Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 212 of 214
Found at i:62690543 original size:53 final size:53
Alignment explanation
Indices: 62690400--62690543 Score: 145
Period size: 53 Copynumber: 2.8 Consensus size: 53
62690390 AACAGTTTTT
** * * *
62690400 TAAATAATAT-ATAAAAATTTTAAATG--ATAATATAT-ATAATAGTTTAAAA
1 TAAATAATATAATAAAAAACTTAAAAGAAATAATAGATAAAAATAGTTTAAAA
* * * * *
62690449 TAAGTAATATAATAAAAAATTTTAAAGAAATAATAGGTAAAAATAGTTTAGAA
1 TAAATAATATAATAAAAAACTTAAAAGAAATAATAGATAAAAATAGTTTAAAA
*
62690502 TAAATAATATATATAAAAAACTTAAAATAAATAATA-ATAAAA
1 TAAATAATATA-ATAAAAAACTTAAAAGAAATAATAGATAAAA
62690544 TAGGTCTTTT
Statistics
Matches: 77, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
49 9 0.12
50 13 0.17
52 7 0.09
53 27 0.35
54 21 0.27
ACGTcount: A:0.61, C:0.01, G:0.06, T:0.33
Consensus pattern (53 bp):
TAAATAATATAATAAAAAACTTAAAAGAAATAATAGATAAAAATAGTTTAAAA
Found at i:62693767 original size:20 final size:18
Alignment explanation
Indices: 62693743--62693855 Score: 75
Period size: 20 Copynumber: 5.7 Consensus size: 18
62693733 AATATTTAGC
62693743 ATAATTCTTGGTATTTCTT
1 ATAATT-TTGGTATTTCTT
* * *
62693762 CATAATAATTGATATACTCTT
1 -ATAAT-TTTGGTAT-TTCTT
*
62693783 ATAATGTTTGATATTTCTT
1 ATAAT-TTTGGTATTTCTT
*
62693802 CATAATTTTTGGTACACTT-TT
1 -ATAA-TTTTGGT--ATTTCTT
62693823 ATAATTTTTGGTATTCTCTT
1 ATAA-TTTTGGTATT-TCTT
62693843 ATAATTTTGGTAT
1 ATAATTTTGGTAT
62693856 AGTTTCGAAC
Statistics
Matches: 76, Mismatches: 9, Indels: 17
0.75 0.09 0.17
Matches are distributed among these distances:
18 2 0.03
19 14 0.18
20 50 0.66
21 7 0.09
22 3 0.04
ACGTcount: A:0.27, C:0.10, G:0.10, T:0.54
Consensus pattern (18 bp):
ATAATTTTGGTATTTCTT
Found at i:62693848 original size:40 final size:40
Alignment explanation
Indices: 62693743--62693854 Score: 129
Period size: 40 Copynumber: 2.8 Consensus size: 40
62693733 AATATTTAGC
* ** * *
62693743 ATAATTCTTGGTATTTCTTCATAATAATTGATATACTCTT
1 ATAATTTTTGGTATTTCTTCATAATTTTTGGTACACTCTT
* * *
62693783 ATAATGTTTGATATTTCTTCATAATTTTTGGTACACTTTT
1 ATAATTTTTGGTATTTCTTCATAATTTTTGGTACACTCTT
62693823 ATAATTTTTGGTATTCTCTT-ATAA-TTTTGGTA
1 ATAATTTTTGGTATT-TCTTCATAATTTTTGGTA
62693855 TAGTTTCGAA
Statistics
Matches: 61, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
39 8 0.13
40 49 0.80
41 4 0.07
ACGTcount: A:0.27, C:0.10, G:0.10, T:0.54
Consensus pattern (40 bp):
ATAATTTTTGGTATTTCTTCATAATTTTTGGTACACTCTT
Found at i:62695050 original size:11 final size:11
Alignment explanation
Indices: 62695020--62695067 Score: 53
Period size: 11 Copynumber: 4.5 Consensus size: 11
62695010 AAATATAGAA
62695020 ATTTAG-TTTT
1 ATTTAGATTTT
** *
62695030 ATAAAGATTTC
1 ATTTAGATTTT
62695041 ATTTAGATTTT
1 ATTTAGATTTT
*
62695052 ATTCAGATTTT
1 ATTTAGATTTT
62695063 ATTTA
1 ATTTA
62695068 CTAAAGAATA
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
10 4 0.14
11 25 0.86
ACGTcount: A:0.31, C:0.04, G:0.08, T:0.56
Consensus pattern (11 bp):
ATTTAGATTTT
Found at i:62695059 original size:22 final size:21
Alignment explanation
Indices: 62695020--62695067 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
62695010 AAATATAGAA
62695020 ATTTAGTTTTATAAAGATTTC
1 ATTTAGTTTTATAAAGATTTC
** *
62695041 ATTTAGATTTTATTCAGATTTT
1 ATTTAG-TTTTATAAAGATTTC
62695063 ATTTA
1 ATTTA
62695068 CTAAAGAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.31, C:0.04, G:0.08, T:0.56
Consensus pattern (21 bp):
ATTTAGTTTTATAAAGATTTC
Found at i:62698607 original size:29 final size:29
Alignment explanation
Indices: 62698561--62698616 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
62698551 CATAAATTTT
*
62698561 AAATTTAATCCTTGTACTT-TTATTTATAA
1 AAATTTAATCCTTCTACTTATT-TTTATAA
62698590 AAATTTAAT-CTATCTACTTATTTTTAT
1 AAATTTAATCCT-TCTACTTATTTTTAT
62698617 TAGTATTCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 2 0.08
29 20 0.83
30 2 0.08
ACGTcount: A:0.34, C:0.11, G:0.02, T:0.54
Consensus pattern (29 bp):
AAATTTAATCCTTCTACTTATTTTTATAA
Found at i:62702032 original size:29 final size:29
Alignment explanation
Indices: 62701986--62702041 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
62701976 CATAAATTTT
*
62701986 AAATTTAATCCTTGTACTT-TTATTTATAG
1 AAATTTAAACCTTGTACTTATT-TTTATAG
62702015 AAATTTAAACCATT-TACTTATTTTTAT
1 AAATTTAAACC-TTGTACTTATTTTTAT
62702042 TAGTATTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
29 20 0.83
30 4 0.17
ACGTcount: A:0.34, C:0.11, G:0.04, T:0.52
Consensus pattern (29 bp):
AAATTTAAACCTTGTACTTATTTTTATAG
Found at i:62709202 original size:17 final size:17
Alignment explanation
Indices: 62709180--62709213 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
62709170 AAAAAGTATT
* *
62709180 TTAAAAATATTTTAAAA
1 TTAAAAAAAATTTAAAA
62709197 TTAAAAAAAATTTAAAA
1 TTAAAAAAAATTTAAAA
62709214 ATATATATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TTAAAAAAAATTTAAAA
Found at i:62718954 original size:56 final size:56
Alignment explanation
Indices: 62718887--62719001 Score: 230
Period size: 56 Copynumber: 2.1 Consensus size: 56
62718877 ACTAACCTAA
62718887 TCCTTTGCATGTGTCCAAATCCAATAATAAATAGGAAAAGAAAACTTAAACATTCT
1 TCCTTTGCATGTGTCCAAATCCAATAATAAATAGGAAAAGAAAACTTAAACATTCT
62718943 TCCTTTGCATGTGTCCAAATCCAATAATAAATAGGAAAAGAAAACTTAAACATTCT
1 TCCTTTGCATGTGTCCAAATCCAATAATAAATAGGAAAAGAAAACTTAAACATTCT
62718999 TCC
1 TCC
62719002 AAACCCATAC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 59 1.00
ACGTcount: A:0.42, C:0.19, G:0.10, T:0.29
Consensus pattern (56 bp):
TCCTTTGCATGTGTCCAAATCCAATAATAAATAGGAAAAGAAAACTTAAACATTCT
Found at i:62722594 original size:18 final size:17
Alignment explanation
Indices: 62722555--62722596 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
62722545 CATTATTCTT
62722555 ACATCTCTAAATTTTTA
1 ACATCTCTAAATTTTTA
*
62722572 TCATCT-TAAATTAGTTTA
1 ACATCTCTAAATT--TTTA
62722590 ACATCTC
1 ACATCTC
62722597 AATTTCTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 4
0.77 0.08 0.15
Matches are distributed among these distances:
16 6 0.30
17 5 0.25
18 9 0.45
ACGTcount: A:0.33, C:0.19, G:0.02, T:0.45
Consensus pattern (17 bp):
ACATCTCTAAATTTTTA
Found at i:62731485 original size:22 final size:22
Alignment explanation
Indices: 62731459--62731521 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
62731449 CATGGCTCTC
62731459 CTCTCTTTCTCTCGCTCTTTCA
1 CTCTCTTTCTCTCGCTCTTTCA
62731481 CTCTCCTTTC-CTCGC-CATTTCA
1 CTCT-CTTTCTCTCGCTC-TTTCA
*
62731503 CT-TCTTT-TCTC-CTCGTTCA
1 CTCTCTTTCTCTCGCTCTTTCA
62731522 ATCCGCCGTC
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
19 5 0.14
20 8 0.22
21 2 0.06
22 16 0.44
23 5 0.14
ACGTcount: A:0.06, C:0.41, G:0.05, T:0.48
Consensus pattern (22 bp):
CTCTCTTTCTCTCGCTCTTTCA
Found at i:62742556 original size:25 final size:26
Alignment explanation
Indices: 62742525--62742577 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
62742515 TTTTTACAAA
62742525 TTTAG-AATTTAGT-TCTATTTTTATT
1 TTTAGAAATTTAGTCTCTATTTTT-TT
*
62742550 TTTAGAAATTTAGTCTCTCTTTTTTT
1 TTTAGAAATTTAGTCTCTATTTTTTT
62742576 TT
1 TT
62742578 ATATTTCAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 5 0.20
26 12 0.48
27 8 0.32
ACGTcount: A:0.21, C:0.08, G:0.08, T:0.64
Consensus pattern (26 bp):
TTTAGAAATTTAGTCTCTATTTTTTT
Found at i:62744160 original size:22 final size:23
Alignment explanation
Indices: 62744135--62744178 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
62744125 TAATTTAAAT
*
62744135 TTTAATACT-TTTATATATATTA
1 TTTAATAATATTTATATATATTA
*
62744157 TTTATTAATAATTTATATATAT
1 TTTAATAAT-ATTTATATATAT
62744179 AGTACTCTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.39
24 11 0.61
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
TTTAATAATATTTATATATATTA
Found at i:62744549 original size:29 final size:30
Alignment explanation
Indices: 62744508--62744605 Score: 128
Period size: 29 Copynumber: 3.3 Consensus size: 30
62744498 ACAAAATAGT
*
62744508 ATTTTGACCCCTAAATTTTCTTAAAATTAT
1 ATTTTGACCCCTAAATTTTCTTAAAATTAC
* *
62744538 ATTCTGA-CCCTAAACTTTCTTAAAATTAC
1 ATTTTGACCCCTAAATTTTCTTAAAATTAC
* *
62744567 ATTTTAACCCCTAAATTTTC-CAAAATTAC
1 ATTTTGACCCCTAAATTTTCTTAAAATTAC
*
62744596 ACTTTGACCC
1 ATTTTGACCC
62744606 TAGAAGTTTT
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
29 41 0.71
30 17 0.29
ACGTcount: A:0.34, C:0.23, G:0.03, T:0.40
Consensus pattern (30 bp):
ATTTTGACCCCTAAATTTTCTTAAAATTAC
Found at i:62745100 original size:4 final size:4
Alignment explanation
Indices: 62745091--62745172 Score: 56
Period size: 4 Copynumber: 22.0 Consensus size: 4
62745081 GGCTGATCGG
*
62745091 GAAA GAAA G-AA -AAA GAGAA GAAA GAAA GAAA G-AA GAAGA GGAA G-AA
1 GAAA GAAA GAAA GAAA GA-AA GAAA GAAA GAAA GAAA GAA-A GAAA GAAA
*
62745137 G-AA GAAA GGAAA -AAA AAAA G-AA -AAA GAAA -AAA GAAA
1 GAAA GAAA -GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
62745173 ACAATTTTTT
Statistics
Matches: 65, Mismatches: 2, Indels: 22
0.73 0.02 0.25
Matches are distributed among these distances:
3 23 0.35
4 31 0.48
5 11 0.17
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:62745113 original size:15 final size:15
Alignment explanation
Indices: 62745093--62745173 Score: 68
Period size: 15 Copynumber: 5.7 Consensus size: 15
62745083 CTGATCGGGA
62745093 AAGAAAGAAAAAGAG
1 AAGAAAGAAAAAGAG
62745108 AAGAAAGAAAGAA-AG
1 AAGAAAGAAA-AAGAG
**
62745123 AAG-AAGAGGAAGAAG
1 AAGAAAGAAAAAG-AG
*
62745138 AAGAAAGGAAAA-A-
1 AAGAAAGAAAAAGAG
62745151 AA-AAAGAAAAAGA-
1 AAGAAAGAAAAAGAG
62745164 AA-AAAGAAAA
1 AAGAAAGAAAA
62745174 CAATTTTTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
12 8 0.15
13 15 0.27
14 5 0.09
15 20 0.36
16 7 0.13
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (15 bp):
AAGAAAGAAAAAGAG
Found at i:62745123 original size:12 final size:11
Alignment explanation
Indices: 62745091--62745172 Score: 71
Period size: 11 Copynumber: 7.4 Consensus size: 11
62745081 GGCTGATCGG
62745091 GAAAGAAAGAA
1 GAAAGAAAGAA
62745102 -AAAGAGAAGAAA
1 GAAAGA-AAG-AA
62745114 GAAAGAAAGAA
1 GAAAGAAAGAA
*
62745125 GAAGAGGAAGAA
1 GAA-AGAAAGAA
62745137 G-AAGAAAGGAA
1 GAAAGAAA-GAA
* *
62745148 AAAAAAAAGAA
1 GAAAGAAAGAA
*
62745159 -AAAGAAAAAA
1 GAAAGAAAGAA
62745169 GAAA
1 GAAA
62745173 ACAATTTTTT
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
10 17 0.29
11 18 0.31
12 18 0.31
13 5 0.09
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (11 bp):
GAAAGAAAGAA
Found at i:62745501 original size:14 final size:14
Alignment explanation
Indices: 62745482--62745532 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
62745472 GAAAAAAAAT
62745482 AAAAAAAAGGAGAG
1 AAAAAAAAGGAGAG
* *
62745496 AAAAAAGAGAAGA-
1 AAAAAAAAGGAGAG
62745509 AAAAAAAAGG-GAAG
1 AAAAAAAAGGAG-AG
*
62745523 AAGAAAAAGG
1 AAAAAAAAGG
62745533 GGGTTCAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
12 1 0.03
13 9 0.30
14 20 0.67
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (14 bp):
AAAAAAAAGGAGAG
Found at i:62745533 original size:14 final size:15
Alignment explanation
Indices: 62745496--62745530 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
62745486 AAAAGGAGAG
*
62745496 AAAAAAGAGAAGAAA
1 AAAAAAGGGAAGAAA
62745511 AAAAAAGGGAAGAAGA
1 AAAAAAGGGAAGAA-A
62745527 AAAA
1 AAAA
62745531 GGGGGTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
AAAAAAGGGAAGAAA
Found at i:62745909 original size:17 final size:17
Alignment explanation
Indices: 62745867--62746194 Score: 155
Period size: 17 Copynumber: 18.6 Consensus size: 17
62745857 TTTCAAAAAA
* * *
62745867 GTTTCAAAAATTGTCGC
1 GTTTCAAAAATTTTTGT
*
62745884 GTTTTAAAAATTTTTGT
1 GTTTCAAAAATTTTTGT
*
62745901 GATTCAAAAATTGTCTTGT
1 GTTTCAAAAATT-T-TTGT
*
62745920 -TTT--AAAATTTTTCAT
1 GTTTCAAAAATTTTT-GT
* **
62745935 GTTTCTAAAGATTTCCGT
1 GTTTC-AAAAATTTTTGT
*
62745953 GTTTTCAAAAATTTTCGT
1 G-TTTCAAAAATTTTTGT
*
62745971 AATTTCAAAAATTTTTGT
1 -GTTTCAAAAATTTTTGT
*
62745989 GTTTTCTAAAAATTTCTGT
1 G-TTTC-AAAAATTTTTGT
62746008 GTTTCAAAAATTTTCATGT
1 GTTTCAAAAATTTT--TGT
* *
62746027 -TTTCAAAAATTGTCGT
1 GTTTCAAAAATTTTTGT
*
62746043 GTTTTCCAAAATTTTCT-T
1 G-TTTCAAAAATTTT-TGT
*
62746061 GTTTCACAAATTTTTGT
1 GTTTCAAAAATTTTTGT
* * **
62746078 ATTTTAAATTTTTTTTGT
1 GTTTCAAA-AATTTTTGT
* * * *
62746096 CTTTTGAAAATAATTCTTAT
1 -GTTT-CAAA-AATTTTTGT
* * *
62746116 GTTTCAAAAGTTGTCGT
1 GTTTCAAAAATTTTTGT
* *
62746133 GTTTTAAAAATTTTCGT
1 GTTTCAAAAATTTTTGT
* * *
62746150 GTTTTAAAAATTCTAGT
1 GTTTCAAAAATTTTTGT
*
62746167 GTTTTCAAAAATTCTCT-T
1 G-TTTCAAAAATT-TTTGT
62746185 GTTTCAAAAA
1 GTTTCAAAAA
62746195 CATTCGTTTT
Statistics
Matches: 237, Mismatches: 52, Indels: 44
0.71 0.16 0.13
Matches are distributed among these distances:
14 2 0.01
15 2 0.01
16 12 0.05
17 92 0.39
18 85 0.36
19 35 0.15
20 9 0.04
ACGTcount: A:0.30, C:0.10, G:0.11, T:0.50
Consensus pattern (17 bp):
GTTTCAAAAATTTTTGT
Found at i:62745966 original size:18 final size:18
Alignment explanation
Indices: 62745868--62746194 Score: 212
Period size: 18 Copynumber: 18.5 Consensus size: 18
62745858 TTCAAAAAAG
* *
62745868 TTTCAAAAATTGTCGCGT
1 TTTCAAAAATTTTCGTGT
*
62745886 TTT-AAAAATTTTTGTG-
1 TTTCAAAAATTTTCGTGT
* * *
62745902 ATTCAAAAATTGTCTTGT
1 TTTCAAAAATTTTCGTGT
* *
62745920 TTT-AAAATTTTTCATG-
1 TTTCAAAAATTTTCGTGT
* *
62745936 TTTCTAAAGATTTCCGTGT
1 TTTC-AAAAATTTTCGTGT
**
62745955 TTTCAAAAATTTTCGTAA
1 TTTCAAAAATTTTCGTGT
*
62745973 TTTCAAAAATTTTTGTGT
1 TTTCAAAAATTTTCGTGT
62745991 TTTCTAAAAA-TTTC-TGT
1 TTTC-AAAAATTTTCGTGT
*
62746008 GTTTCAAAAATTTTCATGT
1 -TTTCAAAAATTTTCGTGT
*
62746027 TTTCAAAAATTGTCGTGT
1 TTTCAAAAATTTTCGTGT
* *
62746045 TTTCCAAAATTTTCTTG-
1 TTTCAAAAATTTTCGTGT
* * *
62746062 TTTCACAAATTTTTGTAT
1 TTTCAAAAATTTTCGTGT
** * *
62746080 TTT-AAATTTTTTTTGTCT
1 TTTCAAA-AATTTTCGTGT
* *
62746098 TTTGAAAATAATTCTT-ATG-
1 TTT-CAAA-AATT-TTCGTGT
* *
62746117 TTTCAAAAGTTGTCGTGT
1 TTTCAAAAATTTTCGTGT
62746135 TTT-AAAAATTTTCGTGT
1 TTTCAAAAATTTTCGTGT
* *
62746152 TTT-AAAAATTCTAGTGT
1 TTTCAAAAATTTTCGTGT
* *
62746169 TTTCAAAAATTCTCTTG-
1 TTTCAAAAATTTTCGTGT
62746186 TTTCAAAAA
1 TTTCAAAAA
62746195 CATTCGTTTT
Statistics
Matches: 241, Mismatches: 51, Indels: 35
0.74 0.16 0.11
Matches are distributed among these distances:
16 6 0.02
17 96 0.40
18 115 0.48
19 15 0.06
20 7 0.03
21 2 0.01
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (18 bp):
TTTCAAAAATTTTCGTGT
Found at i:62749363 original size:17 final size:17
Alignment explanation
Indices: 62749330--62749363 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
62749320 ATGATTCCAG
* *
62749330 CTCGAAATTATTTAAAA
1 CTCGAAATGATTCAAAA
62749347 CTCGAAATGATTCAAAA
1 CTCGAAATGATTCAAAA
62749364 TTTTTGAAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.15, G:0.09, T:0.29
Consensus pattern (17 bp):
CTCGAAATGATTCAAAA
Found at i:62770443 original size:57 final size:56
Alignment explanation
Indices: 62770346--62770469 Score: 203
Period size: 57 Copynumber: 2.2 Consensus size: 56
62770336 CTTCAAATCT
*
62770346 CATATCTCAATTTCCAATTCACATATCAATTCACAATTTCACTTTCTCATTTCTTTC
1 CATAGCTCAATTTCCAATTCACATATCAATTCACAATTTCACTTTCTCATTTC-TTC
* * *
62770403 CATAGCTCGATTTCCAATTCACATATCAATTCACGATTTCACTTTCTTATTTCTTC
1 CATAGCTCAATTTCCAATTCACATATCAATTCACAATTTCACTTTCTCATTTCTTC
62770459 CATAGCTCAAT
1 CATAGCTCAAT
62770470 CAATCACACT
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
56 13 0.21
57 49 0.79
ACGTcount: A:0.27, C:0.27, G:0.03, T:0.42
Consensus pattern (56 bp):
CATAGCTCAATTTCCAATTCACATATCAATTCACAATTTCACTTTCTCATTTCTTC
Found at i:62772488 original size:30 final size:29
Alignment explanation
Indices: 62772454--62772513 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 29
62772444 AGCCTCAAAA
*
62772454 TTATATATGAATTTTGATTTATGTGTAATT
1 TTATATATAAATTTTGATTT-TGTGTAATT
62772484 TTATATATAAATTTTGATTTTGTGTAATT
1 TTATATATAAATTTTGATTTTGTGTAATT
62772513 T
1 T
62772514 CATACACAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 10 0.34
30 19 0.66
ACGTcount: A:0.30, C:0.00, G:0.12, T:0.58
Consensus pattern (29 bp):
TTATATATAAATTTTGATTTTGTGTAATT
Found at i:62772526 original size:30 final size:30
Alignment explanation
Indices: 62772463--62772533 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
62772453 ATTATATATG
* * *
62772463 AATTTTGATTTATGTGTAATTTTATATATA
1 AATTTTGATTTATGTGTAATTTCATACAAA
62772493 AATTTTGATTT-TGTGTAATTTCATACACAA
1 AATTTTGATTTATGTGTAATTTCATACA-AA
*
62772523 AATTTTAATTT
1 AATTTTGATTT
62772534 GATCTAATTC
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 14 0.39
30 22 0.61
ACGTcount: A:0.34, C:0.04, G:0.08, T:0.54
Consensus pattern (30 bp):
AATTTTGATTTATGTGTAATTTCATACAAA
Found at i:62772534 original size:29 final size:29
Alignment explanation
Indices: 62772463--62772534 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 29
62772453 ATTATATATG
* * * *
62772463 AATTTTGATTTATGTGTAATTTTATATATA
1 AATTTTGAATT-TGTGTAATTTCATACAAA
*
62772493 AATTTTGATTTTGTGTAATTTCATACACAA
1 AATTTTGAATTTGTGTAATTTCATACA-AA
62772523 AATTTT-AATTTG
1 AATTTTGAATTTG
62772535 ATCTAATTCT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 19 0.51
30 18 0.49
ACGTcount: A:0.33, C:0.04, G:0.10, T:0.53
Consensus pattern (29 bp):
AATTTTGAATTTGTGTAATTTCATACAAA
Found at i:62772682 original size:31 final size:32
Alignment explanation
Indices: 62772641--62772726 Score: 92
Period size: 31 Copynumber: 2.8 Consensus size: 32
62772631 AATAAATGTA
*
62772641 TATAA-TTGAACCAAAATTAAAGTTTCAT-T-
1 TATAATTTGAACCAAAATTAAAGTTCCATATG
* * *
62772670 TATACATTTGAACCACAATAAAAATTCCATATG
1 TATA-ATTTGAACCAAAATTAAAGTTCCATATG
62772703 TATAATTT-AACC-AAATTAAAGTTC
1 TATAATTTGAACCAAAATTAAAGTTC
62772727 ATGTATCAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 7
0.77 0.12 0.12
Matches are distributed among these distances:
29 4 0.09
30 10 0.22
31 23 0.50
32 5 0.11
33 4 0.09
ACGTcount: A:0.45, C:0.14, G:0.06, T:0.35
Consensus pattern (32 bp):
TATAATTTGAACCAAAATTAAAGTTCCATATG
Found at i:62773173 original size:23 final size:22
Alignment explanation
Indices: 62773117--62773180 Score: 57
Period size: 23 Copynumber: 3.0 Consensus size: 22
62773107 TCCTAAGTGA
62773117 AATAAAAATA--A-TAAATTTT
1 AATAAAAATATTATTAAATTTT
* *
62773136 AATTAAGATATTATTTAAATTTT
1 AATAAAAATATTA-TTAAATTTT
62773159 ATATAAAAATA-TATT-AATTTT
1 A-ATAAAAATATTATTAAATTTT
62773180 A
1 A
62773181 CTTTATTAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
19 8 0.22
21 8 0.22
22 2 0.06
23 11 0.31
24 7 0.19
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
AATAAAAATATTATTAAATTTT
Found at i:62773265 original size:30 final size:31
Alignment explanation
Indices: 62773194--62773266 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 31
62773184 TATTAGAAAA
* *
62773194 AAATAATATTTAATAAATAAAATTACATTTAT
1 AAATATTA-TTAATAAATAAAATTACATTAAT
* * *
62773226 AAATTTTATTAA-AAATACAATTTCATTAAT
1 AAATATTATTAATAAATAAAATTACATTAAT
*
62773256 TAATATTATTA
1 AAATATTATTA
62773267 TAATTTAAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
30 24 0.71
31 4 0.12
32 6 0.18
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (31 bp):
AAATATTATTAATAAATAAAATTACATTAAT
Found at i:62774069 original size:22 final size:21
Alignment explanation
Indices: 62774036--62774077 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
62774026 TTAAATTCTT
* *
62774036 AAAAATAATATTAATTATACA
1 AAAAAAAATATTAATAATACA
62774057 AAAAAAAACTATTAATAATAC
1 AAAAAAAA-TATTAATAATAC
62774078 TTGAAAAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (21 bp):
AAAAAAAATATTAATAATACA
Found at i:62782157 original size:29 final size:29
Alignment explanation
Indices: 62782124--62782181 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
62782114 AAAAAATATA
*
62782124 ATTTTAAAGGATTAAATTAAAATTTTATC
1 ATTTTAAAGGATTAAAATAAAATTTTATC
* * *
62782153 ATTTTAGAGGGTTAAAATATAATTTTATC
1 ATTTTAAAGGATTAAAATAAAATTTTATC
62782182 TTCACTAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.45
Consensus pattern (29 bp):
ATTTTAAAGGATTAAAATAAAATTTTATC
Found at i:62782256 original size:2 final size:2
Alignment explanation
Indices: 62782249--62782273 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
62782239 GCTTCTGGTG
62782249 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
62782274 AATGATGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:62784791 original size:13 final size:11
Alignment explanation
Indices: 62784759--62784801 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
62784749 CATTTTTTTA
*
62784759 AATAAAATAAT
1 AATAAAATATT
62784770 AAT-AAATATCT
1 AATAAAATAT-T
62784781 AAGTAAAATATT
1 AA-TAAAATATT
62784793 AATAAAATA
1 AATAAAATA
62784802 ATATTGAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 5 0.18
11 13 0.46
12 4 0.14
13 6 0.21
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (11 bp):
AATAAAATATT
Found at i:62785184 original size:3 final size:3
Alignment explanation
Indices: 62785176--62785225 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
62785166 CTTCTTAATC
62785176 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
62785224 AT
1 AT
62785226 ACTCCTCAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:62785859 original size:20 final size:20
Alignment explanation
Indices: 62785831--62785891 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
62785821 TTATTCTGCA
62785831 TCTTAAATTTTTTATTGATT
1 TCTTAAATTTTTTATTGATT
* * * *
62785851 TCTTTAATTCTTTAATAATAT
1 TCTTAAATTTTTTATTGAT-T
62785872 T-TTAAATTTTTTATTGATT
1 TCTTAAATTTTTTATTGATT
62785891 T
1 T
62785892 AAAATATGCC
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
19 2 0.06
20 28 0.88
21 2 0.06
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (20 bp):
TCTTAAATTTTTTATTGATT
Found at i:62795086 original size:17 final size:16
Alignment explanation
Indices: 62795064--62795099 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
62795054 AATTTGATCA
62795064 TTTTTAGTTCCTGTAAT
1 TTTTTAGTT-CTGTAAT
*
62795081 TTTTTAGTTTTGTAAT
1 TTTTTAGTTCTGTAAT
62795097 TTT
1 TTT
62795100 AGTCTTGACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.17, C:0.06, G:0.11, T:0.67
Consensus pattern (16 bp):
TTTTTAGTTCTGTAAT
Found at i:62796035 original size:40 final size:40
Alignment explanation
Indices: 62795946--62796042 Score: 99
Period size: 40 Copynumber: 2.4 Consensus size: 40
62795936 CGTTTGAACA
62795946 AAAAACGCCGCTAAAAATCGAGCATTAGCGGTGCTTTTAG
1 AAAAACGCCGCTAAAAATCGAGCATTAGCGGTGCTTTTAG
* * * * * *
62795986 TACAGCGCCGCTAAAAAT-GATCATTCGCGACGT-TTTTTAG
1 AAAAACGCCGCTAAAAATCGAGCATTAGCG--GTGCTTTTAG
*
62796026 AAAAACGCCGCAAAAAA
1 AAAAACGCCGCTAAAAA
62796043 CCTAAGCCCA
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
39 9 0.20
40 34 0.76
41 2 0.04
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (40 bp):
AAAAACGCCGCTAAAAATCGAGCATTAGCGGTGCTTTTAG
Found at i:62796157 original size:41 final size:41
Alignment explanation
Indices: 62796112--62796208 Score: 104
Period size: 41 Copynumber: 2.4 Consensus size: 41
62796102 TGCTCAGAGC
* * * ** *
62796112 TTTAGCTGTGTTTTTTATAAAGCGCGGCTAAAGATCTGGCT
1 TTTAGCTGCGTTTTTAAAAAAGCGCCACTAAAGATCGGGCT
* * * *
62796153 TTTAGCGGCGGTTCTAAAAAAGTGCCACTAAAGATCGGGCT
1 TTTAGCTGCGTTTTTAAAAAAGCGCCACTAAAGATCGGGCT
62796194 TTTAGCTGCGTTTTT
1 TTTAGCTGCGTTTTT
62796209 GAAATAGCAT
Statistics
Matches: 43, Mismatches: 13, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.36
Consensus pattern (41 bp):
TTTAGCTGCGTTTTTAAAAAAGCGCCACTAAAGATCGGGCT
Found at i:62796264 original size:41 final size:41
Alignment explanation
Indices: 62796201--62796306 Score: 108
Period size: 41 Copynumber: 2.6 Consensus size: 41
62796191 GCTTTTAGCT
**
62796201 GCGTTTTTG-AAATAGCATCGCTAATGCTAAGAGC-TGCAGCG
1 GCGTTTTTGAAAAT-GCGCCGCTAATGCTAAG-GCTTGCAGCG
** **
62796242 GCGTTTTTGAAAATGCGCCGCTAATGCTTTGGCTTTTAGCG
1 GCGTTTTTGAAAATGCGCCGCTAATGCTAAGGCTTGCAGCG
* *
62796283 GCGTTTTTAAAAAAGCGCCGCTAA
1 GCGTTTTTGAAAATGCGCCGCTAA
62796307 AACATTTTAT
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
40 2 0.04
41 49 0.89
42 4 0.07
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (41 bp):
GCGTTTTTGAAAATGCGCCGCTAATGCTAAGGCTTGCAGCG
Found at i:62796448 original size:26 final size:26
Alignment explanation
Indices: 62796400--62796449 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
62796390 AAAATGGATA
** * *
62796400 AATTTGAAATAATGACACGTAGAACT
1 AATTTGAAATAAAAAAACATAGAACT
62796426 AATTTGAAATAAAAAAACATAGAA
1 AATTTGAAATAAAAAAACATAGAA
62796450 AAATATTTGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.56, C:0.08, G:0.12, T:0.24
Consensus pattern (26 bp):
AATTTGAAATAAAAAAACATAGAACT
Found at i:62796741 original size:14 final size:15
Alignment explanation
Indices: 62796715--62796747 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
62796705 AACATTTATA
62796715 GATTATGGAATTAGG
1 GATTATGGAATTAGG
62796730 GATTAT-GAATTAGG
1 GATTATGGAATTAGG
62796744 GATT
1 GATT
62796748 TTGGTTTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.33, C:0.00, G:0.30, T:0.36
Consensus pattern (15 bp):
GATTATGGAATTAGG
Found at i:62796924 original size:81 final size:83
Alignment explanation
Indices: 62796836--62796986 Score: 218
Period size: 83 Copynumber: 1.8 Consensus size: 83
62796826 CAGGTTAAGC
* **
62796836 TTTAGGGTTTAGATTAATTAGTATATTTT-AA-TT-TATATTAAATAAGATTTAGGGGTTAGGAG
1 TTTAGGGTTTAGATTAATTAGTAT-TTTTAAATTTATATATTAAATAAGACTTAGGGGTTAACAG
62796898 TTAGGGATTCGGGCTATGA
65 TTAGGGATTCGGGCTATGA
* * *
62796917 TTTAGGGTTTAGATTAATTATTGTTTTTAAATTTATATATTAAATAAGGCTTAGGGGTTAACAGT
1 TTTAGGGTTTAGATTAATTAGTATTTTTAAATTTATATATTAAATAAGACTTAGGGGTTAACAGT
62796982 TAGGG
66 TAGGG
62796987 GTTTGGGGTT
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
80 4 0.07
81 24 0.39
82 2 0.03
83 31 0.51
ACGTcount: A:0.31, C:0.03, G:0.23, T:0.43
Consensus pattern (83 bp):
TTTAGGGTTTAGATTAATTAGTATTTTTAAATTTATATATTAAATAAGACTTAGGGGTTAACAGT
TAGGGATTCGGGCTATGA
Found at i:62797023 original size:28 final size:28
Alignment explanation
Indices: 62796967--62797024 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
62796957 TAAATAAGGC
* * *
62796967 TTAGGGGTTAACAGTTAGGGGTTTGGGG
1 TTAGAGGTTAACAGTTAGGGATTTAGGG
* *
62796995 TTAGAGGTTAAGAGTTAGTGATTTAGGG
1 TTAGAGGTTAACAGTTAGGGATTTAGGG
62797023 TT
1 TT
62797025 TAAAGACTCG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.22, C:0.02, G:0.40, T:0.36
Consensus pattern (28 bp):
TTAGAGGTTAACAGTTAGGGATTTAGGG
Found at i:62797129 original size:7 final size:7
Alignment explanation
Indices: 62797117--62797155 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
62797107 ATTGTAAAAG
62797117 AGGGGTT
1 AGGGGTT
62797124 AGGGGTT
1 AGGGGTT
*
62797131 AGAGGTT
1 AGGGGTT
* *
62797138 AAGGATT
1 AGGGGTT
62797145 AGGGGTT
1 AGGGGTT
62797152 AGGG
1 AGGG
62797156 ATATACTTAC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.51, T:0.26
Consensus pattern (7 bp):
AGGGGTT
Found at i:62797604 original size:15 final size:16
Alignment explanation
Indices: 62797578--62797612 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
62797568 ATTTATAAAT
62797578 TTTAATATTGATAGTA
1 TTTAATATTGATAGTA
62797594 TTTAA-ATTGATAGTA
1 TTTAATATTGATAGTA
62797609 TTTA
1 TTTA
62797613 TAAATTTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.51
Consensus pattern (16 bp):
TTTAATATTGATAGTA
Found at i:62800233 original size:29 final size:30
Alignment explanation
Indices: 62800180--62800239 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
62800170 TCCAAGCCTT
*
62800180 GGGGCAAAAATGTAATTATGTAAAAATTTA
1 GGGGCAAAAATGTAATTATGTAAAAAGTTA
* *
62800210 GGGGCAAAATTGTAATTTTG-AAAAAGTTA
1 GGGGCAAAAATGTAATTATGTAAAAAGTTA
62800239 G
1 G
62800240 AGTCGAGGGC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 9 0.33
30 18 0.67
ACGTcount: A:0.43, C:0.03, G:0.23, T:0.30
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGTAAAAAGTTA
Found at i:62800467 original size:13 final size:13
Alignment explanation
Indices: 62800449--62800480 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
62800439 TTTCCAGCAA
62800449 TTATGAATTTATT
1 TTATGAATTTATT
62800462 TTATGAATTTATT
1 TTATGAATTTATT
*
62800475 TGATGA
1 TTATGA
62800481 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:62800688 original size:50 final size:50
Alignment explanation
Indices: 62800575--62800816 Score: 288
Period size: 50 Copynumber: 4.7 Consensus size: 50
62800565 ATTTGGGTAA
* * **
62800575 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCTTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-C--CGAGA-C--G
*
62800631 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
62800681 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
62800731 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
62800781 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
62800817 TTTGGCATGT
Statistics
Matches: 165, Mismatches: 19, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.18
52 1 0.01
53 3 0.02
55 1 0.01
56 39 0.24
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:62800764 original size:100 final size:103
Alignment explanation
Indices: 62800575--62800824 Score: 355
Period size: 100 Copynumber: 2.4 Consensus size: 103
62800565 ATTTGGGTAA
62800575 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCTTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATC--T-AGATCATGAGAGGTCCC
* *
62800640 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * * *
62800681 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-C-CGA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCTAGATCATGAGAGGTCCCCTA
62800743 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
62800781 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
62800825 GTTATTATCG
Statistics
Matches: 132, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.39
101 39 0.30
105 1 0.01
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCTAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:62802696 original size:45 final size:45
Alignment explanation
Indices: 62802620--62802716 Score: 149
Period size: 45 Copynumber: 2.2 Consensus size: 45
62802610 ATAAGTTTTC
* * * *
62802620 TAAATTTATAAGTTTTCTAAGTAAATTTTCTAAATTTATTAGTAT
1 TAAAATTATAAGTTTTCTAAATAAATGTTCTAAATTTATTAGTAA
*
62802665 TAAAATTATAAGTTTTCTAAATAAGTGTTCTAAATTTATTAGTAA
1 TAAAATTATAAGTTTTCTAAATAAATGTTCTAAATTTATTAGTAA
62802710 TAAAATT
1 TAAAATT
62802717 TATTAGTATT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.47
Consensus pattern (45 bp):
TAAAATTATAAGTTTTCTAAATAAATGTTCTAAATTTATTAGTAA
Found at i:62802783 original size:12 final size:12
Alignment explanation
Indices: 62802766--62802975 Score: 65
Period size: 12 Copynumber: 19.1 Consensus size: 12
62802756 ATAAGCTTGC
62802766 ATAACTTACATA
1 ATAACTTACATA
62802778 ATAACTTAC---
1 ATAACTTACATA
62802787 ATAACTTACATA
1 ATAACTTACATA
** *
62802799 ATACAC-CCCTTA
1 ATA-ACTTACATA
*
62802811 CATAACTTATAT-
1 -ATAACTTACATA
*
62802823 ATAA-TAACATA
1 ATAACTTACATA
62802834 ATAACTTAC---
1 ATAACTTACATA
*
62802843 ATAACTTATAT-
1 ATAACTTACATA
*
62802854 ATAA-TAACATA
1 ATAACTTACATA
*
62802865 ATAAATTAC---
1 ATAACTTACATA
62802874 ATAA--TACATA
1 ATAACTTACATA
*
62802884 ATAACATA-ATA
1 ATAACTTACATA
*
62802895 CATAACTTATATA
1 -ATAACTTACATA
* *
62802908 GA-AGCTTGC---
1 -ATAACTTACATA
62802917 ATAACTTACATA
1 ATAACTTACATA
62802929 ATAACTTAC---
1 ATAACTTACATA
62802938 ATAACTTACATA
1 ATAACTTACATA
* *
62802950 ATACAC-CACTTA
1 ATA-ACTTACATA
62802962 CATAACTTACATA
1 -ATAACTTACATA
62802975 A
1 A
62802976 CTTACATAGC
Statistics
Matches: 144, Mismatches: 25, Indels: 58
0.63 0.11 0.26
Matches are distributed among these distances:
7 3 0.02
8 1 0.01
9 35 0.24
10 12 0.08
11 19 0.13
12 55 0.38
13 19 0.13
ACGTcount: A:0.49, C:0.18, G:0.01, T:0.32
Consensus pattern (12 bp):
ATAACTTACATA
Found at i:62802790 original size:9 final size:9
Alignment explanation
Indices: 62802778--62803299 Score: 178
Period size: 9 Copynumber: 61.4 Consensus size: 9
62802768 AACTTACATA
62802778 ATAACTTAC
1 ATAACTTAC
62802787 ATAACTTAC
1 ATAACTTAC
62802796 ATAA--TAC
1 ATAACTTAC
***
62802803 ACCCCTTAC
1 ATAACTTAC
*
62802812 ATAACTTAT
1 ATAACTTAC
62802821 AT-A--TA-
1 ATAACTTAC
*
62802826 ATAACATA-
1 ATAACTTAC
62802834 ATAACTTAC
1 ATAACTTAC
*
62802843 ATAACTTAT
1 ATAACTTAC
62802852 AT-A--TA-
1 ATAACTTAC
*
62802857 ATAACATA-
1 ATAACTTAC
*
62802865 ATAAATTAC
1 ATAACTTAC
62802874 ATAA--TAC
1 ATAACTTAC
*
62802881 ATAA-TAAC
1 ATAACTTAC
62802889 ATAA--TAC
1 ATAACTTAC
*
62802896 ATAACTTAT
1 ATAACTTAC
*
62802905 ATAGAAGCTTGC
1 AT--AA-CTTAC
62802917 ATAACTTAC
1 ATAACTTAC
62802926 ATAATAACTTAC
1 ---ATAACTTAC
62802938 ATAACTTAC
1 ATAACTTAC
62802947 ATAA--TAC
1 ATAACTTAC
**
62802954 ACCACTTAC
1 ATAACTTAC
62802963 ATAACTTAC
1 ATAACTTAC
62802972 ATAACTTAC
1 ATAACTTAC
*
62802981 ATAGCTTAC
1 ATAACTTAC
*
62802990 AT-TC-TAC
1 ATAACTTAC
* *
62802997 ACAACTTGC
1 ATAACTTAC
*
62803006 ATAACATAC
1 ATAACTTAC
*
62803015 ATAA--TGC
1 ATAACTTAC
*
62803022 AGAACTTAC
1 ATAACTTAC
* *
62803031 ATAA--AAT
1 ATAACTTAC
*
62803038 ATAATTTAC
1 ATAACTTAC
*
62803047 ATATCTTAC
1 ATAACTTAC
62803056 ATAA--TAC
1 ATAACTTAC
62803063 A-ACACTTAC
1 ATA-ACTTAC
* *
62803072 ACAACTTAA
1 ATAACTTAC
*
62803081 ATAACTTGC
1 ATAACTTAC
62803090 ATAA--TAC
1 ATAACTTAC
* *
62803097 ATAGCCTAC
1 ATAACTTAC
*
62803106 ATCAA-TTAT
1 AT-AACTTAC
*
62803115 ATAACTTTC
1 ATAACTTAC
**
62803124 ATAAAATA-
1 ATAACTTAC
62803132 A-AACTTAC
1 ATAACTTAC
**
62803140 ATATTTTAC
1 ATAACTTAC
*
62803149 ATAAAACTTAT
1 AT--AACTTAC
62803160 ATAA--TAC
1 ATAACTTAC
62803167 ATAACTTAC
1 ATAACTTAC
62803176 ATAA--TAC
1 ATAACTTAC
**
62803183 AGCACTTAC
1 ATAACTTAC
* *
62803192 ACAACTTAA
1 ATAACTTAC
*
62803201 ATAACTTGC
1 ATAACTTAC
62803210 ATAA--TAC
1 ATAACTTAC
* *
62803217 ATAGCCTAC
1 ATAACTTAC
*
62803226 ATAACTTAT
1 ATAACTTAC
62803235 ATAACATT-C
1 ATAAC-TTAC
**
62803244 ATAAAATAC
1 ATAACTTAC
62803253 --AACTTAC
1 ATAACTTAC
**
62803260 ATATTTTAC
1 ATAACTTAC
*
62803269 ATAAAACTTAT
1 AT--AACTTAC
62803280 ATAA--TAC
1 ATAACTTAC
62803287 ATAACTTAC
1 ATAACTTAC
62803296 ATAA
1 ATAA
62803300 TACAGCACTT
Statistics
Matches: 374, Mismatches: 86, Indels: 106
0.66 0.15 0.19
Matches are distributed among these distances:
5 4 0.01
6 7 0.02
7 77 0.21
8 32 0.09
9 220 0.59
10 6 0.02
11 14 0.04
12 14 0.04
ACGTcount: A:0.47, C:0.19, G:0.02, T:0.32
Consensus pattern (9 bp):
ATAACTTAC
Found at i:62802834 original size:19 final size:19
Alignment explanation
Indices: 62802810--62802865 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 19
62802800 TACACCCCTT
62802810 ACATAACTTATATATAATA
1 ACATAACTTATATATAATA
*
62802829 ACATAA--TA-A-CT--T-
1 ACATAACTTATATATAATA
62802841 ACATAACTTATATATAATA
1 ACATAACTTATATATAATA
62802860 ACATAA
1 ACATAA
62802866 TAAATTACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 14
0.64 0.05 0.32
Matches are distributed among these distances:
12 6 0.21
13 1 0.04
14 2 0.07
15 2 0.07
16 2 0.07
17 2 0.07
18 1 0.04
19 12 0.43
ACGTcount: A:0.54, C:0.12, G:0.00, T:0.34
Consensus pattern (19 bp):
ACATAACTTATATATAATA
Found at i:62802836 original size:8 final size:8
Alignment explanation
Indices: 62802823--62802899 Score: 62
Period size: 8 Copynumber: 10.5 Consensus size: 8
62802813 TAACTTATAT
62802823 ATAATAAC
1 ATAATAAC
62802831 ATAATAAC
1 ATAATAAC
*
62802839 TTACATAAC
1 ATA-ATAAC
* *
62802848 -TTAT-AT
1 ATAATAAC
62802854 ATAATAAC
1 ATAATAAC
62802862 ATAATAA-
1 ATAATAAC
62802869 AT--T-AC
1 ATAATAAC
62802874 ATAAT-AC
1 ATAATAAC
62802881 ATAATAAC
1 ATAATAAC
62802889 ATAAT-AC
1 ATAATAAC
62802896 ATAA
1 ATAA
62802900 CTTATATAGA
Statistics
Matches: 57, Mismatches: 5, Indels: 15
0.74 0.06 0.19
Matches are distributed among these distances:
4 1 0.02
5 3 0.05
6 1 0.02
7 21 0.37
8 26 0.46
9 5 0.09
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (8 bp):
ATAATAAC
Found at i:62802845 original size:31 final size:31
Alignment explanation
Indices: 62802807--62802877 Score: 133
Period size: 31 Copynumber: 2.3 Consensus size: 31
62802797 TAATACACCC
62802807 CTTACATAACTTATATATAATAACATAATAA
1 CTTACATAACTTATATATAATAACATAATAA
62802838 CTTACATAACTTATATATAATAACATAATAA
1 CTTACATAACTTATATATAATAACATAATAA
*
62802869 ATTACATAA
1 CTTACATAA
62802878 TACATAATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (31 bp):
CTTACATAACTTATATATAATAACATAATAA
Found at i:62802852 original size:27 final size:28
Alignment explanation
Indices: 62802820--62802894 Score: 98
Period size: 31 Copynumber: 2.6 Consensus size: 28
62802810 ACATAACTTA
*
62802820 TATATAATAACATAATAACTTACATAACTT
1 TATATAATAACATAATAAATTACATAA--T
62802850 ATATATAATAACATAATAAATTACATAA-
1 -TATATAATAACATAATAAATTACATAAT
*
62802878 TACATAATAACATAATA
1 TATATAATAACATAATA
62802895 CATAACTTAT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
27 16 0.38
31 26 0.62
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (28 bp):
TATATAATAACATAATAAATTACATAAT
Found at i:62802960 original size:25 final size:21
Alignment explanation
Indices: 62802756--62802991 Score: 159
Period size: 21 Copynumber: 11.0 Consensus size: 21
62802746 ATAATTATAT
*
62802756 ATAAGCTTGCATAACTTACATA
1 ATAA-CTTACATAACTTACATA
62802778 ATAACTTACATAACTTACATA
1 ATAACTTACATAACTTACATA
*
62802799 ATACACCCCTTACATAACTTATATATA
1 ATA-A---CTTACATAAC-T-TACATA
*
62802826 ATAACATA-ATAACTTAC---
1 ATAACTTACATAACTTACATA
* * *
62802843 ATAACTTATATATAATAACATA
1 ATAACTTACATA-ACTTACATA
*
62802865 ATAAATTACATAA--TACATA
1 ATAACTTACATAACTTACATA
*
62802884 ATAACATAATACATAACTTATATA
1 ATAAC-T--TACATAACTTACATA
* *
62802908 GA-AGCTTGCATAACTTACATA
1 -ATAACTTACATAACTTACATA
62802929 ATAACTTACATAACTTACATA
1 ATAACTTACATAACTTACATA
62802950 ATACACCACTTACATAACTTAC---
1 AT--A--ACTTACATAACTTACATA
*
62802972 ATAACTTACATAGCTTACAT
1 ATAACTTACATAACTTACAT
62802992 TCTACACAAC
Statistics
Matches: 172, Mismatches: 18, Indels: 50
0.72 0.08 0.21
Matches are distributed among these distances:
17 7 0.04
18 17 0.10
19 13 0.08
20 5 0.03
21 53 0.31
22 29 0.17
23 5 0.03
24 7 0.04
25 26 0.15
26 2 0.01
27 8 0.05
ACGTcount: A:0.47, C:0.19, G:0.03, T:0.32
Consensus pattern (21 bp):
ATAACTTACATAACTTACATA
Found at i:62803015 original size:25 final size:25
Alignment explanation
Indices: 62802969--62803085 Score: 60
Period size: 25 Copynumber: 4.7 Consensus size: 25
62802959 TTACATAACT
* * *
62802969 TACATAACTTACATAGCTTACATTC
1 TACACAACTTACATAACATACATTC
* **
62802994 TACACAACTTGCATAACATACATAA
1 TACACAACTTACATAACATACATTC
* * * *
62803019 TGCAGAACTTACATAAAATATAATT-
1 TACACAACTTACATAACATA-CATTC
* * *
62803044 TACATATCTTACATAATACA-ACACT-
1 TACACAACTTACAT-A-ACATACATTC
*
62803069 TACACAACTTAAATAAC
1 TACACAACTTACATAAC
62803086 TTGCATAATA
Statistics
Matches: 68, Mismatches: 21, Indels: 8
0.70 0.22 0.08
Matches are distributed among these distances:
23 2 0.03
24 1 0.01
25 59 0.87
26 4 0.06
27 2 0.03
ACGTcount: A:0.45, C:0.21, G:0.03, T:0.30
Consensus pattern (25 bp):
TACACAACTTACATAACATACATTC
Found at i:62803174 original size:16 final size:16
Alignment explanation
Indices: 62802865--62803303 Score: 128
Period size: 16 Copynumber: 26.1 Consensus size: 16
62802855 TAATAACATA
*
62802865 ATAAATTACATAATAC
1 ATAACTTACATAATAC
*
62802881 ATAA-TAACATAATAC
1 ATAACTTACATAATAC
* *
62802896 ATAACTTATATAGAAGCTTGC
1 ATAACTTACAT--AA---TAC
62802917 ATAACTTACATAATAACTTAC
1 ATAACTTAC---ATAA--TAC
62802938 ATAACTTACATAATAC
1 ATAACTTACATAATAC
**
62802954 ACCACTTACATAACTTAC
1 ATAACTTACATAA--TAC
*
62802972 ATAACTTACATAGCTTAC
1 ATAACTTACATA--ATAC
* * *
62802990 AT-TC-TACACAACTTGC
1 ATAACTTACATAA--TAC
* *
62803006 ATAACATACATAATGC
1 ATAACTTACATAATAC
*
62803022 AGAACTTACATAA-A-
1 ATAACTTACATAATAC
*
62803036 AT-A--TA-AT-TTAC
1 ATAACTTACATAATAC
*
62803047 ATATCTTACATAATAC
1 ATAACTTACATAATAC
* *
62803063 A-ACACTTACACAACTTAA
1 ATA-ACTTACATAA--TAC
*
62803081 ATAACTTGCATAATAC
1 ATAACTTACATAATAC
* * *
62803097 ATAGCCTACATCAATTAT
1 ATAACTTACAT-AA-TAC
* * *
62803115 ATAACTTTCATAAAAT
1 ATAACTTACATAATAC
* *
62803131 AAAACTTACATATTTTAC
1 ATAACTTACATA--ATAC
*
62803149 ATAAAACTTATATAATAC
1 AT--AACTTACATAATAC
62803167 ATAACTTACATAATAC
1 ATAACTTACATAATAC
** * *
62803183 AGCACTTACACAACTTAA
1 ATAACTTACATAA--TAC
*
62803201 ATAACTTGCATAATAC
1 ATAACTTACATAATAC
* * *
62803217 ATAGCCTACATAACTTAT
1 ATAACTTACATAA--TAC
* *
62803235 ATAACATT-CATAAAAT
1 ATAAC-TTACATAATAC
* *
62803251 ACAACTTACATATTTTAC
1 ATAACTTACATA--ATAC
*
62803269 ATAAAACTTATATAATAC
1 AT--AACTTACATAATAC
62803287 ATAACTTACATAATAC
1 ATAACTTACATAATAC
62803303 A
1 A
62803304 GCACTTACAC
Statistics
Matches: 308, Mismatches: 71, Indels: 88
0.66 0.15 0.19
Matches are distributed among these distances:
10 3 0.01
11 4 0.01
13 1 0.00
14 3 0.01
15 19 0.06
16 138 0.45
17 6 0.02
18 87 0.28
19 2 0.01
20 18 0.06
21 23 0.07
22 2 0.01
24 2 0.01
ACGTcount: A:0.47, C:0.19, G:0.03, T:0.32
Consensus pattern (16 bp):
ATAACTTACATAATAC
Found at i:62803197 original size:120 final size:120
Alignment explanation
Indices: 62803044--62803313 Score: 488
Period size: 120 Copynumber: 2.2 Consensus size: 120
62803034 AAATATAATT
* *
62803044 TACATATCTTACATAATACAACACTTACACAACTTAAATAACTTGCATAATACATAGCCTACATC
1 TACATAACTTACATAATACAGCACTTACACAACTTAAATAACTTGCATAATACATAGCCTACAT-
*
62803109 AA-TTATATAACTTTCATAAAATAAAACTTACATATTTTACATAAAACTTATATAA
65 AACTTATATAACATTCATAAAATAAAACTTACATATTTTACATAAAACTTATATAA
62803164 TACATAACTTACATAATACAGCACTTACACAACTTAAATAACTTGCATAATACATAGCCTACATA
1 TACATAACTTACATAATACAGCACTTACACAACTTAAATAACTTGCATAATACATAGCCTACATA
*
62803229 ACTTATATAACATTCATAAAATACAACTTACATATTTTACATAAAACTTATATAA
66 ACTTATATAACATTCATAAAATAAAACTTACATATTTTACATAAAACTTATATAA
62803284 TACATAACTTACATAATACAGCACTTACAC
1 TACATAACTTACATAATACAGCACTTACAC
62803314 GACAGAACAC
Statistics
Matches: 145, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
119 2 0.01
120 143 0.99
ACGTcount: A:0.46, C:0.20, G:0.02, T:0.32
Consensus pattern (120 bp):
TACATAACTTACATAATACAGCACTTACACAACTTAAATAACTTGCATAATACATAGCCTACATA
ACTTATATAACATTCATAAAATAAAACTTACATATTTTACATAAAACTTATATAA
Found at i:62803232 original size:34 final size:33
Alignment explanation
Indices: 62803167--62803247 Score: 85
Period size: 34 Copynumber: 2.4 Consensus size: 33
62803157 TATATAATAC
62803167 ATAACTTACATAATACAGCACTTACACAACTTAA
1 ATAACTT-CATAATACAGCACTTACACAACTTAA
* *
62803201 ATAACTTGCATAATACATAGC-C-TACATAACTTAT
1 ATAACTT-CATAATAC--AGCACTTACACAACTTAA
62803235 ATAACATTCATAA
1 ATAAC-TTCATAA
62803248 AATACAACTT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
34 35 0.85
35 3 0.07
36 3 0.07
ACGTcount: A:0.46, C:0.21, G:0.04, T:0.30
Consensus pattern (33 bp):
ATAACTTCATAATACAGCACTTACACAACTTAA
Found at i:62803309 original size:16 final size:16
Alignment explanation
Indices: 62803273--62803312 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
62803263 TTTTACATAA
* *
62803273 AACTTATATAATACAT
1 AACTTACATAATACAG
62803289 AACTTACATAATACAG
1 AACTTACATAATACAG
*
62803305 CACTTACA
1 AACTTACA
62803313 CGACAGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.47, C:0.20, G:0.03, T:0.30
Consensus pattern (16 bp):
AACTTACATAATACAG
Found at i:62805346 original size:19 final size:19
Alignment explanation
Indices: 62805322--62805359 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
62805312 GTAAATATTT
*
62805322 TTATCATTTTGACTTTTAA
1 TTATCATTTTAACTTTTAA
62805341 TTATCATTTTAACTTTTAA
1 TTATCATTTTAACTTTTAA
62805360 CATTTTTGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.03, T:0.58
Consensus pattern (19 bp):
TTATCATTTTAACTTTTAA
Found at i:62805629 original size:43 final size:43
Alignment explanation
Indices: 62805558--62805875 Score: 449
Period size: 43 Copynumber: 7.4 Consensus size: 43
62805548 CATTTTTAAA
* * *
62805558 AAAAACGCCACTAAAAGTCATGGTCTTTAGCGGCGTTTGTGGG
1 AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGG
* *
62805601 AAAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTTTGTGGA
1 AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGG
* *
62805644 AAAAGCGTCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGT
1 AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGG
* * * *
62805687 AAAAGCGCCGCTAAAGATTATGGTCTATAGCGGCGTTTGTGGTA
1 AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGG-G
62805731 AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGT-GG
1 AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGG
* * *
62805773 AAAAGGCGCCGCTAAAGGTCTTGGTCTTTAGTGGCGTTTGTGAG
1 AAAA-GCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGG
* * *
62805817 AAAAGCGCGGCTAAAGGTCTTGGTCTTTAGTGGCGTTTGTGGG
1 AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGG
*
62805860 AAAAGCGCCACTAAAG
1 AAAAGCGCCGCTAAAG
62805876 TTAGCGACGC
Statistics
Matches: 248, Mismatches: 24, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
42 4 0.02
43 202 0.81
44 42 0.17
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (43 bp):
AAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGG
Found at i:62805752 original size:130 final size:130
Alignment explanation
Indices: 62805577--62805875 Score: 460
Period size: 130 Copynumber: 2.3 Consensus size: 130
62805567 ACTAAAAGTC
62805577 ATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTTTGTG
1 ATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTTTGTG
*
62805642 GAAAAAGCGTCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTG-GTAAAAGCGCCGCTAAAGAT-
66 GAAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGAG-AAAAGCGCCGCTAAAGATC
62805705 T
130 T
* * *
62805706 ATGGTCTATAGCGGCGTTTGTGGTAAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGT
1 ATGGTCTTTAGCGGCGTTTGTGG-GAAAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTTTGT
* * * * *
62805771 GGAAAAGGCGCCGCTAAAGGTCTTGGTCTTTAGTGGCGTTTGTGAGAAAAGCGCGGCTAAAGGTC
65 GGAAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGATC
62805836 T
130 T
* *
62805837 -TGGTCTTTAGTGGCGTTTGTGGGAAAAGCGCCACTAAAG
1 ATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAG
62805876 TTAGCGACGC
Statistics
Matches: 154, Mismatches: 13, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
129 37 0.24
130 115 0.75
131 2 0.01
ACGTcount: A:0.23, C:0.17, G:0.33, T:0.28
Consensus pattern (130 bp):
ATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCATGATCTTTAGCGGCGTTTGTG
GAAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGATCT
Found at i:62805866 original size:173 final size:173
Alignment explanation
Indices: 62805557--62805875 Score: 500
Period size: 173 Copynumber: 1.8 Consensus size: 173
62805547 GCATTTTTAA
62805557 AAAAAACGCCACTAAAAGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCAT
1 AAAAAACGCCACTAAAAGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCAT
*
62805622 GATCTTTAGCGGCGTTTGTGGAAAAAGCGTCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGT
66 GATCTTTAGCGGCGTTTGTGGAAAAAGCGTCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGG
*
62805687 AAAAGCGCCGCTAAAGATTATGGTCTATAGCGGCGTTTGTGGT
131 AAAAGCGCCACTAAAGATTATGGTCTATAGCGGCGTTTGTGGT
* * * *
62805730 AAAAAGCGCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGT-GGAAAAGGCGCCGCTAAAGGTCT
1 AAAAAACGCCACTAAAAGTCATGGTCTTTAGCGGCGTTTGTGGGAAAA-GCGCCGCTAAAGGTCA
* * * *
62805794 TGGTCTTTAGTGGCGTTTGT-GAGAAAAGCG-CGGCTAAAGGTCTTGGTCTTTAGTGGCGTTTGT
65 TGATCTTTAGCGGCGTTTGTGGA-AAAAGCGTC-GCTAAAGGTCATGGTCTTTAGCGGCGTTTGT
62805857 GGGAAAAGCGCCACTAAAG
128 GGGAAAAGCGCCACTAAAG
62805876 TTAGCGACGC
Statistics
Matches: 133, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
172 9 0.07
173 124 0.93
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (173 bp):
AAAAAACGCCACTAAAAGTCATGGTCTTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTCAT
GATCTTTAGCGGCGTTTGTGGAAAAAGCGTCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTGGG
AAAAGCGCCACTAAAGATTATGGTCTATAGCGGCGTTTGTGGT
Found at i:62807434 original size:23 final size:22
Alignment explanation
Indices: 62807399--62807442 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
62807389 TTAGTTTCAA
62807399 TTTTCATTAAATTATAATAATT
1 TTTTCATTAAATTATAATAATT
* *
62807421 TTTTTATTATAATTATATTAAT
1 TTTTCATTA-AATTATAATAAT
62807443 AAAAATATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTTCATTAAATTATAATAATT
Found at i:62813162 original size:36 final size:38
Alignment explanation
Indices: 62813112--62813187 Score: 102
Period size: 36 Copynumber: 2.0 Consensus size: 38
62813102 CCTACATGTC
62813112 TGTTTTCTAATGGACATAC-ATA-ATGTCCTTAAAGTT
1 TGTTTTCTAATGGACATACAATAGATGTCCTTAAAGTT
* *
62813148 TGTTTTGTATTGGACATACATATATGATGTCCTTAAAGTT
1 TGTTTTCTAATGGACATACA-ATA-GATGTCCTTAAAGTT
62813188 GGCAATAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 17 0.50
38 3 0.09
40 14 0.41
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.43
Consensus pattern (38 bp):
TGTTTTCTAATGGACATACAATAGATGTCCTTAAAGTT
Found at i:62827336 original size:19 final size:19
Alignment explanation
Indices: 62827290--62827336 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
62827280 TCATCAGCTA
62827290 TAGG-CAAATAGATAGCAT
1 TAGGACAAATAGATAGCAT
*
62827308 TAGGATAAATAGATAGCAT
1 TAGGACAAATAGATAGCAT
*
62827327 TATGACAAAT
1 TAGGACAAAT
62827337 TTTCCAAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
18 4 0.16
19 21 0.84
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.26
Consensus pattern (19 bp):
TAGGACAAATAGATAGCAT
Found at i:62831684 original size:4 final size:4
Alignment explanation
Indices: 62831675--62831704 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
62831665 AGAATGCATG
62831675 TTTA TTTA TTTA TTTA TTTA TTTA -TTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
62831705 GGAACATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:62835247 original size:9 final size:9
Alignment explanation
Indices: 62835233--62835262 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
62835223 CTTAACTGTT
62835233 AAAAAAAGA
1 AAAAAAAGA
62835242 AAAAAAAGA
1 AAAAAAAGA
62835251 AAAAAAAGA
1 AAAAAAAGA
62835260 AAA
1 AAA
62835263 GACTAGATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:62840337 original size:31 final size:29
Alignment explanation
Indices: 62840301--62840375 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 29
62840291 AATTAAATTA
62840301 AAATTAAAATTT-TATGTATATATTTGAACC
1 AAATTAAAATTTATATGTATA-A-TTGAACC
** *
62840331 ACAATTAAGGTTTCATATGTATAATTGTACC
1 A-AATTAAAATTT-ATATGTATAATTGAACC
62840362 AAATTAAAATTTAT
1 AAATTAAAATTTAT
62840376 TTATTGAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
29 2 0.05
30 10 0.27
31 16 0.43
32 1 0.03
33 8 0.22
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (29 bp):
AAATTAAAATTTATATGTATAATTGAACC
Found at i:62846459 original size:23 final size:23
Alignment explanation
Indices: 62846409--62846459 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
62846399 AATTTAGACC
* * *
62846409 TTTAATAATTTATAAAATTTTAA
1 TTTAATAAATGATAAAATTATAA
* *
62846432 ATTAATAAATGATAAAATTATAT
1 TTTAATAAATGATAAAATTATAA
62846455 TTTAA
1 TTTAA
62846460 CTCTCAAAAA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
TTTAATAAATGATAAAATTATAA
Found at i:62850673 original size:30 final size:30
Alignment explanation
Indices: 62850627--62850750 Score: 203
Period size: 30 Copynumber: 4.1 Consensus size: 30
62850617 TTTTATTATG
*
62850627 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
62850658 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
62850688 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * *
62850718 CTATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
62850748 CCA
1 CCA
62850751 TAAATATGGA
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
30 81 0.92
31 7 0.08
ACGTcount: A:0.26, C:0.24, G:0.06, T:0.44
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:62850682 original size:15 final size:15
Alignment explanation
Indices: 62850637--62850744 Score: 78
Period size: 15 Copynumber: 7.2 Consensus size: 15
62850627 CCAATATCTC
62850637 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
62850652 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
62850667 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
62850682 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
62850697 GATACCCATATCTTT
1 GATACCCATATCTTT
** * *
62850712 GACTTTCTAT-TATTT
1 GA-TACCCATATCTTT
62850727 GATACCCATATCTTT
1 GATACCCATATCTTT
62850742 GAT
1 GAT
62850745 TTTCCATAAA
Statistics
Matches: 67, Mismatches: 20, Indels: 12
0.68 0.20 0.12
Matches are distributed among these distances:
14 12 0.18
15 43 0.64
16 12 0.18
ACGTcount: A:0.26, C:0.22, G:0.07, T:0.44
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:62855371 original size:30 final size:30
Alignment explanation
Indices: 62855321--62855444 Score: 194
Period size: 30 Copynumber: 4.1 Consensus size: 30
62855311 TTTTATTATG
*
62855321 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
*
62855352 CCAATATTTGATACTCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
62855382 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * *
62855412 CTATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
62855442 CCA
1 CCA
62855445 TAAATATGGA
Statistics
Matches: 86, Mismatches: 7, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
30 79 0.92
31 7 0.08
ACGTcount: A:0.26, C:0.23, G:0.06, T:0.44
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:62858421 original size:30 final size:31
Alignment explanation
Indices: 62858364--62858421 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 31
62858354 ATATTTCAAG
**
62858364 TCCCTGTATTTTTTGTTTATTTAAAATTTAA
1 TCCCTGTATTTTTTGTGGATTTAAAATTTAA
* *
62858395 TCCCTTTATTTTTT-TGGATTTGAAATT
1 TCCCTGTATTTTTTGTGGATTTAAAATT
62858422 CAGGTCTACG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
30 10 0.43
31 13 0.57
ACGTcount: A:0.22, C:0.10, G:0.09, T:0.59
Consensus pattern (31 bp):
TCCCTGTATTTTTTGTGGATTTAAAATTTAA
Found at i:62860303 original size:21 final size:21
Alignment explanation
Indices: 62860279--62860327 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
62860269 ATTAAAGAGC
*
62860279 AAATTGATAT-TTTTTGTTAAA
1 AAATTGATATATTTATGTT-AA
* *
62860300 AAATTCATCTATTTATGTTAA
1 AAATTGATATATTTATGTTAA
62860321 AAATTGA
1 AAATTGA
62860328 CATAATTAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.41, C:0.04, G:0.08, T:0.47
Consensus pattern (21 bp):
AAATTGATATATTTATGTTAA
Found at i:62864972 original size:205 final size:204
Alignment explanation
Indices: 62864508--62865186 Score: 984
Period size: 205 Copynumber: 3.3 Consensus size: 204
62864498 AGCAGTTAAC
*
62864508 ATACAGTTTTCAAGCATTACAAGATGGAAACACTATATCATGCATCCATCTTAAGGCATTCAACT
1 ATACAGTTTTCAAGCATTACAAGATGGAAACACTATATCATGCATCCATATTAAGGCATTCAACT
* * * * **
62864573 TGCATTTTATATGGTACAATTATCCAAAAGAAATCAAGGCAGAGCAGTGGAACAAT-AAAATCAG
66 TACA-TTTATATGGTACAAATATCCAAATGAAAACAAGGCAGAGCAGCAGAAC-ATGAAAATCAG
*
62864637 CAGTTCAATGACAGAAATATTACTAATTTTTGAAACACAAAACACAA-ATGCAATTATACTTTCA
129 CAGTT-AATGACAGAAATATTACTAA-TTTTGATACACAAAACACAAGATGCAATTATACTTTCA
62864701 TCCACTCTGGTTTAT
192 TCCACTCTGG-TT-T
62864716 ATACAGTTTTCAAGCATTACAAGATGGAAACACTATATCATGCATCCATATTAAGGCATTCAACT
1 ATACAGTTTTCAAGCATTACAAGATGGAAACACTATATCATGCATCCATATTAAGGCATTCAACT
* * *
62864781 TACATCTTATATGGTACAACTATCCAAATGAAAACAAGGGAGAGCAGCAGAACATGAAAATTAGC
66 TACAT-TTATATGGTACAAATATCCAAATGAAAACAAGGCAGAGCAGCAGAACATGAAAATCAGC
* *
62864846 AGTTAATGACAGAAATATTGCTAATTTTGATACACAAAACACAAGATGCAATAATAC-TTCAATC
130 AGTTAATGACAGAAATATTACTAATTTTGATACACAAAACACAAGATGCAATTATACTTTC-ATC
62864910 CACTCTGGTTT
194 CACTCTGGTTT
62864921 ATACAGTTTTCAAGCATTACAAGATGGAAACACTATATCATGCATCCATATTAAGGCATTCAACT
1 ATACAGTTTTCAAGCATTACAAGATGGAAACACTATATCATGCATCCATATTAAGGCATTCAACT
*
62864986 TACATTATATATGGTA-AAATCATCCAAATGAAAACAAGGCAGAGCAGCAGAACATGCAAATCAG
66 TACATT-TATATGGTACAAAT-ATCCAAATGAAAACAAGGCAGAGCAGCAGAACATGAAAATCAG
* *
62865050 CAGTTAATGACGGAAATATTAATAA-TTT--T----AAAACACAAGATGCAATTATACTTTCATC
129 CAGTTAATGACAGAAATATTACTAATTTTGATACACAAAACACAAGATGCAATTATACTTTCATC
*
62865108 CATTCTGGTTT
194 CACTCTGGTTT
* * * *
62865119 ATACACAGTTTTCAAGCATTACAAGATAGAAACACCATACCATGCATCCTTATTAAGGCATTCAA
1 AT--ACAGTTTTCAAGCATTACAAGATGGAAACACTATATCATGCATCCATATTAAGGCATTCAA
62865184 CTT
64 CTT
62865187 TCTAATTTCT
Statistics
Matches: 437, Mismatches: 25, Indels: 26
0.90 0.05 0.05
Matches are distributed among these distances:
198 36 0.08
199 3 0.01
200 60 0.14
202 1 0.00
204 7 0.02
205 142 0.32
206 24 0.05
207 44 0.10
208 120 0.27
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.28
Consensus pattern (204 bp):
ATACAGTTTTCAAGCATTACAAGATGGAAACACTATATCATGCATCCATATTAAGGCATTCAACT
TACATTTATATGGTACAAATATCCAAATGAAAACAAGGCAGAGCAGCAGAACATGAAAATCAGCA
GTTAATGACAGAAATATTACTAATTTTGATACACAAAACACAAGATGCAATTATACTTTCATCCA
CTCTGGTTT
Found at i:62870053 original size:33 final size:33
Alignment explanation
Indices: 62870008--62870072 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
62869998 CAAAAACAGA
*
62870008 ACCAATACCAAAACAAAATACACTCTCTCATGT
1 ACCAATACCAAAACAAAATACACTCTCCCATGT
* *
62870041 ACCAATATCAAAACAAAATGCACTCTCCCATG
1 ACCAATACCAAAACAAAATACACTCTCCCATG
62870073 GATAAAAACA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.45, C:0.31, G:0.05, T:0.20
Consensus pattern (33 bp):
ACCAATACCAAAACAAAATACACTCTCCCATGT
Found at i:62872565 original size:12 final size:12
Alignment explanation
Indices: 62872548--62872580 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
62872538 TCATTGTGTG
62872548 TGTTCTTTTTGT
1 TGTTCTTTTTGT
62872560 TGTTC-TTTTGT
1 TGTTCTTTTTGT
62872571 TGCTTCTTTT
1 TG-TTCTTTT
62872581 AGCATAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 8 0.42
12 8 0.42
13 3 0.16
ACGTcount: A:0.00, C:0.12, G:0.15, T:0.73
Consensus pattern (12 bp):
TGTTCTTTTTGT
Found at i:62875878 original size:14 final size:16
Alignment explanation
Indices: 62875842--62875881 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 16
62875832 TAAATTATTA
62875842 ATAAATTTATATTTTC
1 ATAAATTTATATTTTC
*
62875858 AT-TATTT-TATTTT-
1 ATAAATTTATATTTTC
62875871 ATAAATTTATA
1 ATAAATTTATA
62875882 AAATAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 5
0.74 0.07 0.19
Matches are distributed among these distances:
13 2 0.10
14 10 0.50
15 6 0.30
16 2 0.10
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (16 bp):
ATAAATTTATATTTTC
Found at i:62876454 original size:18 final size:20
Alignment explanation
Indices: 62876431--62876468 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
62876421 TTTTTTATTA
62876431 AAATAATA-TAAAA-AATTT
1 AAATAATATTAAAATAATTT
62876449 AAATAATATTAAAATAATTT
1 AAATAATATTAAAATAATTT
62876469 TTTTATTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.44
19 5 0.28
20 5 0.28
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAATAATATTAAAATAATTT
Found at i:62876463 original size:11 final size:11
Alignment explanation
Indices: 62876426--62876466 Score: 54
Period size: 11 Copynumber: 4.1 Consensus size: 11
62876416 GGGGTTTTTT
62876426 TATTAAAATAA
1 TATTAAAATAA
62876437 TA-TAAAA-AA
1 TATTAAAATAA
62876446 T-TT-AAATAA
1 TATTAAAATAA
62876455 TATTAAAATAA
1 TATTAAAATAA
62876466 T
1 T
62876467 TTTTTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
8 3 0.12
9 7 0.27
10 7 0.27
11 9 0.35
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
TATTAAAATAA
Found at i:62882944 original size:3 final size:3
Alignment explanation
Indices: 62882894--62882932 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
62882884 GCTTCCCTTC
62882894 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
62882933 CGTTGTTATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:62895114 original size:37 final size:37
Alignment explanation
Indices: 62894996--62895115 Score: 97
Period size: 37 Copynumber: 3.3 Consensus size: 37
62894986 TTAGGCACTG
*
62894996 AATATTTAAAAAATGTG-AAAAA-CATTATTTGTTGAAT
1 AATATTT-AAAAATGTGAAAAAAGCATT-TTTGTTGAAA
* * ** * *
62895033 AATA-ATAATAACAT-AAAAAAGACATTTTTTTTGTTAA
1 AATATTTAAAAATGTGAAAAAAG-CATTTTTGTTG-AAA
*
62895070 AA-CTTTAAAAATGTGAAAAAAGCATTTTTGTTGAAA
1 AATATTTAAAAATGTGAAAAAAGCATTTTTGTTGAAA
62895106 AATATTTAAA
1 AATATTTAAA
62895116 TTAATAATTT
Statistics
Matches: 61, Mismatches: 15, Indels: 14
0.68 0.17 0.16
Matches are distributed among these distances:
35 10 0.16
36 11 0.18
37 33 0.54
38 7 0.11
ACGTcount: A:0.50, C:0.04, G:0.09, T:0.37
Consensus pattern (37 bp):
AATATTTAAAAATGTGAAAAAAGCATTTTTGTTGAAA
Found at i:62906440 original size:3 final size:3
Alignment explanation
Indices: 62906427--62906456 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
62906417 CCATTTCATA
62906427 ATT ATT A-T ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
62906457 ATTTATTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:62907755 original size:15 final size:16
Alignment explanation
Indices: 62907735--62907764 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
62907725 AATGTTTAAA
62907735 ATATTTTTA-AATTTT
1 ATATTTTTACAATTTT
62907750 ATATTTTTACAATTT
1 ATATTTTTACAATTT
62907765 CTTGTAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (16 bp):
ATATTTTTACAATTTT
Found at i:62907832 original size:26 final size:27
Alignment explanation
Indices: 62907792--62907842 Score: 79
Period size: 26 Copynumber: 1.9 Consensus size: 27
62907782 ATTTAATCAA
62907792 ATTTATTTTTTTATTT-TTT-AAATAT
1 ATTTATTTTTTTATTTCTTTGAAATAT
62907817 ATTTAATTTTTTTATTTCTTTGAAAT
1 ATTT-ATTTTTTTATTTCTTTGAAAT
62907843 TTTAACAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 4 0.17
26 12 0.52
27 3 0.13
28 4 0.17
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (27 bp):
ATTTATTTTTTTATTTCTTTGAAATAT
Found at i:62909680 original size:14 final size:14
Alignment explanation
Indices: 62909661--62909687 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
62909651 GCTCCCTGCT
62909661 TCATTGCATGCATA
1 TCATTGCATGCATA
62909675 TCATTGCATGCAT
1 TCATTGCATGCAT
62909688 GAATGCATGC
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:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (14 bp):
TCATTGCATGCATA
Found at i:62911218 original size:33 final size:33
Alignment explanation
Indices: 62911181--62911256 Score: 107
Period size: 33 Copynumber: 2.3 Consensus size: 33
62911171 GTTGTCAGCC
62911181 TCATCTTCATCGTCATCATCAACAAATTCGCTA
1 TCATCTTCATCGTCATCATCAACAAATTCGCTA
* ** * *
62911214 TCATCTTCATTGTGGTCGTCAACGAATTCGCTA
1 TCATCTTCATCGTCATCATCAACAAATTCGCTA
62911247 TCATCTTCAT
1 TCATCTTCAT
62911257 AATCATCAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.25, C:0.28, G:0.11, T:0.37
Consensus pattern (33 bp):
TCATCTTCATCGTCATCATCAACAAATTCGCTA
Found at i:62911575 original size:42 final size:42
Alignment explanation
Indices: 62911516--62911600 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
62911506 CCGAGATGGG
*
62911516 ATCAAACTGGTCATGCTCGCCTGAGCCCCTATTATTATCATC
1 ATCAAACTGGCCATGCTCGCCTGAGCCCCTATTATTATCATC
*
62911558 ATCAAACTGGCCATGCTCGCCTGAGCTCCTATTATTATCATC
1 ATCAAACTGGCCATGCTCGCCTGAGCCCCTATTATTATCATC
62911600 A
1 A
62911601 CCACCATCTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.25, C:0.31, G:0.14, T:0.31
Consensus pattern (42 bp):
ATCAAACTGGCCATGCTCGCCTGAGCCCCTATTATTATCATC
Found at i:62912116 original size:17 final size:17
Alignment explanation
Indices: 62912094--62912132 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
62912084 GTGGTGCTTA
62912094 TTTCCGTAAATAATTCT
1 TTTCCGTAAATAATTCT
62912111 TTTCCGTAAATAATTCT
1 TTTCCGTAAATAATTCT
62912128 TTTCC
1 TTTCC
62912133 TATCCTATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.26, C:0.21, G:0.05, T:0.49
Consensus pattern (17 bp):
TTTCCGTAAATAATTCT
Found at i:62916009 original size:19 final size:19
Alignment explanation
Indices: 62915985--62916021 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
62915975 CAGACGCATG
62915985 AATAACAAAAACTCGAACC
1 AATAACAAAAACTCGAACC
* *
62916004 AATAACATAATCTCGAAC
1 AATAACAAAAACTCGAAC
62916022 TACATTACTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.54, C:0.24, G:0.05, T:0.16
Consensus pattern (19 bp):
AATAACAAAAACTCGAACC
Found at i:62918925 original size:29 final size:30
Alignment explanation
Indices: 62918875--62918943 Score: 70
Period size: 29 Copynumber: 2.3 Consensus size: 30
62918865 TCGCAAACTT
* *
62918875 AAAATTTAATCCTTATAATTTT-ATTTTTA
1 AAAATTTAATCCTTATAATTTTAAATTTCA
**
62918904 AAAATTTAATCTCTT-TGCTTTTCAAATTTCA
1 AAAATTTAATC-CTTATAATTTT-AAATTTCA
62918935 AAAATTTAA
1 AAAATTTAA
62918944 ATCCAATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 16 0.48
30 3 0.09
31 14 0.42
ACGTcount: A:0.39, C:0.10, G:0.01, T:0.49
Consensus pattern (30 bp):
AAAATTTAATCCTTATAATTTTAAATTTCA
Found at i:62919025 original size:30 final size:30
Alignment explanation
Indices: 62918989--62919074 Score: 102
Period size: 30 Copynumber: 2.8 Consensus size: 30
62918979 TAAATTGAAT
*
62918989 CTAAATTTTAAAATTTAAAAATTAGAAAGA
1 CTAAATTTTAAAATTTAAAAATTACAAAGA
* *
62919019 CTAAATTCTTAAAA-ATAAAAATAACAAAGA
1 CTAAATT-TTAAAATTTAAAAATTACAAAGA
*
62919049 CTAAATTTTAAATTTATAAGAAATTA
1 CTAAATTTTAAAATT-TAA-AAATTA
62919075 AAACATATTT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
29 5 0.11
30 27 0.59
31 9 0.20
32 5 0.11
ACGTcount: A:0.57, C:0.06, G:0.05, T:0.33
Consensus pattern (30 bp):
CTAAATTTTAAAATTTAAAAATTACAAAGA
Found at i:62919436 original size:18 final size:18
Alignment explanation
Indices: 62919413--62919450 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
62919403 ATTATTATGT
62919413 TGAGTTTGGTGTACATGA
1 TGAGTTTGGTGTACATGA
62919431 TGAGTTTGGTGTACATGA
1 TGAGTTTGGTGTACATGA
62919449 TG
1 TG
62919451 TTATCAGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.05, G:0.34, T:0.39
Consensus pattern (18 bp):
TGAGTTTGGTGTACATGA
Found at i:62925938 original size:59 final size:59
Alignment explanation
Indices: 62925846--62925967 Score: 244
Period size: 59 Copynumber: 2.1 Consensus size: 59
62925836 GCCCAGTATG
62925846 TTAATCTAGAAGGAAGTGTCATGCAAAGATCCAACAAGTTTTGGACTGGATATGCACGC
1 TTAATCTAGAAGGAAGTGTCATGCAAAGATCCAACAAGTTTTGGACTGGATATGCACGC
62925905 TTAATCTAGAAGGAAGTGTCATGCAAAGATCCAACAAGTTTTGGACTGGATATGCACGC
1 TTAATCTAGAAGGAAGTGTCATGCAAAGATCCAACAAGTTTTGGACTGGATATGCACGC
62925964 TTAA
1 TTAA
62925968 AACTGGAACT
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 63 1.00
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.26
Consensus pattern (59 bp):
TTAATCTAGAAGGAAGTGTCATGCAAAGATCCAACAAGTTTTGGACTGGATATGCACGC
Found at i:62929360 original size:21 final size:21
Alignment explanation
Indices: 62929331--62929370 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
62929321 ATATTTAATG
* *
62929331 TTTATTTTTTATTACTTTAAC
1 TTTAATTTTTATTAATTTAAC
*
62929352 TTTAATTTTTTTTAATTTA
1 TTTAATTTTTATTAATTTA
62929371 GCCCTTATTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTAATTTTTATTAATTTAAC
Found at i:62930304 original size:21 final size:22
Alignment explanation
Indices: 62930274--62930315 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
62930264 TTATTTTTAC
62930274 TTAATTAT-AAAATACATAAATA
1 TTAATTATAAAAATACA-AAATA
62930296 TTAA-TATAAAAATACAAAAT
1 TTAATTATAAAAATACAAAAT
62930316 GTCGTGTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (22 bp):
TTAATTATAAAAATACAAAATA
Found at i:62933590 original size:17 final size:18
Alignment explanation
Indices: 62933546--62933591 Score: 51
Period size: 17 Copynumber: 2.6 Consensus size: 18
62933536 GTGTATGTGT
* *
62933546 ATATATATGTATATAAAA
1 ATATATAAGTACATAAAA
62933564 AT-TATAAAGTACA-AAAA
1 ATATAT-AAGTACATAAAA
62933581 ATATATAAGTA
1 ATATATAAGTA
62933592 GGTATACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
17 14 0.58
18 10 0.42
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.33
Consensus pattern (18 bp):
ATATATAAGTACATAAAA
Found at i:62934809 original size:18 final size:18
Alignment explanation
Indices: 62934786--62934829 Score: 65
Period size: 16 Copynumber: 2.6 Consensus size: 18
62934776 AAATGTACAA
62934786 ATATATAAAAAATATAAT
1 ATATATAAAAAATATAAT
*
62934804 ATATAT--GAAATATAAT
1 ATATATAAAAAATATAAT
62934820 ATATATAAAA
1 ATATATAAAA
62934830 GTTAAAAGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 15 0.68
18 7 0.32
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (18 bp):
ATATATAAAAAATATAAT
Found at i:62935242 original size:3 final size:3
Alignment explanation
Indices: 62935224--62935258 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
62935214 GAATATACAG
* *
62935224 ATA ATG ATA GTA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
62935259 TTTTTTTTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:62940175 original size:16 final size:16
Alignment explanation
Indices: 62940134--62940179 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
62940124 AATCTAAAAA
62940134 TATAAAAAAATAAATT
1 TATAAAAAAATAAATT
*
62940150 TATTAAAAAATAAATT
1 TATAAAAAAATAAATT
62940166 TA-AAAGAAAA-AAAT
1 TATAAA-AAAATAAAT
62940180 CACATCAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 6 0.22
16 21 0.78
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (16 bp):
TATAAAAAAATAAATT
Found at i:62960427 original size:20 final size:20
Alignment explanation
Indices: 62960392--62960447 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
62960382 CACTAAAAAA
* *
62960392 ATATAAAACTAGAAATAAAT
1 ATATAAAAATAAAAATAAAT
**
62960412 ATATAAAAATAAAAATGTAT
1 ATATAAAAATAAAAATAAAT
*
62960432 TTATAAAATATAAAAA
1 ATATAAAA-ATAAAAA
62960448 ACATATAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 23 0.77
21 7 0.23
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.29
Consensus pattern (20 bp):
ATATAAAAATAAAAATAAAT
Found at i:62960456 original size:18 final size:18
Alignment explanation
Indices: 62960385--62960476 Score: 62
Period size: 18 Copynumber: 4.9 Consensus size: 18
62960375 ATATATACAC
62960385 TAAAAAA-ATATAAAACTA
1 TAAAAAATATATAAAA-TA
*
62960403 GAAATAAATATATAAAA-A
1 TAAA-AAATATATAAAATA
*
62960421 TAAAAATGTATTTATAAAATA
1 TAAAAA---ATATATAAAATA
* * *
62960442 TAAAAAACATATAAATTG
1 TAAAAAATATATAAAATA
*
62960460 TAAAAAAAATTATAAAA
1 TAAAAAATA-TATAAAA
62960477 AAATAAAATT
Statistics
Matches: 58, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
17 2 0.03
18 23 0.40
19 9 0.16
20 17 0.29
21 7 0.12
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.27
Consensus pattern (18 bp):
TAAAAAATATATAAAATA
Found at i:62960468 original size:29 final size:27
Alignment explanation
Indices: 62960436--62960499 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 27
62960426 ATGTATTTAT
62960436 AAAATATAAAAAACATATAAATTGTA-AAA
1 AAAATATAAAAAA-ATA-AAATT-TACAAA
62960465 AAAATTATAAAAAAATAAAATTTACAAA
1 AAAA-TATAAAAAAATAAAATTTACAAA
62960493 AGAAATA
1 A-AAATA
62960500 CGAAAAGAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
27 2 0.06
28 11 0.34
29 10 0.31
30 9 0.28
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.23
Consensus pattern (27 bp):
AAAATATAAAAAAATAAAATTTACAAA
Found at i:62960565 original size:18 final size:19
Alignment explanation
Indices: 62960523--62960558 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
62960513 GTTGAAATTA
*
62960523 ATAATATTATTAAAAAAGT
1 ATAAAATTATTAAAAAAGT
62960542 ATAAAATTA-TAAAAAAG
1 ATAAAATTATTAAAAAAG
62960559 CTTAAAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.31
Consensus pattern (19 bp):
ATAAAATTATTAAAAAAGT
Found at i:62964598 original size:21 final size:22
Alignment explanation
Indices: 62964569--62964615 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
62964559 CAGAAGGAGT
*
62964569 GAGTAGTACTTCACAGCAGGTG
1 GAGTAGTACTCCACAGCAGGTG
*
62964591 GAGT-GTACTCCGCAGCAGGTG
1 GAGTAGTACTCCACAGCAGGTG
62964612 GAGT
1 GAGT
62964616 TTGAGCAGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.23, C:0.19, G:0.36, T:0.21
Consensus pattern (22 bp):
GAGTAGTACTCCACAGCAGGTG
Found at i:62976384 original size:12 final size:12
Alignment explanation
Indices: 62976367--62976400 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
62976357 TAAACAAGTC
**
62976367 ATAAACGAGCTT
1 ATAAACGAGCCA
62976379 ATAAACGAGCCA
1 ATAAACGAGCCA
62976391 ATAAACGAGC
1 ATAAACGAGC
62976401 ATAGACGAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.47, C:0.21, G:0.18, T:0.15
Consensus pattern (12 bp):
ATAAACGAGCCA
Found at i:62978067 original size:7 final size:7
Alignment explanation
Indices: 62978055--62978079 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
62978045 TTCAGTAAGT
62978055 TTTTAAA
1 TTTTAAA
62978062 TTTTAAA
1 TTTTAAA
62978069 TTTTAAA
1 TTTTAAA
62978076 TTTT
1 TTTT
62978080 TTCTGGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (7 bp):
TTTTAAA
Found at i:62981153 original size:102 final size:102
Alignment explanation
Indices: 62980982--62981191 Score: 393
Period size: 102 Copynumber: 2.1 Consensus size: 102
62980972 TTTCCTTCTT
*
62980982 ATCTCTCTTCCCCTTTGCACTCTCTTTATTTCTGGATTCATTTCAACTTACTTGCATGTGTTTAT
1 ATCTGTCTTCCCCTTTGCACTCTCTTTATTTCTGGATTCATTTCAACTTACTTGCATGTGTTTAT
62981047 TTATTCAGATTTCAAACCCAATTGAGTCACCAAGTCC
66 TTATTCAGATTTCAAACCCAATTGAGTCACCAAGTCC
*
62981084 ATCTGTCTTCCCCTTTGCACTCTCTTTATTTCTGGATTCATTTCAACTTACTTGTATGTGTTTAT
1 ATCTGTCTTCCCCTTTGCACTCTCTTTATTTCTGGATTCATTTCAACTTACTTGCATGTGTTTAT
*
62981149 TTATTCAGATTTTAAACCCAATTGAGTCACCAAGTCC
66 TTATTCAGATTTCAAACCCAATTGAGTCACCAAGTCC
62981186 ATCTGT
1 ATCTGT
62981192 GAAGAAGTGT
Statistics
Matches: 105, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
102 105 1.00
ACGTcount: A:0.21, C:0.25, G:0.10, T:0.43
Consensus pattern (102 bp):
ATCTGTCTTCCCCTTTGCACTCTCTTTATTTCTGGATTCATTTCAACTTACTTGCATGTGTTTAT
TTATTCAGATTTCAAACCCAATTGAGTCACCAAGTCC
Found at i:62988123 original size:5 final size:5
Alignment explanation
Indices: 62988113--62988137 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
62988103 ATATCAACAT
62988113 TTTAA TTTAA TTTAA TTTAA TTTAA
1 TTTAA TTTAA TTTAA TTTAA TTTAA
62988138 ACAATTATCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTTAA
Found at i:62990514 original size:28 final size:28
Alignment explanation
Indices: 62990465--62990520 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
62990455 TTTAAAATAT
* * **
62990465 TTTTAAAATACTTTTTTTAATTTTTTAA
1 TTTTAAAATACGTCTTAAAATTTTTTAA
62990493 TTTTAAAATACGTCTTAAAATTTTTTAA
1 TTTTAAAATACGTCTTAAAATTTTTTAA
62990521 AATAAAAATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (28 bp):
TTTTAAAATACGTCTTAAAATTTTTTAA
Found at i:63000380 original size:31 final size:31
Alignment explanation
Indices: 63000344--63000404 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
63000334 TTAGTCCCTG
*
63000344 AACTTGACAATTGTTCCCAGATTAGGGCCTA
1 AACTTGACAATTGTTCCCACATTAGGGCCTA
*
63000375 AACTTGACAATTGTTCCCACATTATGGCCT
1 AACTTGACAATTGTTCCCACATTAGGGCCT
63000405 GAACCATGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (31 bp):
AACTTGACAATTGTTCCCACATTAGGGCCTA
Found at i:63000849 original size:4 final size:4
Alignment explanation
Indices: 63000840--63000888 Score: 98
Period size: 4 Copynumber: 12.2 Consensus size: 4
63000830 CTTATGAGAC
63000840 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
63000888 C
1 C
63000889 CTTAGAGCTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:63004374 original size:13 final size:13
Alignment explanation
Indices: 63004347--63004383 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
63004337 CATTTTTAAG
*
63004347 TTTATA-ATAATT
1 TTTATATATTATT
63004359 TTTATATATTATT
1 TTTATATATTATT
63004372 TTTATATATTAT
1 TTTATATATTAT
63004384 GTAATTTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 6 0.26
13 17 0.74
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
TTTATATATTATT
Found at i:63004464 original size:11 final size:10
Alignment explanation
Indices: 63004448--63004499 Score: 50
Period size: 11 Copynumber: 5.0 Consensus size: 10
63004438 TAATTAAACA
63004448 TTAAAATAAT
1 TTAAAATAAT
63004458 GTTAAAATAAT
1 -TTAAAATAAT
* *
63004469 ATAATATAATT
1 TTAAAATAA-T
*
63004480 TTAAAAAAAT
1 TTAAAATAAT
*
63004490 TCAAAATAAT
1 TTAAAATAAT
63004500 ATGGGTGGGC
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
10 16 0.48
11 17 0.52
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (10 bp):
TTAAAATAAT
Found at i:63004498 original size:21 final size:21
Alignment explanation
Indices: 63004449--63004499 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
63004439 AATTAAACAT
*
63004449 TAAAATAATGTTAAAATAATA
1 TAAAATAATGTTAAAAAAATA
* *
63004470 TAATATAATTTTAAAAAAAT-
1 TAAAATAATGTTAAAAAAATA
63004490 TCAAAATAAT
1 T-AAAATAAT
63004500 ATGGGTGGGC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 1 0.04
21 24 0.96
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (21 bp):
TAAAATAATGTTAAAAAAATA
Found at i:63012339 original size:24 final size:24
Alignment explanation
Indices: 63012312--63012363 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
63012302 TTAGTAAGTC
*
63012312 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
63012336 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
63012360 AAAT
1 AAAT
63012364 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Done.