGTTA
**
32546377 AAAGCGGTAATTTTGGTGAAATCGGGGTTA
1 AAAATGG-AATTTTGGTGAAATCGGGGTTA
32546407 AAAAT-GAGATTTT-G-GAAAGTTCGAGGG-T-
1 AAAATGGA-ATTTTGGTGAAA--TCG-GGGTTA
**
32546435 AAAATGGTAATTTTGGTGAAATTAGGGTTA
1 AAAATGG-AATTTTGGTGAAATCGGGGTTA
*
32546465 AAAATGGAATATTGG
1 AAAATGGAATTTTGG
32546480 AAAGTTCAGG
Statistics
Matches: 102, Mismatches: 9, Indels: 42
0.67 0.06 0.27
Matches are distributed among these distances:
27 9 0.09
28 18 0.18
29 40 0.39
30 20 0.20
31 13 0.13
32 2 0.02
ACGTcount: A:0.35, C:0.03, G:0.30, T:0.32
Consensus pattern (29 bp):
AAAATGGAATTTTGGTGAAATCGGGGTTA
Found at i:32546418 original size:58 final size:58
Alignment explanation
Indices: 32546253--32546490 Score: 250
Period size: 58 Copynumber: 4.1 Consensus size: 58
32546243 TGGATGCCCG
* * * * * * *
32546253 GGGGCAAAATGGTAATTTTTAGG-AAAATCGAGGTAAAAAAATGAAATTTTAGAAAGTTTA
1 GGGGTAAAATGGTAA-TTTT-GGTGAAATCGGGGT-TAAAAATGAGATTTTGGAAAGTTCA
* * *
32546313 AGGGTAAAATGGTAATTTTTGGTGTAATCGAGGTTAAAAAT-AGGATTTTGGAAAGTTCA
1 GGGGTAAAATGGTAA-TTTTGGTGAAATCGGGGTTAAAAATGA-GATTTTGGAAAGTTCA
**
32546372 GGGGTAAAGCGGTAATTTTGGTGAAATCGGGGTTAAAAATGAGATTTTGGAAAGTTC-
1 GGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGAGATTTTGGAAAGTTCA
** *
32546429 GAGGGTAAAATGGTAATTTTGGTGAAATTAGGGTTAAAAATG-GAATATTGGAAAGTTCA
1 G-GGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGAG-ATTTTGGAAAGTTCA
32546488 GGG
1 GGG
32546491 ACCTATAAAA
Statistics
Matches: 154, Mismatches: 18, Indels: 14
0.83 0.10 0.08
Matches are distributed among these distances:
57 2 0.01
58 90 0.58
59 35 0.23
60 27 0.18
ACGTcount: A:0.37, C:0.03, G:0.29, T:0.30
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTGGTGAAATCGGGGTTAAAAATGAGATTTTGGAAAGTTCA
Found at i:32546490 original size:29 final size:29
Alignment explanation
Indices: 32546344--32546490 Score: 105
Period size: 29 Copynumber: 5.1 Consensus size: 29
32546334 GTGTAATCGA
32546344 GGTTAAAAATAGG-ATTTTGGAAAGTTCAG
1 GGTTAAAAAT-GGAATTTTGGAAAGTTCAG
* ** *
32546373 GGGT-AAAGCGGTAATTTTGGTGAAA--TCGG
1 GGTTAAAAATGG-AATTTT-G-GAAAGTTCAG
32546402 GGTTAAAAAT-GAGATTTTGGAAAGTTCGAG
1 GGTTAAAAATGGA-ATTTTGGAAAGTTC-AG
32546432 GG-T-AAAATGGTAATTTTGGTGAAA-TT-AG
1 GGTTAAAAATGG-AATTTT-G-GAAAGTTCAG
*
32546460 GGTTAAAAATGGAATATTGGAAAGTTCAG
1 GGTTAAAAATGGAATTTTGGAAAGTTCAG
32546489 GG
1 GG
32546491 ACCTATAAAA
Statistics
Matches: 92, Mismatches: 9, Indels: 34
0.68 0.07 0.25
Matches are distributed among these distances:
27 10 0.11
28 17 0.18
29 39 0.42
30 18 0.20
31 8 0.09
ACGTcount: A:0.35, C:0.03, G:0.31, T:0.30
Consensus pattern (29 bp):
GGTTAAAAATGGAATTTTGGAAAGTTCAG
Found at i:32547099 original size:29 final size:29
Alignment explanation
Indices: 32547049--32547106 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
32547039 TCCGTTCACC
* * *
32547049 GCGTGAGCGCGCGTCATTGACGCCCCCAG
1 GCGTGAGCGCACATCATCGACGCCCCCAG
*
32547078 GCGTGAGCGCACATTATCGACGCCCCCAG
1 GCGTGAGCGCACATCATCGACGCCCCCAG
32547107 CCACGCGTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.17, C:0.38, G:0.31, T:0.14
Consensus pattern (29 bp):
GCGTGAGCGCACATCATCGACGCCCCCAG
Found at i:32548388 original size:6 final size:6
Alignment explanation
Indices: 32548377--32548492 Score: 82
Period size: 6 Copynumber: 20.0 Consensus size: 6
32548367 TATAATGATT
* * * *
32548377 TTTAAA TTTAAA -ATAAA TTTAGA TTTAAA -TTAAA TTCAAA TTTATAG
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA-AA
* * * *
32548424 TTTAAT TTTAAT TTTAAA TTTGAAA --TAAA TCTAAA TTTAAA -TCAAA
1 TTTAAA TTTAAA TTTAAA TTT-AAA TTTAAA TTTAAA TTTAAA TTTAAA
* *
32548470 TTTAAT TTTAAA -ATAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA
32548493 AGGGCCCGAT
Statistics
Matches: 86, Mismatches: 16, Indels: 16
0.73 0.14 0.14
Matches are distributed among these distances:
4 3 0.03
5 18 0.21
6 57 0.66
7 8 0.09
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:32548402 original size:17 final size:17
Alignment explanation
Indices: 32548377--32548492 Score: 81
Period size: 17 Copynumber: 6.4 Consensus size: 17
32548367 TATAATGATT
32548377 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
* *
32548394 TTTAGATTTAAATTAAA
1 TTTAAATTTAAAATAAA
* *
32548411 TTCAAATTTATAGTTTAATTTTAAT
1 TTTAAATTTA-A----AA---TAAA
*
32548436 TTTAAATTTGAAATAAA
1 TTTAAATTTAAAATAAA
*
32548453 TCTAAATTT-AAATCAAA
1 TTTAAATTTAAAAT-AAA
*
32548470 TTTAATTTTAAAATAAA
1 TTTAAATTTAAAATAAA
32548487 TTTAAA
1 TTTAAA
32548493 AGGGCCCGAT
Statistics
Matches: 76, Mismatches: 13, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
16 4 0.05
17 52 0.68
18 5 0.07
20 2 0.03
22 1 0.01
24 1 0.01
25 11 0.14
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:32548404 original size:23 final size:25
Alignment explanation
Indices: 32548377--32548434 Score: 68
Period size: 23 Copynumber: 2.4 Consensus size: 25
32548367 TATAATGATT
32548377 TTTAAATTTAAAAT-AAATTTAGA-
1 TTTAAATTTAAAATCAAATTTAGAG
* *
32548400 TTTAAA-TTAAATTCAAATTTATAG
1 TTTAAATTTAAAATCAAATTTAGAG
*
32548424 TTTAATTTTAA
1 TTTAAATTTAA
32548435 TTTTAAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 6 0.21
23 14 0.48
24 5 0.17
25 4 0.14
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (25 bp):
TTTAAATTTAAAATCAAATTTAGAG
Found at i:32548986 original size:19 final size:19
Alignment explanation
Indices: 32548962--32549001 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
32548952 ATATAATAAT
*
32548962 AAATTTAA-ATTTTATATTA
1 AAATTTAATA-TTAATATTA
32548981 AAATTTAATATTAATATTA
1 AAATTTAATATTAATATTA
32549000 AA
1 AA
32549002 TAAATACAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 18 0.95
20 1 0.05
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AAATTTAATATTAATATTA
Found at i:32548987 original size:12 final size:13
Alignment explanation
Indices: 32548968--32549022 Score: 56
Period size: 13 Copynumber: 4.2 Consensus size: 13
32548958 TAATAAATTT
*
32548968 AAATTTTATATTA
1 AAATTTAATATTA
32548981 AAATTTAATATTA
1 AAATTTAATATTA
* * *
32548994 ATATTAAATAAATA
1 AAATTTAAT-ATTA
*
32549008 CAATTTAATATTA
1 AAATTTAATATTA
32549021 AA
1 AA
32549023 TAAAATTAAA
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
13 23 0.72
14 9 0.28
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (13 bp):
AAATTTAATATTA
Done.