Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold364
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: 2089110
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 10
Found at i:1942597 original size:7 final size:7
Alignment explanation
Indices: 1942579--1942669 Score: 64
Period size: 7 Copynumber: 12.9 Consensus size: 7
1942569 ATTTTCATAA
1942579 TTTAAA-
1 TTTAAAT
1942585 TTTAAAT
1 TTTAAAT
1942592 TTTAAAT
1 TTTAAAT
1942599 TTTAAAT
1 TTTAAAT
1942606 TTTAAA-
1 TTTAAAT
* *
1942612 ATAAAAT
1 TTTAAAT
**
1942619 TTTGATTT
1 TTT-AAAT
1942627 TATCTAAATT
1 T-T-TAAA-T
1942637 TTTAGAA-
1 TTTA-AAT
*
1942644 TCTAAA-
1 TTTAAAT
1942650 TTTAAAT
1 TTTAAAT
1942657 TTTAAAT
1 TTTAAAT
1942664 TTTAAA
1 TTTAAA
1942670 ATTAAATTCT
Statistics
Matches: 67, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
6 17 0.25
7 37 0.55
8 5 0.07
9 5 0.07
10 3 0.04
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (7 bp):
TTTAAAT
Found at i:1942599 original size:65 final size:65
Alignment explanation
Indices: 1942530--1942669 Score: 199
Period size: 65 Copynumber: 2.2 Consensus size: 65
1942520 ATTATTATCA
* * * * * *
1942530 AAATTTTAAATTTTACATTTAAATTCTGATTTTATCCCAATTTTCATAATTTAAATTTAAATTTT
1 AAATTTTAAATTTTAAAATAAAATTCTGATTTTATCCAAATTTTCAGAATCTAAATTTAAATTTT
* * *
1942595 AAATTTTAAATTTTAAAATAAAATTTTGATTTTATCTAAATTTTTAGAATCTAAATTTAAATTTT
1 AAATTTTAAATTTTAAAATAAAATTCTGATTTTATCCAAATTTTCAGAATCTAAATTTAAATTTT
1942660 AAATTTTAAA
1 AAATTTTAAA
1942670 ATTAAATTCT
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.41, C:0.06, G:0.02, T:0.51
Consensus pattern (65 bp):
AAATTTTAAATTTTAAAATAAAATTCTGATTTTATCCAAATTTTCAGAATCTAAATTTAAATTTT
Found at i:1949168 original size:21 final size:21
Alignment explanation
Indices: 1949142--1949217 Score: 66
Period size: 21 Copynumber: 3.7 Consensus size: 21
1949132 TTTAATTTAA
1949142 TTAATATATTTAAAATAATAT
1 TTAATATATTTAAAATAATAT
* *
1949163 TTAATAAATTTAAAATTAAAAT
1 TTAATATATTTAAAA-TAATAT
* * *
1949185 TTTA-ATATTTATAAT-TTAT
1 TTAATATATTTAAAATAATAT
**
1949204 TTTTTATATTTAAA
1 TTAATATATTTAAA
1949218 TTACGATTTA
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
19 5 0.11
20 9 0.20
21 22 0.50
22 8 0.18
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
TTAATATATTTAAAATAATAT
Found at i:1951705 original size:24 final size:24
Alignment explanation
Indices: 1951682--1951727 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1951672 TTTATTAATA
*
1951682 ATTTATTT-AATATAAGTTAAAAT
1 ATTTATTTGAATATAAATTAAAAT
1951705 ATTTATTTGAATATAAATTAAAA
1 ATTTATTTGAATATAAATTAAAA
1951728 ATAAAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 8 0.38
24 13 0.62
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (24 bp):
ATTTATTTGAATATAAATTAAAAT
Found at i:1951763 original size:28 final size:28
Alignment explanation
Indices: 1951699--1951779 Score: 101
Period size: 28 Copynumber: 2.8 Consensus size: 28
1951689 TAATATAAGT
* *
1951699 TAAAATATTTATTTGAATATAAATTAAAAA
1 TAAAAAATTTATTT-AA-ATAAAGTAAAAA
*
1951729 TAAAAAATTTATTTAAATACAGTAAAAA
1 TAAAAAATTTATTTAAATAAAGTAAAAA
1951757 TATAAAAA-TTATTTAAATAAAGT
1 TA-AAAAATTTATTTAAATAAAGT
1951780 GATTTGGAAG
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
28 26 0.57
29 7 0.15
30 13 0.28
ACGTcount: A:0.58, C:0.01, G:0.04, T:0.37
Consensus pattern (28 bp):
TAAAAAATTTATTTAAATAAAGTAAAAA
Found at i:1955628 original size:24 final size:22
Alignment explanation
Indices: 1955569--1955632 Score: 69
Period size: 24 Copynumber: 2.9 Consensus size: 22
1955559 AATAAAATTT
* *
1955569 TTTAAATTTTA-TATAAAATAA
1 TTTAAATTTTATTTTAAAAAAA
1955590 TTTAAA-TTTATTTTTAAATAAAA
1 TTTAAATTTTA-TTTTAAA-AAAA
1955613 TTTAAAATTTTATTTTAAAA
1 TTT-AAATTTTATTTTAAAA
1955633 TTTTATTAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
20 4 0.11
21 6 0.17
22 5 0.14
23 7 0.19
24 10 0.28
25 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTAAATTTTATTTTAAAAAAA
Found at i:1955629 original size:13 final size:13
Alignment explanation
Indices: 1955613--1955639 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1955603 TTAAATAAAA
1955613 TTTAAAATTTTAT
1 TTTAAAATTTTAT
1955626 TTTAAAATTTTAT
1 TTTAAAATTTTAT
1955639 T
1 T
1955640 AACATTTAAA
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:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTAAAATTTTAT
Found at i:1959764 original size:18 final size:18
Alignment explanation
Indices: 1959741--1959785 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1959731 TACGGCTCTG
* *
1959741 CTTTGTTCTCTCAAGATC
1 CTTTGTCCTCCCAAGATC
1959759 CTTTGTCCTCCCAAGATC
1 CTTTGTCCTCCCAAGATC
1959777 CTTTGTCCT
1 CTTTGTCCT
1959786 GGAACGCTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.13, C:0.33, G:0.11, T:0.42
Consensus pattern (18 bp):
CTTTGTCCTCCCAAGATC
Found at i:1960112 original size:22 final size:20
Alignment explanation
Indices: 1960087--1960138 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 20
1960077 AAAAAAATTT
1960087 TAAATTTATCATTTTATTTAAA
1 TAAATTT-T-ATTTTATTTAAA
1960109 TAAAATTTTATATTTATTTAAA
1 T-AAATTTTAT-TTTATTTAAA
*
1960131 TTAATTTT
1 TAAATTTT
1960139 TAATTTTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
21 8 0.30
22 13 0.48
23 6 0.22
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (20 bp):
TAAATTTTATTTTATTTAAA
Found at i:1960139 original size:22 final size:23
Alignment explanation
Indices: 1960099--1960161 Score: 74
Period size: 22 Copynumber: 2.7 Consensus size: 23
1960089 AATTTATCAT
1960099 TTTATTTAAATAAAATTTT-ATA
1 TTTATTTAAATAAAATTTTAATA
* * *
1960121 TTTATTTAAATTAATTTTTAATT
1 TTTATTTAAATAAAATTTTAATA
1960144 TTTAATTTAAATCAAAAT
1 TTT-ATTTAAAT-AAAAT
1960162 AAATTATTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
22 17 0.52
23 5 0.15
24 8 0.24
25 3 0.09
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
TTTATTTAAATAAAATTTTAATA
Found at i:1968887 original size:17 final size:16
Alignment explanation
Indices: 1968848--1968894 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
1968838 TGATTTGATC
*
1968848 TATTTTAAATTTTTTT
1 TATTTTAAATTTTTTA
*
1968864 TATTTTTACATTTTTTAA
1 TA-TTTTAAATTTTTT-A
1968882 TATTTTAAATTTT
1 TATTTTAAATTTT
1968895 GTTAGACTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 2 0.08
17 22 0.85
18 2 0.08
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (16 bp):
TATTTTAAATTTTTTA
Found at i:1969108 original size:25 final size:24
Alignment explanation
Indices: 1969069--1969117 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
1969059 ATATTTCAAA
1969069 TTAAAATATAAAATA-TTTGTTATT
1 TTAAAATATAAAATACTTT-TTATT
*
1969093 TTAAAATTTTAAAATACTTTTTATT
1 TTAAAA-TATAAAATACTTTTTATT
1969118 AAACTTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 6 0.27
25 13 0.59
26 3 0.14
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (24 bp):
TTAAAATATAAAATACTTTTTATT
Found at i:1969354 original size:19 final size:19
Alignment explanation
Indices: 1969330--1969367 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1969320 TTATTTTCAC
1969330 GTAACTTTTTAACTTACTT
1 GTAACTTTTTAACTTACTT
1969349 GTAACTTTTTAACTTACTT
1 GTAACTTTTTAACTTACTT
1969368 TTAAATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.16, G:0.05, T:0.53
Consensus pattern (19 bp):
GTAACTTTTTAACTTACTT
Found at i:1969376 original size:19 final size:19
Alignment explanation
Indices: 1969330--1969376 Score: 67
Period size: 19 Copynumber: 2.5 Consensus size: 19
1969320 TTATTTTCAC
*
1969330 GTAACTTTTTAACTTACTT
1 GTAAATTTTTAACTTACTT
*
1969349 GTAACTTTTTAACTTACTT
1 GTAAATTTTTAACTTACTT
*
1969368 TTAAATTTT
1 GTAAATTTT
1969377 ATTATTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.28, C:0.13, G:0.04, T:0.55
Consensus pattern (19 bp):
GTAAATTTTTAACTTACTT
Found at i:1970277 original size:21 final size:21
Alignment explanation
Indices: 1970232--1970277 Score: 51
Period size: 20 Copynumber: 2.2 Consensus size: 21
1970222 TTTTCTAATT
* *
1970232 TAATAAAAATAATATATTAAA
1 TAATTAAAATAATATAATAAA
1970253 -AATTAAAATAA-ATAAATAAA
1 TAATTAAAATAATAT-AATAAA
1970273 TAATT
1 TAATT
1970278 TTTATAGATA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
19 2 0.10
20 15 0.71
21 4 0.19
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
TAATTAAAATAATATAATAAA
Found at i:1977336 original size:20 final size:20
Alignment explanation
Indices: 1977311--1977453 Score: 69
Period size: 19 Copynumber: 7.4 Consensus size: 20
1977301 ACATTATAAG
1977311 AATATAATATTAAAAATATA
1 AATATAATATTAAAAATATA
*
1977331 AATAT-ATA-TAATATATATA
1 AATATAATATTAA-AAATATA
* **
1977350 AA-ATTAT-TTAAATTTATA
1 AATATAATATTAAAAATATA
1977368 TAATATAA-ATTATTAAAATATA
1 -AATATAATATTA--AAAATATA
*
1977390 AA-A-AAT-TATATAAATATA
1 AATATAATAT-TAAAAATATA
*
1977408 TAATAT--T-TT--AAATACA
1 -AATATAATATTAAAAATATA
1977424 AATATAATATATAAAAATATA
1 AATATAATAT-TAAAAATATA
1977445 TAATATAAT
1 -AATATAAT
1977454 TTGTTATAAA
Statistics
Matches: 95, Mismatches: 8, Indels: 38
0.67 0.06 0.27
Matches are distributed among these distances:
15 5 0.05
16 6 0.06
17 1 0.01
18 20 0.21
19 26 0.27
20 15 0.16
21 8 0.08
22 14 0.15
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (20 bp):
AATATAATATTAAAAATATA
Found at i:1977343 original size:15 final size:15
Alignment explanation
Indices: 1977325--1977452 Score: 77
Period size: 15 Copynumber: 8.5 Consensus size: 15
1977315 TAATATTAAA
1977325 AATATAAATATATAT
1 AATATAAATATATAT
* *
1977340 AATATATATA-AAAT
1 AATATAAATATATAT
* * *
1977354 TATTTAAATTTATAT
1 AATATAAATATATAT
*
1977369 AATATAAAT-TATTAA
1 AATATAAATATA-TAT
*
1977384 AATATAAAAAATTATAT
1 AATAT-AAATA-TATAT
*
1977401 AAATATATAATAT-TTT
1 -AATATA-AATATATAT
*
1977417 AAATACAAATATA-AT
1 -AATATAAATATATAT
*
1977432 -ATATAAAAATATAT
1 AATATAAATATATAT
1977446 AATATAA
1 AATATAA
1977453 TTTGTTATAA
Statistics
Matches: 85, Mismatches: 18, Indels: 20
0.69 0.15 0.16
Matches are distributed among these distances:
13 9 0.11
14 13 0.15
15 38 0.45
16 11 0.13
17 4 0.05
18 10 0.12
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (15 bp):
AATATAAATATATAT
Found at i:1977350 original size:33 final size:32
Alignment explanation
Indices: 1977312--1977434 Score: 96
Period size: 33 Copynumber: 3.9 Consensus size: 32
1977302 CATTATAAGA
1977312 ATATAATATTAAAAATATAAATATATATAATAT
1 ATATAATATT-AAAATATAAATATATATAATAT
* * *
1977345 ATATAAAATT---ATTTAAATTTATATAATAT
1 ATATAATATTAAAATATAAATATATATAATAT
* *
1977374 A-A-ATTATTAAAATATAAAAAATTATATAA-AT
1 ATATAATATTAAAATAT-AAATA-TATATAATAT
* *
1977405 ATATAATATTTTAAATACAAATATAATATA
1 ATATAATA-TTAAAATATAAATAT-ATATA
1977435 TAAAAATATA
Statistics
Matches: 69, Mismatches: 12, Indels: 18
0.70 0.12 0.18
Matches are distributed among these distances:
27 4 0.06
28 1 0.01
29 18 0.26
30 3 0.04
31 6 0.09
32 9 0.13
33 21 0.30
34 7 0.10
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.41
Consensus pattern (32 bp):
ATATAATATTAAAATATAAATATATATAATAT
Found at i:1977377 original size:24 final size:24
Alignment explanation
Indices: 1977341--1977386 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
1977331 AATATATATA
*
1977341 ATATATATAAAATTATTTAAATTT
1 ATATATATAAAATTATTAAAATTT
1977365 ATATA-ATATAAATTATTAAAAT
1 ATATATATA-AAATTATTAAAAT
1977387 ATAAAAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
ATATATATAAAATTATTAAAATTT
Found at i:1977397 original size:18 final size:20
Alignment explanation
Indices: 1977333--1977410 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
1977323 AAAATATAAA
*
1977333 TATATATAATATATATAAAAT
1 TATATA-AATATATAAAAAAT
*
1977354 TATTTAAATTTATATAATATAAAT
1 TATATAAA--TATATAA-A-AAAT
1977378 TAT-TAAA-ATATAAAAAAT
1 TATATAAATATATAAAAAAT
1977396 TATATAAATATATAA
1 TATATAAATATATAA
1977411 TATTTTAAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
18 7 0.14
19 5 0.10
20 14 0.29
21 5 0.10
22 6 0.12
23 5 0.10
24 7 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
TATATAAATATATAAAAAAT
Found at i:1977404 original size:42 final size:42
Alignment explanation
Indices: 1977325--1977413 Score: 119
Period size: 42 Copynumber: 2.1 Consensus size: 42
1977315 TAATATTAAA
* * *
1977325 AATATAAATATATATAATATATATAAAATTATTTAAATTTATAT
1 AATATAAATATATATAAAATATAAAAAATTATATAAA--TATAT
1977369 AATATAAAT-TAT-TAAAATATAAAAAATTATATAAATATAT
1 AATATAAATATATATAAAATATAAAAAATTATATAAATATAT
1977409 AATAT
1 AATAT
1977414 TTTAAATACA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
40 10 0.24
42 20 0.48
43 3 0.07
44 9 0.21
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (42 bp):
AATATAAATATATATAAAATATAAAAAATTATATAAATATAT
Found at i:1982435 original size:4 final size:4
Alignment explanation
Indices: 1982426--1982452 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
1982416 CAACCCTCAT
1982426 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1982453 CAAATTGATA
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:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:1984455 original size:23 final size:21
Alignment explanation
Indices: 1984414--1984458 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 21
1984404 TTTTAATCAG
1984414 ATTTATTAATAAAAAAATTAA
1 ATTTATTAATAAAAAAATTAA
*
1984435 ATTTATTTAATTAAAATAATTAA
1 ATTTA-TTAA-TAAAAAAATTAA
1984458 A
1 A
1984459 ACAAAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.24
22 4 0.19
23 12 0.57
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
ATTTATTAATAAAAAAATTAA
Found at i:1984469 original size:30 final size:31
Alignment explanation
Indices: 1984433--1984490 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 31
1984423 TAAAAAAATT
*
1984433 AAATTTATTTAATTAA-AATAATTAAAACAA
1 AAATTTATATAATTAATAATAATTAAAACAA
* *
1984463 AAATTTATATATTTAATATTAATTAAAA
1 AAATTTATATAATTAATAATAATTAAAA
1984491 TATTTTTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 14 0.58
31 10 0.42
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (31 bp):
AAATTTATATAATTAATAATAATTAAAACAA
Found at i:1991181 original size:2 final size:2
Alignment explanation
Indices: 1991176--1991206 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1991166 TGTTTGGAAC
*
1991176 AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1991207 AAAAAATAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1994843 original size:2 final size:2
Alignment explanation
Indices: 1994836--1994913 Score: 84
Period size: 2 Copynumber: 39.0 Consensus size: 2
1994826 ACCTAAAATA
* * * *
1994836 AT AT AT AT AT GT AT AT GT GT AT AT AT AT AG AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
1994878 AT AT AT AT CT AT AT CT AT TT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1994914 TAATATTAAT
Statistics
Matches: 62, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1994861 original size:20 final size:20
Alignment explanation
Indices: 1994836--1994913 Score: 95
Period size: 20 Copynumber: 3.9 Consensus size: 20
1994826 ACCTAAAATA
* *
1994836 ATATATATATGTATATGTGT
1 ATATATATATGTATATATAT
1994856 ATATATATA-GATATATATAT
1 ATATATATATG-TATATATAT
* *
1994876 ATATATATATCTATATCTAT
1 ATATATATATGTATATATAT
*
1994896 TTATATATATGTATATAT
1 ATATATATATGTATATAT
1994914 TAATATTAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
19 1 0.02
20 48 0.98
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (20 bp):
ATATATATATGTATATATAT
Found at i:1996334 original size:3 final size:3
Alignment explanation
Indices: 1996326--1996355 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
1996316 TGCACTTTAA
1996326 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1996356 TACAGATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2001658 original size:19 final size:20
Alignment explanation
Indices: 2001617--2001658 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
2001607 CACACTTTAC
* *
2001617 AAAAATAAATTTTCACAGTTA
1 AAAAATAAATCTACACAG-TA
2001638 AAAAATAAATCTACACA-TA
1 AAAAATAAATCTACACAGTA
2001657 AA
1 AA
2001659 TGATAACATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 4 0.21
21 15 0.79
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (20 bp):
AAAAATAAATCTACACAGTA
Found at i:2003458 original size:2 final size:2
Alignment explanation
Indices: 2003451--2003491 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
2003441 TGCTGATTGT
2003451 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2003492 CACACATTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2004991 original size:15 final size:16
Alignment explanation
Indices: 2004971--2005003 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
2004961 TTTTTTAATT
2004971 TTTTAAAAAAT-ATAA
1 TTTTAAAAAATAATAA
*
2004986 TTTTAAAAGATAATAA
1 TTTTAAAAAATAATAA
2005002 TT
1 TT
2005004 AAAAATTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (16 bp):
TTTTAAAAAATAATAA
Found at i:2005051 original size:20 final size:19
Alignment explanation
Indices: 2005026--2005082 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 19
2005016 TTATCTTAAA
2005026 ATTTTAAAATTATTTTTTAT
1 ATTTTAAAA-TATTTTTTAT
* *
2005046 ATTTTAAAAATAATTATTAT
1 ATTTT-AAAATATTTTTTAT
2005066 ATTTTAAAA-ATTTTTTA
1 ATTTTAAAATATTTTTTA
2005083 AATCTTGAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 6 0.19
19 4 0.12
20 18 0.56
21 4 0.12
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTTTAAAATATTTTTTAT
Found at i:2005440 original size:16 final size:17
Alignment explanation
Indices: 2005421--2005457 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
2005411 ATTAATAATT
2005421 TATTATATA-TATTTTA
1 TATTATATATTATTTTA
*
2005437 TATT-TATATTATTTTT
1 TATTATATATTATTTTA
2005453 TATTA
1 TATTA
2005458 ATTTTTATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TATTATATATTATTTTA
Found at i:2005441 original size:20 final size:21
Alignment explanation
Indices: 2005402--2005498 Score: 71
Period size: 20 Copynumber: 4.8 Consensus size: 21
2005392 ATAATATAAA
*
2005402 ATTATATATA-TTAATAATTT
1 ATTATATATATTTTATAATTT
2005422 ATTATATATATTTTAT-ATTT
1 ATTATATATATTTTATAATTT
*
2005442 A-TAT-TATTTTTTATTAATTT
1 ATTATATATATTTTA-TAATTT
* *
2005462 -TTATATTATGTTGTTATTATTT
1 ATTATA-TATATT-TTATAATTT
* *
2005484 TTTATAT-TTTTTTAT
1 ATTATATATATTTTAT
2005499 TATTCAATTT
Statistics
Matches: 64, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
18 8 0.12
19 4 0.06
20 26 0.41
21 7 0.11
22 11 0.17
23 8 0.12
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (21 bp):
ATTATATATATTTTATAATTT
Found at i:2005494 original size:10 final size:11
Alignment explanation
Indices: 2005434--2005502 Score: 65
Period size: 11 Copynumber: 6.5 Consensus size: 11
2005424 TATATATATT
*
2005434 TTATATTTATA
1 TTATTTTTATA
2005445 TTATTTTT-TA
1 TTATTTTTATA
2005455 TTAATTTTTATA
1 TT-ATTTTTATA
*
2005467 TTATGTTGT-TA
1 TTAT-TTTTATA
2005478 TTATTTTT-TA
1 TTATTTTTATA
*
2005488 -TATTTTTTTA
1 TTATTTTTATA
2005498 TTATT
1 TTATT
2005503 CAATTTAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
9 7 0.14
10 11 0.22
11 25 0.50
12 7 0.14
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (11 bp):
TTATTTTTATA
Found at i:2005501 original size:23 final size:22
Alignment explanation
Indices: 2005439--2005508 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 22
2005429 ATATTTTATA
2005439 TTTATATTATTTTTTATTAATT
1 TTTATATTATTTTTTATTAATT
* *
2005461 TTTATATTATGTTGTTATTATTT
1 TTTATATTAT-TTTTTATTAATT
*
2005484 TTTATATTTTTTTATTATTCAATT
1 TTTATATTATTTT-TTATT-AATT
2005508 T
1 T
2005509 AAAAAAATTA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
22 12 0.30
23 24 0.60
24 4 0.10
ACGTcount: A:0.24, C:0.01, G:0.03, T:0.71
Consensus pattern (22 bp):
TTTATATTATTTTTTATTAATT
Found at i:2006769 original size:15 final size:16
Alignment explanation
Indices: 2006739--2006783 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
2006729 TTGTGTACGG
*
2006739 AAAAAATAAATATTTA-
1 AAAAAATTAAT-TTTAT
2006755 AAAAAATTAATTTTAT
1 AAAAAATTAATTTTAT
*
2006771 AATAAATTAATTT
1 AAAAAATTAATTT
2006784 AATTTTAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
15 4 0.15
16 22 0.85
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AAAAAATTAATTTTAT
Found at i:2007519 original size:17 final size:18
Alignment explanation
Indices: 2007481--2007534 Score: 62
Period size: 17 Copynumber: 3.2 Consensus size: 18
2007471 CATATAATTT
2007481 AATAA-TATTAAATATAA
1 AATAATTATTAAATATAA
* *
2007498 TATAATTATTTAATA-AA
1 AATAATTATTAAATATAA
2007515 AATAATTA--AAATATAA
1 AATAATTATTAAATATAA
2007531 AATA
1 AATA
2007535 TAAGATAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
15 4 0.13
16 6 0.19
17 13 0.42
18 8 0.26
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AATAATTATTAAATATAA
Found at i:2007527 original size:28 final size:27
Alignment explanation
Indices: 2007477--2007573 Score: 79
Period size: 28 Copynumber: 3.5 Consensus size: 27
2007467 TTCACATATA
* * * *
2007477 ATTTAATAATATTAAATATAATATAATT
1 ATTTAATAAAAATAATTAAAATATAA-T
*
2007505 ATTTAATAAAAATAATTAAAATATAAA
1 ATTTAATAAAAATAATTAAAATATAAT
* * * *
2007532 ATATAAGATAAATAAATATAAATATAAT
1 ATTTAATAAAAATAATTA-AAATATAAT
2007560 A-TTAATAATAAATA
1 ATTTAATAA-AAATA
2007574 TTTTAAATTT
Statistics
Matches: 54, Mismatches: 13, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
27 18 0.33
28 36 0.67
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (27 bp):
ATTTAATAAAAATAATTAAAATATAAT
Found at i:2007556 original size:21 final size:22
Alignment explanation
Indices: 2007523--2007567 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
2007513 AAAATAATTA
2007523 AAATATAAAATATAAGATAAAT
1 AAATATAAAATATAAGATAAAT
* *
2007545 AAATAT-AAATATAATATTAAT
1 AAATATAAAATATAAGATAAAT
2007566 AA
1 AA
2007568 TAAATATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (22 bp):
AAATATAAAATATAAGATAAAT
Found at i:2007900 original size:24 final size:24
Alignment explanation
Indices: 2007866--2007918 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
2007856 ATATTGATTA
2007866 AAAATTAATTAATTAT-TATTTTTT
1 AAAATTAATTAATTATATA-TTTTT
*
2007890 AAAATTTATTAATTATATATTTTT
1 AAAATTAATTAATTATATATTTTT
2007914 AAAAT
1 AAAAT
2007919 CATCTTAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 25 0.93
25 2 0.07
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
AAAATTAATTAATTATATATTTTT
Found at i:2007926 original size:25 final size:24
Alignment explanation
Indices: 2007873--2007929 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 24
2007863 TTAAAAATTA
*
2007873 ATTAATTATTATTTTTTAAAATTT
1 ATTAATTATTATTTTTTAAAATAT
2007897 ATTAATTA-TATATTTTTAAAATCAT
1 ATTAATTATTAT-TTTTTAAAAT-AT
*
2007922 CTTAATTA
1 ATTAATTA
2007930 AAATGTTAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 3 0.10
24 18 0.62
25 8 0.28
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (24 bp):
ATTAATTATTATTTTTTAAAATAT
Found at i:2010551 original size:21 final size:21
Alignment explanation
Indices: 2010520--2010578 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
2010510 TTTAATTAAA
*
2010520 TTATTTATATTTAAAAT-T-T
1 TTATTTTTATTTAAAATATAT
*
2010539 TATATTTTTTATTAAAAATATAT
1 T-TA-TTTTTATTTAAAATATAT
2010562 TTATTTTTATTTCAAAA
1 TTATTTTTATTT-AAAA
2010579 AGTTATTTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
19 1 0.03
20 2 0.06
21 20 0.62
22 7 0.22
23 2 0.06
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
TTATTTTTATTTAAAATATAT
Found at i:2012865 original size:17 final size:19
Alignment explanation
Indices: 2012829--2012866 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
2012819 AAGAATATTA
*
2012829 TTTTATTTTTTAATTAATC
1 TTTTATTTTTTAAATAATC
2012848 TTTT-TTTTTTAAAT-ATC
1 TTTTATTTTTTAAATAATC
2012865 TT
1 TT
2012867 AATAAAAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 9 0.50
19 4 0.22
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTTATTTTTTAAATAATC
Found at i:2013170 original size:2 final size:2
Alignment explanation
Indices: 2013163--2013191 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2013153 ACAAAACAAC
2013163 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2013192 TTAAGTTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2014665 original size:16 final size:16
Alignment explanation
Indices: 2014644--2014675 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2014634 ATATTCATCC
*
2014644 AAGAAAAGAAAAAGGG
1 AAGAAAAAAAAAAGGG
2014660 AAGAAAAAAAAAAGGG
1 AAGAAAAAAAAAAGGG
2014676 GAGGAATTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (16 bp):
AAGAAAAAAAAAAGGG
Found at i:2019959 original size:15 final size:16
Alignment explanation
Indices: 2019915--2019960 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
2019905 AATTTAAATT
2019915 AAATATAATGTAATTTTA
1 AAATA-AAT-TAATTTTA
*
2019933 AAATATATTAATTTTA
1 AAATAAATTAATTTTA
2019949 AAA-AAATTAATT
1 AAATAAATTAATT
2019961 AAAAAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
15 8 0.31
16 11 0.42
17 2 0.08
18 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (16 bp):
AAATAAATTAATTTTA
Found at i:2022655 original size:69 final size:69
Alignment explanation
Indices: 2022548--2022683 Score: 254
Period size: 69 Copynumber: 2.0 Consensus size: 69
2022538 ACGAAAACTG
2022548 TTGCTTGCAGCAATTCATGCTTACTTGGTAGGTTTTTTGTTCTTAGGCTACAATAGTATGATTTT
1 TTGCTTGCAGCAATTCATGCTTACTTGGTAGGTTTTTTGTTCTTAGGCTACAATAGTATGATTTT
2022613 GTTA
66 GTTA
* *
2022617 TTGCTTGCAGCAATTCATGCTTACTTGGTAGGTTTTTTGTTCTTAGGGTGCAATAGTATGATTTT
1 TTGCTTGCAGCAATTCATGCTTACTTGGTAGGTTTTTTGTTCTTAGGCTACAATAGTATGATTTT
2022682 GT
66 GT
2022684 AATCCAATTA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
69 65 1.00
ACGTcount: A:0.19, C:0.12, G:0.22, T:0.46
Consensus pattern (69 bp):
TTGCTTGCAGCAATTCATGCTTACTTGGTAGGTTTTTTGTTCTTAGGCTACAATAGTATGATTTT
GTTA
Found at i:2024516 original size:25 final size:25
Alignment explanation
Indices: 2024488--2024550 Score: 58
Period size: 25 Copynumber: 2.4 Consensus size: 25
2024478 AATGATTAAA
2024488 TTATTAATAATA-AAAAATTAAATAT
1 TTATTAATAATATAAAAATT-AATAT
* *
2024513 TTA-TAATTTATATAAAAATTGATAT
1 TTATTAA-TAATATAAAAATTAATAT
2024538 TTAATTCAATAAT
1 TT-ATT-AATAAT
2024551 TCAAAATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
24 3 0.10
25 13 0.43
26 8 0.27
27 4 0.13
28 2 0.07
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (25 bp):
TTATTAATAATATAAAAATTAATAT
Found at i:2030232 original size:2 final size:2
Alignment explanation
Indices: 2030220--2030263 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
2030210 GTGAAATTTG
* * *
2030220 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2030262 AT
1 AT
2030264 TGTGTTTATC
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2041874 original size:20 final size:20
Alignment explanation
Indices: 2041846--2041893 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
2041836 AATATAAATA
*
2041846 ATTTTAAAAAA-TTATTTATT
1 ATTTAAAAAAATTTA-TTATT
2041866 ATTTAAAAAAATTTATTATT
1 ATTTAAAAAAATTTATTATT
*
2041886 TTTTAAAA
1 ATTTAAAA
2041894 TATCACTCCA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 22 0.88
21 3 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
ATTTAAAAAAATTTATTATT
Found at i:2041894 original size:17 final size:17
Alignment explanation
Indices: 2041848--2041886 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
2041838 TATAAATAAT
2041848 TTTAAAAAATTATTTATTA
1 TTTAAAAAA--ATTTATTA
2041867 TTTAAAAAAATTTATTA
1 TTTAAAAAAATTTATTA
2041884 TTT
1 TTT
2041887 TTTAAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 11 0.55
19 9 0.45
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TTTAAAAAAATTTATTA
Found at i:2041921 original size:16 final size:16
Alignment explanation
Indices: 2041902--2041934 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2041892 AATATCACTC
2041902 CATTAAA-AAAATATTA
1 CATTAAATAAAA-ATTA
2041918 CATTAAATAAAAATTA
1 CATTAAATAAAAATTA
2041934 C
1 C
2041935 TCTGCTGATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (16 bp):
CATTAAATAAAAATTA
Found at i:2042056 original size:3 final size:3
Alignment explanation
Indices: 2042050--2042086 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
2042040 ATGAAAGGTC
2042050 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2042087 ATCTATAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2042388 original size:20 final size:21
Alignment explanation
Indices: 2042358--2042396 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
2042348 TTTAAAAATA
*
2042358 AATATAAATAATTTTATTTTT
1 AATATAAATAATATTATTTTT
2042379 AATA-AAATAATATTATTT
1 AATATAAATAATATTATTT
2042397 CATAAATTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AATATAAATAATATTATTTTT
Found at i:2046906 original size:34 final size:34
Alignment explanation
Indices: 2046844--2047063 Score: 334
Period size: 34 Copynumber: 6.5 Consensus size: 34
2046834 AGTAGTTTGT
* *
2046844 CATTGTTGACTAAAT-GGAGATTTGGTAGCTTAC
1 CATTGTTGATTAAATGGGAAATTTGGTAGCTTAC
2046877 CATTGTTGATTAAATGGGAAATTTGGTAGCTTAC
1 CATTGTTGATTAAATGGGAAATTTGGTAGCTTAC
*
2046911 CATTGTTGATTAAATGAGAAATTTGGTAGCTTAC
1 CATTGTTGATTAAATGGGAAATTTGGTAGCTTAC
2046945 CATTGTTGATTAAATGGGAAATTTGGTAGCTTAC
1 CATTGTTGATTAAATGGGAAATTTGGTAGCTTAC
* ** *
2046979 CATTTTTGATTAAATGGGTGATTTGGTGGCTTAC
1 CATTGTTGATTAAATGGGAAATTTGGTAGCTTAC
* * * *
2047013 CATTGTTGACTAAATGGGAGATTTGGTAGGTTGC
1 CATTGTTGATTAAATGGGAAATTTGGTAGCTTAC
2047047 CATTGTTGATTAAATGG
1 CATTGTTGATTAAATGG
2047064 TGGTTTTTAC
Statistics
Matches: 171, Mismatches: 15, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
33 14 0.08
34 157 0.92
ACGTcount: A:0.27, C:0.09, G:0.25, T:0.39
Consensus pattern (34 bp):
CATTGTTGATTAAATGGGAAATTTGGTAGCTTAC
Found at i:2047425 original size:19 final size:19
Alignment explanation
Indices: 2047369--2047431 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
2047359 TGGTTGTCGA
**
2047369 GGTACTATTCACGTATATA
1 GGTACTATTCACGTATACG
2047388 GGTACTATTCACGTATACG
1 GGTACTATTCACGTATACG
*
2047407 GGTACTATTCAAGTATACG
1 GGTACTATTCACGTATACG
*
2047426 GTTACT
1 GGTACT
2047432 GTACACGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTACTATTCACGTATACG
Found at i:2051591 original size:34 final size:34
Alignment explanation
Indices: 2051497--2051748 Score: 357
Period size: 34 Copynumber: 7.5 Consensus size: 34
2051487 AAGTGGGAGA
* * *
2051497 ATTGTTGATTAAATGGTG--ATTTAGTAGTTTGCC
1 ATTGTTGATTAAATGG-GAAATTTGGTAGCTTACC
* *
2051530 ATTGTTGACTAAAT-GGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
2051563 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
2051597 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
2051631 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
* ** *
2051665 ATTTTTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
* * * *
2051699 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
2051733 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
2051749 TGGTTTTTAC
Statistics
Matches: 199, Mismatches: 17, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
31 1 0.01
32 1 0.01
33 38 0.19
34 159 0.80
ACGTcount: A:0.27, C:0.08, G:0.25, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
Found at i:2052500 original size:14 final size:14
Alignment explanation
Indices: 2052464--2052507 Score: 63
Period size: 14 Copynumber: 3.1 Consensus size: 14
2052454 TTAAAAAAAA
2052464 TAATATTTAATAATTT
1 TAATATTT-A-AATTT
2052480 T-ATATTTAAATTT
1 TAATATTTAAATTT
2052493 TAATATTTAAATTT
1 TAATATTTAAATTT
2052507 T
1 T
2052508 TTTATTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 6 0.22
14 14 0.52
15 6 0.22
16 1 0.04
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TAATATTTAAATTT
Found at i:2052513 original size:14 final size:14
Alignment explanation
Indices: 2052466--2052514 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
2052456 AAAAAAAATA
*
2052466 ATATTTAATAATTTT
1 ATATTTAA-ATTTTT
*
2052481 ATATTTAAATTTTA
1 ATATTTAAATTTTT
2052495 ATATTTAAATTTTT
1 ATATTTAAATTTTT
*
2052509 TTATTT
1 ATATTT
2052515 TTAAATTATA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
14 22 0.73
15 8 0.27
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
ATATTTAAATTTTT
Found at i:2052518 original size:30 final size:30
Alignment explanation
Indices: 2052463--2052543 Score: 94
Period size: 30 Copynumber: 2.7 Consensus size: 30
2052453 TTTAAAAAAA
**
2052463 ATAATATTT-AATAATTTTATATTTAAATT
1 ATAATATTTAAATTTTTTTATATTTAAATT
* *
2052492 TTAATATTTAAATTTTTTTATTTTTAAATT
1 ATAATATTTAAATTTTTTTATATTTAAATT
*
2052522 ATAAT-TTTATATTTTATTTATA
1 ATAATATTTAAATTTT-TTTATA
2052544 CAAAATTTTA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 17 0.40
30 26 0.60
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (30 bp):
ATAATATTTAAATTTTTTTATATTTAAATT
Found at i:2055632 original size:23 final size:24
Alignment explanation
Indices: 2055606--2055658 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
2055596 ATTTAGTAAT
*
2055606 AATTAATTTTTTTAAAAA-AATTA
1 AATTAATTATTTTAAAAATAATTA
* *
2055629 AATTTATTATTTTAAAAATATTTA
1 AATTAATTATTTTAAAAATAATTA
2055653 AATTAA
1 AATTAA
2055659 AATTATTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 16 0.64
24 9 0.36
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
AATTAATTATTTTAAAAATAATTA
Found at i:2064354 original size:2 final size:2
Alignment explanation
Indices: 2064347--2064376 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2064337 AAAAAGTTTC
*
2064347 TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2064377 GAAAGAGATA
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):
TA
Found at i:2064555 original size:4 final size:4
Alignment explanation
Indices: 2064546--2064572 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2064536 CTCGAAAATT
2064546 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
2064573 TTTTAGAAAA
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:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:2064873 original size:6 final size:6
Alignment explanation
Indices: 2064862--2064891 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
2064852 TAGAAAAGAG
2064862 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
2064892 TTTGTCGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:2066928 original size:2 final size:2
Alignment explanation
Indices: 2066921--2066948 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2066911 ATCAAGACAA
2066921 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
2066949 GTGTCGTTAA
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:2067002 original size:27 final size:26
Alignment explanation
Indices: 2066972--2067022 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
2066962 TAAACACGCA
2066972 ATTTGAGAAAATTTTTTAGTAATTAAG
1 ATTTGA-AAAATTTTTTAGTAATTAAG
** *
2066999 ATTTGATTAATTTTTTAGTTATTA
1 ATTTGAAAAATTTTTTAGTAATTA
2067023 CTAATATATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 15 0.71
27 6 0.29
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (26 bp):
ATTTGAAAAATTTTTTAGTAATTAAG
Found at i:2067667 original size:3 final size:3
Alignment explanation
Indices: 2067659--2067684 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2067649 ATCACAGCAA
2067659 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
2067685 AGAAATAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2070578 original size:13 final size:13
Alignment explanation
Indices: 2070560--2070584 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2070550 TCCGGCATTT
2070560 AAAAAAAGAAAAA
1 AAAAAAAGAAAAA
2070573 AAAAAAAGAAAA
1 AAAAAAAGAAAA
2070585 GATGAAAGCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (13 bp):
AAAAAAAGAAAAA
Found at i:2076784 original size:3 final size:3
Alignment explanation
Indices: 2076776--2076805 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2076766 CGCCGCGTGC
2076776 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2076806 TTGCATTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2077497 original size:23 final size:24
Alignment explanation
Indices: 2077463--2077515 Score: 74
Period size: 23 Copynumber: 2.3 Consensus size: 24
2077453 TTTTATAATT
2077463 TAATT-TTAATTTTTATTTAAAAA
1 TAATTATTAATTTTTATTTAAAAA
**
2077486 TAATTATT-ATTTTTATTTAAATT
1 TAATTATTAATTTTTATTTAAAAA
2077509 TAATTAT
1 TAATTAT
2077516 AAATATTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 25 0.93
24 2 0.07
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TAATTATTAATTTTTATTTAAAAA
Found at i:2079773 original size:20 final size:20
Alignment explanation
Indices: 2079736--2079773 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2079726 TAATAAAATT
*
2079736 TTATTTTTATTTAAATTTAA
1 TTATTTTTATATAAATTTAA
2079756 TTATTTTTA-ATAATATTT
1 TTATTTTTATATAA-ATTT
2079774 TAAATGATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TTATTTTTATATAAATTTAA
Found at i:2083013 original size:27 final size:27
Alignment explanation
Indices: 2082981--2083034 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
2082971 TTTATTGGTT
2082981 ATAATT-ATTATATTATTATTTTATAAA
1 ATAATTAATTATATT-TTATTTTATAAA
*
2083008 ATAATTAATTTTATTTTATTTTATAAA
1 ATAATTAATTATATTTTATTTTATAAA
2083035 GTTATGAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 18 0.72
28 7 0.28
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
ATAATTAATTATATTTTATTTTATAAA
Found at i:2083880 original size:32 final size:32
Alignment explanation
Indices: 2083842--2083904 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
2083832 TATTAGTAAA
* *
2083842 TTATATTATATAAATTAT-TTATTTTTATATTT
1 TTATATTATAT-AATTATATAATATTTATATTT
2083874 TTATATTATATAATTATATAATATTTATATT
1 TTATATTATATAATTATATAATATTTATATT
2083905 ATCGGATAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 6 0.21
32 22 0.79
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (32 bp):
TTATATTATATAATTATATAATATTTATATTT
Found at i:2086105 original size:18 final size:18
Alignment explanation
Indices: 2086065--2086168 Score: 68
Period size: 21 Copynumber: 5.3 Consensus size: 18
2086055 TATTTTATTT
2086065 ATATTTAATTATAAAATATA
1 ATATTTAA-TATAAAA-ATA
*
2086085 TAAATATTAATATAAAAATA
1 -ATAT-TTAATATAAAAATA
2086105 ATATTTAATATAAATAAATA
1 ATATTTAATAT-AA-AAATA
*
2086125 ATAATTTAAATTTATAAAATCA
1 AT-ATTT-AATATA-AAAAT-A
* *
2086147 A-ATTAAATATAAATATA
1 ATATTTAATATAAAAATA
2086164 A-ATTT
1 ATATTT
2086169 TAAAATTTTT
Statistics
Matches: 69, Mismatches: 7, Indels: 18
0.73 0.07 0.19
Matches are distributed among these distances:
17 5 0.07
18 11 0.16
19 10 0.14
20 13 0.19
21 19 0.28
22 11 0.16
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (18 bp):
ATATTTAATATAAAAATA
Found at i:2086129 original size:16 final size:16
Alignment explanation
Indices: 2086084--2086135 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
2086074 TATAAAATAT
2086084 ATAAATATTAATATAA
1 ATAAATATTAATATAA
*
2086100 AAATAATATTTAATATAA
1 ATA-AATA-TTAATATAA
* *
2086118 ATAAATAATAATTTAA
1 ATAAATATTAATATAA
2086134 AT
1 AT
2086136 TTATAAAATC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
16 11 0.37
17 8 0.27
18 11 0.37
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATAAATATTAATATAA
Found at i:2086142 original size:20 final size:20
Alignment explanation
Indices: 2086065--2086133 Score: 72
Period size: 18 Copynumber: 3.4 Consensus size: 20
2086055 TATTTTATTT
*
2086065 ATATTTAATTATAAAATATATA
1 ATATTTAA-TAT-AAATAAATA
2086087 A-ATATTAATAT-AA-AAATA
1 ATAT-TTAATATAAATAAATA
2086105 ATATTTAATATAAATAAATA
1 ATATTTAATATAAATAAATA
2086125 ATAATTTAA
1 AT-ATTTAA
2086134 ATTTATAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
18 12 0.29
19 6 0.15
20 7 0.17
21 11 0.27
22 5 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
ATATTTAATATAAATAAATA
Found at i:2086144 original size:21 final size:20
Alignment explanation
Indices: 2086067--2086157 Score: 73
Period size: 22 Copynumber: 4.5 Consensus size: 20
2086057 TTTTATTTAT
2086067 ATTTAAT-TATAAAATATATAA
1 ATTTAATATATAAAATA-AT-A
2086088 ATATTAATATA-AAAATAAT-
1 AT-TTAATATATAAAATAATA
*
2086107 ATTTAATATAAATAAATAATA
1 ATTTAATATATA-AAATAATA
* *
2086128 ATTTAAATTTATAAAATCA-A
1 ATTT-AATATATAAAATAATA
*
2086148 ATTAAATATA
1 ATTTAATATA
2086158 AATATAAATT
Statistics
Matches: 59, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
18 8 0.14
19 8 0.14
20 11 0.19
21 13 0.22
22 17 0.29
23 2 0.03
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (20 bp):
ATTTAATATATAAAATAATA
Found at i:2087696 original size:2 final size:2
Alignment explanation
Indices: 2087689--2087718 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2087679 AATATACAAA
2087689 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2087719 GGGTGATGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2087849 original size:3 final size:3
Alignment explanation
Indices: 2087843--2087869 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2087833 TTCTCTTTTT
2087843 TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC
2087870 ATCCTTTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Done.