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 18 of 193
Found at i:6197748 original size:5 final size:5
Alignment explanation
Indices: 6197738--6197765 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
6197728 TGGTATATTT
6197738 TAAAA TAAAA TAAAA TAAAA TAAAA TAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAA
6197766 GTGAATTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (5 bp):
TAAAA
Found at i:6209231 original size:16 final size:16
Alignment explanation
Indices: 6209212--6209258 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
6209202 AAATTTTAAT
6209212 AAATAAAAAATATATA
1 AAATAAAAAATATATA
**
6209228 AAATTATTAAATAT-TA
1 AAA-TAAAAAATATATA
6209244 AAATAAAATAATATA
1 AAATAAAA-AATATA
6209259 AATATTTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
15 3 0.12
16 13 0.54
17 8 0.33
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATAAAAAATATATA
Found at i:6212545 original size:29 final size:29
Alignment explanation
Indices: 6212500--6212555 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
6212490 TGTTAGTGGA
* *
6212500 TAATAATATTTTATTATTTAGAAAAAAAT
1 TAATAATATTATATTATTAAGAAAAAAAT
*
6212529 TAATAA-ATTATAGTTATTAATAAAAAA
1 TAATAATATTATA-TTATTAAGAAAAAA
6212556 TTGTGTTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 5 0.22
29 18 0.78
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (29 bp):
TAATAATATTATATTATTAAGAAAAAAAT
Found at i:6212622 original size:31 final size:33
Alignment explanation
Indices: 6212552--6212624 Score: 96
Period size: 34 Copynumber: 2.2 Consensus size: 33
6212542 TTATTAATAA
* *
6212552 AAAATTGTGTTATAAAGATATAATTTTTACACGT
1 AAAATTATCTTATAAAGATATAATTTTTA-ACGT
*
6212586 AAAATTATCTTATAAAGATATAA-TTTT-ATGT
1 AAAATTATCTTATAAAGATATAATTTTTAACGT
6212617 AAAATTAT
1 AAAATTAT
6212625 TTTGTAAACC
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
31 11 0.31
33 4 0.11
34 21 0.58
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.42
Consensus pattern (33 bp):
AAAATTATCTTATAAAGATATAATTTTTAACGT
Found at i:6219031 original size:3 final size:3
Alignment explanation
Indices: 6219023--6219058 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
6219013 CATACACATC
*
6219023 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCA TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
6219059 ACCCTTTTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.03, C:0.33, G:0.00, T:0.64
Consensus pattern (3 bp):
TCT
Found at i:6220590 original size:29 final size:29
Alignment explanation
Indices: 6220532--6220593 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
6220522 GTTACGGATA
* **
6220532 TAGTACATATACTTTTTTTTTTTGAATTT
1 TAGTACATATACTTTATTTGGTTGAATTT
*
6220561 TAGTACATATACTTTAATTTGGTT-ATTTT
1 TAGTACATATACTTT-ATTTGGTTGAATTT
6220590 TAGT
1 TAGT
6220594 CTTTGTATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 23 0.82
30 5 0.18
ACGTcount: A:0.26, C:0.06, G:0.10, T:0.58
Consensus pattern (29 bp):
TAGTACATATACTTTATTTGGTTGAATTT
Found at i:6241883 original size:19 final size:19
Alignment explanation
Indices: 6241829--6241885 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 19
6241819 AAAAAAAATC
*
6241829 AAAATAATTTTCAAAAATTG
1 AAAATGATTTT-AAAAATTG
*
6241849 AAAATGATTTTTAAAATTG
1 AAAATGATTTTAAAAATTG
6241868 AAAAT-ATTTATAAAAATT
1 AAAATGATTT-TAAAAATT
6241886 TTAAAATTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 4 0.12
19 19 0.58
20 10 0.30
ACGTcount: A:0.54, C:0.02, G:0.05, T:0.39
Consensus pattern (19 bp):
AAAATGATTTTAAAAATTG
Found at i:6252469 original size:33 final size:33
Alignment explanation
Indices: 6252431--6252500 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
6252421 TCAGTCCAGA
*
6252431 AGCTTAATTCTGGACGAATGCAGCCATAAGATC
1 AGCTTAATTCTAGACGAATGCAGCCATAAGATC
6252464 AGCTTAATTCTAGACGAATGCAGCCATAAGATC
1 AGCTTAATTCTAGACGAATGCAGCCATAAGATC
6252497 AGCT
1 AGCT
6252501 GGAAATTGCG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.24
Consensus pattern (33 bp):
AGCTTAATTCTAGACGAATGCAGCCATAAGATC
Found at i:6256826 original size:21 final size:21
Alignment explanation
Indices: 6256802--6256859 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
6256792 CAGTGCAAGT
*
6256802 TTCTACCGATACATGTGA-TAG
1 TTCTACCGATACAAGTGACT-G
*
6256823 TTCTACCGATACAAGTGACTT
1 TTCTACCGATACAAGTGACTG
*
6256844 TTCTACCGATGCAAGT
1 TTCTACCGATACAAGT
6256860 TTTACCTCTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 32 0.97
22 1 0.03
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (21 bp):
TTCTACCGATACAAGTGACTG
Found at i:6267308 original size:2 final size:2
Alignment explanation
Indices: 6267301--6267342 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
6267291 AGCTGGCTAG
* * *
6267301 AT AT AT AT AT AT AT AT AT AT GT AT GT AT GT AT A- 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
6267342 A
1 A
6267343 CCCTTTGGGT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6267362 original size:6 final size:6
Alignment explanation
Indices: 6267351--6267400 Score: 100
Period size: 6 Copynumber: 8.3 Consensus size: 6
6267341 TACCCTTTGG
6267351 GTGGCA GTGGCA GTGGCA GTGGCA GTGGCA GTGGCA GTGGCA GTGGCA
1 GTGGCA GTGGCA GTGGCA GTGGCA GTGGCA GTGGCA GTGGCA GTGGCA
6267399 GT
1 GT
6267401 ACCATATTTA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.16, C:0.16, G:0.50, T:0.18
Consensus pattern (6 bp):
GTGGCA
Found at i:6270698 original size:2 final size:2
Alignment explanation
Indices: 6270691--6270721 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
6270681 ATGAACAGCT
6270691 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6270722 GTTCCATGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:6272499 original size:41 final size:43
Alignment explanation
Indices: 6272383--6272623 Score: 170
Period size: 43 Copynumber: 5.7 Consensus size: 43
6272373 ATAATGGTAT
* * * *
6272383 ACACAGTGCATAATTAGACA-AGCCAAAGCAATTATACTGGCAC
1 ACACAGTGCATCATTGGATATA-CCAAAGTAATTATACTGGCAC
* * * * * *
6272426 ACATAGTGCATCATT-TAGTAAACTAAAATAATTATGCTGGCAC
1 ACACAGTGCATCATTGGA-TATACCAAAGTAATTATACTGGCAC
* * *
6272469 ATA-AGTGCAT-ATTGGATATACCAAAGTAATTATACAGACAC
1 ACACAGTGCATCATTGGATATACCAAAGTAATTATACTGGCAC
* * * *
6272510 ACACAATGCATCATTGGATATACCAAAGAAACTATACTAGCAC
1 ACACAGTGCATCATTGGATATACCAAAGTAATTATACTGGCAC
* * * * * *
6272553 A-A-GGTGCATCATCGAATATATCGAAGTAATTATACTCGCAC
1 ACACAGTGCATCATTGGATATACCAAAGTAATTATACTGGCAC
* * * * *
6272594 ATAGAGTGCATCATCGGATAAACCGAAGTA
1 ACACAGTGCATCATTGGATATACCAAAGTA
6272624 TAGCATGTAC
Statistics
Matches: 155, Mismatches: 36, Indels: 14
0.76 0.18 0.07
Matches are distributed among these distances:
41 55 0.35
42 17 0.11
43 82 0.53
44 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.24
Consensus pattern (43 bp):
ACACAGTGCATCATTGGATATACCAAAGTAATTATACTGGCAC
Found at i:6278062 original size:21 final size:21
Alignment explanation
Indices: 6278032--6278089 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
6278022 TCAGAATGTC
*
6278032 AGTCCTATGAATAGTGAAGTCA
1 AGTCC-ATGAATAGTGAAATCA
*
6278054 AGTCCATGAAAAGTGAAATCA
1 AGTCCATGAATAGTGAAATCA
* *
6278075 AAT-CACGAATAGTGA
1 AGTCCATGAATAGTGA
6278090 TAGTATGTAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
20 10 0.32
21 16 0.52
22 5 0.16
ACGTcount: A:0.43, C:0.14, G:0.21, T:0.22
Consensus pattern (21 bp):
AGTCCATGAATAGTGAAATCA
Found at i:6286475 original size:30 final size:31
Alignment explanation
Indices: 6286408--6286476 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
6286398 AAATTTTAAA
* *
6286408 TTAATAAA-GATAAAATTATACTTTAGTCTCC
1 TTAA-AAATGATAAAATTATAATTTAATCTCC
* *
6286439 TTAAAAATGATAAAATTTTAATTTAATC-CT
1 TTAAAAATGATAAAATTATAATTTAATCTCC
6286469 TTAAAAAT
1 TTAAAAAT
6286477 TTTACTTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 12 0.36
31 21 0.64
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.41
Consensus pattern (31 bp):
TTAAAAATGATAAAATTATAATTTAATCTCC
Found at i:6286605 original size:33 final size:33
Alignment explanation
Indices: 6286567--6286666 Score: 191
Period size: 33 Copynumber: 3.0 Consensus size: 33
6286557 TGGAGTTCTC
6286567 AGCATGGAGCAATGGTGGTGAAGGTGGAATGTG
1 AGCATGGAGCAATGGTGGTGAAGGTGGAATGTG
6286600 AGCATGGAGCAATGGTGGTGAAGGTGGAATGTG
1 AGCATGGAGCAATGGTGGTGAAGGTGGAATGTG
*
6286633 AGCATGGAGCAATGGTGGTGAAGGGGGAATGTG
1 AGCATGGAGCAATGGTGGTGAAGGTGGAATGTG
6286666 A
1 A
6286667 TAATGTTAAT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
33 66 1.00
ACGTcount: A:0.28, C:0.06, G:0.46, T:0.20
Consensus pattern (33 bp):
AGCATGGAGCAATGGTGGTGAAGGTGGAATGTG
Found at i:6287053 original size:12 final size:12
Alignment explanation
Indices: 6286986--6287056 Score: 54
Period size: 12 Copynumber: 5.8 Consensus size: 12
6286976 CTTCTACTTG
*
6286986 TATTTTTTATTT
1 TATTTTTTAATT
*
6286998 TATTTTTTTAAAT
1 TA-TTTTTTAATT
6287011 T-TTTTTTAATTT
1 TATTTTTTAA-TT
** * *
6287023 TAATTAATAAATA
1 T-ATTTTTTAATT
6287036 TATTTTTTAATT
1 TATTTTTTAATT
6287048 TATTTTTTA
1 TATTTTTTA
6287057 TTAATAAGTC
Statistics
Matches: 44, Mismatches: 11, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
11 8 0.18
12 20 0.45
13 11 0.25
14 5 0.11
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (12 bp):
TATTTTTTAATT
Found at i:6289430 original size:16 final size:16
Alignment explanation
Indices: 6289409--6289439 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
6289399 CATATTGAAG
6289409 CATATAAATTTAAAAT
1 CATATAAATTTAAAAT
*
6289425 CATATATATTTAAAA
1 CATATAAATTTAAAA
6289440 GTTTTTTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (16 bp):
CATATAAATTTAAAAT
Found at i:6289599 original size:17 final size:20
Alignment explanation
Indices: 6289559--6289604 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 20
6289549 ATTCTTTAGT
6289559 TTTTTAAAAAAATTATATATA
1 TTTTT-AAAAAATTATATATA
6289580 TTTTTAAAAAA-TATA-A-A
1 TTTTTAAAAAATTATATATA
6289597 TTTTTAAA
1 TTTTTAAA
6289605 CTTTTATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 9 0.36
18 1 0.04
19 4 0.16
20 6 0.24
21 5 0.20
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
TTTTTAAAAAATTATATATA
Found at i:6289612 original size:18 final size:17
Alignment explanation
Indices: 6289568--6289639 Score: 54
Period size: 17 Copynumber: 4.1 Consensus size: 17
6289558 TTTTTTAAAA
* *
6289568 AAATTATATATATTTTT
1 AAATTTTATAAATTTTT
***
6289585 AAAAAATATAAATTTTT
1 AAATTTTATAAATTTTT
6289602 AAACTTTTATAAATATTTT
1 AAA-TTTTATAAAT-TTTT
* *
6289621 GAATTTTTTATAATTTTT
1 AAATTTTATA-AATTTTT
6289639 A
1 A
6289640 TTGAAAGAGA
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
17 17 0.40
18 17 0.40
19 9 0.21
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (17 bp):
AAATTTTATAAATTTTT
Found at i:6295424 original size:18 final size:18
Alignment explanation
Indices: 6295384--6295426 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
6295374 TTTTCAGTTA
6295384 TAATTAATTTAAAATTTT
1 TAATTAATTTAAAATTTT
* *
6295402 CAATTAA-TTAAATTTATT
1 TAATTAATTTAAAATT-TT
6295420 TAATTAA
1 TAATTAA
6295427 AAAATTATTC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTAATTTAAAATTTT
Found at i:6296019 original size:21 final size:21
Alignment explanation
Indices: 6295970--6296030 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
6295960 TTAGATAACT
*
6295970 ATGT-TTATTTTCTTTAAATTA
1 ATGTATTATTTT-TTTAATTTA
*
6295991 A-G-AATATTTTTTTAATTTA
1 ATGTATTATTTTTTTAATTTA
*
6296010 ATGTATTATTTTTTTATTTTA
1 ATGTATTATTTTTTTAATTTA
6296031 TTGTTTTTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
19 9 0.27
20 8 0.24
21 16 0.48
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.64
Consensus pattern (21 bp):
ATGTATTATTTTTTTAATTTA
Found at i:6301586 original size:67 final size:67
Alignment explanation
Indices: 6301478--6301603 Score: 216
Period size: 67 Copynumber: 1.9 Consensus size: 67
6301468 AAAAAACACA
** * *
6301478 TATAATTGGATTCAATACATTAAAGGCTTAATACTACCCCTTATGAATATGAAGGGGCAGCAATC
1 TATAATTGGACCCAATACATAAAAGGCCTAATACTACCCCTTATGAATATGAAGGGGCAGCAATC
6301543 CT
66 CT
6301545 TATAATTGGACCCAATACATAAAAGGCCTAATACTACCCCTTATGAATATGAAGGGGCA
1 TATAATTGGACCCAATACATAAAAGGCCTAATACTACCCCTTATGAATATGAAGGGGCA
6301604 ACAGCCCTAA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
67 55 1.00
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (67 bp):
TATAATTGGACCCAATACATAAAAGGCCTAATACTACCCCTTATGAATATGAAGGGGCAGCAATC
CT
Found at i:6301617 original size:67 final size:67
Alignment explanation
Indices: 6301479--6301617 Score: 206
Period size: 67 Copynumber: 2.1 Consensus size: 67
6301469 AAAAACACAT
** * * * *
6301479 ATAATTGGATTCAATACATTAAAGGCTTAATACTACCCCTTATGAATATGAAGGGGCAGCAATCC
1 ATAATTGGACCCAATACATAAAAGGCCTAATACTACCCCTTATGAATATGAAGGGGCAACAACCC
*
6301544 TT
66 TA
*
6301546 ATAATTGGACCCAATACATAAAAGGCCTAATACTACCCCTTATGAATATGAAGGGGCAACAGCCC
1 ATAATTGGACCCAATACATAAAAGGCCTAATACTACCCCTTATGAATATGAAGGGGCAACAACCC
6301611 TA
66 TA
6301613 ATAAT
1 ATAAT
6301618 ATTTATTAAG
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
67 64 1.00
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (67 bp):
ATAATTGGACCCAATACATAAAAGGCCTAATACTACCCCTTATGAATATGAAGGGGCAACAACCC
TA
Found at i:6305226 original size:31 final size:31
Alignment explanation
Indices: 6305174--6305235 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
6305164 TCATTTCAGG
*
6305174 CTCTAATGTTATCAAATGTTCTCAGTTTAGT
1 CTCTAATGTTATCAAACGTTCTCAGTTTAGT
* * *
6305205 CTCTAATGTTATTAGACGTTCTCGGTTTAGT
1 CTCTAATGTTATCAAACGTTCTCAGTTTAGT
6305236 GTTTTGAACA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.23, C:0.16, G:0.16, T:0.45
Consensus pattern (31 bp):
CTCTAATGTTATCAAACGTTCTCAGTTTAGT
Found at i:6305491 original size:16 final size:17
Alignment explanation
Indices: 6305460--6305502 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
6305450 TTTTTTTTAA
6305460 AATATATTACAAATTTT
1 AATATATTACAAATTTT
*
6305477 AATATTTTA-AAATTTT
1 AATATATTACAAATTTT
*
6305493 -ATAAATTACA
1 AATATATTACA
6305503 TCTATTAGAG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
15 6 0.27
16 8 0.36
17 8 0.36
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (17 bp):
AATATATTACAAATTTT
Found at i:6307351 original size:14 final size:15
Alignment explanation
Indices: 6307332--6307388 Score: 66
Period size: 14 Copynumber: 3.9 Consensus size: 15
6307322 TAGCAAAATT
6307332 AATAATAA-AATAAA
1 AATAATAACAATAAA
*
6307346 AATAATAA-AATATCTA
1 AATAATAACAATA--AA
6307362 AATAATAACAAT-AA
1 AATAATAACAATAAA
6307376 AATAATAACAATA
1 AATAATAACAATA
6307389 TAACAACGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
14 25 0.68
16 9 0.24
17 3 0.08
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (15 bp):
AATAATAACAATAAA
Found at i:6307368 original size:30 final size:31
Alignment explanation
Indices: 6307314--6307389 Score: 97
Period size: 30 Copynumber: 2.5 Consensus size: 31
6307304 TAAATATCTT
* *
6307314 TAAAATAATAGCAAAAT-T-AATAATAA-AA
1 TAAAATAATAACAATATCTAAATAATAACAA
6307342 TAAAAATAATAA-AATATCTAAATAATAACAA
1 T-AAAATAATAACAATATCTAAATAATAACAA
6307373 TAAAATAATAACAATAT
1 TAAAATAATAACAATAT
6307390 AACAACGAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
28 5 0.12
29 10 0.24
30 18 0.44
31 8 0.20
ACGTcount: A:0.67, C:0.05, G:0.01, T:0.26
Consensus pattern (31 bp):
TAAAATAATAACAATATCTAAATAATAACAA
Found at i:6326586 original size:38 final size:36
Alignment explanation
Indices: 6326501--6326591 Score: 85
Period size: 38 Copynumber: 2.4 Consensus size: 36
6326491 TTGTAAAACT
6326501 ATTTTTTAAAAAATAAAAAAAATTGTAAATATTTAAA
1 ATTTTTTAAAAAATAAAAAAAATTGTAAATA-TTAAA
* * * *
6326538 AATTTGTAAAAAATGATAAAAAATTGTGAGAATA-TAAT
1 ATTTTTTAAAAAAT-AAAAAAAATTGT-A-AATATTAAA
*
6326576 TTTTTTTAAAATAATA
1 ATTTTTTAAAA-AATA
6326592 TTTACAAGTT
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
37 12 0.28
38 23 0.53
39 4 0.09
40 4 0.09
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (36 bp):
ATTTTTTAAAAAATAAAAAAAATTGTAAATATTAAA
Found at i:6326963 original size:62 final size:62
Alignment explanation
Indices: 6326866--6326991 Score: 216
Period size: 62 Copynumber: 2.0 Consensus size: 62
6326856 TTTCATTTTA
* *
6326866 AATTTTAATATTTTCAATCTTGAAATTCAGGATAAAAGTGTCGATGTGACATTAAATTATTG
1 AATTTCAATATTTTCAATCTCGAAATTCAGGATAAAAGTGTCGATGTGACATTAAATTATTG
* *
6326928 AATTTCAATATTTTTAATCTCGAAATTCAGGATAAAAGTGTCGATGTGATATTAAATTATTG
1 AATTTCAATATTTTCAATCTCGAAATTCAGGATAAAAGTGTCGATGTGACATTAAATTATTG
6326990 AA
1 AA
6326992 AAAAATATAC
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 60 1.00
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.40
Consensus pattern (62 bp):
AATTTCAATATTTTCAATCTCGAAATTCAGGATAAAAGTGTCGATGTGACATTAAATTATTG
Found at i:6334993 original size:39 final size:41
Alignment explanation
Indices: 6334923--6335000 Score: 106
Period size: 39 Copynumber: 1.9 Consensus size: 41
6334913 GATTAAAGCA
* *
6334923 ATGGTGGGGAAGATGGGGAGAGAATCGGAGTAGG-GGGAGGG
1 ATGGTGGGGAAGA-GGGGAAAGAATCAGAGTAGGAGGGAGGG
*
6334964 ATGGTGGGGGAGA-GGGAAAGAATCAGAGTAGGAGGGA
1 ATGGTGGGGAAGAGGGGAAAGAATCAGAGTAGGAGGGA
6335001 TGGTGAGGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 17 0.52
40 4 0.12
41 12 0.36
ACGTcount: A:0.31, C:0.03, G:0.55, T:0.12
Consensus pattern (41 bp):
ATGGTGGGGAAGAGGGGAAAGAATCAGAGTAGGAGGGAGGG
Found at i:6335080 original size:30 final size:30
Alignment explanation
Indices: 6335046--6335119 Score: 139
Period size: 30 Copynumber: 2.5 Consensus size: 30
6335036 ATAGGGGGAT
6335046 GGAAAATGGCAGCTCCATTAAGTTTGTAAC
1 GGAAAATGGCAGCTCCATTAAGTTTGTAAC
6335076 GGAAAATGGCAGCTCCATTAAGTTTGTAAC
1 GGAAAATGGCAGCTCCATTAAGTTTGTAAC
*
6335106 GGAAAATGGTAGCT
1 GGAAAATGGCAGCT
6335120 TCGTTACATC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.34, C:0.15, G:0.26, T:0.26
Consensus pattern (30 bp):
GGAAAATGGCAGCTCCATTAAGTTTGTAAC
Found at i:6335134 original size:30 final size:30
Alignment explanation
Indices: 6335046--6335145 Score: 121
Period size: 30 Copynumber: 3.3 Consensus size: 30
6335036 ATAGGGGGAT
* *
6335046 GGAAAATGGCAGCTCCATTAAGTTTGTAAC
1 GGAAAATGGTAGCTCCATTAAGTCTGTAAC
* *
6335076 GGAAAATGGCAGCTCCATTAAGTTTGTAAC
1 GGAAAATGGTAGCTCCATTAAGTCTGTAAC
* * *
6335106 GGAAAATGGTAGCTTCGTTACA-TCTGTAAT
1 GGAAAATGGTAGCTCCATTA-AGTCTGTAAC
6335136 GGAAAATGGT
1 GGAAAATGGT
6335146 TAGTAGTGAC
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
30 63 0.98
31 1 0.02
ACGTcount: A:0.33, C:0.14, G:0.25, T:0.28
Consensus pattern (30 bp):
GGAAAATGGTAGCTCCATTAAGTCTGTAAC
Found at i:6338143 original size:228 final size:228
Alignment explanation
Indices: 6337735--6338201 Score: 763
Period size: 228 Copynumber: 2.0 Consensus size: 228
6337725 ATACAAAGGA
*
6337735 TCTGAAACAACTAGAGCAAATTGATAAGATGCATAAGTGTCATCAGTATATTTCGGATTCGGCTT
1 TCTGAAACAACTAGAGCAAATTGATAAGACGCATAAGTGTCATCAGTATATTTCGGATTCGGCTT
* *
6337800 TCTGACCCTTATTGATCTTCTTAGTGAAATTGGTTCTTCAGAAGATTCTTCAAGTGTTATAGATA
66 TCTGACCCTTATTGATCTCCTTAGTGAAATTGGTTCTTCAAAAGATTCTTCAAGTGTTATAGATA
* *
6337865 TTGCTGGTGCCGACTCTTGTTTTTCATCTGAAGAATCTTTAATAGGAAAAGAAATCTCCTGTTGT
131 TTGCTGGTACCGACTCTTGTTTTTCATCTGAAGAATCTTCAATAGGAAAAGAAATCTCCTGTTGT
* *
6337930 ACCTGCTTTACAGTCATATCCCAGCTTGCATTT
196 ACCTACTCTACAGTCATATCCCAGCTTGCATTT
* *
6337963 TCTGAAACAACTAGAGCAAATTGATAGGACGCATAAGTGTCATTAGTATATTTCGGATTCGGCTT
1 TCTGAAACAACTAGAGCAAATTGATAAGACGCATAAGTGTCATCAGTATATTTCGGATTCGGCTT
* * * *
6338028 TCTGATCCTTGTTGATCTCCTTAGTGAAATTGGTTCTTTAAAAGATTCTTCAAGTGTTATAGATG
66 TCTGACCCTTATTGATCTCCTTAGTGAAATTGGTTCTTCAAAAGATTCTTCAAGTGTTATAGATA
* *
6338093 TTGCTGGTACCGACTCTTGTTTTTCATCTGGAGAATCTTCAATGGGAAAAGAAATCTCCTGTTGT
131 TTGCTGGTACCGACTCTTGTTTTTCATCTGAAGAATCTTCAATAGGAAAAGAAATCTCCTGTTGT
* *
6338158 ACCTACTCTACGGTCATATCCCATCTTGCATTT
196 ACCTACTCTACAGTCATATCCCAGCTTGCATTT
*
6338191 TCGTCAAACAA
1 TC-TGAAACAA
6338202 TATATCTCTT
Statistics
Matches: 220, Mismatches: 18, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
228 213 0.97
229 7 0.03
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (228 bp):
TCTGAAACAACTAGAGCAAATTGATAAGACGCATAAGTGTCATCAGTATATTTCGGATTCGGCTT
TCTGACCCTTATTGATCTCCTTAGTGAAATTGGTTCTTCAAAAGATTCTTCAAGTGTTATAGATA
TTGCTGGTACCGACTCTTGTTTTTCATCTGAAGAATCTTCAATAGGAAAAGAAATCTCCTGTTGT
ACCTACTCTACAGTCATATCCCAGCTTGCATTT
Found at i:6339288 original size:17 final size:17
Alignment explanation
Indices: 6339268--6339300 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
6339258 TTGAACATTG
6339268 TCCAAAATTTTTCCTTC
1 TCCAAAATTTTTCCTTC
6339285 TCCAAAATTTTTCCTT
1 TCCAAAATTTTTCCTT
6339301 TTCTATGGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.48
Consensus pattern (17 bp):
TCCAAAATTTTTCCTTC
Found at i:6340934 original size:14 final size:14
Alignment explanation
Indices: 6340910--6340951 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
6340900 AGATTTTAAC
6340910 AAATT-TTTTATTT
1 AAATTATTTTATTT
* *
6340923 ACATTATTTTATTC
1 AAATTATTTTATTT
*
6340937 AAATTATGTTATTT
1 AAATTATTTTATTT
6340951 A
1 A
6340952 TCTCTATACT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
13 4 0.17
14 19 0.83
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (14 bp):
AAATTATTTTATTT
Found at i:6352354 original size:31 final size:31
Alignment explanation
Indices: 6352302--6352392 Score: 89
Period size: 31 Copynumber: 3.0 Consensus size: 31
6352292 AAAAAATTAA
*
6352302 ATGTATACAATTGAATCAAAATCGAAA-TTTT
1 ATGTATACAATTGAAACAAAATC-AAAGTTTT
*
6352333 ATGTATAC-ATTTAAACAAAAATCAAAGTTTT
1 ATGTATACAATTGAAAC-AAAATCAAAGTTTT
* * * *
6352364 ATGTGTATAATT-ACACAAAATAAAAGTTT
1 ATGTATACAATTGAAACAAAATCAAAGTTT
6352393 ACGTATCAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
30 21 0.41
31 27 0.53
32 3 0.06
ACGTcount: A:0.47, C:0.09, G:0.09, T:0.35
Consensus pattern (31 bp):
ATGTATACAATTGAAACAAAATCAAAGTTTT
Found at i:6353549 original size:19 final size:19
Alignment explanation
Indices: 6353524--6353580 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
6353514 AATTACAAAA
6353524 AAAAATTCAAAATAATTT-T
1 AAAAATTCAAAAT-ATTTAT
*
6353543 TAAAATTCAAAATATTTAT
1 AAAAATTCAAAATATTTAT
*
6353562 AAAAATTCCAAA-ATTTAT
1 AAAAATTCAAAATATTTAT
6353580 A
1 A
6353581 TTTTTTAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 11 0.32
19 23 0.68
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:6353625 original size:35 final size:35
Alignment explanation
Indices: 6353558--6353627 Score: 95
Period size: 35 Copynumber: 2.0 Consensus size: 35
6353548 TTCAAAATAT
* ** *
6353558 TTATAAAAATTCCAAAATTTATATTTTTTAAAAAA
1 TTATAAAAATTCCAAAATATATATAATATAAAAAA
*
6353593 TTATAAAAATTCCAATATATATATAATATAAAAAA
1 TTATAAAAATTCCAAAATATATATAATATAAAAAA
6353628 GGTTAAAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (35 bp):
TTATAAAAATTCCAAAATATATATAATATAAAAAA
Found at i:6360182 original size:11 final size:12
Alignment explanation
Indices: 6360166--6360220 Score: 64
Period size: 11 Copynumber: 4.8 Consensus size: 12
6360156 AATATTTATT
6360166 TATATTAT-TAA
1 TATATTATATAA
6360177 TATATTATATAAA
1 TATATTATAT-AA
6360190 TATATTATATAA
1 TATATTATATAA
6360202 -ATATT-TA-AA
1 TATATTATATAA
*
6360211 TAAATTATAT
1 TATATTATAT
6360221 TTTGCAATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
9 2 0.05
10 6 0.16
11 15 0.39
12 3 0.08
13 12 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
TATATTATATAA
Found at i:6360191 original size:13 final size:13
Alignment explanation
Indices: 6360166--6360221 Score: 73
Period size: 13 Copynumber: 4.5 Consensus size: 13
6360156 AATATTTATT
6360166 TATATTAT-T-AA
1 TATATTATATAAA
6360177 TATATTATATAAA
1 TATATTATATAAA
6360190 TATATTATATAAA
1 TATATTATATAAA
*
6360203 TAT-TTAAATAAA
1 TATATTATATAAA
6360215 TTATATT
1 -TATATT
6360222 TTGCAATAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
11 8 0.20
12 9 0.22
13 21 0.52
14 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TATATTATATAAA
Found at i:6360210 original size:21 final size:21
Alignment explanation
Indices: 6360155--6360220 Score: 62
Period size: 21 Copynumber: 3.0 Consensus size: 21
6360145 CCTTTAAATA
**
6360155 AAATATTTATTTATATTAT-T
1 AAATATTTAAATATATTATAT
6360175 AATATATTATATAAATATATTATAT
1 AA-ATA-T-T-TAAATATATTATAT
*
6360200 AAATATTTAAATAAATTATAT
1 AAATATTTAAATATATTATAT
6360221 TTTGCAATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
20 2 0.05
21 16 0.42
22 2 0.05
23 2 0.05
24 13 0.34
25 3 0.08
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AAATATTTAAATATATTATAT
Found at i:6363301 original size:49 final size:49
Alignment explanation
Indices: 6363222--6363323 Score: 177
Period size: 49 Copynumber: 2.1 Consensus size: 49
6363212 GTTAAAGATA
*
6363222 TATACAACTACAATTGAATAAACTTCGTCCTAGGTTAAAGTGTCCTGTG
1 TATACAACTACAATTCAATAAACTTCGTCCTAGGTTAAAGTGTCCTGTG
* *
6363271 TATACAACTACAATTCAATACACTTTGTCCTAGGTTAAAGTGTCCTGTG
1 TATACAACTACAATTCAATAAACTTCGTCCTAGGTTAAAGTGTCCTGTG
6363320 TATA
1 TATA
6363324 ATATAATGGG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (49 bp):
TATACAACTACAATTCAATAAACTTCGTCCTAGGTTAAAGTGTCCTGTG
Found at i:6366720 original size:20 final size:19
Alignment explanation
Indices: 6366682--6366744 Score: 67
Period size: 20 Copynumber: 3.3 Consensus size: 19
6366672 TTTTAGTGTT
* *
6366682 AAATATAAAAT-TGTTTAA
1 AAATTTAAAATGTATTTAA
6366700 AAATTTAAAAT-TATTTTTAA
1 AAATTTAAAATGTA--TTTAA
*
6366720 AATTTTAAAATGTATTTAA
1 AAATTTAAAATGTATTTAA
6366739 AAATTT
1 AAATTT
6366745 TATTGTAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
18 11 0.29
19 10 0.26
20 15 0.39
21 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (19 bp):
AAATTTAAAATGTATTTAA
Found at i:6366745 original size:20 final size:20
Alignment explanation
Indices: 6366695--6366746 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
6366685 TATAAAATTG
6366695 TTTAAAAA-TTTAAAATTAT
1 TTTAAAAATTTTAAAATTAT
*
6366714 TTTTAAAATTTTAAAATGTA-
1 TTTAAAAATTTTAAAAT-TAT
6366734 TTTAAAAATTTTA
1 TTTAAAAATTTTA
6366747 TTGTAAAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 7 0.24
20 20 0.69
21 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
TTTAAAAATTTTAAAATTAT
Found at i:6367342 original size:59 final size:57
Alignment explanation
Indices: 6367230--6367346 Score: 155
Period size: 59 Copynumber: 2.0 Consensus size: 57
6367220 GATAATTAAC
**
6367230 ACGTAATATTTCAAATATAAGTGACTAAAATATTGTAACGTGATAACGTAAGTGACTAA
1 ACGTAATATTTCAAATATAAGTGACTAAAATA-T-TAACGTGATAACAAAAGTGACTAA
*
6367289 ACGTAATATTTCAAATATAAGTGACTAAAATA-TAACTTGAGGTAAACAAAAGTGACTA
1 ACGTAATATTTCAAATATAAGTGACTAAAATATTAACGTGA--T-AACAAAAGTGACTA
6367347 TTTTAACAGT
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
56 7 0.13
58 1 0.02
59 44 0.85
ACGTcount: A:0.46, C:0.10, G:0.15, T:0.29
Consensus pattern (57 bp):
ACGTAATATTTCAAATATAAGTGACTAAAATATTAACGTGATAACAAAAGTGACTAA
Found at i:6368293 original size:30 final size:30
Alignment explanation
Indices: 6368259--6368317 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 30
6368249 TATTTTATTG
* *
6368259 TTAATTTTGTTATTATTTTAGAGACATTTC
1 TTAATTTTGTTACTATTTTAGAAACATTTC
6368289 TTAATTTTGTTACTATTTTAGAAACATTT
1 TTAATTTTGTTACTATTTTAGAAACATTT
6368318 ATTTGTTAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.29, C:0.07, G:0.08, T:0.56
Consensus pattern (30 bp):
TTAATTTTGTTACTATTTTAGAAACATTTC
Found at i:6368391 original size:25 final size:24
Alignment explanation
Indices: 6368359--6368409 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
6368349 ATATATTTTT
6368359 TAAAATTTATTTTCAAT-TTATTAG
1 TAAAATTTATTTT-AATGTTATTAG
*
6368383 TAAATATTTATTTTAATGTTTTTAG
1 TAAA-ATTTATTTTAATGTTATTAG
6368408 TA
1 TA
6368410 TTTTTAATGC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.57
Consensus pattern (24 bp):
TAAAATTTATTTTAATGTTATTAG
Found at i:6368461 original size:25 final size:25
Alignment explanation
Indices: 6368432--6368488 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
6368422 TATATATATA
*
6368432 TATATATATATATATATTT-AAAAAT
1 TATATATAAATA-ATATTTAAAAAAT
*
6368457 TATATAAAAATAATATTTAAAAAAT
1 TATATATAAATAATATTTAAAAAAT
6368482 TA-ATATA
1 TATATATA
6368489 GGCGGGTCGG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 10 0.36
25 18 0.64
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
TATATATAAATAATATTTAAAAAAT
Found at i:6368462 original size:2 final size:2
Alignment explanation
Indices: 6368422--6368448 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6368412 TTTAATGCAT
6368422 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
6368449 TTAAAAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6376845 original size:45 final size:44
Alignment explanation
Indices: 6376794--6376983 Score: 191
Period size: 45 Copynumber: 4.2 Consensus size: 44
6376784 AGAGCTATAC
* *
6376794 TCTTCCAAAATAGTATCATTTTCTGATGCAGGATCAATCCTCTTT
1 TCTTCCAAAAGAGTATCATTTT-TGATGCAAGATCAATCCTCTTT
* *
6376839 TCTTCCAAAAGAGTATCATTATTTGATGTAAGATCAATTCTCTTT
1 TCTTCCAAAAGAGTATCATT-TTTGATGCAAGATCAATCCTCTTT
* ** *
6376884 TCTTCCAAAAGAGTATCGTCAATGGATGCAAGATCAATCCTCTTT
1 TCTTCCAAAAGAGTATCAT-TTTTGATGCAAGATCAATCCTCTTT
* * ** * * * *
6376929 TCATCCAAAATAGTATCAGTTTCAGATGTAAGATCAAACTTGTTT
1 TCTTCCAAAAGAGTATCA-TTTTTGATGCAAGATCAATCCTCTTT
*
6376974 CCTTCCAAAA
1 TCTTCCAAAA
6376984 CAACCTGATC
Statistics
Matches: 119, Mismatches: 23, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
45 116 0.97
46 3 0.03
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (44 bp):
TCTTCCAAAAGAGTATCATTTTTGATGCAAGATCAATCCTCTTT
Found at i:6376979 original size:90 final size:90
Alignment explanation
Indices: 6376818--6376983 Score: 230
Period size: 90 Copynumber: 1.8 Consensus size: 90
6376808 ATCATTTTCT
* * ** *
6376818 GATGCAGGATCAATCCTCTTTTCTTCCAAAAGAGTATCATTATTTGATGTAAGATCAATTCTCTT
1 GATGCAAGATCAATCCTCTTTTCATCCAAAAGAGTATCATTATCAGATGTAAGATCAATACTCTT
6376883 TTCTTCCAAAAGAGTATCGTCAATG
66 TTCTTCCAAAAGAGTATCGTCAATG
*
6376908 GATGCAAGATCAATCCTCTTTTCATCCAAAATAGTATCAGTT-TCAGATGTAAGATCAA-ACT-T
1 GATGCAAGATCAATCCTCTTTTCATCCAAAAGAGTATCA-TTATCAGATGTAAGATCAATACTCT
6376970 GTTTCCTTCCAAAA
65 -TTT-CTTCCAAAA
6376984 CAACCTGATC
Statistics
Matches: 67, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
88 1 0.01
89 5 0.07
90 59 0.88
91 2 0.03
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (90 bp):
GATGCAAGATCAATCCTCTTTTCATCCAAAAGAGTATCATTATCAGATGTAAGATCAATACTCTT
TTCTTCCAAAAGAGTATCGTCAATG
Found at i:6382574 original size:31 final size:31
Alignment explanation
Indices: 6382539--6382616 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 31
6382529 TAATTTTATT
6382539 ATTTTAATAATTTTAAAAGA-TTAAAATCAAA
1 ATTTTAATAATTTTAAAAGAGTTAAAAT-AAA
* * * *
6382570 ATTTTATTATTTTTAAGAGAGTTAAAATATA
1 ATTTTAATAATTTTAAAAGAGTTAAAATAAA
6382601 ATTTT-ATAATTATTAA
1 ATTTTAATAATT-TTAA
6382617 TTTAAAATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
30 4 0.10
31 28 0.72
32 7 0.18
ACGTcount: A:0.47, C:0.01, G:0.05, T:0.46
Consensus pattern (31 bp):
ATTTTAATAATTTTAAAAGAGTTAAAATAAA
Found at i:6382616 original size:22 final size:23
Alignment explanation
Indices: 6382591--6382636 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
6382581 TTTAAGAGAG
*
6382591 TTAAAATATAATTTTAT-AATTA
1 TTAAAATAAAATTTTATAAATTA
**
6382613 TTAATTTAAAATTTTATAAATTA
1 TTAAAATAAAATTTTATAAATTA
6382636 T
1 T
6382637 AAATGATCGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TTAAAATAAAATTTTATAAATTA
Found at i:6386220 original size:3 final size:3
Alignment explanation
Indices: 6386214--6386272 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
6386204 GAGGAGGAGG
6386214 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
6386262 AGA AGA AGA AG
1 AGA AGA AGA AG
6386273 CAGCAGCTTT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:6386645 original size:4 final size:4
Alignment explanation
Indices: 6386636--6386708 Score: 101
Period size: 4 Copynumber: 18.2 Consensus size: 4
6386626 TAAATATTCC
* *
6386636 TGTA TGTA TGTC TGTA TGTC TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
* * *
6386684 AGTA AGTA AGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA T
6386709 AATGGTGGCC
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
4 63 1.00
ACGTcount: A:0.26, C:0.03, G:0.25, T:0.47
Consensus pattern (4 bp):
TGTA
Found at i:6393121 original size:20 final size:20
Alignment explanation
Indices: 6393093--6393145 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
6393083 TCTAAATAAT
*
6393093 AAAAGAAAATATTAATTAAG
1 AAAATAAAATATTAATTAAG
* * *
6393113 AAAATAAAAGATTATTTACG
1 AAAATAAAATATTAATTAAG
*
6393133 AAAATAATATATT
1 AAAATAAAATATT
6393146 TTCTATGTTA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.30
Consensus pattern (20 bp):
AAAATAAAATATTAATTAAG
Found at i:6393746 original size:19 final size:18
Alignment explanation
Indices: 6393715--6393750 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
6393705 CCCTTTTAAA
6393715 ATTAAAATATTTTTATTAC
1 ATTAAAA-ATTTTTATTAC
*
6393734 ATTAATAATTTTTATTA
1 ATTAAAAATTTTTATTA
6393751 AAATATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTAAAAATTTTTATTAC
Found at i:6393760 original size:14 final size:14
Alignment explanation
Indices: 6393715--6393760 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 14
6393705 CCCTTTTAAA
6393715 ATTAAAATATTTTT
1 ATTAAAATATTTTT
6393729 ATTACATTAATAATTTTT
1 ATTA-A--AAT-ATTTTT
6393747 ATTAAAATATTTTT
1 ATTAAAATATTTTT
6393761 TTTTATAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
14 10 0.36
15 4 0.14
17 4 0.14
18 10 0.36
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTAAAATATTTTT
Found at i:6394113 original size:24 final size:24
Alignment explanation
Indices: 6394065--6394115 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 24
6394055 TTATAAAATA
* *
6394065 TTATATATTTTTATTATTTTAATT
1 TTATATATTTTTATAAATTTAATT
*
6394089 TTATATAATTTTTATAAATTTATTT
1 TTATAT-ATTTTTATAAATTTAATT
6394114 TT
1 TT
6394116 TCCTGCTAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 6 0.26
25 17 0.74
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (24 bp):
TTATATATTTTTATAAATTTAATT
Found at i:6396514 original size:30 final size:30
Alignment explanation
Indices: 6396446--6396514 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 30
6396436 AAAGGCTCAT
*
6396446 TTTCAAA--ATTACTTATGGAAATGAATCA
1 TTTCAAATGATTACTTACGGAAATGAATCA
* * *
6396474 TTTCAGATGATTATTTACGGAAATGAATCG
1 TTTCAAATGATTACTTACGGAAATGAATCA
*
6396504 TTTTAAATGAT
1 TTTCAAATGAT
6396515 AAAATTAATA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
28 6 0.18
30 27 0.82
ACGTcount: A:0.38, C:0.09, G:0.14, T:0.39
Consensus pattern (30 bp):
TTTCAAATGATTACTTACGGAAATGAATCA
Found at i:6398452 original size:16 final size:16
Alignment explanation
Indices: 6398433--6398485 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
6398423 GGTCAAAGTG
6398433 ATTTTTTATTGTTATT
1 ATTTTTTATTGTTATT
* * *
6398449 ATTTTTTTTTGGTGGATA
1 ATTTTTTATT-GT-TATT
*
6398467 ATTTCTTATTGTTATT
1 ATTTTTTATTGTTATT
6398483 ATT
1 ATT
6398486 GAATCTGGAG
Statistics
Matches: 28, Mismatches: 7, Indels: 4
0.72 0.18 0.10
Matches are distributed among these distances:
16 14 0.50
17 4 0.14
18 10 0.36
ACGTcount: A:0.19, C:0.02, G:0.11, T:0.68
Consensus pattern (16 bp):
ATTTTTTATTGTTATT
Found at i:6399710 original size:6 final size:6
Alignment explanation
Indices: 6399699--6399725 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
6399689 AGAGGAAAAA
6399699 GCAATG GCAATG GCAATG GCAATG GCA
1 GCAATG GCAATG GCAATG GCAATG GCA
6399726 GTGACGATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.19, G:0.33, T:0.15
Consensus pattern (6 bp):
GCAATG
Found at i:6403581 original size:31 final size:31
Alignment explanation
Indices: 6403540--6403602 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
6403530 AGTCCGAGGA
6403540 ACATAAGAATTTTCTATTCTTACTCGAGTCT
1 ACATAAGAATTTTCTATTCTTACTCGAGTCT
* *
6403571 ACATAGGAATTTTCTATTCTTACTTGAGTCT
1 ACATAAGAATTTTCTATTCTTACTCGAGTCT
6403602 A
1 A
6403603 TAGAAGTGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.29, C:0.17, G:0.11, T:0.43
Consensus pattern (31 bp):
ACATAAGAATTTTCTATTCTTACTCGAGTCT
Found at i:6406598 original size:28 final size:28
Alignment explanation
Indices: 6406558--6406616 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 28
6406548 GTTAGTTTTT
* *
6406558 ATTGAATAAAAACTCCCATTTTATTGGG
1 ATTGAATAAAAACCCCCATTCTATTGGG
6406586 ATTGAATAAAAACCCCCATTCTATTGGG
1 ATTGAATAAAAACCCCCATTCTATTGGG
6406614 ATT
1 ATT
6406617 CATGATTGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.34
Consensus pattern (28 bp):
ATTGAATAAAAACCCCCATTCTATTGGG
Found at i:6411617 original size:23 final size:23
Alignment explanation
Indices: 6411560--6411605 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
6411550 CTGAAGTGGC
*
6411560 ATCCAATCAGCAGCTTCTAGAAG
1 ATCCAATCAGCAGCTTCCAGAAG
*
6411583 ATCCAATTAGCAGCTTCCAGAAG
1 ATCCAATCAGCAGCTTCCAGAAG
6411606 GTCTAGTCAG
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:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (23 bp):
ATCCAATCAGCAGCTTCCAGAAG
Found at i:6424520 original size:137 final size:137
Alignment explanation
Indices: 6424074--6424618 Score: 804
Period size: 137 Copynumber: 4.0 Consensus size: 137
6424064 TCATAGATAA
* * *
6424074 AATTAATATATGAATTTAATTCATACAAAATATTAATTGTATATATTTTATCTAATTTATTAATA
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCTAAATTATTAATA
* * * *
6424139 TAAATAATTATATTAATTAATTTCAATCAAAATAT------ATGGAAATTAATATTCTTTTGGAA
66 TAAATAATTATATTAATTAATTTCGACCAAAATATAAAAAAATGAAAATTAATATTCTTTCGGAA
*
6424198 AAAATAT
131 AGAATAT
*
6424205 AATTAATATATGAATTTGATTCATTCAAAATATTAATTGTATATATTTTACC-AAATTTATTAAT
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCTAAA-TTATTAAT
* * *
6424269 ATAAATAGTTATATTAATTAATTTCGATCAAAATATAAAATACATGAAAATTAATATT-TTT-GG
65 ATAAATAATTATATTAATTAATTTCGACCAAAATATAAAA-AAATGAAAATTAATATTCTTTCGG
6424332 AAA-AATAT
129 AAAGAATAT
* *
6424340 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATATTACCGAAATTATTAATA
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCTAAATTATTAATA
* *
6424405 TAAATAATTATATTAATTAATTTTGACCAAAATATAAAAAAATGGAAATTAATATTCTTTCGGAA
66 TAAATAATTATATTAATTAATTTCGACCAAAATATAAAAAAATGAAAATTAATATTCTTTCGGAA
6424470 AGAATAT
131 AGAATAT
* *
6424477 AATTAATATATGAATTTGATTTATACAAAATATTAATTGTATATATTTTACCTAATTTATTAATA
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCTAAATTATTAATA
* * *
6424542 TAAACAGTTATATTAATTAATTTCGACCAAAATATAAAAAATATGAAAATTAATGTTCTTTCGGA
66 TAAATAATTATATTAATTAATTTCGACCAAAATATAAAAAA-ATGAAAATTAATATTCTTTCGGA
6424607 AAGAATAT
130 AAGAATAT
6424615 AATT
1 AATT
6424619 CATTTTTCTA
Statistics
Matches: 378, Mismatches: 23, Indels: 19
0.90 0.05 0.05
Matches are distributed among these distances:
130 2 0.01
131 91 0.24
134 15 0.04
135 103 0.27
136 13 0.03
137 107 0.28
138 47 0.12
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (137 bp):
AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCTAAATTATTAATA
TAAATAATTATATTAATTAATTTCGACCAAAATATAAAAAAATGAAAATTAATATTCTTTCGGAA
AGAATAT
Found at i:6424554 original size:272 final size:269
Alignment explanation
Indices: 6424074--6424618 Score: 853
Period size: 272 Copynumber: 2.0 Consensus size: 269
6424064 TCATAGATAA
* * * *
6424074 AATTAATATATGAATTTAATTCATACAAAATATTAATTGTATATATTTTATCTAATTTATTAATA
1 AATTAATATATGAATTTAATTCATACAAAATATTAATTGTATATATATTACCGAAATTATTAATA
* *
6424139 TAAATAATTATATTAATTAATTTCAATCAAAATATATGGAAATTAATATTCTTTTGGAAAAAATA
66 TAAATAATTATATTAATTAATTTCAACCAAAATATATGGAAATTAATATTCTTTCGGAAAAAATA
*
6424204 TAATTAATATATGAATTTGATTCATTCAAAATATTAATTGTATATATTTTACCAAATTTATTAAT
131 TAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTATTAAT
* * *
6424269 ATAAATAGTTATATTAATTAATTTCGATCAAAATATAAAATACATGAAAATTAATATT-TTT-GG
196 ATAAACAGTTATATTAATTAATTTCGACCAAAATATAAAAAACATGAAAATTAATATTCTTTCGG
6424332 AAA-AATAT
261 AAAGAATAT
*
6424340 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATATTACCGAAATTATTAATA
1 AATTAATATATGAATTTAATTCATACAAAATATTAATTGTATATATATTACCGAAATTATTAATA
**
6424405 TAAATAATTATATTAATTAATTTTGACCAAAATATAAAAAAATGGAAATTAATATTCTTTCGGAA
66 TAAATAATTATATTAATTAATTTCAACCAAAATAT------ATGGAAATTAATATTCTTTCGGAA
* * *
6424470 AGAATATAATTAATATATGAATTTGATTTATACAAAATATTAATTGTATATATTTTACCTAATTT
125 AAAATATAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTT
* *
6424535 ATTAATATAAACAGTTATATTAATTAATTTCGACCAAAATATAAAAAATATGAAAATTAATGTTC
190 ATTAATATAAACAGTTATATTAATTAATTTCGACCAAAATATAAAAAACATGAAAATTAATATTC
6424600 TTTCGGAAAGAATAT
255 TTTCGGAAAGAATAT
6424615 AATT
1 AATT
6424619 CATTTTTCTA
Statistics
Matches: 252, Mismatches: 18, Indels: 9
0.90 0.06 0.03
Matches are distributed among these distances:
266 92 0.37
272 143 0.57
273 3 0.01
274 5 0.02
275 9 0.04
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (269 bp):
AATTAATATATGAATTTAATTCATACAAAATATTAATTGTATATATATTACCGAAATTATTAATA
TAAATAATTATATTAATTAATTTCAACCAAAATATATGGAAATTAATATTCTTTCGGAAAAAATA
TAATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACCAAATTTATTAAT
ATAAACAGTTATATTAATTAATTTCGACCAAAATATAAAAAACATGAAAATTAATATTCTTTCGG
AAAGAATAT
Found at i:6424676 original size:60 final size:60
Alignment explanation
Indices: 6424606--6424723 Score: 193
Period size: 60 Copynumber: 2.0 Consensus size: 60
6424596 GTTCTTTCGG
*
6424606 AAAGAATATAATTCATTTTTCTAACTTTCCATTTATC-TTCTCTATTAATAAGGGAATATA
1 AAAGAATATAATTCATTTTTCTAACTTTCCATTT-GCATTCTCTATTAATAAGGGAATATA
* *
6424666 AAAGAATATAATTTATTTTTCTAATTTTCCATTTGCATTCTCTATTAATAAGGGAATA
1 AAAGAATATAATTCATTTTTCTAACTTTCCATTTGCATTCTCTATTAATAAGGGAATA
6424724 ATCTTGATTT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
59 1 0.02
60 53 0.98
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (60 bp):
AAAGAATATAATTCATTTTTCTAACTTTCCATTTGCATTCTCTATTAATAAGGGAATATA
Found at i:6428148 original size:17 final size:18
Alignment explanation
Indices: 6428126--6428160 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
6428116 TTTATTAAAA
6428126 TAAATTAATTTTC-CAAT
1 TAAATTAATTTTCTCAAT
6428143 TAAATTAATTTTCTCAAT
1 TAAATTAATTTTCTCAAT
6428161 CTAATTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (18 bp):
TAAATTAATTTTCTCAAT
Found at i:6436121 original size:2 final size:2
Alignment explanation
Indices: 6436114--6436151 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
6436104 TAAAATTTTA
6436114 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
6436152 TCTAATATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6440512 original size:17 final size:17
Alignment explanation
Indices: 6440468--6440503 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
6440458 GTACCATTAT
6440468 TTAAAA-AA-TAACTAA
1 TTAAAATAATTAACTAA
6440483 TTAAAATAATTAACTAA
1 TTAAAATAATTAACTAA
6440500 TTAA
1 TTAA
6440504 GATGCTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.32
16 2 0.11
17 11 0.58
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (17 bp):
TTAAAATAATTAACTAA
Found at i:6447264 original size:57 final size:58
Alignment explanation
Indices: 6447164--6447284 Score: 158
Period size: 57 Copynumber: 2.1 Consensus size: 58
6447154 TAAATGAACT
*
6447164 CATTTCCATTTTCATTTTGGAGAAAATCACATTAATTTCCAAATG-ATTTCATTTCTC
1 CATTTCCATTTTCATTTTGGAGAAAATCACATTAATTTACAAATGTATTTCATTTCTC
* * * *
6447221 CATTTTCATTTTCATTTTGGAGAAAACCTTA-ATT-ATTTACAAATGTTTTTTATTTCTC
1 CATTTCCATTTTCATTTTGGAGAAAA--TCACATTAATTTACAAATGTATTTCATTTCTC
6447279 CATTTC
1 CATTTC
6447285 ACCATTTCTG
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
57 35 0.64
58 18 0.33
59 2 0.04
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.48
Consensus pattern (58 bp):
CATTTCCATTTTCATTTTGGAGAAAATCACATTAATTTACAAATGTATTTCATTTCTC
Found at i:6447863 original size:21 final size:21
Alignment explanation
Indices: 6447837--6447884 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
6447827 TTAACTATCT
6447837 AGACTTGTATGTCAAGTCTCG
1 AGACTTGTATGTCAAGTCTCG
* *
6447858 AGACTTGTCTTTCAAGTCTCG
1 AGACTTGTATGTCAAGTCTCG
6447879 AGACTT
1 AGACTT
6447885 ACTCCATTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (21 bp):
AGACTTGTATGTCAAGTCTCG
Found at i:6450683 original size:2 final size:2
Alignment explanation
Indices: 6450676--6450701 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6450666 AAGGGATATT
6450676 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
6450702 TTACAAGTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6451558 original size:20 final size:20
Alignment explanation
Indices: 6451541--6451578 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
6451531 TCAAGTTATT
6451541 TTTTAGTCACTTATGTTACG
1 TTTTAGTCACTTATGTTACG
*
6451561 TTTTAGTTACTTATGTTA
1 TTTTAGTCACTTATGTTA
6451579 ATATGTTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.11, G:0.13, T:0.55
Consensus pattern (20 bp):
TTTTAGTCACTTATGTTACG
Found at i:6451974 original size:47 final size:47
Alignment explanation
Indices: 6451905--6452002 Score: 151
Period size: 47 Copynumber: 2.1 Consensus size: 47
6451895 ACACGTCAGT
* *
6451905 TTACCATTATACCGTTAACGGCAATTAATAACTCAATGACTAAAATG
1 TTACCATTACACCGTTAACGGCAATTAACAACTCAATGACTAAAATG
* **
6451952 TTACCATTACACCGTTAACGGCAATTAACGACTCGGTGACTAAAATG
1 TTACCATTACACCGTTAACGGCAATTAACAACTCAATGACTAAAATG
6451999 TTAC
1 TTAC
6452003 AATATGTTAA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.29
Consensus pattern (47 bp):
TTACCATTACACCGTTAACGGCAATTAACAACTCAATGACTAAAATG
Found at i:6453840 original size:35 final size:34
Alignment explanation
Indices: 6453803--6453869 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
6453793 CAAGATTTTT
*
6453803 AAATAAAAAGTATAAAAATTTAATGTCTCAAAATTA
1 AAATAAAAAG-AAAAAAATTTAAT-TCTCAAAATTA
* *
6453839 AAATATAAAGAAAAAAATTTAATTTTCAAAA
1 AAATAAAAAGAAAAAAATTTAATTCTCAAAA
6453870 AAAGATAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 7 0.25
35 12 0.43
36 9 0.32
ACGTcount: A:0.61, C:0.04, G:0.04, T:0.30
Consensus pattern (34 bp):
AAATAAAAAGAAAAAAATTTAATTCTCAAAATTA
Found at i:6454922 original size:28 final size:26
Alignment explanation
Indices: 6454881--6454935 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 26
6454871 ATTAATTTTT
*
6454881 ATTAAGTAATAATTCCTTAATTTATAGA
1 ATTAAGTAATAATT--TGAATTTATAGA
6454909 ATTAAGTAGA-AATTTGAATTTATAGA
1 ATTAAGTA-ATAATTTGAATTTATAGA
6454935 A
1 A
6454936 AAATTTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 12 0.48
28 12 0.48
29 1 0.04
ACGTcount: A:0.45, C:0.04, G:0.11, T:0.40
Consensus pattern (26 bp):
ATTAAGTAATAATTTGAATTTATAGA
Found at i:6455276 original size:21 final size:20
Alignment explanation
Indices: 6455250--6455298 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
6455240 TGAACAAAAA
6455250 AAATATAAAAAATTTGTAAAT
1 AAATATAAAAAATTT-TAAAT
* * **
6455271 AAATATTAATAATTTTATTT
1 AAATATAAAAAATTTTAAAT
6455291 AAATATAA
1 AAATATAA
6455299 TTAAACAATA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (20 bp):
AAATATAAAAAATTTTAAAT
Found at i:6455400 original size:21 final size:23
Alignment explanation
Indices: 6455368--6455417 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
6455358 GTGTTTAATG
6455368 GTTTAGAATCTAG-G-CTCTCGA
1 GTTTAGAATCTAGTGTCTCTCGA
*
6455389 GTTTA-AAGTCTAGTGTCTCTCGG
1 GTTTAGAA-TCTAGTGTCTCTCGA
6455412 GTTTAG
1 GTTTAG
6455418 GTTTCAAGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
20 2 0.08
21 10 0.42
22 1 0.04
23 11 0.46
ACGTcount: A:0.20, C:0.16, G:0.26, T:0.38
Consensus pattern (23 bp):
GTTTAGAATCTAGTGTCTCTCGA
Found at i:6457492 original size:17 final size:16
Alignment explanation
Indices: 6457472--6457507 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
6457462 TTTTAATGAT
*
6457472 TATTTGAATTATTACAA
1 TATTTGAATAATTA-AA
6457489 TATTTGAATAATTAAA
1 TATTTGAATAATTAAA
6457505 TAT
1 TAT
6457508 AGTATAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.28
17 13 0.72
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (16 bp):
TATTTGAATAATTAAA
Found at i:6457616 original size:17 final size:17
Alignment explanation
Indices: 6457594--6457641 Score: 78
Period size: 17 Copynumber: 2.8 Consensus size: 17
6457584 GATGTTTGAA
*
6457594 CATGAGTTTAAATAAAG
1 CATGAGTTCAAATAAAG
6457611 CATGAGTTCAAATAAAG
1 CATGAGTTCAAATAAAG
*
6457628 CATAAGTTCAAATA
1 CATGAGTTCAAATA
6457642 GAACATAGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.48, C:0.10, G:0.15, T:0.27
Consensus pattern (17 bp):
CATGAGTTCAAATAAAG
Found at i:6458970 original size:24 final size:24
Alignment explanation
Indices: 6458942--6458987 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
6458932 TACGCTGAGC
6458942 GATAAAGCTCAGTGGTACTTTCAT
1 GATAAAGCTCAGTGGTACTTTCAT
*
6458966 GATAAAGCTCAGTGGTATTTTC
1 GATAAAGCTCAGTGGTACTTTC
6458988 TTGGTTCAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.35
Consensus pattern (24 bp):
GATAAAGCTCAGTGGTACTTTCAT
Found at i:6465698 original size:156 final size:156
Alignment explanation
Indices: 6465414--6465727 Score: 565
Period size: 156 Copynumber: 2.0 Consensus size: 156
6465404 TGAACAGATG
*
6465414 CAGCAGAGGGAGTTTTATCCTCAGCTAGATGTGTTTCTACCTGCTCTTCAGAAATACTTCTGATT
1 CAGCAGAGGGAGTTTTATCCTCAGCTAGAGGTGTTTCTACCTGCTCTTCAGAAATACTTCTGATT
* *
6465479 TCTTCCTCCTGAACTGATGCAGCAACCGATGTTTCATCCTCAGCTAGGGGAGCTTCCTCTTGTAC
66 TCTTCCTCCTGAACTGATGCAGCAACCGATGTTTCATCCTCAGCTAGGGCAACTTCCTCTTGTAC
*
6465544 TACACCTTTTTGTGTAGACTCTTCAT
131 TACACCTTTTTGTCTAGACTCTTCAT
* *
6465570 CAGCAGAGGGAGTTTTATCCTCAGCTAGAGGTGTTTCTACCTGCTCTTCGGGAATACTTCTGATT
1 CAGCAGAGGGAGTTTTATCCTCAGCTAGAGGTGTTTCTACCTGCTCTTCAGAAATACTTCTGATT
6465635 TCTTCCTCCTGAACTGATGCAGCAACCGATGTTTCATCCTCAGCTAGGGCAACTTCCTCTTGTAC
66 TCTTCCTCCTGAACTGATGCAGCAACCGATGTTTCATCCTCAGCTAGGGCAACTTCCTCTTGTAC
*
6465700 TACATCTTTTTGTCTAGACTCTTCAT
131 TACACCTTTTTGTCTAGACTCTTCAT
6465726 CA
1 CA
6465728 ACTGAATTTT
Statistics
Matches: 151, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
156 151 1.00
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.35
Consensus pattern (156 bp):
CAGCAGAGGGAGTTTTATCCTCAGCTAGAGGTGTTTCTACCTGCTCTTCAGAAATACTTCTGATT
TCTTCCTCCTGAACTGATGCAGCAACCGATGTTTCATCCTCAGCTAGGGCAACTTCCTCTTGTAC
TACACCTTTTTGTCTAGACTCTTCAT
Found at i:6465840 original size:231 final size:231
Alignment explanation
Indices: 6465570--6466014 Score: 827
Period size: 231 Copynumber: 1.9 Consensus size: 231
6465560 GACTCTTCAT
* *
6465570 CAGCAGAGGGAGTTTTATCCTCAGCTAGAGGTGTTTCTACCTGCTCTTCGGGAATACTTCTGATT
1 CAGCAGAGGGAGTTTTATCCTCAGCTAGAGGTGTTTCTACCTGCTCTTCAGGAATACTTCCGATT
*
6465635 TCTTCCTCCTGAACTGATGCAGCAACCGATGTTTCATCCTCAGCTAGGGCAACTTCCTCTTGTAC
66 TCTTCCTCCTGAACTGATGCAGCAACCGATGTTTCATCCACAGCTAGGGCAACTTCCTCTTGTAC
*
6465700 TACATCTTTTTGTCTAGACTCTTCATCAACTGAATTTTTGGAAGTCACTTGGTCAACTACTTCTC
131 TACATCTTTTTGTCTAGACTCTTCATCAACTGAATTTTCGGAAGTCACTTGGTCAACTACTTCTC
6465765 CAGATGATCCAGCTATTTCTTCTTCTTCAACAGATC
196 CAGATGATCCAGCTATTTCTTCTTCTTCAACAGATC
6465801 CAGCAGAGGGAGTTTTATCCTCAGCTAGAGGTGTTTCTACCTGCTCTTCAGGAATACTTCCGATT
1 CAGCAGAGGGAGTTTTATCCTCAGCTAGAGGTGTTTCTACCTGCTCTTCAGGAATACTTCCGATT
* *
6465866 TCTTCCTCCTGAACTGATGCAGCAACCGATGTTTCATCCACAGCTAGGGGAGCTTCCTCTTGTAC
66 TCTTCCTCCTGAACTGATGCAGCAACCGATGTTTCATCCACAGCTAGGGCAACTTCCTCTTGTAC
*
6465931 TACATCTTTTTGTGTAGACTCTTCATCAACTGAATTTTCGGAAGTCACTTGGTCAACTACTTCTC
131 TACATCTTTTTGTCTAGACTCTTCATCAACTGAATTTTCGGAAGTCACTTGGTCAACTACTTCTC
6465996 CAGATGATCCAGCTATTTC
196 CAGATGATCCAGCTATTTC
6466015 ATCACTTCCC
Statistics
Matches: 207, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
231 207 1.00
ACGTcount: A:0.22, C:0.26, G:0.18, T:0.35
Consensus pattern (231 bp):
CAGCAGAGGGAGTTTTATCCTCAGCTAGAGGTGTTTCTACCTGCTCTTCAGGAATACTTCCGATT
TCTTCCTCCTGAACTGATGCAGCAACCGATGTTTCATCCACAGCTAGGGCAACTTCCTCTTGTAC
TACATCTTTTTGTCTAGACTCTTCATCAACTGAATTTTCGGAAGTCACTTGGTCAACTACTTCTC
CAGATGATCCAGCTATTTCTTCTTCTTCAACAGATC
Found at i:6468877 original size:2 final size:2
Alignment explanation
Indices: 6468870--6468894 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6468860 AGTCTTAAGC
6468870 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
6468895 GGATATAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6469516 original size:12 final size:12
Alignment explanation
Indices: 6469499--6469527 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
6469489 CTTTACTAAC
6469499 TTGATATATATA
1 TTGATATATATA
6469511 TTGATATATATA
1 TTGATATATATA
6469523 TTGAT
1 TTGAT
6469528 CGTCACATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.52
Consensus pattern (12 bp):
TTGATATATATA
Found at i:6472506 original size:41 final size:41
Alignment explanation
Indices: 6472449--6472533 Score: 170
Period size: 41 Copynumber: 2.1 Consensus size: 41
6472439 GATTGCAAGA
6472449 AGAGAAGACAGTTTCATTAAAGGTCACGTGGCGTGAAATAT
1 AGAGAAGACAGTTTCATTAAAGGTCACGTGGCGTGAAATAT
6472490 AGAGAAGACAGTTTCATTAAAGGTCACGTGGCGTGAAATAT
1 AGAGAAGACAGTTTCATTAAAGGTCACGTGGCGTGAAATAT
6472531 AGA
1 AGA
6472534 CTCTTTCATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.38, C:0.12, G:0.27, T:0.24
Consensus pattern (41 bp):
AGAGAAGACAGTTTCATTAAAGGTCACGTGGCGTGAAATAT
Found at i:6474299 original size:23 final size:22
Alignment explanation
Indices: 6474236--6474314 Score: 113
Period size: 22 Copynumber: 3.5 Consensus size: 22
6474226 TTCGCACTTC
* *
6474236 GTGTGTCTACTGATTGCACTAT
1 GTGTGCCTACTGATTGCACTGT
*
6474258 GTGCGCCTACTGATTGCACTGT
1 GTGTGCCTACTGATTGCACTGT
6474280 GTGTGCCTACTGGATTGCACTGT
1 GTGTGCCTACT-GATTGCACTGT
*
6474303 GTGTGCTTACTG
1 GTGTGCCTACTG
6474315 TTTCCCCAGC
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
22 30 0.59
23 21 0.41
ACGTcount: A:0.14, C:0.22, G:0.28, T:0.37
Consensus pattern (22 bp):
GTGTGCCTACTGATTGCACTGT
Found at i:6478782 original size:26 final size:26
Alignment explanation
Indices: 6478750--6478799 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
6478740 AAGATAAATC
*
6478750 TTTATGATAATTA-AATAATATTTAGA
1 TTTATGATAAATATAAT-ATATTTAGA
6478776 TTTATGATAAATATAATATATTTA
1 TTTATGATAAATATAATATATTTA
6478800 TATATTATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 19 0.86
27 3 0.14
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (26 bp):
TTTATGATAAATATAATATATTTAGA
Found at i:6479447 original size:61 final size:59
Alignment explanation
Indices: 6479351--6479478 Score: 161
Period size: 61 Copynumber: 2.1 Consensus size: 59
6479341 TAAATTTAGA
*
6479351 TATCAAATTGGATCTAAAAAAGCTTAGGTACCAAATTAGGAAAAAAAA-ATGCCAAGTTCAAG
1 TATCAAATTGGATCTAAAAAAGCTTAAGTACCAAATTA--AAAAAAAATAT--CAAGTTCAAG
* * *
6479413 TATCAAATTGGGTC-AAAAAAGTTTAAGTACCAAATTAAAAAAAAATATCAAGTTCAGG
1 TATCAAATTGGATCTAAAAAAGCTTAAGTACCAAATTAAAAAAAAATATCAAGTTCAAG
*
6479471 TACCAAAT
1 TATCAAAT
6479479 ATTATATTAA
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
58 16 0.27
59 8 0.13
60 2 0.03
61 21 0.35
62 13 0.22
ACGTcount: A:0.49, C:0.12, G:0.14, T:0.24
Consensus pattern (59 bp):
TATCAAATTGGATCTAAAAAAGCTTAAGTACCAAATTAAAAAAAAATATCAAGTTCAAG
Found at i:6484935 original size:32 final size:31
Alignment explanation
Indices: 6484886--6484950 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 31
6484876 TCATATCATC
* *
6484886 AAAAATAATATTGAGTTGTAAAATTTAATTAA
1 AAAAATAAAATTGAGTTGCAAAATTTAA-TAA
6484918 AAAAATCAAAATT-AGTTGCAAAATTTAATAA
1 AAAAAT-AAAATTGAGTTGCAAAATTTAATAA
6484949 AA
1 AA
6484951 TTTAAAGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
31 5 0.17
32 20 0.67
33 5 0.17
ACGTcount: A:0.57, C:0.03, G:0.08, T:0.32
Consensus pattern (31 bp):
AAAAATAAAATTGAGTTGCAAAATTTAATAA
Found at i:6492925 original size:24 final size:24
Alignment explanation
Indices: 6492897--6492955 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
6492887 TAGACTAATA
*
6492897 AGAGTTTGACTCAAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
* *
6492921 AGAGTTTAATTGAAACAAATAAAC
1 AGAGTTTAACTCAAACAAATAAAC
6492945 AGAGTTTAACT
1 AGAGTTTAACT
6492956 AAAAGATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.49, C:0.12, G:0.14, T:0.25
Consensus pattern (24 bp):
AGAGTTTAACTCAAACAAATAAAC
Found at i:6494640 original size:2 final size:2
Alignment explanation
Indices: 6494633--6494659 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6494623 TTCTATTGTG
6494633 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
6494660 GGCTTTATGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6496738 original size:58 final size:61
Alignment explanation
Indices: 6496609--6496743 Score: 172
Period size: 58 Copynumber: 2.3 Consensus size: 61
6496599 AATATTATAT
* * * *
6496609 ATTATAATTTTTACT-AATTCATATTTTAATAATAATTATATTAAAAATGTTATTAAATTA
1 ATTATTATTTTTATTAAATTCATATTTTAATAATAATTATATTAAAAATATAATTAAATTA
* *
6496669 ATTATTA-TTTTATTAAATT-ATA-TTTAATAATAATTATGTT-AGAATATAATTAAATTA
1 ATTATTATTTTTATTAAATTCATATTTTAATAATAATTATATTAAAAATATAATTAAATTA
*
6496726 TTTATTATTTTTATTAAA
1 ATTATTATTTTTATTAAA
6496744 AAAAGAAGTT
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
57 20 0.30
58 27 0.41
59 9 0.14
60 10 0.15
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (61 bp):
ATTATTATTTTTATTAAATTCATATTTTAATAATAATTATATTAAAAATATAATTAAATTA
Found at i:6519565 original size:16 final size:16
Alignment explanation
Indices: 6519500--6519569 Score: 95
Period size: 16 Copynumber: 4.4 Consensus size: 16
6519490 TTTGGTTCGC
*
6519500 TGTAATGGAATAGAGC
1 TGTAATGGAATAGAGT
*
6519516 TGTAATGTAATAGAGT
1 TGTAATGGAATAGAGT
* *
6519532 TGTAATGAAATGGAGT
1 TGTAATGGAATAGAGT
*
6519548 TGTAATGGAATAGGGT
1 TGTAATGGAATAGAGT
6519564 TGTAAT
1 TGTAAT
6519570 CAGTAATTCA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.36, C:0.01, G:0.30, T:0.33
Consensus pattern (16 bp):
TGTAATGGAATAGAGT
Found at i:6519655 original size:39 final size:40
Alignment explanation
Indices: 6519546--6519656 Score: 93
Period size: 44 Copynumber: 2.6 Consensus size: 40
6519536 ATGAAATGGA
6519546 GTTGTAATGGAATAGG-GTTGTAATCAGTAATTCAATTGTTTG
1 GTTG-AATGGAAT-GGTGTTGTAAT-AGTAATTCAATTGTTTG
* * *
6519588 GTTGAATGGAATGGAATAGAGCTATAATAGT-ATTC-TTGTGTTTG
1 GTTGAATGGAATGG--T---GTTGTAATAGTAATTCAAT-TGTTTG
6519632 GTTGAATGGAATGGTGTTGTAATAG
1 GTTGAATGGAATGGTGTTGTAATAG
6519657 CATAAGAAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 17
0.72 0.06 0.22
Matches are distributed among these distances:
39 8 0.14
40 2 0.04
41 8 0.14
42 5 0.09
43 1 0.02
44 24 0.42
45 3 0.05
46 6 0.11
ACGTcount: A:0.29, C:0.04, G:0.29, T:0.39
Consensus pattern (40 bp):
GTTGAATGGAATGGTGTTGTAATAGTAATTCAATTGTTTG
Found at i:6519812 original size:26 final size:26
Alignment explanation
Indices: 6519783--6519870 Score: 68
Period size: 26 Copynumber: 3.2 Consensus size: 26
6519773 AATAAATAAT
6519783 TTAATTATATTTTAACATAATTATTA
1 TTAATTATATTTTAACATAATTATTA
* * * *
6519809 TTAAATATAATTTAACAAAATAATAAATAA
1 TTAATTATATTTTAAC---ATAAT-TATTA
* *
6519839 TTTAATAATATTTTTAATATAATTATTA
1 -TTAATTATA-TTTTAACATAATTATTA
6519867 TTAA
1 TTAA
6519871 AATATGAATT
Statistics
Matches: 46, Mismatches: 10, Indels: 11
0.69 0.15 0.16
Matches are distributed among these distances:
26 14 0.30
27 4 0.09
28 3 0.07
29 10 0.22
30 3 0.07
31 7 0.15
32 5 0.11
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (26 bp):
TTAATTATATTTTAACATAATTATTA
Found at i:6519850 original size:57 final size:59
Alignment explanation
Indices: 6519744--6519894 Score: 218
Period size: 58 Copynumber: 2.6 Consensus size: 59
6519734 AAATAAGATT
*
6519744 ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATTATA-TTTTAACATA
1 ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATAATATTTTTAACATA
* *
6519802 ATTATTATTAAATATAATTTAA-CAAAATAATAAATAATTTAATAATATTTTTAATATA
1 ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATAATATTTTTAACATA
* *
6519860 ATTATTATTAAAATATGAA-TTAGTAAAAATTATAA
1 ATTATTATT-AAATAT-AATTTAATAAAAATAATAA
6519895 TATATAATAT
Statistics
Matches: 83, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
57 23 0.28
58 40 0.48
59 9 0.11
60 11 0.13
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (59 bp):
ATTATTATTAAATATAATTTAATAAAAATAATAAATAATTTAATAATATTTTTAACATA
Found at i:6524104 original size:20 final size:18
Alignment explanation
Indices: 6524065--6524112 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
6524055 CCATTAGTTT
*
6524065 TAATATACTGGACTTTTA
1 TAATATATTGGACTTTTA
6524083 TAATATATTGGACTTATCTA
1 TAATATATTGGACTT-T-TA
*
6524103 TATTATATTG
1 TAATATATTG
6524113 ACGATAGTCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 14 0.54
19 1 0.04
20 11 0.42
ACGTcount: A:0.33, C:0.08, G:0.10, T:0.48
Consensus pattern (18 bp):
TAATATATTGGACTTTTA
Found at i:6534906 original size:85 final size:85
Alignment explanation
Indices: 6534806--6534978 Score: 319
Period size: 85 Copynumber: 2.0 Consensus size: 85
6534796 AACCAGGAGT
6534806 TATTTAGTGCATTAGAATTGTCTTACAACAAAGGGGATGTTATATTGGCTTACTAAAGGGTAAAA
1 TATTTAGTGCATTAGAATTGTCTTACAACAAAGGGGATGTTATATTGGCTTACTAAAGGGTAAAA
*
6534871 ACACAATTTATCTTTGGTAA
66 ACACAATTTATCTTGGGTAA
*
6534891 TATTTAGTGCATTAGAATTGTCTTACAACAAAGGGGGTGTTATATTGGCTTACTAAAGGGTAAAA
1 TATTTAGTGCATTAGAATTGTCTTACAACAAAGGGGATGTTATATTGGCTTACTAAAGGGTAAAA
*
6534956 ACGCAATTTATCTTGGGTAA
66 ACACAATTTATCTTGGGTAA
6534976 TAT
1 TAT
6534979 CTTTTACCTA
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
85 85 1.00
ACGTcount: A:0.34, C:0.10, G:0.20, T:0.35
Consensus pattern (85 bp):
TATTTAGTGCATTAGAATTGTCTTACAACAAAGGGGATGTTATATTGGCTTACTAAAGGGTAAAA
ACACAATTTATCTTGGGTAA
Found at i:6538120 original size:58 final size:57
Alignment explanation
Indices: 6538009--6538127 Score: 168
Period size: 58 Copynumber: 2.1 Consensus size: 57
6537999 ACCCATCAAC
* * *
6538009 AAACTAAACCCAAATATTTTAAACCCAAATATAATTTTATTCTTCAAACACACTTAT
1 AAACTAAACCCAAATATTTTAAACCAAAATATAATTTTATTCTTCAAAAACACTCAT
* *
6538066 AAACTAAACCCAAATACTTTTAAACTAAAATATAATTTTATT-TTTAAATAACACTCAT
1 AAACTAAACCCAAATA-TTTTAAACCAAAATATAATTTTATTCTTCAAA-AACACTCAT
6538124 AAAC
1 AAAC
6538128 AACTCCTTTT
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
57 21 0.38
58 34 0.62
ACGTcount: A:0.48, C:0.18, G:0.00, T:0.34
Consensus pattern (57 bp):
AAACTAAACCCAAATATTTTAAACCAAAATATAATTTTATTCTTCAAAAACACTCAT
Found at i:6542170 original size:2 final size:2
Alignment explanation
Indices: 6542165--6542198 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
6542155 TGTGTGTTTT
6542165 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6542199 AACACGTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6547388 original size:127 final size:127
Alignment explanation
Indices: 6547227--6547507 Score: 422
Period size: 127 Copynumber: 2.2 Consensus size: 127
6547217 TCACATTTCT
* * **
6547227 TTTTCTTAATTCATCCTTAAATTTCTTTAATGTCTATGATTTTATTTACTTTTGCTAAAAAATTA
1 TTTTCTAAAGTCATCCTTAAATTTCTTTAATGTCTATGATTTTATTTACTTTTGCT-AAAAACGA
** *
6547292 AAATTAAATT-AAATTAAATAAGAAGTTCAATTTCATCCAAAATTCTTGCTTAATCAGTCTTC
65 AAAAAAAATTAAAATTAAATAAGAAATTCAATTTCATCCAAAATTCTTGCTTAATCAGTCTTC
** *
6547354 TTTTCTAAAGTCATCCTTACTTTTCTTTATTGTCTATGATTTTATTTACTTTTGCTAAAAACGAA
1 TTTTCTAAAGTCATCCTTAAATTTCTTTAATGTCTATGATTTTATTTACTTTTGCTAAAAACGAA
* *
6547419 AAAAAAATTAAAATTAAATAAGAAATTCAATTTCATCCAAAATTCTTGTTTAATCAGTTTTC
66 AAAAAAATTAAAATTAAATAAGAAATTCAATTTCATCCAAAATTCTTGCTTAATCAGTCTTC
6547481 TTTTCTAAAGTCA-CCATTAAATTTCTT
1 TTTTCTAAAGTCATCC-TTAAATTTCTT
6547508 CCCTTTATTA
Statistics
Matches: 138, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
126 16 0.12
127 122 0.88
ACGTcount: A:0.35, C:0.14, G:0.06, T:0.45
Consensus pattern (127 bp):
TTTTCTAAAGTCATCCTTAAATTTCTTTAATGTCTATGATTTTATTTACTTTTGCTAAAAACGAA
AAAAAAATTAAAATTAAATAAGAAATTCAATTTCATCCAAAATTCTTGCTTAATCAGTCTTC
Found at i:6558170 original size:21 final size:21
Alignment explanation
Indices: 6558146--6558187 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
6558136 TTTACTTTTT
6558146 TTAAGTTAAAAGTCAAAATCA
1 TTAAGTTAAAAGTCAAAATCA
6558167 TTAAGTTAAAAGTCAAAATCA
1 TTAAGTTAAAAGTCAAAATCA
6558188 CGTCGTTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.29
Consensus pattern (21 bp):
TTAAGTTAAAAGTCAAAATCA
Found at i:6561940 original size:18 final size:19
Alignment explanation
Indices: 6561895--6561961 Score: 75
Period size: 19 Copynumber: 3.5 Consensus size: 19
6561885 ATAACAAAAT
6561895 AATTCAAAATAATTTTCAA
1 AATTCAAAATAATTTTCAA
*
6561914 AATTCAAAATAATTTT-TA
1 AATTCAAAATAATTTTCAA
* *
6561932 AATTTAAAAT-ATTTATAAA
1 AATTCAAAATAATTT-TCAA
6561951 AATTTCAAAAT
1 AA-TTCAAAAT
6561962 TTATATTTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
17 4 0.10
18 11 0.27
19 19 0.46
20 7 0.17
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (19 bp):
AATTCAAAATAATTTTCAA
Found at i:6561965 original size:18 final size:19
Alignment explanation
Indices: 6561931--6562006 Score: 65
Period size: 19 Copynumber: 4.2 Consensus size: 19
6561921 AATAATTTTT
6561931 AAATTTAAAATATTTATAA
1 AAATTTAAAATATTTATAA
*
6561950 AAATTTCAAA-ATTTAT--
1 AAATTTAAAATATTTATAA
*
6561966 --ATTTAAAAATTTTTATAA
1 AAATTT-AAAATATTTATAA
*
6561984 AAATTATAAAA-AATTATAA
1 AAATT-TAAAATATTTATAA
6562003 AAAT
1 AAAT
6562007 ATATATAAAA
Statistics
Matches: 45, Mismatches: 5, Indels: 14
0.70 0.08 0.22
Matches are distributed among these distances:
14 4 0.09
15 3 0.07
16 5 0.11
18 6 0.13
19 19 0.42
20 7 0.16
21 1 0.02
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (19 bp):
AAATTTAAAATATTTATAA
Found at i:6561995 original size:10 final size:10
Alignment explanation
Indices: 6561978--6562025 Score: 64
Period size: 10 Copynumber: 4.8 Consensus size: 10
6561968 TTAAAAATTT
6561978 TTAT-AAAAA
1 TTATAAAAAA
6561987 TTATAAAAAA
1 TTATAAAAAA
6561997 TTATAAAAATA
1 TTATAAAAA-A
6562008 TATATAAAAAA
1 T-TATAAAAAA
6562019 TT-TAAAA
1 TTATAAAA
6562026 GTTTAAAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
9 9 0.25
10 15 0.42
11 4 0.11
12 8 0.22
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
TTATAAAAAA
Found at i:6562015 original size:12 final size:11
Alignment explanation
Indices: 6561964--6562025 Score: 55
Period size: 10 Copynumber: 6.0 Consensus size: 11
6561954 TTCAAAATTT
6561964 ATATT-TAAAA
1 ATATTATAAAA
*
6561974 AT-TTTTATAAA
1 ATATTATA-AAA
6561985 A-ATTATAAAA
1 ATATTATAAAA
6561995 A-ATTATAAAA
1 ATATTATAAAA
6562005 ATATATATAAAA
1 ATAT-TATAAAA
6562017 A-ATT-TAAAA
1 ATATTATAAAA
6562026 GTTTAAAATT
Statistics
Matches: 46, Mismatches: 1, Indels: 11
0.79 0.02 0.19
Matches are distributed among these distances:
9 7 0.15
10 19 0.41
11 12 0.26
12 8 0.17
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
ATATTATAAAA
Found at i:6562018 original size:22 final size:21
Alignment explanation
Indices: 6561931--6562025 Score: 81
Period size: 21 Copynumber: 4.5 Consensus size: 21
6561921 AATAATTTTT
*
6561931 AAATTT-AAAATATTTAT-AA
1 AAATTTAAAAATATATATAAA
* *
6561950 AAATTTCAAAATTTATATTTAAA
1 AAATTT-AAAA-ATATATATAAA
*
6561973 AATTTTTATAAAA-AT-TATAAA
1 AA-ATTTA-AAAATATATATAAA
6561994 AAATTATAAAAATATATATAAA
1 AAATT-TAAAAATATATATAAA
6562016 AAATTTAAAA
1 AAATTTAAAA
6562026 GTTTAAAATT
Statistics
Matches: 60, Mismatches: 7, Indels: 16
0.72 0.08 0.19
Matches are distributed among these distances:
19 6 0.10
20 6 0.10
21 19 0.32
22 18 0.30
23 5 0.08
24 6 0.10
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (21 bp):
AAATTTAAAAATATATATAAA
Found at i:6567646 original size:22 final size:22
Alignment explanation
Indices: 6567593--6567646 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
6567583 TAAGAGAGAT
* *
6567593 CAAAGTTAAATTGTAATTTTTA
1 CAAAATTAAAATGTAATTTTTA
* *
6567615 CAATAGTAAAATGTAATTTTTA
1 CAAAATTAAAATGTAATTTTTA
6567637 -AAGAATTAAA
1 CAA-AATTAAA
6567647 TTAAAATTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 2 0.08
22 23 0.92
ACGTcount: A:0.48, C:0.04, G:0.09, T:0.39
Consensus pattern (22 bp):
CAAAATTAAAATGTAATTTTTA
Found at i:6574794 original size:18 final size:20
Alignment explanation
Indices: 6574757--6574802 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
6574747 TAAAATACAA
*
6574757 ATTTTAGAATTTTCATAAA-T
1 ATTTT-GAATTTTCAAAAATT
6574777 ATTTTGAATTTT-AAAAATT
1 ATTTTGAATTTTCAAAAATT
6574796 ATTTTGA
1 ATTTTGA
6574803 TTATTTTGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 15 0.62
20 5 0.21
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.52
Consensus pattern (20 bp):
ATTTTGAATTTTCAAAAATT
Found at i:6579973 original size:211 final size:212
Alignment explanation
Indices: 6579613--6580033 Score: 684
Period size: 211 Copynumber: 2.0 Consensus size: 212
6579603 GAAAGGTAAT
* *
6579613 TTTTTTGTGTTTATTGTTAAATTTATTTTTAAAATTATTTAAGTTGTTAGTTAGTAATAGTTATT
1 TTTTTTGTGTTTATTGTTAAATTTATTTTTAAAATTATTTAAGTTATTAGTTAGTAATAGTAATT
* *
6579678 TTTTTGTTATTTTTATACATAGTTTAGGCAAATAATGTTTAGTTTGATATTAATTTGTTATAAAT
66 TTTTTGTTATTTTTATACACAGTTTAGGCAAATAATGTTTAATTTGATATTAATTTGTTATAAAT
* *
6579743 TTATAGTAGTAAGGTATATTTTTAAATTTTTATTTTATTTA-TTTTTAATAGATTTATTGAATAT
131 TTATAGTAGTAAGGTATATTTTTAAATTTTTATTTTATTTATTTTTTAACAGATTTATTGAAGAT
*
6579807 GGATAATC-ATTTTTAA
196 GAATAATCAATTTTTAA
* * * *
6579823 TTTTTTGTTTTTATTGTTAAATTTATTTTTAAAGTTATTTAATTTATTAGTTAGTAGTAGTAATT
1 TTTTTTGTGTTTATTGTTAAATTTATTTTTAAAATTATTTAAGTTATTAGTTAGTAATAGTAA-T
*
6579888 TTTTTTGTTATTTTTATACACAGTTTAGGCAATTAATGTTTAATTTGATATTAATTTGTTATAAA
65 TTTTTTGTTATTTTTATACACAGTTTAGGCAAATAATGTTTAATTTGATATTAATTTGTTATAAA
** *
6579953 TTTATTTTAGTAGGGTATATTTTTAAATTTTTATTTTATTTATTTTTTAACAGATTTATTGAAGA
130 TTTATAGTAGTAAGGTATATTTTTAAATTTTTATTTTATTTATTTTTTAACAGATTTATTGAAGA
6580018 TGAATAATCAATTTTT
195 TGAATAATCAATTTTT
6580034 TGTATGCATT
Statistics
Matches: 193, Mismatches: 15, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
210 57 0.30
211 102 0.53
212 28 0.15
213 6 0.03
ACGTcount: A:0.30, C:0.02, G:0.11, T:0.57
Consensus pattern (212 bp):
TTTTTTGTGTTTATTGTTAAATTTATTTTTAAAATTATTTAAGTTATTAGTTAGTAATAGTAATT
TTTTTGTTATTTTTATACACAGTTTAGGCAAATAATGTTTAATTTGATATTAATTTGTTATAAAT
TTATAGTAGTAAGGTATATTTTTAAATTTTTATTTTATTTATTTTTTAACAGATTTATTGAAGAT
GAATAATCAATTTTTAA
Found at i:6582760 original size:28 final size:27
Alignment explanation
Indices: 6582701--6582785 Score: 75
Period size: 28 Copynumber: 3.1 Consensus size: 27
6582691 GACATTTTTC
* **
6582701 ATTTGAAATTAATTAAGTTTATGAATGA
1 ATTTGAAATTAATTATGTTTAT-TTTGA
*
6582729 ATTTGAAATTAATTATGTTTAATTTTGT
1 ATTTGAAATTAATTATGTTT-ATTTTGA
* * *
6582757 ATTT--AATTAATAATTTTTATTTTGC
1 ATTTGAAATTAATTATGTTTATTTTGA
6582782 ATTT
1 ATTT
6582786 TGGTTTAAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
25 10 0.20
26 12 0.24
28 25 0.51
29 2 0.04
ACGTcount: A:0.35, C:0.01, G:0.09, T:0.54
Consensus pattern (27 bp):
ATTTGAAATTAATTATGTTTATTTTGA
Found at i:6582775 original size:26 final size:25
Alignment explanation
Indices: 6582735--6582785 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
6582725 ATGAATTTGA
* *
6582735 AATTAATTATGTTTAATTTTGTATTT
1 AATTAATAATGTTT-ATTTTGCATTT
*
6582761 AATTAATAATTTTTATTTTGCATTT
1 AATTAATAATGTTTATTTTGCATTT
6582786 TGGTTTAAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (25 bp):
AATTAATAATGTTTATTTTGCATTT
Found at i:6582785 original size:25 final size:26
Alignment explanation
Indices: 6582735--6582785 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
6582725 ATGAATTTGA
* *
6582735 AATTAATTATGTTTAATTTTGTATTT
1 AATTAATAATGTTTAATTTTGCATTT
*
6582761 AATTAATAAT-TTTTATTTTGCATTT
1 AATTAATAATGTTTAATTTTGCATTT
6582786 TGGTTTAAGG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 13 0.59
26 9 0.41
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (26 bp):
AATTAATAATGTTTAATTTTGCATTT
Found at i:6582815 original size:15 final size:14
Alignment explanation
Indices: 6582797--6582871 Score: 62
Period size: 15 Copynumber: 5.1 Consensus size: 14
6582787 GGTTTAAGGG
6582797 TTTAGTGTTTTGAAT
1 TTTAG-GTTTTGAAT
* *
6582812 TTTAGGGTTTTTAAA
1 TTTA-GGTTTTGAAT
*
6582827 TTTAGGATTT-AAT
1 TTTAGGTTTTGAAT
*
6582840 GTTAAGGGTTTTGAAT
1 -TTTA-GGTTTTGAAT
*
6582856 TTGAGGTTTTGAAT
1 TTTAGGTTTTGAAT
6582870 TT
1 TT
6582872 AGGGTTTAAG
Statistics
Matches: 49, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
13 2 0.04
14 20 0.41
15 23 0.47
16 4 0.08
ACGTcount: A:0.24, C:0.00, G:0.23, T:0.53
Consensus pattern (14 bp):
TTTAGGTTTTGAAT
Found at i:6582856 original size:28 final size:28
Alignment explanation
Indices: 6582805--6582878 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 28
6582795 GGTTTAGTGT
6582805 TTTGAATTTTAGGGTTTTTAAATTT-AGGA
1 TTTGAA-TTTAGGG-TTTTAAATTTGAGGA
* *
6582834 TTT-AATGTTAAGGGTTTTGAATTTGAGGT
1 TTTGAAT-TT-AGGGTTTTAAATTTGAGGA
6582863 TTTGAATTTAGGGTTT
1 TTTGAATTTAGGGTTT
6582879 AAGGTTTTGA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
27 1 0.03
28 20 0.51
29 15 0.38
30 3 0.08
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (28 bp):
TTTGAATTTAGGGTTTTAAATTTGAGGA
Found at i:6582877 original size:14 final size:14
Alignment explanation
Indices: 6582797--6582878 Score: 71
Period size: 14 Copynumber: 5.7 Consensus size: 14
6582787 GGTTTAAGGG
*
6582797 TTTAGTGTTTTGAA
1 TTTAGGGTTTTGAA
*
6582811 TTTTAGGGTTTTTAAA
1 -TTTAGGG-TTTTGAA
*
6582827 TTTA-GGATTT-AA
1 TTTAGGGTTTTGAA
6582839 TGTTAAGGGTTTTGAA
1 T-TT-AGGGTTTTGAA
6582855 TTT-GAGGTTTTGAA
1 TTTAG-GGTTTTGAA
6582869 TTTAGGGTTT
1 TTTAGGGTTT
6582879 AAGGTTTTGA
Statistics
Matches: 56, Mismatches: 4, Indels: 15
0.75 0.05 0.20
Matches are distributed among these distances:
12 3 0.05
13 6 0.11
14 20 0.36
15 18 0.32
16 9 0.16
ACGTcount: A:0.23, C:0.00, G:0.24, T:0.52
Consensus pattern (14 bp):
TTTAGGGTTTTGAA
Done.