Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold158
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: 1811518
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 13
Found at i:1646013 original size:5 final size:5
Alignment explanation
Indices: 1645994--1646067 Score: 60
Period size: 5 Copynumber: 14.4 Consensus size: 5
1645984 TATATCGTAT
* * * * *
1645994 TTATA TTATTT TTATA TTATA TTTTA TTATA TTATA TTTTAA CTAT- TTATT
1 TTATA TTA-TA TTATA TTATA TTATA TTATA TTATA TTAT-A TTATA TTATA
*
1646045 TTATA TTATA TTGATA ATATA TT
1 TTATA TTATA TT-ATA TTATA TT
1646068 CAAATCTACC
Statistics
Matches: 54, Mismatches: 11, Indels: 8
0.74 0.15 0.11
Matches are distributed among these distances:
4 3 0.06
5 40 0.74
6 11 0.20
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (5 bp):
TTATA
Found at i:1646023 original size:10 final size:10
Alignment explanation
Indices: 1645949--1646031 Score: 53
Period size: 11 Copynumber: 8.1 Consensus size: 10
1645939 TAAATTATTA
1645949 TATATTTTAT
1 TATATTTTAT
* *
1645959 ATAAATTTTAA
1 -TATATTTTAT
*
1645970 TA-AATTTA-
1 TATATTTTAT
1645978 TATATTTATAT
1 TATATTT-TAT
**
1645989 CGTATTTATAT
1 TATATTT-TAT
*
1646000 TATTTTTATAT
1 TATATTT-TAT
1646011 TATATTTTAT
1 TATATTTTAT
*
1646021 TATATTATAT
1 TATATTTTAT
1646031 T
1 T
1646032 TTAACTATTT
Statistics
Matches: 58, Mismatches: 11, Indels: 7
0.76 0.14 0.09
Matches are distributed among these distances:
8 2 0.03
9 8 0.14
10 17 0.29
11 31 0.53
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (10 bp):
TATATTTTAT
Found at i:1646425 original size:17 final size:18
Alignment explanation
Indices: 1646403--1646440 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1646393 ATAATTTAAA
*
1646403 TTAAATTT-TTAATTTTT
1 TTAAATTTGTCAATTTTT
1646420 TTAAATTTGTCAATTTTT
1 TTAAATTTGTCAATTTTT
1646438 TTA
1 TTA
1646441 GTGACCTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.66
Consensus pattern (18 bp):
TTAAATTTGTCAATTTTT
Found at i:1648800 original size:2 final size:2
Alignment explanation
Indices: 1648756--1648783 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1648746 AATCTAATTG
1648756 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
1648784 TAAATTCTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1652421 original size:76 final size:74
Alignment explanation
Indices: 1652322--1652475 Score: 281
Period size: 76 Copynumber: 2.1 Consensus size: 74
1652312 AAGTTTAGAT
1652322 AAATATTTTTATAGTCATAAAAAATTGTGACTTAACATAAAACTAATATATCTAGGTTTTAAAAC
1 AAATATTTTTATAGTCATAAAAAATTGTGACTTAACATAAAACTAATATATCTAGGTTTTAAAAC
1652387 CTTAAACTA
66 CTTAAACTA
*
1652396 AAATATTTTTATATAGTCATAAAAAATTGTGACTTAATATAAAACTAATATATCTAGGTTTTAAA
1 AAATA-TTTT-TATAGTCATAAAAAATTGTGACTTAACATAAAACTAATATATCTAGGTTTTAAA
1652461 ACCTTAAACTA
64 ACCTTAAACTA
1652472 AAAT
1 AAAT
1652476 TTATATATTT
Statistics
Matches: 77, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
74 5 0.06
75 4 0.05
76 68 0.88
ACGTcount: A:0.47, C:0.10, G:0.06, T:0.37
Consensus pattern (74 bp):
AAATATTTTTATAGTCATAAAAAATTGTGACTTAACATAAAACTAATATATCTAGGTTTTAAAAC
CTTAAACTA
Found at i:1656515 original size:31 final size:32
Alignment explanation
Indices: 1656474--1656535 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 32
1656464 TCGATCGGAT
*
1656474 ATATTCAAAATTATT-TATTATTATTTAAAATA
1 ATATTCAAAATT-TTATATTAATATTTAAAATA
1656506 ATATT-AAAATTTTATATTAATATTTAAAAT
1 ATATTCAAAATTTTATATTAATATTTAAAAT
1656536 TAAATTTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 2 0.07
31 21 0.75
32 5 0.18
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (32 bp):
ATATTCAAAATTTTATATTAATATTTAAAATA
Found at i:1657024 original size:23 final size:21
Alignment explanation
Indices: 1656990--1657031 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
1656980 AATAAAATAT
*
1656990 TTTATAATTATTATTGAATATGA
1 TTTATAACTATT-TT-AATATGA
1657013 TTTATAACTATTTTAATAT
1 TTTATAACTATTTTAATAT
1657032 ATTATTATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 2 0.11
23 11 0.61
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (21 bp):
TTTATAACTATTTTAATATGA
Found at i:1657052 original size:36 final size:34
Alignment explanation
Indices: 1656987--1657053 Score: 82
Period size: 36 Copynumber: 1.9 Consensus size: 34
1656977 AAAAATAAAA
**
1656987 TATTTTATAATTATTATTGAATATGATTTATAAC
1 TATTTTATAATTATTATTGAATAACATTTATAAC
1657021 TATTTTAATATATTATTA-TGTAATAACATTTAT
1 TATTTT-ATA-ATTATTATTG-AATAACATTTAT
1657054 TACATAAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
34 6 0.21
35 5 0.18
36 17 0.61
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TATTTTATAATTATTATTGAATAACATTTATAAC
Found at i:1657257 original size:2 final size:2
Alignment explanation
Indices: 1657250--1657281 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1657240 GAAAATTGTA
1657250 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
1657282 CAAATGAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1657516 original size:16 final size:16
Alignment explanation
Indices: 1657495--1657525 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1657485 TTTAATATTA
1657495 AATAAATATTAAATAT
1 AATAAATATTAAATAT
*
1657511 AATAAATATTTAATA
1 AATAAATATTAAATA
1657526 AAAATATATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AATAAATATTAAATAT
Found at i:1657531 original size:17 final size:17
Alignment explanation
Indices: 1657474--1657539 Score: 64
Period size: 17 Copynumber: 3.9 Consensus size: 17
1657464 ATTTAAATAT
*
1657474 TAAAAATTAAT-TTTAA
1 TAAAAATAAATATTTAA
* *
1657490 TATTAAATAAATATTAAA
1 TA-AAAATAAATATTTAA
*
1657508 T-ATAATAAATATTTAA
1 TAAAAATAAATATTTAA
*
1657524 TAAAAATATATATTTA
1 TAAAAATAAATATTTA
1657540 GCTAAATAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
16 15 0.38
17 19 0.49
18 5 0.13
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAAAATAAATATTTAA
Found at i:1657552 original size:19 final size:18
Alignment explanation
Indices: 1657509--1657562 Score: 56
Period size: 17 Copynumber: 2.9 Consensus size: 18
1657499 AATATTAAAT
*
1657509 ATAATAAATATTTAATAA
1 ATAATATATATTTAATAA
*
1657527 A-AATATATATTTAGCTAA
1 ATAATATATATTTA-ATAA
*
1657545 ATAATATAGTCTTTAATA
1 ATAATATA-TATTTAATA
1657563 TAGATATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
17 11 0.38
18 5 0.17
19 8 0.28
20 5 0.17
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.41
Consensus pattern (18 bp):
ATAATATATATTTAATAA
Found at i:1658507 original size:19 final size:18
Alignment explanation
Indices: 1658485--1658565 Score: 64
Period size: 18 Copynumber: 4.5 Consensus size: 18
1658475 AGAAATAATT
1658485 AAAATATAATATA-ATATA
1 AAAATATAATATATATA-A
*
1658503 AAAA-ATAATAT-TTTAA
1 AAAATATAATATATATAA
*
1658519 ATATATATAAT-TATGATAA
1 A-AAATATAATATAT-ATAA
1658538 AAAATATAA-ATATAATAA
1 AAAATATAATATAT-ATAA
1658556 AAATATATAA
1 AAA-ATATAA
1658566 ATTTTCATAT
Statistics
Matches: 51, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
16 2 0.04
17 12 0.24
18 27 0.53
19 10 0.20
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (18 bp):
AAAATATAATATATATAA
Found at i:1658510 original size:17 final size:16
Alignment explanation
Indices: 1658479--1658513 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
1658469 GATATAAGAA
*
1658479 ATAATTAAAATATAAT
1 ATAATTAAAAAATAAT
1658495 ATAATATAAAAAATAAT
1 ATAAT-TAAAAAATAAT
1658512 AT
1 AT
1658514 TTTAAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
ATAATTAAAAAATAAT
Found at i:1658565 original size:28 final size:29
Alignment explanation
Indices: 1658461--1658566 Score: 83
Period size: 31 Copynumber: 3.5 Consensus size: 29
1658451 AATTACTGAT
*
1658461 ATAAAAATGATATAAGAAATAATTAAAATATA
1 ATAAAAAT-ATATAAAAAAT-ATT-AAATATA
* *
1658493 AT-ATAATATAAAAAATAATATTTTAAATAT-
1 ATAAAAATATATAAAA-AATA--TTAAATATA
* *
1658523 ATATAATTATGATAAAAAATA-TAAATATA
1 ATAAAAATAT-ATAAAAAATATTAAATATA
1658552 ATAAAAATATATAAA
1 ATAAAAATATATAAA
1658567 TTTTCATATC
Statistics
Matches: 59, Mismatches: 9, Indels: 16
0.70 0.11 0.19
Matches are distributed among these distances:
28 12 0.20
29 8 0.14
30 9 0.15
31 21 0.36
32 9 0.15
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (29 bp):
ATAAAAATATATAAAAAATATTAAATATA
Found at i:1659136 original size:12 final size:12
Alignment explanation
Indices: 1659119--1659144 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1659109 AAGAAACTTA
1659119 AACTGTCACAAG
1 AACTGTCACAAG
1659131 AACTGTCACAAG
1 AACTGTCACAAG
1659143 AA
1 AA
1659145 AATTAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.23, G:0.15, T:0.15
Consensus pattern (12 bp):
AACTGTCACAAG
Found at i:1662645 original size:21 final size:23
Alignment explanation
Indices: 1662602--1662646 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
1662592 TTCAGTTTTA
1662602 TATATTATATTAATTATTATATT
1 TATATTATATTAATTATTATATT
1662625 TATATTATA-TAATTA-TATATT
1 TATATTATATTAATTATTATATT
1662646 T
1 T
1662647 CATGAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 7 0.32
22 6 0.27
23 9 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TATATTATATTAATTATTATATT
Found at i:1662734 original size:6 final size:6
Alignment explanation
Indices: 1662725--1662771 Score: 58
Period size: 6 Copynumber: 7.3 Consensus size: 6
1662715 AAATTAATTA
*
1662725 AATTTT AATTTT AATTTTT AATATTT AATTATT AATTTT AATATT AA
1 AATTTT AATTTT AA-TTTT AAT-TTT AATT-TT AATTTT AATTTT AA
1662772 ATAAATATTA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
6 19 0.51
7 18 0.49
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (6 bp):
AATTTT
Found at i:1662740 original size:21 final size:20
Alignment explanation
Indices: 1662722--1662769 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
1662712 TTTAAATTAA
1662722 TTAAAT-TTTAATTTTAATT
1 TTAAATATTTAATTTTAATT
*
1662741 TTTAATATTTAATTATTAATT
1 TTAAATATTTAATT-TTAATT
1662762 TT-AATATT
1 TTAAATATT
1662770 AAATAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 5 0.19
20 13 0.50
21 8 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTAAATATTTAATTTTAATT
Found at i:1662740 original size:27 final size:27
Alignment explanation
Indices: 1662710--1662773 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 27
1662700 ATCGAATCAA
1662710 AATTTAAATTAATTAAATT-TTAATTTT
1 AATTTAAATT-ATTAAATTATTAATTTT
* *
1662737 AATTTTTAA-TATTTAATTATTAATTTT
1 AA-TTTAAATTATTAAATTATTAATTTT
1662764 AATATTAAAT
1 AAT-TTAAAT
1662774 AAATATTAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
26 8 0.27
27 17 0.57
28 5 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
AATTTAAATTATTAAATTATTAATTTT
Found at i:1662743 original size:7 final size:7
Alignment explanation
Indices: 1662722--1662763 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
1662712 TTTAAATTAA
*
1662722 TTAAATT
1 TTAATTT
1662729 TTAA-TT
1 TTAATTT
1662735 TTAATTT
1 TTAATTT
*
1662742 TTAATAT
1 TTAATTT
*
1662749 TTAATTA
1 TTAATTT
1662756 TTAATTT
1 TTAATTT
1662763 T
1 T
1662764 AATATTAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 6 0.20
7 24 0.80
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (7 bp):
TTAATTT
Found at i:1662751 original size:20 final size:20
Alignment explanation
Indices: 1662728--1662769 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1662718 TTAATTAAAT
1662728 TTTAATT-TTAATTTTTAATA
1 TTTAATTATTAA-TTTTAATA
1662748 TTTAATTATTAATTTTAATA
1 TTTAATTATTAATTTTAATA
1662768 TT
1 TT
1662770 AAATAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTAATTATTAATTTTAATA
Found at i:1663343 original size:32 final size:32
Alignment explanation
Indices: 1663313--1663374 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
1663303 TAATTAAATT
* *
1663313 TTATTAAACT-ATATTTATTTTAAA-AATAAA
1 TTATTAAAATCATATTTATATTAAATAATAAA
*
1663343 TTATTAAAATCATCTTTATATTAAATAATAAA
1 TTATTAAAATCATATTTATATTAAATAATAAA
1663375 ATATATAACT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 9 0.33
31 12 0.44
32 6 0.22
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (32 bp):
TTATTAAAATCATATTTATATTAAATAATAAA
Found at i:1663367 original size:31 final size:31
Alignment explanation
Indices: 1663238--1663374 Score: 96
Period size: 35 Copynumber: 4.1 Consensus size: 31
1663228 AATAATTTTT
*
1663238 AATTATTAAAATTATATTTATATTAAATAACAA
1 AATTATTAAAA-TATATTTATATTAAATAA-TA
* * *
1663271 AATATAAATAAAATTATATTTATGTGAAATAATAATTA
1 AAT-T-ATTAAAA-TATATTTATAT--TA-AATAA-TA
* *
1663309 AATTTTATTAAACTATATTTATTTTAAA-AATA
1 AA--TTATTAAAATATATTTATATTAAATAATA
*
1663341 AATTATTAAAATCATCTTTATATTAAATAATA
1 AATTATTAAAAT-ATATTTATATTAAATAATA
1663373 AA
1 AA
1663375 ATATATAACT
Statistics
Matches: 83, Mismatches: 12, Indels: 19
0.73 0.11 0.17
Matches are distributed among these distances:
30 9 0.11
31 12 0.14
32 10 0.12
33 5 0.06
34 3 0.04
35 18 0.22
37 11 0.13
38 13 0.16
39 1 0.01
40 1 0.01
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.43
Consensus pattern (31 bp):
AATTATTAAAATATATTTATATTAAATAATA
Found at i:1663388 original size:37 final size:36
Alignment explanation
Indices: 1663244--1663391 Score: 130
Period size: 37 Copynumber: 4.2 Consensus size: 36
1663234 TTTTAATTAT
*
1663244 TAAAATTATATTTATATTAAATAACAAAATATA-AA
1 TAAAATTATATTTATATTAAATAATAAAATATATAA
* * * *
1663279 TAAAATTATATTTATGTGAAATAATAATTAA-ATTTTA
1 TAAAATTATATTTATATTAAATAATAA--AATATATAA
* * *
1663316 TTAAACTATATTTATTTTAAA-AAT-AAAT-TAT--
1 TAAAATTATATTTATATTAAATAATAAAATATATAA
* *
1663347 TAAAATCATCTTTATATTAAATAATAAAATATATAA
1 TAAAATTATATTTATATTAAATAATAAAATATATAA
1663383 CTAAAATTA
1 -TAAAATTA
1663392 AAAATTATGC
Statistics
Matches: 87, Mismatches: 16, Indels: 18
0.72 0.13 0.15
Matches are distributed among these distances:
31 16 0.18
32 3 0.03
33 8 0.09
34 3 0.03
35 25 0.29
36 5 0.06
37 27 0.31
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.42
Consensus pattern (36 bp):
TAAAATTATATTTATATTAAATAATAAAATATATAA
Found at i:1663620 original size:5 final size:5
Alignment explanation
Indices: 1663612--1663685 Score: 51
Period size: 5 Copynumber: 14.2 Consensus size: 5
1663602 TATGACTTAA
* * * *
1663612 AAATT AAATT AAA-T ATATT TAATT ATTATTT AAATT AAAATT AAATC
1 AAATT AAATT AAATT AAATT AAATT A--AATT AAATT -AAATT AAATT
* *
1663659 AAATT TAATAA AAATT AAATT AAATT A
1 AAATT AAAT-T AAATT AAATT AAATT A
1663686 TGGGATAGAT
Statistics
Matches: 52, Mismatches: 12, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
4 3 0.06
5 37 0.71
6 8 0.15
7 4 0.08
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (5 bp):
AAATT
Found at i:1663655 original size:11 final size:11
Alignment explanation
Indices: 1663641--1663682 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
1663631 TAATTATTAT
1663641 TTAAATTAAAA
1 TTAAATTAAAA
*
1663652 TTAAA-TCAAA
1 TTAAATTAAAA
* *
1663662 TTTAATAAAAA
1 TTAAATTAAAA
1663673 TTAAATTAAA
1 TTAAATTAAA
1663683 TTATGGGATA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
10 8 0.33
11 16 0.67
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (11 bp):
TTAAATTAAAA
Found at i:1663674 original size:21 final size:22
Alignment explanation
Indices: 1663639--1663684 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
1663629 TTTAATTATT
*
1663639 ATTTAAATTAAAATTAAATCAA
1 ATTTAAATAAAAATTAAATCAA
*
1663661 ATTT-AATAAAAATTAAATTAA
1 ATTTAAATAAAAATTAAATCAA
1663682 ATT
1 ATT
1663685 ATGGGATAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
ATTTAAATAAAAATTAAATCAA
Found at i:1663901 original size:29 final size:29
Alignment explanation
Indices: 1663869--1664024 Score: 77
Period size: 29 Copynumber: 5.2 Consensus size: 29
1663859 ATATTTTTAC
1663869 ATTATATTTATATTTTTTTATATATTATA
1 ATTATATTTATATTTTTTTATATATTATA
* * * *
1663898 ATTATTTTTAAAATTTTATATAT-TTAT-
1 ATTATATTTATATTTTTTTATATATTATA
* * * *
1663925 A-TAAATTTTAATATATTATTAATATAATTTTTA
1 ATTATA-TTT-ATAT-TTTTTTATAT-A-TTATA
* * * *
1663958 A-TATATTTATATATTTATATTAAATTTTA
1 ATTATATTTATATTTTTTTA-TATATTATA
* * *
1663987 ATTATTTTTAATATTATATTTATATTTTATA
1 ATTATATTT-ATATT-TTTTTATATATTATA
1664018 ATTATAT
1 ATTATAT
1664025 CATATTAGAA
Statistics
Matches: 90, Mismatches: 26, Indels: 20
0.66 0.19 0.15
Matches are distributed among these distances:
26 2 0.02
27 4 0.04
28 6 0.07
29 32 0.36
30 10 0.11
31 22 0.24
32 10 0.11
33 4 0.04
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (29 bp):
ATTATATTTATATTTTTTTATATATTATA
Found at i:1663905 original size:20 final size:20
Alignment explanation
Indices: 1663882--1664023 Score: 55
Period size: 20 Copynumber: 6.8 Consensus size: 20
1663872 ATATTTATAT
1663882 TTTTTTATATATTATAATTA
1 TTTTTTATATATTATAATTA
* * *
1663902 TTTTTAAAATTTTATATATTTA
1 TTTTTTATATATTATA-A-TTA
1663924 TATAAATTTTAATATATTATTAATATAA
1 T-T---TTTT-ATATATTA-TAAT-T-A
*
1663952 TTTTTAATATATT-T-ATATA
1 TTTTTTATATATTATAAT-TA
*
1663971 TTTATATTA-A-ATTTTAATTA
1 TTT-T-TTATATATTATAATTA
*
1663991 -TTTTTA-ATATTATATTTA
1 TTTTTTATATATTATAATTA
*
1664009 TATTTTATA-ATTATA
1 TTTTTTATATATTATA
1664024 TCATATTAGA
Statistics
Matches: 94, Mismatches: 11, Indels: 35
0.67 0.08 0.25
Matches are distributed among these distances:
17 4 0.04
18 9 0.10
19 20 0.21
20 23 0.24
21 6 0.06
22 4 0.04
23 8 0.09
24 3 0.03
26 4 0.04
27 9 0.10
28 4 0.04
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTTTTATATATTATAATTA
Found at i:1663949 original size:23 final size:23
Alignment explanation
Indices: 1663914--1664000 Score: 79
Period size: 23 Copynumber: 3.6 Consensus size: 23
1663904 TTTAAAATTT
*
1663914 TATA-TATTTATATAAATTTTAA
1 TATATTATTAATATAAATTTTAA
*
1663936 TATATTATTAATATAATTTTTAA
1 TATATTATTAATATAAATTTTAA
1663959 TATATTTATATATTTATATTAAATTTTAA
1 TATA-TTAT-TA---ATA-TAAATTTTAA
*
1663988 T-TATTTTTAATAT
1 TATATTATTAATAT
1664001 TATATTTATA
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
22 5 0.09
23 23 0.43
24 4 0.07
25 2 0.04
26 2 0.04
27 3 0.06
28 5 0.09
29 10 0.19
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TATATTATTAATATAAATTTTAA
Found at i:1663958 original size:12 final size:12
Alignment explanation
Indices: 1663923--1663962 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
1663913 TTATATATTT
*
1663923 ATATAAATTTTA
1 ATATAATTTTTA
*
1663935 ATAT-ATTATTA
1 ATATAATTTTTA
1663946 ATATAATTTTTA
1 ATATAATTTTTA
1663958 ATATA
1 ATATA
1663963 TTTATATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
ATATAATTTTTA
Found at i:1664335 original size:40 final size:41
Alignment explanation
Indices: 1664267--1664352 Score: 106
Period size: 40 Copynumber: 2.1 Consensus size: 41
1664257 AATTAAATAT
1664267 AATTTAAATAATATACATATAATAAAAAATT-TTAATATCAA
1 AATTTAAATAATATACATATAATAAAAAATTATT-ATATCAA
* * *
1664308 AATTTATA-AATATACA-ATATATTAAAAATTATTATATTAA
1 AATTTAAATAATATACATATA-ATAAAAAATTATTATATCAA
1664348 AATTT
1 AATTT
1664353 TTTAGTATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
39 3 0.08
40 28 0.70
41 9 0.22
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (41 bp):
AATTTAAATAATATACATATAATAAAAAATTATTATATCAA
Found at i:1664692 original size:6 final size:6
Alignment explanation
Indices: 1664661--1664704 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
1664651 ATTTTTTATT
1664661 AATATCA AAT-TA AATAT- -ATA-A AATATA AATATA AATATA AATAT
1 AATAT-A AATATA AATATA AATATA AATATA AATATA AATATA AATAT
1664705 TATTCAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
4 3 0.09
5 7 0.21
6 20 0.61
7 3 0.09
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (6 bp):
AATATA
Found at i:1664930 original size:29 final size:29
Alignment explanation
Indices: 1664898--1664961 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 29
1664888 TTTAAAAATA
*
1664898 AATATA-ATAATTATACTTTTTTA-ATAGAT
1 AATATATATAATT-TA-TTTTTAATATAGAT
1664927 AATATGATATAATTTATTTTTAATATAGAT
1 AATAT-ATATAATTTATTTTTAATATAGAT
1664957 -ATATA
1 AATATA
1664962 CCAATAATGC
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
28 1 0.03
29 15 0.48
30 9 0.29
31 6 0.19
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (29 bp):
AATATATATAATTTATTTTTAATATAGAT
Found at i:1665734 original size:22 final size:21
Alignment explanation
Indices: 1665707--1665757 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1665697 TCACGATTTG
*
1665707 ATAATATTAAATATGATAAAAA
1 ATAATATTAAATACGAT-AAAA
*
1665729 ATAATA-TAAATACGATATAA
1 ATAATATTAAATACGATAAAA
1665749 AT-ATATTAA
1 ATAATATTAA
1665758 TGTTTTAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 3 0.12
20 8 0.31
21 9 0.35
22 6 0.23
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (21 bp):
ATAATATTAAATACGATAAAA
Found at i:1668661 original size:2 final size:2
Alignment explanation
Indices: 1668654--1668685 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
1668644 AATATTGCAC
*
1668654 AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1668686 TTTAAAAAGG
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:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1670815 original size:2 final size:2
Alignment explanation
Indices: 1670808--1670852 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
1670798 TTTTGTGTTC
1670808 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
1670850 TA T
1 TA T
1670853 TATTTTCTCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1671759 original size:22 final size:22
Alignment explanation
Indices: 1671734--1671789 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
1671724 AAATACTTAT
*
1671734 CTTTTTATTTAAAAAAATCTCA
1 CTTTTTATTTAAAAAAATATCA
*
1671756 CTTTTTATTTTAAAAAACTATCA
1 CTTTTTA-TTTAAAAAAATATCA
*
1671779 ATTTTT-TTTAA
1 CTTTTTATTTAA
1671790 TTTTAATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 5 0.17
22 7 0.23
23 18 0.60
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.52
Consensus pattern (22 bp):
CTTTTTATTTAAAAAAATATCA
Found at i:1672366 original size:30 final size:30
Alignment explanation
Indices: 1672310--1672366 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
1672300 GTATCAAAAT
*
1672310 TTATATAAATATAAAATACTTTAAATATGA
1 TTATATAAATATAAAATACTTAAAATATGA
1672340 TTATAATAAA-ATAAAATA-TATAAAATA
1 TTAT-ATAAATATAAAATACT-TAAAATA
1672367 ATATAAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
29 1 0.04
30 18 0.75
31 5 0.21
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (30 bp):
TTATATAAATATAAAATACTTAAAATATGA
Found at i:1677787 original size:19 final size:18
Alignment explanation
Indices: 1677762--1677858 Score: 97
Period size: 19 Copynumber: 5.8 Consensus size: 18
1677752 ATTTCAACAA
1677762 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1677780 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
1677796 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1677812 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
1677828 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1677844 TTTTGTATCGATACA
1 -TTTGTATCGATACA
1677859 ATGTATCGCT
Statistics
Matches: 66, Mismatches: 0, Indels: 25
0.73 0.00 0.27
Matches are distributed among these distances:
13 22 0.33
15 4 0.06
17 4 0.06
18 1 0.02
19 35 0.53
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:1677801 original size:13 final size:13
Alignment explanation
Indices: 1677783--1677839 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
1677773 ACATAAGTGT
1677783 TGTATCGATACAA
1 TGTATCGATACAA
1677796 TGTATCGATACATAA
1 TGTATCGATAC--AA
1677811 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
1677828 TGTATCGATACA
1 TGTATCGATACA
1677840 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1677801 original size:32 final size:32
Alignment explanation
Indices: 1677764--1677866 Score: 197
Period size: 32 Copynumber: 3.2 Consensus size: 32
1677754 TTCAACAATT
1677764 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1677796 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
1677828 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1677860 TGTATCG
1 TGTATCG
1677867 CTACGAAGCT
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
32 70 1.00
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:1677947 original size:33 final size:33
Alignment explanation
Indices: 1677890--1677956 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
1677880 GCCAAGGAAA
**
1677890 TGTATCGATACATTACTCAATGTATTGATACAT
1 TGTATCGATACATTACTCAATGTATCAATACAT
**
1677923 TGTATCGATACATTGA-TCTTTGTATCAATACAT
1 TGTATCGATACATT-ACTCAATGTATCAATACAT
1677956 T
1 T
1677957 TGGGAAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 28 0.97
34 1 0.03
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (33 bp):
TGTATCGATACATTACTCAATGTATCAATACAT
Found at i:1684345 original size:38 final size:36
Alignment explanation
Indices: 1684303--1684395 Score: 104
Period size: 33 Copynumber: 2.6 Consensus size: 36
1684293 ATTTTTAATG
1684303 TAAATATAATATTAATAATGTTTAATTATTATTAAACA
1 TAAATATAAT-TTAATAAT-TTTAATTATTATTAAACA
* *
1684341 TAAATATAATTTAATAAATTTT-ATTA-TA--CAATA
1 TAAATATAATTTAAT-AATTTTAATTATTATTAAACA
1684374 TAAATATAATTTTAATAATTTT
1 TAAATATAA-TTTAATAATTTT
1684396 TAGTTATTTA
Statistics
Matches: 51, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
33 18 0.35
34 6 0.12
35 2 0.04
36 4 0.08
37 8 0.16
38 13 0.25
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.47
Consensus pattern (36 bp):
TAAATATAATTTAATAATTTTAATTATTATTAAACA
Found at i:1684365 original size:33 final size:35
Alignment explanation
Indices: 1684328--1684403 Score: 104
Period size: 33 Copynumber: 2.2 Consensus size: 35
1684318 TAATGTTTAA
1684328 TTATTATTA-AACATAAATATAA-TTTAATAAATT
1 TTATTATTACAACATAAATATAATTTTAATAAATT
* *
1684361 TTATTA-TACAATATAAATATAATTTTAATAATTT
1 TTATTATTACAACATAAATATAATTTTAATAAATT
1684395 TTAGTTATT
1 TTA-TTATT
1684404 TATTAGATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
32 2 0.05
33 18 0.49
34 13 0.35
35 3 0.08
36 1 0.03
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (35 bp):
TTATTATTACAACATAAATATAATTTTAATAAATT
Found at i:1685474 original size:24 final size:26
Alignment explanation
Indices: 1685437--1685490 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 26
1685427 ATTTTAAGAT
* * *
1685437 AAATTCATTAAATTATTTTTATTT-A
1 AAATTAATTAAATTAATATTATTTGA
1685462 AAATTAATT-AATTAATATTATTTGA
1 AAATTAATTAAATTAATATTATTTGA
1685487 AAAT
1 AAAT
1685491 GTTAAGTGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 12 0.48
25 13 0.52
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (26 bp):
AAATTAATTAAATTAATATTATTTGA
Found at i:1686089 original size:20 final size:20
Alignment explanation
Indices: 1686061--1686135 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
1686051 TCATACCCTG
1686061 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
1686081 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * * *
1686101 ATGTATTGATATATTCTACA
1 ATGTATCGATACATTTTTCA
1686121 ATGTATCGATACATT
1 ATGTATCGATACATT
1686136 ATGTCTTTTT
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1686128 original size:40 final size:39
Alignment explanation
Indices: 1686061--1686138 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
1686051 TCATACCCTG
* *
1686061 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* * *
1686101 ATGTATTGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
1686139 TCTTTTTACC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.41
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:1693220 original size:16 final size:18
Alignment explanation
Indices: 1693199--1693248 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 18
1693189 AAAGTCAAAA
*
1693199 GCAAAAGCACAAAAAA-T
1 GCAAAAGCAAAAAAAAGT
1693216 G-AAAAG-AAAAAAAAGT
1 GCAAAAGCAAAAAAAAGT
1693232 GCAAAAGCAAAATAAAA
1 GCAAAAGCAAAA-AAAA
1693249 AAAAGAGAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
15 7 0.25
16 7 0.25
17 6 0.21
18 4 0.14
19 4 0.14
ACGTcount: A:0.70, C:0.10, G:0.14, T:0.06
Consensus pattern (18 bp):
GCAAAAGCAAAAAAAAGT
Found at i:1693227 original size:23 final size:23
Alignment explanation
Indices: 1693184--1693226 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
1693174 CTTCAAAATG
*
1693184 ACAAAAAAGTCAAAAGCAAAAGC
1 ACAAAAAAGTCAAAAGAAAAAGC
*
1693207 ACAAAAAA-TGAAAAGAAAAA
1 ACAAAAAAGTCAAAAGAAAAA
1693227 AAAGTGCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.72, C:0.12, G:0.12, T:0.05
Consensus pattern (23 bp):
ACAAAAAAGTCAAAAGAAAAAGC
Found at i:1693252 original size:39 final size:39
Alignment explanation
Indices: 1693186--1693266 Score: 103
Period size: 38 Copynumber: 2.1 Consensus size: 39
1693176 TCAAAATGAC
* *
1693186 AAAAAAGTCAAAAGCAAAAGCACAAAAAA-TGAA-AAGAA
1 AAAAAAGTCAAAAGCAAAAG-AAAAAAAAGAGAACAAGAA
*
1693224 AAAAAAGTGCAAAAGCAAAATAAAAAAAAGAGAACAAGAA
1 AAAAAAGT-CAAAAGCAAAAGAAAAAAAAGAGAACAAGAA
1693264 AAA
1 AAA
1693267 TAAAAAACGA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
38 15 0.41
39 14 0.38
40 8 0.22
ACGTcount: A:0.73, C:0.09, G:0.14, T:0.05
Consensus pattern (39 bp):
AAAAAAGTCAAAAGCAAAAGAAAAAAAAGAGAACAAGAA
Found at i:1693266 original size:23 final size:23
Alignment explanation
Indices: 1693217--1693273 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
1693207 ACAAAAAATG
* * *
1693217 AAAAGAAAAAAAAGTGCAAAAGC
1 AAAATAAAAAAAAGAGCAAAAGA
1693240 AAAATAAAAAAAAGAG-AACAAGA
1 AAAATAAAAAAAAGAGCAA-AAGA
1693263 AAAATAAAAAA
1 AAAATAAAAAA
1693274 CGAGGACATG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
22 2 0.07
23 28 0.93
ACGTcount: A:0.77, C:0.05, G:0.12, T:0.05
Consensus pattern (23 bp):
AAAATAAAAAAAAGAGCAAAAGA
Found at i:1693546 original size:20 final size:20
Alignment explanation
Indices: 1693517--1693555 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1693507 CCCAATCCTA
1693517 AAAAAAAAAAACAAAAAAAC
1 AAAAAAAAAAACAAAAAAAC
*
1693537 AAAAACAAAAACAAAAAAA
1 AAAAAAAAAAACAAAAAAA
1693556 AACCCTTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAAACAAAAAAAC
Found at i:1694648 original size:27 final size:27
Alignment explanation
Indices: 1694609--1695469 Score: 1461
Period size: 27 Copynumber: 31.5 Consensus size: 27
1694599 GTGGCATTTT
* * *
1694609 CTTTTAAACTCCACAACTCTGTGGCATC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
1694637 TTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1694664 CTTTTAAAGTCCACAACTCCGTGGCATC
1 CTTTT-AAGTCCACAACTCCGTGGCACC
*
1694692 TTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1694719 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1694746 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1694773 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1694800 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1694827 CTTTTAAGTCCACAACTCCGTGGCACCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
1694855 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
1694882 CTTTTTAGTCCACAACTCCGTGGTACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1694909 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1694936 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1694963 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1694990 CTTTTTAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1695017 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1695044 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1695071 CTTTTAAGTCCACAACTCCGTGGCACCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
1695099 CTTTTAAGTCCACAACTCCGTGGCATCT
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
1695127 CTTTTAAGTCCACAACTCCGTGGCACCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
1695155 CTTTTAAGTCCACACCTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1695182 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
1695209 CTTTTAAGTCCACAACTCCGTAGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1695236 CTTTTAAGTCCACAACTCCGTGGCACT
1 CTTTTAAGTCCACAACTCCGTGGCACC
1695263 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1695290 CTTTTAAGTCCACAACTCCGTGGCACCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
1695318 CTTTTAAGTCCACAACTCCGTGGCACCC
1 CTTTTAAGTCCACAACTCCGTGGCA-CC
*
1695346 CTTTTAAGTCCACACCTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
1695373 CTTTTAAGTCCACAACTCCGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1695400 CTTTTAAGTCCACAACTCCGTGGCATC
1 CTTTTAAGTCCACAACTCCGTGGCACC
* *
1695427 CTTTTAAATCCACAACTCTGTGGCACC
1 CTTTTAAGTCCACAACTCCGTGGCACC
*
1695454 CATTTCAAAGTCCACA
1 C-TTT-TAAGTCCACA
1695470 CAAGTCGGTG
Statistics
Matches: 792, Mismatches: 35, Indels: 11
0.95 0.04 0.01
Matches are distributed among these distances:
27 593 0.75
28 191 0.24
29 8 0.01
ACGTcount: A:0.22, C:0.36, G:0.14, T:0.27
Consensus pattern (27 bp):
CTTTTAAGTCCACAACTCCGTGGCACC
Found at i:1695492 original size:32 final size:32
Alignment explanation
Indices: 1695437--1696038 Score: 992
Period size: 32 Copynumber: 18.8 Consensus size: 32
1695427 CTTTTAAATC
* * *
1695437 CACAACTCTGTGGC-ACCCATTTCAAAGTCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1695468 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
1695500 CACAAGTCAGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* *
1695532 CACAAATCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
1695564 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1695596 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
1695628 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
1695660 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
1695692 CACAAGTCGGTGGCAACCCATTTTAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
1695724 CACAAGTCGGTGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1695756 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
1695788 CACAAGTCGGTGGCAACCCATTGCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
*
1695820 CACAAGTCGGTGGCAACCCATTGCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1695852 CACAAGTCGGTGGCAACCC-TTTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTT-CAAAGCCCA
1695884 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1695916 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1695948 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
* * *
1695980 CACGAGTCGATGGCAACCCATTCCAAAGCCCA
1 CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
** * *
1696012 TGCAAGTCAGTGGCAACCCTTTTCAAA
1 CACAAGTCGGTGGCAACCCATTTCAAA
1696039 TCACCATTTT
Statistics
Matches: 541, Mismatches: 27, Indels: 5
0.94 0.05 0.01
Matches are distributed among these distances:
31 14 0.03
32 524 0.97
33 3 0.01
ACGTcount: A:0.31, C:0.35, G:0.18, T:0.15
Consensus pattern (32 bp):
CACAAGTCGGTGGCAACCCATTTCAAAGCCCA
Found at i:1696597 original size:20 final size:20
Alignment explanation
Indices: 1696569--1696643 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
1696559 TCATACCCTG
1696569 ATGTATCGATACATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
1696589 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
* * * *
1696609 ATGTATTGATATATTCTACA
1 ATGTATCGATACATTTTTCA
1696629 ATGTATCGATACATT
1 ATGTATCGATACATT
1696644 ATGTCTTTTT
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1696636 original size:40 final size:39
Alignment explanation
Indices: 1696569--1696646 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
1696559 TCATACCCTG
* *
1696569 ATGTATCGATACATTTTTCAATATATCGATACATGTATGA
1 ATGTATCGATACATTCTACAATATATCGATACAT-TATGA
* * *
1696609 ATGTATTGATATATTCTACAATGTATCGATACATTATG
1 ATGTATCGATACATTCTACAATATATCGATACATTATG
1696647 TCTTTTTACC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.41
Consensus pattern (39 bp):
ATGTATCGATACATTCTACAATATATCGATACATTATGA
Found at i:1700678 original size:18 final size:19
Alignment explanation
Indices: 1700645--1700692 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
1700635 TATAATTAAA
*
1700645 TTTAAATAAAATATATTAT
1 TTTAATTAAAATATATTAT
1700664 TTTAATTAAAA-ATATTAT
1 TTTAATTAAAATATATTAT
1700682 TTTAAATTAAA
1 TTT-AATTAAA
1700693 TTTAAATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
18 10 0.37
19 17 0.63
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
TTTAATTAAAATATATTAT
Found at i:1700923 original size:15 final size:15
Alignment explanation
Indices: 1700903--1700932 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1700893 TAAAAGTATT
1700903 TATAATTTAAATTAA
1 TATAATTTAAATTAA
*
1700918 TATAATTTAATTTAA
1 TATAATTTAAATTAA
1700933 ATTATTATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TATAATTTAAATTAA
Found at i:1700930 original size:20 final size:19
Alignment explanation
Indices: 1700905--1700954 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 19
1700895 AAAGTATTTA
1700905 TAATTTAAATTAATATAATT
1 TAATTTAAATTAATAT-ATT
* *
1700925 TAATTTAAATTATTATTTT
1 TAATTTAAATTAATATATT
*
1700944 TTATTTAAATT
1 TAATTTAAATT
1700955 TAATTATAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TAATTTAAATTAATATATT
Found at i:1701026 original size:20 final size:20
Alignment explanation
Indices: 1700905--1701027 Score: 63
Period size: 23 Copynumber: 5.7 Consensus size: 20
1700895 AAAGTATTTA
*
1700905 TAATTTAAA-TTAATATAATT
1 TAATTTAAATTTAAT-TTATT
*
1700925 TAATTTAAATTATTATTT-TT
1 TAATTTAAATT-TAATTTATT
1700945 T-ATTTAAATTTAATTATAAATAT
1 TAATTTAAATTTAATT-T--AT-T
* **
1700968 TAATATAAAAATAATTTTTATTT
1 TAATTTAAATTTAA--TTTA-TT
*
1700991 TTATTTAAATTTTTTAATTTATT
1 TAATTTAAA---TTTAATTTATT
1701014 TAATTTAAATTTAA
1 TAATTTAAATTTAA
1701028 ATAAAAAATT
Statistics
Matches: 78, Mismatches: 11, Indels: 28
0.67 0.09 0.24
Matches are distributed among these distances:
18 4 0.05
19 10 0.13
20 17 0.22
21 2 0.03
22 4 0.05
23 21 0.27
24 14 0.18
25 1 0.01
26 5 0.06
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TAATTTAAATTTAATTTATT
Found at i:1702123 original size:15 final size:15
Alignment explanation
Indices: 1702103--1702135 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
1702093 GTCCAGCAAG
1702103 AATAATAATAATAAC
1 AATAATAATAATAAC
1702118 AATAATAATAATAAC
1 AATAATAATAATAAC
1702133 AAT
1 AAT
1702136 TAATTAATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (15 bp):
AATAATAATAATAAC
Found at i:1702945 original size:28 final size:29
Alignment explanation
Indices: 1702910--1702973 Score: 78
Period size: 29 Copynumber: 2.3 Consensus size: 29
1702900 TTTTTATTAA
*
1702910 TTTT-TTTTA-TTATGTTCAAATAAATTT
1 TTTTATTTTATTTATATTCAAATAAATTT
* *
1702937 TTTTATTTTATTTATATTTAAATATATTT
1 TTTTATTTTATTTATATTCAAATAAATTT
*
1702966 TTTAATTT
1 TTTTATTT
1702974 AAATAAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 4 0.13
28 5 0.16
29 22 0.71
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (29 bp):
TTTTATTTTATTTATATTCAAATAAATTT
Found at i:1702988 original size:16 final size:16
Alignment explanation
Indices: 1702967--1703017 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
1702957 AATATATTTT
1702967 TTAATTTAAATAAAAA
1 TTAATTTAAATAAAAA
*
1702983 TTAATTTAAATTAAAA
1 TTAATTTAAATAAAAA
* *
1702999 TTTATTT-AATATAAA
1 TTAATTTAAATAAAAA
1703014 TTAA
1 TTAA
1703018 AAGTTAAAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 9 0.30
16 21 0.70
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAATTTAAATAAAAA
Found at i:1703007 original size:21 final size:20
Alignment explanation
Indices: 1702943--1703019 Score: 67
Period size: 21 Copynumber: 4.0 Consensus size: 20
1702933 ATTTTTTTAT
*
1702943 TTTATTTATATTTAAAT-ATA
1 TTTATTTA-ATTTAAATAAAA
1702963 TTT-TTTAATTTAAATAAAA
1 TTTATTTAATTTAAATAAAA
1702982 ---A-TTAATTTAAATTAAAA
1 TTTATTTAATTTAAA-TAAAA
*
1702999 TTTATTTAATATAAATTAAAA
1 TTTATTTAATTTAAA-TAAAA
1703020 GTTAAAATTT
Statistics
Matches: 48, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
16 10 0.21
17 5 0.10
18 8 0.17
19 6 0.12
20 4 0.08
21 15 0.31
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTATTTAATTTAAATAAAA
Found at i:1703071 original size:30 final size:28
Alignment explanation
Indices: 1702995--1703089 Score: 99
Period size: 30 Copynumber: 3.4 Consensus size: 28
1702985 AATTTAAATT
1702995 AAAATTTATTTAATATAAATTAAAAGTT-
1 AAAATTTATTTAA-ATAAATTAAAAGTTA
1703023 AAAATTT-TTT--ATAAATTAAAAGTTA
1 AAAATTTATTTAAATAAATTAAAAGTTA
* *
1703048 AAAGATTTATTTAAAACAAATTAAATGTTA
1 AAA-ATTTATTT-AAATAAATTAAAAGTTA
* *
1703078 ATAATTTTTTTA
1 AAAATTTATTTA
1703090 GGTGGAATAA
Statistics
Matches: 57, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
24 14 0.25
25 3 0.05
26 4 0.07
27 6 0.11
28 8 0.14
29 7 0.12
30 15 0.26
ACGTcount: A:0.51, C:0.01, G:0.04, T:0.44
Consensus pattern (28 bp):
AAAATTTATTTAAATAAATTAAAAGTTA
Found at i:1703283 original size:22 final size:22
Alignment explanation
Indices: 1703258--1703299 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1703248 ATTTTTAATT
1703258 TAAAT-TTAATTATAAAAATATA
1 TAAATATTAA-TATAAAAATATA
1703280 TAAATATTAATATAAAAATA
1 TAAATATTAATATAAAAATA
1703300 ATTTTTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
TAAATATTAATATAAAAATATA
Found at i:1704354 original size:20 final size:19
Alignment explanation
Indices: 1704329--1704367 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
1704319 TTTCATCTTG
1704329 CAAGATCTTGAAAACTGCTA
1 CAAGATCTTGAAAA-TGCTA
1704349 CAAGATCTTGAAAATGCTA
1 CAAGATCTTGAAAATGCTA
1704368 TATATATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.41, C:0.18, G:0.15, T:0.26
Consensus pattern (19 bp):
CAAGATCTTGAAAATGCTA
Found at i:1704373 original size:2 final size:2
Alignment explanation
Indices: 1704366--1704404 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1704356 TTGAAAATGC
1704366 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 T
1704405 TACTTTTCTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1704532 original size:51 final size:51
Alignment explanation
Indices: 1704466--1704562 Score: 158
Period size: 51 Copynumber: 1.9 Consensus size: 51
1704456 TCATCTTATA
* * *
1704466 ACCATAATCATAATAGTCGAGACTTAATTTAATTGATCGATTCTTACAATT
1 ACCATAATCATAATAGCCGAGACTTAATTCAATTGACCGATTCTTACAATT
*
1704517 ACCATAATCATAATAGCCGAGACTTAATTCAGTTGACCGATTCTTA
1 ACCATAATCATAATAGCCGAGACTTAATTCAATTGACCGATTCTTA
1704563 TAACTACTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.36, C:0.19, G:0.11, T:0.34
Consensus pattern (51 bp):
ACCATAATCATAATAGCCGAGACTTAATTCAATTGACCGATTCTTACAATT
Found at i:1706648 original size:25 final size:27
Alignment explanation
Indices: 1706614--1706665 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
1706604 ATTTCAATTT
1706614 GTGATAGAATTT-A-GTGACAAAAAAA
1 GTGATAGAATTTAATGTGACAAAAAAA
*
1706639 GTGATGGAATTTAAATGTGACAAAAAA
1 GTGATAGAATTT-AATGTGACAAAAAA
1706666 TTATGATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 11 0.48
27 1 0.04
28 11 0.48
ACGTcount: A:0.50, C:0.04, G:0.21, T:0.25
Consensus pattern (27 bp):
GTGATAGAATTTAATGTGACAAAAAAA
Found at i:1708863 original size:93 final size:93
Alignment explanation
Indices: 1708752--1708935 Score: 359
Period size: 93 Copynumber: 2.0 Consensus size: 93
1708742 TGTGCATTGC
1708752 AACTTTAATTTTTCTTCATATTGCCTCCTTCTTCTATACTTAAATTAATGTGTAAATCCATTAAT
1 AACTTTAATTTTTCTTCATATTGCCTCCTTCTTCTATACTTAAATTAATGTGTAAATCCATTAAT
1708817 CATGGTTGCATATGATGGAGCAAGTTTT
66 CATGGTTGCATATGATGGAGCAAGTTTT
*
1708845 AACTTTAATTTTTCTTCATATTGCCTCCTTCTTCTATACTTAAATTAATGTGTAAATCTATTAAT
1 AACTTTAATTTTTCTTCATATTGCCTCCTTCTTCTATACTTAAATTAATGTGTAAATCCATTAAT
1708910 CATGGTTGCATATGATGGAGCAAGTT
66 CATGGTTGCATATGATGGAGCAAGTT
1708936 AAAACTTGAA
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 90 1.00
ACGTcount: A:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (93 bp):
AACTTTAATTTTTCTTCATATTGCCTCCTTCTTCTATACTTAAATTAATGTGTAAATCCATTAAT
CATGGTTGCATATGATGGAGCAAGTTTT
Found at i:1709535 original size:21 final size:22
Alignment explanation
Indices: 1709492--1709551 Score: 63
Period size: 21 Copynumber: 2.8 Consensus size: 22
1709482 TGATATTTTA
1709492 AATTTAAA--ATTGATTTAATTT
1 AATTTAAATTATT-ATTTAATTT
1709513 AATTTAAATTATTATTTAA-TT
1 AATTTAAATTATTATTTAATTT
**
1709534 AATAAAAATTTATTATTT
1 AATTTAAA-TTATTATTT
1709552 TAATATTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
21 16 0.47
22 15 0.44
23 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
AATTTAAATTATTATTTAATTT
Found at i:1709546 original size:22 final size:22
Alignment explanation
Indices: 1709504--1709551 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1709494 TTTAAAATTG
**
1709504 ATTTAATTTAATTTAAATTATT
1 ATTTAATTTAATAAAAATTATT
1709526 ATTTAA-TTAATAAAAATTTATT
1 ATTTAATTTAATAAAAA-TTATT
1709548 ATTT
1 ATTT
1709552 TAATATTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
ATTTAATTTAATAAAAATTATT
Found at i:1709772 original size:19 final size:19
Alignment explanation
Indices: 1709748--1709804 Score: 73
Period size: 19 Copynumber: 3.1 Consensus size: 19
1709738 TGTACGTGAT
1709748 AATATTAAATATAAAATAA
1 AATATTAAATATAAAATAA
*
1709767 AATATTAAATAAAAAATAA
1 AATATTAAATATAAAATAA
*
1709786 AA-A-TATAATATAATATAA
1 AATATTA-AATATAAAATAA
1709804 A
1 A
1709805 TGTATAAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
17 2 0.06
18 12 0.35
19 20 0.59
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
AATATTAAATATAAAATAA
Found at i:1709795 original size:25 final size:26
Alignment explanation
Indices: 1709754--1709804 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
1709744 TGATAATATT
1709754 AAATATAAAATAAAATATTAA-ATAAA
1 AAATATAAAATAAAATA-TAATATAAA
*
1709780 AAATA-AAAATATAATATAATATAAA
1 AAATATAAAATAAAATATAATATAAA
1709805 TGTATAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 3 0.13
25 15 0.65
26 5 0.22
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (26 bp):
AAATATAAAATAAAATATAATATAAA
Found at i:1709896 original size:18 final size:16
Alignment explanation
Indices: 1709873--1709915 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 16
1709863 AAAATATTTT
1709873 TTAAAATATATTATAATA
1 TTAAAATATA-TATAA-A
*
1709891 TTAAAAAATATATAAA
1 TTAAAATATATATAAA
1709907 TATAAAATA
1 T-TAAAATA
1709916 AATAAATAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 2 0.09
17 11 0.50
18 9 0.41
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TTAAAATATATATAAA
Found at i:1710165 original size:20 final size:20
Alignment explanation
Indices: 1710119--1710167 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
1710109 ATATTAAATT
*
1710119 AAATTTGAATATAAAATTTA
1 AAATTTTAATATAAAATTTA
1710139 AAATTTTAATATAAAATTTA
1 AAATTTTAATATAAAATTTA
1710159 AAATTTTAA
1 AAATTTTAA
1710168 GTTAAGATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
AAATTTTAATATAAAATTTA
Found at i:1710393 original size:23 final size:21
Alignment explanation
Indices: 1710367--1710409 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1710357 TTATATAATT
1710367 TAATATAAAAAATTAAATAAAAA
1 TAAT-TAAAAAA-TAAATAAAAA
*
1710390 TAATTTAAAAATAAATAAAA
1 TAATTAAAAAATAAATAAAA
1710410 TCAAAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.47
22 6 0.32
23 4 0.21
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (21 bp):
TAATTAAAAAATAAATAAAAA
Found at i:1711307 original size:20 final size:20
Alignment explanation
Indices: 1711282--1711326 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
1711272 GCTCCTTATA
1711282 GAATTGATTCATGTAAGTTT
1 GAATTGATTCATGTAAGTTT
*
1711302 GAATTGATTCATGTACGTTT
1 GAATTGATTCATGTAAGTTT
*
1711322 AAATT
1 GAATT
1711327 TTGGTCATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.31, C:0.07, G:0.18, T:0.44
Consensus pattern (20 bp):
GAATTGATTCATGTAAGTTT
Found at i:1716703 original size:30 final size:30
Alignment explanation
Indices: 1716644--1716703 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
1716634 AGGAATTAAA
* *
1716644 TAATTAAAAAATATATATTTTATTTAAAAT
1 TAATTAAAAAATATATATTATATTAAAAAT
*
1716674 TAATTATAAAATATATATTGATA-TAAAAAT
1 TAATTAAAAAATATATATT-ATATTAAAAAT
1716704 AAAATTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 24 0.92
31 2 0.08
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (30 bp):
TAATTAAAAAATATATATTATATTAAAAAT
Found at i:1717418 original size:33 final size:33
Alignment explanation
Indices: 1717381--1717446 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1717371 ATGTCTATAT
1717381 TTAGACAAT-TTTTCAATAAAATAAGTTTATACA
1 TTAGACAATATTTT-AATAAAATAAGTTTATACA
* *
1717414 TTAGACAATATTTTATTAAGATAAGTTTATACA
1 TTAGACAATATTTTAATAAAATAAGTTTATACA
1717447 AGATGTAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 26 0.87
34 4 0.13
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.41
Consensus pattern (33 bp):
TTAGACAATATTTTAATAAAATAAGTTTATACA
Found at i:1717526 original size:14 final size:14
Alignment explanation
Indices: 1717507--1717562 Score: 67
Period size: 14 Copynumber: 3.8 Consensus size: 14
1717497 ATTTTTTCTT
1717507 AATTAAATTTATTC
1 AATTAAATTTATTC
* *
1717521 AATTAAATTTTTTA
1 AATTAAATTTATTC
1717535 AATTTAACATTTTATTC
1 AA-TTAA-A-TTTATTC
1717552 AATTAAATTTA
1 AATTAAATTTA
1717563 ACTTAATTAG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
14 18 0.51
15 5 0.14
16 5 0.14
17 7 0.20
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (14 bp):
AATTAAATTTATTC
Found at i:1722327 original size:149 final size:150
Alignment explanation
Indices: 1722120--1722405 Score: 398
Period size: 150 Copynumber: 1.9 Consensus size: 150
1722110 TTTAGAATTG
* * * * * *
1722120 AGCCTTATGAAACTGCCTGGTCACTTCTATGCCGAGGGTATGGATTAGGTGTAAGTTCGCTTTTA
1 AGCCCTATGAAACTACCTGGTCACTTCTATGCCAAAGGTACGGATTAGGCGTAAGTTCGCTTTTA
* * * * * * *
1722185 -TTTTTCAAGTTCTCTAGGATTACTAGGCACTTCTAAGTCGATGGTAAATCTTAAGGACCTTTTA
66 CTTTTTCAAATCCTCTAGGATCACCAGACACTTCTAAGTCGATGGTAAACCTTAAAGACCTTTTA
1722249 GCATTTTTTCCTTGAAACCT
131 GCATTTTTTCCTTGAAACCT
*
1722269 AGCCCTATGAAACTACC-GAGTCACTTCTATGCCAAAGGTACGTATTAGGCG-AATGTTCGCTTT
1 AGCCCTATGAAACTACCTG-GTCACTTCTATGCCAAAGGTACGGATTAGGCGTAA-GTTCGCTTT
*
1722332 TACTTTTTCAAATCCTCTAGGATCACCAGACACTTCTAAGTCGATGGTAGACCTTAAAGACCTTT
64 TACTTTTTCAAATCCTCTAGGATCACCAGACACTTCTAAGTCGATGGTAAACCTTAAAGACCTTT
1722397 TAGCATTTT
129 TAGCATTTT
1722406 CACCAAAATC
Statistics
Matches: 119, Mismatches: 15, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
148 3 0.03
149 53 0.45
150 63 0.53
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.35
Consensus pattern (150 bp):
AGCCCTATGAAACTACCTGGTCACTTCTATGCCAAAGGTACGGATTAGGCGTAAGTTCGCTTTTA
CTTTTTCAAATCCTCTAGGATCACCAGACACTTCTAAGTCGATGGTAAACCTTAAAGACCTTTTA
GCATTTTTTCCTTGAAACCT
Found at i:1722688 original size:96 final size:96
Alignment explanation
Indices: 1722524--1722715 Score: 366
Period size: 96 Copynumber: 2.0 Consensus size: 96
1722514 GTACCTTTAT
1722524 GTCTAAGCTGAGTCTTAAGTTTTTTATCTTTGTTCTAATTAAATTTGAATATTTTTGTAACACAA
1 GTCTAAGCTGAGTCTTAAGTTTTTTATCTTTGTTCTAATTAAATTTGAATATTTTTGTAACACAA
*
1722589 AGGCAATGTCTCGGAATTAAAATAGTACATG
66 AGGCAATGTCTCGGAATGAAAATAGTACATG
*
1722620 GTCTAAGCTGAGTCTTAGGTTTTTTATCTTTGTTCTAATTAAATTTGAATATTTTTGTAACACAA
1 GTCTAAGCTGAGTCTTAAGTTTTTTATCTTTGTTCTAATTAAATTTGAATATTTTTGTAACACAA
1722685 AGGCAATGTCTCGGAATGAAAATAGTACATG
66 AGGCAATGTCTCGGAATGAAAATAGTACATG
1722716 CAATTTTTTC
Statistics
Matches: 94, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
96 94 1.00
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.40
Consensus pattern (96 bp):
GTCTAAGCTGAGTCTTAAGTTTTTTATCTTTGTTCTAATTAAATTTGAATATTTTTGTAACACAA
AGGCAATGTCTCGGAATGAAAATAGTACATG
Found at i:1723818 original size:17 final size:17
Alignment explanation
Indices: 1723798--1723837 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
1723788 AAAAAATAAT
*
1723798 ATTTATCATATATCTAA
1 ATTTATCAAATATCTAA
* *
1723815 ATTTATTAAATATTTAA
1 ATTTATCAAATATCTAA
1723832 ATTTAT
1 ATTTAT
1723838 TAATCAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTATCAAATATCTAA
Found at i:1723838 original size:17 final size:17
Alignment explanation
Indices: 1723807--1723840 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1723797 TATTTATCAT
1723807 ATATCTAAATTTATTAA
1 ATATCTAAATTTATTAA
*
1723824 ATATTTAAATTTATTAA
1 ATATCTAAATTTATTAA
1723841 TCAAAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATCTAAATTTATTAA
Found at i:1724851 original size:14 final size:15
Alignment explanation
Indices: 1724832--1724864 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
1724822 ATTTAAAAAT
1724832 TTTTAAA-TATTTAA
1 TTTTAAATTATTTAA
1724846 TTTTAAATTTATTTAA
1 TTTTAAA-TTATTTAA
1724862 TTT
1 TTT
1724865 ATTTAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.41
16 10 0.59
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTTAAATTATTTAA
Found at i:1724879 original size:40 final size:44
Alignment explanation
Indices: 1724832--1724924 Score: 106
Period size: 43 Copynumber: 2.2 Consensus size: 44
1724822 ATTTAAAAAT
1724832 TTTTAAA-TATTTA-ATTTTAAAT-TTATTT-AATTT-ATTTAA
1 TTTTAAATTATTTATATTTTAAATATTATTTAAATTTCATTTAA
* *
1724871 TATTTAAATTTATTTATTTTTTACATATTATTTAAATTTGCATTTAA
1 T-TTTAAA-TTATTTATATTTTAAATATTATTTAAATTT-CATTTAA
1724918 TTTTAAA
1 TTTTAAA
1724925 AAGTAATATT
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
39 1 0.02
40 6 0.14
42 6 0.14
43 7 0.16
44 6 0.14
45 5 0.11
46 6 0.14
47 7 0.16
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.60
Consensus pattern (44 bp):
TTTTAAATTATTTATATTTTAAATATTATTTAAATTTCATTTAA
Found at i:1724882 original size:17 final size:17
Alignment explanation
Indices: 1724855--1724909 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
1724845 ATTTTAAATT
1724855 TATTT-AATTTATTTAA
1 TATTTAAATTTATTTAA
*
1724871 TATTTAAATTTATTTAT
1 TATTTAAATTTATTTAA
* *
1724888 TTTTTACATATTATTTAA
1 TATTTAAAT-TTATTTAA
1724906 -ATTT
1 TATTT
1724910 GCATTTAATT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
16 5 0.16
17 20 0.62
18 7 0.22
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.64
Consensus pattern (17 bp):
TATTTAAATTTATTTAA
Found at i:1724889 original size:25 final size:26
Alignment explanation
Indices: 1724839--1724899 Score: 92
Period size: 25 Copynumber: 2.4 Consensus size: 26
1724829 AATTTTTAAA
1724839 TATTTAAT-TTTAAATTTATTTAATT
1 TATTTAATATTTAAATTTATTTAATT
1724864 TATTTAATATTTAAATTTATTT-ATT
1 TATTTAATATTTAAATTTATTTAATT
1724889 T-TTTACATATT
1 TATTTA-ATATT
1724900 ATTTAAATTT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
24 4 0.12
25 17 0.50
26 13 0.38
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (26 bp):
TATTTAATATTTAAATTTATTTAATT
Found at i:1725398 original size:4 final size:4
Alignment explanation
Indices: 1725391--1725417 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1725381 TTCAAAAAAA
1725391 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1725418 CTTCACCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:1726751 original size:23 final size:23
Alignment explanation
Indices: 1726725--1726769 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1726715 AGAAAATGTA
1726725 AAATGAATA-AAGAAGAGAAAGAC
1 AAATG-ATAGAAGAAGAGAAAGAC
*
1726748 AAATGATAGAAGAAGGGAAAGA
1 AAATGATAGAAGAAGAGAAAGA
1726770 GCTGAGCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.62, C:0.02, G:0.27, T:0.09
Consensus pattern (23 bp):
AAATGATAGAAGAAGAGAAAGAC
Found at i:1728343 original size:23 final size:24
Alignment explanation
Indices: 1728313--1728358 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
1728303 AATATATTTT
1728313 TATAAA-TTAATAAATTTATATTA
1 TATAAATTTAATAAATTTATATTA
*
1728336 TATAAATTTTAATAAGTTTATAT
1 TATAAA-TTTAATAAATTTATAT
1728359 ATTTGCATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
25 14 0.70
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
TATAAATTTAATAAATTTATATTA
Found at i:1728593 original size:14 final size:15
Alignment explanation
Indices: 1728576--1728613 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
1728566 TTATATTTTA
1728576 ATTAT-TTTATCTAT
1 ATTATATTTATCTAT
*
1728590 ATTATATTTATGTAT
1 ATTATATTTATCTAT
1728605 -TTATATTTA
1 ATTATATTTA
1728614 AAGTTATCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 14 0.64
15 8 0.36
ACGTcount: A:0.32, C:0.03, G:0.03, T:0.63
Consensus pattern (15 bp):
ATTATATTTATCTAT
Found at i:1729134 original size:14 final size:14
Alignment explanation
Indices: 1729087--1729135 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
1729077 ATATTTTAGT
*
1729087 TTTATATTATTAAA
1 TTTATATTTTTAAA
**
1729101 TTTAATATTTTTATT
1 TTT-ATATTTTTAAA
1729116 TTTATATTTTTAAA
1 TTTATATTTTTAAA
*
1729130 ATTATA
1 TTTATA
1729136 ACAAATAAGA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
14 17 0.61
15 11 0.39
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTATATTTTTAAA
Found at i:1730330 original size:2 final size:2
Alignment explanation
Indices: 1730323--1730363 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
1730313 AAGGCTAATA
*
1730323 AT AT AT AT AT AT AT AT AT AT AG 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 AT AT AT AT AT A
1730364 AGAAAAGAGA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1737867 original size:26 final size:26
Alignment explanation
Indices: 1737838--1737890 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
1737828 AATTCAGTCT
* *
1737838 TTACATATGTAGGAACAGTATTCTTC
1 TTACATACGTAGGAACAATATTCTTC
1737864 TTACATACGTAGGAACAATATTCTTC
1 TTACATACGTAGGAACAATATTCTTC
1737890 T
1 T
1737891 CATTTTGTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (26 bp):
TTACATACGTAGGAACAATATTCTTC
Found at i:1741955 original size:13 final size:14
Alignment explanation
Indices: 1741933--1741965 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
1741923 AAAAAATAAC
1741933 ATAAACAAATATTT
1 ATAAACAAATATTT
1741947 ATAAA-AAATATTT
1 ATAAACAAATATTT
1741960 A-AAACA
1 ATAAACA
1741966 CAACATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.17
13 10 0.56
14 5 0.28
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (14 bp):
ATAAACAAATATTT
Found at i:1742017 original size:18 final size:17
Alignment explanation
Indices: 1741978--1742033 Score: 67
Period size: 17 Copynumber: 3.2 Consensus size: 17
1741968 ACATAAAAAT
* *
1741978 AATATACATATAATATA
1 AATATACATAAAATAAA
* *
1741995 AATATACTTACATATAAA
1 AATATACATA-AAATAAA
1742013 AATATACATAAAATAAA
1 AATATACATAAAATAAA
1742030 AATA
1 AATA
1742034 AATTATTAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
17 19 0.59
18 13 0.41
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.30
Consensus pattern (17 bp):
AATATACATAAAATAAA
Found at i:1742787 original size:32 final size:33
Alignment explanation
Indices: 1742711--1742787 Score: 81
Period size: 33 Copynumber: 2.4 Consensus size: 33
1742701 AAAAATATAC
*
1742711 ATAAAATAAA-ATAAATTATTAATATATAAAAA
1 ATAAAATAAATATAAATTATTAATATACAAAAA
1742743 ATATATAA-AAATATAATATT-TT-ATATACAAAAA
1 ATA-A-AATAAATATAA-ATTATTAATATACAAAAA
*
1742776 ATAACATAAATA
1 ATAAAATAAATA
1742788 CGAAAATATA
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
31 1 0.03
32 9 0.24
33 17 0.45
34 8 0.21
35 3 0.08
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (33 bp):
ATAAAATAAATATAAATTATTAATATACAAAAA
Found at i:1742822 original size:17 final size:17
Alignment explanation
Indices: 1742800--1742855 Score: 58
Period size: 17 Copynumber: 3.1 Consensus size: 17
1742790 AAAATATAAA
*
1742800 TTTTTTTAATTTTTTTC
1 TTTTTTTAATTTCTTTC
*
1742817 TTTTTTTTCTCATTTCTTTC
1 --TTTTTT-TAATTTCTTTC
*
1742837 TTTTTTTTATTTCTTTC
1 TTTTTTTAATTTCTTTC
1742854 TT
1 TT
1742856 CCTTTCTCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
17 12 0.36
18 6 0.18
19 6 0.18
20 9 0.27
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.80
Consensus pattern (17 bp):
TTTTTTTAATTTCTTTC
Found at i:1743127 original size:15 final size:15
Alignment explanation
Indices: 1743109--1743138 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1743099 TTATTTTACG
1743109 TTAAATTAATTTAAA
1 TTAAATTAATTTAAA
*
1743124 TTAAATTATTTTAAA
1 TTAAATTAATTTAAA
1743139 ATTTTGGATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TTAAATTAATTTAAA
Found at i:1743300 original size:31 final size:32
Alignment explanation
Indices: 1743229--1743300 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 32
1743219 ATTTTTTAAA
* **
1743229 TTTAAATTAAGAGTTATAATTATTTAATTATT
1 TTTAAATTTAGAGTTATAATTACCTAATTATT
* *
1743261 TTAAAATTTAG-GTTGTAATTACCTAATTATT
1 TTTAAATTTAGAGTTATAATTACCTAATTATT
1743292 TTTAAATTT
1 TTTAAATTT
1743301 TAATTATTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 25 0.74
32 9 0.26
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.53
Consensus pattern (32 bp):
TTTAAATTTAGAGTTATAATTACCTAATTATT
Found at i:1743318 original size:17 final size:18
Alignment explanation
Indices: 1743284--1743366 Score: 64
Period size: 17 Copynumber: 4.7 Consensus size: 18
1743274 TGTAATTACC
*
1743284 TAATTATTTTTAAA-TTT
1 TAATTATTTTAAAATTTT
1743301 TAATTA-TTTAAAATTTT
1 TAATTATTTTAAAATTTT
* * * *
1743318 TAA-TAGTTTATAATCATC
1 TAATTATTTTAAAAT-TTT
*
1743336 TAATTATTTTAAAAATTT
1 TAATTATTTTAAAATTTT
* *
1743354 TGATTAATTTAAA
1 TAATTATTTTAAA
1743367 TTCTTAAATC
Statistics
Matches: 51, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
16 8 0.16
17 19 0.37
18 16 0.31
19 8 0.16
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (18 bp):
TAATTATTTTAAAATTTT
Found at i:1743540 original size:38 final size:37
Alignment explanation
Indices: 1743457--1743532 Score: 102
Period size: 38 Copynumber: 2.1 Consensus size: 37
1743447 ATGTTAATTA
**
1743457 AAATTT-AAAATAATTAAACAATTACAACTTTTAATTT
1 AAATTTAAAAATAATTAAACAATTACAAC-TTTAAACT
*
1743494 AAATTTAAAAATAATTAAACAATTATAA-TTTAAACT
1 AAATTTAAAAATAATTAAACAATTACAACTTTAAACT
1743530 AAA
1 AAA
1743533 GTTTTAAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 9 0.26
37 6 0.17
38 20 0.57
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (37 bp):
AAATTTAAAAATAATTAAACAATTACAACTTTAAACT
Found at i:1743678 original size:19 final size:19
Alignment explanation
Indices: 1743647--1743695 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 19
1743637 TAATAAAAAC
1743647 TATTAAATAATAATAATATGTTT
1 TATT-AATAAT-ATAATA--TTT
1743670 TATTAATAATATAATATTT
1 TATTAATAATATAATATTT
1743689 TATTAAT
1 TATTAAT
1743696 TTTAAAACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 10 0.38
21 6 0.23
22 6 0.23
23 4 0.15
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
TATTAATAATATAATATTT
Found at i:1744003 original size:29 final size:30
Alignment explanation
Indices: 1743959--1744023 Score: 107
Period size: 29 Copynumber: 2.2 Consensus size: 30
1743949 TTTTTACAAA
1743959 TTAAAA-TAATAATATTTTGATAATTTA-T
1 TTAAAATTAATAATATTTTGATAATTTATT
*
1743987 TTAAAATTAATATTATTTTGATAATTTATT
1 TTAAAATTAATAATATTTTGATAATTTATT
1744017 TTAAAAT
1 TTAAAAT
1744024 CAAGATATTT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
28 6 0.18
29 20 0.59
30 8 0.24
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (30 bp):
TTAAAATTAATAATATTTTGATAATTTATT
Found at i:1744015 original size:13 final size:13
Alignment explanation
Indices: 1743971--1744018 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
1743961 AAAATAATAA
1743971 TATTTTGATAATT
1 TATTTTGATAATT
**
1743984 TATTTAAAATTAATAT
1 TATTT-TGA-TAAT-T
1744000 TATTTTGATAATT
1 TATTTTGATAATT
1744013 TATTTT
1 TATTTT
1744019 AAAATCAAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
13 12 0.43
14 5 0.18
15 5 0.18
16 6 0.21
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.60
Consensus pattern (13 bp):
TATTTTGATAATT
Found at i:1744032 original size:29 final size:28
Alignment explanation
Indices: 1743970--1744034 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 28
1743960 TAAAATAATA
* *
1743970 ATATTTTGATAATTTATTTAAAATTAAT
1 ATATTTTGATAATTTATTTAAAATCAAG
1743998 ATTATTTTGATAATTTATTTTAAAATCAAG
1 A-TATTTTGATAATTTA-TTTAAAATCAAG
1744028 ATATTTT
1 ATATTTT
1744035 TATCGTTTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 1 0.03
29 21 0.64
30 11 0.33
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.54
Consensus pattern (28 bp):
ATATTTTGATAATTTATTTAAAATCAAG
Found at i:1744846 original size:34 final size:34
Alignment explanation
Indices: 1744803--1744920 Score: 173
Period size: 34 Copynumber: 3.4 Consensus size: 34
1744793 TAAAATATCT
* *
1744803 TGCTCACCTAACACATTACCTAACACATCTAATA
1 TGCTTACCTAACACATCACCTAACACATCTAATA
* * *
1744837 TGCTTACCTAACGCATCACCTAATACACCTAATA
1 TGCTTACCTAACACATCACCTAACACATCTAATA
1744871 TGCTTCACCTAACACATCACCTAACACATCTAATA
1 TGCTT-ACCTAACACATCACCTAACACATCTAATA
*
1744906 TGTTTACCTAACACA
1 TGCTTACCTAACACA
1744921 CTTAACAAAG
Statistics
Matches: 74, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
34 44 0.59
35 30 0.41
ACGTcount: A:0.36, C:0.32, G:0.04, T:0.27
Consensus pattern (34 bp):
TGCTTACCTAACACATCACCTAACACATCTAATA
Found at i:1744892 original size:12 final size:12
Alignment explanation
Indices: 1744875--1744900 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1744865 CTAATATGCT
1744875 TCACCTAACACA
1 TCACCTAACACA
1744887 TCACCTAACACA
1 TCACCTAACACA
1744899 TC
1 TC
1744901 TAATATGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.42, G:0.00, T:0.19
Consensus pattern (12 bp):
TCACCTAACACA
Found at i:1744939 original size:69 final size:69
Alignment explanation
Indices: 1744806--1744939 Score: 171
Period size: 69 Copynumber: 1.9 Consensus size: 69
1744796 AATATCTTGC
* * * * * *
1744806 TCACCTAACACATTACCTAACACATCTAATATGCTTACCTAACGCATCACCTAATACACCTAATA
1 TCACCTAACACATCACCTAACACATCTAATATGCTTACCTAACACATCAACAAAGACAACTAATA
1744871 TGCT
66 TGCT
* * *
1744875 TCACCTAACACATCACCTAACACATCTAATATGTTTACCTAACACACTTAACAAAGA-AATTAAT
1 TCACCTAACACATCACCTAACACATCTAATATGCTTACCTAACACA-TCAACAAAGACAACTAAT
1744939 A
65 A
1744940 AAAATATATA
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
69 49 0.89
70 6 0.11
ACGTcount: A:0.40, C:0.29, G:0.04, T:0.27
Consensus pattern (69 bp):
TCACCTAACACATCACCTAACACATCTAATATGCTTACCTAACACATCAACAAAGACAACTAATA
TGCT
Found at i:1749694 original size:34 final size:35
Alignment explanation
Indices: 1749655--1749732 Score: 131
Period size: 34 Copynumber: 2.3 Consensus size: 35
1749645 AAATATCTTA
*
1749655 TTCACCTAACACATTACCTAACACACCTAATATGC
1 TTCACCTAACACATCACCTAACACACCTAATATGC
*
1749690 -TCACCTAACACATCACCTAACACACTTAATATGC
1 TTCACCTAACACATCACCTAACACACCTAATATGC
1749724 TTCACCTAA
1 TTCACCTAA
1749733 AATACTTAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
34 32 0.80
35 8 0.20
ACGTcount: A:0.37, C:0.35, G:0.03, T:0.26
Consensus pattern (35 bp):
TTCACCTAACACATCACCTAACACACCTAATATGC
Found at i:1749707 original size:12 final size:12
Alignment explanation
Indices: 1749656--1749713 Score: 52
Period size: 12 Copynumber: 5.0 Consensus size: 12
1749646 AATATCTTAT
1749656 TCACCTAACACA
1 TCACCTAACACA
*
1749668 TTACCT-A-ACA
1 TCACCTAACACA
*
1749678 -CACCTAATATGC-
1 TCACCTAACA--CA
1749690 TCACCTAACACA
1 TCACCTAACACA
1749702 TCACCTAACACA
1 TCACCTAACACA
1749714 CTTAATATGC
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
9 4 0.11
10 4 0.11
11 3 0.08
12 17 0.46
13 9 0.24
ACGTcount: A:0.40, C:0.38, G:0.02, T:0.21
Consensus pattern (12 bp):
TCACCTAACACA
Found at i:1749761 original size:22 final size:23
Alignment explanation
Indices: 1749702--1749765 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
1749692 ACCTAACACA
1749702 TCACCTAACACACTTAATATGCT
1 TCACCTAACACACTTAATATGCT
* *
1749725 TCACCTAAAATACTTAATATG-T
1 TCACCTAACACACTTAATATGCT
*
1749747 TTACCTAACACACTTAATA
1 TCACCTAACACACTTAATA
1749766 AAAAAATTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
22 17 0.47
23 19 0.53
ACGTcount: A:0.39, C:0.25, G:0.03, T:0.33
Consensus pattern (23 bp):
TCACCTAACACACTTAATATGCT
Found at i:1755295 original size:2 final size:2
Alignment explanation
Indices: 1755288--1755319 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1755278 TGTAAGCAAC
1755288 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
1755320 CGATTCCATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1756380 original size:2 final size:2
Alignment explanation
Indices: 1756373--1756407 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1756363 TAAAATATGC
1756373 AT AT 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 AT AT A
1756408 GTGCATGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1757351 original size:17 final size:18
Alignment explanation
Indices: 1757310--1757353 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
1757300 ACAAATATTT
1757310 TTATT-AATTTTTAAAAA
1 TTATTAAATTTTTAAAAA
1757327 TTATTAAATTTTTAAAAA
1 TTATTAAATTTTTAAAAA
1757345 TT-TTAAATT
1 TTATTAAATT
1757354 AAATTAATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTATTAAATTTTTAAAAA
Done.