Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold33
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: 2032796
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.32
Warning! 48244 characters in sequence are not A, C, G, or T
File 11 of 13
Found at i:1653174 original size:32 final size:33
Alignment explanation
Indices: 1653100--1653182 Score: 91
Period size: 32 Copynumber: 2.5 Consensus size: 33
1653090 ATTTTAAATT
* *
1653100 TTTATA-ATTTATATATTCATATTATATTTATGTA
1 TTTATATATTTATATAAT-A-ATTATATTTATATA
*
1653134 TTTTTATATTT-TATAATAATTATATTTA-ATA
1 TTTATATATTTATATAATAATTATATTTATATA
1653165 TGTTATATATTTATATAA
1 T-TTATATATTTATATAA
1653183 ATTTTAATGT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
31 3 0.07
32 19 0.45
33 6 0.14
34 10 0.24
35 4 0.10
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.59
Consensus pattern (33 bp):
TTTATATATTTATATAATAATTATATTTATATA
Found at i:1653180 original size:8 final size:8
Alignment explanation
Indices: 1653100--1653181 Score: 62
Period size: 8 Copynumber: 10.0 Consensus size: 8
1653090 ATTTTAAATT
1653100 TTTATA-A
1 TTTATATA
1653107 TTTATATA
1 TTTATATA
1653115 TTCATATTATA
1 TT--TA-TATA
*
1653126 TTTATGTA
1 TTTATATA
*
1653134 TTTTTATA
1 TTTATATA
1653142 TTT-TATA
1 TTTATATA
* *
1653149 ATAATTATA
1 TTTA-TATA
1653158 TTTA-ATA
1 TTTATATA
1653165 TGTTATATA
1 T-TTATATA
1653174 TTTATATA
1 TTTATATA
1653182 AATTTTAATG
Statistics
Matches: 60, Mismatches: 7, Indels: 15
0.73 0.09 0.18
Matches are distributed among these distances:
7 15 0.25
8 25 0.42
9 12 0.20
10 2 0.03
11 6 0.10
ACGTcount: A:0.37, C:0.01, G:0.02, T:0.60
Consensus pattern (8 bp):
TTTATATA
Found at i:1655752 original size:2 final size:2
Alignment explanation
Indices: 1655745--1655791 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1655735 ATTTTTCTTC
1655745 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
1655787 TA TA T
1 TA TA T
1655792 TCTTTTTTGG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1658551 original size:26 final size:25
Alignment explanation
Indices: 1658521--1658573 Score: 70
Period size: 26 Copynumber: 2.1 Consensus size: 25
1658511 GGGTTACAAA
* * *
1658521 ATTAAATGTTATATTTTTAATATATT
1 ATTAAATATAATATATTTAAT-TATT
1658547 ATTAAATATAATATATTTAATTATT
1 ATTAAATATAATATATTTAATTATT
1658572 AT
1 AT
1658574 ATTATATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
25 6 0.25
26 18 0.75
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (25 bp):
ATTAAATATAATATATTTAATTATT
Found at i:1658583 original size:48 final size:44
Alignment explanation
Indices: 1658530--1658638 Score: 125
Period size: 43 Copynumber: 2.4 Consensus size: 44
1658520 AATTAAATGT
1658530 TATATT-TTTAATATATTATTAAATATAATATATTTAATTATTATATTA
1 TATATTATTTAATA-ATT-TT--ATA-AATATATTTAATTATTATATTA
*
1658578 TATATTATTT-ATAATTTTCTAAATATATTTAATTATTATATTA
1 TATATTATTTAATAATTTTATAAATATATTTAATTATTATATTA
* *
1658621 TACATTGTTT-ATAATTTT
1 TATATTATTTAATAATTTT
1658639 CAAAATGCAT
Statistics
Matches: 57, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
43 38 0.67
44 2 0.04
46 2 0.04
47 3 0.05
48 9 0.16
49 3 0.05
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (44 bp):
TATATTATTTAATAATTTTATAAATATATTTAATTATTATATTA
Found at i:1658605 original size:43 final size:43
Alignment explanation
Indices: 1658556--1658644 Score: 151
Period size: 43 Copynumber: 2.1 Consensus size: 43
1658546 TATTAAATAT
* *
1658556 AATATATTTAATTATTATATTATATATTATTTATAATTTTCTA
1 AATATATTTAATTATTATATTATACATTATTTATAATTTTCAA
*
1658599 AATATATTTAATTATTATATTATACATTGTTTATAATTTTCAA
1 AATATATTTAATTATTATATTATACATTATTTATAATTTTCAA
1658642 AAT
1 AAT
1658645 GCATTAAACT
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.55
Consensus pattern (43 bp):
AATATATTTAATTATTATATTATACATTATTTATAATTTTCAA
Found at i:1659372 original size:25 final size:25
Alignment explanation
Indices: 1659328--1659410 Score: 71
Period size: 25 Copynumber: 3.2 Consensus size: 25
1659318 AATGTTAAAT
*
1659328 ATTTAAATTATTTTTTATTTATAATGA
1 ATTTAAA-TA-TTTTAATTTATAATGA
**
1659355 ATTTAAATATTTTAATTTA-ATATTT
1 ATTTAAATATTTTAATTTATA-ATGA
* *
1659380 ATTTAAATA-TTTAATTTTTATTAGA
1 ATTTAAATATTTTAATTTATAAT-GA
1659405 ATTTAA
1 ATTTAA
1659411 TTAATAAATT
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
24 10 0.22
25 27 0.59
26 2 0.04
27 7 0.15
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (25 bp):
ATTTAAATATTTTAATTTATAATGA
Found at i:1659381 original size:36 final size:34
Alignment explanation
Indices: 1659306--1659388 Score: 96
Period size: 36 Copynumber: 2.4 Consensus size: 34
1659296 TCACTTAGAT
* *
1659306 TTTAGTTTAAATAATGTTAAATATTTAAATTATTT
1 TTTA-TTTAAATAATGTTAAATATTTAAATTAATA
*
1659341 TTTATTTATAATGAAT-TTAAATATTTTAATTTAATA
1 TTTATTTA-AAT-AATGTTAAATA-TTTAAATTAATA
1659377 TTTATTTAAATA
1 TTTATTTAAATA
1659389 TTTAATTTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
34 5 0.12
35 17 0.40
36 20 0.48
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (34 bp):
TTTATTTAAATAATGTTAAATATTTAAATTAATA
Found at i:1659388 original size:12 final size:12
Alignment explanation
Indices: 1659355--1659392 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
1659345 TTTATAATGA
1659355 ATTTAAATATTTT
1 ATTTAAATA-TTT
1659368 AATTT-AATATTT
1 -ATTTAAATATTT
1659380 ATTTAAATATTT
1 ATTTAAATATTT
1659392 A
1 A
1659393 ATTTTTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 4 0.17
12 11 0.48
13 4 0.17
14 4 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
ATTTAAATATTT
Found at i:1659396 original size:17 final size:17
Alignment explanation
Indices: 1659376--1659445 Score: 52
Period size: 17 Copynumber: 3.9 Consensus size: 17
1659366 TTAATTTAAT
1659376 ATTTATTTAAATATTTA
1 ATTTATTTAAATATTTA
* *
1659393 ATTTTTATTAGA-ATTTA
1 ATTTAT-TTAAATATTTA
1659410 ATTAATAAATTTAAATATTTA
1 ATT--T--ATTTAAATATTTA
**
1659431 ATAGATTTAAATATT
1 ATTTATTTAAATATT
1659446 CAAAATAACT
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
17 24 0.59
18 4 0.10
19 1 0.02
20 4 0.10
21 8 0.20
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
ATTTATTTAAATATTTA
Found at i:1659908 original size:25 final size:25
Alignment explanation
Indices: 1659880--1659929 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
1659870 AAAAATTTAA
1659880 TTAAAA-ATCAAATAAA-TAAAATCTT
1 TTAAAACAT-AAA-AAATTAAAATCTT
1659905 TTAAAACATAAAAAATTAAAATCTT
1 TTAAAACATAAAAAATTAAAATCTT
1659930 AGACCAACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 3 0.13
25 18 0.78
26 2 0.09
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (25 bp):
TTAAAACATAAAAAATTAAAATCTT
Found at i:1662242 original size:118 final size:117
Alignment explanation
Indices: 1662082--1662307 Score: 425
Period size: 118 Copynumber: 1.9 Consensus size: 117
1662072 TAATTTAAGG
*
1662082 ACCTGGAGAGGGTTTGCAAGTGAAAAATGCATAGTTTGAAAGTTTCAATTTAGCAGCACTTTCTT
1 ACCTGGAGAGGGTTTGCAAGTGAAAAATGCATAGTTTGAAAGTTTCAATTTAGAAGCACTTTCTT
1662147 TATTGCACATGCTTATTTTCCATCTACTGTTGATGCCTTTTTTTTTTCCCCCC
66 TATTGCACATGCTTATTTTCCATCTACTGTTGATG-CTTTTTTTTTTCCCCCC
*
1662200 ACCTGGAGAGGGTTTGCAAGTGAAAATTGCATAGTTTGAAAGTTTCAATTTAGAAGCACTTTCTT
1 ACCTGGAGAGGGTTTGCAAGTGAAAAATGCATAGTTTGAAAGTTTCAATTTAGAAGCACTTTCTT
1662265 TATTGCACATGCTTATTTTCCATCTACTGTTGATGCTTTTTTT
66 TATTGCACATGCTTATTTTCCATCTACTGTTGATGCTTTTTTT
1662308 CCCCCCTTCT
Statistics
Matches: 106, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
117 8 0.08
118 98 0.92
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.41
Consensus pattern (117 bp):
ACCTGGAGAGGGTTTGCAAGTGAAAAATGCATAGTTTGAAAGTTTCAATTTAGAAGCACTTTCTT
TATTGCACATGCTTATTTTCCATCTACTGTTGATGCTTTTTTTTTTCCCCCC
Found at i:1664936 original size:29 final size:29
Alignment explanation
Indices: 1664903--1664974 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
1664893 TCATCTCCAT
*
1664903 CTAAACTGATCTTCTTGATTGGGCA-CTCC
1 CTAAACTGATCTTCTTGATT-GGAAGCTCC
* ** *
1664932 CTAAATTGATAATCTTGATTGGAAGCTCT
1 CTAAACTGATCTTCTTGATTGGAAGCTCC
1664961 CTAAACTGATCTTC
1 CTAAACTGATCTTC
1664975 AGGACTTGAT
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.36
Consensus pattern (29 bp):
CTAAACTGATCTTCTTGATTGGAAGCTCC
Found at i:1667999 original size:3 final size:3
Alignment explanation
Indices: 1667993--1668027 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1667983 AAAAAAACCC
1667993 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1668028 ACCTCGACCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1669345 original size:21 final size:21
Alignment explanation
Indices: 1669319--1669372 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 21
1669309 TTTTAAGTCG
1669319 TATTTTTAAATTTTATTTTAA
1 TATTTTTAAATTTTATTTTAA
* *
1669340 TATTTTT-ATTTTTATTTTTA
1 TATTTTTAAATTTTATTTTAA
1669360 T-TTTTTAAATTTT
1 TATTTTTAAATTTT
1669373 TTATTATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 5 0.17
20 17 0.59
21 7 0.24
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (21 bp):
TATTTTTAAATTTTATTTTAA
Found at i:1669351 original size:6 final size:6
Alignment explanation
Indices: 1669319--1669364 Score: 56
Period size: 6 Copynumber: 7.2 Consensus size: 6
1669309 TTTTAAGTCG
*
1669319 TATTTT TAAATTT TATTTT AATATTTT TATTTT TATTTT TATTTT T
1 TATTTT T-ATTTT TATTTT --TATTTT TATTTT TATTTT TATTTT T
1669365 TAAATTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
6 24 0.69
7 5 0.14
8 6 0.17
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (6 bp):
TATTTT
Found at i:1669382 original size:21 final size:21
Alignment explanation
Indices: 1669321--1669383 Score: 55
Period size: 21 Copynumber: 3.1 Consensus size: 21
1669311 TTAAGTCGTA
1669321 TTTTTAAATTTTATT-TTA-AT
1 TTTTTAAATTTT-TTATTATAT
*
1669341 ATTTTT--A-TTTTTATTTTTAT
1 -TTTTTAAATTTTTTA-TTATAT
1669361 TTTTTAAATTTTTTATTATAT
1 TTTTTAAATTTTTTATTATAT
1669382 TT
1 TT
1669384 ATTGATTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
17 2 0.06
18 3 0.09
19 8 0.24
20 2 0.06
21 13 0.38
22 6 0.18
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTTTAAATTTTTTATTATAT
Found at i:1671637 original size:21 final size:21
Alignment explanation
Indices: 1671613--1671661 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
1671603 CCAATGGGTG
*
1671613 ATGTATCGATACATTCATATA
1 ATGTATCGATACATTCACATA
*
1671634 ATGTATAGATACATTCACATA
1 ATGTATCGATACATTCACATA
1671655 ATGTATC
1 ATGTATC
1671662 AATATAGGGC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (21 bp):
ATGTATCGATACATTCACATA
Found at i:1673221 original size:342 final size:342
Alignment explanation
Indices: 1672591--1673277 Score: 1266
Period size: 342 Copynumber: 2.0 Consensus size: 342
1672581 ATTCTTGTAT
1672591 ATCGACGGACTTGTGGTGTTATTTTGACAATCAAAATCCTTTATTTTTTCTCTTCGTAATGTAGA
1 ATCGACGGACTTGTGGTGTTATTTTGACAATCAAAATCCTTTATTTTTTCTCTTCGTAATGTAGA
* * *
1672656 CCTGTTTTGGTTGTTTAGTATCATGGCATTATTTCTTATGCTCCACCCATGCTAATATGTGCTCA
66 CCTATTTTGGTTGTTTACTACCATGGCATTATTTCTTATGCTCCACCCATGCTAATATGTGCTCA
*
1672721 TGAAACATACCTTGATGATGTCCATGCATTTGAGCTTTGCTTTATGTGTCAAAAATGTTTTTATG
131 TGAAACATACCTTGATGATGTCCATGCATTTGAGCTTTGCTTTATGTGTCAAAAATGTTTTGATG
* *
1672786 ATGTTGGTTTTATGTCTTGTATGTTTTATGCTTCTGATGAAGTTTTAGCTTATCACATGCTTGTA
196 ATGTTGGTTCTATGTCTTGTATGTTTTATGCTTCGGATGAAGTTTTAGCTTATCACATGCTTGTA
1672851 AAAATGCTTGTTTTATGCCTCCCTGATGTATGCTAAAATATGTTTTTGCAAAACCCCTCAAGTTA
261 AAAATGCTTGTTTTATGCCTCCCTGATGTATGCTAAAATATGTTTTTGCAAAACCCCTCAAGTTA
1672916 GATTAATATTGGTTCTA
326 GATTAATATTGGTTCTA
*
1672933 ATCGACGGACTTGTGGTGTTATTTTGACAATCAAAATCCTTTATTTTTTCTCTTGGTAATGTAGA
1 ATCGACGGACTTGTGGTGTTATTTTGACAATCAAAATCCTTTATTTTTTCTCTTCGTAATGTAGA
*
1672998 CCTATTTTGGTTGTTTACTACCATGGCATTATTTCTTATGCTCCATCCATGCTAATATGTGCTCA
66 CCTATTTTGGTTGTTTACTACCATGGCATTATTTCTTATGCTCCACCCATGCTAATATGTGCTCA
*
1673063 TGAAACATACCTTGATGATGTCCATGCATTTGAGTTTTGCTTTATGTGTCAAAAATGTTTTGATG
131 TGAAACATACCTTGATGATGTCCATGCATTTGAGCTTTGCTTTATGTGTCAAAAATGTTTTGATG
1673128 ATGTTGGTTCTATGTCTTGTATGTTTTATGCTTCGGATGAAGTTTTAGCTTATCACATGCTTGTA
196 ATGTTGGTTCTATGTCTTGTATGTTTTATGCTTCGGATGAAGTTTTAGCTTATCACATGCTTGTA
* * *
1673193 AAAATGCTTGTTTTATGCCTCTCTGATGTATGCTAAAATCTGTTTTTGCAAAACCCCTTAAGTTA
261 AAAATGCTTGTTTTATGCCTCCCTGATGTATGCTAAAATATGTTTTTGCAAAACCCCTCAAGTTA
1673258 GATTAATATTGGTTCTA
326 GATTAATATTGGTTCTA
1673275 ATC
1 ATC
1673278 AATGGGATTA
Statistics
Matches: 333, Mismatches: 12, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
342 333 1.00
ACGTcount: A:0.24, C:0.16, G:0.17, T:0.43
Consensus pattern (342 bp):
ATCGACGGACTTGTGGTGTTATTTTGACAATCAAAATCCTTTATTTTTTCTCTTCGTAATGTAGA
CCTATTTTGGTTGTTTACTACCATGGCATTATTTCTTATGCTCCACCCATGCTAATATGTGCTCA
TGAAACATACCTTGATGATGTCCATGCATTTGAGCTTTGCTTTATGTGTCAAAAATGTTTTGATG
ATGTTGGTTCTATGTCTTGTATGTTTTATGCTTCGGATGAAGTTTTAGCTTATCACATGCTTGTA
AAAATGCTTGTTTTATGCCTCCCTGATGTATGCTAAAATATGTTTTTGCAAAACCCCTCAAGTTA
GATTAATATTGGTTCTA
Found at i:1679492 original size:2 final size:2
Alignment explanation
Indices: 1679485--1679514 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1679475 CCATTCCTCA
*
1679485 TC TC TC TC TC CC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1679515 CTCCCTGTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
TC
Found at i:1680454 original size:6 final size:7
Alignment explanation
Indices: 1680428--1680453 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
1680418 AAAAATATAA
1680428 TTAAAAT
1 TTAAAAT
1680435 TTAAAAT
1 TTAAAAT
1680442 TTAAAAT
1 TTAAAAT
1680449 TTAAA
1 TTAAA
1680454 TAATAATTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
TTAAAAT
Found at i:1682094 original size:19 final size:19
Alignment explanation
Indices: 1682059--1682098 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
1682049 ATCTTGTAAA
1682059 TTTTATTTAAATTTATTATT
1 TTTTATTT-AATTTATTATT
1682079 TTTTATTT-ATTATATTATT
1 TTTTATTTAATT-TATTATT
1682098 T
1 T
1682099 ATATATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 3 0.16
19 8 0.42
20 8 0.42
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTATTTAATTTATTATT
Found at i:1686240 original size:19 final size:19
Alignment explanation
Indices: 1686194--1686239 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
1686184 GAATTCTGAC
1686194 ATATTTATATTTTTATATT
1 ATATTTATATTTTTATATT
1686213 ATATTTATATTATTT-T-TT
1 ATATTTATATT-TTTATATT
1686231 ATA-TTATAT
1 ATATTTATAT
1686240 AATCATCTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 6 0.23
18 5 0.19
19 12 0.46
20 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (19 bp):
ATATTTATATTTTTATATT
Found at i:1690431 original size:2 final size:2
Alignment explanation
Indices: 1690420--1690454 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1690410 AAAGTCTATG
1690420 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1690455 CAAGCAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1692785 original size:2 final size:2
Alignment explanation
Indices: 1692778--1692812 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
1692768 CAATCAATAA
*
1692778 AT AT AT AT AT AT AT AT AT AT CT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1692813 GTGTACAAAG
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:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1693934 original size:15 final size:16
Alignment explanation
Indices: 1693914--1693943 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1693904 AATTAAATAT
1693914 ATAAAATAT-TAAAGC
1 ATAAAATATGTAAAGC
1693929 ATAAAATATGTAAAG
1 ATAAAATATGTAAAG
1693944 TTATCCATGT
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:0.60, C:0.03, G:0.10, T:0.27
Consensus pattern (16 bp):
ATAAAATATGTAAAGC
Found at i:1694878 original size:18 final size:18
Alignment explanation
Indices: 1694855--1694915 Score: 67
Period size: 18 Copynumber: 3.6 Consensus size: 18
1694845 AAAATATCAC
1694855 ATATATTTATAAATTTTA
1 ATATATTTATAAATTTTA
* **
1694873 AGATATGAAT-AA-TTT-
1 ATATATTTATAAATTTTA
1694888 ATAT-TTTATAAATTTTA
1 ATATATTTATAAATTTTA
1694905 ATATATTTATA
1 ATATATTTATA
1694916 TTTCATATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
14 3 0.09
15 5 0.15
16 6 0.18
17 6 0.18
18 13 0.39
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52
Consensus pattern (18 bp):
ATATATTTATAAATTTTA
Found at i:1694924 original size:32 final size:32
Alignment explanation
Indices: 1694854--1694988 Score: 100
Period size: 32 Copynumber: 4.2 Consensus size: 32
1694844 TAAAATATCA
*
1694854 CATATATTTATAAATTTTAAGATATGAATAATTT
1 CATAT-TTTATAAATTTTAATATATGAAT-ATTT
**
1694888 -ATATTTTATAAATTTTAATATATTTATATTT
1 CATATTTTATAAATTTTAATATATGAATATTT
* *
1694919 CATATTTATGTTATATTTT-AT-T-TGAATTATTT
1 CATATTT-T-ATAAATTTTAATATATGAA-TATTT
* * * **
1694951 -ATATTATATAAATTTTGACATATTTATATTT
1 CATATTTTATAAATTTTAATATATGAATATTT
1694982 CATATTT
1 CATATTT
1694989 GTGTTATATT
Statistics
Matches: 79, Mismatches: 14, Indels: 18
0.71 0.13 0.16
Matches are distributed among these distances:
29 7 0.09
30 2 0.03
31 17 0.22
32 39 0.49
33 7 0.09
34 7 0.09
ACGTcount: A:0.37, C:0.03, G:0.04, T:0.56
Consensus pattern (32 bp):
CATATTTTATAAATTTTAATATATGAATATTT
Found at i:1694927 original size:63 final size:61
Alignment explanation
Indices: 1694857--1694988 Score: 158
Period size: 63 Copynumber: 2.1 Consensus size: 61
1694847 AATATCACAT
* *
1694857 ATATTTA-TAAATTTTAAGATATGAATAATTTATATTTTATAAATTTTAATATATTTATATTTC
1 ATATTTATTAAATTTT---ATATGAATAATTTATATTATATAAATTTTAACATATTTATATTTC
* * * *
1694920 ATATTTATGTTATATTTTATTTGAATTATTTATATTATATAAATTTTGACATATTTATATTTC
1 ATATTTA--TTAAATTTTATATGAATAATTTATATTATATAAATTTTAACATATTTATATTTC
1694983 ATATTT
1 ATATTT
1694989 GTGTTATATT
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
63 53 0.88
66 7 0.12
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (61 bp):
ATATTTATTAAATTTTATATGAATAATTTATATTATATAAATTTTAACATATTTATATTTC
Found at i:1694994 original size:63 final size:63
Alignment explanation
Indices: 1694878--1695011 Score: 223
Period size: 63 Copynumber: 2.1 Consensus size: 63
1694868 TTTTAAGATA
* * *
1694878 TGAATAATTTATATTTTATAAATTTTAATATATTTATATTTCATATTTATGTTATATTTTATT
1 TGAATTATTTATATTATATAAATTTTAACATATTTATATTTCATATTTATGTTATATTTTATT
* *
1694941 TGAATTATTTATATTATATAAATTTTGACATATTTATATTTCATATTTGTGTTATATTTTATT
1 TGAATTATTTATATTATATAAATTTTAACATATTTATATTTCATATTTATGTTATATTTTATT
1695004 TGAATTAT
1 TGAATTAT
1695012 GTAATTGTGT
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 66 1.00
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (63 bp):
TGAATTATTTATATTATATAAATTTTAACATATTTATATTTCATATTTATGTTATATTTTATT
Found at i:1696914 original size:18 final size:19
Alignment explanation
Indices: 1696887--1696927 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
1696877 AAATATTTTT
*
1696887 TAAATTTAATTATAAAT-A
1 TAAATATAATTATAAATAA
*
1696905 TAAATATAATTTTAAATAA
1 TAAATATAATTATAAATAA
1696924 TAAA
1 TAAA
1696928 ATTAATTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TAAATATAATTATAAATAA
Found at i:1696945 original size:21 final size:21
Alignment explanation
Indices: 1696901--1696941 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
1696891 TTTAATTATA
1696901 AATATAAATATAATTTTAAAT
1 AATATAAATATAATTTTAAAT
1696922 AATA-AAAT-TAATTTTCAAAT
1 AATATAAATATAATTTT-AAAT
1696942 TAATTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
20 8 0.42
21 4 0.21
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
AATATAAATATAATTTTAAAT
Found at i:1696959 original size:30 final size:31
Alignment explanation
Indices: 1696906--1696966 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 31
1696896 TTATAAATAT
*
1696906 AAATATAATTTTAAATAATAAAATTAATTTTC
1 AAATATAATTTTAAATAAAAAAATT-ATTTTC
1696938 AAAT-TAATTTT-AATAAAAAAATTATTTTC
1 AAATATAATTTTAAATAAAAAAATTATTTTC
1696967 TCATGTCACT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 6 0.21
30 11 0.39
31 7 0.25
32 4 0.14
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.44
Consensus pattern (31 bp):
AAATATAATTTTAAATAAAAAAATTATTTTC
Found at i:1699132 original size:10 final size:10
Alignment explanation
Indices: 1699119--1699148 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
1699109 AATTGATTTA
1699119 AATTTAAAAT
1 AATTTAAAAT
1699129 AATTTAAAAT
1 AATTTAAAAT
1699139 AATTTAAAAT
1 AATTTAAAAT
1699149 GATTCAAACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
AATTTAAAAT
Found at i:1703120 original size:15 final size:15
Alignment explanation
Indices: 1703096--1703131 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
1703086 CGGACAATGG
*
1703096 CATAAAACTCTTTGT
1 CATAAGACTCTTTGT
1703111 CATAAGACTCTTTGT
1 CATAAGACTCTTTGT
1703126 CATAAG
1 CATAAG
1703132 TTGAATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.36
Consensus pattern (15 bp):
CATAAGACTCTTTGT
Found at i:1706223 original size:11 final size:11
Alignment explanation
Indices: 1706200--1706233 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
1706190 GAAGTGACAC
1706200 GTGGCAGATGAT
1 GTGGCA-ATGAT
1706212 GTGGCAATGAT
1 GTGGCAATGAT
*
1706223 GTGGCGATGAT
1 GTGGCAATGAT
1706234 TGGACAACTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 15 0.71
12 6 0.29
ACGTcount: A:0.24, C:0.09, G:0.41, T:0.26
Consensus pattern (11 bp):
GTGGCAATGAT
Found at i:1706971 original size:20 final size:20
Alignment explanation
Indices: 1706948--1707020 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1706938 ACAATTCAAA
1706948 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
1706968 GTATCGATACATGAAAAAAAT
1 GTATCGATACATG-TTGCAAT
1706989 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1707009 GTATCGATACAT
1 GTATCGATACAT
1707021 AAAAAGGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1706991 original size:21 final size:21
Alignment explanation
Indices: 1706965--1707041 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
1706955 TACATGTTGC
1706965 AATGTATCGATACATGAAAAA
1 AATGTATCGATACATGAAAAA
****
1706986 AATGTATCGATACATG-TTGC
1 AATGTATCGATACATGAAAAA
1707006 AATGTATCGATACAT-AAAAA
1 AATGTATCGATACATGAAAAA
*
1707026 GGATGTATCGATACAT
1 -AATGTATCGATACAT
1707042 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
AATGTATCGATACATGAAAAA
Found at i:1706999 original size:41 final size:41
Alignment explanation
Indices: 1706948--1707041 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
1706938 ACAATTCAAA
1706948 GTATCGATACATGTTGCAATGTATCGATACATGAAAAA-AAT
1 GTATCGATACATGTTGCAATGTATCGATACAT-AAAAAGAAT
*
1706989 GTATCGATACATGTTGCAATGTATCGATACATAAAAAGGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAGAAT
1707030 GTATCGATACAT
1 GTATCGATACAT
1707042 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 5 0.10
41 46 0.90
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAGAAT
Found at i:1707098 original size:13 final size:13
Alignment explanation
Indices: 1707080--1707105 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1707070 TACAGCAAGT
1707080 ATGTATCGATACA
1 ATGTATCGATACA
1707093 ATGTATCGATACA
1 ATGTATCGATACA
1707106 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1711187 original size:15 final size:15
Alignment explanation
Indices: 1711167--1711197 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1711157 TAAAAATGTC
*
1711167 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1711182 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1711197 C
1 C
1711198 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1713294 original size:13 final size:13
Alignment explanation
Indices: 1713276--1713314 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1713266 ACATTTTTCC
1713276 TTGTATCGATACA
1 TTGTATCGATACA
1713289 TTGTATCGATACA
1 TTGTATCGATACA
*
1713302 CTGTATCGATACA
1 TTGTATCGATACA
1713315 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1715761 original size:20 final size:20
Alignment explanation
Indices: 1715738--1715810 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1715728 ACAATTCAAA
1715738 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
1715758 GTATCGATACATGAAAAAAAT
1 GTATCGATACATG-TTGCAAT
1715779 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
1715799 GTATCGATACAT
1 GTATCGATACAT
1715811 AAAAAGGATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.32
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:1715781 original size:21 final size:21
Alignment explanation
Indices: 1715755--1715831 Score: 86
Period size: 21 Copynumber: 3.7 Consensus size: 21
1715745 TACATGTTGC
1715755 AATGTATCGATACATGAAAAA
1 AATGTATCGATACATGAAAAA
****
1715776 AATGTATCGATACATG-TTGC
1 AATGTATCGATACATGAAAAA
1715796 AATGTATCGATACAT-AAAAA
1 AATGTATCGATACATGAAAAA
*
1715816 GGATGTATCGATACAT
1 -AATGTATCGATACAT
1715832 TTCTTGGCAG
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
20 15 0.33
21 30 0.67
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.29
Consensus pattern (21 bp):
AATGTATCGATACATGAAAAA
Found at i:1715789 original size:41 final size:41
Alignment explanation
Indices: 1715738--1715831 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
1715728 ACAATTCAAA
1715738 GTATCGATACATGTTGCAATGTATCGATACATGAAAAA-AAT
1 GTATCGATACATGTTGCAATGTATCGATACAT-AAAAAGAAT
*
1715779 GTATCGATACATGTTGCAATGTATCGATACATAAAAAGGAT
1 GTATCGATACATGTTGCAATGTATCGATACATAAAAAGAAT
1715820 GTATCGATACAT
1 GTATCGATACAT
1715832 TTCTTGGCAG
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 5 0.10
41 46 0.90
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATAAAAAGAAT
Found at i:1715888 original size:13 final size:13
Alignment explanation
Indices: 1715870--1715895 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1715860 TACAGCAAGT
1715870 ATGTATCGATACA
1 ATGTATCGATACA
1715883 ATGTATCGATACA
1 ATGTATCGATACA
1715896 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1717165 original size:21 final size:21
Alignment explanation
Indices: 1717141--1717184 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
1717131 AGTTACCTTG
1717141 AGGATAATATGGATCAACATC
1 AGGATAATATGGATCAACATC
*
1717162 AGGATGATATGGATCAACATC
1 AGGATAATATGGATCAACATC
1717183 AG
1 AG
1717185 ATACATTGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.14, G:0.23, T:0.23
Consensus pattern (21 bp):
AGGATAATATGGATCAACATC
Found at i:1722060 original size:67 final size:67
Alignment explanation
Indices: 1721952--1722082 Score: 253
Period size: 67 Copynumber: 2.0 Consensus size: 67
1721942 TAATCTTCAC
*
1721952 ACAACTCTTTGTACTATGAATAAAGTATTTACAAACAATTTGAAACTTTAATAGGTGGAAGTTTG
1 ACAACCCTTTGTACTATGAATAAAGTATTTACAAACAATTTGAAACTTTAATAGGTGGAAGTTTG
1722017 CT
66 CT
1722019 ACAACCCTTTGTACTATGAATAAAGTATTTACAAACAATTTGAAACTTTAATAGGTGGAAGTTT
1 ACAACCCTTTGTACTATGAATAAAGTATTTACAAACAATTTGAAACTTTAATAGGTGGAAGTTT
1722083 ACTAAAATTT
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
67 63 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (67 bp):
ACAACCCTTTGTACTATGAATAAAGTATTTACAAACAATTTGAAACTTTAATAGGTGGAAGTTTG
CT
Found at i:1722779 original size:16 final size:15
Alignment explanation
Indices: 1722753--1722783 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
1722743 CAAATATAAC
1722753 TTATTTTATATCAAA
1 TTATTTTATATCAAA
1722768 TTATTATTATATCAAA
1 TTATT-TTATATCAAA
1722784 ATCAAGATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (15 bp):
TTATTTTATATCAAA
Found at i:1727532 original size:11 final size:11
Alignment explanation
Indices: 1727518--1727576 Score: 55
Period size: 11 Copynumber: 5.1 Consensus size: 11
1727508 TTACAACATA
*
1727518 TAAATACTATT
1 TAAATATTATT
*
1727529 TAAAAATTATT
1 TAAATATTATT
*
1727540 TAATTATTATT
1 TAAATATTATT
*
1727551 TAAAAATTATATT
1 TAAATA-T-TATT
1727564 TAATATATTATT
1 TAA-ATATTATT
1727576 T
1 T
1727577 TTATTAAATT
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
11 22 0.58
12 6 0.16
13 8 0.21
14 2 0.05
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (11 bp):
TAAATATTATT
Found at i:1727550 original size:22 final size:25
Alignment explanation
Indices: 1727525--1727576 Score: 83
Period size: 22 Copynumber: 2.2 Consensus size: 25
1727515 ATATAAATAC
1727525 TATTTAAAAA-T-TATTTAAT-TAT
1 TATTTAAAAATTATATTTAATATAT
1727547 TATTTAAAAATTATATTTAATATAT
1 TATTTAAAAATTATATTTAATATAT
1727572 TATTT
1 TATTT
1727577 TTATTAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 10 0.37
23 1 0.04
24 8 0.30
25 8 0.30
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TATTTAAAAATTATATTTAATATAT
Found at i:1727560 original size:14 final size:15
Alignment explanation
Indices: 1727541--1727586 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 15
1727531 AAAATTATTT
1727541 AATTATTATTTAA-A
1 AATTATTATTTAATA
1727555 AATTA-TATTTAATA
1 AATTATTATTTAATA
* *
1727569 TATTATT-TTTATTA
1 AATTATTATTTAATA
1727583 AATT
1 AATT
1727587 TTAAAAAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 7 0.26
14 19 0.70
15 1 0.04
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
AATTATTATTTAATA
Found at i:1727810 original size:30 final size:30
Alignment explanation
Indices: 1727770--1727829 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
1727760 TATTATATAA
* *
1727770 TTTATATTTATTTATTTTGATCAT-CATAT
1 TTTATATTTATTTATATAGATCATGCATAT
1727799 TTTATTATTTATTTATATAGATCATGCATAT
1 TTTA-TATTTATTTATATAGATCATGCATAT
1727830 AAAATTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
29 4 0.15
30 18 0.67
31 5 0.19
ACGTcount: A:0.30, C:0.07, G:0.05, T:0.58
Consensus pattern (30 bp):
TTTATATTTATTTATATAGATCATGCATAT
Found at i:1727816 original size:18 final size:19
Alignment explanation
Indices: 1727739--1727816 Score: 56
Period size: 18 Copynumber: 4.1 Consensus size: 19
1727729 AAATAAATTA
1727739 ATTTTA-TATATT-TTTAT
1 ATTTTATTATATTATTTAT
* *
1727756 AATTTATTATATAATTTAT
1 ATTTTATTATATTATTTAT
* *
1727775 A-TTTATTTATTTTGATCATCAT
1 ATTTTA-TTATATT-AT--TTAT
1727797 ATTTTATTAT-TTATTTAT
1 ATTTTATTATATTATTTAT
1727815 AT
1 AT
1727817 AGATCATGCA
Statistics
Matches: 48, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
17 5 0.10
18 14 0.29
19 11 0.23
20 4 0.08
21 2 0.04
22 8 0.17
23 4 0.08
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (19 bp):
ATTTTATTATATTATTTAT
Found at i:1728020 original size:13 final size:13
Alignment explanation
Indices: 1728002--1728027 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1727992 TCTAACAGTT
1728002 AATTGTTAATATA
1 AATTGTTAATATA
1728015 AATTGTTAATATA
1 AATTGTTAATATA
1728028 TTAACTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.46
Consensus pattern (13 bp):
AATTGTTAATATA
Found at i:1728107 original size:2 final size:2
Alignment explanation
Indices: 1728100--1728131 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1728090 AATATCCCTT
*
1728100 TA TA TA TA TT 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
1728132 ATTCAAGTTA
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:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1729783 original size:27 final size:27
Alignment explanation
Indices: 1729736--1729787 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
1729726 TATATATTTT
*
1729736 ATTTTAAAATATTTTATATTTATATAA
1 ATTTTAAAATATTATATATTTATATAA
*
1729763 ATTTTAATATATTA-ATAATTTATAT
1 ATTTTAAAATATTATAT-ATTTATAT
1729788 TACATATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 2 0.09
27 20 0.91
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
ATTTTAAAATATTATATATTTATATAA
Found at i:1731614 original size:11 final size:11
Alignment explanation
Indices: 1731600--1731667 Score: 77
Period size: 11 Copynumber: 6.3 Consensus size: 11
1731590 TAATACGATT
1731600 ATATAATATAA
1 ATATAATATAA
*
1731611 ATATAATTTAAA
1 ATATAATAT-AA
1731623 ATATAATATAA
1 ATATAATATAA
*
1731634 TTATAATA-AA
1 ATATAATATAA
*
1731644 AAAT-ATATAA
1 ATATAATATAA
*
1731654 ATATTATATAA
1 ATATAATATAA
1731665 ATA
1 ATA
1731668 CATAGATTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
9 3 0.06
10 9 0.19
11 26 0.54
12 10 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
ATATAATATAA
Found at i:1731626 original size:23 final size:21
Alignment explanation
Indices: 1731600--1731667 Score: 75
Period size: 23 Copynumber: 3.1 Consensus size: 21
1731590 TAATACGATT
1731600 ATATAATATAAATATAATTTAAA
1 ATATAATATAAATATAA--TAAA
*
1731623 ATATAATATAATTATAATAAA
1 ATATAATATAAATATAATAAA
* *
1731644 AAAT-ATATAAATATTATATAA
1 ATATAATATAAATATAATA-AA
1731665 ATA
1 ATA
1731668 CATAGATTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
20 12 0.31
21 11 0.28
23 16 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
ATATAATATAAATATAATAAA
Found at i:1732189 original size:16 final size:16
Alignment explanation
Indices: 1732168--1732213 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
1732158 CATAAAAGTA
1732168 AAAATTATAAATATTT
1 AAAATTATAAATATTT
*
1732184 AAAATT-TAAA-ATCT
1 AAAATTATAAATATTT
*
1732198 AAATTTATTAAATATT
1 AAAATTA-TAAATATT
1732214 ATTTTTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
14 8 0.33
15 4 0.17
16 10 0.42
17 2 0.08
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (16 bp):
AAAATTATAAATATTT
Found at i:1733172 original size:16 final size:16
Alignment explanation
Indices: 1733149--1733188 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
1733139 TAATATTATA
1733149 TTATTAAAAT-AAATT
1 TTATTAAAATAAAATT
1733164 TTATGTAAAATAAAATT
1 TTAT-TAAAATAAAATT
*
1733181 TTAATAAA
1 TTATTAAA
1733189 TAGAGTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 4 0.18
16 10 0.45
17 8 0.36
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (16 bp):
TTATTAAAATAAAATT
Found at i:1734483 original size:2 final size:2
Alignment explanation
Indices: 1734478--1734511 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1734468 ATTGTCTCTC
1734478 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1734512 TAGGAATAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1738296 original size:15 final size:16
Alignment explanation
Indices: 1738254--1738320 Score: 64
Period size: 16 Copynumber: 4.2 Consensus size: 16
1738244 AAAAAAAGTT
*
1738254 AAAATTTGAATTTAAA
1 AAAATTTAAATTTAAA
**
1738270 AACTTTTAAATTTAAA
1 AAAATTTAAATTTAAA
1738286 AAAATTT-AATTTAAA
1 AAAATTTAAATTTAAA
** **
1738301 TTAATCAAAATTTAAA
1 AAAATTTAAATTTAAA
1738317 AAAA
1 AAAA
1738321 ATAAACTCAA
Statistics
Matches: 39, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
15 11 0.28
16 28 0.72
ACGTcount: A:0.58, C:0.03, G:0.01, T:0.37
Consensus pattern (16 bp):
AAAATTTAAATTTAAA
Found at i:1738300 original size:21 final size:21
Alignment explanation
Indices: 1738274--1738315 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1738264 TTTAAAAACT
1738274 TTTAAATTTAA-AAAAATTTAA
1 TTTAAA-TTAATAAAAATTTAA
*
1738295 TTTAAATTAATCAAAATTTAA
1 TTTAAATTAATAAAAATTTAA
1738316 AAAAAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
TTTAAATTAATAAAAATTTAA
Found at i:1739977 original size:19 final size:20
Alignment explanation
Indices: 1739953--1740004 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
1739943 GTCTTATTAA
*
1739953 TAATATTTAAATTTT-TTAT
1 TAATATTTAAATTTTATAAT
1739972 TAATATTTATATATTTTATAAT
1 TAATATTTA-A-ATTTTATAAT
1739994 TAA-ATTTAAAT
1 TAATATTTAAAT
1740005 AAAATATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
19 11 0.38
20 2 0.07
21 10 0.34
22 6 0.21
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TAATATTTAAATTTTATAAT
Found at i:1740791 original size:21 final size:20
Alignment explanation
Indices: 1740765--1740811 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
1740755 TTTTAAATAA
1740765 AAATAATTTA-AATATTAAAAT
1 AAATAATTTATAATATT--AAT
1740786 AAATAA-TTATAATATTAAT
1 AAATAATTTATAATATTAAT
1740805 AAATAAT
1 AAATAAT
1740812 AAATATAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 9 0.38
20 3 0.12
21 12 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
AAATAATTTATAATATTAAT
Found at i:1740911 original size:7 final size:7
Alignment explanation
Indices: 1740901--1740931 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
1740891 TTAAAACTCA
1740901 AAAAATT
1 AAAAATT
1740908 AAAAATT
1 AAAAATT
1740915 AAAAATT
1 AAAAATT
1740922 AAAAATT
1 AAAAATT
1740929 AAA
1 AAA
1740932 CAAATTAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
AAAAATT
Found at i:1740911 original size:15 final size:14
Alignment explanation
Indices: 1740900--1740940 Score: 55
Period size: 14 Copynumber: 2.8 Consensus size: 14
1740890 TTTAAAACTC
1740900 AAAAAATTAAAAAT
1 AAAAAATTAAAAAT
*
1740914 TAAAAATTAAAAATT
1 AAAAAATTAAAAA-T
1740929 AAACAAATTAAA
1 AAA-AAATTAAA
1740941 GCTATCTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 12 0.52
15 3 0.13
16 8 0.35
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (14 bp):
AAAAAATTAAAAAT
Found at i:1742626 original size:15 final size:15
Alignment explanation
Indices: 1742602--1742677 Score: 64
Period size: 15 Copynumber: 4.9 Consensus size: 15
1742592 AAATGATTAT
1742602 ATATATATAAATATA
1 ATATATATAAATATA
* * *
1742617 ATATAAATAATTAAA
1 ATATATATAAATATA
1742632 ATATTATATAAATAT-
1 ATA-TATATAAATATA
* *
1742647 ATAGTATAAAAAAATA
1 ATA-TATATAAATATA
*
1742663 TATTTATATAAATAT
1 -ATATATATAAATAT
1742678 TTTAAAATTT
Statistics
Matches: 46, Mismatches: 12, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
15 27 0.59
16 17 0.37
17 2 0.04
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.39
Consensus pattern (15 bp):
ATATATATAAATATA
Found at i:1742643 original size:31 final size:30
Alignment explanation
Indices: 1742600--1742677 Score: 88
Period size: 31 Copynumber: 2.5 Consensus size: 30
1742590 TAAAATGATT
1742600 ATATATATATAAATATA-A-TATAAATAATTAAA
1 ATAT-TATATAAATATATAGTATAAA-AA--AAA
*
1742632 ATATTATATAAATATATAGTATAAAAAAAT
1 ATATTATATAAATATATAGTATAAAAAAAA
1742662 ATATTTATATAAATAT
1 ATA-TTATATAAATAT
1742678 TTTAAAATTT
Statistics
Matches: 42, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
30 5 0.12
31 24 0.57
32 7 0.17
33 6 0.14
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (30 bp):
ATATTATATAAATATATAGTATAAAAAAAA
Found at i:1742649 original size:33 final size:31
Alignment explanation
Indices: 1742578--1742677 Score: 85
Period size: 31 Copynumber: 3.0 Consensus size: 31
1742568 AAAGACTGCG
*
1742578 TAATATTAAAAATAAAATGATTATATATATATAAATA
1 TAATA-TAAAAA-AAAAT-ATT-TATATA-A-ATATA
1742615 TAATATAAATAATTAAAATA-TTATATAAATATA
1 TAATATAAA-AA--AAAATATTTATATAAATATA
* *
1742648 TAGTATAAAAAAATATATTTATATAAATAT
1 TAATATAAAAAAAAATATTTATATAAATAT
1742678 TTTAAAATTT
Statistics
Matches: 57, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
30 5 0.09
31 12 0.21
32 2 0.04
33 12 0.21
34 1 0.02
35 6 0.11
36 5 0.09
37 8 0.14
38 6 0.11
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (31 bp):
TAATATAAAAAAAAATATTTATATAAATATA
Found at i:1742662 original size:37 final size:38
Alignment explanation
Indices: 1742590--1742662 Score: 96
Period size: 37 Copynumber: 1.9 Consensus size: 38
1742580 ATATTAAAAA
* *
1742590 TAAAATGATTATATATATATAAATATAATATAAATAAT
1 TAAAATGATTATATAAATATAAATATAATAAAAATAAT
*
1742628 TAAAAT-ATTATATAAATATATAGTATAA-AAAAATA
1 TAAAATGATTATATAAATATA-AATATAATAAAAATA
1742663 TATTTATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
37 19 0.61
38 12 0.39
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (38 bp):
TAAAATGATTATATAAATATAAATATAATAAAAATAAT
Found at i:1742704 original size:22 final size:20
Alignment explanation
Indices: 1742664--1742704 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
1742654 AAAAAAATAT
*
1742664 ATTTATATAAATATTTTAAA
1 ATTTATATAAAAATTTTAAA
1742684 ATTTATATAATAAATTATTAA
1 ATTTATATAA-AAATT-TTAA
1742705 TATATTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
21 4 0.22
22 4 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
ATTTATATAAAAATTTTAAA
Found at i:1742719 original size:18 final size:18
Alignment explanation
Indices: 1742688--1742737 Score: 52
Period size: 18 Copynumber: 2.8 Consensus size: 18
1742678 TTTAAAATTT
1742688 ATATAATAA-ATTAT-TAA
1 ATATAA-AATATTATGTAA
1742705 TATATTAAAAT-TTATGTAA
1 -ATA-TAAAATATTATGTAA
1742724 ATATAAAATATTAT
1 ATATAAAATATTAT
1742738 AAAAAATATT
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
17 6 0.21
18 16 0.57
19 6 0.21
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (18 bp):
ATATAAAATATTATGTAA
Found at i:1743255 original size:14 final size:14
Alignment explanation
Indices: 1743238--1743275 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
1743228 AATTTAAATA
*
1743238 AAAATATTAAATTT
1 AAAATAATAAATTT
1743252 AAAA-AATAAATTT
1 AAAATAATAAATTT
*
1743265 ATAATAATAAA
1 AAAATAATAAA
1743276 ATTACATCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
AAAATAATAAATTT
Found at i:1747893 original size:24 final size:27
Alignment explanation
Indices: 1747819--1747889 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
1747809 AAACAAGCCT
* *
1747819 CCATATTTGACAAATACAAAGGA-AACCA
1 CCATTTTTGACAAACACAAA--ATAACCA
1747847 CCATTTTTGACAAACACAAAATAACCA
1 CCATTTTTGACAAACACAAAATAACCA
1747874 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
1747890 AATAGGTGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.23
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAATAACCA
Found at i:1749811 original size:21 final size:22
Alignment explanation
Indices: 1749773--1749818 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
1749763 ATTTGTTGAA
* **
1749773 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
1749794 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
1749816 ACT
1 ACT
1749819 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:1752432 original size:28 final size:27
Alignment explanation
Indices: 1752386--1752456 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
1752376 AAACAAGCCT
* *
1752386 CCATATTTGACAAATACAAAGGA-AACCA
1 CCATTTTTGACAAACACAAA--ATAACCA
*
1752414 CCATTTTTGATAAACACAAAATAACCA
1 CCATTTTTGACAAACACAAAATAACCA
1752441 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
1752457 AATGGGTGGC
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 1 0.03
27 20 0.53
28 17 0.45
ACGTcount: A:0.46, C:0.23, G:0.07, T:0.24
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAATAACCA
Found at i:1753037 original size:21 final size:22
Alignment explanation
Indices: 1753012--1753058 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1753002 TCTTTATGAA
*
1753012 TTTAAATT-GTAA-TTTTTAAAT
1 TTTAAATTAG-AACTTTTAAAAT
1753033 TTTAAATTAGAACTTTTAAAAT
1 TTTAAATTAGAACTTTTAAAAT
1753055 TTTA
1 TTTA
1753059 TTTATTTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 10 0.43
22 13 0.57
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (22 bp):
TTTAAATTAGAACTTTTAAAAT
Found at i:1753113 original size:2 final size:2
Alignment explanation
Indices: 1753106--1753136 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1753096 TATTTACATA
1753106 AT AT AT 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 AT AT AT A
1753137 CATGTTTGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1753423 original size:28 final size:26
Alignment explanation
Indices: 1753387--1753451 Score: 71
Period size: 28 Copynumber: 2.5 Consensus size: 26
1753377 CAATTACAAA
*
1753387 ATAAAATATAAATAAATATAATAATATT
1 ATAATATATAAATAAATA-AATAA-ATT
**
1753415 ATAATATATTGATAAATAAATAAATT
1 ATAATATATAAATAAATAAATAAATT
1753441 A-AATA-ATAAAT
1 ATAATATATAAAT
1753452 TAAAGTTTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
24 4 0.12
25 4 0.12
26 4 0.12
27 5 0.16
28 15 0.47
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (26 bp):
ATAATATATAAATAAATAAATAAATT
Found at i:1753448 original size:12 final size:13
Alignment explanation
Indices: 1753427--1753455 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
1753417 AATATATTGA
1753427 TAAATAAATAAAT
1 TAAATAAATAAAT
1753440 TAAAT-AATAAAT
1 TAAATAAATAAAT
1753452 TAAA
1 TAAA
1753456 GTTTATGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (13 bp):
TAAATAAATAAAT
Found at i:1753800 original size:13 final size:15
Alignment explanation
Indices: 1753770--1753801 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
1753760 TGAATGAATT
1753770 TATAAATTTATATAA
1 TATAAATTTATATAA
1753785 TATAAA-TTAT-TAA
1 TATAAATTTATATAA
1753798 TATA
1 TATA
1753802 TATAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 4 0.24
15 6 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TATAAATTTATATAA
Found at i:1754575 original size:21 final size:22
Alignment explanation
Indices: 1754550--1754631 Score: 60
Period size: 25 Copynumber: 3.5 Consensus size: 22
1754540 ATTTCTATAA
1754550 TTTTA-ATATATTAATTATTAT
1 TTTTATATATATTAATTATTAT
* *
1754571 TTTTATATAAATATAACATATTTAT
1 TTTTATATATAT-TAA-TTA-TTAT
*
1754596 ATTTATATATTATTTAATTATT-T
1 TTTTATATA-TA-TTAATTATTAT
*
1754619 TATATATATATAT
1 T-TTTATATATAT
1754632 ATTTGTTTCA
Statistics
Matches: 47, Mismatches: 7, Indels: 13
0.70 0.10 0.19
Matches are distributed among these distances:
21 5 0.11
22 6 0.13
23 6 0.13
24 11 0.23
25 14 0.30
26 4 0.09
27 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (22 bp):
TTTTATATATATTAATTATTAT
Found at i:1757663 original size:2 final size:2
Alignment explanation
Indices: 1757656--1757685 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1757646 ATAAATAAAG
*
1757656 AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1757686 GTATGTATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1757678 original size:14 final size:14
Alignment explanation
Indices: 1757659--1757694 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1757649 AATAAAGATA
1757659 TATATATATATATG
1 TATATATATATATG
1757673 TATATATATATATG
1 TATATATATATATG
*
1757687 TATGTATA
1 TATATATA
1757695 CATTCACATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (14 bp):
TATATATATATATG
Found at i:1765897 original size:3 final size:3
Alignment explanation
Indices: 1765889--1765928 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
1765879 GTTCAGGTAC
1765889 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1765929 TCAATTATAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:1765965 original size:8 final size:7
Alignment explanation
Indices: 1765938--1765964 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
1765928 TTCAATTATA
1765938 AAAAAAT
1 AAAAAAT
1765945 AAAAAAT
1 AAAAAAT
1765952 AAAAAAT
1 AAAAAAT
1765959 AAAAAA
1 AAAAAA
1765965 AAATCATGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (7 bp):
AAAAAAT
Found at i:1766974 original size:29 final size:27
Alignment explanation
Indices: 1766930--1766984 Score: 74
Period size: 29 Copynumber: 2.0 Consensus size: 27
1766920 TTTTTTTTAA
* *
1766930 TTTTATCTCGTCTAAAGAAAAATTATTAT
1 TTTTATCTCATATAAA-AAAAA-TATTAT
1766959 TTTTATCTCATATAAAAAAAATATTA
1 TTTTATCTCATATAAAAAAAATATTA
1766985 CTTTAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 5 0.21
28 5 0.21
29 14 0.58
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.44
Consensus pattern (27 bp):
TTTTATCTCATATAAAAAAAATATTAT
Found at i:1767022 original size:20 final size:20
Alignment explanation
Indices: 1766994--1767035 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1766984 ACTTTAAATA
* *
1766994 ATAATTTCATAAAAAAATTT
1 ATAAATTCATAAAAAAAGTT
1767014 ATAAATTCATAAAAAAAGTT
1 ATAAATTCATAAAAAAAGTT
1767034 AT
1 AT
1767036 TATCTCAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (20 bp):
ATAAATTCATAAAAAAAGTT
Found at i:1772896 original size:182 final size:183
Alignment explanation
Indices: 1772582--1772928 Score: 642
Period size: 182 Copynumber: 1.9 Consensus size: 183
1772572 CAAGCTAAGC
1772582 TAAGCTAAGCTAAGCACTCTTTAAAAGAATGGATTTTTCCAAGTCAAGTCAAGGAAGTGAGAATT
1 TAAGCTAAGCTAAGCACTCTTTAAAAGAATGGATTTTTCCAAGTCAAGTCAAGGAAGTGAGAATT
* * * *
1772647 TTATTTGAACTCCTTTTCATTCTCGAGAACCCCATATGAAGCTGTTTCAATCCAATTTAATGATC
66 TTATTTGAACTCCTTTTCATTCTCAAAAACCCCATATGAAGCTGCTTCAATCCAATTTAACGATC
1772712 TGAACTATGACTACTAAATCAGCTGCTTTTGGGATGGTACCTGATATGTTGGG
131 TGAACTATGACTACTAAATCAGCTGCTTTTGGGATGGTACCTGATATGTTGGG
*
1772765 TAAGCTAAGCTAAGCACTCTTTAAAAGAATGGATTTTTCCAAGTCAAGT-AAGGCAGTGAGAATT
1 TAAGCTAAGCTAAGCACTCTTTAAAAGAATGGATTTTTCCAAGTCAAGTCAAGGAAGTGAGAATT
1772829 TTATTTGAACTCCTTTTCATTCTCAAAAACCCCATATGAAGCTGCTTCAATCCAATTTAACGATC
66 TTATTTGAACTCCTTTTCATTCTCAAAAACCCCATATGAAGCTGCTTCAATCCAATTTAACGATC
1772894 TGAACTATGACTACTAAATCAGCTGCTTTTGGGAT
131 TGAACTATGACTACTAAATCAGCTGCTTTTGGGAT
1772929 TGCGCATGGT
Statistics
Matches: 159, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
182 110 0.69
183 49 0.31
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (183 bp):
TAAGCTAAGCTAAGCACTCTTTAAAAGAATGGATTTTTCCAAGTCAAGTCAAGGAAGTGAGAATT
TTATTTGAACTCCTTTTCATTCTCAAAAACCCCATATGAAGCTGCTTCAATCCAATTTAACGATC
TGAACTATGACTACTAAATCAGCTGCTTTTGGGATGGTACCTGATATGTTGGG
Found at i:1774191 original size:19 final size:21
Alignment explanation
Indices: 1774156--1774194 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 21
1774146 TTTGATGATT
1774156 TTAAATATAACATAAAAATAA
1 TTAAATATAACATAAAAATAA
1774177 TTAAATAT-A-ATAAAAATA
1 TTAAATATAACATAAAAATA
1774195 TGACATGACA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 9 0.50
20 1 0.06
21 8 0.44
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (21 bp):
TTAAATATAACATAAAAATAA
Found at i:1774358 original size:18 final size:18
Alignment explanation
Indices: 1774322--1774374 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 18
1774312 TAAATGTGAT
*
1774322 AGAAAATATGATATGAAATA
1 AGAAAATA--ATATAAAATA
1774342 AGAAAATAATATAAAATA
1 AGAAAATAATATAAAATA
*
1774360 ATATAAAT-ATATAAA
1 AGA-AAATAATATAAA
1774375 TATATTAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 18 0.60
19 4 0.13
20 8 0.27
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (18 bp):
AGAAAATAATATAAAATA
Found at i:1774375 original size:27 final size:27
Alignment explanation
Indices: 1774345--1774457 Score: 92
Period size: 27 Copynumber: 4.1 Consensus size: 27
1774335 TGAAATAAGA
1774345 AAATAATATAAAATAATATA-AATATAT
1 AAAT-ATATAAAATAATATATAATATAT
* *
1774372 AAATATATTAAAAT-TTATATAACATAT
1 AAATATA-TAAAATAATATATAATATAT
*
1774399 -AATATCTTAAATATAAT-TATAATA-AT
1 AAATAT-ATAAA-ATAATATATAATATAT
* *
1774425 AAAAATATATAAATAAAATATAAATATAT
1 AAATATATA-AAATAATATAT-AATATAT
1774454 AAAT
1 AAAT
1774458 CCTTAAATTT
Statistics
Matches: 67, Mismatches: 9, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
26 24 0.36
27 33 0.49
28 5 0.07
29 5 0.07
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (27 bp):
AAATATATAAAATAATATATAATATAT
Found at i:1774378 original size:14 final size:14
Alignment explanation
Indices: 1774345--1774457 Score: 57
Period size: 14 Copynumber: 8.3 Consensus size: 14
1774335 TGAAATAAGA
1774345 AAATAATATAAA-AT
1 AAAT-ATATAAATAT
1774359 -AATATA-AATATAT
1 AAATATATAA-ATAT
1774372 AAATATATTAAA-AT
1 AAATATA-TAAATAT
*
1774386 --TTATATAACATAT
1 AAATATATAA-ATAT
*
1774399 -AATATCTTAAATAT
1 AAATAT-ATAAATAT
* *
1774413 AATTATA-ATAATAA
1 AAATATATA-AATAT
1774427 AAATATATAAATA-
1 AAATATATAAATAT
1774440 AAATATA-AATATAT
1 AAATATATAA-ATAT
1774454 AAAT
1 AAAT
1774458 CCTTAAATTT
Statistics
Matches: 78, Mismatches: 7, Indels: 28
0.69 0.06 0.25
Matches are distributed among these distances:
11 5 0.06
12 11 0.14
13 18 0.23
14 33 0.42
15 9 0.12
16 2 0.03
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (14 bp):
AAATATATAAATAT
Found at i:1774472 original size:8 final size:8
Alignment explanation
Indices: 1774349--1774457 Score: 60
Period size: 8 Copynumber: 12.4 Consensus size: 8
1774339 ATAAGAAAAT
1774349 AATATA-A
1 AATATATA
1774356 AATAATATA
1 AAT-ATATA
1774365 AATATATA
1 AATATATA
1774373 AATATATTAA
1 AATATA-T-A
*
1774383 AATTTATA
1 AATATATA
*
1774391 TAACATAT-
1 -AATATATA
*
1774399 AATATCTTA
1 AATAT-ATA
1774408 AATATAATTA
1 AATAT-A-TA
*
1774418 TAATAATAAA
1 -AAT-ATATA
1774428 AATATATA
1 AATATATA
1774436 AATAAAATATA
1 AAT---ATATA
1774447 AATATATA
1 AATATATA
1774455 AAT
1 AAT
1774458 CCTTAAATTT
Statistics
Matches: 80, Mismatches: 9, Indels: 25
0.70 0.08 0.22
Matches are distributed among these distances:
7 7 0.09
8 31 0.39
9 19 0.24
10 9 0.11
11 12 0.15
12 2 0.03
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (8 bp):
AATATATA
Found at i:1776092 original size:19 final size:19
Alignment explanation
Indices: 1776049--1776094 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
1776039 GTTACTATAT
*
1776049 ATTTTATAATTCCGTCACA
1 ATTTTATAATTCCATCACA
*
1776068 AATTTATAA-TCCATCACA
1 ATTTTATAATTCCATCACA
1776086 ATTTT-TAAT
1 ATTTTATAAT
1776095 ATAAATTATC
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
17 3 0.13
18 12 0.52
19 8 0.35
ACGTcount: A:0.37, C:0.17, G:0.02, T:0.43
Consensus pattern (19 bp):
ATTTTATAATTCCATCACA
Found at i:1776352 original size:26 final size:26
Alignment explanation
Indices: 1776323--1776378 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
1776313 GACATAACTA
* *
1776323 AATTAAAGTC-TTAAAAGTATTTAATT
1 AATTAAA-TCATTAAAAGTATTAAAAT
* *
1776349 AATTTAATCATTAAATGTATTAAAAT
1 AATTAAATCATTAAAAGTATTAAAAT
1776375 AATT
1 AATT
1776379 GATAAATTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 2 0.08
26 23 0.92
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.43
Consensus pattern (26 bp):
AATTAAATCATTAAAAGTATTAAAAT
Found at i:1776362 original size:34 final size:34
Alignment explanation
Indices: 1776324--1776390 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
1776314 ACATAACTAA
* * *
1776324 ATTAAA-GTCTTAAAAGTATTTAATTAATTTAATC
1 ATTAAATGTATTAAAA-TAATTAATAAATTTAATC
*
1776358 ATTAAATGTATTAAAATAATTGATAAATTTAAT
1 ATTAAATGTATTAAAATAATTAATAAATTTAAT
1776391 TATGTTAGGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 20 0.71
35 8 0.29
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.43
Consensus pattern (34 bp):
ATTAAATGTATTAAAATAATTAATAAATTTAATC
Found at i:1776768 original size:25 final size:25
Alignment explanation
Indices: 1776740--1776792 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
1776730 ATTTATATGA
1776740 TATAAATTATTAATATATCAAAACT
1 TATAAATTATTAATATATCAAAACT
* * *
1776765 TATATATTATTAATATATTAAAATT
1 TATAAATTATTAATATATCAAAACT
1776790 TAT
1 TAT
1776793 GTAATATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (25 bp):
TATAAATTATTAATATATCAAAACT
Found at i:1776989 original size:11 final size:11
Alignment explanation
Indices: 1776953--1776995 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
1776943 TATTAATTTA
*
1776953 AATATAATTAT
1 AATATAAATAT
1776964 AATATAAA-AT
1 AATATAAATAT
*
1776974 TATATAAATAT
1 AATATAAATAT
*
1776985 GATATAAATAT
1 AATATAAATAT
1776996 TCAAATTACC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 9 0.32
11 19 0.68
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (11 bp):
AATATAAATAT
Found at i:1781462 original size:17 final size:17
Alignment explanation
Indices: 1781440--1781475 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
1781430 TTTTGTTCTA
1781440 AATAAA-AAAATAATAAT
1 AATAAATAAAATAA-AAT
1781457 AATAAATAAAATAAAAT
1 AATAAATAAAATAAAAT
1781474 AA
1 AA
1781476 AAAGAATAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (17 bp):
AATAAATAAAATAAAAT
Found at i:1781483 original size:26 final size:27
Alignment explanation
Indices: 1781439--1781492 Score: 67
Period size: 26 Copynumber: 2.0 Consensus size: 27
1781429 TTTTTGTTCT
*
1781439 AAATAAAAAAATAATAATA-ATAAATA
1 AAATAAAAAAATAAGAATAGATAAATA
*
1781465 AAATAAAATAAA-AAGAATAGTTAAATA
1 AAATAAAA-AAATAAGAATAGATAAATA
1781492 A
1 A
1781493 GTAGTGCCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 14 0.58
27 10 0.42
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (27 bp):
AAATAAAAAAATAAGAATAGATAAATA
Found at i:1781868 original size:24 final size:24
Alignment explanation
Indices: 1781821--1781870 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
1781811 ATTTTTATAT
*
1781821 TAATATTTATATTTTTAAATGTAA
1 TAATATTTATATTATTAAATGTAA
*
1781845 TAAT-TTTTTATTATTAAATAGTAA
1 TAATATTTATATTATTAAAT-GTAA
1781869 TA
1 TA
1781871 TAAATTGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 13 0.57
24 10 0.43
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (24 bp):
TAATATTTATATTATTAAATGTAA
Found at i:1782502 original size:8 final size:7
Alignment explanation
Indices: 1782485--1782543 Score: 52
Period size: 7 Copynumber: 8.4 Consensus size: 7
1782475 ATATTTTTAA
1782485 ATATT-T
1 ATATTAT
1782491 ATATTAT
1 ATATTAT
1782498 AATATTAT
1 -ATATTAT
1782506 ATATT-T
1 ATATTAT
1782512 ATTATT-T
1 A-TATTAT
*
1782519 ATATGAT
1 ATATTAT
1782526 ATAATTAT
1 AT-ATTAT
*
1782534 ATAATAT
1 ATATTAT
1782541 ATA
1 ATA
1782544 ACTACACGAT
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
6 10 0.22
7 22 0.49
8 13 0.29
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (7 bp):
ATATTAT
Found at i:1782521 original size:13 final size:14
Alignment explanation
Indices: 1782484--1782535 Score: 54
Period size: 13 Copynumber: 3.8 Consensus size: 14
1782474 TATATTTTTA
1782484 AATATTTATATTAT
1 AATATTTATATTAT
1782498 AATATTATATATT-T
1 AATATT-TATATTAT
* *
1782512 ATTATTTATATGAT
1 AATATTTATATTAT
*
1782526 -ATAATTATAT
1 AATATTTATAT
1782536 AATATATAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
13 13 0.41
14 13 0.41
15 6 0.19
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (14 bp):
AATATTTATATTAT
Found at i:1783053 original size:2 final size:2
Alignment explanation
Indices: 1783048--1783083 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
1783038 ACACACACAC
*
1783048 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1783084 TACAAAGTGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1784154 original size:17 final size:18
Alignment explanation
Indices: 1784117--1784155 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
1784107 TTGCTTAGAA
* *
1784117 TTATTTTTTATAAATTTT
1 TTATTTTTTATAAAGTAT
1784135 TTATTTTTT-TAAAGTAT
1 TTATTTTTTATAAAGTAT
1784152 TTAT
1 TTAT
1784156 ATCGATCACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (18 bp):
TTATTTTTTATAAAGTAT
Found at i:1784902 original size:2 final size:2
Alignment explanation
Indices: 1784895--1784923 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1784885 AGTACTTATT
1784895 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1784924 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1788114 original size:13 final size:13
Alignment explanation
Indices: 1788098--1788124 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1788088 TTATGATCAA
1788098 TTATAATAAATAT
1 TTATAATAAATAT
1788111 TTATAATAAATAT
1 TTATAATAAATAT
1788124 T
1 T
1788125 AATGATGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTATAATAAATAT
Found at i:1790809 original size:19 final size:20
Alignment explanation
Indices: 1790771--1790809 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
1790761 TATTTGCATG
* *
1790771 AAAATTATTTTATTTTTTTA
1 AAAATTATTTTATGTATTTA
1790791 AAAATT-TTTTATGTATTTA
1 AAAATTATTTTATGTATTTA
1790810 GAGAATATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (20 bp):
AAAATTATTTTATGTATTTA
Found at i:1791618 original size:14 final size:14
Alignment explanation
Indices: 1791587--1791639 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
1791577 GAAAAAGTAT
* *
1791587 TTTATTTTTTAATC
1 TTTATATTTTAATA
1791601 TTTATATTATTAA-A
1 TTTATATT-TTAATA
*
1791615 TTTAATATTTTAATT
1 TTT-ATATTTTAATA
1791630 TTTATATTTT
1 TTTATATTTT
1791640 GAAATTATTG
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
14 21 0.64
15 12 0.36
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTATATTTTAATA
Found at i:1792051 original size:29 final size:31
Alignment explanation
Indices: 1792003--1792064 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 31
1791993 TTTCCTTATT
*
1792003 TATTACAATTTCAAAAGTATATGGATTAAAA
1 TATTACAATTTCAAAAGTATAGGGATTAAAA
* *
1792034 TATTA-AATTT-AATAGTATAGGGATTTAAA
1 TATTACAATTTCAAAAGTATAGGGATTAAAA
1792063 TA
1 TA
1792065 CCCCTTTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 18 0.64
30 5 0.18
31 5 0.18
ACGTcount: A:0.47, C:0.03, G:0.11, T:0.39
Consensus pattern (31 bp):
TATTACAATTTCAAAAGTATAGGGATTAAAA
Found at i:1793977 original size:154 final size:152
Alignment explanation
Indices: 1793779--1794191 Score: 411
Period size: 154 Copynumber: 2.7 Consensus size: 152
1793769 CCGATAACCT
* * *
1793779 TAAAAGACTTGAATATAACCTAAAAATGTGAACTTATTCGAAATGTACACTTTTGGCATGAAAGC
1 TAAAAGACTTGAATATAACCTAAAAA-GTGAACTTATCCTAAATGCACACTTTTGGCATGAAAGC
* * * ** * *
1793844 ATCTCGGTGATTATCTAAGACTTGGTTCTAGAAAAATTATGAAAATGTCTCTAGAGGTATACTTT
65 ATCTCGGTGACTA-CTAAGACTAGATTCTAGAAAAATTACAAAAATGCCTCTAGAGGTAT-CTAT
1793909 TAACATGAAAA-TATAC-CGGTAAGCC
128 TAACAT-AAAATTAT-CTCGGTAAGCC
* * * *
1793934 TAAAGGACTTGAATATAACCTAAAAAGTGAACCTATCCTAAATGCACA-TCTTTGGTATGAAAAC
1 TAAAAGACTTGAATATAACCTAAAAAGTGAACTTATCCTAAATGCACACT-TTTGGCATGAAAGC
* * * * * *
1793998 ATTTCGGTCACTAGCTAGGACTCGATTCTAGGAAAATTACAAAAATGCCTCTAGGGGTATCTATT
65 ATCTCGGTGACTA-CTAAGACTAGATTCTAGAAAAATTACAAAAATGCCTCTAGAGGTATCTATT
* * * *
1794063 GACATAAAATTATCTCTGTAATCG
129 AACATAAAATTATCTCGGTAAGCC
* * * * * * * *
1794087 TAAAAGACTCGAAAATGATCGT-GAAGGATGAACTTATCCTAAATGCACACCTTTGGCATAAAAG
1 TAAAAGACTTGAATAT-AACCTAAAAAG-TGAACTTATCCTAAATGCACACTTTTGGCATGAAAG
*
1794151 CATCTCGGTGACTACATCAGACTAGATTCTAGAAAAATTAC
64 CATCTCGGTGACTAC-TAAGACTAGATTCTAGAAAAATTAC
1794192 CAAATATACC
Statistics
Matches: 209, Mismatches: 42, Indels: 15
0.79 0.16 0.06
Matches are distributed among these distances:
152 5 0.02
153 35 0.17
154 144 0.69
155 25 0.12
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.29
Consensus pattern (152 bp):
TAAAAGACTTGAATATAACCTAAAAAGTGAACTTATCCTAAATGCACACTTTTGGCATGAAAGCA
TCTCGGTGACTACTAAGACTAGATTCTAGAAAAATTACAAAAATGCCTCTAGAGGTATCTATTAA
CATAAAATTATCTCGGTAAGCC
Found at i:1796514 original size:21 final size:21
Alignment explanation
Indices: 1796490--1796530 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1796480 ACATTTAGAA
1796490 GAAAAAATGCA-TTAGTTGGAT
1 GAAAAAATGCACTT-GTTGGAT
*
1796511 GAAACAATGCACTTGTTGGA
1 GAAAAAATGCACTTGTTGGA
1796531 AGGAAAGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.39, C:0.10, G:0.24, T:0.27
Consensus pattern (21 bp):
GAAAAAATGCACTTGTTGGAT
Found at i:1796852 original size:20 final size:21
Alignment explanation
Indices: 1796813--1796853 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
1796803 TTTGTATAAG
*
1796813 TGTTTTCAAGTCTTAAATTAAA
1 TGTTTTCAAG-CTAAAATTAAA
1796835 TGTTTTCAAG-TAAAATTAA
1 TGTTTTCAAGCTAAAATTAA
1796854 TCCAAAGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
22 10 0.56
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.44
Consensus pattern (21 bp):
TGTTTTCAAGCTAAAATTAAA
Found at i:1797071 original size:20 final size:20
Alignment explanation
Indices: 1797044--1797096 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
1797034 CTAAGTAAAA
*
1797044 TATATCGATACATG-GGACAT
1 TATATCGATACATGAAGA-AT
*
1797064 TGTATCGATACATGAAGAAT
1 TATATCGATACATGAAGAAT
1797084 TATATCGATACAT
1 TATATCGATACAT
1797097 TATGCCCAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 27 0.93
21 2 0.07
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (20 bp):
TATATCGATACATGAAGAAT
Found at i:1803418 original size:21 final size:20
Alignment explanation
Indices: 1803394--1803445 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 20
1803384 CAAATCTTTT
1803394 TCAAAATTCATCT-TTTTCACA
1 TCAAAA-TCATCTATTTT-ACA
*
1803415 TCAAAA-CTATCTATTTTTCA
1 TCAAAATC-ATCTATTTTACA
1803435 TCAAAATCATC
1 TCAAAATCATC
1803446 AACAAAAACA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
19 1 0.04
20 15 0.56
21 11 0.41
ACGTcount: A:0.37, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
TCAAAATCATCTATTTTACA
Found at i:1805671 original size:33 final size:32
Alignment explanation
Indices: 1805627--1805691 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
1805617 ACACACCTAG
* * *
1805627 ATGTATTGATACATTATGCTTTGTATCGATACA
1 ATGTATGGATACATGAT-CATTGTATCGATACA
*
1805660 ATGTATGGATACATGCTCATTGTATCGATACA
1 ATGTATGGATACATGATCATTGTATCGATACA
1805692 TACTCAATTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.38
Consensus pattern (32 bp):
ATGTATGGATACATGATCATTGTATCGATACA
Found at i:1805689 original size:19 final size:20
Alignment explanation
Indices: 1805661--1805713 Score: 72
Period size: 19 Copynumber: 2.7 Consensus size: 20
1805651 ATCGATACAA
* *
1805661 TGTATGGATACATGCTC-AT
1 TGTATCGATACATACTCAAT
1805680 TGTATCGATACATACTCAAT
1 TGTATCGATACATACTCAAT
*
1805700 TGTATTGATACATA
1 TGTATCGATACATA
1805714 AAACTGGTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (20 bp):
TGTATCGATACATACTCAAT
Done.