Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 68 of 120
Found at i:20039370 original size:16 final size:17
Alignment explanation
Indices: 20039343--20039387 Score: 67
Period size: 17 Copynumber: 2.8 Consensus size: 17
20039333 TTTTACTTTG
20039343 AAATTT-AATTTATTTT
1 AAATTTAAATTTATTTT
20039359 -AATTTAAATTTATTTT
1 AAATTTAAATTTATTTT
*
20039375 AAATTTAATTTTA
1 AAATTTAAATTTA
20039388 ATCTGAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 5 0.19
16 10 0.38
17 11 0.42
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
AAATTTAAATTTATTTT
Found at i:20039396 original size:28 final size:28
Alignment explanation
Indices: 20039344--20039427 Score: 100
Period size: 28 Copynumber: 3.1 Consensus size: 28
20039334 TTTACTTTGA
*
20039344 AATTT-AATTT-ATTTTAATTTAAATTT
1 AATTTAAATTTAATTTTAATCTAAATTT
* *
20039370 ATTTTAAATTTAATTTTAATCTGAATTT
1 AATTTAAATTTAATTTTAATCTAAATTT
* * *
20039398 AATTTAAATTTAATATTATTATAAATTT
1 AATTTAAATTTAATTTTAATCTAAATTT
20039426 AA
1 AA
20039428 AAAAAAAGAG
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
26 4 0.08
27 5 0.10
28 39 0.81
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (28 bp):
AATTTAAATTTAATTTTAATCTAAATTT
Found at i:20039403 original size:16 final size:16
Alignment explanation
Indices: 20039343--20039410 Score: 66
Period size: 17 Copynumber: 4.1 Consensus size: 16
20039333 TTTTACTTTG
20039343 AAATTTAATTT-ATTT
1 AAATTTAATTTAATTT
* *
20039358 TAATTTAAATTTATTTT
1 AAATTT-AATTTAATTT
*
20039375 AAATTTAATTTTAATCT
1 AAATTTAA-TTTAATTT
*
20039392 GAATTTAATTTAAATTT
1 AAATTTAATTT-AATTT
20039409 AA
1 AA
20039411 TATTATTATA
Statistics
Matches: 41, Mismatches: 8, Indels: 6
0.75 0.15 0.11
Matches are distributed among these distances:
15 5 0.12
16 10 0.24
17 26 0.63
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (16 bp):
AAATTTAATTTAATTT
Found at i:20039428 original size:6 final size:5
Alignment explanation
Indices: 20039344--20039411 Score: 64
Period size: 5 Copynumber: 12.6 Consensus size: 5
20039334 TTTACTTTGA
* * *
20039344 AATTT AATTT ATTTT AATTT AAATTT ATTTT AAATTT AATTTT AATCTG
1 AATTT AATTT AATTT AATTT -AATTT AATTT -AATTT AA-TTT AAT-TT
20039393 AATTT AATTT AAATTT AAT
1 AATTT AATTT -AATTT AAT
20039412 ATTATTATAA
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
5 29 0.56
6 23 0.44
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (5 bp):
AATTT
Found at i:20040131 original size:3 final size:3
Alignment explanation
Indices: 20040123--20040159 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
20040113 CAATAGCCAT
*
20040123 TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA T-A TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
20040160 TTAAATAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:20041076 original size:162 final size:162
Alignment explanation
Indices: 20040898--20041228 Score: 554
Period size: 162 Copynumber: 2.0 Consensus size: 162
20040888 AGTTTTCAAT
20040898 TTAGTCCTTCGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGCTGATTTATGTA
1 TTAGTCCTTCGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGCTGATTTATGTA
* *
20040963 TCTAGTCCCTGTTATTTTTAATTTGTTTTAATTTAATCCCTAAATCAACTTTTATTTAATTACAA
66 TCTAGTCCATGTTATTTTTAATTTGTTTTAATTTAATCCCTAAATCAACTTTTATTTAACTACAA
* *
20041028 AATTGGCCCAAGAATTTTTAAAGATTTATAAA
131 AATTGGCCCAAGAAATTTTAAAGATTTACAAA
* *
20041060 TTAGTCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGCTTATTTATGTA
1 TTAGTCCTTCGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGCTGATTTATGTA
* *
20041125 TCTAGTCCATGTTATTTTTAATTTGTTTTAATTTAATCCCTAAATCAACTTTTTTTTAACTATAA
66 TCTAGTCCATGTTATTTTTAATTTGTTTTAATTTAATCCCTAAATCAACTTTTATTTAACTACAA
* * * *
20041190 AATTGGCTCAATAAATTTTCAAGATTTACAAT
131 AATTGGCCCAAGAAATTTTAAAGATTTACAAA
20041222 TTAGTCC
1 TTAGTCC
20041229 CTTAACTGCT
Statistics
Matches: 157, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
162 157 1.00
ACGTcount: A:0.27, C:0.17, G:0.13, T:0.43
Consensus pattern (162 bp):
TTAGTCCTTCGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGCTGATTTATGTA
TCTAGTCCATGTTATTTTTAATTTGTTTTAATTTAATCCCTAAATCAACTTTTATTTAACTACAA
AATTGGCCCAAGAAATTTTAAAGATTTACAAA
Found at i:20041456 original size:58 final size:57
Alignment explanation
Indices: 20041338--20041771 Score: 557
Period size: 58 Copynumber: 7.5 Consensus size: 57
20041328 AAAATTTCAA
* *
20041338 AAAATTCCATTTTTAACCCTGATTTCATCACAAATTACCATTTTACCCTCGAACTTTCC
1 AAAATTCCATTTTTAACCCCGATTTCACCA-AAATTACCATTTTACCC-CGAACTTTCC
* * *
20041397 AAAATTCCATTTTTAACCCCGGTTTCAACAAAATTACCATTTTATCCCCAAACTTTCC
1 AAAATTCCATTTTTAACCCCGATTTCACCAAAATTACCATTTTA-CCCCGAACTTTCC
**
20041455 AAAATTCCATTTTTAACCTTGATTTCATCCAAAATTACCATTTTACCCTCGAACTTTCC
1 AAAATTCCATTTTTAACCCCGATTTCA-CCAAAATTACCATTTTACCC-CGAACTTTCC
* * *
20041514 AAAATTCCATTTTTAACCCCGATTTCATCAAAATTACCATTTTACCCCTAAACTTTCT
1 AAAATTCCATTTTTAACCCCGATTTCACCAAAATTACCATTTTACCCC-GAACTTTCC
* *
20041572 AAGATTCCATTTTTAACCCCGATTTCATCAAAATTACCATTTTACCCCCGAACTTTCC
1 AAAATTCCATTTTTAACCCCGATTTCACCAAAATTACCATTTTA-CCCCGAACTTTCC
* * * *
20041630 AAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACTTCTGAACTCTCA
1 AAAATTCCATTTTTAACCCCGATTTCACC-AAAATTACCATTTTAC-CCCGAACTTTCC
* * * *
20041689 AAAATTCCATTTTTAACCCTGATTTCACCAAAATTACCATTTTGCCCCCG--GTATCC
1 AAAATTCCATTTTTAACCCCGATTTCACCAAAATTACCATTTT-ACCCCGAACTTTCC
* *
20041745 AAAAGTCCCATTTTCAACCCCGATTTC
1 AAAA-TTCCATTTTTAACCCCGATTTC
20041772 GTCGTTTATT
Statistics
Matches: 333, Mismatches: 33, Indels: 20
0.86 0.09 0.05
Matches are distributed among these distances:
56 7 0.02
57 20 0.06
58 170 0.51
59 136 0.41
ACGTcount: A:0.31, C:0.29, G:0.04, T:0.36
Consensus pattern (57 bp):
AAAATTCCATTTTTAACCCCGATTTCACCAAAATTACCATTTTACCCCGAACTTTCC
Found at i:20041515 original size:117 final size:115
Alignment explanation
Indices: 20041323--20041771 Score: 623
Period size: 117 Copynumber: 3.9 Consensus size: 115
20041313 TTGCATCTTG
*
20041323 ACCCCAAAATTTCAAAAAATTCCATTTTTAACCCTGATTTCATCACAAATTACCATTTTACCCTC
1 ACCCCAAACTTTC-AAAAATTCCATTTTTAACCCTGATTTCATCA-AAATTACCATTTTACCCTC
*
20041388 GAACTTTCCAAAATTCCATTTTTAACCCCGGTTTCAACAAAATTACCATTTT
64 GAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAACAAAATTACCATTTT
* *
20041440 ATCCCCAAACTTTCCAAAATTCCATTTTTAACCTTGATTTCATCCAAAATTACCATTTTACCCTC
1 A-CCCCAAACTTTCAAAAATTCCATTTTTAACCCTGATTTCAT-CAAAATTACCATTTTACCCTC
*
20041505 GAACTTTCCAAAATTCCATTTTTAACCCCGATTTCATCAAAATTACCATTTT
64 GAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAACAAAATTACCATTTT
* * * *
20041557 ACCCCTAAACTTTCTAAGATTCCATTTTTAACCCCGATTTCATCAAAATTACCATTTTACCCCCG
1 ACCCC-AAACTTTCAAAAATTCCATTTTTAACCCTGATTTCATCAAAATTACCATTTTACCCTCG
*
20041622 AACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTT
65 AACTTTCCAAAATTCCATTTTTAACCCCGATTTCAAC-AAAATTACCATTTT
* ** * * * *
20041674 ACTTCTGAACTCTCAAAAATTCCATTTTTAACCCTGATTTCACCAAAATTACCATTTTGCCCCCG
1 AC-CCCAAACTTTCAAAAATTCCATTTTTAACCCTGATTTCATCAAAATTACCATTTTACCCTCG
* * * *
20041739 --GTATCCAAAAGTCCCATTTTCAACCCCGATTTC
65 AACTTTCCAAAA-TTCCATTTTTAACCCCGATTTC
20041772 GTCGTTTATT
Statistics
Matches: 302, Mismatches: 24, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
115 8 0.03
116 81 0.27
117 199 0.66
118 14 0.05
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.35
Consensus pattern (115 bp):
ACCCCAAACTTTCAAAAATTCCATTTTTAACCCTGATTTCATCAAAATTACCATTTTACCCTCGA
ACTTTCCAAAATTCCATTTTTAACCCCGATTTCAACAAAATTACCATTTT
Found at i:20041630 original size:175 final size:176
Alignment explanation
Indices: 20041337--20041736 Score: 610
Period size: 175 Copynumber: 2.3 Consensus size: 176
20041327 CAAAATTTCA
*
20041337 AAAAATTCCATTTTTAACCCTGATTTCATCACAAATTACCATTTTA-CCCTCGAACTTTCCAAAA
1 AAAAATTCCATTTTTAACCCTGATTTCATCA-AAATTACCATTTTACCCCTCAAACTTTCCAAAA
* *
20041401 TTCCATTTTTAACCCCGGTTTCAACAAAATTACCATTTTATCCCCAAACTTTCCAAAATTCCATT
65 TTCCATTTTTAACCCCGATTTCAACAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATT
** *
20041466 TTTAACCTTGATTTCATCC-AAAATTACCATTTTACC-CTCGAACTTTC
130 TTTAACCCCGATTTCA-CCAAAAATTACCATTTTACCTCT-GAACTCTC
* * * *
20041513 CAAAATTCCATTTTTAACCCCGATTTCATCAAAATTACCATTTTACCCCT-AAACTTTCTAAGAT
1 AAAAATTCCATTTTTAACCCTGATTTCATCAAAATTACCATTTTACCCCTCAAACTTTCCAAAAT
* *
20041577 TCCATTTTTAACCCCGATTTCATCAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCCATTT
66 TCCATTTTTAACCCCGATTTCAACAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTT
*
20041642 TTAACCCCGATTTCACCAAAAATTACCATTTTACTTCTGAACTCTC
131 TTAACCCCGATTTCACCAAAAATTACCATTTTACCTCTGAACTCTC
* *
20041688 AAAAATTCCATTTTTAACCCTGATTTCACCAAAATTACCATTTTGCCCC
1 AAAAATTCCATTTTTAACCCTGATTTCATCAAAATTACCATTTTACCCC
20041737 CGGTATCCAA
Statistics
Matches: 204, Mismatches: 17, Indels: 7
0.89 0.07 0.03
Matches are distributed among these distances:
174 2 0.01
175 167 0.82
176 35 0.17
ACGTcount: A:0.32, C:0.28, G:0.04, T:0.36
Consensus pattern (176 bp):
AAAAATTCCATTTTTAACCCTGATTTCATCAAAATTACCATTTTACCCCTCAAACTTTCCAAAAT
TCCATTTTTAACCCCGATTTCAACAAAATTACCATTTTACCCCCAAACTTTCCAAAATTCCATTT
TTAACCCCGATTTCACCAAAAATTACCATTTTACCTCTGAACTCTC
Found at i:20049566 original size:18 final size:18
Alignment explanation
Indices: 20049543--20049585 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
20049533 GAATAGGTTT
20049543 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
20049561 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
20049579 TTAATTA
1 TTAATTA
20049586 CATATTGAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.22
18 18 0.78
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:20052228 original size:16 final size:16
Alignment explanation
Indices: 20052195--20052242 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
20052185 CAACGTCCAC
*
20052195 TTTTATAT-TTTTTC-
1 TTTTATATATTTATCA
*
20052209 TTTTATTTATTTATCA
1 TTTTATATATTTATCA
*
20052225 TTTTGTATATTTATCA
1 TTTTATATATTTATCA
20052241 TT
1 TT
20052243 AGTTTCTTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 7 0.25
15 5 0.18
16 16 0.57
ACGTcount: A:0.21, C:0.06, G:0.02, T:0.71
Consensus pattern (16 bp):
TTTTATATATTTATCA
Found at i:20066996 original size:11 final size:10
Alignment explanation
Indices: 20066980--20067013 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
20066970 CATATATATA
20066980 TTTTTCTTCTT
1 TTTTTCTT-TT
*
20066991 TTTTTCTTTC
1 TTTTTCTTTT
20067001 TTTTTCTTTT
1 TTTTTCTTTT
20067011 TTT
1 TTT
20067014 ATGTGACTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 13 0.62
11 8 0.38
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:20067633 original size:17 final size:16
Alignment explanation
Indices: 20067577--20067634 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 16
20067567 AAATATATAT
20067577 AGAAATGCAATGACAA
1 AGAAATGCAATGACAA
* * *
20067593 TGAAGATGTAGTGACAA
1 AGAA-ATGCAATGACAA
*
20067610 GAAAAATGCAATGACAA
1 -AGAAATGCAATGACAA
20067627 ACGAAATG
1 A-GAAATG
20067635 TGATGACAGC
Statistics
Matches: 31, Mismatches: 8, Indels: 5
0.70 0.18 0.11
Matches are distributed among these distances:
16 4 0.13
17 25 0.81
18 2 0.06
ACGTcount: A:0.52, C:0.10, G:0.22, T:0.16
Consensus pattern (16 bp):
AGAAATGCAATGACAA
Found at i:20079053 original size:20 final size:20
Alignment explanation
Indices: 20079028--20079071 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
20079018 TGTCAACGCA
20079028 TTTTTACATTTAC-TTTTATC
1 TTTTTACATTTACATTTT-TC
*
20079048 TTTTTACTTTTACATTTTTC
1 TTTTTACATTTACATTTTTC
20079068 TTTT
1 TTTT
20079072 AAATCTTATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.16, C:0.14, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTTACATTTACATTTTTC
Found at i:20079055 original size:14 final size:14
Alignment explanation
Indices: 20079036--20079072 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
20079026 CATTTTTACA
20079036 TTTACTTTTATC-TT
1 TTTACTTTTA-CATT
20079050 TTTACTTTTACATT
1 TTTACTTTTACATT
20079064 TTT-CTTTTA
1 TTTACTTTTA
20079073 AATCTTATGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.16, C:0.14, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTACTTTTACATT
Found at i:20081419 original size:18 final size:18
Alignment explanation
Indices: 20081393--20081429 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
20081383 ATGCATCTTA
*
20081393 TTTAGTTGTCATTGCATT
1 TTTAGTTGTCACTGCATT
*
20081411 TTTATTTGTCACTGCATT
1 TTTAGTTGTCACTGCATT
20081429 T
1 T
20081430 CATTTGTTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.16, C:0.14, G:0.14, T:0.57
Consensus pattern (18 bp):
TTTAGTTGTCACTGCATT
Found at i:20081436 original size:17 final size:17
Alignment explanation
Indices: 20081398--20081451 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
20081388 TCTTATTTAG
* *
20081398 TTGTCATTGCATTTTTAT
1 TTGTCACTGCA-TTTCAT
20081416 TTGTCACTGCATTTCAT
1 TTGTCACTGCATTTCAT
* *
20081433 TTGTTAGTGCATTTGCAT
1 TTGTCACTGCATTT-CAT
20081451 T
1 T
20081452 GTAGTTGCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
17 17 0.55
18 14 0.45
ACGTcount: A:0.17, C:0.15, G:0.15, T:0.54
Consensus pattern (17 bp):
TTGTCACTGCATTTCAT
Found at i:20081468 original size:17 final size:16
Alignment explanation
Indices: 20081423--20081464 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
20081413 TATTTGTCAC
20081423 TGCATTTCATTTGTTAG
1 TGCATTTCA-TTGTTAG
20081440 TGCATTTGCATTG-TAG
1 TGCATTT-CATTGTTAG
20081456 TTGCATTTC
1 -TGCATTTC
20081465 CATTCTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
16 4 0.17
17 17 0.74
18 2 0.09
ACGTcount: A:0.17, C:0.14, G:0.19, T:0.50
Consensus pattern (16 bp):
TGCATTTCATTGTTAG
Found at i:20082240 original size:23 final size:23
Alignment explanation
Indices: 20082210--20082267 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
20082200 CTGACGTGGC
*
20082210 ATCCAGTCAGCAGCTTTTAGAAG
1 ATCCAGTCAGCAGCTTCTAGAAG
20082233 ATCCAGTCAGCAGCTTCTAGAAG
1 ATCCAGTCAGCAGCTTCTAGAAG
* *
20082256 GTCTAGTCAGCA
1 ATCCAGTCAGCA
20082268 AGGATGGACG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.24
Consensus pattern (23 bp):
ATCCAGTCAGCAGCTTCTAGAAG
Found at i:20086953 original size:17 final size:17
Alignment explanation
Indices: 20086933--20086965 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
20086923 AAATCACAAA
20086933 AAGAAAGAAAA-AGAAAG
1 AAGAAA-AAAAGAGAAAG
20086950 AAGAAAAAAAGAGAAA
1 AAGAAAAAAAGAGAAA
20086966 ATAAAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (17 bp):
AAGAAAAAAAGAGAAAG
Found at i:20088062 original size:29 final size:29
Alignment explanation
Indices: 20088020--20088076 Score: 114
Period size: 29 Copynumber: 2.0 Consensus size: 29
20088010 GTTAGATTAC
20088020 TTTGATTCAAACTTAATTCTTCTCATCTG
1 TTTGATTCAAACTTAATTCTTCTCATCTG
20088049 TTTGATTCAAACTTAATTCTTCTCATCT
1 TTTGATTCAAACTTAATTCTTCTCATCT
20088077 ATTTATTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.25, C:0.21, G:0.05, T:0.49
Consensus pattern (29 bp):
TTTGATTCAAACTTAATTCTTCTCATCTG
Found at i:20099034 original size:631 final size:628
Alignment explanation
Indices: 20097550--20099055 Score: 2107
Period size: 631 Copynumber: 2.4 Consensus size: 628
20097540 CACACGGCTC
* * * * * *
20097550 TGTGACCCACACAACCATGTGGTAGGCCAAATCGATTTCACAAAATTGCACACCAAACAACGAAA
1 TGTGACCCACACGACCATGTGGTAGGCCATATCGATATCACGAAATTGCACACCAAACAATGGAA
* * * * *
20097615 AATCAAAATTTTTAAGTTTTTCGGGCATTCTAAGATGTATATAAGATAAAAATAAGAAACTTGAA
66 AATCAAAA-TTTT-AGGTTTTCGGGCATTCTAAGATGTATATATGACAAAAATAAGAAACTAGGA
* * * *
20097680 GGCAAG-CATCAGAGAATATTCAAGAAAACAACTC-GAAAAATACCATTAAAGCCCACTTTGAAG
129 GG-GAGCCATCAGAGAATATTCAAGAAAACAACTCAAAAAAAT-CCATTGAAGCCGACTTTGAAG
* * *
20097743 CAGATTTCTGTCAAAATTGAAGATTCTCATTTGATTTGATAGTAGATTATCATGAGTTTCTTTAT
192 CAGATTTCCGTCAAGATTGAAGATTCTCATTTGATTTGATAGGAGATTATCATGAGTTTCTTTAT
* * *
20097808 TTTTTTTCGGTTATATTATCTCTTGGATGTTTTTACTTTCAAGAATGAACTAATTTTCTAAATAC
257 TTTCTTTCGGTTATACTATCTCCTGGATGTTTTTACTTTCAAGAATGAACTAATTTTCTAAATAC
*
20097873 CTAGGGAAGATGAAACCTATGATGGATTATGACATTTGATTTTTATTTGGCGCAACAAATACTTA
322 CTAGGGAAGAAGAAACCTATGATGGATTATGACATTTGATTTTTATTTGGCGCAACAAATACTTA
20097938 GTTTTTTCTCTCAATTATGTGTGCTTAAATCGTGAATATTCGATGTTCATTGTAAATTTTATGCT
387 GTTTTTTCTCTCAATTATGTGTGCTTAAATCGTGAATATTCGATGTTCATTGTAAATTTTATGCT
* * * *
20098003 CCTAATCCTTTCAATTCATGTTTTTATGCTTAATATAGTACTAGAAATCAAAAGGAGTGAAAAAT
452 CCTAATCCTTTCAATACATATTTTTATGCTTAATAAAGCACTAGAAATCAAAAGGAGTGAAAAAT
* *
20098068 GAGCGAAAAAAAAATCGGAGCAAGCTATAGGAGCCACACGGGTTGGACCATTCCACTTGGCCATA
517 GAGCGAAAAAAAAATCGGAGCAAGCTATAGGAGCCACACGGGCTGGACCATTCCACATGGCCATA
* * *
20098133 TGATCCTCACGAGTAAAACCATTCCACACGGCCAGACCACATGGTTG
582 TGATCCACACGAGTAAAACCATTCCACACGACCAGACCACATGATTG
** * * *
20098180 TGTGACCCACACGACCATGTCTTAGGCCATATCAATATCACGAAATTGCAAACTAAACAATGGAA
1 TGTGACCCACACGACCATGTGGTAGGCCATATCGATATCACGAAATTGCACACCAAACAATGGAA
*
20098245 AATCATATATTTTAGGTTTTGCGGGCATTCTAAGATGTATATATGAC-AAAATAAGAAACTAGGA
66 AATCA-AAATTTTAGGTTTT-CGGGCATTCTAAGATGTATATATGACAAAAATAAGAAACTAGGA
* * *
20098309 GGGAGCAATCAGAGAGTATTCAAGAAAACAAATCAAAAAACA-CCATTGAAGCCGACTTTGAAGC
129 GGGAGCCATCAGAGAATATTCAAGAAAACAACTCAAAAAA-ATCCATTGAAGCCGACTTTGAAGC
* * * *
20098373 AAATTTCCATTAAGATTGAATATTCTCATTTGATTTGATAGGAGATTATCATGAGTTTCTTTA-T
193 AGATTTCCGTCAAGATTGAAGATTCTCATTTGATTTGATAGGAGATTATCATGAGTTTCTTTATT
* *
20098437 TTCTTTCGGTTATACTGTCTCCTGGATGTTTTTTCCTTTCAAGAATGAACTAATTTTCTAAATAC
258 TTCTTTCGGTTATACTATCTCCTGGATG-TTTTTACTTTCAAGAATGAACTAATTTTCTAAATAC
* * * * * *
20098502 CTAGAGG-AGAAGAACCCTGTGATGGATTATGTCGTTTGATTTTTATTTTGTC-CAA-AAATGCT
322 CTAG-GGAAGAAGAAACCTATGATGGATTATGACATTTGATTTTTA-TTTGGCGCAACAAATACT
* * * * *
20098564 TAGTTTTTTCTCTGAATTATGTGTGCTTAAATTGTGATTATTCGATGTTTATTGTGAATTTTATG
385 TAGTTTTTTCTCTCAATTATGTGTGCTTAAATCGTGAATATTCGATGTTCATTGTAAATTTTATG
* *
20098629 CTCCTAATCTTTTCAATACATATTTTTATGCTTAATAAAGCACTTGAAATCAAAAGGAGTGAAAA
450 CTCCTAATCCTTTCAATACATATTTTTATGCTTAATAAAGCACTAGAAATCAAAAGGAGTGAAAA
* * *
20098694 ATGAGCGAAAATCGAAAAATTGGAGCAAGCTATAGGGGCCACATGGGCTGGACCATTCCACATGG
515 ATGAGCGAAAA---AAAAATCGGAGCAAGCTATAGGAGCCACACGGGCTGGACCATTCCACATGG
*
20098759 CCATATGATCCACACGAGCT-AAAGCATTCCACACGACCTA-ACCACATGATTG
577 CCATATGATCCACACGAG-TAAAACCATTCCACACGACC-AGACCACATGATTG
* * *
20098811 TGTG-CCCACACGACCATGTGGTAGGCCATATCGATATCACGGAATTGCACACCAAATAGTGGAA
1 TGTGACCCACACGACCATGTGGTAGGCCATATCGATATCACGAAATTGCACACCAAACAATGGAA
** * **
20098875 AATCACAAATTTTAGGCTTTTCCAGCATTTTAAGACATATATATGACAAAAATAAGAAACTAGGA
66 AATCA-AAATTTTAGG-TTTTCGGGCATTCTAAGATGTATATATGACAAAAATAAGAAACTAGGA
* *
20098940 GGGAGCCATCAAAGAATATTCAAGAAAACAACTCAAAAAAATCCTTTGAAGCCGACTTTGAAGCA
129 GGGAGCCATCAGAGAATATTCAAGAAAACAACTCAAAAAAATCCATTGAAGCCGACTTTGAAGCA
* *
20099005 GATTTCCGTCAAGATTAAAGATGCTCATTTGATTTGATAGGAGATTATCAT
194 GATTTCCGTCAAGATTGAAGATTCTCATTTGATTTGATAGGAGATTATCAT
20099056 ATACCTAGGG
Statistics
Matches: 771, Mismatches: 89, Indels: 31
0.87 0.10 0.03
Matches are distributed among these distances:
628 163 0.21
629 199 0.26
630 186 0.24
631 221 0.29
632 2 0.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (628 bp):
TGTGACCCACACGACCATGTGGTAGGCCATATCGATATCACGAAATTGCACACCAAACAATGGAA
AATCAAAATTTTAGGTTTTCGGGCATTCTAAGATGTATATATGACAAAAATAAGAAACTAGGAGG
GAGCCATCAGAGAATATTCAAGAAAACAACTCAAAAAAATCCATTGAAGCCGACTTTGAAGCAGA
TTTCCGTCAAGATTGAAGATTCTCATTTGATTTGATAGGAGATTATCATGAGTTTCTTTATTTTC
TTTCGGTTATACTATCTCCTGGATGTTTTTACTTTCAAGAATGAACTAATTTTCTAAATACCTAG
GGAAGAAGAAACCTATGATGGATTATGACATTTGATTTTTATTTGGCGCAACAAATACTTAGTTT
TTTCTCTCAATTATGTGTGCTTAAATCGTGAATATTCGATGTTCATTGTAAATTTTATGCTCCTA
ATCCTTTCAATACATATTTTTATGCTTAATAAAGCACTAGAAATCAAAAGGAGTGAAAAATGAGC
GAAAAAAAAATCGGAGCAAGCTATAGGAGCCACACGGGCTGGACCATTCCACATGGCCATATGAT
CCACACGAGTAAAACCATTCCACACGACCAGACCACATGATTG
Found at i:20101207 original size:632 final size:630
Alignment explanation
Indices: 20099996--20101322 Score: 1853
Period size: 632 Copynumber: 2.1 Consensus size: 630
20099986 TTGTGTGACC
* * * * * *
20099996 CACACGAAACAACGAAAAATTATAATTTTTTTGCTTTTATG-GCATTTTAAGACGTATGTATGAG
1 CACACCAAACAACGAAAAA-TATAA-TTTTTTGGTTTT-TGAGCATTCTAAGATGTATATATGAC
*
20100060 AAAAATAAGAAACTAAAAGGGAGCCATCAGAGAATATTAAAGAAAACAACTCGAAAAACACCATT
63 AAAAATAAGAAACTAAAACGGAGCCATCAGAGAATATTAAAGAAAACAACTCGAAAAACACCATT
** * *
20100125 GAAGCCAATATTGAATTAGATTTCCATCAAGATTGAAGATTCTCATTTGATTTGATTGGAGATTA
128 GAAGCCAATATTGAAGAAGATTTCCATCAAGATTGAAGATTCTCATTTGATTTGATAGGAGACTA
* * *
20100190 TCATGAGTTTATTTATTTCTTTCGACTATATTGTCTCTTAGATGTATTTACTTTCAAGCATAAAC
193 TCATGAGTTTATTTATTTCTTTCGACTATACTGTCTCCTAGATGTATTTACTTTCAAGAATAAAC
20100255 TAAATTTCTAAATACCTAAGGAAGATGAACCCTATGATGGATTATGTCGTTGGAATTGTTATTTT
258 TAAATTTCTAAATACCTAAGGAAGATGAACCCTATGATGGATTATGTCGTTGGAATTGTTATTTT
20100320 GCGCAACAAATACTTAGTTTTCCTCTCAATTATGTGTGCTTAAATCATGATTATTTGATGTTCAT
323 GCGCAACAAATACTTAGTTTTCCTCTCAATTATGTGTGCTTAAATCATGATTATTTGATGTTCAT
* * *
20100385 TGTGAATTTTATGCTCCAATTCCTTTCAATTCATATTTTTATGCTTAATAGAACACTTGAAATCA
388 TATGAATTTTAAGCTCCAATTCCTTTCAATTCATATTTTAATGCTTAATAGAACACTTGAAATCA
* * *
20100450 AAACGAGTGAAAAATGAGCGAAAATAGAAAAATTGGAGTAAGCTGCAAGAGCCACCGGGGCTGGA
453 AAACGAGTGAAAAATGAGCGAAAATAGAAAAATCGGAGCAAGCTACAAGAGCCACCGGGGCTGGA
* *
20100515 CCATTCCACATGGCCATATGATCCGCACGAGCTAAACCATTCCACACGGCCAGACCACACGGTTG
518 CCATTCCACATGGCCATATGATCCGCACGAGCTAAACCATTCCACACAGCCAGACCACACGGTTA
* * *
20100580 TGTGACCCACACGACCATGTGGTAAGCCATATTGATTTCACGGAATTG
583 TGTGACCCACACGACCATGTGGTAAGCCATATCGATATCACGAAATTG
* *
20100628 CATACCAAACAACCAAAAATCATAATTTTTTGGTTTTTCGAGCATTCTAAGATGTATATATGACA
1 CACACCAAACAACGAAAAAT-ATAATTTTTTGGTTTTT-GAGCATTCTAAGATGTATATATGACA
*** * * *
20100693 AAAATAAGAAACTGGGACGGAGCGATCAGAGAATATTCAAGAAAACAACTCGAAAAGCACCATTG
64 AAAATAAGAAACTAAAACGGAGCCATCAGAGAATATTAAAGAAAACAACTCGAAAAACACCATTG
* *
20100758 AAGCCAA-ATTTGAAGAAGATTTCCGTCAAGATTGAAGATTCTGATTTGATTTGATAGGAGACTA
129 AAGCCAATA-TTGAAGAAGATTTCCATCAAGATTGAAGATTCTCATTTGATTTGATAGGAGACTA
* ** * * *
20100822 TCATGAGTTTATTTATTTCTTTTGGTTATACTGTCTCCTGGATGTTTTTACTTTCAAGAATGAAC
193 TCATGAGTTTATTTATTTCTTTCGACTATACTGTCTCCTAGATGTATTTACTTTCAAGAATAAAC
* * * * *
20100887 -AAATATTCTAAATGCCTAGGGGAGATGAACCCTATGATGGATTATGTTGTAT-G-ATTTTTATT
258 TAAAT-TTCTAAATACCTAAGGAAGATGAACCCTATGATGGATTATGTCGT-TGGAATTGTTATT
* *
20100949 TTGCGCAACAAATACTTAGTTTTTTCTCTCAATTATGTGTGCTTAAATCGTGATTATTTGATGTT
321 TTGCGCAACAAATACTTAG-TTTTCCTCTCAATTATGTGTGCTTAAATCATGATTATTTGATGTT
* * * *
20101014 CATTATGAATTTTAAGTTTCTAA-TCCTTTCAATTCATGTTTTAATGCTTAATAGAGA-ATTTGA
385 CATTATGAATTTTAAG-CTCCAATTCCTTTCAATTCATATTTTAATGCTTAATAGA-ACACTTGA
* * * * *
20101077 AATCAAAAGGAGTGAAAAATGAG-GAAAAATCGAAAAATCGGAGCAAGCTACAGGGGCTACAC-G
448 AATCAAAACGAGTGAAAAATGAGCG-AAAATAGAAAAATCGGAGCAAGCTACAAGAGCCAC-CGG
* * *
20101140 GGTTGGACCATTCCACATGGGCATATGATCCGCACGAGCTAAACCATTCCAGACAGCCAGACCAC
511 GGCTGGACCATTCCACATGGCCATATGATCCGCACGAGCTAAACCATTCCACACAGCCAGACCAC
*
20101205 ACGGTTATGTGACCCACACGACCATGTGGTAGGCCATATCGATATCACGAAATTG
576 ACGGTTATGTGACCCACACGACCATGTGGTAAGCCATATCGATATCACGAAATTG
** ** * *
20101260 CACACCAAACAGTGGGAAATATCAATTTTTAGGTTTTTAAGGCATTCTAAGATGTATATATGA
1 CACACCAAACAACGAAAAATAT-AATTTTTTGGTTTTTGA-GCATTCTAAGATGTATATATGA
20101323 TTGCCCTGAG
Statistics
Matches: 613, Mismatches: 69, Indels: 26
0.87 0.10 0.04
Matches are distributed among these distances:
630 1 0.00
631 49 0.08
632 556 0.91
633 7 0.01
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (630 bp):
CACACCAAACAACGAAAAATATAATTTTTTGGTTTTTGAGCATTCTAAGATGTATATATGACAAA
AATAAGAAACTAAAACGGAGCCATCAGAGAATATTAAAGAAAACAACTCGAAAAACACCATTGAA
GCCAATATTGAAGAAGATTTCCATCAAGATTGAAGATTCTCATTTGATTTGATAGGAGACTATCA
TGAGTTTATTTATTTCTTTCGACTATACTGTCTCCTAGATGTATTTACTTTCAAGAATAAACTAA
ATTTCTAAATACCTAAGGAAGATGAACCCTATGATGGATTATGTCGTTGGAATTGTTATTTTGCG
CAACAAATACTTAGTTTTCCTCTCAATTATGTGTGCTTAAATCATGATTATTTGATGTTCATTAT
GAATTTTAAGCTCCAATTCCTTTCAATTCATATTTTAATGCTTAATAGAACACTTGAAATCAAAA
CGAGTGAAAAATGAGCGAAAATAGAAAAATCGGAGCAAGCTACAAGAGCCACCGGGGCTGGACCA
TTCCACATGGCCATATGATCCGCACGAGCTAAACCATTCCACACAGCCAGACCACACGGTTATGT
GACCCACACGACCATGTGGTAAGCCATATCGATATCACGAAATTG
Found at i:20104024 original size:16 final size:16
Alignment explanation
Indices: 20104003--20104038 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
20103993 AAATAATCCC
*
20104003 AAAATTACAAGTCTCA
1 AAAATTAAAAGTCTCA
20104019 AAAATTAAAAGTCTCA
1 AAAATTAAAAGTCTCA
20104035 AAAA
1 AAAA
20104039 CACTTTATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.58, C:0.14, G:0.06, T:0.22
Consensus pattern (16 bp):
AAAATTAAAAGTCTCA
Found at i:20109005 original size:20 final size:21
Alignment explanation
Indices: 20108977--20109016 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
20108967 GTAGGTTCAG
*
20108977 TTTCTTTCTTC-TTTTCTTCC
1 TTTCCTTCTTCTTTTTCTTCC
20108997 TTTCCTTCTTCTTTTTCTTC
1 TTTCCTTCTTCTTTTTCTTC
20109017 ATCCTTCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTCCTTCTTCTTTTTCTTCC
Found at i:20129454 original size:19 final size:20
Alignment explanation
Indices: 20129414--20129454 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
20129404 TAAGTGTTTG
*
20129414 TTTTCTTCTTTTCTCTTTCT
1 TTTTCTTCTTTTCTCTTCCT
20129434 TTTTC-TCTATTTC-CTTCCT
1 TTTTCTTCT-TTTCTCTTCCT
20129453 TT
1 TT
20129455 CTACATTTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTCTTCTTTTCTCTTCCT
Found at i:20130014 original size:16 final size:16
Alignment explanation
Indices: 20129989--20130031 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
20129979 AGGAGATGTC
*
20129989 GTTTTGATTTTTTCTT
1 GTTTTAATTTTTTCTT
* *
20130005 TTTTTAATTTTTTGTT
1 GTTTTAATTTTTTCTT
*
20130021 GTTTAAATTTT
1 GTTTTAATTTT
20130032 AAAAAATATA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.14, C:0.02, G:0.09, T:0.74
Consensus pattern (16 bp):
GTTTTAATTTTTTCTT
Found at i:20135720 original size:17 final size:17
Alignment explanation
Indices: 20135686--20135720 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
20135676 TTTTTAAAAT
* *
20135686 ATATTTTTATAAATTAA
1 ATATTTTTAAAAAATAA
20135703 ATATTTTTAAAAAATAA
1 ATATTTTTAAAAAATAA
20135720 A
1 A
20135721 ATAAAAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATTTTTAAAAAATAA
Found at i:20143919 original size:47 final size:47
Alignment explanation
Indices: 20143868--20143972 Score: 147
Period size: 47 Copynumber: 2.2 Consensus size: 47
20143858 GGGAAAGATC
* *
20143868 GAGGCCGTAACGGCGGATCTAGTACCATAGTTATAAAGGAAAAAGTT
1 GAGGCCGCAACGACGGATCTAGTACCATAGTTATAAAGGAAAAAGTT
* * * *
20143915 GAGGCCACAACGACGGATCTAGTACCATAGTTATGAAGGGAAAGGTT
1 GAGGCCGCAACGACGGATCTAGTACCATAGTTATAAAGGAAAAAGTT
*
20143962 AAGGCCGCAAC
1 GAGGCCGCAAC
20143973 AGTAAACCTG
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.35, C:0.18, G:0.29, T:0.18
Consensus pattern (47 bp):
GAGGCCGCAACGACGGATCTAGTACCATAGTTATAAAGGAAAAAGTT
Found at i:20144008 original size:50 final size:50
Alignment explanation
Indices: 20143946--20144294 Score: 346
Period size: 50 Copynumber: 7.0 Consensus size: 50
20143936 GTACCATAGT
* * * *
20143946 TATGAAGGGAAAGGTTAAGGCCGCAACAGTAAACCTGGTACCTTAGAAGA
1 TATGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTAGAAGA
* * * * **
20143996 TACGAAGGGAAAGGTTAAGGCCACAACGGCGAACTTGGTACCTTAGAAGA
1 TATGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTAGAAGA
* * *** * *
20144046 TGTGACA-GGAAAGGTTGAGACTATAATGGTGAACCCAGTACC--ACGAAGA
1 TATGA-AGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTA-GAAGA
* ** *
20144095 TATGAAGGGAAAGGTTGAGGCCGCAATGGCAAACCCGGTATCTTAGAAGA
1 TATGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTAGAAGA
*
20144145 TGTGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTAGAAGA
1 TATGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTAGAAGA
* * * * *
20144195 TGTGATGAGAAAGGTTGAGGCCGCAACGGTGAACCCGGTATCAT-GAAGA
1 TATGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTAGAAGA
* * * * ** *
20144244 TATGAAGGGAAAGGATAAGGCCACAAAGGCAAACCTGGTACCTTAGAAGA
1 TATGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTAGAAGA
20144294 T
1 T
20144295 GTGACCTTAG
Statistics
Matches: 246, Mismatches: 47, Indels: 12
0.81 0.15 0.04
Matches are distributed among these distances:
48 2 0.01
49 73 0.30
50 169 0.69
51 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.31, T:0.17
Consensus pattern (50 bp):
TATGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTAGAAGA
Found at i:20144140 original size:149 final size:149
Alignment explanation
Indices: 20143946--20144604 Score: 499
Period size: 149 Copynumber: 4.3 Consensus size: 149
20143936 GTACCATAGT
*
20143946 TATGAAGGGAAAGGTTAAGGCCGCAACA-GTAAACCTGGTACCTTAGAAGATACGAAGGGAAAGG
1 TATGAAGGGAAAGGTTAAGGCCGCAA-AGGCAAACCTGGTACCTTAGAAGATACGAAGGGAAAGG
** * * *
20144010 TTAAGGCCACAACGGCGAACTTGGTACCTTAGAAGATGTGACAG-GAAAGGTTGAGACTATAATG
65 TTAAGGCCACAACGGCGAACCCGGTACCTTAGAAGATGTGA-AGAGAAAGGTTGAGACCACAACG
20144074 GTGAACCCAGTACCACGAAGA
129 GTGAACCCAGTACCACGAAGA
* * * * **
20144095 TATGAAGGGAAAGGTTGAGGCCGCAATGGCAAACCCGGTATCTTAGAAGATGTGAAGGGAAAGGT
1 TATGAAGGGAAAGGTTAAGGCCGCAAAGGCAAACCTGGTACCTTAGAAGATACGAAGGGAAAGGT
* * * * * *
20144160 TGAGGCCGCAACGGTGAACCCGGTACCTTAGAAGATGTGATGAGAAAGGTTGAGGCCGCAACGGT
66 TAAGGCCACAACGGCGAACCCGGTACCTTAGAAGATGTGAAGAGAAAGGTTGAGACCACAACGGT
* * *
20144225 GAACCCGGTATCATGAAGA
131 GAACCCAGTACCACGAAGA
* *
20144244 TATGAAGGGAAAGGATAAGGCCACAAAGGCAAACCTGGTACCTTAGAAGATGTGACCTTAGAAGA
1 TATGAAGGGAAAGGTTAAGGCCGCAAAGGCAAACCTGGTACCTTAGAAGA--T-A-C------GA
* * * * *
20144309 TGTGATGGGAAAGGTTGAGGCCACAACGGCGAGCCCGGTA-C-TATTAAGATATGAAGGGAAAGG
56 ----A-GGGAAAGGTTAAGGCCACAACGGCGAACCCGGTACCTTA-GAAGATGTGAAGAGAAAGG
* * * * * *
20144372 TTGAGGCCGCAAAGGCGAA-CCTGATACCTTA-AAAGA
115 TTGAGACCACAACGGTGAACCCAG-TACC--ACGAAGA
* ** * * * ** *
20144408 TGTGAAGGGAAAGGTCGAGGCCGCAATA-GCGAACCCGATACCTTAGAAGATGTGATGGGAAAGG
1 TATGAAGGGAAAGGTTAAGGCCGCAA-AGGCAAACCTGGTACCTTAGAAGATACGAAGGGAAAGG
* ** ** * * * * * *
20144472 TTAAGGCCGCAACGGTAAACTTGGTATCGT-GAAGATATGAAGGGAAAGGTTGAGGCCGCAACGG
65 TTAAGGCCACAACGGCGAACCCGGTACCTTAGAAGATGTGAAGAGAAAGGTTGAGACCACAACGG
* *
20144536 TGAACTCGGTACCTTA-GAAGA
130 TGAACCCAGTACC--ACGAAGA
* * * *
20144557 TATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCTAGTACCTTAGAA
1 TATGAAGGGAAAGGTTAAGGCCGCAAAGGCAAACCTGGTACCTTAGAA
20144605 ACATGACAGG
Statistics
Matches: 413, Mismatches: 71, Indels: 52
0.77 0.13 0.10
Matches are distributed among these distances:
148 1 0.00
149 283 0.69
150 3 0.01
151 2 0.00
154 2 0.00
159 2 0.00
162 6 0.01
163 37 0.09
164 75 0.18
165 2 0.00
ACGTcount: A:0.34, C:0.17, G:0.32, T:0.17
Consensus pattern (149 bp):
TATGAAGGGAAAGGTTAAGGCCGCAAAGGCAAACCTGGTACCTTAGAAGATACGAAGGGAAAGGT
TAAGGCCACAACGGCGAACCCGGTACCTTAGAAGATGTGAAGAGAAAGGTTGAGACCACAACGGT
GAACCCAGTACCACGAAGA
Found at i:20144176 original size:99 final size:99
Alignment explanation
Indices: 20143946--20144604 Score: 477
Period size: 99 Copynumber: 6.5 Consensus size: 99
20143936 GTACCATAGT
* * * *
20143946 TATGAAGGGAAAGGTTAAGGCCGCAACAGTAAACCTGGTACCTTAGAAGATACGAAGGGAAAGGT
1 TATGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCTGGTACC-TAGAAGATATGAAGGGAAAGGT
* * **
20144011 TAAGGCCACAACGGCGAACTTGGTACCTTAGAAGA
65 TGAGGCCGCAACGGCGAACCCGGTACCTTAGAAGA
* * *** * **
20144046 TGTGACA-GGAAAGGTTGAGACTATAATGGTGAACCCAGTACC-ACGAAGATATGAAGGGAAAGG
1 TATGA-AGGGAAAGGTTGAGGCCGCAACGGTGAACCTGGTACCTA-GAAGATATGAAGGGAAAGG
* * *
20144109 TTGAGGCCGCAATGGCAAACCCGGTATCTTAGAAGA
64 TTGAGGCCGCAACGGCGAACCCGGTACCTTAGAAGA
* * * * *
20144145 TGTGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCCGGTACCTTAGAAGATGTGATGAGAAAGGT
1 TATGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCTGGTACC-TAGAAGATATGAAGGGAAAGGT
* * *
20144210 TGAGGCCGCAACGGTGAACCCGGTATCAT-GAAGA
65 TGAGGCCGCAACGGCGAACCCGGTACCTTAGAAGA
* * * * ** * **** *
20144244 TATGAAGGGAAAGGATAAGGCCACAAAGGCAAACCTGGTACCTTAGAAGATGTGACCTTAGAAGA
1 TATGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCTGGTACC-TAGAAGATATGAAGGGA-AAGG
* * * * *
20144309 TGTGATGG--G-AAAGGTTGAGGCCACAACGGCGAGCCCGGTACTATTAAGA
64 T-TGA-GGCCGCAACGG-CGA----AC-CCGG-TA--CC--T--TA-GAAGA
* * * * *
20144358 TATGAAGGGAAAGGTTGAGGCCGCAAAGGCGAACCTGATACCTTAAAAGATGTGAAGGGAAAGGT
1 TATGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCTGGTACC-TAGAAGATATGAAGGGAAAGGT
* ** *
20144423 CGAGGCCGCAATAGCGAACCCGATACCTTAGAAGA
65 TGAGGCCGCAACGGCGAACCCGGTACCTTAGAAGA
* * * * * *
20144458 TGTGATGGGAAAGGTTAAGGCCGCAACGGTAAACTTGGTATCGT-GAAGATATGAAGGGAAAGGT
1 TATGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCTGGTA-CCTAGAAGATATGAAGGGAAAGGT
* *
20144522 TGAGGCCGCAACGGTGAACTCGGTACCTTAGAAGA
65 TGAGGCCGCAACGGCGAACCCGGTACCTTAGAAGA
* *
20144557 TATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCTAGTACCTTAGAA
1 TATGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCTGGTACC-TAGAA
20144605 ACATGACAGG
Statistics
Matches: 435, Mismatches: 95, Indels: 58
0.74 0.16 0.10
Matches are distributed among these distances:
98 3 0.01
99 219 0.50
100 119 0.27
101 8 0.02
102 2 0.00
103 1 0.00
104 2 0.00
105 5 0.01
106 1 0.00
107 1 0.00
108 3 0.01
109 2 0.00
111 2 0.00
112 3 0.01
113 7 0.02
114 57 0.13
ACGTcount: A:0.34, C:0.17, G:0.32, T:0.17
Consensus pattern (99 bp):
TATGAAGGGAAAGGTTGAGGCCGCAACGGTGAACCTGGTACCTAGAAGATATGAAGGGAAAGGTT
GAGGCCGCAACGGCGAACCCGGTACCTTAGAAGA
Found at i:20144303 original size:15 final size:15
Alignment explanation
Indices: 20144283--20144313 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
20144273 CAAACCTGGT
20144283 ACCTTAGAAGATGTG
1 ACCTTAGAAGATGTG
20144298 ACCTTAGAAGATGTG
1 ACCTTAGAAGATGTG
20144313 A
1 A
20144314 TGGGAAAGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.13, G:0.26, T:0.26
Consensus pattern (15 bp):
ACCTTAGAAGATGTG
Found at i:20144358 original size:114 final size:114
Alignment explanation
Indices: 20144184--20144412 Score: 343
Period size: 114 Copynumber: 2.0 Consensus size: 114
20144174 TGAACCCGGT
* *
20144184 ACCTTAGAAGATGTGATGAGAAAGGTTGAGGCCGCAACGGTGAACCCGGTATCATGAAGATATGA
1 ACCTTAGAAGATGTGATGAGAAAGGTTGAGGCCACAACGGCGAACCCGGTATCATGAAGATATGA
* *
20144249 AGGGAAAGGATAAGGCCACAAAGGCAAACCTGGTACCTTAGAAGATGTG
66 AGGGAAAGGATAAGGCCACAAAGGCAAACCTGATACCTTAAAAGATGTG
* * *
20144298 ACCTTAGAAGATGTGATGGGAAAGGTTGAGGCCACAACGGCGAGCCCGGTA-CTATTAAGATATG
1 ACCTTAGAAGATGTGATGAGAAAGGTTGAGGCCACAACGGCGAACCCGGTATC-ATGAAGATATG
* * * *
20144362 AAGGGAAAGGTTGAGGCCGCAAAGGCGAACCTGATACCTTAAAAGATGTG
65 AAGGGAAAGGATAAGGCCACAAAGGCAAACCTGATACCTTAAAAGATGTG
20144412 A
1 A
20144413 AGGGAAAGGT
Statistics
Matches: 103, Mismatches: 11, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
113 1 0.01
114 102 0.99
ACGTcount: A:0.35, C:0.16, G:0.31, T:0.18
Consensus pattern (114 bp):
ACCTTAGAAGATGTGATGAGAAAGGTTGAGGCCACAACGGCGAACCCGGTATCATGAAGATATGA
AGGGAAAGGATAAGGCCACAAAGGCAAACCTGATACCTTAAAAGATGTG
Found at i:20144429 original size:50 final size:50
Alignment explanation
Indices: 20144298--20144604 Score: 327
Period size: 50 Copynumber: 6.2 Consensus size: 50
20144288 AGAAGATGTG
* * * * * *
20144298 ACCTTAGAAGATGTGATGGGAAAGGTTGAGGCCACAACGGCGAGCCCGGT
1 ACCTTAGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCTGAT
* *
20144348 A-C-TATTAAGATATGAAGGGAAAGGTTGAGGCCGCAAAGGCGAACCTGAT
1 ACCTTA-GAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCTGAT
* * * ** *
20144397 ACCTTAAAAGATGTGAAGGGAAAGGTCGAGGCCGCAATAGCGAACCCGAT
1 ACCTTAGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCTGAT
* * * ** * *
20144447 ACCTTAGAAGATGTGATGGGAAAGGTTAAGGCCGCAACGGTAAACTTGGT
1 ACCTTAGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCTGAT
* * * *
20144497 ATCGT-GAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGTGAA-CTCGGT
1 ACCTTAGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCT-GAT
20144546 ACCTTAGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCT-AGT
1 ACCTTAGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCTGA-T
20144596 ACCTTAGAA
1 ACCTTAGAA
20144605 ACATGACAGG
Statistics
Matches: 214, Mismatches: 36, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
48 3 0.01
49 78 0.36
50 129 0.60
51 4 0.02
ACGTcount: A:0.33, C:0.17, G:0.32, T:0.18
Consensus pattern (50 bp):
ACCTTAGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCTGAT
Found at i:20144507 original size:263 final size:263
Alignment explanation
Indices: 20144035--20144557 Score: 715
Period size: 263 Copynumber: 2.0 Consensus size: 263
20144025 CGAACTTGGT
* * * *
20144035 ACCTTAGAAGATGTGACAGGAAAGGTTGAGACTATAATGGTGAACCCAGTACCACGAAGATATGA
1 ACCTTAGAAGATGTGACAGGAAAGGTTGAGACCACAACGGCGAACCCAGTACCACGAAGATATGA
* * * * *
20144100 AGGGAAAGGTTGAGGCCGCAATGGCAAACCCGGTATCTTAGAAGATGTGAAGGGAAAGGTTGAGG
66 AGGGAAAGGTTGAGGCCGCAAAGGCAAACCCGATACCTTAAAAGATGTGAAGGGAAAGGTCGAGG
* * * * *
20144165 CCGCAACGGTGAACCCGGTACCTTAGAAGATGTGATGAGAAAGGTTGAGGCCGCAACGGTGAACC
131 CCGCAACAGCGAACCCGATACCTTAGAAGATGTGATGAGAAAGGTTAAGGCCGCAACGGTAAACC
20144230 CGGTATCATGAAGATATGAAGGGAAAGGATAAGGCCACAAAGGCAAAC-CTGGTACCTTAGAAGA
196 CGGTATCATGAAGATATGAAGGGAAAGGATAAGGCCACAAAGGCAAACTC-GGTACCTTAGAAGA
20144294 TGTG
260 TGTG
** * * * * **
20144298 ACCTTAGAAGATGTGATGGGAAAGGTTGAGGCCACAACGGCGAGCCCGGTACTATTAAGATATGA
1 ACCTTAGAAGATGTGACAGGAAAGGTTGAGACCACAACGGCGAACCCAGTACCACGAAGATATGA
* *
20144363 AGGGAAAGGTTGAGGCCGCAAAGGCGAACCTGATACCTTAAAAGATGTGAAGGGAAAGGTCGAGG
66 AGGGAAAGGTTGAGGCCGCAAAGGCAAACCCGATACCTTAAAAGATGTGAAGGGAAAGGTCGAGG
* * *
20144428 CCGCAATAGCGAACCCGATACCTTAGAAGATGTGATGGGAAAGGTTAAGGCCGCAACGGTAAACT
131 CCGCAACAGCGAACCCGATACCTTAGAAGATGTGATGAGAAAGGTTAAGGCCGCAACGGTAAACC
* * * * * * **
20144493 TGGTATCGTGAAGATATGAAGGGAAAGGTTGAGGCCGCAACGGTGAACTCGGTACCTTAGAAGAT
196 CGGTATCATGAAGATATGAAGGGAAAGGATAAGGCCACAAAGGCAAACTCGGTACCTTAGAAGAT
20144558 ATGAAGGGAA
Statistics
Matches: 224, Mismatches: 35, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
263 223 1.00
264 1 0.00
ACGTcount: A:0.34, C:0.16, G:0.32, T:0.18
Consensus pattern (263 bp):
ACCTTAGAAGATGTGACAGGAAAGGTTGAGACCACAACGGCGAACCCAGTACCACGAAGATATGA
AGGGAAAGGTTGAGGCCGCAAAGGCAAACCCGATACCTTAAAAGATGTGAAGGGAAAGGTCGAGG
CCGCAACAGCGAACCCGATACCTTAGAAGATGTGATGAGAAAGGTTAAGGCCGCAACGGTAAACC
CGGTATCATGAAGATATGAAGGGAAAGGATAAGGCCACAAAGGCAAACTCGGTACCTTAGAAGAT
GTG
Found at i:20144648 original size:99 final size:97
Alignment explanation
Indices: 20144354--20144650 Score: 269
Period size: 99 Copynumber: 3.0 Consensus size: 97
20144344 CGGTACTATT
* *
20144354 AAGATATGAAGGGAAAGGTTGAGGCCGCAAAGGCGAACCTGATACCTTA-AAAGATGTGAAGGGA
1 AAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCTG-TACCTTAGAAACA--TGAAGGGA
* * *
20144418 AAGGTCGAGGCCGCAA-TAGCGAACCCGATACCTTAG
63 AAGGTTGAGGCCGCAACGA-CGAA-CTGATACCTTAG
* * * ** * * * *
20144454 AAGATGTGATGGGAAAGGTTAAGGCCGCAACGGTAAACTTGGTATCGT-GAAGATATGAAGGGAA
1 AAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCT-GTACCTTAGAA-ACATGAAGGGAA
** *
20144518 AGGTTGAGGCCGCAACGGTGAACTCGGTACCTTAG
64 AGGTTGAGGCCGCAACGACGAACT-GATACCTTAG
*
20144553 AAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCTAGTACCTTAGAAACATGACA-GGCA
1 AAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCT-GTACCTTAGAAACATGA-AGGGAA
* * * *
20144617 AGATTGAGGCCACAACGACAAATCTTATACCTTA
64 AGGTTGAGGCCGCAACGACGAA-CTGATACCTTA
20144651 CCCCAATCAT
Statistics
Matches: 155, Mismatches: 34, Indels: 17
0.75 0.17 0.08
Matches are distributed among these distances:
98 1 0.01
99 106 0.68
100 45 0.29
101 3 0.02
ACGTcount: A:0.35, C:0.18, G:0.30, T:0.18
Consensus pattern (97 bp):
AAGATATGAAGGGAAAGGTTGAGGCCGCAACGGCGAACCTGTACCTTAGAAACATGAAGGGAAAG
GTTGAGGCCGCAACGACGAACTGATACCTTAG
Found at i:20146693 original size:23 final size:23
Alignment explanation
Indices: 20146663--20146707 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
20146653 TTTCATTTTA
20146663 ATTCAATCCA-TT-TTTTTAAAAG
1 ATTCAAT-CATTTGTTTTTAAAAG
20146685 ATTCGAATCATTTGTTTTTAAAA
1 ATTC-AATCATTTGTTTTTAAAA
20146708 AAGAAAGGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 6 0.30
23 5 0.25
24 9 0.45
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.47
Consensus pattern (23 bp):
ATTCAATCATTTGTTTTTAAAAG
Found at i:20157608 original size:16 final size:17
Alignment explanation
Indices: 20157581--20157616 Score: 65
Period size: 16 Copynumber: 2.2 Consensus size: 17
20157571 ATTATTTACT
20157581 TATATGTTATTATATTA
1 TATATGTTATTATATTA
20157598 TATAT-TTATTATATTA
1 TATATGTTATTATATTA
20157614 TAT
1 TAT
20157617 TTACGCATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
TATATGTTATTATATTA
Found at i:20166424 original size:10 final size:10
Alignment explanation
Indices: 20166406--20166439 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
20166396 AAAGCAAAAA
*
20166406 TCATATTCTT
1 TCATTTTCTT
20166416 TCATTTTCTT
1 TCATTTTCTT
20166426 TCATTTTCTT
1 TCATTTTCTT
20166436 TCAT
1 TCAT
20166440 GTTAAGGCAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.15, C:0.21, G:0.00, T:0.65
Consensus pattern (10 bp):
TCATTTTCTT
Found at i:20167304 original size:16 final size:17
Alignment explanation
Indices: 20167278--20167312 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
20167268 TTATTTCCTC
20167278 ATATCTTATTATATTAT
1 ATATCTTATTATATTAT
20167295 ATAT-TTATTATATTAT
1 ATATCTTATTATATTAT
20167311 AT
1 AT
20167313 TTACGCATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (17 bp):
ATATCTTATTATATTAT
Found at i:20167893 original size:17 final size:17
Alignment explanation
Indices: 20167871--20167905 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
20167861 TTTTTATTGT
20167871 TTAAATATTAAAATATA
1 TTAAATATTAAAATATA
*
20167888 TTAAATTTTAAAATATA
1 TTAAATATTAAAATATA
20167905 T
1 T
20167906 ATATATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
TTAAATATTAAAATATA
Found at i:20169147 original size:24 final size:25
Alignment explanation
Indices: 20169111--20169158 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
20169101 ACATTATTAA
*
20169111 AACAACTTCTAAA-AGAAACTCAAG
1 AACAACTTCTAAAGAAAAACTCAAG
20169135 AACAA-TTCTTAAAGAAAAACTCAA
1 AACAACTTC-TAAAGAAAAACTCAA
20169159 AGAGAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 3 0.14
24 9 0.43
25 9 0.43
ACGTcount: A:0.56, C:0.19, G:0.06, T:0.19
Consensus pattern (25 bp):
AACAACTTCTAAAGAAAAACTCAAG
Found at i:20173995 original size:17 final size:17
Alignment explanation
Indices: 20173973--20174011 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
20173963 AGGTGGAGAA
* *
20173973 CTTGTTCGTTGAGAGTT
1 CTTGTTCGTAGAGAATT
20173990 CTTGTTCGTAGAGAATT
1 CTTGTTCGTAGAGAATT
20174007 CTTGT
1 CTTGT
20174012 CAAAGTGGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.13, G:0.26, T:0.46
Consensus pattern (17 bp):
CTTGTTCGTAGAGAATT
Found at i:20177046 original size:19 final size:19
Alignment explanation
Indices: 20176996--20177047 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
20176986 TAAGTGTTTC
*
20176996 TTTTCTACTTTCT-CTTTCT
1 TTTTCT-CTTTCTCCTTCCT
*
20177015 TTTTCTCTATCTCCTTCCT
1 TTTTCTCTTTCTCCTTCCT
*
20177034 TTTTCTTTTTCTCC
1 TTTTCTCTTTCTCC
20177048 ATCCCCCACA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 5 0.18
19 23 0.82
ACGTcount: A:0.04, C:0.31, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTCTCTTTCTCCTTCCT
Found at i:20177151 original size:16 final size:17
Alignment explanation
Indices: 20177117--20177161 Score: 69
Period size: 16 Copynumber: 2.8 Consensus size: 17
20177107 TCTATTTGCA
20177117 TTATT-TATT-TATATC
1 TTATTATATTATATATC
20177132 TTATTATATTATATAT-
1 TTATTATATTATATATC
20177148 TTATTATATTATAT
1 TTATTATATTATAT
20177162 TTACGCATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.18
16 18 0.64
17 5 0.18
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (17 bp):
TTATTATATTATATATC
Found at i:20177623 original size:7 final size:8
Alignment explanation
Indices: 20177604--20177633 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
20177594 TAGGAGATAT
20177604 TTTTTTAA
1 TTTTTTAA
20177612 TTTTTTAA
1 TTTTTTAA
20177620 TTTTTTAA
1 TTTTTTAA
20177628 TTTTTT
1 TTTTTT
20177634 GTTATTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTTTAA
Found at i:20187683 original size:40 final size:40
Alignment explanation
Indices: 20187630--20187736 Score: 153
Period size: 40 Copynumber: 2.7 Consensus size: 40
20187620 TTGGAAAGAA
*
20187630 GCTTTCACGTGGAAACGCTTTTGTTGACAGAAGGAAAAGC
1 GCTTCCACGTGGAAACGCTTTTGTTGACAGAAGGAAAAGC
* *
20187670 GCTTCCACATGGAAGA-GCTTTTGTTTACAGAAGGAAAAGC
1 GCTTCCACGTGGAA-ACGCTTTTGTTGACAGAAGGAAAAGC
* *
20187710 GCTTCCACGTGGAAGCGCTTTTCTTGA
1 GCTTCCACGTGGAAACGCTTTTGTTGA
20187737 ATTCCCCCTG
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
40 57 0.98
41 1 0.02
ACGTcount: A:0.27, C:0.20, G:0.26, T:0.27
Consensus pattern (40 bp):
GCTTCCACGTGGAAACGCTTTTGTTGACAGAAGGAAAAGC
Found at i:20188240 original size:16 final size:17
Alignment explanation
Indices: 20188213--20188248 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
20188203 ATTATTTGCT
*
20188213 TATATCTTATTATGTTA
1 TATATCTTATTATATTA
20188230 TATAT-TTATTATATTA
1 TATATCTTATTATATTA
20188246 TAT
1 TAT
20188249 TTATGCATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (17 bp):
TATATCTTATTATATTA
Found at i:20199973 original size:6 final size:7
Alignment explanation
Indices: 20199931--20199956 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
20199921 ACACACCATT
20199931 TTTTTAG
1 TTTTTAG
20199938 TTTTTAG
1 TTTTTAG
20199945 TTTTTAG
1 TTTTTAG
20199952 TTTTT
1 TTTTT
20199957 GCTTTGTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.77
Consensus pattern (7 bp):
TTTTTAG
Found at i:20216943 original size:51 final size:51
Alignment explanation
Indices: 20216672--20216935 Score: 440
Period size: 51 Copynumber: 5.2 Consensus size: 51
20216662 TAAACGAAAA
*
20216672 GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTA-GGATTAAAA
1 GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAG
20216722 GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAG
1 GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAG
*
20216773 GTCCGATGACTAAGTGTCATCGTGATTAAATGAATCCTTTACGGATTAAAG
1 GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAG
*
20216824 GTCCGATGACTAAGTGTCATCGTGAATAAATGAATCCTTTACGGATTAAAG
1 GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAG
* * * * *
20216875 GTCCGATGACTAAATGTCATCGTGAGTAAATGAATCCATGATGAATTAAAG
1 GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAG
*
20216926 GTTCGATGAC
1 GTCCGATGAC
20216936 AATATGTCTT
Statistics
Matches: 203, Mismatches: 10, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
50 41 0.20
51 162 0.80
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (51 bp):
GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTAAAG
Found at i:20218936 original size:15 final size:15
Alignment explanation
Indices: 20218917--20218956 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
20218907 TAACCAACAG
*
20218917 AAAGATAAGGAAGAA
1 AAAGAGAAGGAAGAA
*
20218932 GAAGAGAAGGAAGAA
1 AAAGAGAAGGAAGAA
20218947 AAAGAAGAAG
1 AAAG-AGAAG
20218957 AGAATGAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 16 0.76
16 5 0.24
ACGTcount: A:0.65, C:0.00, G:0.33, T:0.03
Consensus pattern (15 bp):
AAAGAGAAGGAAGAA
Found at i:20219191 original size:17 final size:17
Alignment explanation
Indices: 20219169--20219203 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
20219159 TCCACTTAAG
20219169 TTATTGATACTGCATTT
1 TTATTGATACTGCATTT
*
20219186 TTATTGTTACTGCATTT
1 TTATTGATACTGCATTT
20219203 T
1 T
20219204 CTGTTGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.20, C:0.11, G:0.11, T:0.57
Consensus pattern (17 bp):
TTATTGATACTGCATTT
Found at i:20223146 original size:20 final size:20
Alignment explanation
Indices: 20223117--20223157 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
20223107 TGTATTCTCT
* * *
20223117 ACAACTATTGCAAATGGGAA
1 ACAACGATTGAAAACGGGAA
20223137 ACAACGATTGAAAACGGGAA
1 ACAACGATTGAAAACGGGAA
20223157 A
1 A
20223158 GATAGAAAGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.15, G:0.22, T:0.15
Consensus pattern (20 bp):
ACAACGATTGAAAACGGGAA
Found at i:20226920 original size:12 final size:12
Alignment explanation
Indices: 20226905--20226942 Score: 67
Period size: 12 Copynumber: 3.2 Consensus size: 12
20226895 AATTAAAGAA
20226905 ATAATAGCATTC
1 ATAATAGCATTC
*
20226917 ATAATAGCATGC
1 ATAATAGCATTC
20226929 ATAATAGCATTC
1 ATAATAGCATTC
20226941 AT
1 AT
20226943 CATGATAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.42, C:0.16, G:0.11, T:0.32
Consensus pattern (12 bp):
ATAATAGCATTC
Found at i:20230579 original size:97 final size:97
Alignment explanation
Indices: 20230413--20230606 Score: 284
Period size: 97 Copynumber: 2.0 Consensus size: 97
20230403 AACCTCGAAA
* *
20230413 AAGGGAATTCAATTATCCCGATTTGAAGAAAAGTCGCGCCTAGTAAGTTAAGGCACAAATTTTCA
1 AAGGGAATTCAATTATCCCGATTTGAAGAAAAATCGAGCCTAGTAAGTTAAGGCACAAATTTTCA
* *
20230478 AAACCAGAGAT-AAGGAAACATTGCCTCGATTT
66 AAACCAGAAATAAAGG-AACATTACCTCGATTT
* *
20230510 AAGGGTATTCGATTATCCC-AGTTTGAAGAAAAATCGAGCCTAGTAAGTTAAGGCACAAATTTTC
1 AAGGGAATTCAATTATCCCGA-TTTGAAGAAAAATCGAGCCTAGTAAGTTAAGGCACAAATTTTC
* *
20230574 AAAACCCGAAATAAAGGAATATTACCTCGATTT
65 AAAACCAGAAATAAAGGAACATTACCTCGATTT
20230607 TAAATATTTT
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
96 1 0.01
97 82 0.94
98 4 0.05
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.26
Consensus pattern (97 bp):
AAGGGAATTCAATTATCCCGATTTGAAGAAAAATCGAGCCTAGTAAGTTAAGGCACAAATTTTCA
AAACCAGAAATAAAGGAACATTACCTCGATTT
Found at i:20230899 original size:30 final size:29
Alignment explanation
Indices: 20230859--20231086 Score: 137
Period size: 29 Copynumber: 7.8 Consensus size: 29
20230849 CAGAGAATTT
* *
20230859 AGGGTTAAAATGCAATTTTGGAAAGTTTTA
1 AGGGTAAAAATGTAATTTTGGAAAG-TTTA
*
20230889 AGGGTAAAAATGTCATTTTAGGAAA-TTT-
1 AGGGTAAAAATGTAATTTT-GGAAAGTTTA
* * * *
20230917 GGGGTAAAAATGGAGTTTTTGG-AAGTTCA
1 AGGGTAAAAATGTA-ATTTTGGAAAGTTTA
* * * *
20230946 GGGGGTAATAATGTGATTTTTGGAAA-TTCA
1 -AGGGTAAAAATGT-AATTTTGGAAAGTTTA
* * *
20230976 GGGGTAAAAATGTGATTTTTGAGAAGTTT-
1 AGGGTAAAAATGTAATTTTGGA-AAGTTTA
* * *
20231005 AGGGTAAAAATGTGATTTTTGAAAG-TTC
1 AGGGTAAAAATGTAATTTTGGAAAGTTTA
* *
20231033 AGCGGTAAAAATGTAATTTTTGAAAG-TTC
1 AG-GGTAAAAATGTAATTTTGGAAAGTTTA
* * *
20231062 GGAGGTCAAAATGTAATTTTTGAAA
1 AG-GGTAAAAATGTAATTTTGGAAA
20231087 AGTACGGAGG
Statistics
Matches: 167, Mismatches: 20, Indels: 23
0.80 0.10 0.11
Matches are distributed among these distances:
27 4 0.02
28 26 0.16
29 89 0.53
30 40 0.24
31 8 0.05
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.35
Consensus pattern (29 bp):
AGGGTAAAAATGTAATTTTGGAAAGTTTA
Found at i:20230916 original size:58 final size:56
Alignment explanation
Indices: 20230854--20231060 Score: 184
Period size: 58 Copynumber: 3.6 Consensus size: 56
20230844 AGTTTCAGAG
* * * *
20230854 AATTTAGGGTTAAAATGCAATTTTGGAAAGTTTTAAGGGTAAAAATGTCATTTTAGGA
1 AATTCAGGGTAAAAATGTAATTTTGGAAAG-TTTAAGGGTAAAAATGTGATTTT-GGA
** * * * * *
20230912 AATTTGGGGTAAAAATGGAGTTTTTGG-AAGTTCAGGGGGTAATAATGTGATTTTTGGA
1 AATTCAGGGTAAAAATGTA-ATTTTGGAAAGTTTA-AGGGTAAAAATGTGA-TTTTGGA
* * *
20230970 AATTCAGGGGTAAAAATGTGATTTTTGAGAAGTTT-AGGGTAAAAATGTGATTTTTGA
1 AATTCA-GGGTAAAAATGTAATTTTGGA-AAGTTTAAGGGTAAAAATGTGATTTTGGA
*
20231027 AAGTTCAGCGGTAAAAATGTAATTTTTGAAAGTT
1 AA-TTCAG-GGTAAAAATGTAATTTTGGAAAGTT
20231061 CGGAGGTCAA
Statistics
Matches: 122, Mismatches: 19, Indels: 17
0.77 0.12 0.11
Matches are distributed among these distances:
57 17 0.14
58 79 0.65
59 21 0.17
60 5 0.04
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (56 bp):
AATTCAGGGTAAAAATGTAATTTTGGAAAGTTTAAGGGTAAAAATGTGATTTTGGA
Found at i:20230949 original size:29 final size:29
Alignment explanation
Indices: 20230890--20231083 Score: 207
Period size: 29 Copynumber: 6.7 Consensus size: 29
20230880 AAAGTTTTAA
* * * *
20230890 GGGTAAAAATGTCATTTTAGGAAATT-TG
1 GGGTAAAAATGTGATTTTTGGAAGTTCAG
20230918 GGGTAAAAATG-GAGTTTTTGGAAGTTCAGG
1 GGGTAAAAATGTGA-TTTTTGGAAGTTCA-G
* *
20230948 GGGTAATAATGTGATTTTTGGAAATTCAG
1 GGGTAAAAATGTGATTTTTGGAAGTTCAG
*
20230977 GGGTAAAAATGTGATTTTTGAGAAGTTTA-
1 GGGTAAAAATGTGATTTTTG-GAAGTTCAG
*
20231006 GGGTAAAAATGTGATTTTTGAAAGTTCAG
1 GGGTAAAAATGTGATTTTTGGAAGTTCAG
* * *
20231035 CGGTAAAAATGTAATTTTTGAAAGTTC-G
1 GGGTAAAAATGTGATTTTTGGAAGTTCAG
* *
20231063 GAGGTCAAAATGTAATTTTTG
1 G-GGTAAAAATGTGATTTTTG
20231084 AAAAGTACGG
Statistics
Matches: 144, Mismatches: 15, Indels: 13
0.84 0.09 0.08
Matches are distributed among these distances:
27 1 0.01
28 28 0.19
29 83 0.58
30 30 0.21
31 2 0.01
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.36
Consensus pattern (29 bp):
GGGTAAAAATGTGATTTTTGGAAGTTCAG
Found at i:20231082 original size:87 final size:88
Alignment explanation
Indices: 20230890--20231089 Score: 239
Period size: 87 Copynumber: 2.3 Consensus size: 88
20230880 AAAGTTTTAA
* * * * * *
20230890 GGGTAAAAATGTCATTTTAG-GAAATTTGGGGTAAAAATGGAGTTTTTGGAAGTTCAGGGGGTAA
1 GGGTAAAAATGTAATTTTTGAGAAGTTTAGGGTAAAAATGGAGTTTTTGAAAGTTCAGGCGGTAA
* *
20230954 TAATGTGATTTTTGGAAATTCAG
66 AAATGTAATTTTTGGAAATTCAG
*
20230977 GGGTAAAAATGTGATTTTTGAGAAGTTTAGGGTAAAAATGTGA-TTTTTGAAAGTTCA-GCGGTA
1 GGGTAAAAATGTAATTTTTGAGAAGTTTAGGGTAAAAATG-GAGTTTTTGAAAGTTCAGGCGGTA
20231040 AAAATGTAATTTTT-GAAAGTTC-G
65 AAAATGTAATTTTTGGAAA-TTCAG
* *
20231063 GAGGTCAAAATGTAATTTTTGAAAAGT
1 G-GGTAAAAATGTAATTTTTGAGAAGT
20231090 ACGGAGGTCA
Statistics
Matches: 98, Mismatches: 11, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
86 6 0.06
87 60 0.61
88 30 0.31
89 2 0.02
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.35
Consensus pattern (88 bp):
GGGTAAAAATGTAATTTTTGAGAAGTTTAGGGTAAAAATGGAGTTTTTGAAAGTTCAGGCGGTAA
AAATGTAATTTTTGGAAATTCAG
Found at i:20231084 original size:29 final size:29
Alignment explanation
Indices: 20230891--20231176 Score: 192
Period size: 29 Copynumber: 9.8 Consensus size: 29
20230881 AAGTTTTAAG
* * *
20230891 GGTAAAAATGTCATTTTAGGAAA-TTTGG-
1 GGTAAAAATGTAATTTT-TGAAAGTTCGGA
* * * *
20230919 GGTAAAAATGGAGTTTTTGGAAGTTCAGGG
1 GGTAAAAATGTAATTTTTGAAAGTTC-GGA
* *
20230949 GGTAATAATGTGATTTTTGGAAA-TTCAGG-
1 GGTAAAAATGTAATTTTT-GAAAGTTC-GGA
* **
20230978 GGTAAAAATGTGATTTTTGAGAAGTTTAG-
1 GGTAAAAATGTAATTTTTGA-AAGTTCGGA
* * *
20231007 GGTAAAAATGTGATTTTTGAAAGTTCAGC
1 GGTAAAAATGTAATTTTTGAAAGTTCGGA
20231036 GGTAAAAATGTAATTTTTGAAAGTTCGGA
1 GGTAAAAATGTAATTTTTGAAAGTTCGGA
* *
20231065 GGTCAAAATGTAATTTTTGAAAAGTACGGA
1 GGTAAAAATGTAATTTTTG-AAAGTTCGGA
* * * *
20231095 GGTCAGAATATAATTTTTGGAAAGCTC-GA
1 GGTAAAAATGTAATTTTT-GAAAGTTCGGA
* * *
20231124 TGGTCAAAATGAAATTTTTAGAGAA-TTCGGG
1 -GGTAAAAATGTAATTTTT-GA-AAGTTCGGA
* *
20231155 GGTTAAAATGTGATTTTT-AAAG
1 GGTAAAAATGTAATTTTTGAAAG
20231177 AGTTTAGGGA
Statistics
Matches: 212, Mismatches: 33, Indels: 26
0.78 0.12 0.10
Matches are distributed among these distances:
27 5 0.02
28 26 0.12
29 88 0.42
30 86 0.41
31 7 0.03
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.34
Consensus pattern (29 bp):
GGTAAAAATGTAATTTTTGAAAGTTCGGA
Found at i:20231133 original size:60 final size:58
Alignment explanation
Indices: 20231011--20231142 Score: 149
Period size: 59 Copynumber: 2.2 Consensus size: 58
20231001 GTTTAGGGTA
* * * * *
20231011 AAAATGTGATTTTTGAAAGTTCAGCGGTAAAAATGTAATTTTTGAAAGTTCGGAGGTC
1 AAAATGTAATTTTTGAAAGTACAGAGGTAAAAATATAATTTTTGAAAGCTCGGAGGTC
* * *
20231069 AAAATGTAATTTTTGAAAAGTACGGAGGTCAGAATATAATTTTTGGAAAGCTC-GATGGTC
1 AAAATGTAATTTTTG-AAAGTACAGAGGTAAAAATATAATTTTT-GAAAGCTCGGA-GGTC
*
20231129 AAAATGAAATTTTT
1 AAAATGTAATTTTT
20231143 AGAGAATTCG
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
58 14 0.23
59 24 0.39
60 24 0.39
ACGTcount: A:0.37, C:0.07, G:0.22, T:0.34
Consensus pattern (58 bp):
AAAATGTAATTTTTGAAAGTACAGAGGTAAAAATATAATTTTTGAAAGCTCGGAGGTC
Found at i:20231171 original size:60 final size:59
Alignment explanation
Indices: 20231040--20231176 Score: 145
Period size: 60 Copynumber: 2.3 Consensus size: 59
20231030 TTCAGCGGTA
* *
20231040 AAAATGTAATTTTTGAAAGTTCGGAGGTCAAAATGTAATTTTTGAAAAGTACGGAGGTC
1 AAAATGTAATTTTTGAAAGCTCGGAGGTCAAAATGAAATTTTTGAAAAGTACGGAGGTC
* * * * * *
20231099 AGAATATAATTTTTGGAAAGCTC-GATGGTCAAAATGAAATTTTTAGAGAA-TTCGGGGGTT
1 AAAATGTAATTTTT-GAAAGCTCGGA-GGTCAAAATGAAATTTTT-GAAAAGTACGGAGGTC
*
20231159 AAAATGTGATTTTT-AAAG
1 AAAATGTAATTTTTGAAAG
20231177 AGTTTAGGGA
Statistics
Matches: 64, Mismatches: 11, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
58 4 0.06
59 14 0.22
60 42 0.66
61 4 0.06
ACGTcount: A:0.37, C:0.06, G:0.23, T:0.34
Consensus pattern (59 bp):
AAAATGTAATTTTTGAAAGCTCGGAGGTCAAAATGAAATTTTTGAAAAGTACGGAGGTC
Found at i:20233035 original size:6 final size:6
Alignment explanation
Indices: 20233018--20233111 Score: 50
Period size: 6 Copynumber: 15.8 Consensus size: 6
20233008 GACTTTTTAA
* ** *
20233018 TTAAATT TTAAAT TTAAAT TCAAA- ACAAAT TTAAAT TTAAA- ATAAAT
1 TTAAA-T TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
** * * * * *
20233065 TTAAACT CAAAAA ATAAGT TTAAAT TTAAA- ATAAAT TTAAAC TTAAA
1 TTAAA-T TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
20233112 ATAAATAAAT
Statistics
Matches: 65, Mismatches: 18, Indels: 9
0.71 0.20 0.10
Matches are distributed among these distances:
5 12 0.18
6 44 0.68
7 9 0.14
ACGTcount: A:0.56, C:0.05, G:0.01, T:0.37
Consensus pattern (6 bp):
TTAAAT
Found at i:20233047 original size:17 final size:17
Alignment explanation
Indices: 20233026--20233117 Score: 105
Period size: 17 Copynumber: 5.3 Consensus size: 17
20233016 AATTAAATTT
20233026 TAAATTTAAATTCAAAA
1 TAAATTTAAATTCAAAA
* *
20233043 CAAATTTAAATTTAAAA
1 TAAATTTAAATTCAAAA
*
20233060 TAAATTTAAACTCAAAAAA
1 TAAATTTAAATTC--AAAA
* *
20233079 TAAGTTTAAATTTAAAA
1 TAAATTTAAATTCAAAA
20233096 TAAATTTAAACTT-AAAA
1 TAAATTTAAA-TTCAAAA
20233113 TAAAT
1 TAAAT
20233118 AAATTTTAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
17 47 0.75
18 2 0.03
19 14 0.22
ACGTcount: A:0.59, C:0.05, G:0.01, T:0.35
Consensus pattern (17 bp):
TAAATTTAAATTCAAAA
Found at i:20233087 original size:36 final size:34
Alignment explanation
Indices: 20233026--20233129 Score: 131
Period size: 36 Copynumber: 3.0 Consensus size: 34
20233016 AATTAAATTT
* *
20233026 TAAATTTAAATTCAAAACAAATTTAAATTTAAAA
1 TAAATTTAAACTCAAAAAAAATTTAAATTTAAAA
20233060 TAAATTTAAACTCAAAAAATAAGTTTAAATTTAAAA
1 TAAATTTAAACTCAAAAAA-AA-TTTAAATTTAAAA
* *
20233096 TAAATTTAAACTTAAAATAAA--TAAATTTTAAAA
1 TAAATTTAAACTCAAAAAAAATTTAAA-TTTAAAA
20233129 T
1 T
20233130 TTTAAAATTG
Statistics
Matches: 63, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
32 4 0.06
33 8 0.13
34 17 0.27
35 4 0.06
36 30 0.48
ACGTcount: A:0.59, C:0.05, G:0.01, T:0.36
Consensus pattern (34 bp):
TAAATTTAAACTCAAAAAAAATTTAAATTTAAAA
Found at i:20233959 original size:208 final size:209
Alignment explanation
Indices: 20233600--20234761 Score: 1717
Period size: 208 Copynumber: 5.6 Consensus size: 209
20233590 AATCGTATTT
* * * *
20233600 GATTTGGTCTACCTT-TCTGTATCTCATCAGGAAGATGACTGCATCACTTGTTTTAATCCACTTC
1 GATTTGGTATA-CTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTTAATCCGCTTC
* * * *
20233664 TCTATATCTCATCAGGAAGACGGATTTGGTTCACTTTTCTGTATCTCATCAGGAAGCTGACCATT
65 TCTGTATCTCATCAGGAAGATGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTGACCATT
* *
20233729 TTATTGCTTCGACCTACTTCTCAGTATCTCATCAGGAAGCT-GGGTTCGAAGTTTCCCTCACATT
130 TTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTTCCCTCATATT
20233793 GAGCTTTGTTCCATC
195 GAGCTTTGTTCCATC
* *
20233808 GATTTGGTATACTTCTCTGTATCTCATTAGGAAGATGACCGCCTCACTTGTTTTAATTCGCTTCT
1 GATTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTTAATCCGCTTCT
*
20233873 CTGTATCTCATCAGGAAGATGGATTTGGTCCACTTCTTTGTATCTCATCAGGAAGCTGACCATTT
66 CTGTATCTCATCAGGAAGATGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTGACCATTT
* *
20233938 TATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCT-AGGTTCAAAGTTTCCCTCATATTG
131 TATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTTCCCTCATATTG
20234002 AGCTTTGTTCCATC
196 AGCTTTGTTCCATC
*
20234016 GATTTGGTATACTTCTCTGTATCTCATCAGGAAGATGATCGCCTCACTTGTTTTAATCCGCTTCT
1 GATTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTTAATCCGCTTCT
* * * * *
20234081 CCGTATGTCATCAGGAATATGGATTTAGTCCACTTCTCTATATCTCATCAGGAAGCTGACCATTT
66 CTGTATCTCATCAGGAAGATGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTGACCATTT
* *
20234146 TATTGCTTCGACCTGCTTCTCAGTA-CTCATCAGGAAGCTGGGGTTCGAAGTTTCTCTCATATTA
131 TATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTTCCCTCATATTG
* *
20234210 AGCCTTGTTTCATC
196 AGCTTTGTTCCATC
* * *
20234224 GATTTGGTTTACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTTTAATTCACTTC
1 GATTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTG-TTTTAATCCGCTTC
* * * *
20234289 TCTATATCTTATCAGGAAGACGGATTTGGTCCACTTCTCTGTATCTCATTAGGAAGCTGACCATT
65 TCTGTATCTCATCAGGAAGATGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTGACCATT
* * *
20234354 TTATTGCTTCGACCTGCTTCTCAATATCTCATCAGAAAGCTGGGGTTCGAAGTTTCGCTCATATT
130 TTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTTCCCTCATATT
* * *
20234419 GAGCCTTGTTTCATT
195 GAGCTTTGTTCCATC
* *
20234434 GATTTGGTATACTTCTCTGTATCTCATCAAGAAGATGACCGCCTCACTTGTTTTAATCCGCTTTT
1 GATTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTTAATCCGCTTCT
* * * * * *
20234499 CTGTATCACATCAAGAAGATGGATTTGGTCCACTTCTTTGCATCTCATCAGGAAGTTAACCATTT
66 CTGTATCTCATCAGGAAGATGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTGACCATTT
* **
20234564 TATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTAGGGTTCGAAGTTTTGCTC-TATTG
131 TATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTTCCCTCATATTG
*
20234628 AGCTTTGCTT-CATT
196 AGCTTTG-TTCCATC
* ** * * *
20234642 GATTTGGTCTACTTCTCAATATCTCATCAAGAAGATGACCGCATCACTTGTTTTAATTCG-TATC
1 GATTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTTAATCCGCT-TC
* *
20234706 TCTGTATCTCATCAGGAAGATGAATTTGGTCCGCTTCTCTGTATCTCATCAGGAAG
65 TCTGTATCTCATCAGGAAGATGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAG
20234762 ACGATCGCTT
Statistics
Matches: 868, Mismatches: 80, Indels: 12
0.90 0.08 0.01
Matches are distributed among these distances:
207 18 0.02
208 536 0.62
209 217 0.25
210 97 0.11
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.38
Consensus pattern (209 bp):
GATTTGGTATACTTCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTTAATCCGCTTCT
CTGTATCTCATCAGGAAGATGGATTTGGTCCACTTCTCTGTATCTCATCAGGAAGCTGACCATTT
TATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGTTTCCCTCATATTG
AGCTTTGTTCCATC
Found at i:20234994 original size:39 final size:39
Alignment explanation
Indices: 20234792--20235221 Score: 213
Period size: 39 Copynumber: 10.9 Consensus size: 39
20234782 GATAACTACA
* * * * *
20234792 ATCTGCCCCATGATCGGAGTAAGAGATTGGATGGCT-GTG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCT-GATGGTG
* *
20234831 ATCTG-CACATG-TCGGGGTAAGAGATCAAGTGGCTGATGGTG
1 ATCTGCCCCAAGCTCGGGGTAAGAGAT----TGGCTGATGGTG
* ** * * *
20234872 ATCTGCCCCAGGCTCAAGGCAAGAGATAGGTTGATGGTG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTG
* * * * ** **
20234911 ATCTGCCCCAGGCTTGAGGTAAAAAGATTGAATGACT-GCA
1 ATCTGCCCCAAGCTCGGGGT-AAGAGATTGGCTGA-TGGTG
*
20234951 ATCTGCCCCAAGCTCGGGGTGAGAGATTGGCTGATGGTG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTG
* **
20234990 ATCTGCCCCAAGCTCGGGGTAAAAGA-T--CAAATGGTG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTG
* * *
20235026 ACAATCTGCCCTAGGCTCAGGGTAAGAGATTGGCTGATGGTG
1 ---ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTG
* * ** *
20235068 ATCTGCCCCAAGCTCGAGGTAAAAGA-T--CAAATAGCTG
1 ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGAT-GGTG
* * *
20235105 CAATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGATG
1 --ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTG
** * *
20235146 ATCTATCCCAGGCTCGAGGGTAAAAGA-T--C-GAATGGCTG
1 ATCTGCCCCAAGCTCG-GGGTAAGAGATTGGCTG-ATGG-TG
* **
20235184 CAATCTGCCCCAGGCTCAAGGTAAGAGATTGGCTGATG
1 --ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATG
20235222 TAGTTTGAAT
Statistics
Matches: 296, Mismatches: 64, Indels: 59
0.71 0.15 0.14
Matches are distributed among these distances:
36 11 0.04
37 20 0.07
38 10 0.03
39 154 0.52
40 55 0.19
41 16 0.05
42 18 0.06
43 12 0.04
ACGTcount: A:0.26, C:0.20, G:0.31, T:0.22
Consensus pattern (39 bp):
ATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGGTG
Found at i:20235057 original size:78 final size:77
Alignment explanation
Indices: 20234872--20235221 Score: 448
Period size: 78 Copynumber: 4.5 Consensus size: 77
20234862 GCTGATGGTG
* * * * * *
20234872 ATCTGCCCCAGGCTCAAGGCAAGAGATAGGTTGATGGTGATCTGCCCCAGGCTTGAGGTAAAAAG
1 ATCTGCCCCAGGCTCAGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGAGGT-AAAAG
**
20234937 ATTGAATGACTGCA
65 ATCAAATG-CTGCA
* * * *
20234951 ATCTGCCCCAAGCTCGGGGTGAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGGGTAAAAGA
1 ATCTGCCCCAGGCTCAGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGAGGTAAAAGA
*
20235016 TCAAATGGTGACA
66 TCAAATGCTG-CA
*
20235029 ATCTGCCCTAGGCTCAGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGAGGTAAAAGA
1 ATCTGCCCCAGGCTCAGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGAGGTAAAAGA
20235094 TCAAATAGCTGCA
66 TCAAAT-GCTGCA
* * * ** *
20235107 ATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGATGATCTATCCCAGGCTCGAGGGTAAAAG
1 ATCTGCCCCAGGCTCAGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGA-GGTAAAAG
*
20235172 ATCGAATGGCTGCA
65 ATCAAAT-GCTGCA
*
20235186 ATCTGCCCCAGGCTCAAGGTAAGAGATTGGCTGATG
1 ATCTGCCCCAGGCTCAGGGTAAGAGATTGGCTGATG
20235222 TAGTTTGAAT
Statistics
Matches: 239, Mismatches: 29, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
77 2 0.01
78 132 0.55
79 105 0.44
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (77 bp):
ATCTGCCCCAGGCTCAGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGAGGTAAAAGA
TCAAATGCTGCA
Found at i:20235087 original size:157 final size:157
Alignment explanation
Indices: 20234872--20235221 Score: 499
Period size: 157 Copynumber: 2.2 Consensus size: 157
20234862 GCTGATGGTG
* * * * *
20234872 ATCTGCCCCAGGCTCAAGGCAAGAGATAGGTTGATGGTGATCTGCCCCAGGCTTGAGGTAAAAAG
1 ATCTGCCCCAGGCTCAAGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGAGGT-AAAAG
** * * *
20234937 ATTGAAT-GACTGCAATCTGCCCCAAGCTCGGGGTGAGAGATTGGCTGATGGTGATCTGCCCCAA
65 ATCAAATAG-CTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGATGATCTACCCCAA
20235001 GCTCG-GGGTAAAAGATCAAATGG-TGACA
129 GCTCGAGGGTAAAAGATCAAATGGCTG-CA
* *
20235029 ATCTGCCCTAGGCTCAGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGAGGTAAAAGA
1 ATCTGCCCCAGGCTCAAGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGAGGTAAAAGA
* * * *
20235094 TCAAATAGCTGCAATCTGCCCTAGGCTCGGGGTAAGAGATTGGCTGATGATGATCTATCCCAGGC
66 TCAAATAGCTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGATGATCTACCCCAAGC
*
20235159 TCGAGGGTAAAAGATCGAATGGCTGCA
131 TCGAGGGTAAAAGATCAAATGGCTGCA
20235186 ATCTGCCCCAGGCTCAAGGTAAGAGATTGGCTGATG
1 ATCTGCCCCAGGCTCAAGGTAAGAGATTGGCTGATG
20235222 TAGTTTGAAT
Statistics
Matches: 171, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
156 63 0.37
157 106 0.62
158 2 0.01
ACGTcount: A:0.27, C:0.21, G:0.30, T:0.22
Consensus pattern (157 bp):
ATCTGCCCCAGGCTCAAGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGAGGTAAAAGA
TCAAATAGCTGCAATCTGCCCCAAGCTCGGGGTAAGAGATTGGCTGATGATGATCTACCCCAAGC
TCGAGGGTAAAAGATCAAATGGCTGCA
Found at i:20235522 original size:49 final size:49
Alignment explanation
Indices: 20235464--20235825 Score: 304
Period size: 49 Copynumber: 7.4 Consensus size: 49
20235454 GTGTTTGTCG
* * * *
20235464 TTGCAGCCTCAACCTTTCCCTTAAAATCTTCATGGTACTGGGTTTGTCA
1 TTGCGGCCTCAACCTTTCCCTTCAAATCTTCATGGTACTGGGTTCGCCA
* * *
20235513 TTGCGGCCTCAACCTTTCCCTTAAAATCTTCATGGTACCGGGTTTGCCA
1 TTGCGGCCTCAACCTTTCCCTTCAAATCTTCATGGTACTGGGTTCGCCA
* * * * *
20235562 TTGCGGCCTCAACCTTTCCCATCACAT-TTCATGGTACTGGATTCACCG
1 TTGCGGCCTCAACCTTTCCCTTCAAATCTTCATGGTACTGGGTTCGCCA
* * * * *
20235610 TTGCAGCCTCAATCTTTCCCATCACATCGTTTGA-GGTA-TCGGGTTCGCCA
1 TTGCGGCCTCAACCTTTCCCTTCAAATC--TTCATGGTACT-GGGTTCGCCA
* * * * * * * *
20235660 TTGGGGCCTCAACCTTT-CTTGTCACATCTTTAAGGTCCCGGGTTCGCCG
1 TTGCGGCCTCAACCTTTCCCT-TCAAATCTTCATGGTACTGGGTTCGCCA
* * * *
20235709 TTACGGCCTCAACCTTTCCCTTCAAATCTTCATGGTACTGGGTTTGTCG
1 TTGCGGCCTCAACCTTTCCCTTCAAATCTTCATGGTACTGGGTTCGCCA
* * * * * **
20235758 TTACGGCCTCAACCTTTTCCATCATAT-TTCATGGTA-TCGGATTCATCA
1 TTGCGGCCTCAACCTTTCCCTTCAAATCTTCATGGTACT-GGGTTCGCCA
*
20235806 TTGCGGCCTCAATCTTTCCC
1 TTGCGGCCTCAACCTTTCCC
20235826 ATCGCATCTT
Statistics
Matches: 258, Mismatches: 46, Indels: 19
0.80 0.14 0.06
Matches are distributed among these distances:
47 1 0.00
48 76 0.29
49 144 0.56
50 34 0.13
51 3 0.01
ACGTcount: A:0.18, C:0.30, G:0.18, T:0.34
Consensus pattern (49 bp):
TTGCGGCCTCAACCTTTCCCTTCAAATCTTCATGGTACTGGGTTCGCCA
Found at i:20236803 original size:12 final size:13
Alignment explanation
Indices: 20236786--20236818 Score: 52
Period size: 12 Copynumber: 2.7 Consensus size: 13
20236776 CGACCTCTCC
20236786 TTTTCTTTT-CTT
1 TTTTCTTTTGCTT
20236798 TTTTCTTTTGCTT
1 TTTTCTTTTGCTT
20236811 TTTT-TTTT
1 TTTTCTTTT
20236819 AATCCGAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 13 0.65
13 7 0.35
ACGTcount: A:0.00, C:0.12, G:0.03, T:0.85
Consensus pattern (13 bp):
TTTTCTTTTGCTT
Found at i:20236816 original size:17 final size:17
Alignment explanation
Indices: 20236785--20236818 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
20236775 TCGACCTCTC
20236785 CTTTTCTTTTCTTTTTT
1 CTTTTCTTTTCTTTTTT
20236802 CTTTTGCTTTT-TTTTTT
1 CTTTT-CTTTTCTTTTTT
20236819 AATCCGAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (17 bp):
CTTTTCTTTTCTTTTTT
Found at i:20241386 original size:97 final size:97
Alignment explanation
Indices: 20241196--20241389 Score: 275
Period size: 97 Copynumber: 2.0 Consensus size: 97
20241186 AACCTCGAAA
* * *
20241196 AAGGGTATTCGATTATCCCGATTTGAAGAAAAGTCGCGCCTAGTAAGTTAAGGCACAAATTTTCA
1 AAGGGTATTCGATTATCCCGATTTAAAGAAAAATCGCGCCTAGTAAATTAAGGCACAAATTTTCA
* * *
20241261 AAACCAGAGACAAAGAAACATTGTCTCGATTT
66 AAACCAGAAAAAAAGAAACATTGCCTCGATTT
* *
20241293 AAGGGTGTTCGATTATCCCGGTTTAAAGAAAAATCGCGCCTAGTAAATTAAGGCACAAATTTTCA
1 AAGGGTATTCGATTATCCCGATTTAAAGAAAAATCGCGCCTAGTAAATTAAGGCACAAATTTTCA
*
20241358 AAACCCA-AAATAAAAG-AATATTGCCTCGATTT
66 AAA-CCAGAAA-AAAAGAAACATTGCCTCGATTT
20241390 TAAATATTTT
Statistics
Matches: 86, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
97 79 0.92
98 7 0.08
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (97 bp):
AAGGGTATTCGATTATCCCGATTTAAAGAAAAATCGCGCCTAGTAAATTAAGGCACAAATTTTCA
AAACCAGAAAAAAAGAAACATTGCCTCGATTT
Found at i:20241672 original size:29 final size:29
Alignment explanation
Indices: 20241637--20241924 Score: 180
Period size: 29 Copynumber: 9.9 Consensus size: 29
20241627 AGTTTCAGAG
*
20241637 AGTTT-AGGGTTAAAATGTAATTTTGAAA
1 AGTTTGAGGGTAAAAATGTAATTTTGAAA
*
20241665 AGGTTT-AGGGGT-AAAATGTCATTTTAGGAAA
1 A-GTTTGA-GGGTAAAAATGTAATTTT--GAAA
* * * * *
20241696 A--TTCAGGGTAAAAACGGAGTTTTTG-GA
1 AGTTTGAGGGTAAAAATGTA-ATTTTGAAA
* * *
20241723 AGTTTGAGGGGCAAAAATGTGATCTTTGGAA
1 AGTTTGA-GGGTAAAAATGTAAT-TTTGAAA
* * *
20241754 A-TTTGAGGGCAAAAATGTGATTTTTGAGA
1 AGTTTGAGGGTAAAAATGT-AATTTTGAAA
* *
20241783 AGTTT-AGGGTAAAAATGTTATTTTTAAA
1 AGTTTGAGGGTAAAAATGTAATTTTGAAA
20241811 AGTTTGAGGGTAAAAATGTAATTTTTG-AA
1 AGTTTGAGGGTAAAAATGTAA-TTTTGAAA
* * * *
20241840 AGTTTAAGGGTCAAAATGTAGTTTTTAGAA
1 AGTTTGAGGGTAAAAATGTAATTTTGA-AA
* * * * *
20241870 AGTTTAAGGGTTAGAATATAATTTTTGGAA
1 AGTTTGAGGGTAAAAATGTAA-TTTTGAAA
* *
20241900 AGTTCGAGGGTTAAAATGTAATTTT
1 AGTTTGAGGGTAAAAATGTAATTTT
20241925 TAGAGAGTTT
Statistics
Matches: 203, Mismatches: 38, Indels: 37
0.73 0.14 0.13
Matches are distributed among these distances:
27 2 0.01
28 23 0.11
29 95 0.47
30 72 0.35
31 11 0.05
ACGTcount: A:0.36, C:0.03, G:0.25, T:0.36
Consensus pattern (29 bp):
AGTTTGAGGGTAAAAATGTAATTTTGAAA
Found at i:20241740 original size:59 final size:57
Alignment explanation
Indices: 20241657--20241855 Score: 145
Period size: 59 Copynumber: 3.4 Consensus size: 57
20241647 TAAAATGTAA
* ** *
20241657 TTTTGAAAAGGTTTAGGGGTAAAATGTCATTTTAGGAAAATTCAGGGTAAAAACG-GAGT
1 TTTTGAGAA-GTTTAGGGCAAAAATGTCATTTT-GGAAAATTCAGGGCAAAAACGTGA-T
* * * *
20241716 TTTTG-GAAGTTTGAGGGGCAAAAATGTGATCTTTGGAAATTTGAGGGCAAAAATGTGAT
1 TTTTGAGAAGTTT-A-GGGCAAAAATGTCAT-TTTGGAAAATTCAGGGCAAAAACGTGAT
* * * * * * *
20241775 TTTTGAGAAGTTTAGGGTAAAAATGTTATTTT-TAAAAGTTTGAGGGTAAAAATGTAAT
1 TTTTGAGAAGTTTAGGGCAAAAATGTCATTTTGGAAAA--TTCAGGGCAAAAACGTGAT
20241833 TTTTGA-AAGTTTAAGGGTCAAAA
1 TTTTGAGAAGTTT-AGGG-CAAAA
20241856 TGTAGTTTTT
Statistics
Matches: 116, Mismatches: 15, Indels: 18
0.78 0.10 0.12
Matches are distributed among these distances:
56 3 0.03
57 13 0.11
58 43 0.37
59 45 0.39
60 12 0.10
ACGTcount: A:0.36, C:0.04, G:0.26, T:0.34
Consensus pattern (57 bp):
TTTTGAGAAGTTTAGGGCAAAAATGTCATTTTGGAAAATTCAGGGCAAAAACGTGAT
Found at i:20241751 original size:30 final size:29
Alignment explanation
Indices: 20241715--20241953 Score: 164
Period size: 29 Copynumber: 8.1 Consensus size: 29
20241705 AAAAACGGAG
20241715 TTTTTGGAAGTTTGAGGGGCAAAAATGTGA
1 TTTTTGGAAGTTTGA-GGGCAAAAATGTGA
* *
20241745 TCTTTGGAAATTTGAGGGCAAAAATGTGA
1 TTTTTGGAAGTTTGAGGGCAAAAATGTGA
* *
20241774 TTTTTGAGAAGTTT-AGGGTAAAAATGTTA
1 TTTTTG-GAAGTTTGAGGGCAAAAATGTGA
** * *
20241803 TTTTTAAAAGTTTGAGGGTAAAAATGTAA
1 TTTTTGGAAGTTTGAGGGCAAAAATGTGA
* *
20241832 TTTTTGAAAGTTTAAGGGTC-AAAATGT-A
1 TTTTTGGAAGTTTGAGGG-CAAAAATGTGA
* * ** * * *
20241860 GTTTTTAGAAAGTTTAAGGGTTAGAATATAA
1 -TTTTT-GGAAGTTTGAGGGCAAAAATGTGA
* ** *
20241891 TTTTTGGAAAGTTCGAGGGTTAAAATGTAA
1 TTTTTGG-AAGTTTGAGGGCAAAAATGTGA
*
20241921 TTTTTAGAGAGTTTG-GGTGTC-AAAATGTGA
1 TTTTTGGA-AGTTTGAGG-G-CAAAAATGTGA
20241951 TTT
1 TTT
20241954 ATGAAGAGTT
Statistics
Matches: 174, Mismatches: 24, Indels: 22
0.79 0.11 0.10
Matches are distributed among these distances:
28 7 0.04
29 83 0.48
30 83 0.48
31 1 0.01
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.38
Consensus pattern (29 bp):
TTTTTGGAAGTTTGAGGGCAAAAATGTGA
Found at i:20241817 original size:58 final size:59
Alignment explanation
Indices: 20241715--20241935 Score: 207
Period size: 58 Copynumber: 3.7 Consensus size: 59
20241705 AAAAACGGAG
* * * * * *
20241715 TTTTTGGAAGTTTGAGGGGCAAAAATGTGATCTTTGGAAA-TTTGAGGGCAAAAATGTGA
1 TTTTTGGAAGTTT-AAGGGTAAAAATGTTATTTTTAGAAAGTTTGAGGGCAAAAATGTAA
*
20241774 TTTTTGAGAAGTTT-AGGGTAAAAATGTTATTTTTA-AAAGTTTGAGGGTAAAAATGTAA
1 TTTTTG-GAAGTTTAAGGGTAAAAATGTTATTTTTAGAAAGTTTGAGGGCAAAAATGTAA
* * * ** * *
20241832 TTTTTGAAAGTTTAAGGGTCAAAATG-TAGTTTTTAGAAAGTTTAAGGGTTAGAATATAA
1 TTTTTGGAAGTTTAAGGGTAAAAATGTTA-TTTTTAGAAAGTTTGAGGGCAAAAATGTAA
** * * *
20241891 TTTTTGGAAAGTTCGAGGGTTAAAATGTAATTTTTAGAGAGTTTG
1 TTTTTGG-AAGTTTAAGGGTAAAAATGTTATTTTTAGAAAGTTTG
20241936 GGTGTCAAAA
Statistics
Matches: 135, Mismatches: 20, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
57 11 0.08
58 56 0.41
59 31 0.23
60 36 0.27
61 1 0.01
ACGTcount: A:0.34, C:0.02, G:0.25, T:0.38
Consensus pattern (59 bp):
TTTTTGGAAGTTTAAGGGTAAAAATGTTATTTTTAGAAAGTTTGAGGGCAAAAATGTAA
Found at i:20241964 original size:60 final size:58
Alignment explanation
Indices: 20241765--20241965 Score: 185
Period size: 60 Copynumber: 3.4 Consensus size: 58
20241755 TTTGAGGGCA
* * *
20241765 AAAATGTGATTTTTGAGAAGTT-TAGGGTAAAAATGTTATTTTTA-AAAGTTTGAGG-GT
1 AAAATGTAATTTTTGA-AAGTTCAAGGGTAAAAATGTAATTTTTAGAAAGTTTG-GGTGT
* * *
20241822 AAAAATGTAATTTTTGAAAGTTTAAGGGTCAAAATGTAGTTTTTAGAAAGTTTAAGGGT-T
1 -AAAATGTAATTTTTGAAAGTTCAAGGGTAAAAATGTAATTTTTAGAAAGTTT--GGGTGT
* * * * *
20241882 AGAATATAATTTTTGGAAAGTTCGAGGGTTAAAATGTAATTTTTAGAGAGTTTGGGTGT
1 AAAATGTAATTTTT-GAAAGTTCAAGGGTAAAAATGTAATTTTTAGAAAGTTTGGGTGT
* *
20241941 CAAAATGTGATTTATGAAGAGTTCA
1 -AAAATGTAATTTTTGAA-AGTTCA
20241966 GGAACCTTTT
Statistics
Matches: 117, Mismatches: 17, Indels: 16
0.78 0.11 0.11
Matches are distributed among these distances:
57 5 0.04
58 37 0.32
59 23 0.20
60 51 0.44
61 1 0.01
ACGTcount: A:0.36, C:0.02, G:0.24, T:0.38
Consensus pattern (58 bp):
AAAATGTAATTTTTGAAAGTTCAAGGGTAAAAATGTAATTTTTAGAAAGTTTGGGTGT
Found at i:20243772 original size:6 final size:6
Alignment explanation
Indices: 20243755--20243841 Score: 52
Period size: 6 Copynumber: 14.3 Consensus size: 6
20243745 AACTTTTTAA
* * ** *
20243755 TTAAATT TTAAAT TTAAAT TCAAA- ATAAAT TTAAAT TTAAACT CAAAAA
1 TTAAA-T TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA-T TTAAAT
* * * *
20243804 ATAAGT TTAAAT TTAAA- ATAATT TTAAATT TTAAAT TT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAA-T TTAAAT TT
20243842 TAAAATTGGG
Statistics
Matches: 59, Mismatches: 17, Indels: 9
0.69 0.20 0.11
Matches are distributed among these distances:
5 6 0.10
6 38 0.64
7 15 0.25
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (6 bp):
TTAAAT
Found at i:20243812 original size:25 final size:23
Alignment explanation
Indices: 20243756--20243820 Score: 85
Period size: 25 Copynumber: 2.7 Consensus size: 23
20243746 ACTTTTTAAT
*
20243756 TAAATTTTAAATTTAAATTCAAAA
1 TAAA-TTTAAATTTAAACTCAAAA
20243780 TAAATTTAAATTTAAACTCAAAAAA
1 TAAATTTAAATTTAAACTC--AAAA
*
20243805 TAAGTTTAAATTTAAA
1 TAAATTTAAATTTAAA
20243821 ATAATTTTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
23 14 0.38
24 4 0.11
25 19 0.51
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (23 bp):
TAAATTTAAATTTAAACTCAAAA
Found at i:20243823 original size:17 final size:17
Alignment explanation
Indices: 20243801--20243839 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
20243791 TTAAACTCAA
20243801 AAAATAAGTTTAAATTT
1 AAAATAAGTTTAAATTT
*
20243818 AAAATAATTTTAAATTT
1 AAAATAAGTTTAAATTT
*
20243835 TAAAT
1 AAAAT
20243840 TTTAAAATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
AAAATAAGTTTAAATTT
Found at i:20248460 original size:16 final size:17
Alignment explanation
Indices: 20248433--20248464 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
20248423 ATTATTTGCT
20248433 TATATCTTATTATATTA
1 TATATCTTATTATATTA
20248450 TATAT-TTATTATATT
1 TATATCTTATTATATT
20248465 TACGCATCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
TATATCTTATTATATTA
Found at i:20263305 original size:26 final size:26
Alignment explanation
Indices: 20263265--20263333 Score: 88
Period size: 26 Copynumber: 2.7 Consensus size: 26
20263255 GAAATGATAC
*
20263265 CTGTATCTGTCGACTGTA-CAATCGAA
1 CTGTATCTGTTGACTGTATCAA-CGAA
*
20263291 CTGTAAT-TGTTGACTGTATGAACGAA
1 CTGT-ATCTGTTGACTGTATCAACGAA
20263317 CTGTATCTGTTGACTGT
1 CTGTATCTGTTGACTGT
20263334 GTAGTTGGTA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
25 2 0.05
26 32 0.84
27 4 0.11
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (26 bp):
CTGTATCTGTTGACTGTATCAACGAA
Found at i:20267563 original size:12 final size:12
Alignment explanation
Indices: 20267541--20267579 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
20267531 AATTTGTTTG
20267541 AAAGCATAAAATA
1 AAAG-ATAAAATA
20267554 AAAGATAAAATA
1 AAAGATAAAATA
* *
20267566 AAATAGAAAATA
1 AAAGATAAAATA
20267578 AA
1 AA
20267580 GGCAAAGTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 20 0.83
13 4 0.17
ACGTcount: A:0.74, C:0.03, G:0.08, T:0.15
Consensus pattern (12 bp):
AAAGATAAAATA
Found at i:20267568 original size:17 final size:17
Alignment explanation
Indices: 20267546--20267579 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
20267536 GTTTGAAAGC
20267546 ATAAAATA-AAAGATAAA
1 ATAAAATAGAAA-ATAAA
20267563 ATAAAATAGAAAATAAA
1 ATAAAATAGAAAATAAA
20267580 GGCAAAGTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (17 bp):
ATAAAATAGAAAATAAA
Found at i:20269170 original size:24 final size:24
Alignment explanation
Indices: 20269120--20269178 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
20269110 TTCTTTCCTT
*
20269120 TTATGTCTCACTCCATCTCACCCCC
1 TTATTTCTC-CTCCATCTCACCCCC
*
20269145 TTATTTCTCCTCC-TCTCACCATCC
1 TTATTTCTCCTCCATCTCACC-CCC
*
20269169 TTTTTTCTCC
1 TTATTTCTCC
20269179 ATTTTAGGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 7 0.23
24 15 0.50
25 8 0.27
ACGTcount: A:0.12, C:0.44, G:0.02, T:0.42
Consensus pattern (24 bp):
TTATTTCTCCTCCATCTCACCCCC
Found at i:20269349 original size:21 final size:22
Alignment explanation
Indices: 20269317--20269358 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
20269307 ATTCACATGT
20269317 TTTCTAACTCATGATTCTTTTG
1 TTTCTAACTCATGATTCTTTTG
**
20269339 TTTCT-ACTCATTTTTCTTTT
1 TTTCTAACTCATGATTCTTTT
20269359 CTTTTTGATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.14, C:0.19, G:0.05, T:0.62
Consensus pattern (22 bp):
TTTCTAACTCATGATTCTTTTG
Found at i:20275202 original size:13 final size:14
Alignment explanation
Indices: 20275173--20275202 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
20275163 TTCTGTACAT
20275173 TGACATTTAACCTC
1 TGACATTTAACCTC
20275187 TGACATTTAA-CTC
1 TGACATTTAACCTC
20275200 TGA
1 TGA
20275203 TTGCATTGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (14 bp):
TGACATTTAACCTC
Found at i:20282562 original size:20 final size:21
Alignment explanation
Indices: 20282537--20282583 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
20282527 AAGACCAGTT
20282537 GAAGGAAAAAGA-AAAAAAGA
1 GAAGGAAAAAGAGAAAAAAGA
* *
20282557 GAAGGAAGAAGAGAATAAAGA
1 GAAGGAAAAAGAGAAAAAAGA
20282578 GAAGGA
1 GAAGGA
20282584 CCCTGTCCAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 11 0.46
21 13 0.54
ACGTcount: A:0.66, C:0.00, G:0.32, T:0.02
Consensus pattern (21 bp):
GAAGGAAAAAGAGAAAAAAGA
Found at i:20283662 original size:13 final size:13
Alignment explanation
Indices: 20283641--20283681 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
20283631 CAGTCACTTG
20283641 AAAAA-AGAAAAA
1 AAAAAGAGAAAAA
*
20283653 AAAAAGAGAAAAG
1 AAAAAGAGAAAAA
20283666 AAAAAGAAGAAAAA
1 AAAAAG-AGAAAAA
20283680 AA
1 AA
20283682 TTATATTTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 5 0.20
13 12 0.48
14 8 0.32
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAGAGAAAAA
Found at i:20287226 original size:7 final size:7
Alignment explanation
Indices: 20287214--20287247 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
20287204 GCTATAAATA
20287214 GAAGAAT
1 GAAGAAT
20287221 GAAGAAT
1 GAAGAAT
20287228 GAAGAAT
1 GAAGAAT
*
20287235 AAAGAAT
1 GAAGAAT
20287242 GAAGAA
1 GAAGAA
20287248 ATCATCAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.62, C:0.00, G:0.26, T:0.12
Consensus pattern (7 bp):
GAAGAAT
Found at i:20291576 original size:10 final size:11
Alignment explanation
Indices: 20291546--20291591 Score: 60
Period size: 10 Copynumber: 4.3 Consensus size: 11
20291536 TGGCAATATA
20291546 TTTCTTTTCTT
1 TTTCTTTTCTT
20291557 TTCTCTTTTCTT
1 TT-TCTTTTCTT
*
20291569 TTTC-TTTCAT
1 TTTCTTTTCTT
20291579 TTTC-TTTCTT
1 TTTCTTTTCTT
20291589 TTT
1 TTT
20291592 GTGATTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
10 17 0.53
11 4 0.12
12 11 0.34
ACGTcount: A:0.02, C:0.20, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTCTTTTCTT
Found at i:20292710 original size:11 final size:11
Alignment explanation
Indices: 20292688--20292721 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
20292678 TTCCTTTCCT
20292688 TCATTCTCCTTC
1 TCATT-TCCTTC
20292700 TCATTTCCTTC
1 TCATTTCCTTC
20292711 TCATTT-CTTC
1 TCATTTCCTTC
20292721 T
1 T
20292722 TCTTTTTCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 5 0.23
11 12 0.55
12 5 0.23
ACGTcount: A:0.09, C:0.35, G:0.00, T:0.56
Consensus pattern (11 bp):
TCATTTCCTTC
Found at i:20312133 original size:26 final size:26
Alignment explanation
Indices: 20312070--20312136 Score: 66
Period size: 26 Copynumber: 2.6 Consensus size: 26
20312060 CAGAATTGCA
**
20312070 CCCAAAATTGTCACTGCATGATGATG
1 CCCAAAATTGTCGTTGCATGATGATG
* *
20312096 -TCAAGAAATGTCGTTGCATGA-GCATG
1 CCCAA-AATTGTCGTTGCATGATG-ATG
20312122 CCCAAAATTGTCGTT
1 CCCAAAATTGTCGTT
20312137 ATAGGAACTT
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
25 4 0.12
26 25 0.78
27 3 0.09
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (26 bp):
CCCAAAATTGTCGTTGCATGATGATG
Found at i:20313383 original size:23 final size:22
Alignment explanation
Indices: 20313353--20313412 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 22
20313343 CTTGTTTCTC
*
20313353 TTTT-TTTTGTTTTCACATTTTA
1 TTTTATTTTGTTTTCA-AGTTTA
*
20313375 TTTTATTTTATTTTCAAGTTTA
1 TTTTATTTTGTTTTCAAGTTTA
20313397 TTTTACGTTTTGTTTT
1 TTTTA--TTTTGTTTT
20313413 TGTAGAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 14 0.44
23 10 0.31
24 8 0.25
ACGTcount: A:0.15, C:0.07, G:0.07, T:0.72
Consensus pattern (22 bp):
TTTTATTTTGTTTTCAAGTTTA
Found at i:20315668 original size:37 final size:38
Alignment explanation
Indices: 20315602--20315675 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 38
20315592 GAGTCAATTC
* * *
20315602 AGAATTGCGCCCAGAATTGTCACTACATGACGATGTCT
1 AGAATTGCACCCAAAATTATCACTACATGACGATGTCT
*
20315640 AGAA-TGCACCCAAAATTATCACTGCATGACGATGTC
1 AGAATTGCACCCAAAATTATCACTACATGACGATGTC
20315676 CAAAAATGTC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 28 0.88
38 4 0.12
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.24
Consensus pattern (38 bp):
AGAATTGCACCCAAAATTATCACTACATGACGATGTCT
Found at i:20327882 original size:23 final size:22
Alignment explanation
Indices: 20327851--20327894 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
20327841 AACGAAATAA
*
20327851 AATTAACCCAATTTAATTAATT
1 AATTAACCCAAATTAATTAATT
*
20327873 AATTCAACCCAAATTATTTAAT
1 AATT-AACCCAAATTAATTAAT
20327895 GAAATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.45, C:0.16, G:0.00, T:0.39
Consensus pattern (22 bp):
AATTAACCCAAATTAATTAATT
Found at i:20335553 original size:17 final size:18
Alignment explanation
Indices: 20335518--20335579 Score: 67
Period size: 17 Copynumber: 3.6 Consensus size: 18
20335508 CATTAAATTA
20335518 CAATGACAA-ATGGAAATG
1 CAATGACAATAT-GAAATG
20335536 CAATGACAATAT-AAATG
1 CAATGACAATATGAAATG
* *
20335553 CAGTGACAAT-TAAAATG
1 CAATGACAATATGAAATG
*
20335570 TAATGACAAT
1 CAATGACAAT
20335580 GGGAATGTGA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
16 1 0.03
17 27 0.69
18 9 0.23
19 2 0.05
ACGTcount: A:0.50, C:0.11, G:0.16, T:0.23
Consensus pattern (18 bp):
CAATGACAATATGAAATG
Found at i:20350107 original size:24 final size:24
Alignment explanation
Indices: 20350080--20350136 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
20350070 AAGCCTAATT
*
20350080 CTAATCAATGCAAAATATATTATG
1 CTAATAAATGCAAAATATATTATG
* *
20350104 CTAATAAATGCTAAATATATTATA
1 CTAATAAATGCAAAATATATTATG
*
20350128 CTACTAAAT
1 CTAATAAAT
20350137 CTTCTAGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.35
Consensus pattern (24 bp):
CTAATAAATGCAAAATATATTATG
Found at i:20350202 original size:36 final size:35
Alignment explanation
Indices: 20350155--20350231 Score: 109
Period size: 36 Copynumber: 2.2 Consensus size: 35
20350145 AAGATAATAT
* *
20350155 ATTTTGTTTAACTTCACTTGCAAGTAATTCTCTTAG
1 ATTTTGTTTAACTTAACTTGCAAGCAA-TCTCTTAG
*
20350191 ATTTTGTTTAACTTAACTTGGAAGCAATCTCTTAG
1 ATTTTGTTTAACTTAACTTGCAAGCAATCTCTTAG
*
20350226 AATTTG
1 ATTTTG
20350232 GATCACACAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
35 13 0.35
36 24 0.65
ACGTcount: A:0.27, C:0.14, G:0.13, T:0.45
Consensus pattern (35 bp):
ATTTTGTTTAACTTAACTTGCAAGCAATCTCTTAG
Found at i:20351603 original size:13 final size:13
Alignment explanation
Indices: 20351587--20351611 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20351577 TCTTATTATG
20351587 ACCAAAAATTACT
1 ACCAAAAATTACT
20351600 ACCAAAAATTAC
1 ACCAAAAATTAC
20351612 AGATATAAGC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.24, G:0.00, T:0.20
Consensus pattern (13 bp):
ACCAAAAATTACT
Found at i:20351931 original size:19 final size:20
Alignment explanation
Indices: 20351892--20351931 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
20351882 AAAACTCGAA
20351892 TTGAATTAACAACATGCATTGT
1 TTGAATTAACAACA--CATTGT
20351914 TTGAATTAACAACA-ATTG
1 TTGAATTAACAACACATTG
20351932 CAAAATTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
22 14 0.78
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (20 bp):
TTGAATTAACAACACATTGT
Found at i:20352299 original size:17 final size:17
Alignment explanation
Indices: 20352277--20352309 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
20352267 TCATACCTGA
*
20352277 ATTTTAATTTTTTTATT
1 ATTTTAATATTTTTATT
20352294 ATTTTAATATTTTTAT
1 ATTTTAATATTTTTAT
20352310 GTAATTATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
ATTTTAATATTTTTATT
Found at i:20352367 original size:14 final size:14
Alignment explanation
Indices: 20352348--20352374 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
20352338 CATCTGATAC
20352348 ACTAACCCGATTCA
1 ACTAACCCGATTCA
20352362 ACTAACCCGATTC
1 ACTAACCCGATTC
20352375 TTGGGATGTG
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:0.33, C:0.37, G:0.07, T:0.22
Consensus pattern (14 bp):
ACTAACCCGATTCA
Found at i:20352633 original size:17 final size:18
Alignment explanation
Indices: 20352594--20352632 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
20352584 ATTGCTTCTC
*
20352594 AAAAGCACTTTTGAGATA
1 AAAAGCACTTTTGAAATA
*
20352612 AAAAGTACTTTTGAAATA
1 AAAAGCACTTTTGAAATA
20352630 AAA
1 AAA
20352633 GCATTGCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.08, G:0.13, T:0.28
Consensus pattern (18 bp):
AAAAGCACTTTTGAAATA
Found at i:20354472 original size:16 final size:17
Alignment explanation
Indices: 20354446--20354477 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
20354436 TTATTTGCTT
20354446 ATATCTTATTATATTAC
1 ATATCTTATTATATTAC
20354463 ATAT-TTATTATATTA
1 ATATCTTATTATATTA
20354478 TTTACGCATC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (17 bp):
ATATCTTATTATATTAC
Found at i:20363668 original size:16 final size:16
Alignment explanation
Indices: 20363617--20363672 Score: 60
Period size: 16 Copynumber: 3.3 Consensus size: 16
20363607 AACTATTAAC
*
20363617 AAATAAATATTAGTAT
1 AAATAAATATTCGTAT
20363633 AAATATATAATAATTC-TAT
1 -AA-ATA-AAT-ATTCGTAT
20363652 AAATAAATATTCGTAT
1 AAATAAATATTCGTAT
20363668 AAATA
1 AAATA
20363673 TATAAATATA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
15 4 0.12
16 11 0.32
17 5 0.15
18 5 0.15
19 6 0.18
20 3 0.09
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.38
Consensus pattern (16 bp):
AAATAAATATTCGTAT
Found at i:20365073 original size:15 final size:15
Alignment explanation
Indices: 20365048--20365093 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
20365038 TCCCAGACGT
*
20365048 ATAATAAATAAATAA
1 ATAAAAAATAAATAA
* *
20365063 ATAGAAAATAAAAAA
1 ATAAAAAATAAATAA
*
20365078 ATAAAAAAAAAATAA
1 ATAAAAAATAAATAA
20365093 A
1 A
20365094 AATTGGGTTG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.17
Consensus pattern (15 bp):
ATAAAAAATAAATAA
Found at i:20365074 original size:19 final size:19
Alignment explanation
Indices: 20365050--20365095 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
20365040 CCAGACGTAT
* * *
20365050 AATAAATAAATAAATAGAA
1 AATAAAAAAATAAAAAAAA
20365069 AATAAAAAAATAAAAAAAA
1 AATAAAAAAATAAAAAAAA
20365088 AATAAAAA
1 AATAAAAA
20365096 TTGGGTTGCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.02, T:0.15
Consensus pattern (19 bp):
AATAAAAAAATAAAAAAAA
Found at i:20369138 original size:21 final size:21
Alignment explanation
Indices: 20369096--20369140 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
20369086 ATGCCTCAGT
* *
20369096 TTGCTTTTGAAAATCTGCAGA
1 TTGCTTTTGAAAAACTACAGA
*
20369117 TTGCTTTTGAAAAACTATAGA
1 TTGCTTTTGAAAAACTACAGA
20369138 TTG
1 TTG
20369141 ATGCTGAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (21 bp):
TTGCTTTTGAAAAACTACAGA
Found at i:20370718 original size:16 final size:15
Alignment explanation
Indices: 20370680--20370718 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
20370670 TCTGGGGAAC
20370680 AATAAAAATAAAAGA
1 AATAAAAATAAAAGA
20370695 AA-ACAAAATTAAAAGA
1 AATA-AAAA-TAAAAGA
20370711 AATAAAAA
1 AATAAAAA
20370719 ATAGGAGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 1 0.05
15 6 0.29
16 13 0.62
17 1 0.05
ACGTcount: A:0.79, C:0.03, G:0.05, T:0.13
Consensus pattern (15 bp):
AATAAAAATAAAAGA
Found at i:20371483 original size:14 final size:14
Alignment explanation
Indices: 20371464--20371493 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
20371454 TTCAAACTCT
*
20371464 AAAAGATAAATATA
1 AAAAGATAAACATA
20371478 AAAAGATAAACATA
1 AAAAGATAAACATA
20371492 AA
1 AA
20371494 TTAAATACAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.73, C:0.03, G:0.07, T:0.17
Consensus pattern (14 bp):
AAAAGATAAACATA
Found at i:20372182 original size:26 final size:26
Alignment explanation
Indices: 20372153--20372207 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
20372143 TACGTGTTTC
* *
20372153 TTTTTTAAAATTTATTAAAT-AATATA
1 TTTTATAAAATTTA-AAAATAAATATA
*
20372179 TTTTATAAATTTTAAAAATAAATATA
1 TTTTATAAAATTTAAAAATAAATATA
20372205 TTT
1 TTT
20372208 ACTAATTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 4 0.16
26 21 0.84
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
TTTTATAAAATTTAAAAATAAATATA
Found at i:20375701 original size:21 final size:21
Alignment explanation
Indices: 20375650--20375706 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
20375640 AGTGTAGACC
*
20375650 TCTACCAATACAAGTGACAGT
1 TCTACCGATACAAGTGACAGT
20375671 TCTACCGATACAAGTGACAGT
1 TCTACCGATACAAGTGACAGT
**
20375692 TCTATTGATACAAGT
1 TCTACCGATACAAGT
20375707 CTTACTTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (21 bp):
TCTACCGATACAAGTGACAGT
Found at i:20380965 original size:18 final size:18
Alignment explanation
Indices: 20380939--20380983 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
20380929 TCGCACAAAT
*
20380939 TACAAGTTCTCAAATCAA
1 TACAGGTTCTCAAATCAA
20380957 TACAGGTTCTCAAATCAA
1 TACAGGTTCTCAAATCAA
*
20380975 TATAGGTTC
1 TACAGGTTC
20380984 GCACCTAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.38, C:0.20, G:0.11, T:0.31
Consensus pattern (18 bp):
TACAGGTTCTCAAATCAA
Found at i:20381639 original size:16 final size:16
Alignment explanation
Indices: 20381588--20381643 Score: 69
Period size: 16 Copynumber: 3.3 Consensus size: 16
20381578 AACTATTAAC
20381588 AAATAAATATTCGTAT
1 AAATAAATATTCGTAT
20381604 AAATATATAATAATTC-TAT
1 -AA-ATA-AAT-ATTCGTAT
20381623 AAATAAATATTCGTAT
1 AAATAAATATTCGTAT
20381639 AAATA
1 AAATA
20381644 TATAGCATTG
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
15 4 0.11
16 11 0.31
17 5 0.14
18 5 0.14
19 6 0.17
20 4 0.11
ACGTcount: A:0.54, C:0.05, G:0.04, T:0.38
Consensus pattern (16 bp):
AAATAAATATTCGTAT
Found at i:20381779 original size:5 final size:5
Alignment explanation
Indices: 20381769--20381871 Score: 63
Period size: 5 Copynumber: 20.4 Consensus size: 5
20381759 AAAATATAAT
* *
20381769 TTATA TTATA TTA-A TTTCTA TTATA CTTCATA TTATA TTATG TT-TGCA
1 TTATA TTATA TTATA -TTATA TTATA -TT-ATA TTATA TTATA TTAT--A
** * *
20381817 TTAT- TT-GC TTATA TCATA TTATA TTATA TTTTAA TTATA TT-TA TTATA
1 TTATA TTATA TTATA TTATA TTATA TTATA TTAT-A TTATA TTATA TTATA
20381865 TTATA TT
1 TTATA TT
20381872 TACACATCAT
Statistics
Matches: 76, Mismatches: 11, Indels: 22
0.70 0.10 0.20
Matches are distributed among these distances:
4 10 0.13
5 51 0.67
6 11 0.14
7 4 0.05
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (5 bp):
TTATA
Found at i:20383033 original size:26 final size:27
Alignment explanation
Indices: 20382986--20383044 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
20382976 TTTACGTGTT
*
20382986 TATTTTTAAAATTTTATTAAAT-AATA
1 TATTTTTAAAATTTTATAAAATAAATA
20383012 TATTTTTATAAATTTTA-AAAATAAATA
1 TATTTTTA-AAATTTTATAAAATAAATA
20383039 TATTTT
1 TATTTT
20383045 CTAATTAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 12 0.40
27 18 0.60
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
TATTTTTAAAATTTTATAAAATAAATA
Found at i:20383797 original size:5 final size:5
Alignment explanation
Indices: 20383787--20383818 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
20383777 TGAGCATTCG
20383787 ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA AT
1 ATCGA ATCGA ATCGA ATCGA ATCGA ATCGA AT
20383819 GAAAATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (5 bp):
ATCGA
Done.