Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 76 of 135
Found at i:22965784 original size:5 final size:6
Alignment explanation
Indices: 22965752--22965783 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
22965742 TTGTCTATCT
22965752 TCCCTA TCCCTA TCCCTA TCCCTA T-CCTA TCC
1 TCCCTA TCCCTA TCCCTA TCCCTA TCCCTA TCC
22965784 TTCCATTCTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.16, C:0.50, G:0.00, T:0.34
Consensus pattern (6 bp):
TCCCTA
Found at i:22974430 original size:16 final size:16
Alignment explanation
Indices: 22974386--22974432 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
22974376 GGGGAATGTG
*
22974386 TAAAAAAACAT-AAACA
1 TAAATAAACATGAAA-A
*
22974402 TAAATATACATGAAAA
1 TAAATAAACATGAAAA
*
22974418 TAAATAAAGATGAAA
1 TAAATAAACATGAAA
22974433 TAAGAATAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
16 23 0.88
17 3 0.12
ACGTcount: A:0.68, C:0.06, G:0.06, T:0.19
Consensus pattern (16 bp):
TAAATAAACATGAAAA
Found at i:22975165 original size:148 final size:148
Alignment explanation
Indices: 22974996--22975278 Score: 385
Period size: 148 Copynumber: 1.9 Consensus size: 148
22974986 TTTCTTTTTC
* * * *
22974996 TTTTTAAACAAAAACACTACTTTTCTTAAAAATCAAAATTTTTATTTTGAAAT-GATTAAAAAAA
1 TTTTTAAAAAAAAAAACTACTTTTCTTAAAAATCAAAACTTTTATTTCGAAATAG-TTAAAAAAA
22975060 ATC-AAACTTTATTTAAAAAATTAAAATTTTT-CTTTAAAAT-ACCTAAAAAAACAGATTTTTAT
65 ATCAAAACTTTATTTAAAAAATTAAAATTTTTCCTTTAAAATGA-CT--AAAAACAGATTTTTAT
22975122 TTTTAAAAACCTAAAGTTTCTT
127 TTTTAAAAACCTAAAGTTTCTT
* * * *
22975144 TTTTTAAAAAAAAAAATTACTTTTTTTAAACATCAAAGCTTTTATTTCGAAATAGTTAAAAAAAA
1 TTTTTAAAAAAAAAAACTACTTTTCTTAAAAATCAAAACTTTTATTTCGAAATAGTTAAAAAAAA
* ** **
22975209 TCAAAACTTTATTTAAAAATTTAATTTTTTTCCTTTAAAATGACTAAAAATTGATTTTTATTTTT
66 TCAAAACTTTATTTAAAAAATTAAAATTTTTCCTTTAAAATGACTAAAAACAGATTTTTATTTTT
22975274 AAAAA
131 AAAAA
22975279 TCTATTTTTT
Statistics
Matches: 118, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
148 80 0.68
149 26 0.22
150 11 0.09
151 1 0.01
ACGTcount: A:0.46, C:0.09, G:0.03, T:0.42
Consensus pattern (148 bp):
TTTTTAAAAAAAAAAACTACTTTTCTTAAAAATCAAAACTTTTATTTCGAAATAGTTAAAAAAAA
TCAAAACTTTATTTAAAAAATTAAAATTTTTCCTTTAAAATGACTAAAAACAGATTTTTATTTTT
AAAAACCTAAAGTTTCTT
Found at i:22976044 original size:16 final size:16
Alignment explanation
Indices: 22976023--22976054 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
22976013 TTCTTGGCAC
22976023 TATATTTTCCACAAAA
1 TATATTTTCCACAAAA
22976039 TATATTTTCCACAAAA
1 TATATTTTCCACAAAA
22976055 AAGTGATCGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (16 bp):
TATATTTTCCACAAAA
Found at i:22976110 original size:16 final size:16
Alignment explanation
Indices: 22976075--22976114 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
22976065 AAAAGAGCAG
* *
22976075 AAAAAAATAAAATACG
1 AAAAAAATAAAAAACA
*
22976091 AAAAAAATAAAAAATA
1 AAAAAAATAAAAAACA
22976107 AAAAAAAT
1 AAAAAAAT
22976115 TTTGTGGGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.12
Consensus pattern (16 bp):
AAAAAAATAAAAAACA
Found at i:22983872 original size:3 final size:3
Alignment explanation
Indices: 22983864--22983983 Score: 213
Period size: 3 Copynumber: 40.0 Consensus size: 3
22983854 ATTAAAGTTT
* *
22983864 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAT GAA GAA GAA AAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
*
22983912 GAC GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
22983960 GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA
22983984 AAAGTGATAA
Statistics
Matches: 111, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 111 1.00
ACGTcount: A:0.66, C:0.01, G:0.33, T:0.01
Consensus pattern (3 bp):
GAA
Found at i:22984007 original size:21 final size:21
Alignment explanation
Indices: 22983981--22984024 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
22983971 AGAAGAAGAA
22983981 GAAAAAGTGATAAATTTTAAG
1 GAAAAAGTGATAAATTTTAAG
22984002 GAAAAAGTGATAAATTTTAAG
1 GAAAAAGTGATAAATTTTAAG
22984023 GA
1 GA
22984025 CTTTTAACCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.20, T:0.27
Consensus pattern (21 bp):
GAAAAAGTGATAAATTTTAAG
Found at i:22985269 original size:53 final size:53
Alignment explanation
Indices: 22985206--22985310 Score: 140
Period size: 53 Copynumber: 2.0 Consensus size: 53
22985196 TTTAGGGGAG
* * *
22985206 ACACGGGCTGGACACACGGGCTTGTGCTAGA-TCGTGTGTGTATACTATTTTGA
1 ACACGGGCTGGACACACAGGCGTGTGCTAGACT-GTGTGTGCATACTATTTTGA
* * *
22985259 ACACGGGCTGGACACATAGGCGTGTGTTAGACTGTGTGTGCATACTGTTTTG
1 ACACGGGCTGGACACACAGGCGTGTGCTAGACTGTGTGTGCATACTATTTTG
22985311 GGAATTAAGG
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
53 44 0.98
54 1 0.02
ACGTcount: A:0.20, C:0.18, G:0.31, T:0.30
Consensus pattern (53 bp):
ACACGGGCTGGACACACAGGCGTGTGCTAGACTGTGTGTGCATACTATTTTGA
Found at i:22991581 original size:40 final size:40
Alignment explanation
Indices: 22991533--22991613 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
22991523 CTATTCGAAG
* * *
22991533 GCACACGGGCATGTGTTAGACCGTGTGTGTATACTATTTT
1 GCACACGGGCATGTGTCAGACCATGTGAGTATACTATTTT
* *
22991573 GCACACGGGCGTGTGTCAGACCATGTGAGTATACTGTTTT
1 GCACACGGGCATGTGTCAGACCATGTGAGTATACTATTTT
22991613 G
1 G
22991614 GAATTACAGG
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.20, C:0.19, G:0.30, T:0.32
Consensus pattern (40 bp):
GCACACGGGCATGTGTCAGACCATGTGAGTATACTATTTT
Found at i:22996876 original size:18 final size:18
Alignment explanation
Indices: 22996853--22996894 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
22996843 AAAACAAAGA
22996853 AGAGAAGAGAAGGGAGCT
1 AGAGAAGAGAAGGGAGCT
22996871 AGAGAAGAGAAGGGAGCT
1 AGAGAAGAGAAGGGAGCT
22996889 AGAGAA
1 AGAGAA
22996895 TGGGACGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.48, C:0.05, G:0.43, T:0.05
Consensus pattern (18 bp):
AGAGAAGAGAAGGGAGCT
Found at i:23003405 original size:21 final size:21
Alignment explanation
Indices: 23003372--23003424 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
23003362 GAAGGAAAGA
* * *
23003372 GAAGAGAAAGAAGAAGAGAGT
1 GAAGAGAAGGAAGAAGAAAAT
*
23003393 GAGGAGAAGGAAGAAGAAAAT
1 GAAGAGAAGGAAGAAGAAAAT
23003414 GAAGAGAAGGA
1 GAAGAGAAGGA
23003425 CCCTACCAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.57, C:0.00, G:0.40, T:0.04
Consensus pattern (21 bp):
GAAGAGAAGGAAGAAGAAAAT
Found at i:23004508 original size:10 final size:10
Alignment explanation
Indices: 23004480--23004526 Score: 50
Period size: 9 Copynumber: 5.2 Consensus size: 10
23004470 CAGTCATTTG
23004480 AAAAGGAA-A
1 AAAAGGAAGA
*
23004489 AAAATG-AGA
1 AAAAGGAAGA
23004498 AAAAGGAAG-
1 AAAAGGAAGA
23004507 AAAA--AAGA
1 AAAAGGAAGA
23004515 AAAAGGAAGA
1 AAAAGGAAGA
23004525 AA
1 AA
23004527 TTTTTGATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
7 3 0.10
8 5 0.16
9 15 0.48
10 8 0.26
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.02
Consensus pattern (10 bp):
AAAAGGAAGA
Found at i:23004515 original size:17 final size:18
Alignment explanation
Indices: 23004480--23004526 Score: 71
Period size: 17 Copynumber: 2.7 Consensus size: 18
23004470 CAGTCATTTG
23004480 AAAAGGAA-AAAAATGAGA
1 AAAAGGAAGAAAAA-GAGA
23004498 AAAAGGAAGAAAAA-AGA
1 AAAAGGAAGAAAAAGAGA
23004515 AAAAGGAAGAAA
1 AAAAGGAAGAAA
23004527 TTTTTGATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 15 0.54
18 8 0.29
19 5 0.18
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.02
Consensus pattern (18 bp):
AAAAGGAAGAAAAAGAGA
Found at i:23005662 original size:16 final size:16
Alignment explanation
Indices: 23005641--23005672 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
23005631 TAACTTGTTC
23005641 TTGGGTATTCAACGTT
1 TTGGGTATTCAACGTT
23005657 TTGGGTATTCAACGTT
1 TTGGGTATTCAACGTT
23005673 GTTCACACTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.12, G:0.25, T:0.44
Consensus pattern (16 bp):
TTGGGTATTCAACGTT
Found at i:23022682 original size:38 final size:39
Alignment explanation
Indices: 23022629--23022704 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 39
23022619 TTCGTACGTT
* *
23022629 GTTCGAACAGCAAAAAAAATAGAGAAAAAAAAGCAAAAG
1 GTTCGAAAAGCAAAAAAAAGAGAGAAAAAAAAGCAAAAG
* * *
23022668 GTTCGAAAAG-AAAAAAAAGGGAGAAAAAGAAGGAAAA
1 GTTCGAAAAGCAAAAAAAAGAGAGAAAAAAAAGCAAAA
23022705 AAACATGGTT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
38 23 0.72
39 9 0.28
ACGTcount: A:0.64, C:0.07, G:0.22, T:0.07
Consensus pattern (39 bp):
GTTCGAAAAGCAAAAAAAAGAGAGAAAAAAAAGCAAAAG
Found at i:23046711 original size:25 final size:26
Alignment explanation
Indices: 23046683--23046738 Score: 62
Period size: 26 Copynumber: 2.2 Consensus size: 26
23046673 ATAAAATACA
*
23046683 TTTTCAG-TATCATTAAGTAAACTTT
1 TTTTCAGATATCATAAAGTAAACTTT
* *
23046708 TTTT-AGATTATTATAAAGTACACTTT
1 TTTTCAGA-TATCATAAAGTAAACTTT
23046734 TTTTC
1 TTTTC
23046739 TTTTAAATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
24 2 0.08
25 4 0.16
26 19 0.76
ACGTcount: A:0.30, C:0.11, G:0.07, T:0.52
Consensus pattern (26 bp):
TTTTCAGATATCATAAAGTAAACTTT
Found at i:23050859 original size:34 final size:34
Alignment explanation
Indices: 23050811--23050893 Score: 157
Period size: 34 Copynumber: 2.4 Consensus size: 34
23050801 CTAAGGAAAG
23050811 AAAATAAGAGGGAGAGGAGACTTGGGAAAATAAAT
1 AAAA-AAGAGGGAGAGGAGACTTGGGAAAATAAAT
23050846 AAAAAAGAGGGAGAGGAGACTTGGGAAAATAAAT
1 AAAAAAGAGGGAGAGGAGACTTGGGAAAATAAAT
23050880 AAAAAAGAGGGAGA
1 AAAAAAGAGGGAGA
23050894 AAGAAACTAG
Statistics
Matches: 48, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
34 44 0.92
35 4 0.08
ACGTcount: A:0.54, C:0.02, G:0.33, T:0.11
Consensus pattern (34 bp):
AAAAAAGAGGGAGAGGAGACTTGGGAAAATAAAT
Found at i:23064759 original size:23 final size:23
Alignment explanation
Indices: 23064728--23065033 Score: 427
Period size: 23 Copynumber: 13.3 Consensus size: 23
23064718 CTTATATCTA
*
23064728 TGCTCAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
23064751 TGCTTAAATATTAATATGATTTA
1 TGCTTAAATATTAATGTGATTTG
*
23064774 TGATTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
23064797 TGCTTAAGA-ATTAATGTGATTTG
1 TGCTTAA-ATATTAATGTGATTTG
* *
23064820 TGCTTAAGTATT-ATGTGATTTA
1 TGCTTAAATATTAATGTGATTTG
*
23064842 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
23064865 TGCTCAAATATTAATGTGATTTA
1 TGCTTAAATATTAATGTGATTTG
* *
23064888 TACTTAAATATTAATGTGATTTA
1 TGCTTAAATATTAATGTGATTTG
*
23064911 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
23064934 TGCTAAAATATTAATGTGATTTA
1 TGCTTAAATATTAATGTGATTTG
23064957 TGCTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
* *
23064980 TGCTTAAATATTAATATGATTTA
1 TGCTTAAATATTAATGTGATTTG
*
23065003 TGATTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
*
23065026 TGTTTAAA
1 TGCTTAAA
23065034 GAATTAAGAT
Statistics
Matches: 249, Mismatches: 31, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
22 20 0.08
23 228 0.92
24 1 0.00
ACGTcount: A:0.35, C:0.04, G:0.14, T:0.47
Consensus pattern (23 bp):
TGCTTAAATATTAATGTGATTTG
Found at i:23075428 original size:52 final size:52
Alignment explanation
Indices: 23075359--23075701 Score: 449
Period size: 52 Copynumber: 6.6 Consensus size: 52
23075349 TTCTCATTTG
* ** * * *
23075359 ATACTCACGATGGCACATAGTCATCAAACATCGTAATCCGAAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
23075411 ATACTCATGATGACACATAGTTATCGGACCTCATAATCCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * *
23075463 ATACTCATGATGACACATAGTCATCGGACCTTATAATCTGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* * *
23075515 ATACTCTCACGATGACAC--AGACATCGGACCTTATAATTCGTAAAGGATTCAT
1 ATA--CTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* ** * *
23075567 ATACTCATGATGACACATAGTCATCAAACCTTATAATCCATAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
* *
23075619 ATACTCACGATGACACATTGTCATCGGACCTCATAATTCGTAAAGGATTCAT
1 ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
23075671 ATACTCACGATGACACATAGAT-ATCGGACCT
1 ATACTCACGATGACACATAG-TCATCGGACCT
23075702 TTTGCATTTA
Statistics
Matches: 257, Mismatches: 29, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
50 12 0.05
52 232 0.90
53 1 0.00
54 12 0.05
ACGTcount: A:0.36, C:0.22, G:0.15, T:0.27
Consensus pattern (52 bp):
ATACTCACGATGACACATAGTCATCGGACCTCATAATCCGTAAAGGATTCAT
Found at i:23076273 original size:18 final size:16
Alignment explanation
Indices: 23076242--23076277 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
23076232 CCTCAATACC
23076242 ATTTCATTTCAATTTA
1 ATTTCATTTCAATTTA
23076258 ATTTCATTCCTCAATTTA
1 ATTTCATT--TCAATTTA
23076276 AT
1 AT
23076278 ATTTACTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
18 10 0.56
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTCATTTCAATTTA
Found at i:23082011 original size:7 final size:7
Alignment explanation
Indices: 23081977--23082048 Score: 74
Period size: 7 Copynumber: 10.4 Consensus size: 7
23081967 TCTGAAAAGC
23081977 CAACGGT
1 CAACGGT
*
23081984 CAA-AGT
1 CAACGGT
*
23081990 CAACGAT
1 CAACGGT
23081997 CAACGGT
1 CAACGGT
*
23082004 CAATGGT
1 CAACGGT
*
23082011 CAACAGT
1 CAACGGT
23082018 CAACGGT
1 CAACGGT
*
23082025 CAATGGT
1 CAACGGT
*
23082032 CAACAGT
1 CAACGGT
*
23082039 CAATGGT
1 CAACGGT
23082046 CAA
1 CAA
23082049 AGTCAATAGT
Statistics
Matches: 51, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
6 5 0.10
7 46 0.90
ACGTcount: A:0.36, C:0.24, G:0.22, T:0.18
Consensus pattern (7 bp):
CAACGGT
Found at i:23082014 original size:21 final size:21
Alignment explanation
Indices: 23081977--23082048 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
23081967 TCTGAAAAGC
*
23081977 CAACGGTCAA-AGTCAAC-GAT
1 CAACGGTCAATGGTCAACAG-T
23081997 CAACGGTCAATGGTCAACAGT
1 CAACGGTCAATGGTCAACAGT
23082018 CAACGGTCAATGGTCAACAGT
1 CAACGGTCAATGGTCAACAGT
*
23082039 CAATGGTCAA
1 CAACGGTCAA
23082049 AGTCAATAGT
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
20 10 0.21
21 37 0.77
22 1 0.02
ACGTcount: A:0.36, C:0.24, G:0.22, T:0.18
Consensus pattern (21 bp):
CAACGGTCAATGGTCAACAGT
Found at i:23082054 original size:13 final size:14
Alignment explanation
Indices: 23082016--23082055 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
23082006 ATGGTCAACA
*
23082016 GTCAACGGTCAATG
1 GTCAACAGTCAATG
23082030 GTCAACAGTCAATG
1 GTCAACAGTCAATG
23082044 GTCAA-AGTCAAT
1 GTCAACAGTCAAT
23082056 AGTACGGGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 7 0.28
14 18 0.72
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.23
Consensus pattern (14 bp):
GTCAACAGTCAATG
Found at i:23088258 original size:20 final size:20
Alignment explanation
Indices: 23088235--23088283 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
23088225 CCAAAAAACC
*
23088235 CACACGCCTATATGAAAAGA
1 CACACGCCCATATGAAAAGA
* * *
23088255 CACACACCCGTGTGAAAAGA
1 CACACGCCCATATGAAAAGA
23088275 CACACGCCC
1 CACACGCCC
23088284 GTGTGCAAAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.39, C:0.35, G:0.16, T:0.10
Consensus pattern (20 bp):
CACACGCCCATATGAAAAGA
Found at i:23088284 original size:20 final size:20
Alignment explanation
Indices: 23088247--23088288 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
23088237 CACGCCTATA
23088247 TGAAAAGACACACACCCGTG
1 TGAAAAGACACACACCCGTG
*
23088267 TGAAAAGACACACGCCCGTG
1 TGAAAAGACACACACCCGTG
23088287 TG
1 TG
23088289 CAAACCACTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.36, C:0.29, G:0.24, T:0.12
Consensus pattern (20 bp):
TGAAAAGACACACACCCGTG
Found at i:23092719 original size:24 final size:24
Alignment explanation
Indices: 23092692--23092751 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
23092682 AAACATTCAT
*
23092692 ACTACCGATACATCAGTACCATAA
1 ACTACCGATACATCAGTAACATAA
* * *
23092716 ACTATCGATACATCTGTAATATAA
1 ACTACCGATACATCAGTAACATAA
23092740 ACTACCGATACA
1 ACTACCGATACA
23092752 ACCCAAGTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.42, C:0.25, G:0.08, T:0.25
Consensus pattern (24 bp):
ACTACCGATACATCAGTAACATAA
Found at i:23103136 original size:5 final size:5
Alignment explanation
Indices: 23103113--23103139 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
23103103 AAAAATAAAA
23103113 AAATT AAATT AAATT AAATT AAATT AA
1 AAATT AAATT AAATT AAATT AAATT AA
23103140 TAAATCATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (5 bp):
AAATT
Found at i:23104171 original size:19 final size:19
Alignment explanation
Indices: 23104149--23104187 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
23104139 ATCTATAGTG
23104149 TACGCTTGCATAATATTGC
1 TACGCTTGCATAATATTGC
23104168 TACGCTTGCATAATATTGC
1 TACGCTTGCATAATATTGC
23104187 T
1 T
23104188 GTGACATTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (19 bp):
TACGCTTGCATAATATTGC
Found at i:23104658 original size:29 final size:29
Alignment explanation
Indices: 23104616--23104671 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
23104606 GCTGGGAATT
23104616 TTGAACTCAAGCCTGTAATGTTTCAAATG
1 TTGAACTCAAGCCTGTAATGTTTCAAATG
23104645 TTGAACTCAAGCCTGTAATGTTTCAAA
1 TTGAACTCAAGCCTGTAATGTTTCAAA
23104672 CGTAGGTCTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Consensus pattern (29 bp):
TTGAACTCAAGCCTGTAATGTTTCAAATG
Found at i:23112809 original size:11 final size:11
Alignment explanation
Indices: 23112793--23112822 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
23112783 ATCACAAATC
23112793 ATTCAAATTCA
1 ATTCAAATTCA
23112804 ATTCAAATTCA
1 ATTCAAATTCA
23112815 ATTCAAAT
1 ATTCAAAT
23112823 ATACTATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.37
Consensus pattern (11 bp):
ATTCAAATTCA
Found at i:23115869 original size:37 final size:38
Alignment explanation
Indices: 23115827--23115914 Score: 92
Period size: 38 Copynumber: 2.3 Consensus size: 38
23115817 GGACACGTTC
*
23115827 ATGCAGCGACA-TTCCTAGG-TGCAA-TTGAAGAATACTT
1 ATGCAGCGACAGTT-CT-GGATGAAATTTGAAGAATACTT
* * *
23115864 ATGCAGTGATAGTTCTGGATGAAATTTGAAGAATATTT
1 ATGCAGCGACAGTTCTGGATGAAATTTGAAGAATACTT
*
23115902 ATGCAGCAACAGT
1 ATGCAGCGACAGT
23115915 CTTGGGTGCA
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
36 2 0.05
37 15 0.37
38 24 0.59
ACGTcount: A:0.34, C:0.14, G:0.23, T:0.30
Consensus pattern (38 bp):
ATGCAGCGACAGTTCTGGATGAAATTTGAAGAATACTT
Found at i:23116564 original size:6 final size:6
Alignment explanation
Indices: 23116553--23116617 Score: 71
Period size: 6 Copynumber: 10.8 Consensus size: 6
23116543 TTAAATTGAT
* * *
23116553 TTTAAA TTTAAA TTT-AT TTTAAA TTTAAA TTTACCTA TTTAAA TTT-AC
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTA--AA TTTAAA TTTAAA
23116601 TTTAAA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAA
23116618 TCAAATTTAA
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
5 8 0.16
6 36 0.73
8 5 0.10
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:23116584 original size:17 final size:17
Alignment explanation
Indices: 23116542--23116616 Score: 93
Period size: 17 Copynumber: 4.6 Consensus size: 17
23116532 TAATTAAGAG
*
23116542 TTTAAATTGATTTTAAA
1 TTTAAATTTATTTTAAA
23116559 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
**
23116576 TTTAAATTTA-CCT--A
1 TTTAAATTTATTTTAAA
*
23116590 TTTAAATTTACTTTAAA
1 TTTAAATTTATTTTAAA
23116607 TTTAAATTTA
1 TTTAAATTTA
23116617 ATCAAATTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
14 11 0.22
15 1 0.02
16 1 0.02
17 37 0.74
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.55
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:23116596 original size:31 final size:31
Alignment explanation
Indices: 23116558--23116616 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
23116548 TTGATTTTAA
*
23116558 ATTTAAATTTATTTTAAATTTAAATTTACCT
1 ATTTAAATTTACTTTAAATTTAAATTTACCT
23116589 ATTTAAATTTACTTTAAATTTAAATTTA
1 ATTTAAATTTACTTTAAATTTAAATTTA
23116617 ATCAAATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (31 bp):
ATTTAAATTTACTTTAAATTTAAATTTACCT
Found at i:23116647 original size:12 final size:12
Alignment explanation
Indices: 23116624--23116656 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
23116614 TTAATCAAAT
23116624 TTAAAA-TAATA
1 TTAAAATTAATA
*
23116635 TTAAACTTAATA
1 TTAAAATTAATA
23116647 TTAAAATTAA
1 TTAAAATTAA
23116657 AAGTCCAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
11 5 0.26
12 14 0.74
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (12 bp):
TTAAAATTAATA
Found at i:23117347 original size:12 final size:13
Alignment explanation
Indices: 23117330--23117380 Score: 54
Period size: 12 Copynumber: 4.2 Consensus size: 13
23117320 CTACATATTT
23117330 TAATAATAT-TAA
1 TAATAATATATAA
*
23117342 TAATAAT-TGTAA
1 TAATAATATATAA
23117354 TAATAA-ATATAA
1 TAATAATATATAA
* *
23117366 CAATAATAAATAA
1 TAATAATATATAA
23117379 TA
1 TA
23117381 TTAAACATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
11 1 0.03
12 25 0.78
13 6 0.19
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (13 bp):
TAATAATATATAA
Found at i:23118452 original size:30 final size:29
Alignment explanation
Indices: 23118418--23118655 Score: 206
Period size: 30 Copynumber: 8.0 Consensus size: 29
23118408 CTAAACTATC
23118418 CAAAAATAGTATTTTGACCCCAAAACTTTT
1 CAAAAATA-TATTTTGACCCCAAAACTTTT
* * * *
23118448 CAAAAATTACATTTTAATCCCTAAACTTTT
1 CAAAAA-TATATTTTGACCCCAAAACTTTT
* * *
23118478 CCAAAATTATATTTTGATCCTAAAACTTTT
1 -CAAAAATATATTTTGACCCCAAAACTTTT
* *
23118508 CAAAAATTACATTTTGACCCCTAAACTTTT
1 CAAAAA-TATATTTTGACCCCAAAACTTTT
*
23118538 CTAAAATTATATTTTGACCCCAAAACTTTT
1 C-AAAAATATATTTTGACCCCAAAACTTTT
*** * **
23118568 TGTAAATTTCATTTTGACCCTTAAACTTTT
1 CAAAAATAT-ATTTTGACCCCAAAACTTTT
* *
23118598 CCAAAATTATATTTTGACCCTAAAACTTTT
1 -CAAAAATATATTTTGACCCCAAAACTTTT
* * * * *
23118628 TAAAATTACATTTTTACCCCTAAACTTT
1 CAAAAATATATTTTGACCCCAAAACTTT
23118656 CTAAAACTCC
Statistics
Matches: 167, Mismatches: 35, Indels: 13
0.78 0.16 0.06
Matches are distributed among these distances:
29 32 0.19
30 120 0.72
31 15 0.09
ACGTcount: A:0.36, C:0.20, G:0.03, T:0.41
Consensus pattern (29 bp):
CAAAAATATATTTTGACCCCAAAACTTTT
Found at i:23118503 original size:60 final size:60
Alignment explanation
Indices: 23118406--23118655 Score: 342
Period size: 60 Copynumber: 4.2 Consensus size: 60
23118396 CCCTGAAAGT
* * * *
23118406 CCCTAAAC-TATCCAAAAATAGTATTTTGACCCCAAAACTTTTCAAAAATTACATTTTAAT
1 CCCTAAACTTTTCCAAAATTA-TATTTTGACCCCAAAACTTTTCAAAAATTACATTTTGAC
* *
23118466 CCCTAAACTTTTCCAAAATTATATTTTGATCCTAAAACTTTTCAAAAATTACATTTTGAC
1 CCCTAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTTCAAAAATTACATTTTGAC
* *** *
23118526 CCCTAAACTTTTCTAAAATTATATTTTGACCCCAAAACTTTTTGTAAATTTCATTTTGAC
1 CCCTAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTTCAAAAATTACATTTTGAC
* * * *
23118586 CCTTAAACTTTTCCAAAATTATATTTTGACCCTAAAACTTTT-TAAAATTACATTTTTAC
1 CCCTAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTTCAAAAATTACATTTTGAC
23118645 CCCTAAACTTT
1 CCCTAAACTTT
23118656 CTAAAACTCC
Statistics
Matches: 168, Mismatches: 21, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
59 23 0.14
60 135 0.80
61 10 0.06
ACGTcount: A:0.36, C:0.21, G:0.03, T:0.40
Consensus pattern (60 bp):
CCCTAAACTTTTCCAAAATTATATTTTGACCCCAAAACTTTTCAAAAATTACATTTTGAC
Found at i:23118564 original size:90 final size:90
Alignment explanation
Indices: 23118428--23118655 Score: 291
Period size: 90 Copynumber: 2.5 Consensus size: 90
23118418 CAAAAATAGT
* * *
23118428 ATTTTGACCCCAAAACTTTTCAAAAATTACATTTTAATCCCTAAACTTTTCCAAAATTAT-ATTT
1 ATTTTGACCCCTAAACTTTTCTAAAATTACATTTTAACCCCTAAACTTTTCCAAAATT-TCATTT
*
23118492 TGATCCTAAAACTTTTCAAAAATTAC
65 TGACCCTAAAACTTTTCAAAAATTAC
* * * ***
23118518 ATTTTGACCCCTAAACTTTTCTAAAATTATATTTTGACCCCAAAACTTTTTGTAAATTTCATTTT
1 ATTTTGACCCCTAAACTTTTCTAAAATTACATTTTAACCCCTAAACTTTTCCAAAATTTCATTTT
* * *
23118583 GACCCTTAAACTTTTCCAAAATTAT
66 GACCCTAAAACTTTTCAAAAATTAC
*
23118608 ATTTTGA-CCCTAAAACTTTT-TAAAATTACATTTTTACCCCTAAACTTT
1 ATTTTGACCCCT-AAACTTTTCTAAAATTACATTTTAACCCCTAAACTTT
23118656 CTAAAACTCC
Statistics
Matches: 120, Mismatches: 16, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
89 30 0.25
90 90 0.75
ACGTcount: A:0.35, C:0.20, G:0.03, T:0.42
Consensus pattern (90 bp):
ATTTTGACCCCTAAACTTTTCTAAAATTACATTTTAACCCCTAAACTTTTCCAAAATTTCATTTT
GACCCTAAAACTTTTCAAAAATTAC
Found at i:23118692 original size:59 final size:59
Alignment explanation
Indices: 23118629--23118769 Score: 212
Period size: 59 Copynumber: 2.4 Consensus size: 59
23118619 AAAACTTTTT
* *
23118629 AAAATTA-CATTTTTACCCCTAAACTTTCTAAAACTCCATTTTTAACCTCGATTTCACCA
1 AAAATTACCA-TTTTACCCCTAAACTTTCCAAAACCCCATTTTTAACCTCGATTTCACCA
* * *
23118688 AAAATTACCATTTTACCCATAAACTTTCCAAAACCCCATTTTTAACCTTGATTTTACCA
1 AAAATTACCATTTTACCCCTAAACTTTCCAAAACCCCATTTTTAACCTCGATTTCACCA
*
23118747 AAAATTACCATTTTGCCCCTAAA
1 AAAATTACCATTTTACCCCTAAA
23118770 AGTCCAAAAT
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
59 72 0.97
60 2 0.03
ACGTcount: A:0.35, C:0.27, G:0.02, T:0.35
Consensus pattern (59 bp):
AAAATTACCATTTTACCCCTAAACTTTCCAAAACCCCATTTTTAACCTCGATTTCACCA
Found at i:23118719 original size:30 final size:29
Alignment explanation
Indices: 23118406--23118720 Score: 194
Period size: 30 Copynumber: 10.6 Consensus size: 29
23118396 CCCTGAAAGT
* *
23118406 CCCTAAACTATCCAAAAA-TAGTATTTTGA
1 CCCTAAACTTTCCAAAAATTA-CATTTTGA
* * *
23118435 CCCCAAAACTTTTCAAAAATTACATTTTAA
1 -CCCTAAACTTTCCAAAAATTACATTTTGA
*
23118465 TCCCTAAACTTTTCC-AAAATTATATTTTGA
1 -CCCTAAAC-TTTCCAAAAATTACATTTTGA
* *
23118495 TCCTAAAACTTTTCAAAAATTACATTTTGA
1 CCCT-AAACTTTCCAAAAATTACATTTTGA
* * *
23118525 CCCCTAAACTTTTCTAAAATTATATTTTGA
1 -CCCTAAACTTTCCAAAAATTACATTTTGA
* **** *
23118555 CCCCAAAACTTTTTGTAAATTTCATTTTGA
1 -CCCTAAACTTTCCAAAAATTACATTTTGA
*
23118585 CCCTTAAACTTTTCC-AAAATTATATTTTGA
1 CCC-TAAAC-TTTCCAAAAATTACATTTTGA
** *
23118615 CCCTAAAACTTT-TTAAAATTACATTTTTA
1 CCCT-AAACTTTCCAAAAATTACATTTTGA
* * * *
23118644 CCCCTAAACTTT-CTAAAACTCCATTTTTA
1 -CCCTAAACTTTCCAAAAATTACATTTTGA
* **
23118673 ACCTCGA-TTTCACCAAAAATTACCATTTT-A
1 CCCTAAACTTT--CCAAAAATTA-CATTTTGA
23118703 CCCATAAACTTTCCAAAA
1 CCC-TAAACTTTCCAAAA
23118721 CCCCATTTTT
Statistics
Matches: 226, Mismatches: 43, Indels: 32
0.75 0.14 0.11
Matches are distributed among these distances:
27 3 0.01
28 4 0.02
29 48 0.21
30 148 0.65
31 20 0.09
32 3 0.01
ACGTcount: A:0.37, C:0.22, G:0.03, T:0.38
Consensus pattern (29 bp):
CCCTAAACTTTCCAAAAATTACATTTTGA
Found at i:23119186 original size:96 final size:96
Alignment explanation
Indices: 23119021--23119202 Score: 228
Period size: 96 Copynumber: 1.9 Consensus size: 96
23119011 AAAACTTTAA
* * * **
23119021 AATCGAGGCAATATTCTTTTATTTCGAGTTTTGAAACTTTGTGCCTTAACGTACTAGGTGCGATT
1 AATCGAGGCAATATTCTTTTATTTCGAGTTTTGAAAATTTGCGCCTTAACGTACTAGGTGCAACC
23119086 TTTCTTCAAATCGAAATAATCGAATATCCTT
66 TTTCTTCAAATCGAAATAATCGAATATCCTT
* *
23119117 AATCGAGGCAATGTT-TTCTTATCTTCG-GTTATT-AAAATTTGCGCCTTAA-TTCACTAGGTGC
1 AATCGAGGCAATATTCTT-TTAT-TTCGAGTT-TTGAAAATTTGCGCCTTAACGT-ACTAGGTGC
*
23119178 AACCTTTCTTCAAATCGAGATAATC
62 AACCTTTCTTCAAATCGAAATAATC
23119203 AAACACCCTT
Statistics
Matches: 74, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
95 3 0.04
96 65 0.88
97 6 0.08
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.38
Consensus pattern (96 bp):
AATCGAGGCAATATTCTTTTATTTCGAGTTTTGAAAATTTGCGCCTTAACGTACTAGGTGCAACC
TTTCTTCAAATCGAAATAATCGAATATCCTT
Found at i:23121476 original size:16 final size:16
Alignment explanation
Indices: 23121452--23121483 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
23121442 TACTTACAAA
*
23121452 TTTATTCCTTTAACAT
1 TTTAATCCTTTAACAT
23121468 TTTAATCCTTTAACAT
1 TTTAATCCTTTAACAT
23121484 AAAAATTACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.19, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTAATCCTTTAACAT
Found at i:23127064 original size:23 final size:23
Alignment explanation
Indices: 23127034--23127165 Score: 174
Period size: 23 Copynumber: 5.7 Consensus size: 23
23127024 CTTATATCCA
23127034 TGCTTAAATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
* * *
23127057 TGCTTAAATTTTAATATGATTTA
1 TGCTTAAATATTAATGTGATTTG
* *
23127080 TGATTAGATATTAATGTGATTTG
1 TGCTTAAATATTAATGTGATTTG
* * *
23127103 TGCTTAAGTATTAATCTGATTTA
1 TGCTTAAATATTAATGTGATTTG
*
23127126 TGCTTAAATATTAATATGATTTG
1 TGCTTAAATATTAATGTGATTTG
*
23127149 TGCTCAAATATTAATGT
1 TGCTTAAATATTAATGT
23127166 AACACCCCTT
Statistics
Matches: 91, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 91 1.00
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.48
Consensus pattern (23 bp):
TGCTTAAATATTAATGTGATTTG
Found at i:23127145 original size:69 final size:69
Alignment explanation
Indices: 23127034--23127165 Score: 192
Period size: 69 Copynumber: 1.9 Consensus size: 69
23127024 CTTATATCCA
* * * * *
23127034 TGCTTAAATATTAATGTGATTTGTGCTTAAATTTTAATATGATTTATGATTAGATATTAATGTGA
1 TGCTTAAATATTAATCTGATTTATGCTTAAATATTAATATGATTTATGATCAAATATTAATGTGA
23127099 TTTG
66 TTTG
* * *
23127103 TGCTTAAGTATTAATCTGATTTATGCTTAAATATTAATATGATTTGTGCTCAAATATTAATGT
1 TGCTTAAATATTAATCTGATTTATGCTTAAATATTAATATGATTTATGATCAAATATTAATGT
23127166 AACACCCCTT
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
69 55 1.00
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.48
Consensus pattern (69 bp):
TGCTTAAATATTAATCTGATTTATGCTTAAATATTAATATGATTTATGATCAAATATTAATGTGA
TTTG
Found at i:23130570 original size:23 final size:23
Alignment explanation
Indices: 23130537--23130719 Score: 267
Period size: 23 Copynumber: 8.0 Consensus size: 23
23130527 GACTGTTACA
*
23130537 ATTAATGTGATTTGTGCTCAAAT
1 ATTAATGTGATTTGTGCTTAAAT
* *
23130560 ATTAATATGATTTGTGCTCAAAT
1 ATTAATGTGATTTGTGCTTAAAT
* * *
23130583 ATTAGTGTGATTTATACTTAAAT
1 ATTAATGTGATTTGTGCTTAAAT
23130606 ATTAATGTGATTTGTGCTTAAAT
1 ATTAATGTGATTTGTGCTTAAAT
*
23130629 ACTAATGTGATTTGTGCTTAAAT
1 ATTAATGTGATTTGTGCTTAAAT
* * *
23130652 ATTGATATGATTTGTGCTCAAAT
1 ATTAATGTGATTTGTGCTTAAAT
23130675 ATTAATGTGATTTGTGCTTAAAT
1 ATTAATGTGATTTGTGCTTAAAT
*
23130698 ATTAATATGATTTGTGCTTAAA
1 ATTAATGTGATTTGTGCTTAAA
23130720 GAATTAAGAT
Statistics
Matches: 142, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 142 1.00
ACGTcount: A:0.32, C:0.07, G:0.16, T:0.45
Consensus pattern (23 bp):
ATTAATGTGATTTGTGCTTAAAT
Found at i:23134320 original size:16 final size:16
Alignment explanation
Indices: 23134293--23134335 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
23134283 GAGATCTAAG
23134293 TAAAAATAAAAAAAAAT
1 TAAAAAT-AAAAAAAAT
*
23134310 TAAAAATAAAAGAAAT
1 TAAAAATAAAAAAAAT
*
23134326 AAAAAATAAA
1 TAAAAATAAA
23134336 GAAATCAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
16 17 0.71
17 7 0.29
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.16
Consensus pattern (16 bp):
TAAAAATAAAAAAAAT
Found at i:23134328 original size:15 final size:15
Alignment explanation
Indices: 23134293--23134350 Score: 55
Period size: 15 Copynumber: 3.7 Consensus size: 15
23134283 GAGATCTAAG
*
23134293 TAAAAATAAAAAAAAA
1 TAAAAAT-AAAAGAAA
23134309 TTAAAAATAAAAGAAA
1 -TAAAAATAAAAGAAA
23134325 TAAAAA-ATAAAGAAA
1 TAAAAATA-AAAGAAA
* *
23134340 TCAAAGTAAAA
1 TAAAAATAAAA
23134351 ATAAATAGTA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
14 1 0.03
15 20 0.56
16 8 0.22
17 7 0.19
ACGTcount: A:0.78, C:0.02, G:0.05, T:0.16
Consensus pattern (15 bp):
TAAAAATAAAAGAAA
Found at i:23135137 original size:30 final size:29
Alignment explanation
Indices: 23135099--23135175 Score: 86
Period size: 30 Copynumber: 2.7 Consensus size: 29
23135089 AAATAAACAT
23135099 AAATTAAATACAAATAAATAATAT-CTTTA
1 AAATTAAATACAAATAAA-AATATACTTTA
* * *
23135128 AATATTAAATCCTAATAAAAATATATTTTA
1 AA-ATTAAATACAAATAAAAATATACTTTA
*
23135158 AAATAAAATA-AAATAAAA
1 AAATTAAATACAAATAAAA
23135176 CCAAGTCTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
28 7 0.17
29 13 0.32
30 20 0.50
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (29 bp):
AAATTAAATACAAATAAAAATATACTTTA
Found at i:23137917 original size:21 final size:21
Alignment explanation
Indices: 23137891--23137941 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
23137881 TTAGATGCCT
23137891 CAGTTTGCTTTTGAAAATCTA
1 CAGTTTGCTTTTGAAAATCTA
23137912 CAGTTTGCTTTTGAAAATCTA
1 CAGTTTGCTTTTGAAAATCTA
* *
23137933 TAGATTGCT
1 CAGTTTGCT
23137942 GCTGAAATTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.43
Consensus pattern (21 bp):
CAGTTTGCTTTTGAAAATCTA
Found at i:23137947 original size:21 final size:21
Alignment explanation
Indices: 23137902--23137948 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
23137892 AGTTTGCTTT
* **
23137902 TGAAAATCTACAGTTTGCTTT
1 TGAAAATCTACAGATTGCTGC
*
23137923 TGAAAATCTATAGATTGCTGC
1 TGAAAATCTACAGATTGCTGC
23137944 TGAAA
1 TGAAA
23137949 TTCAAGAACA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (21 bp):
TGAAAATCTACAGATTGCTGC
Found at i:23143846 original size:53 final size:52
Alignment explanation
Indices: 23143687--23143863 Score: 184
Period size: 50 Copynumber: 3.4 Consensus size: 52
23143677 TAATACTGAT
** * *
23143687 GATGACA-TATAGTCATCGGACC-TTATAATCCACGAGGGATTCGTATACTCAC
1 GATGACACT-TAGTCATCGGACCTTTA-AATCCATAAAGGATTCATATACTCAC
* *** * *
23143739 GATGACAC--AGTCATCGAACCTCTT-AATTTGTAAAGGATCCATATACTCAT
1 GATGACACTTAGTCATCGGACCT-TTAAATCCATAAAGGATTCATATACTCAC
*
23143789 GATGACACTTAGTCATCAGACCTTTAAATCCATAAAGGATTTCATATACTCAC
1 GATGACACTTAGTCATCGGACCTTTAAATCCATAAAGGA-TTCATATACTCAC
23143842 GATGACACTTAGTCATCGGACC
1 GATGACACTTAGTCATCGGACC
23143864 CTTTTCATTT
Statistics
Matches: 100, Mismatches: 18, Indels: 13
0.76 0.14 0.10
Matches are distributed among these distances:
50 36 0.36
51 2 0.02
52 30 0.30
53 32 0.32
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (52 bp):
GATGACACTTAGTCATCGGACCTTTAAATCCATAAAGGATTCATATACTCAC
Found at i:23150290 original size:3 final size:3
Alignment explanation
Indices: 23150282--23150346 Score: 66
Period size: 3 Copynumber: 22.7 Consensus size: 3
23150272 CAGGGCAACG
* *
23150282 TCT TCT TCT TTT TCT TCCT T-T TCT TCT TTT TCT TCT TCT TCT T-T
1 TCT TCT TCT TCT TCT T-CT TCT TCT TCT TCT TCT TCT TCT TCT TCT
*
23150326 TCT T-T T-T TCT TCT TCT GCT TC
1 TCT TCT TCT TCT TCT TCT TCT TC
23150347 AATACCCACA
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
2 8 0.15
3 41 0.79
4 3 0.06
ACGTcount: A:0.00, C:0.28, G:0.02, T:0.71
Consensus pattern (3 bp):
TCT
Found at i:23150307 original size:18 final size:17
Alignment explanation
Indices: 23150284--23150339 Score: 75
Period size: 18 Copynumber: 3.5 Consensus size: 17
23150274 GGGCAACGTC
23150284 TTCTTCTTTTTCTTCCTT
1 TTCTTCTTTTTCTT-CTT
23150302 TTCTTCTTTTTCTTC--
1 TTCTTCTTTTTCTTCTT
23150317 TTCTTC-TTTTCTT-TT
1 TTCTTCTTTTTCTTCTT
23150332 TTCTTCTT
1 TTCTTCTT
23150340 CTGCTTCAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
14 7 0.20
15 12 0.34
16 1 0.03
17 1 0.03
18 14 0.40
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (17 bp):
TTCTTCTTTTTCTTCTT
Found at i:23150340 original size:18 final size:20
Alignment explanation
Indices: 23150282--23150346 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 20
23150272 CAGGGCAACG
23150282 TCTTCTTCTTTTTCTTCCTT-T
1 TCTTCTT-TTTTTCTT-CTTCT
23150303 TCTTCTTTTTCTTCTTCTTCT
1 TCTTCTTTTT-TTCTTCTTCT
23150324 T-TTC-TTTTTTCTTCTTCT
1 TCTTCTTTTTTTCTTCTTCT
*
23150342 GCTTC
1 TCTTC
23150347 AATACCCACA
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
18 10 0.25
19 7 0.17
20 9 0.22
21 14 0.35
ACGTcount: A:0.00, C:0.28, G:0.02, T:0.71
Consensus pattern (20 bp):
TCTTCTTTTTTTCTTCTTCT
Found at i:23152163 original size:24 final size:24
Alignment explanation
Indices: 23152118--23152165 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
23152108 TACAAAAACT
23152118 AAAGAAACAAATTAAAGTAAAATA
1 AAAGAAACAAATTAAAGTAAAATA
*
23152142 AAAGACAA-AAATTAACAGAAAAAT
1 AAAGA-AACAAATTAA-AGTAAAAT
23152166 TACAATGACA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.71, C:0.06, G:0.08, T:0.15
Consensus pattern (24 bp):
AAAGAAACAAATTAAAGTAAAATA
Found at i:23166775 original size:24 final size:24
Alignment explanation
Indices: 23166747--23166833 Score: 129
Period size: 24 Copynumber: 3.6 Consensus size: 24
23166737 AGAAATAATC
*
23166747 TTTCAGTTAAACTCTGTTTAATTG
1 TTTCAGTTAAACTCTGTTTATTTG
* *
23166771 TTTCATTTAAACTTTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTATTTG
*
23166795 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTATTTG
*
23166819 TTTGAGTTAAACTCT
1 TTTCAGTTAAACTCT
23166834 TATTAGTTTA
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 56 1.00
ACGTcount: A:0.24, C:0.11, G:0.10, T:0.54
Consensus pattern (24 bp):
TTTCAGTTAAACTCTGTTTATTTG
Found at i:23175961 original size:34 final size:35
Alignment explanation
Indices: 23175909--23175974 Score: 125
Period size: 34 Copynumber: 1.9 Consensus size: 35
23175899 TAGCACCATC
23175909 ATAGATGGTTTTGTGTAATGTGTATGTTACAAGCT
1 ATAGATGGTTTTGTGTAATGTGTATGTTACAAGCT
23175944 ATAGATGG-TTTGTGTAATGTGTATGTTACAA
1 ATAGATGGTTTTGTGTAATGTGTATGTTACAA
23175975 TACTTTAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 23 0.74
35 8 0.26
ACGTcount: A:0.27, C:0.05, G:0.26, T:0.42
Consensus pattern (35 bp):
ATAGATGGTTTTGTGTAATGTGTATGTTACAAGCT
Found at i:23181023 original size:31 final size:31
Alignment explanation
Indices: 23180988--23181046 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
23180978 ATGTGTATAG
* *
23180988 TTGAACCAGAATCAAAATTTCATTTATACAT
1 TTGAACCAAAATCAAAATTTCATGTATACAT
* *
23181019 TTGAACCAAAATTAAAGTTTCATGTATA
1 TTGAACCAAAATCAAAATTTCATGTATA
23181047 TAATAAATAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.36
Consensus pattern (31 bp):
TTGAACCAAAATCAAAATTTCATGTATACAT
Found at i:23185983 original size:23 final size:26
Alignment explanation
Indices: 23185945--23185996 Score: 83
Period size: 24 Copynumber: 2.1 Consensus size: 26
23185935 GCTTTATTTC
23185945 TTTCTTGTAATTTAGG-TTTAGTTAT
1 TTTCTTGTAATTTAGGTTTTAGTTAT
23185970 TTTCTT-T-ATTTAGGTTTTAGTTAT
1 TTTCTTGTAATTTAGGTTTTAGTTAT
23185994 TTT
1 TTT
23185997 TACTTTTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
23 7 0.27
24 13 0.50
25 6 0.23
ACGTcount: A:0.17, C:0.04, G:0.13, T:0.65
Consensus pattern (26 bp):
TTTCTTGTAATTTAGGTTTTAGTTAT
Found at i:23189067 original size:18 final size:19
Alignment explanation
Indices: 23189044--23189081 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
23189034 ATCCAAAATT
23189044 ATAAG-TCTTAAAAATAAA
1 ATAAGTTCTTAAAAATAAA
* *
23189062 ATAAGTTTTTAAAATTAAA
1 ATAAGTTCTTAAAAATAAA
23189081 A
1 A
23189082 GTTCAACACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (19 bp):
ATAAGTTCTTAAAAATAAA
Found at i:23190196 original size:21 final size:21
Alignment explanation
Indices: 23190170--23190215 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
23190160 AGGCATTGTG
23190170 ACTTGGAGTGAGTCCCCCTGC
1 ACTTGGAGTGAGTCCCCCTGC
* *
23190191 ACTTGGTGTGAGTCCCCTTGC
1 ACTTGGAGTGAGTCCCCCTGC
23190212 ACTT
1 ACTT
23190216 AATGTTCGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.13, C:0.30, G:0.26, T:0.30
Consensus pattern (21 bp):
ACTTGGAGTGAGTCCCCCTGC
Found at i:23208051 original size:21 final size:20
Alignment explanation
Indices: 23208022--23208062 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
23208012 TCAGTCACTT
*
23208022 GAAAAAAAATGAGAAAAAAAA
1 GAAAAAAAAAGA-AAAAAAAA
*
23208043 GAAAGAAAAAGAAAAAAAAA
1 GAAAAAAAAAGAAAAAAAAA
23208063 TTGTTGAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (20 bp):
GAAAAAAAAAGAAAAAAAAA
Found at i:23208062 original size:10 final size:10
Alignment explanation
Indices: 23208022--23208062 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
23208012 TCAGTCACTT
*
23208022 GAAAAAAAAT
1 GAAAAAAAAA
23208032 GAGAAAAAAAA
1 GA-AAAAAAAA
*
23208043 GAAAGAAAAA
1 GAAAAAAAAA
23208053 GAAAAAAAAA
1 GAAAAAAAAA
23208063 TTGTTGAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
10 18 0.67
11 9 0.33
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:23213050 original size:37 final size:37
Alignment explanation
Indices: 23213000--23213227 Score: 303
Period size: 37 Copynumber: 6.2 Consensus size: 37
23212990 CTTCTAAGAA
* * ** *
23213000 ATTCGAGCTATGTGCCTAGAAGGCTTTATGCCTGTGT
1 ATTCGGGCTATGTGCCTAGCAGGCTTCGTGCCGGTGT
23213037 ATTCGGGCTATGTGCCTAGCAGGCTTCGTGCCGGTGT
1 ATTCGGGCTATGTGCCTAGCAGGCTTCGTGCCGGTGT
* * * * * *
23213074 ATTCAGGCTATGTTCCTAGTAGGCTTTGTTCCTGTGT
1 ATTCGGGCTATGTGCCTAGCAGGCTTCGTGCCGGTGT
23213111 ATTCGGGCTATGTGCCTAGCAGGCTTCGTGCCGGTGT
1 ATTCGGGCTATGTGCCTAGCAGGCTTCGTGCCGGTGT
* *
23213148 ATTCGAGCTATTTGCCTAGCAGGCTTCGTGCCGGTGT
1 ATTCGGGCTATGTGCCTAGCAGGCTTCGTGCCGGTGT
* * * *
23213185 ATTTGAGCTATGTGCCTAGCAGGCTTCTTGTCGGTGT
1 ATTCGGGCTATGTGCCTAGCAGGCTTCGTGCCGGTGT
23213222 ATTCGG
1 ATTCGG
23213228 ACTGTCTGTC
Statistics
Matches: 166, Mismatches: 25, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 166 1.00
ACGTcount: A:0.14, C:0.21, G:0.30, T:0.35
Consensus pattern (37 bp):
ATTCGGGCTATGTGCCTAGCAGGCTTCGTGCCGGTGT
Found at i:23218573 original size:134 final size:134
Alignment explanation
Indices: 23218333--23218604 Score: 508
Period size: 134 Copynumber: 2.0 Consensus size: 134
23218323 GTGCTTCGTC
23218333 GTTATAGATCAGATCCCTCCCACGTGTTATCAGTGGAAGATATTGAGTTGCAACCCGATTTAACC
1 GTTATAGATCAGATCCCTCCCACGTGTTATCAGTGGAAGATATTGAGTTGCAACCCGATTTAACC
* *
23218398 AAAACTGAGGAGCCTATCAAAATTTTGGCTCGAGAAGTGAAAGAGTTGTGAAACAAAAAGGTTGA
66 AAAACTAAGGAGCCTATCAAAATTTTGGCTCGAGAAGTGAAAGAGTTGTGAAACAAAAAGGTTAA
23218463 GTTA
131 GTTA
*
23218467 GTTATAGATCAGATCCCTCCCACGTGTTATCAGTGGAAGATATTGTGTTGCAACCCGATTTAACC
1 GTTATAGATCAGATCCCTCCCACGTGTTATCAGTGGAAGATATTGAGTTGCAACCCGATTTAACC
*
23218532 TAAACTAAGGAGCCTATCAAAATTTTGGCTCGAGAAGTGAAAGAGTTGTGAAACAAAAAGGTTAA
66 AAAACTAAGGAGCCTATCAAAATTTTGGCTCGAGAAGTGAAAGAGTTGTGAAACAAAAAGGTTAA
23218597 GTTA
131 GTTA
23218601 GTTA
1 GTTA
23218605 AAGTACTGTG
Statistics
Matches: 134, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
134 134 1.00
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.27
Consensus pattern (134 bp):
GTTATAGATCAGATCCCTCCCACGTGTTATCAGTGGAAGATATTGAGTTGCAACCCGATTTAACC
AAAACTAAGGAGCCTATCAAAATTTTGGCTCGAGAAGTGAAAGAGTTGTGAAACAAAAAGGTTAA
GTTA
Found at i:23219482 original size:37 final size:37
Alignment explanation
Indices: 23219432--23219574 Score: 196
Period size: 37 Copynumber: 3.9 Consensus size: 37
23219422 ACTTCTAAGA
* *
23219432 ATTCGAGCTATGTGCCTAACAGGCTTCGTGCCTGTGT
1 ATTCGGGCTATGTGCCTAACAGGCTTCGTGCCGGTGT
*
23219469 ATTCGGGCTATGTGCCTAGCAGGCTTCGTGCCGGTGT
1 ATTCGGGCTATGTGCCTAACAGGCTTCGTGCCGGTGT
* * * *
23219506 ATTCGGGCTATGTGCCTAGCAGGTTTTGTGTCGGTGT
1 ATTCGGGCTATGTGCCTAACAGGCTTCGTGCCGGTGT
* * *
23219543 ATTCAGGCTACGTGCCTAACAGGCTACGTGCC
1 ATTCGGGCTATGTGCCTAACAGGCTTCGTGCC
23219575 TAACAGGCTT
Statistics
Matches: 93, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 93 1.00
ACGTcount: A:0.15, C:0.24, G:0.31, T:0.31
Consensus pattern (37 bp):
ATTCGGGCTATGTGCCTAACAGGCTTCGTGCCGGTGT
Found at i:23219567 original size:16 final size:16
Alignment explanation
Indices: 23219546--23219590 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
23219536 TCGGTGTATT
23219546 CAGGCTACGTGCCTAA
1 CAGGCTACGTGCCTAA
23219562 CAGGCTACGTGCCTAA
1 CAGGCTACGTGCCTAA
*
23219578 CAGGCTTCGTGCC
1 CAGGCTACGTGCC
23219591 GGAGTATTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.20, C:0.33, G:0.27, T:0.20
Consensus pattern (16 bp):
CAGGCTACGTGCCTAA
Found at i:23219598 original size:53 final size:53
Alignment explanation
Indices: 23219511--23219620 Score: 130
Period size: 53 Copynumber: 2.1 Consensus size: 53
23219501 GGTGTATTCG
* * * * * *
23219511 GGCTATGTGCCTAGCAGGTTTTGTGTCGGTGTATTCAGGCTACGTGCCTAACA
1 GGCTACGTGCCTAACAGGCTTCGTGCCGGAGTATTCAGGCTACGTGCCTAACA
** * *
23219564 GGCTACGTGCCTAACAGGCTTCGTGCCGGAGTATTTGGGCTATGTGCCTAGCA
1 GGCTACGTGCCTAACAGGCTTCGTGCCGGAGTATTCAGGCTACGTGCCTAACA
23219617 GGCT
1 GGCT
23219621 TCATGCTGAT
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
53 47 1.00
ACGTcount: A:0.16, C:0.23, G:0.32, T:0.29
Consensus pattern (53 bp):
GGCTACGTGCCTAACAGGCTTCGTGCCGGAGTATTCAGGCTACGTGCCTAACA
Found at i:23227000 original size:17 final size:17
Alignment explanation
Indices: 23226978--23227013 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
23226968 ATACACTAAC
*
23226978 ATTAAAATGCAATGACA
1 ATTAAAATGCAACGACA
23226995 ATTAAAATGCAACGACA
1 ATTAAAATGCAACGACA
23227012 AT
1 AT
23227014 GTGCACTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.53, C:0.14, G:0.11, T:0.22
Consensus pattern (17 bp):
ATTAAAATGCAACGACA
Found at i:23238043 original size:24 final size:23
Alignment explanation
Indices: 23237995--23238044 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
23237985 TTTCTTGTAA
*
23237995 TTTAGGTTTAGTTATTTTCTTTC
1 TTTAGGTTTAGTTATTTTCTCTC
23238018 TTTAGGTTTTAGTTATTTT-TACTC
1 TTTAGG-TTTAGTTATTTTCT-CTC
23238042 TTT
1 TTT
23238045 TTATGGAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 7 0.29
24 17 0.71
ACGTcount: A:0.14, C:0.08, G:0.12, T:0.66
Consensus pattern (23 bp):
TTTAGGTTTAGTTATTTTCTCTC
Found at i:23247065 original size:6 final size:6
Alignment explanation
Indices: 23247054--23247104 Score: 75
Period size: 6 Copynumber: 8.5 Consensus size: 6
23247044 TGAGCAAAAT
* * *
23247054 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG
23247102 TGA
1 TGA
23247105 TATGAATTGT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 41 1.00
ACGTcount: A:0.47, C:0.00, G:0.31, T:0.22
Consensus pattern (6 bp):
TGAAAG
Found at i:23251822 original size:51 final size:51
Alignment explanation
Indices: 23251746--23251932 Score: 214
Period size: 51 Copynumber: 3.6 Consensus size: 51
23251736 CTATAAACGA
* *
23251746 AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT
* * *
23251797 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGATGTATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT
* ** * * **
23251848 AAGGGTCCGATGACTTTGTGTCATCGTGAGTATATGAATTCCTATATGGAAC
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAA-TCCTTTATGGATT
* *
23251900 AAGAGGTCAGATGACTATA-TGTCATCGTTAGTA
1 AA-AGGTCCGATGACTA-AGTGTCATCGTGAGTA
23251933 TTAAATGAAA
Statistics
Matches: 113, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
51 80 0.71
52 9 0.08
53 24 0.21
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTATGGATT
Found at i:23258995 original size:27 final size:27
Alignment explanation
Indices: 23258963--23259030 Score: 66
Period size: 28 Copynumber: 2.4 Consensus size: 27
23258953 TCTAAAACTC
*
23258963 ACAAAACCTTAACACTA-ATTTAAATAA
1 ACAAAACC-TAACACTACATTTAAAAAA
* * *
23258990 ACAAAAACCTAGCCCTACTTTTAAAAAA
1 AC-AAAACCTAACACTACATTTAAAAAA
23259018 ACAAAACCCTAAC
1 ACAAAA-CCTAAC
23259031 CTTAAAGAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
27 12 0.36
28 21 0.64
ACGTcount: A:0.53, C:0.25, G:0.01, T:0.21
Consensus pattern (27 bp):
ACAAAACCTAACACTACATTTAAAAAA
Found at i:23269398 original size:20 final size:20
Alignment explanation
Indices: 23269375--23269443 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
23269365 TTAAAATTCT
23269375 TAAAATTATTTTTTTAAATA
1 TAAAATTATTTTTTTAAATA
***
23269395 TAAAATTATTAAAATT-AAT-
1 TAAAATTATT-TTTTTAAATA
*
23269414 TAAAATTATTTTTTAAAATA
1 TAAAATTATTTTTTTAAATA
23269434 TAAAATTATT
1 TAAAATTATT
23269444 AAAATCATCA
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
18 1 0.03
19 13 0.33
20 23 0.59
21 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TAAAATTATTTTTTTAAATA
Found at i:23269407 original size:38 final size:39
Alignment explanation
Indices: 23269365--23269448 Score: 143
Period size: 39 Copynumber: 2.2 Consensus size: 39
23269355 ACAAATGATT
* *
23269365 TTAAAATT-CTTAAAATTATTTTTTTAAATATAAAATTA
1 TTAAAATTAATTAAAATTATTTTTTAAAATATAAAATTA
23269403 TTAAAATTAATTAAAATTATTTTTTAAAATATAAAATTA
1 TTAAAATTAATTAAAATTATTTTTTAAAATATAAAATTA
23269442 TTAAAAT
1 TTAAAAT
23269449 CATCATCATC
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
38 8 0.19
39 35 0.81
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (39 bp):
TTAAAATTAATTAAAATTATTTTTTAAAATATAAAATTA
Found at i:23269409 original size:9 final size:9
Alignment explanation
Indices: 23269395--23269448 Score: 50
Period size: 9 Copynumber: 6.7 Consensus size: 9
23269385 TTTTTAAATA
23269395 TAAAATTAT
1 TAAAATTAT
23269404 TAAAATTAAT
1 TAAAATT-AT
23269414 TAAAATTAT
1 TAAAATTAT
23269423 T----TT-T
1 TAAAATTAT
23269427 TAAAA-TA-
1 TAAAATTAT
23269434 TAAAATTAT
1 TAAAATTAT
23269443 TAAAAT
1 TAAAAT
23269449 CATCATCATC
Statistics
Matches: 37, Mismatches: 0, Indels: 16
0.70 0.00 0.30
Matches are distributed among these distances:
4 2 0.05
5 2 0.05
7 6 0.16
8 2 0.05
9 16 0.43
10 9 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
TAAAATTAT
Found at i:23269837 original size:22 final size:21
Alignment explanation
Indices: 23269809--23269850 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
23269799 TATAAGAAAG
23269809 ATTATTTAAGTCTAAGTAAGAC
1 ATTATTTAAGT-TAAGTAAGAC
*
23269831 ATTATTTAAGTTAATTAAGA
1 ATTATTTAAGTTAAGTAAGA
23269851 GTCTAACTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.43, C:0.05, G:0.12, T:0.40
Consensus pattern (21 bp):
ATTATTTAAGTTAAGTAAGAC
Found at i:23271122 original size:21 final size:21
Alignment explanation
Indices: 23271073--23271124 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
23271063 GGAGTTTTTA
23271073 GTATCGGTAGAAGCATGACTT
1 GTATCGGTAGAAGCATGACTT
* * *
23271094 AT-TCCGGTAGAAGCTTTACTT
1 GTAT-CGGTAGAAGCATGACTT
23271115 GTATCGGTAG
1 GTATCGGTAG
23271125 GACTATCACA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 1 0.04
21 23 0.92
22 1 0.04
ACGTcount: A:0.25, C:0.15, G:0.27, T:0.33
Consensus pattern (21 bp):
GTATCGGTAGAAGCATGACTT
Found at i:23276025 original size:50 final size:50
Alignment explanation
Indices: 23275950--23276052 Score: 152
Period size: 50 Copynumber: 2.1 Consensus size: 50
23275940 CACAGGTTTA
* *
23275950 TTTCATACTAGCACTTATTCTTTTATCAATAAATTATATTTGTACATAAT
1 TTTCATACTACCACTTATTCTTTTATCAATAAATTATACTTGTACATAAT
* * * *
23276000 TTTCATAGTACCACTTATTCTTTTATCAATGAATTATACTTGTATATACT
1 TTTCATACTACCACTTATTCTTTTATCAATAAATTATACTTGTACATAAT
23276050 TTT
1 TTT
23276053 TTTTCGTATT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.31, C:0.15, G:0.05, T:0.50
Consensus pattern (50 bp):
TTTCATACTACCACTTATTCTTTTATCAATAAATTATACTTGTACATAAT
Found at i:23276299 original size:26 final size:26
Alignment explanation
Indices: 23276270--23276325 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
23276260 AAATGGTTTT
23276270 TTATTTTAAATTCTAATGTTAATTTC
1 TTATTTTAAATTCTAATGTTAATTTC
* * *
23276296 TTATTTTATATTTTGATGTTAATTTC
1 TTATTTTAAATTCTAATGTTAATTTC
23276322 TTAT
1 TTAT
23276326 GTCCCATGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.27, C:0.05, G:0.05, T:0.62
Consensus pattern (26 bp):
TTATTTTAAATTCTAATGTTAATTTC
Found at i:23276817 original size:16 final size:18
Alignment explanation
Indices: 23276788--23276821 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
23276778 TCATAAATCA
23276788 AAGATATTTCCAGAAGCT
1 AAGATATTTCCAGAAGCT
23276806 AAGAT-TTT-CAGAAGCT
1 AAGATATTTCCAGAAGCT
23276822 GATATAACAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 3 0.19
18 5 0.31
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.29
Consensus pattern (18 bp):
AAGATATTTCCAGAAGCT
Found at i:23282609 original size:44 final size:44
Alignment explanation
Indices: 23282550--23282722 Score: 247
Period size: 44 Copynumber: 3.9 Consensus size: 44
23282540 AGACTTGGTG
* *
23282550 ATTACTAAATGGAAGAATTTATGTCTCGGTTAGAGCATAAGATT
1 ATTAGTAAATGGAAGAACTTATGTCTCGGTTAGAGCATAAGATT
*
23282594 ATTAGTAAATGGAAGAACTTAAGTCTCGGTTAGAGCATAAGATT
1 ATTAGTAAATGGAAGAACTTATGTCTCGGTTAGAGCATAAGATT
* * *
23282638 ATTTGTAAATGGAAGAAATTATGTCTCGGCTAGAGCATAAGATT
1 ATTAGTAAATGGAAGAACTTATGTCTCGGTTAGAGCATAAGATT
* * * * *
23282682 ATTTGTAATTGGAAGAACTTATGACTCAGATAGAGCATAAG
1 ATTAGTAAATGGAAGAACTTATGTCTCGGTTAGAGCATAAG
23282723 GTTAATTCAG
Statistics
Matches: 117, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 117 1.00
ACGTcount: A:0.38, C:0.09, G:0.22, T:0.31
Consensus pattern (44 bp):
ATTAGTAAATGGAAGAACTTATGTCTCGGTTAGAGCATAAGATT
Found at i:23284187 original size:27 final size:27
Alignment explanation
Indices: 23284130--23284188 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 27
23284120 CATGGCACCT
* * * *
23284130 TCTAAATGGACTGCCTTTGTAGTGTAG
1 TCTAAATGGACTACCCTTGTAGCGTAC
*
23284157 TCTAAATGGACTACCCTTGTGGCGTAC
1 TCTAAATGGACTACCCTTGTAGCGTAC
23284184 TCTAA
1 TCTAA
23284189 TAAGGCCTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (27 bp):
TCTAAATGGACTACCCTTGTAGCGTAC
Found at i:23288327 original size:29 final size:29
Alignment explanation
Indices: 23288275--23288331 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
23288265 TTACATTTTG
*
23288275 TTGTGTGATATTACTCCTTATTGTGTTAA
1 TTGTGTGATATTACTCCTGATTGTGTTAA
23288304 TTGTGTGATATTACT-CTGAGTTGTGTTA
1 TTGTGTGATATTACTCCTGA-TTGTGTTA
23288332 TTAGTATGAC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 3 0.12
29 23 0.88
ACGTcount: A:0.19, C:0.09, G:0.21, T:0.51
Consensus pattern (29 bp):
TTGTGTGATATTACTCCTGATTGTGTTAA
Found at i:23305478 original size:58 final size:58
Alignment explanation
Indices: 23305432--23305618 Score: 201
Period size: 58 Copynumber: 3.3 Consensus size: 58
23305422 ATATTATAAT
23305432 TTTTACT-AATTCATATTTTAATAATAATTATATTAAAAATGTTATTAAATTATATATTA
1 TTTTACTAAATT-ATA-TTTAATAATAATTATATTAAAAATGTTATTAAATTATATATTA
* * * * * *
23305491 TTTTATTAAATTGTATTTAATAATAATTATGTT-AAAATATAATTAAATTATTTATTA
1 TTTTACTAAATTATATTTAATAATAATTATATTAAAAATGTTATTAAATTATATATTA
* *
23305548 TTCTTATTAAATTATATTTAATAATAATCT-TATT-AAAAT-TAAATTAAATTATAT-TTA
1 TT-TTACTAAATTATATTTAATAATAAT-TATATTAAAAATGT-TATTAAATTATATATTA
23305605 -TTTAC-AAATTATAT
1 TTTTACTAAATTATAT
23305619 GGATTAAGTG
Statistics
Matches: 114, Mismatches: 10, Indels: 13
0.83 0.07 0.09
Matches are distributed among these distances:
54 9 0.08
55 3 0.03
56 1 0.01
57 27 0.24
58 61 0.54
59 9 0.08
60 4 0.04
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (58 bp):
TTTTACTAAATTATATTTAATAATAATTATATTAAAAATGTTATTAAATTATATATTA
Found at i:23305560 original size:26 final size:28
Alignment explanation
Indices: 23305531--23305593 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 28
23305521 GTTAAAATAT
* * *
23305531 AATTAAATTAT-TTATTATTCTTATT-A
1 AATTAAATTATAATAATAATCTTATTAA
*
23305557 AATTATATT-TAATAATAATCTTATTAA
1 AATTAAATTATAATAATAATCTTATTAA
23305584 AATTAAATTA
1 AATTAAATTA
23305594 AATTATATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
25 1 0.03
26 19 0.66
27 9 0.31
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (28 bp):
AATTAAATTATAATAATAATCTTATTAA
Found at i:23306153 original size:18 final size:20
Alignment explanation
Indices: 23306116--23306153 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
23306106 AAACATTGGA
*
23306116 CTCATAGAGTCGAAATATAT
1 CTCATAGAGTCGAAACATAT
23306136 CTCATA-AGT-GAAACATAT
1 CTCATAGAGTCGAAACATAT
23306154 AGCTAACACT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 8 0.47
19 3 0.18
20 6 0.35
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (20 bp):
CTCATAGAGTCGAAACATAT
Found at i:23306425 original size:14 final size:14
Alignment explanation
Indices: 23306403--23306434 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
23306393 ATAATTAGTC
23306403 ACATGGCATGAAGA
1 ACATGGCATGAAGA
*
23306417 ACATTGCATGAAGA
1 ACATGGCATGAAGA
23306431 ACAT
1 ACAT
23306435 ACCCACATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.44, C:0.16, G:0.22, T:0.19
Consensus pattern (14 bp):
ACATGGCATGAAGA
Found at i:23310747 original size:21 final size:19
Alignment explanation
Indices: 23310694--23310747 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 19
23310684 AAACATTATT
* *
23310694 TAATTAAAATATATTACTA
1 TAATTAAAATATTTTAATA
23310713 TAA-TAAAATAATTTCTAATCA
1 TAATTAAAAT-ATTT-TAAT-A
23310734 TAATTAAAATATTT
1 TAATTAAAATATTT
23310748 GTACGACATT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
18 6 0.21
19 6 0.21
20 3 0.10
21 8 0.28
22 6 0.21
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.43
Consensus pattern (19 bp):
TAATTAAAATATTTTAATA
Found at i:23311907 original size:3 final size:3
Alignment explanation
Indices: 23311899--23311955 Score: 105
Period size: 3 Copynumber: 19.0 Consensus size: 3
23311889 TCCCCCATTT
*
23311899 TTC TTC TTC TTC TTC TTT TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
23311947 TTC TTC TTC
1 TTC TTC TTC
23311956 ATCAACCCAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:23312831 original size:13 final size:13
Alignment explanation
Indices: 23312813--23312881 Score: 50
Period size: 14 Copynumber: 5.1 Consensus size: 13
23312803 TGATTTAAGT
23312813 TATTATTAATTAA
1 TATTATTAATTAA
23312826 TATTA-TAATATAA
1 TATTATTAAT-TAA
* * *
23312839 TAGTATAAATTAT
1 TATTATTAATTAA
*
23312852 TATTTATTAATATTA
1 TA-TTATTAAT-TAA
*
23312867 TCTTATTATATTAA
1 TATTATTA-ATTAA
23312881 T
1 T
23312882 GAAATATATA
Statistics
Matches: 42, Mismatches: 9, Indels: 9
0.70 0.15 0.15
Matches are distributed among these distances:
12 4 0.10
13 16 0.38
14 18 0.43
15 4 0.10
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (13 bp):
TATTATTAATTAA
Found at i:23313127 original size:14 final size:14
Alignment explanation
Indices: 23313108--23313134 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
23313098 GCTTAAACGA
23313108 AAAAGGGAAGGAAG
1 AAAAGGGAAGGAAG
23313122 AAAAGGGAAGGAA
1 AAAAGGGAAGGAA
23313135 AAAGAAAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (14 bp):
AAAAGGGAAGGAAG
Found at i:23313539 original size:17 final size:18
Alignment explanation
Indices: 23313517--23313552 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
23313507 TAAACGAGTT
23313517 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
*
23313534 AATTAGGGTATAAATTGG
1 AATTAGGATATAAATTGG
23313552 A
1 A
23313553 TAGAAATTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.42, C:0.00, G:0.25, T:0.33
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:23315592 original size:30 final size:30
Alignment explanation
Indices: 23315541--23315602 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
23315531 GGAGAGTTGG
*
23315541 ATGAGAGGGAAGTAAAAGTTTTAGGAGGAAA
1 ATGAGAGAGAAGTAAAAGTTTTAGGA-GAAA
*
23315572 ATGAGAGAGAA-TAGAAGTTTTAGGAGAAA
1 ATGAGAGAGAAGTAAAAGTTTTAGGAGAAA
23315601 AT
1 AT
23315603 AAAGAGTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 6 0.21
30 13 0.45
31 10 0.34
ACGTcount: A:0.47, C:0.00, G:0.32, T:0.21
Consensus pattern (30 bp):
ATGAGAGAGAAGTAAAAGTTTTAGGAGAAA
Found at i:23315778 original size:21 final size:21
Alignment explanation
Indices: 23315744--23315785 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
23315734 AGGTGAAAGT
*
23315744 GGGAAGAAGTAAAAGTTTTGG
1 GGGAAGAAGTAAAAGGTTTGG
23315765 GGGAA-AAGTAAAAAGGTTTGG
1 GGGAAGAAGT-AAAAGGTTTGG
23315786 AGTTTGGAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.40, C:0.00, G:0.38, T:0.21
Consensus pattern (21 bp):
GGGAAGAAGTAAAAGGTTTGG
Found at i:23320318 original size:21 final size:21
Alignment explanation
Indices: 23320294--23320349 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
23320284 GTTGAGATGG
**
23320294 TTCTACCGATACAA-TGGTGAC
1 TTCTACCGATACAACTCATG-C
* *
23320315 TTCTATCGAAACAACTCATGC
1 TTCTACCGATACAACTCATGC
23320336 TTCTACCGATACAA
1 TTCTACCGATACAA
23320350 GTAAACGATC
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
21 25 0.89
22 3 0.11
ACGTcount: A:0.32, C:0.27, G:0.12, T:0.29
Consensus pattern (21 bp):
TTCTACCGATACAACTCATGC
Found at i:23321042 original size:25 final size:26
Alignment explanation
Indices: 23320979--23321044 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 26
23320969 CTTCCAAAAT
* * *
23320979 TTTAGCTCA-ATGAGCCTAGACATAG
1 TTTAGCTCATACGAGCCCAGACAGAG
*
23321004 TTTAGCTCTTACGAGCCCAGACAGA-
1 TTTAGCTCATACGAGCCCAGACAGAG
*
23321029 TTTCGCTCATACGAGC
1 TTTAGCTCATACGAGC
23321045 TAGTTAGAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
25 22 0.65
26 12 0.35
ACGTcount: A:0.27, C:0.26, G:0.20, T:0.27
Consensus pattern (26 bp):
TTTAGCTCATACGAGCCCAGACAGAG
Found at i:23321078 original size:25 final size:25
Alignment explanation
Indices: 23321050--23321098 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
23321040 CGAGCTAGTT
*
23321050 AGAATAACGCTCTTGCGAACCAGAC
1 AGAATAACGCTCTTACGAACCAGAC
* *
23321075 AGAATATCGCTCTTACGAGCCAGA
1 AGAATAACGCTCTTACGAACCAGA
23321099 ATCCAAATTA
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:0.35, C:0.27, G:0.20, T:0.18
Consensus pattern (25 bp):
AGAATAACGCTCTTACGAACCAGAC
Found at i:23327710 original size:3 final size:3
Alignment explanation
Indices: 23327702--23327745 Score: 61
Period size: 3 Copynumber: 14.3 Consensus size: 3
23327692 AAAAGCTCAA
* *
23327702 ATT ATT ATT ATA ATT ACT ATT AATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT A
23327746 AGGTTTCATG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:23327729 original size:19 final size:19
Alignment explanation
Indices: 23327705--23327742 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
23327695 AGCTCAAATT
23327705 ATTATTATAATTACTATTA
1 ATTATTATAATTACTATTA
* *
23327724 ATTATTATTATTATTATTA
1 ATTATTATAATTACTATTA
23327743 TTAAGGTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTATTATAATTACTATTA
Found at i:23327729 original size:22 final size:22
Alignment explanation
Indices: 23327701--23327746 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
23327691 CAAAAGCTCA
23327701 AATTATTATTATAATTACTATT
1 AATTATTATTATAATTACTATT
* *
23327723 AATTATTATTATTATTATTATT
1 AATTATTATTATAATTACTATT
23327745 AA
1 AA
23327747 GGTTTCATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
AATTATTATTATAATTACTATT
Found at i:23328602 original size:21 final size:22
Alignment explanation
Indices: 23328566--23328608 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
23328556 CAACAAATGA
* *
23328566 TTTTAAAATTATTAAACTTATT
1 TTTTAAAAATATTAAAATTATT
23328588 TTTTAAAAATA-TAAAATTATT
1 TTTTAAAAATATTAAAATTATT
23328609 AAAATTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (22 bp):
TTTTAAAAATATTAAAATTATT
Found at i:23328605 original size:30 final size:32
Alignment explanation
Indices: 23328569--23328630 Score: 101
Period size: 30 Copynumber: 2.0 Consensus size: 32
23328559 CAAATGATTT
*
23328569 TAAAATTATTAAACTTATTTTTT-AAA-AATA
1 TAAAATTATTAAAATTATTTTTTGAAATAATA
23328599 TAAAATTATTAAAATTATTTTTTGAAATAATA
1 TAAAATTATTAAAATTATTTTTTGAAATAATA
23328631 ATAATTAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 22 0.76
31 3 0.10
32 4 0.14
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (32 bp):
TAAAATTATTAAAATTATTTTTTGAAATAATA
Found at i:23329673 original size:147 final size:146
Alignment explanation
Indices: 23329188--23329686 Score: 727
Period size: 147 Copynumber: 3.4 Consensus size: 146
23329178 TTATTATGCT
* * * *
23329188 TTTTTTTAATTATTTTGAAATAAAAGTTTAGATTTTTTAG-AAAATAGTGATTTTCATTAAAAAA
1 TTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGTAAAGTAGTGATTTTCATTAAAAAA
* * *
23329252 GGAGAAAGTTTATA-TTTTAAACACAAAAATCTGTTTTTCAGTTATTTTAAAGAAAAAGTTTAAA
66 --AGAAAGTTTATATTTTTAAAAATAAAAATATGTTTTT-AGTTATTTTAAAGAAAAAGTTTAAA
23329316 TTTTTAAATAAAGTTTTGA
128 TTTTTAAATAAAGTTTTGA
*
23329335 TTTTTTTAAACTATTTCGAAATAAAAGTTTGGATTTTTAAGTAAAGTAGTGATTTTCATTAAAAA
1 TTTTTTT-AACTATTTCGAAATAAAAGTTTAGATTTTTAAGTAAAGTAGTGATTTTCATT--AAA
* * *
23329400 ATAAAGAAATTTTATATTTTTAAAAAT-AAAATTTTTTTATTAGTTATTTTAAAGAAAAAGTTTA
63 A-AAAGAAAGTTTATATTTTTAAAAATAAAAATATGTTT-TTAGTTATTTTAAAGAAAAAGTTTA
23329464 AATTTTTAAATAAAGTTTTGA
126 AATTTTTAAATAAAGTTTTGA
23329485 TTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGTAAAGTAGTGATTTTCATTAAAAAA
1 TTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGTAAAGTAGTGATTTTCATTAAAAAA
* *
23329550 AGAAAGTTTAGATTTTTAAAAATAAAAATATGTTTTTAGTGATTTTAAAGAAAAAAGTTTAAATT
66 AGAAAGTTTATATTTTTAAAAATAAAAATATGTTTTTAGTTATTTTAAAG-AAAAAGTTTAAATT
*
23329615 TTTAAATAAAATTTTGA
130 TTTAAATAAAGTTTTGA
* * *
23329632 TTTTTTTAACTATTTCGAAATAAAAGTTTTG-TTTCTGAAGTAAAGTTGTGATTTT
1 TTTTTTTAACTATTTCGAAATAAAAGTTTAGATTT-TTAAGTAAAGTAGTGATTTT
23329687 GTTTTAATCA
Statistics
Matches: 322, Mismatches: 20, Indels: 20
0.89 0.06 0.06
Matches are distributed among these distances:
146 40 0.12
147 98 0.30
148 29 0.09
149 68 0.21
150 71 0.22
151 14 0.04
152 2 0.01
ACGTcount: A:0.41, C:0.03, G:0.11, T:0.45
Consensus pattern (146 bp):
TTTTTTTAACTATTTCGAAATAAAAGTTTAGATTTTTAAGTAAAGTAGTGATTTTCATTAAAAAA
AGAAAGTTTATATTTTTAAAAATAAAAATATGTTTTTAGTTATTTTAAAGAAAAAGTTTAAATTT
TTAAATAAAGTTTTGA
Found at i:23331122 original size:239 final size:238
Alignment explanation
Indices: 23330703--23331171 Score: 751
Period size: 239 Copynumber: 2.0 Consensus size: 238
23330693 AAAATCATAA
* * *
23330703 TAATGATAAAAGATCGAATGAGTTGTAGATGAATTTTAATATTTCTCTTAATTCATTAGTAACTT
1 TAATGATAAAAGATCGAATAAGTTGTAGATGAATTTTAATATTTATCTTAATTAATTAGTAACTT
* *
23330768 TTAGGTTTTTTTTAGGATTCTAAAATAAAATTAATTTTAAGAATTGAAGGTATTTTACTATAATT
66 TTAGGTTTTTTTTAGGATTCTAAAATAAAATTAATTTTAAGAATTGAAAGTATTTTACTAGAATT
* *
23330833 ATTTAAGTATCTTTTAGGATTCTCGTCAGAAGTAAAAATCTCTGATTTAAGTTTTAAATTAGATA
131 ATTTAAGTATCTTTTAGGATTCTCATCAGAAGTAAAAATCTCTAATTTAAGTTTTAAATTAGATA
23330898 AGTTTAGTGAACACGTCTTAATCAAGTTACAAGTATATCAGAG
196 AGTTTAGTGAACACGTCTTAATCAAGTTACAAGTATATCAGAG
*
23330941 TAATGATAAAAGATCGAATAAGTTGTAGATGAATTTTAATATTTATCTTAATTAATTAGTAATTT
1 TAATGATAAAAGATCGAATAAGTTGTAGATGAATTTTAATATTTATCTTAATTAATTAGTAA--C
**
23331006 TTTTAGG-TTTTTTTAGGATTCTAAAATGCAATTAATTTTAAGAATTGAAAGTATTTTACTAGAA
64 TTTTAGGTTTTTTTTAGGATTCTAAAATAAAATTAATTTTAAGAATTGAAAGTATTTTACTAGAA
* * * * * *
23331070 TTATTTAGGTATCTTTTAGGGTTCTTATTAGGAGTAAAATTCTCTAATTTAAGTTTTAAATTAGA
129 TTATTTAAGTATCTTTTAGGATTCTCATCAGAAGTAAAAATCTCTAATTTAAGTTTTAAATTAGA
* *
23331135 TAAGTTTGGTGAACACGTCTTAGTCAAGTTACAAGTA
194 TAAGTTTAGTGAACACGTCTTAATCAAGTTACAAGTA
23331172 AATTGGAGGC
Statistics
Matches: 211, Mismatches: 18, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
238 59 0.28
239 145 0.69
240 7 0.03
ACGTcount: A:0.36, C:0.07, G:0.15, T:0.42
Consensus pattern (238 bp):
TAATGATAAAAGATCGAATAAGTTGTAGATGAATTTTAATATTTATCTTAATTAATTAGTAACTT
TTAGGTTTTTTTTAGGATTCTAAAATAAAATTAATTTTAAGAATTGAAAGTATTTTACTAGAATT
ATTTAAGTATCTTTTAGGATTCTCATCAGAAGTAAAAATCTCTAATTTAAGTTTTAAATTAGATA
AGTTTAGTGAACACGTCTTAATCAAGTTACAAGTATATCAGAG
Found at i:23343235 original size:42 final size:42
Alignment explanation
Indices: 23343176--23343760 Score: 825
Period size: 42 Copynumber: 13.9 Consensus size: 42
23343166 AAGGAAAGCA
*
23343176 TTCATTGCATTTAGAGGCCCAGGTGTAGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * *
23343218 TTCATCGCATTCAGAGGCCTAGGTGTGGAGG-CTCATTTACTA
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTC-CATTTACTT
* *
23343260 TTCATTGTATTTAGAGGCCCAAGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
23343302 TTCATTACATTTAGAGGCCC-GCGTGTGGAGTTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAG-GTGTGGAGGTCCATTTACTT
* * *
23343344 TTCATTGCATTTATAGGCCTAGGTGTGAAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
*
23343386 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
** *
23343428 TTCATTGCATTTAGAGGCCCAGGTGTGGAGACCCATTTATTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* *
23343470 TTCATTGCATTTAGATGCCCAAGTGTGGAGGTCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
*
23343512 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
23343554 TTCATTGCATTTAAAGGCCTAGGTGTGGAGGTCTATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * * *
23343596 TTCATTACATTTAGAGGCTCAGGTGTGGTGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
* * *
23343638 TTCATTGCATTTAGAGGCCGAGGTGTAGAGGCCCATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
23343680 TTCATTGCATTTAGAGGCCCAGGTGTGGAGG-CCTATTTACTT
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCC-ATTTACTT
* * * *
23343722 TTTATTGCATTTAGAGGCCTAGGGGTAGAGGTCCATTTA
1 TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTA
23343761 TTTATTTTTT
Statistics
Matches: 481, Mismatches: 56, Indels: 12
0.88 0.10 0.02
Matches are distributed among these distances:
41 3 0.01
42 474 0.99
43 4 0.01
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (42 bp):
TTCATTGCATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
Found at i:23344227 original size:3 final size:3
Alignment explanation
Indices: 23344221--23344255 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
23344211 TTATTATCAT
23344221 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
23344256 TTATTATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
TAC
Found at i:23344260 original size:3 final size:3
Alignment explanation
Indices: 23344254--23344285 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
23344244 CTACTACTAC
23344254 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
23344286 AGGTTTCATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:23345030 original size:147 final size:149
Alignment explanation
Indices: 23344816--23345086 Score: 408
Period size: 148 Copynumber: 1.8 Consensus size: 149
23344806 TTATTTTTTC
* * * *
23344816 GAAAAATTTAAATTTTTAAATATAGTTTTGATTTTTTTAAATTATTTCAAAATAAAGGTTTAGAT
1 GAAAAATTTAAATTTTTAAATAAAATTTTGATTTTTTTAAACTATTTCAAAATAAAAGTTTAGAT
* * *
23344881 TTTTAAG-AAATTAGTGATTTTCA-TTAAAAAAGAATAAAGTTTATATTTTTAAAAATAAAAATA
66 TTTTAAGTAAAGTAGTGATTTTCATTTAAAAAA-AAGAAAATTTATATTTTTAAAAATAAAAATA
23344944 TGTTTTTCAGTTATTTTAGA
130 TGTTTTTCAGTTATTTTAGA
*
23344964 GAAAAAGTTTAAATTTTTAAATAAAATTTT-ATTTTTTT-AACTATTTCGAAATAAAAGTTT-GA
1 GAAAAA-TTTAAATTTTTAAATAAAATTTTGATTTTTTTAAACTATTTCAAAATAAAAGTTTAG-
23345026 ATTTTTAAGTAAAGTAGTGATTTTCATTTAAAAAAAAGAAAATTTATATTTTTAAAAATAA
64 ATTTTTAAGTAAAGTAGTGATTTTCATTTAAAAAAAAGAAAATTTATATTTTTAAAAATAA
23345087 GAAGATTAAG
Statistics
Matches: 111, Mismatches: 8, Indels: 8
0.87 0.06 0.06
Matches are distributed among these distances:
146 1 0.01
147 28 0.25
148 53 0.48
149 29 0.26
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.45
Consensus pattern (149 bp):
GAAAAATTTAAATTTTTAAATAAAATTTTGATTTTTTTAAACTATTTCAAAATAAAAGTTTAGAT
TTTTAAGTAAAGTAGTGATTTTCATTTAAAAAAAAGAAAATTTATATTTTTAAAAATAAAAATAT
GTTTTTCAGTTATTTTAGA
Found at i:23345653 original size:25 final size:23
Alignment explanation
Indices: 23345602--23345674 Score: 58
Period size: 25 Copynumber: 2.9 Consensus size: 23
23345592 TAATGATTTA
* *
23345602 TATTTATTCATACTTGCATAATTTT
1 TATTTATTC-TA-TTTCATATTTTT
23345627 TATTTATTCTTATTTCATATTTGTT
1 TATTTATTC-TATTTCATATTT-TT
23345652 TACTTTCATGTCTATTT-ATATTT
1 TA-TTT-AT-TCTATTTCATATTT
23345675 ATGTTTTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
24 8 0.20
25 15 0.37
26 9 0.22
27 7 0.17
28 2 0.05
ACGTcount: A:0.23, C:0.11, G:0.04, T:0.62
Consensus pattern (23 bp):
TATTTATTCTATTTCATATTTTT
Found at i:23346504 original size:239 final size:237
Alignment explanation
Indices: 23346078--23346557 Score: 764
Period size: 239 Copynumber: 2.0 Consensus size: 237
23346068 AAATATTTTA
* * *
23346078 AAATCATAATAATGATAAATGATCGAATAAGTTGTAGATGAGTTTTAATATTTCTCTTAATTCAT
1 AAATCAGAATAATGATAAAAGATCGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTCAT
*
23346143 TAGTAACTTTTAGGTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAAAATTGAAGGTATTTTA
66 TAGTAACTTTTAGGTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAAAATTGAAAGTATTTTA
*
23346208 CTAGAATTATTTAAGTATCTTGTAGGATTCTCGTTAGAAGTAAAAATCTCTAATTTAAGTTTTAA
131 CTAGAATTATTTAAGTATCTTGTAGGATTCTCATTAGAAGTAAAAATCTCTAATTTAAGTTTTAA
* *
23346273 ATTAGATAAGTTTGGTGAACATGCCTTAGTCAAGTTACAAGT
196 ATTAGATAAGTTTAGTGAACACGCCTTAGTCAAGTTACAAGT
*
23346315 AAATCAGAGTAATGATAAAAGATCGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTCAT
1 AAATCAGAATAATGATAAAAGATCGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTCAT
* *
23346380 TAGTAATTTTTTTAGGTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAGAATTGAAAGTATTT
66 TAGTAA--CTTTTAGGTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAAAATTGAAAGTATTT
* * * * *
23346445 TATTAGAATTATTTAGGTATCGTT-TAGGGTTCTTATTAGGAGTAAAAATCTCTAATTTAAGTTT
129 TACTAGAATTATTTAAGTATC-TTGTAGGATTCTCATTAGAAGTAAAAATCTCTAATTTAAGTTT
* * *
23346509 TAAATTAGCTAAGTTTAGTGAACACGTCTTAGTTAAGTTACAAGT
193 TAAATTAGATAAGTTTAGTGAACACGCCTTAGTCAAGTTACAAGT
23346554 AAAT
1 AAAT
23346558 TTGAGGCATT
Statistics
Matches: 222, Mismatches: 18, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
237 67 0.30
239 153 0.69
240 2 0.01
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (237 bp):
AAATCAGAATAATGATAAAAGATCGAATAAGTTGTAGATGAATTTTAATATTTCTCTTAATTCAT
TAGTAACTTTTAGGTTTTTTTAGGATTCTAAAATAGAATTAATTTTAAAAATTGAAAGTATTTTA
CTAGAATTATTTAAGTATCTTGTAGGATTCTCATTAGAAGTAAAAATCTCTAATTTAAGTTTTAA
ATTAGATAAGTTTAGTGAACACGCCTTAGTCAAGTTACAAGT
Found at i:23347595 original size:19 final size:19
Alignment explanation
Indices: 23347571--23347611 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
23347561 ATGTGAAAGT
23347571 CATTCGTAGTTTTCTTAGG
1 CATTCGTAGTTTTCTTAGG
*
23347590 CATTCGTAGTTTTCTTGGG
1 CATTCGTAGTTTTCTTAGG
23347609 CAT
1 CAT
23347612 GCAAGATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.15, C:0.17, G:0.22, T:0.46
Consensus pattern (19 bp):
CATTCGTAGTTTTCTTAGG
Found at i:23357508 original size:27 final size:27
Alignment explanation
Indices: 23357470--23357644 Score: 235
Period size: 27 Copynumber: 6.5 Consensus size: 27
23357460 CTGAGTAATA
*
23357470 AGCGATATTCTGTATTTTGCTCGAATG
1 AGCGATATTCTGTATTTGGCTCGAATG
23357497 AGCGATATTCTGTATTTGGCTCGAATG
1 AGCGATATTCTGTATTTGGCTCGAATG
*
23357524 AGCGATATTCTGTATCTGGCTCGAATG
1 AGCGATATTCTGTATTTGGCTCGAATG
* *
23357551 AGCGATA-TCTTGTATCTCGCTCGAATG
1 AGCGATATTC-TGTATTTGGCTCGAATG
* ** * *
23357578 AGTGGCATTTTGTATTTGGCTCAAATG
1 AGCGATATTCTGTATTTGGCTCGAATG
* *
23357605 AGCGATATTCTTTATTTGGCTCGAACG
1 AGCGATATTCTGTATTTGGCTCGAATG
23357632 AGCGATATTCTGT
1 AGCGATATTCTGT
23357645 TATTGTTGAA
Statistics
Matches: 128, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
26 2 0.02
27 125 0.98
28 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.24, T:0.37
Consensus pattern (27 bp):
AGCGATATTCTGTATTTGGCTCGAATG
Found at i:23366952 original size:46 final size:46
Alignment explanation
Indices: 23366895--23366995 Score: 114
Period size: 46 Copynumber: 2.2 Consensus size: 46
23366885 TAATTTTTAT
* * **
23366895 ATTTTTCCATGATATTG-TTTTGTTGTCATGACATTTTTGTAGTTGC
1 ATTTTGCCATGATA-TGATTTTGTTATCATGACATTTTCATAGTTGC
* * *
23366941 ATTTTGCCATGATATGATTTTTTTATCATGGCATTTTCATATTTGC
1 ATTTTGCCATGATATGATTTTGTTATCATGACATTTTCATAGTTGC
*
23366987 ATATTGCCA
1 ATTTTGCCA
23366996 CGGTATAGTT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
45 2 0.04
46 44 0.96
ACGTcount: A:0.21, C:0.13, G:0.15, T:0.51
Consensus pattern (46 bp):
ATTTTGCCATGATATGATTTTGTTATCATGACATTTTCATAGTTGC
Found at i:23375470 original size:30 final size:29
Alignment explanation
Indices: 23375346--23375471 Score: 74
Period size: 30 Copynumber: 4.2 Consensus size: 29
23375336 TATTTTGTTT
* *
23375346 AAAATTATATTTTAACCCTAAACTTTCCCA
1 AAAATTTTATTTTAACCCTAAACTTT-CTA
** * *
23375376 AAAATTCAAATTTAACCCCCAAACTTTCT-
1 AAAATTTTATTTTAA-CCCTAAACTTTCTA
* ** * * * *
23375405 AAAATTTCATTTTTGTTCCCTTATCTTTTTG
1 AAAATTTTA-TTTT-AACCCTAAACTTTCTA
*
23375436 AAAATTTTATTTTGACCCTCAAACTTTCTA
1 AAAATTTTATTTTAACCCT-AAACTTTCTA
23375466 AAAATT
1 AAAATT
23375472 ACAATTTAAC
Statistics
Matches: 70, Mismatches: 21, Indels: 10
0.69 0.21 0.10
Matches are distributed among these distances:
29 11 0.16
30 41 0.59
31 18 0.26
ACGTcount: A:0.35, C:0.21, G:0.02, T:0.42
Consensus pattern (29 bp):
AAAATTTTATTTTAACCCTAAACTTTCTA
Found at i:23375615 original size:18 final size:18
Alignment explanation
Indices: 23375594--23375636 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
23375584 CTTTTAAAAT
23375594 TTTTTA-TATAAAATTTCA
1 TTTTTATTA-AAAATTTCA
* *
23375612 TTTTGATTAAAAATTTCC
1 TTTTTATTAAAAATTTCA
23375630 TTTTTAT
1 TTTTTAT
23375637 CCTCTTTTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 19 0.90
19 2 0.10
ACGTcount: A:0.33, C:0.07, G:0.02, T:0.58
Consensus pattern (18 bp):
TTTTTATTAAAAATTTCA
Found at i:23380326 original size:80 final size:81
Alignment explanation
Indices: 23380166--23380335 Score: 238
Period size: 80 Copynumber: 2.1 Consensus size: 81
23380156 ATGGAGGCAG
23380166 TTAA-CAAGAATATCAAGAAGATCGAGACCTACAAAGATTGACATAGGAAGTTATCATTTGCTCT
1 TTAATCAAGAATATCAAGAAGATCGAGACCTACAAAGATTGACATAGGAAGTTATCATTTGCTCT
* * *
23380230 CTATGCTTATTGAACA
66 CTACGCCTATTAAACA
* * *
23380246 TTAATCAAGAA-ATCAAGAAGATCGAGACTTGCAAAGATTGGCAT-GAGAAGTTATCATTTGCTC
1 TTAATCAAGAATATCAAGAAGATCGAGACCTACAAAGATTGACATAG-GAAGTTATCATTTGCTC
*
23380309 TTTACGCCTATTAAACA
65 TCTACGCCTATTAAACA
*
23380326 TCAATCAAGA
1 TTAATCAAGA
23380336 TTTTGTTGGA
Statistics
Matches: 80, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
79 1 0.01
80 73 0.91
81 6 0.08
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.28
Consensus pattern (81 bp):
TTAATCAAGAATATCAAGAAGATCGAGACCTACAAAGATTGACATAGGAAGTTATCATTTGCTCT
CTACGCCTATTAAACA
Found at i:23380801 original size:7 final size:7
Alignment explanation
Indices: 23380769--23380828 Score: 52
Period size: 7 Copynumber: 8.7 Consensus size: 7
23380759 CCAAAAAAAT
*
23380769 AAAAATA
1 AAAAAGA
23380776 AAAAAGA
1 AAAAAGA
**
23380783 GGAAAGA
1 AAAAAGA
23380790 GAAAAAGA
1 -AAAAAGA
23380798 AAAAAG-
1 AAAAAGA
*
23380804 AAAGA-A
1 AAAAAGA
23380810 AAAAAGA
1 AAAAAGA
*
23380817 AAAAGGA
1 AAAAAGA
23380824 AAAAA
1 AAAAA
23380829 AGAGAGGTCG
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
6 8 0.20
7 28 0.68
8 5 0.12
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (7 bp):
AAAAAGA
Found at i:23380808 original size:19 final size:19
Alignment explanation
Indices: 23380784--23380829 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
23380774 TAAAAAAGAG
*
23380784 GAAAGAGAAAAAGAAAAAA
1 GAAAGAAAAAAAGAAAAAA
*
23380803 GAAAGAAAAAAAGAAAAAG
1 GAAAGAAAAAAAGAAAAAA
23380822 GAAA-AAAA
1 GAAAGAAAA
23380830 GAGAGGTCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 4 0.16
19 21 0.84
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (19 bp):
GAAAGAAAAAAAGAAAAAA
Done.