Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold498
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: 1804022
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.36
File 14 of 17
Found at i:1422017 original size:30 final size:30
Alignment explanation
Indices: 1421976--1422032 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
1421966 TCTACTTCTG
* *
1421976 GTTGCCGATCTGGTTTTGATTGCTGTTACT
1 GTTGCCGATCTGCTTCTGATTGCTGTTACT
* *
1422006 GTTGTCGATCTGCTTCTGGTTGCTGTT
1 GTTGCCGATCTGCTTCTGATTGCTGTT
1422033 GTGATTGTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.07, C:0.18, G:0.28, T:0.47
Consensus pattern (30 bp):
GTTGCCGATCTGCTTCTGATTGCTGTTACT
Found at i:1422105 original size:22 final size:22
Alignment explanation
Indices: 1422047--1422098 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
1422037 TTGTTGATTG
* * *
1422047 TTGCTATTGCTATTAGGTTTAT
1 TTGCTACTGCTGTTAGGTTTAA
*
1422069 TTGCTGCTGCTGTTAGGTTTAA
1 TTGCTACTGCTGTTAGGTTTAA
1422091 TTGCTACT
1 TTGCTACT
1422099 AGTGTTAAGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.15, C:0.13, G:0.21, T:0.50
Consensus pattern (22 bp):
TTGCTACTGCTGTTAGGTTTAA
Found at i:1422273 original size:45 final size:45
Alignment explanation
Indices: 1422177--1422275 Score: 153
Period size: 45 Copynumber: 2.2 Consensus size: 45
1422167 TTTGTTACTT
* * *
1422177 TTTTTAATTGGGTTTTAATTGGATTTATGTTTAAGTTTATATAGA
1 TTTTTAGTTGGGTTTGAATTGGATTTAGGTTTAAGTTTATATAGA
* *
1422222 TTTTTAGTTGGGTTTGAATTGGGTTTGGGTTTAAGTTTATATAGA
1 TTTTTAGTTGGGTTTGAATTGGATTTAGGTTTAAGTTTATATAGA
1422267 TTTTTAGTT
1 TTTTTAGTT
1422276 TGTGTTAAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.56
Consensus pattern (45 bp):
TTTTTAGTTGGGTTTGAATTGGATTTAGGTTTAAGTTTATATAGA
Found at i:1422300 original size:45 final size:45
Alignment explanation
Indices: 1422177--1422305 Score: 136
Period size: 45 Copynumber: 2.9 Consensus size: 45
1422167 TTTGTTACTT
* * * * *
1422177 TTTTTAATTGGGTTTTAATTGGATTTATGTTTAAGTTTATATAGA
1 TTTTTAGTTGGGTTTGAAATGGGTTTACGTTTAAGTTTATATAGA
* **
1422222 TTTTTAGTTGGGTTTGAATTGGGTTTGGGTTTAAGTTTATATAGA
1 TTTTTAGTTGGGTTTGAAATGGGTTTACGTTTAAGTTTATATAGA
* *
1422267 TTTTTAGTT-TGTGTT-AAATGGGTTTAACTTTTAAGTTTA
1 TTTTTAGTTGGGT-TTGAAATGGGTTT-ACGTTTAAGTTTA
1422306 AATTTATATT
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
44 11 0.15
45 61 0.85
ACGTcount: A:0.23, C:0.01, G:0.22, T:0.54
Consensus pattern (45 bp):
TTTTTAGTTGGGTTTGAAATGGGTTTACGTTTAAGTTTATATAGA
Found at i:1424593 original size:25 final size:27
Alignment explanation
Indices: 1424544--1424594 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
1424534 ATTACGTCTT
* *
1424544 ATATTTTATATTATAATTATATTTAAA
1 ATATTATATATTATAATAATATTTAAA
1424571 ATATTATATATT-TAATAAT-TTTAA
1 ATATTATATATTATAATAATATTTAA
1424595 TATGATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 5 0.23
26 6 0.27
27 11 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
ATATTATATATTATAATAATATTTAAA
Found at i:1426502 original size:13 final size:13
Alignment explanation
Indices: 1426475--1426509 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
1426465 TTTCATGTGT
*
1426475 AAATATTT-TTTA
1 AAATATTTAATTA
1426487 AAATATTTAATTA
1 AAATATTTAATTA
1426500 AAATATTTAA
1 AAATATTTAA
1426510 ATTTTATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 8 0.38
13 13 0.62
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (13 bp):
AAATATTTAATTA
Found at i:1426523 original size:45 final size:45
Alignment explanation
Indices: 1426438--1426524 Score: 106
Period size: 45 Copynumber: 1.9 Consensus size: 45
1426428 AAAAATTAAA
* * *
1426438 TTTAAGATATTTAATTATAATTAAAATTTTCATGTGTAAATATTT
1 TTTAAAATATTTAATTAAAATTAAAATTTTCATATGTAAATATTT
*
1426483 TTTAAAATATTTAATTAAAATATTTAAATTTT-ATAT-TAAATA
1 TTTAAAATATTTAATT-AAA-ATTAAAATTTTCATATGTAAATA
1426525 ATATTTATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
45 21 0.58
46 5 0.14
47 10 0.28
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (45 bp):
TTTAAAATATTTAATTAAAATTAAAATTTTCATATGTAAATATTT
Found at i:1428719 original size:108 final size:108
Alignment explanation
Indices: 1428511--1428731 Score: 275
Period size: 108 Copynumber: 2.0 Consensus size: 108
1428501 AATACTTTGC
* * * * * *
1428511 AATCACCTGCAGAAGATGAAATTGACTGGATAAAGATGAATAACTTTCTAAGTGCAATGCCTGAG
1 AATCGCCTGCAGAACATGAAATTGAATGGATAAAGATGAACAACTTGCTAAGTGCAATACCTGAG
* * *
1428576 AAAAAATCATGTAAACTGAGAGATGAGACGAATGCTGACTGCA
66 AAAAAATCATGTAAACAGACAGATCAGACGAATGCTGACTGCA
* *
1428619 AATCGCCTGCTGAACATGAAATTGAATGGGTAAAGATGAACAACTTGCTAAGTGCAA-ACCATGA
1 AATCGCCTGCAGAACATGAAATTGAATGGATAAAGATGAACAACTTGCTAAGTGCAATACC-TGA
** * *
1428683 GAAAAGTTTATGTAAACAGACAGATCAGAC-AGATGCTGACTGCC
65 GAAAAAATCATGTAAACAGACAGATCAGACGA-ATGCTGACTGCA
1428727 AATCG
1 AATCG
1428732 GCTCTTCTCC
Statistics
Matches: 96, Mismatches: 15, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
107 3 0.03
108 93 0.97
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.22
Consensus pattern (108 bp):
AATCGCCTGCAGAACATGAAATTGAATGGATAAAGATGAACAACTTGCTAAGTGCAATACCTGAG
AAAAAATCATGTAAACAGACAGATCAGACGAATGCTGACTGCA
Found at i:1430786 original size:15 final size:16
Alignment explanation
Indices: 1430750--1430789 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
1430740 TTTAATATTT
*
1430750 ATAAAATTTTTAATTAA
1 ATAAAA-TTATAATTAA
1430767 ATAAAATTATAATT-A
1 ATAAAATTATAATTAA
1430782 ATAAAATT
1 ATAAAATT
1430790 TATTTTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.41
16 7 0.32
17 6 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAAAATTATAATTAA
Found at i:1430792 original size:16 final size:17
Alignment explanation
Indices: 1430750--1430792 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
1430740 TTTAATATTT
*
1430750 ATAAAATTTTTAATTAA
1 ATAAAATTTATAATTAA
1430767 ATAAAA-TTATAATT-A
1 ATAAAATTTATAATTAA
1430782 ATAAAATTTAT
1 ATAAAATTTAT
1430793 TTTAAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 7 0.29
16 11 0.46
17 6 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAAAATTTATAATTAA
Found at i:1431912 original size:17 final size:17
Alignment explanation
Indices: 1431872--1431920 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
1431862 AATCCCTTCC
1431872 CTTTCCTTTTCTTTCTA
1 CTTTCCTTTTCTTTCTA
** *
1431889 CGCTCCTTTTCTTTCTT
1 CTTTCCTTTTCTTTCTA
*
1431906 TTTTCCTTGTTCTTT
1 CTTTCCTT-TTCTTT
1431921 TGTTTGCTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
17 19 0.76
18 6 0.24
ACGTcount: A:0.02, C:0.29, G:0.04, T:0.65
Consensus pattern (17 bp):
CTTTCCTTTTCTTTCTA
Found at i:1432397 original size:16 final size:16
Alignment explanation
Indices: 1432368--1432412 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
1432358 ATATACAATA
* *
1432368 TTTTTCTTTCTCTCCT
1 TTTTTTTTTTTCTCCT
1432384 TTTTTTTTTTTCTCCT
1 TTTTTTTTTTTCTCCT
1432400 TTCTTTCTTTTTT
1 TT-TTT-TTTTTT
1432413 TTTTCTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 16 0.64
17 3 0.12
18 6 0.24
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTTTTTTTTCTCCT
Found at i:1432420 original size:19 final size:19
Alignment explanation
Indices: 1432368--1432431 Score: 58
Period size: 19 Copynumber: 3.2 Consensus size: 19
1432358 ATATACAATA
* *
1432368 TTTTTCTTTCTCTCCTTT-T
1 TTTTTTTTTCT-TTCTTTCT
1432387 TTTTTTTTCTCCTTTCTTTCT
1 TTTTTTTT-T-CTTTCTTTCT
*
1432408 TTTTTTTTTCTTTATTTCT
1 TTTTTTTTTCTTTCTTTCT
1432427 GTTTT
1 -TTTT
1432432 CACCAAACAT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
19 16 0.42
20 11 0.29
21 11 0.29
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.78
Consensus pattern (19 bp):
TTTTTTTTTCTTTCTTTCT
Found at i:1432515 original size:3 final size:3
Alignment explanation
Indices: 1432507--1432549 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
1432497 GTATATATAG
1432507 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1432550 GATAATCCGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1434277 original size:310 final size:310
Alignment explanation
Indices: 1433715--1434320 Score: 933
Period size: 310 Copynumber: 2.0 Consensus size: 310
1433705 AGATCAGGTA
* * * * *
1433715 CTAGTCCAAATTCTTTCAGTTGAGTCAGCATAACAGCAACTTCATCAATCCATCTCTGTTTTCCA
1 CTAGTCCAAATTATTTCAGTTCAGTCAGCACAACAGCAACTTAATCAATCCATCTCTGTTGTCCA
* * * *
1433780 TAAATATTGATCGTAATGTTGAATGTATAGTGGTTTAAAGCAAAATTCAATTCCTTCATCCTCTG
66 TAAATATTGATCATAATGTTGAATGTAGAGTGGTCTAAACCAAAATTCAATTCCTTCATCCTCTG
** * *
1433845 CAAGACACTTCTAAATTTCTCCATTGGCCTTCATTCCCATATGCATCCAACACACAATTGTAGGC
131 CAAGACACTTCTAAATTAATCCATTGACCTTCATTCCCATATGCATCCAACACACAATCGTAGGC
1433910 TTCAAGGGAAACTAAAAAACCATTGAATTGCATTTCCCAAACAGTTGATGACATCTTCTTGGAGT
196 TTCAAGGGAAACTAAAAAACCATTGAATTGCATTTCCCAAACAGTTGATGACATCTTCTTGGAGT
**
1433975 CCTTATTTTGACCATAGGCAGATTATAATAGTATTGCAACAGTTCAGTTG
261 CCTTATTTCAACCATAGGCAGATTATAATAGTATTGCAACAGTTCAGTTG
* ***
1434025 CTAGTCCAAATTATTTCATTTCAGTCAGCACAGTGGCAACTTAATCAATCCATCTCTGTTGTCCA
1 CTAGTCCAAATTATTTCAGTTCAGTCAGCACAACAGCAACTTAATCAATCCATCTCTGTTGTCCA
* * *
1434090 TAAATATTGATCATAATGTTGAATGTAGAGTGGTCTAAACCACATTTCAATTGCTTCATCCTCTG
66 TAAATATTGATCATAATGTTGAATGTAGAGTGGTCTAAACCAAAATTCAATTCCTTCATCCTCTG
* * *
1434155 CAAGACACTTTTAAATTAATCCATTGACCTTCTTTCCCATATGCATCCAACATACAATCGTAGGC
131 CAAGACACTTCTAAATTAATCCATTGACCTTCATTCCCATATGCATCCAACACACAATCGTAGGC
* ** * *
1434220 TTCAAGGGAAACTGAAAAACCATTGAATTGCATTTTTCTAACAGTTGATGACATCTTCTTGGCGT
196 TTCAAGGGAAACTAAAAAACCATTGAATTGCATTTCCCAAACAGTTGATGACATCTTCTTGGAGT
*
1434285 CCTTATTTCAACCATTGGCAGATTATAATAGTATTG
261 CCTTATTTCAACCATAGGCAGATTATAATAGTATTG
1434321 TAAGGGATTA
Statistics
Matches: 265, Mismatches: 31, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
310 265 1.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (310 bp):
CTAGTCCAAATTATTTCAGTTCAGTCAGCACAACAGCAACTTAATCAATCCATCTCTGTTGTCCA
TAAATATTGATCATAATGTTGAATGTAGAGTGGTCTAAACCAAAATTCAATTCCTTCATCCTCTG
CAAGACACTTCTAAATTAATCCATTGACCTTCATTCCCATATGCATCCAACACACAATCGTAGGC
TTCAAGGGAAACTAAAAAACCATTGAATTGCATTTCCCAAACAGTTGATGACATCTTCTTGGAGT
CCTTATTTCAACCATAGGCAGATTATAATAGTATTGCAACAGTTCAGTTG
Found at i:1435015 original size:22 final size:23
Alignment explanation
Indices: 1434990--1435036 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
1434980 ATCATAAACT
1434990 AACAAAA-AAAAATAAAAAAG-GA
1 AACAAAAGAAAAA-AAAAAAGAGA
*
1435012 AACAAAAGCAAAAAAAAAAGAGA
1 AACAAAAGAAAAAAAAAAAGAGA
1435035 AA
1 AA
1435037 AAGAATGGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.81, C:0.06, G:0.11, T:0.02
Consensus pattern (23 bp):
AACAAAAGAAAAAAAAAAAGAGA
Found at i:1435751 original size:20 final size:20
Alignment explanation
Indices: 1435711--1435753 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
1435701 GTTAGGTAAG
* *
1435711 AAAGAAAGAAAGAAGATGAA
1 AAAGAAAGAAAGAAAAAGAA
*
1435731 AAAGAAAGGAAGAAAAAGAA
1 AAAGAAAGAAAGAAAAAGAA
1435751 AAA
1 AAA
1435754 AATATGAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.02
Consensus pattern (20 bp):
AAAGAAAGAAAGAAAAAGAA
Found at i:1436141 original size:2 final size:2
Alignment explanation
Indices: 1436128--1436162 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1436118 TTATTTTATT
*
1436128 TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1436163 TGAAAATCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1438952 original size:46 final size:46
Alignment explanation
Indices: 1438902--1439029 Score: 168
Period size: 46 Copynumber: 2.8 Consensus size: 46
1438892 TTAAGAAATA
* * *
1438902 AATTAAATTAAATTAATTAATAGATAGATAAAAAAAATTTAT-TATT
1 AATTAAATTAAATTAATTAAGAGATAAATAAAAAAAATTTATCT-CT
* *
1438948 AATTAAATTAAATTAATTAAGAGATAAATAAAATAATTTTATCTCT
1 AATTAAATTAAATTAATTAAGAGATAAATAAAAAAAATTTATCTCT
* * *
1438994 AATTAAATTTAATTAACTAAGAGATAAATGAAAAAA
1 AATTAAATTAAATTAATTAAGAGATAAATAAAAAAA
1439030 TAAGTTTTTT
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
46 71 0.99
47 1 0.01
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.36
Consensus pattern (46 bp):
AATTAAATTAAATTAATTAAGAGATAAATAAAAAAAATTTATCTCT
Found at i:1448172 original size:22 final size:20
Alignment explanation
Indices: 1448151--1448200 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
1448141 AAAGTTATAT
1448151 TTTAAGATAAAAATATAAATA
1 TTTAA-ATAAAAATATAAATA
* * *
1448172 TTTAAATATAAATTTAAATT
1 TTTAAATAAAAATATAAATA
1448192 TATTAAATA
1 T-TTAAATA
1448201 TTATTTTTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (20 bp):
TTTAAATAAAAATATAAATA
Found at i:1451463 original size:15 final size:16
Alignment explanation
Indices: 1451435--1451474 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
1451425 TAATAAACTA
*
1451435 TTATTATCACTATTTT
1 TTATTATCACTATTAT
1451451 TTATTAT-ACTATTAT
1 TTATTATCACTATTAT
*
1451466 TTATGATCA
1 TTATTATCA
1451475 TAAATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.30, C:0.10, G:0.03, T:0.57
Consensus pattern (16 bp):
TTATTATCACTATTAT
Found at i:1452194 original size:26 final size:27
Alignment explanation
Indices: 1452139--1452201 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 27
1452129 ATTGCCGATA
*
1452139 TATAAAATTTATATATTCTTAATAAAT
1 TATAAAATATATATATTCTTAATAAAT
*
1452166 TATAAAATAT-TAT-TTCGTTAATAATT
1 TATAAAATATATATATTC-TTAATAAAT
*
1452192 TATTAAATAT
1 TATAAAATAT
1452202 CAATAGACTC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 3 0.09
26 20 0.62
27 9 0.28
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.49
Consensus pattern (27 bp):
TATAAAATATATATATTCTTAATAAAT
Found at i:1453623 original size:27 final size:26
Alignment explanation
Indices: 1453585--1453638 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
1453575 CCAATTGAAC
* *
1453585 TTTTTTTAATTATATAATATATTTTA
1 TTTTTATAATTATATAATATATATTA
*
1453611 TTTTTATATATTATATAATTTATATTA
1 TTTTTATA-ATTATATAATATATATTA
1453638 T
1 T
1453639 ATAAAAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (26 bp):
TTTTTATAATTATATAATATATATTA
Found at i:1453764 original size:17 final size:17
Alignment explanation
Indices: 1453738--1453773 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
1453728 TAAAGATTAA
*
1453738 ATTTTTAAAAAAATAAT
1 ATTTTGAAAAAAATAAT
1453755 ATTTTGAAAAAAATAAT
1 ATTTTGAAAAAAATAAT
1453772 AT
1 AT
1453774 GAATAATCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
ATTTTGAAAAAAATAAT
Found at i:1455321 original size:16 final size:16
Alignment explanation
Indices: 1455290--1455331 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
1455280 TTTTAAAAAA
*
1455290 ATTAAATA-TATTTAT
1 ATTAAATATTTTTTAT
1455305 ATTAAATATTTTTTAT
1 ATTAAATATTTTTTAT
*
1455321 ATTTAATATTT
1 ATTAAATATTT
1455332 AATTCAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 8 0.33
16 16 0.67
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATTAAATATTTTTTAT
Found at i:1455892 original size:31 final size:30
Alignment explanation
Indices: 1455837--1455902 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 30
1455827 TTAAATTTTT
*
1455837 TAAAAATTATTTTATTATTTATTAT-ATTAA
1 TAAAAATTATTTTATTATTAATTATCA-TAA
1455867 TAAAATATTATTTTA-TATTAAATTATCATAA
1 TAAAA-ATTATTTTATTATT-AATTATCATAA
1455898 TAAAA
1 TAAAA
1455903 CTTAAATTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
30 9 0.28
31 22 0.69
32 1 0.03
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (30 bp):
TAAAAATTATTTTATTATTAATTATCATAA
Found at i:1455993 original size:15 final size:15
Alignment explanation
Indices: 1455956--1455995 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
1455946 TAAATTAATT
1455956 TTAAATTTATAAAAA
1 TTAAATTTATAAAAA
** *
1455971 TTTTATTTATATAAA
1 TTAAATTTATAAAAA
1455986 TTAAATTTAT
1 TTAAATTTAT
1455996 CTAGTTGATC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTAAATTTATAAAAA
Found at i:1456344 original size:11 final size:11
Alignment explanation
Indices: 1456328--1456417 Score: 55
Period size: 11 Copynumber: 8.3 Consensus size: 11
1456318 AATGTATTTT
*
1456328 TATTTTAATCA
1 TATTTTAATTA
*
1456339 TATTTTTATTA
1 TATTTTAATTA
1456350 T-TTTATAATTA
1 TATTT-TAATTA
1456361 TA-TTTAA-TA
1 TATTTTAATTA
1456370 TATTTTATATT-
1 TATTTTA-ATTA
* *
1456381 TATATTAATTT
1 TATTTTAATTA
*
1456392 TATTAT-ATTAA
1 TATTTTAATT-A
*
1456403 TAATTTATATTA
1 TATTTTA-ATTA
1456415 TAT
1 TAT
1456418 AAATTTAAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 17
0.69 0.11 0.20
Matches are distributed among these distances:
9 4 0.07
10 16 0.27
11 33 0.55
12 4 0.07
13 3 0.05
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (11 bp):
TATTTTAATTA
Found at i:1456363 original size:22 final size:22
Alignment explanation
Indices: 1456333--1456413 Score: 65
Period size: 22 Copynumber: 3.5 Consensus size: 22
1456323 ATTTTTATTT
*
1456333 TAATCATATTTTTATTATTTTA
1 TAATTATATTTTTATTATTTTA
*
1456355 TAATTATA-TTTAATATATTTTA
1 TAATTATATTTTTAT-TATTTTA
* *
1456377 TATTTATATTAATTTTATTATATTAA
1 TAATTATA-T--TTTTATTAT-TTTA
1456403 TAATTTATATT
1 TAA-TTATATT
1456414 ATATAAATTT
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
21 5 0.11
22 21 0.46
24 1 0.02
25 3 0.07
26 11 0.24
27 5 0.11
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (22 bp):
TAATTATATTTTTATTATTTTA
Found at i:1456366 original size:20 final size:20
Alignment explanation
Indices: 1456322--1456386 Score: 62
Period size: 22 Copynumber: 3.2 Consensus size: 20
1456312 AAAATTAATG
*
1456322 TATTT-TTATTTTAATCA-TA
1 TATTTATTATTTT-ATAATTA
*
1456341 TTTTTATTATTTTATAATTA
1 TATTTATTATTTTATAATTA
*
1456361 TATTTAATATATTTTATATTTA
1 TATTT-AT-TATTTTATAATTA
1456383 TATT
1 TATT
1456387 AATTTTATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
19 7 0.18
20 13 0.34
21 2 0.05
22 16 0.42
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (20 bp):
TATTTATTATTTTATAATTA
Found at i:1456387 original size:27 final size:27
Alignment explanation
Indices: 1456327--1456417 Score: 80
Period size: 27 Copynumber: 3.2 Consensus size: 27
1456317 TAATGTATTT
1456327 TTAT-TTTAATCATATTTTTATTATTTTATAA
1 TTATATTTAAT-ATA-TTTTA-TA-TTTAT-A
1456358 TTATATTTAATATATTTTATATTTATA
1 TTATATTTAATATATTTTATATTTATA
* *
1456385 TTA-ATTTTAT-TATATTAATAATTTATA
1 TTATATTTAATATAT-TTTAT-ATTTATA
1456412 TTATAT
1 TTATAT
1456418 AAATTTAAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
25 3 0.06
26 10 0.19
27 14 0.26
28 7 0.13
29 2 0.04
30 5 0.09
31 7 0.13
32 6 0.11
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (27 bp):
TTATATTTAATATATTTTATATTTATA
Found at i:1456416 original size:38 final size:38
Alignment explanation
Indices: 1456338--1456435 Score: 100
Period size: 38 Copynumber: 2.7 Consensus size: 38
1456328 TATTTTAATC
* * *
1456338 ATATTTTTATTATTTTATAATTATATTTAATATATTTT
1 ATATTTATATTAATTTATAATTATATTTAATATATATT
1456376 ATATTTATATTAATTT-T-ATTATA-TTAATA-AT-TT
1 ATATTTATATTAATTTATAATTATATTTAATATATATT
* *
1456409 ATA-TTATATAAATTTAAAATATATATT
1 ATATTTATATTAATTTATAAT-TATATT
1456436 CATAGCTTAT
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
32 11 0.21
33 5 0.10
34 4 0.08
35 10 0.19
36 7 0.13
37 1 0.02
38 14 0.27
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (38 bp):
ATATTTATATTAATTTATAATTATATTTAATATATATT
Found at i:1458810 original size:32 final size:33
Alignment explanation
Indices: 1458760--1458828 Score: 77
Period size: 32 Copynumber: 2.1 Consensus size: 33
1458750 TTTTAAATTT
** *
1458760 ATATAAATTTTTATATATTAAT-AATTTATATG
1 ATATAAATTTAAAAATATTAATGAATTTATATG
* * *
1458792 ATATAAATTTAAAAATATTTATGTATTTATATT
1 ATATAAATTTAAAAATATTAATGAATTTATATG
1458825 ATAT
1 ATAT
1458829 TATATTTTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
32 18 0.60
33 12 0.40
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (33 bp):
ATATAAATTTAAAAATATTAATGAATTTATATG
Found at i:1459374 original size:16 final size:17
Alignment explanation
Indices: 1459336--1459374 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
1459326 TGAGTTAATT
1459336 GATTTAATATCATTTTA
1 GATTTAATATCATTTTA
1459353 -AGTTTAA-ATCATTTTA
1 GA-TTTAATATCATTTTA
1459369 GATTTA
1 GATTTA
1459375 TAGTTGAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.36, C:0.05, G:0.08, T:0.51
Consensus pattern (17 bp):
GATTTAATATCATTTTA
Found at i:1459544 original size:11 final size:12
Alignment explanation
Indices: 1459517--1459550 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
1459507 TATTAATTTT
*
1459517 TTTAATTAAATA
1 TTTAAATAAATA
1459529 TTTAAATAAA-A
1 TTTAAATAAATA
1459540 TTTAAATAAAT
1 TTTAAATAAAT
1459551 TAATCAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TTTAAATAAATA
Found at i:1459873 original size:16 final size:16
Alignment explanation
Indices: 1459854--1460000 Score: 74
Period size: 16 Copynumber: 8.8 Consensus size: 16
1459844 GTATTAAAAT
1459854 ATTTTATATTATATAA
1 ATTTTATATTATATAA
1459870 ATTTTA-A-TATATTAA
1 ATTTTATATTATA-TAA
*
1459885 TTATTTATATATTACATAA
1 --ATTT-TATATTATATAA
1459904 ATTTTAGTA-TAT-TAA
1 ATTTTA-TATTATATAA
1459919 CGA-TTTATATTATATAA
1 --ATTTTATATTATATAA
* *
1459936 ATTTTATTATT-TTTAT
1 ATTTTA-TATTATATAA
1459952 ATATTTATATTAATTTATATA
1 AT-TTTATATT-A--TATA-A
* *
1459973 TTTTTATATTATATTAT
1 ATTTTATATTATA-TAA
1459990 ATTTTA-ATTAT
1 ATTTTATATTAT
1460001 TTTTATCATA
Statistics
Matches: 102, Mismatches: 9, Indels: 40
0.68 0.06 0.26
Matches are distributed among these distances:
14 4 0.04
15 10 0.10
16 35 0.34
17 29 0.28
18 4 0.04
19 5 0.05
20 14 0.14
21 1 0.01
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (16 bp):
ATTTTATATTATATAA
Found at i:1459890 original size:17 final size:18
Alignment explanation
Indices: 1459858--1459918 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 18
1459848 TAAAATATTT
1459858 TATATTATATAAATTTTAA
1 TATATTA-ATAAATTTTAA
*
1459877 TATATTAAT-TA-TTT-A
1 TATATTAATAAATTTTAA
*
1459892 TATATTACATAAATTTTAG
1 TATATTA-ATAAATTTTAA
1459911 TATATTAA
1 TATATTAA
1459919 CGATTTATAT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
15 8 0.23
16 5 0.14
17 2 0.06
18 6 0.17
19 14 0.40
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (18 bp):
TATATTAATAAATTTTAA
Found at i:1459893 original size:32 final size:32
Alignment explanation
Indices: 1459856--1459963 Score: 126
Period size: 34 Copynumber: 3.3 Consensus size: 32
1459846 ATTAAAATAT
1459856 TTTATATTATATAAATTTTAATATATTAATTA
1 TTTATATTATATAAATTTTAATATATTAATTA
* * **
1459888 TTTATATATTACATAAATTTTAGTATATTAACGA
1 -TT-TATATTATATAAATTTTAATATATTAATTA
* * *
1459922 TTTATATTATATAAATTTTATTATTTTTATATA
1 TTTATATTATATAAATTTTAATATATTAAT-TA
1459955 TTTATATTA
1 TTTATATTA
1459964 ATTTATATAT
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
32 23 0.37
33 14 0.22
34 26 0.41
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (32 bp):
TTTATATTATATAAATTTTAATATATTAATTA
Found at i:1459951 original size:20 final size:18
Alignment explanation
Indices: 1459923--1460003 Score: 60
Period size: 19 Copynumber: 4.4 Consensus size: 18
1459913 TATTAACGAT
*
1459923 TTATATTATATAAATTTTA
1 TTATTTTATAT-AATTTTA
1459942 TTATTTT-TATATATTTATA
1 TTATTTTATATA-ATTT-TA
* *
1459961 TTAATTTATATATTTTTA
1 TTATTTTATATAATTTTA
*
1459979 -TATTATAT-TATATTTTAA
1 TTATTTTATATA-ATTTT-A
1459997 TTATTTT
1 TTATTTT
1460004 TATCATATAA
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
16 2 0.04
17 11 0.22
18 10 0.20
19 22 0.45
20 4 0.08
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TTATTTTATATAATTTTA
Found at i:1460017 original size:28 final size:26
Alignment explanation
Indices: 1459936--1460018 Score: 82
Period size: 28 Copynumber: 3.0 Consensus size: 26
1459926 TATTATATAA
1459936 ATTTTATTATTTTTATATAT--TTAT
1 ATTTTATTATTTTTATATATAATTAT
1459960 ATTAATTTATATATTTTTATAT-TATATTAT
1 A-T--TTTAT-TATTTTTATATATA-ATTAT
1459990 ATTTTAATTATTTTTATCATATAATTAT
1 ATTTT-ATTATTTTTAT-ATATAATTAT
1460018 A
1 A
1460019 CGGTGCTTCT
Statistics
Matches: 49, Mismatches: 0, Indels: 16
0.75 0.00 0.25
Matches are distributed among these distances:
24 1 0.02
25 1 0.02
27 18 0.37
28 21 0.43
29 3 0.06
30 5 0.10
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (26 bp):
ATTTTATTATTTTTATATATAATTAT
Found at i:1461427 original size:2 final size:2
Alignment explanation
Indices: 1461420--1461463 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1461410 TTAATTTGAT
1461420 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1461462 TA
1 TA
1461464 AAATTAGAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1463306 original size:21 final size:22
Alignment explanation
Indices: 1463264--1463307 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
1463254 ATAATTTAAT
*
1463264 TTTTCATATATTTTATATTGTA
1 TTTTCATATATTTTATAATGTA
1463286 TTTT-ATA-ATTTCTATAATGTA
1 TTTTCATATATTT-TATAATGTA
1463307 T
1 T
1463308 AATAATGTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
20 4 0.20
21 12 0.60
22 4 0.20
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.61
Consensus pattern (22 bp):
TTTTCATATATTTTATAATGTA
Found at i:1465988 original size:19 final size:19
Alignment explanation
Indices: 1465964--1466016 Score: 106
Period size: 19 Copynumber: 2.8 Consensus size: 19
1465954 TTTTGACCTA
1465964 AATGTATCGATACATATTC
1 AATGTATCGATACATATTC
1465983 AATGTATCGATACATATTC
1 AATGTATCGATACATATTC
1466002 AATGTATCGATACAT
1 AATGTATCGATACAT
1466017 TATCGATACA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (19 bp):
AATGTATCGATACATATTC
Found at i:1474742 original size:24 final size:24
Alignment explanation
Indices: 1474706--1474755 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1474696 TTTGGTAAGA
*
1474706 TTGATTTTCATTT-TACTTGATAAT
1 TTGATTTTCATTTATA-TTAATAAT
*
1474730 TTGATTTTTATTTATATTAATAAT
1 TTGATTTTCATTTATATTAATAAT
1474754 TT
1 TT
1474756 TGCTTTTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 21 0.91
25 2 0.09
ACGTcount: A:0.28, C:0.04, G:0.06, T:0.62
Consensus pattern (24 bp):
TTGATTTTCATTTATATTAATAAT
Found at i:1476438 original size:165 final size:166
Alignment explanation
Indices: 1476166--1476493 Score: 541
Period size: 165 Copynumber: 2.0 Consensus size: 166
1476156 ACACTCGCGA
*
1476166 GTTTTCCATTCACGAGAAGAAAAATCGCACCAAGATGTTCAAAGATTCAGAAAACAATGAGATTT
1 GTTTTCCATTCACGAGAAGAAAAATCGCACCAAGATGCTCAAAGATTCAGAAAACAATGAGATTT
* *
1476231 GCAGTTAGCAGTAGAGGAATCAGAATCAGTACTTAAAATCAGCAATGAAAATGCCAAAGAAAGCA
66 GCAGTTAGCAGCAGAGGAATCAGAATCAGTACTTAAAATCAGCAATGAAAATGCCAAAGAAAGAA
* *
1476296 GAAAT-TTGGTAGAAAATCCCTAGTTCATGAGATTC
131 GAAATCTAGCTAGAAAATCCCTAGTTCATGAGATTC
* *
1476331 GTTTTCCATTCGCGAGAAGAAAAATTGCACCAAGATGCTCAAAGATTCAGAAAACAATGAGATTT
1 GTTTTCCATTCACGAGAAGAAAAATCGCACCAAGATGCTCAAAGATTCAGAAAACAATGAGATTT
* * * * *
1476396 GTAGTTAGCAGCAGTGGAATCAGAATTAGTACTTGAAATCAGCAATGAAAATGCTAAAGAAAGAA
66 GCAGTTAGCAGCAGAGGAATCAGAATCAGTACTTAAAATCAGCAATGAAAATGCCAAAGAAAGAA
1476461 GAAATCTAGCTAGAAAATCCCTAGTTCATGAGA
131 GAAATCTAGCTAGAAAATCCCTAGTTCATGAGA
1476494 GTCATGCTAA
Statistics
Matches: 150, Mismatches: 12, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
165 125 0.83
166 25 0.17
ACGTcount: A:0.42, C:0.15, G:0.20, T:0.23
Consensus pattern (166 bp):
GTTTTCCATTCACGAGAAGAAAAATCGCACCAAGATGCTCAAAGATTCAGAAAACAATGAGATTT
GCAGTTAGCAGCAGAGGAATCAGAATCAGTACTTAAAATCAGCAATGAAAATGCCAAAGAAAGAA
GAAATCTAGCTAGAAAATCCCTAGTTCATGAGATTC
Found at i:1477581 original size:19 final size:19
Alignment explanation
Indices: 1477557--1477598 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
1477547 GATATTTAAA
*
1477557 AAATTTAAATAA-AAATATT
1 AAATTTAAAAAATAAAT-TT
1477576 AAATTTAAAAAATAAATTT
1 AAATTTAAAAAATAAATTT
1477595 AAAT
1 AAAT
1477599 AAAATAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
AAATTTAAAAAATAAATTT
Found at i:1477610 original size:19 final size:18
Alignment explanation
Indices: 1477557--1477610 Score: 55
Period size: 19 Copynumber: 3.2 Consensus size: 18
1477547 GATATTTAAA
1477557 AAATTTAAATAAAAATATT
1 AAATTTAAATAAAAA-ATT
1477576 AAA-TT---TAAAAAA-T
1 AAATTTAAATAAAAAATT
1477589 AAATTTAAATAAAATAATT
1 AAATTTAAATAAAA-AATT
1477608 AAA
1 AAA
1477611 CTTATTTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
13 4 0.14
14 3 0.10
15 6 0.21
17 5 0.17
18 4 0.14
19 7 0.24
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAATTTAAATAAAAAATT
Found at i:1477668 original size:5 final size:5
Alignment explanation
Indices: 1477658--1477682 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1477648 TTAAAGCTTA
1477658 AATCT AATCT AATCT AATCT AATCT
1 AATCT AATCT AATCT AATCT AATCT
1477683 CTTTTTTTAA
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:0.20, G:0.00, T:0.40
Consensus pattern (5 bp):
AATCT
Found at i:1479429 original size:19 final size:19
Alignment explanation
Indices: 1479407--1479445 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
1479397 ATTAAAAAGT
* *
1479407 TAAATTAAAATTATAGATA
1 TAAAATAAAATTAAAGATA
1479426 TAAAATAAAATTAAAGATA
1 TAAAATAAAATTAAAGATA
1479445 T
1 T
1479446 TTAAGTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (19 bp):
TAAAATAAAATTAAAGATA
Found at i:1482321 original size:2 final size:2
Alignment explanation
Indices: 1482314--1482342 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1482304 GAAAATGGAT
1482314 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1482343 GTTTTGATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1483652 original size:32 final size:32
Alignment explanation
Indices: 1483615--1483679 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
1483605 AAAAATATGA
*
1483615 ATATAATATAAATATATAAATTTATTAA-ATTT
1 ATATAATATAAAT-TATAAATATATTAACATTT
* *
1483647 ATATAATATTAATTATTAATATATTAACATTT
1 ATATAATATAAATTATAAATATATTAACATTT
1483679 A
1 A
1483680 AGATAATTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 12 0.41
32 17 0.59
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (32 bp):
ATATAATATAAATTATAAATATATTAACATTT
Found at i:1494371 original size:29 final size:29
Alignment explanation
Indices: 1494329--1494417 Score: 98
Period size: 27 Copynumber: 3.2 Consensus size: 29
1494319 TATTTATTTG
*
1494329 TATAA-ATAAATAATATTTTAAATATAAT
1 TATAATATAAATAATATTTTAAATATAAA
** *
1494357 TATAATATGTATAATA--TTATATATAAA
1 TATAATATAAATAATATTTTAAATATAAA
1494384 TATAATATAAAT-ATATTATTAAATATAAA
1 TATAATATAAATAATATT-TTAAATATAAA
1494413 -ATAAT
1 TATAAT
1494418 CACTTAAATA
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
26 3 0.06
27 19 0.38
28 10 0.20
29 18 0.36
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (29 bp):
TATAATATAAATAATATTTTAAATATAAA
Found at i:1494387 original size:33 final size:30
Alignment explanation
Indices: 1494347--1494417 Score: 83
Period size: 29 Copynumber: 2.3 Consensus size: 30
1494337 AATAATATTT
*
1494347 TAAATATAATTATAATATGTATAATATTATATA
1 TAAATATAATTATAA-A--TATAATATTAAATA
*
1494380 TAAATATAA-TATAAATATATTATTAAATA
1 TAAATATAATTATAAATATAATATTAAATA
1494409 TAAA-ATAAT
1 TAAATATAAT
1494418 CACTTAAATA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
28 4 0.11
29 16 0.46
31 1 0.03
32 5 0.14
33 9 0.26
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.42
Consensus pattern (30 bp):
TAAATATAATTATAAATATAATATTAAATA
Found at i:1494392 original size:23 final size:24
Alignment explanation
Indices: 1494366--1494417 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 24
1494356 TTATAATATG
1494366 TATAATAT-TA-TATATAAATATAA
1 TATAATATATATTAT-TAAATATAA
1494389 TATAA-ATATATTATTAAATATAA
1 TATAATATATATTATTAAATATAA
*
1494412 AATAAT
1 TATAAT
1494418 CACTTAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
22 2 0.08
23 20 0.80
24 3 0.12
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
TATAATATATATTATTAAATATAA
Found at i:1494408 original size:12 final size:11
Alignment explanation
Indices: 1494329--1494416 Score: 58
Period size: 11 Copynumber: 7.9 Consensus size: 11
1494319 TATTTATTTG
1494329 TATAA-ATAAA
1 TATAATATAAA
* *
1494339 TAATATTTTAAA
1 T-ATAATATAAA
1494351 TATAAT-TATAA
1 TATAATATA-AA
*
1494362 TAT-GTAT-AA
1 TATAATATAAA
1494371 TATTATATATAAA
1 TA-TA-ATATAAA
1494384 TATAATATAAA
1 TATAATATAAA
*
1494395 TATATTATTAAA
1 TATAATA-TAAA
*
1494407 TATAAAATAA
1 TATAATATAA
1494417 TCACTTAAAT
Statistics
Matches: 61, Mismatches: 8, Indels: 17
0.71 0.09 0.20
Matches are distributed among these distances:
9 4 0.07
10 5 0.08
11 29 0.48
12 19 0.31
13 4 0.07
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (11 bp):
TATAATATAAA
Found at i:1494676 original size:32 final size:32
Alignment explanation
Indices: 1494615--1494682 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
1494605 CCATTAGATA
*
1494615 TTTTT-AAAAAAAATTGAATAAAAATAATAAT
1 TTTTTAAAAAAAAATTAAATAAAAATAATAAT
1494646 TTTTTAAAAAATAAATTTAAATAAAAAATAAT-AT
1 TTTTTAAAAAA-AAA-TTAAAT-AAAAATAATAAT
1494680 TTT
1 TTT
1494683 AATTTTAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
31 5 0.16
32 5 0.16
33 3 0.09
34 10 0.31
35 9 0.28
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (32 bp):
TTTTTAAAAAAAAATTAAATAAAAATAATAAT
Found at i:1494683 original size:32 final size:32
Alignment explanation
Indices: 1494612--1494684 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
1494602 TATCCATTAG
* *
1494612 ATATTTTTAAAAAAAATTGAATAAAAATAATA
1 ATATTTTAAAAAAAAATTAAATAAAAATAATA
*
1494644 ATTTTTTAAAAAATAAATTTAAAT-AAAA-AATA
1 ATATTTTAAAAAA-AAA-TTAAATAAAAATAATA
1494676 ATATTTTAA
1 ATATTTTAA
1494685 TTTTAATACG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
32 23 0.66
33 7 0.20
34 5 0.14
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (32 bp):
ATATTTTAAAAAAAAATTAAATAAAAATAATA
Found at i:1495596 original size:23 final size:24
Alignment explanation
Indices: 1495568--1495640 Score: 64
Period size: 24 Copynumber: 3.0 Consensus size: 24
1495558 ATATAATATG
1495568 TATATTAAATATATTATTTTAATA
1 TATATTAAATATATTATTTTAATA
1495592 -ATATTTAAATA-ATTTATTATTAA-A
1 TATA-TTAAATATA-TTATT-TTAATA
1495616 TATATTGATAATATAATT-TTTTAAT
1 TATATT-A-AATAT-ATTATTTTAAT
1495641 TTTATAAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 16
0.71 0.00 0.29
Matches are distributed among these distances:
23 4 0.10
24 15 0.38
25 12 0.30
26 6 0.15
27 2 0.05
28 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.53
Consensus pattern (24 bp):
TATATTAAATATATTATTTTAATA
Found at i:1495830 original size:6 final size:6
Alignment explanation
Indices: 1495805--1495839 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
1495795 ATATTATATC
*
1495805 ATATTT ATTATTT ATTTTT ATATTT ATATTT ATAT
1 ATATTT A-TATTT ATATTT ATATTT ATATTT ATAT
1495840 ATAAAATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
ATATTT
Found at i:1496116 original size:37 final size:41
Alignment explanation
Indices: 1496054--1496144 Score: 120
Period size: 37 Copynumber: 2.3 Consensus size: 41
1496044 TTTATTTATT
*
1496054 TTATTTTTATATTTATTTTTAAATATAAATATAA-TTTTAA
1 TTATTTTTATATTTATTTTTAAATATAAATACAATTTTTAA
1496094 -TATTTTTA-A-TTATTATTT-AATATAAATACAATTTTTAA
1 TTATTTTTATATTTATT-TTTAAATATAAATACAATTTTTAA
1496132 TTATTTATTATAT
1 TTATTT-TTATAT
1496145 ATACATATTT
Statistics
Matches: 44, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
37 17 0.39
38 10 0.23
39 13 0.30
40 3 0.07
41 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (41 bp):
TTATTTTTATATTTATTTTTAAATATAAATACAATTTTTAA
Found at i:1496161 original size:29 final size:28
Alignment explanation
Indices: 1496097--1496162 Score: 82
Period size: 26 Copynumber: 2.4 Consensus size: 28
1496087 ATTTTAATAT
*
1496097 TTTTAATTATTATTTAATATAAATACAA
1 TTTTAATAATTATTTAATATAAATACAA
* *
1496125 TTTT--TAATTATTTATTATATATACATA
1 TTTTAATAATTATTTAATATAAATACA-A
1496152 TTTTAATAATT
1 TTTTAATAATT
1496163 TTTCATCATA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
26 18 0.56
27 5 0.16
28 4 0.12
29 5 0.16
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (28 bp):
TTTTAATAATTATTTAATATAAATACAA
Found at i:1496191 original size:21 final size:21
Alignment explanation
Indices: 1496132--1496192 Score: 54
Period size: 22 Copynumber: 2.9 Consensus size: 21
1496122 CAATTTTTAA
*
1496132 TTAT-TTATTATATATACATATT
1 TTATATTATTAT-TAT-CATAAT
* *
1496154 TTA-ATAATTTTTCATCATAAT
1 TTATATTATTATT-ATCATAAT
1496175 TTATATTATTATTATCAT
1 TTATATTATTATTATCAT
1496193 TACAATAACA
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
21 14 0.45
22 17 0.55
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (21 bp):
TTATATTATTATTATCATAAT
Found at i:1496654 original size:29 final size:30
Alignment explanation
Indices: 1496621--1496704 Score: 91
Period size: 29 Copynumber: 2.8 Consensus size: 30
1496611 TAAAAGGTAA
1496621 TTATTGTTTAAATTTTTATAAAAATA-TAT
1 TTATTGTTTAAATTTTTATAAAAATATTAT
* *
1496650 TTATTGTTTTAATATTTA-AAAAATATTTAT
1 TTATTGTTTAAATTTTTATAAAAATA-TTAT
* * *
1496680 TTATTATTTTAAAATTTAATAAAAA
1 TTATT-GTTTAAATTTTTATAAAAA
1496705 AAATATTTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
28 7 0.16
29 16 0.36
30 8 0.18
31 8 0.18
32 5 0.11
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (30 bp):
TTATTGTTTAAATTTTTATAAAAATATTAT
Found at i:1496681 original size:30 final size:28
Alignment explanation
Indices: 1496621--1496703 Score: 94
Period size: 30 Copynumber: 2.8 Consensus size: 28
1496611 TAAAAGGTAA
* *
1496621 TTATTGTTTAAATTTTTATAAAAATATAT
1 TTATTGTTTTAATATTTA-AAAAATATAT
1496650 TTATTGTTTTAATATTTAAAAAATATTTAT
1 TTATTGTTTTAATATTTAAAAAATA--TAT
* *
1496680 TTATTATTTTAAAATTTAATAAAA
1 TTATTGTTTTAATATTTAA-AAAA
1496704 AAAATATTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
28 7 0.15
29 16 0.34
30 20 0.43
31 4 0.09
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (28 bp):
TTATTGTTTTAATATTTAAAAAATATAT
Found at i:1497003 original size:23 final size:24
Alignment explanation
Indices: 1496958--1497008 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
1496948 AACTTTGAAA
* *
1496958 TAAATTTATTAAAATATTTTTATT
1 TAAATTAATTAAAATATTATTATT
*
1496982 TAAATTAATT-AACTATTATTATT
1 TAAATTAATTAAAATATTATTATT
1497005 TAAA
1 TAAA
1497009 ATTTAATGAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (24 bp):
TAAATTAATTAAAATATTATTATT
Found at i:1497466 original size:17 final size:16
Alignment explanation
Indices: 1497444--1497490 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 16
1497434 ATCTTAATAG
1497444 TAATTAAAGATAAT-TTT
1 TAATTAAA-A-AATATTT
1497461 TAATTAAAAAATATTT
1 TAATTAAAAAATATTT
1497477 TAAGTTAAAAAATA
1 TAA-TTAAAAAATA
1497491 AAAATAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.11
16 7 0.25
17 18 0.64
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.40
Consensus pattern (16 bp):
TAATTAAAAAATATTT
Found at i:1497620 original size:23 final size:23
Alignment explanation
Indices: 1497563--1497621 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 23
1497553 TTTAAAAGAT
* *
1497563 AAATATATTTTATAATAAATTAAA
1 AAATATAATTTA-AGTAAATTAAA
*
1497587 AAATATTATTTAAGTAAATTACAA
1 AAATATAATTTAAGTAAATTA-AA
1497611 AAATA-AATTTA
1 AAATATAATTTA
1497622 CAGGTATTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 13 0.43
24 17 0.57
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (23 bp):
AAATATAATTTAAGTAAATTAAA
Found at i:1497852 original size:26 final size:25
Alignment explanation
Indices: 1497822--1497880 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 25
1497812 AAAAAAATTA
*
1497822 TATTTATGTATTTTTATATCATATTT
1 TATTTATGTATTTTTAAATCAT-TTT
* *
1497848 TATTTATTTATTTTTAAATTATTTT
1 TATTTATGTATTTTTAAATCATTTT
1497873 TATATTAT
1 TAT-TTAT
1497881 ATTTAAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 6 0.21
26 23 0.79
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.68
Consensus pattern (25 bp):
TATTTATGTATTTTTAAATCATTTT
Found at i:1497871 original size:11 final size:11
Alignment explanation
Indices: 1497855--1497889 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
1497845 TTTTATTTAT
1497855 TTATTTTTAAA
1 TTATTTTTAAA
*
1497866 TTATTTTTATA
1 TTATTTTTAAA
*
1497877 TTATATTTAAA
1 TTATTTTTAAA
1497888 TT
1 TT
1497890 TATCTCATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TTATTTTTAAA
Found at i:1497871 original size:37 final size:40
Alignment explanation
Indices: 1497830--1497911 Score: 107
Period size: 37 Copynumber: 2.1 Consensus size: 40
1497820 TATATTTATG
*
1497830 TATTTTTATATCATATTT-TATTTAT-T-TATTTTTAAAT
1 TATTTTTATATCATATTTAAATTTATCTATATTTTTAAAT
* *
1497867 TATTTTTATATTATATTTAAATTTATCTCATATTTTTAATT
1 TATTTTTATATCATATTTAAATTTATCT-ATATTTTTAAAT
1497908 TATT
1 TATT
1497912 AAATTATTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
37 17 0.45
38 6 0.16
39 1 0.03
41 14 0.37
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (40 bp):
TATTTTTATATCATATTTAAATTTATCTATATTTTTAAAT
Found at i:1498344 original size:22 final size:21
Alignment explanation
Indices: 1498295--1498344 Score: 50
Period size: 22 Copynumber: 2.3 Consensus size: 21
1498285 TTTTTTAGTC
*
1498295 TATTAAATTATTTGATTTTAA
1 TATTAAATTATTTGATTTAAA
1498316 T-TCTAAATTTATTT-ATTTAAGA
1 TAT-TAAA-TTATTTGATTTAA-A
1498338 TATTAAA
1 TATTAAA
1498345 ATAAAAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
20 1 0.04
21 10 0.42
22 12 0.50
23 1 0.04
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (21 bp):
TATTAAATTATTTGATTTAAA
Found at i:1499257 original size:15 final size:15
Alignment explanation
Indices: 1499207--1499271 Score: 51
Period size: 15 Copynumber: 4.3 Consensus size: 15
1499197 ATTTGAATTA
* * *
1499207 TTTTTAAATCTAATT
1 TTTTTAGATTTAAAT
1499222 TTTTTAGATTTAAAT
1 TTTTTAGATTTAAAT
**
1499237 CATTTAGATATT-AAT
1 TTTTTAGAT-TTAAAT
*
1499252 TTTTTAAATTTAAAAT
1 TTTTTAGATTT-AAAT
1499268 TTTT
1 TTTT
1499272 CAAATTTGAA
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
14 2 0.05
15 28 0.72
16 9 0.23
ACGTcount: A:0.35, C:0.03, G:0.03, T:0.58
Consensus pattern (15 bp):
TTTTTAGATTTAAAT
Found at i:1499626 original size:21 final size:21
Alignment explanation
Indices: 1499600--1499668 Score: 77
Period size: 21 Copynumber: 3.1 Consensus size: 21
1499590 AAGATATACT
1499600 TTATTATTAATTTTAATTTTA
1 TTATTATTAATTTTAATTTTA
*
1499621 TTATTA-TAATAATTAATTTTA
1 TTATTATTAAT-TTTAATTTTA
*
1499642 TTATTATAATTACTTTTAATTTTA
1 TTA-T-T-ATTAATTTTAATTTTA
1499666 TTA
1 TTA
1499669 AAATTAATCT
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
20 4 0.10
21 18 0.45
22 1 0.03
23 1 0.03
24 13 0.32
25 3 0.08
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (21 bp):
TTATTATTAATTTTAATTTTA
Found at i:1499659 original size:39 final size:39
Alignment explanation
Indices: 1499599--1499676 Score: 90
Period size: 39 Copynumber: 2.0 Consensus size: 39
1499589 TAAGATATAC
*
1499599 TTTATTATTAATTTTAATTTT-ATTATTA-TAATAATTAAT
1 TTTATTATTAATATTAATTTTAATT-TTATTAA-AATTAAT
*
1499638 TTTATTATT-ATAATTACTTTTAATTTTATTAAAATTAAT
1 TTTATTATTAAT-ATTAATTTTAATTTTATTAAAATTAAT
1499677 CTCATCATCT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
38 2 0.06
39 26 0.76
40 6 0.18
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.60
Consensus pattern (39 bp):
TTTATTATTAATATTAATTTTAATTTTATTAAAATTAAT
Found at i:1499666 original size:18 final size:18
Alignment explanation
Indices: 1499599--1499659 Score: 61
Period size: 18 Copynumber: 3.2 Consensus size: 18
1499589 TAAGATATAC
*
1499599 TTTATTATTA-ATTTTAAT
1 TTTATTATTATA-ATTAAT
1499617 TTTATTATTATAATAATTAAT
1 TTTATTA-T-T-ATAATTAAT
*
1499638 TTTATTATTATAATTACT
1 TTTATTATTATAATTAAT
1499656 TTTA
1 TTTA
1499660 ATTTTATTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
18 19 0.51
19 2 0.05
20 2 0.05
21 13 0.35
22 1 0.03
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (18 bp):
TTTATTATTATAATTAAT
Found at i:1500411 original size:28 final size:26
Alignment explanation
Indices: 1500375--1500427 Score: 70
Period size: 28 Copynumber: 2.0 Consensus size: 26
1500365 AATTTATATT
*
1500375 AATATTTTTTATATTAAATTTAAATAAA
1 AATAATTTTTATATT--ATTTAAATAAA
*
1500403 AATAATTTTTTTATTATTTAAATAA
1 AATAATTTTTATATTATTTAAATAA
1500428 TAATTTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 10 0.43
28 13 0.57
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
AATAATTTTTATATTATTTAAATAAA
Found at i:1500421 original size:40 final size:41
Alignment explanation
Indices: 1500335--1500421 Score: 99
Period size: 41 Copynumber: 2.1 Consensus size: 41
1500325 ATTTAAAAAT
*
1500335 TTATTTTATTATTTAAAATAATATTAAAATAATTTATATTA
1 TTATTTTATTATTTAAAATAATATAAAAATAATTTATATTA
* * *
1500376 ATATTTT-TTATATTAAATTTAA-ATAAAAATAATTT-TTTTA
1 TTATTTTATTAT-TTAAA-ATAATATAAAAATAATTTATATTA
1500416 TTATTT
1 TTATTT
1500422 AAATAATAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
40 13 0.33
41 23 0.59
42 3 0.08
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (41 bp):
TTATTTTATTATTTAAAATAATATAAAAATAATTTATATTA
Found at i:1502627 original size:17 final size:17
Alignment explanation
Indices: 1502605--1502664 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
1502595 GAATAAAATA
1502605 ATTTTATTATTTTTTAT
1 ATTTTATTATTTTTTAT
* *
1502622 ATTTTA-AAATTTTTATT
1 ATTTTATTATTTTTTA-T
*
1502639 ATTTTAATAATCTTTTTTAT
1 ATTTT-AT--TATTTTTTAT
1502659 ATTTTA
1 ATTTTA
1502665 ATTCGTTGCA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 7 0.21
17 12 0.36
18 1 0.03
19 1 0.03
20 6 0.18
21 6 0.18
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTTTATTATTTTTTAT
Found at i:1502661 original size:20 final size:19
Alignment explanation
Indices: 1502614--1502666 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
1502604 AATTTTATTA
1502614 TTTTTTATATTTTAA-AAT
1 TTTTTTATATTTTAATAAT
*
1502632 TTTTAT-TATTTTAATAAT
1 TTTTTTATATTTTAATAAT
1502650 CTTTTTTATATTTTAAT
1 -TTTTTTATATTTTAAT
1502667 TCGTTGCATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 8 0.27
18 8 0.27
19 5 0.17
20 9 0.30
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTTTTATATTTTAATAAT
Found at i:1503250 original size:20 final size:19
Alignment explanation
Indices: 1503211--1503290 Score: 52
Period size: 18 Copynumber: 4.6 Consensus size: 19
1503201 ATATTATGTT
*
1503211 TATATT-TA-AAATATTTTA
1 TATATTATATAAA-ATTTAA
1503229 TAT-TTATATAAAATTTAA
1 TATATTATATAAAATTTAA
1503247 TATATTA-AT--AA-TT--
1 TATATTATATAAAATTTAA
*
1503260 TATATTATATAAATTTTAA
1 TATATTATATAAAATTTAA
*
1503279 AATATTTATATA
1 TATA-TTATATA
1503291 TTTATATTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 18
0.70 0.04 0.26
Matches are distributed among these distances:
13 7 0.14
14 2 0.04
15 2 0.04
16 3 0.06
17 4 0.08
18 15 0.31
19 9 0.18
20 7 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TATATTATATAAAATTTAA
Found at i:1503277 original size:16 final size:16
Alignment explanation
Indices: 1503209--1503300 Score: 57
Period size: 16 Copynumber: 5.6 Consensus size: 16
1503199 TTATATTATG
*
1503209 TTTATATT-TAAAATAT
1 TTTATATTATATAA-AT
1503225 TTTATATTTATATAAAAT
1 TTTATA-TTATAT-AAAT
1503243 TTAATATATTA-AT-AA-
1 TT--TATATTATATAAAT
1503258 TTTATATTATATAAAT
1 TTTATATTATATAAAT
* * * *
1503274 TTTAAAATATTTATAT
1 TTTATATTATATAAAT
1503290 ATTTATATTAT
1 -TTTATATTAT
1503301 TTTTATATTT
Statistics
Matches: 60, Mismatches: 7, Indels: 17
0.71 0.08 0.20
Matches are distributed among these distances:
13 7 0.12
14 2 0.03
15 4 0.07
16 20 0.33
17 10 0.17
18 8 0.13
19 5 0.08
20 4 0.07
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTATATTATATAAAT
Found at i:1503299 original size:33 final size:33
Alignment explanation
Indices: 1503220--1503300 Score: 112
Period size: 32 Copynumber: 2.5 Consensus size: 33
1503210 TTATATTTAA
*
1503220 AATAT-TTTATATTTATATAAAATTTAATATATT
1 AATATATTTATA-TTATATAAAATTTAAAATATT
*
1503253 AATA-ATTTATATTATATAAATTTTAAAATATT
1 AATATATTTATATTATATAAAATTTAAAATATT
*
1503285 TATATATTTATATTAT
1 AATATATTTATATTAT
1503301 TTTTATATTT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
32 22 0.51
33 21 0.49
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (33 bp):
AATATATTTATATTATATAAAATTTAAAATATT
Found at i:1503323 original size:26 final size:27
Alignment explanation
Indices: 1503287--1503344 Score: 93
Period size: 26 Copynumber: 2.2 Consensus size: 27
1503277 AAAATATTTA
1503287 TATATTTATATTAT-TTTT-ATATTTTT
1 TATATTTATATTATATTTTAAT-TTTTT
1503313 TATATTTATATTATATTTTAATTTTTT
1 TATATTTATATTATATTTTAATTTTTT
1503340 TATAT
1 TATAT
1503345 CACGTTCATA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
26 14 0.47
27 14 0.47
28 2 0.07
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (27 bp):
TATATTTATATTATATTTTAATTTTTT
Found at i:1503961 original size:10 final size:12
Alignment explanation
Indices: 1503951--1504005 Score: 51
Period size: 11 Copynumber: 4.5 Consensus size: 12
1503941 AAATCGATTT
1503951 AATT-TTTTTTA
1 AATTATTTTTTA
1503962 AATTATTTTTTTA
1 AATTA-TTTTTTA
*
1503975 ACTTAATATTTTTA
1 AATT-AT-TTTTTA
*
1503989 AATT-TTTTTTT
1 AATTATTTTTTA
1504000 AATTAT
1 AATTAT
1504006 AAAAAAAATT
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
11 13 0.36
12 2 0.06
13 11 0.31
14 10 0.28
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (12 bp):
AATTATTTTTTA
Found at i:1503971 original size:14 final size:14
Alignment explanation
Indices: 1503952--1503999 Score: 55
Period size: 13 Copynumber: 3.6 Consensus size: 14
1503942 AATCGATTTA
1503952 ATTTTTTTTAAATT
1 ATTTTTTTTAAATT
*
1503966 A-TTTTTTTAACTT
1 ATTTTTTTTAAATT
* *
1503979 AATATTTTTAAATT
1 ATTTTTTTTAAATT
1503993 -TTTTTTT
1 ATTTTTTT
1504000 AATTATAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
13 17 0.61
14 11 0.39
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (14 bp):
ATTTTTTTTAAATT
Found at i:1504231 original size:22 final size:20
Alignment explanation
Indices: 1504205--1504268 Score: 53
Period size: 22 Copynumber: 3.1 Consensus size: 20
1504195 TATTTTTTAA
1504205 ATAAATTTAATAATATTATTTT
1 ATAAATTTAATAATATTA--TT
*
1504227 ATAAATAT-ATGAATA-TATT
1 ATAAATTTAAT-AATATTATT
1504246 -TAAATTTATATAATATTAATT
1 ATAAATTTA-ATAATATT-ATT
1504267 AT
1 AT
1504269 TAATATATTT
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
18 6 0.18
19 6 0.18
20 3 0.09
21 7 0.21
22 12 0.35
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
ATAAATTTAATAATATTATT
Found at i:1504280 original size:16 final size:14
Alignment explanation
Indices: 1504238--1504290 Score: 52
Period size: 14 Copynumber: 3.5 Consensus size: 14
1504228 TAAATATATG
1504238 AATATATTTAAATT
1 AATATATTTAAATT
*
1504252 TATATAATATTAATTATT
1 AATAT-AT-TTAA--ATT
1504270 AATATATTTAAATT
1 AATATATTTAAATT
*
1504284 TATATAT
1 AATATAT
1504291 AAAAAATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
14 13 0.41
15 2 0.06
16 8 0.25
17 2 0.06
18 7 0.22
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
AATATATTTAAATT
Found at i:1504291 original size:16 final size:16
Alignment explanation
Indices: 1504239--1504291 Score: 65
Period size: 16 Copynumber: 3.3 Consensus size: 16
1504229 AAATATATGA
1504239 ATATATTTAAATTTAT
1 ATATATTTAAATTTAT
*
1504255 ATA-ATATTAATTATTA-
1 ATATAT-TTAAAT-TTAT
1504271 ATATATTTAAATTTAT
1 ATATATTTAAATTTAT
1504287 ATATA
1 ATATA
1504292 AAAAATATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
15 5 0.16
16 21 0.68
17 5 0.16
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATATATTTAAATTTAT
Found at i:1504309 original size:34 final size:32
Alignment explanation
Indices: 1504229--1504300 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 32
1504219 ATTATTTTAT
* *
1504229 AAATATATGAATATATTTAAATTTATATAATAT
1 AAAT-TATTAATATATTTAAATTTATATAATAA
*
1504262 TAATTATTAATATATTTAAATTTATAT-ATAA
1 AAATTATTAATATATTTAAATTTATATAATAA
*
1504293 AAAATATT
1 AAATTATT
1504301 TTAAATATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 9 0.26
32 22 0.65
33 3 0.09
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (32 bp):
AAATTATTAATATATTTAAATTTATATAATAA
Found at i:1504315 original size:15 final size:15
Alignment explanation
Indices: 1504297--1504340 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
1504287 ATATAAAAAA
*
1504297 TATTTTAAATATAAT
1 TATTATAAATATAAT
1504312 TATTATATAATA-AAT
1 TATTATA-AATATAAT
1504327 TA-TATAAATATAAT
1 TATTATAAATATAAT
1504341 ATGGAGACAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 4 0.15
14 7 0.27
15 11 0.42
16 4 0.15
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TATTATAAATATAAT
Found at i:1505092 original size:13 final size:14
Alignment explanation
Indices: 1505076--1505105 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
1505066 AATTTTTTAC
1505076 TTAAATTT-ATTTT
1 TTAAATTTAATTTT
1505089 TTAAATTTAATTTT
1 TTAAATTTAATTTT
1505103 TTA
1 TTA
1505106 TTTAAACTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TTAAATTTAATTTT
Found at i:1505100 original size:18 final size:17
Alignment explanation
Indices: 1505043--1505110 Score: 66
Period size: 18 Copynumber: 3.9 Consensus size: 17
1505033 AGTCAAGATC
*
1505043 AAATCTATTTTTTAATT
1 AAATTTATTTTTTAATT
* *
1505060 AAACTTAATTTTTTACTT
1 AAA-TTTATTTTTTAATT
1505078 AAATTTATTTTTTAAATT
1 AAATTTATTTTTT-AATT
*
1505096 TAATTT-TTTATTTAA
1 AAATTTATTT-TTTAA
1505111 ACTCTCAAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
17 17 0.40
18 25 0.60
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.60
Consensus pattern (17 bp):
AAATTTATTTTTTAATT
Found at i:1505666 original size:21 final size:22
Alignment explanation
Indices: 1505640--1505681 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
1505630 ACATCCATTG
1505640 AAAGGAAGCTT-CGGCAGCTGC
1 AAAGGAAGCTTCCGGCAGCTGC
*
1505661 AAAGGATGCTTCCGGCAGCTG
1 AAAGGAAGCTTCCGGCAGCTG
1505682 GTTGTCCTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.26, C:0.24, G:0.33, T:0.17
Consensus pattern (22 bp):
AAAGGAAGCTTCCGGCAGCTGC
Found at i:1506152 original size:17 final size:18
Alignment explanation
Indices: 1506113--1506153 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
1506103 TATATTAAAC
*
1506113 ATAAATATTTTAAAAAAT
1 ATAAATATTTCAAAAAAT
*
1506131 A-AAATA-TTCAAATAAT
1 ATAAATATTTCAAAAAAT
1506147 ATAAATA
1 ATAAATA
1506154 ATTATAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 9 0.45
17 10 0.50
18 1 0.05
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.34
Consensus pattern (18 bp):
ATAAATATTTCAAAAAAT
Found at i:1506506 original size:15 final size:15
Alignment explanation
Indices: 1506482--1506519 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
1506472 TGTAAAATTT
*
1506482 TTTATATAATTTAAA
1 TTTATTTAATTTAAA
*
1506497 TTTATTTAATTTAAG
1 TTTATTTAATTTAAA
1506512 TTTATTTA
1 TTTATTTA
1506520 TGTAAATCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.61
Consensus pattern (15 bp):
TTTATTTAATTTAAA
Found at i:1506796 original size:2 final size:2
Alignment explanation
Indices: 1506789--1506829 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1506779 AAATGAATCT
1506789 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1506830 CTAGGCCGAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1509199 original size:15 final size:15
Alignment explanation
Indices: 1509181--1509216 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
1509171 TAAAATATAT
1509181 TTTTTAAAAATTTAA
1 TTTTTAAAAATTTAA
*
1509196 TTTTTAATAATTTAA
1 TTTTTAAAAATTTAA
1509211 TATTTT
1 T-TTTT
1509217 TTACTAAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 15 0.79
16 4 0.21
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTTTAAAAATTTAA
Found at i:1509218 original size:34 final size:35
Alignment explanation
Indices: 1509131--1509218 Score: 85
Period size: 34 Copynumber: 2.5 Consensus size: 35
1509121 TTAAAAATAG
*
1509131 ATAATTTAAT-TTTATTTAAATCAATTCATATTTTT
1 ATAATTTAATATTTTTTTAAA-CAATTCATATTTTT
*
1509166 -TAATTTAAAATATATTTTTTAAA-AATTTA-ATTTTT
1 ATAATTT--AATAT-TTTTTTAAACAATTCATATTTTT
1509201 AATAATTTAATATTTTTT
1 -ATAATTTAATATTTTTT
1509219 ACTAAGTTTC
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
34 11 0.24
35 11 0.24
36 8 0.18
37 7 0.16
38 8 0.18
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (35 bp):
ATAATTTAATATTTTTTTAAACAATTCATATTTTT
Found at i:1509990 original size:24 final size:23
Alignment explanation
Indices: 1509963--1510009 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1509953 TTAATAGTTG
1509963 AAATATAATTATAAAATTAAATAA
1 AAATATAATTAT-AAATTAAATAA
** *
1509987 AAATATTTTTATTAATTAAATAA
1 AAATATAATTATAAATTAAATAA
1510010 TATTTTGAGC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
AAATATAATTATAAATTAAATAA
Found at i:1510006 original size:19 final size:20
Alignment explanation
Indices: 1509978--1510015 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
1509968 TAATTATAAA
1509978 ATTAAATAAA-AATATTTTT
1 ATTAAATAAATAATATTTTT
*
1509997 ATTAATTAAATAATATTTT
1 ATTAAATAAATAATATTTT
1510016 GAGCCTAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTAAATAAATAATATTTTT
Found at i:1510502 original size:23 final size:23
Alignment explanation
Indices: 1510472--1510515 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1510462 TAGACACATC
1510472 AATTTGATCTCTGCTTTTAACTT
1 AATTTGATCTCTGCTTTTAACTT
* *
1510495 AATTTGATCTTTGTTTTTAAC
1 AATTTGATCTCTGCTTTTAAC
1510516 CAAAAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.23, C:0.14, G:0.09, T:0.55
Consensus pattern (23 bp):
AATTTGATCTCTGCTTTTAACTT
Found at i:1510675 original size:21 final size:21
Alignment explanation
Indices: 1510651--1510690 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1510641 TATTTTTATT
*
1510651 TAAAT-TTAATTATAAAATATA
1 TAAATATTAA-TACAAAATATA
1510672 TAAATATTAATACAAAATA
1 TAAATATTAATACAAAATA
1510691 ATTTTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAATATTAATACAAAATATA
Found at i:1511645 original size:32 final size:34
Alignment explanation
Indices: 1511576--1511640 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
1511566 ATTAAATTAA
*
1511576 TTCTTTAAAGCTTATATCTTTATTTTTTTTTTAC
1 TTCTTTAAAGCTTATATCTCTATTTTTTTTTTAC
*
1511610 TTCTTTAAGGCTTATATCTCTATTTTTTTTT
1 TTCTTTAAAGCTTATATCTCTATTTTTTTTT
1511641 CTTCTATCGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.18, C:0.12, G:0.05, T:0.65
Consensus pattern (34 bp):
TTCTTTAAAGCTTATATCTCTATTTTTTTTTTAC
Found at i:1512120 original size:2 final size:2
Alignment explanation
Indices: 1512113--1512164 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
1512103 AATAAGTAAA
*
1512113 AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1512155 AT AT AT AT AT
1 AT AT AT AT AT
1512165 GGAATAAACG
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1517300 original size:11 final size:12
Alignment explanation
Indices: 1517277--1517305 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
1517267 TATCTAACAC
1517277 TAAATTAAATAA
1 TAAATTAAATAA
1517289 TAAATT-AATAA
1 TAAATTAAATAA
1517300 TAAATT
1 TAAATT
1517306 TAATTTTAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TAAATTAAATAA
Found at i:1517308 original size:12 final size:12
Alignment explanation
Indices: 1517277--1517309 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
1517267 TATCTAACAC
*
1517277 TAAATTAAATAA
1 TAAATTTAATAA
1517289 TAAA-TTAATAA
1 TAAATTTAATAA
1517300 TAAATTTAAT
1 TAAATTTAAT
1517310 TTTAGATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
TAAATTTAATAA
Found at i:1517675 original size:14 final size:14
Alignment explanation
Indices: 1517640--1517685 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
1517630 CGATGAATAT
*
1517640 ATATATTTTTAAAA
1 ATATATTTATAAAA
1517654 ATAT-TTTATAAAA
1 ATATATTTATAAAA
* *
1517667 ATTTATTTATGAAA
1 ATATATTTATAAAA
1517681 ATATA
1 ATATA
1517686 AAAATTATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
13 11 0.41
14 16 0.59
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (14 bp):
ATATATTTATAAAA
Found at i:1519199 original size:27 final size:26
Alignment explanation
Indices: 1519153--1519219 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 26
1519143 CATGTTTATT
*
1519153 TATTT-TATTATATTTAATATATTTTA
1 TATTTATATTATATTTAATATA-TTAA
*
1519179 TATTTATATTA-ATTATGATATATTAA
1 TATTTATATTATATT-TAATATATTAA
1519205 TAATTTATATTATAT
1 T-ATTTATATTATAT
1519220 AATATTTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
26 12 0.34
27 21 0.60
28 2 0.06
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (26 bp):
TATTTATATTATATTTAATATATTAA
Found at i:1519657 original size:16 final size:14
Alignment explanation
Indices: 1519637--1519677 Score: 55
Period size: 14 Copynumber: 2.8 Consensus size: 14
1519627 ATTGTTGAAG
1519637 TTTAAATTATAAATT
1 TTTAAA-TATAAATT
*
1519652 TATTAAATATTAATT
1 T-TTAAATATAAATT
1519667 TTTAAATATAA
1 TTTAAATATAA
1519678 TTATATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 9 0.39
15 9 0.39
16 5 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TTTAAATATAAATT
Found at i:1522986 original size:13 final size:13
Alignment explanation
Indices: 1522970--1522994 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1522960 GTGTCATCAA
1522970 AAATTTAAATTTT
1 AAATTTAAATTTT
1522983 AAATTTAAATTT
1 AAATTTAAATTT
1522995 CGATTTTATC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AAATTTAAATTTT
Found at i:1526731 original size:2 final size:2
Alignment explanation
Indices: 1526724--1526759 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1526714 TGAATTACAT
1526724 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1526760 AGACCTATCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1528821 original size:45 final size:41
Alignment explanation
Indices: 1528765--1528848 Score: 105
Period size: 45 Copynumber: 2.0 Consensus size: 41
1528755 AAAAATATAA
* *
1528765 TAATATTAAATAATTATATAATTTAAATATAAAAATAAATAAAGT
1 TAATATAAAATAATTA-A-AAATT-AAT-TAAAAATAAATAAAGT
*
1528810 TAATATAAAATAATTAAAAATTAATTAAATATAAATAAA
1 TAATATAAAATAATTAAAAATTAATTAAAAATAAATAAA
1528849 AACCTTTAAG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
41 13 0.36
42 3 0.08
43 4 0.11
44 1 0.03
45 15 0.42
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (41 bp):
TAATATAAAATAATTAAAAATTAATTAAAAATAAATAAAGT
Found at i:1528833 original size:21 final size:21
Alignment explanation
Indices: 1528790--1528850 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
1528780 ATATAATTTA
*
1528790 AATATAAAAATAAAT-AAAGTT
1 AATAT-AAAATAAATAAAAATT
*
1528811 AATATAAAATAATTAAAAATT
1 AATATAAAATAAATAAAAATT
1528832 AAT-TAAATATAAATAAAAA
1 AATATAAA-ATAAATAAAAA
1528851 CCTTTAAGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 12 0.34
21 23 0.66
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.30
Consensus pattern (21 bp):
AATATAAAATAAATAAAAATT
Found at i:1529484 original size:26 final size:28
Alignment explanation
Indices: 1529455--1529506 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
1529445 ATATTTTATT
*
1529455 ATATAAA-TTTTACATATAT-AAATGTA
1 ATATAAATTTTTAAATATATCAAATGTA
1529481 ATATAAATTTTTAAATATATCAAATG
1 ATATAAATTTTTAAATATATCAAATG
1529507 CGATATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 7 0.30
27 11 0.48
28 5 0.22
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (28 bp):
ATATAAATTTTTAAATATATCAAATGTA
Found at i:1529512 original size:28 final size:26
Alignment explanation
Indices: 1529455--1529513 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
1529445 ATATTTTATT
* *
1529455 ATATAAATTTTACATATATAAATGTA
1 ATATAAATTTTAAATATATAAATGCA
*
1529481 ATATAAATTTTTAAATATATCAAATGCG
1 ATATAAA-TTTTAAATATAT-AAATGCA
1529509 ATATA
1 ATATA
1529514 TATGTATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 7 0.25
27 11 0.39
28 10 0.36
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (26 bp):
ATATAAATTTTAAATATATAAATGCA
Found at i:1534294 original size:23 final size:23
Alignment explanation
Indices: 1534268--1534317 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
1534258 ACCACTACTT
*
1534268 TTCTTTAAGCAAATAAATGGTGC
1 TTCTTGAAGCAAATAAATGGTGC
* *
1534291 TTCTTGGAGCAAATAAATGGTGT
1 TTCTTGAAGCAAATAAATGGTGC
1534314 TTCT
1 TTCT
1534318 GTACATTCCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (23 bp):
TTCTTGAAGCAAATAAATGGTGC
Found at i:1534333 original size:2 final size:2
Alignment explanation
Indices: 1534326--1534358 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1534316 CTGTACATTC
1534326 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1534359 AATGTTTCTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1534830 original size:2 final size:2
Alignment explanation
Indices: 1534825--1534856 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1534815 ATGAACTCTG
*
1534825 TA TA TA TA TC TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1534857 AAAAACAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1538716 original size:25 final size:25
Alignment explanation
Indices: 1538688--1538738 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
1538678 AGGATAATAA
*
1538688 TTTATATT-ATATAAATATTAATTTT
1 TTTATATTCATAT-AATATTAAATTT
*
1538713 TTTATATTCATGTAATATTAAATTT
1 TTTATATTCATATAATATTAAATTT
1538738 T
1 T
1538739 ATATCATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 20 0.87
26 3 0.13
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (25 bp):
TTTATATTCATATAATATTAAATTT
Found at i:1538783 original size:18 final size:18
Alignment explanation
Indices: 1538760--1538794 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1538750 GTATTATTTT
1538760 TATA-TTATATTCAAATTA
1 TATATTTATATT-AAATTA
1538778 TATATTTATATTAAATT
1 TATATTTATATTAAATT
1538795 TAAAATAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (18 bp):
TATATTTATATTAAATTA
Done.