Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold412
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: 4645160
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 12 of 32
Found at i:1672257 original size:29 final size:29
Alignment explanation
Indices: 1672205--1672297 Score: 70
Period size: 29 Copynumber: 3.3 Consensus size: 29
1672195 AATTCAAAAT
* *
1672205 AAATTAAATAAATTTAA--AATATAAA-A
1 AAATTATATAAATTTAATCATTATAAACA
**
1672231 AAATTATATAAATTTAATCATTTATAAATT
1 AAATTATATAAATTTAATCA-TTATAAACA
*
1672261 AAATTCA-ATAAA-TTATTCAATTATAAACA
1 AAATT-ATATAAATTTAATC-ATTATAAACA
*
1672290 AACTTATA
1 AAATTATA
1672298 ACATACAAGT
Statistics
Matches: 53, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
26 16 0.30
28 2 0.04
29 23 0.43
30 11 0.21
31 1 0.02
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (29 bp):
AAATTATATAAATTTAATCATTATAAACA
Found at i:1673811 original size:22 final size:20
Alignment explanation
Indices: 1673773--1673812 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
1673763 ATATTTTATT
1673773 TAAATTTAATTAAAAATATA
1 TAAATTTAATTAAAAATATA
1673793 TAAATATTAATATAAAAATA
1 TAAAT-TTAAT-TAAAAATA
1673813 ATATTTTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 5 0.28
22 8 0.44
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TAAATTTAATTAAAAATATA
Found at i:1674354 original size:16 final size:16
Alignment explanation
Indices: 1674335--1674370 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
1674325 TTTTAAGTTT
1674335 AATTAAA-TTTAAATCA
1 AATTAAATTTTAAAT-A
1674351 AATTAAATTTTAAATA
1 AATTAAATTTTAAATA
1674367 AATT
1 AATT
1674371 TACGTTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
AATTAAATTTTAAATA
Found at i:1674433 original size:2 final size:2
Alignment explanation
Indices: 1674426--1674464 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
1674416 TGTTTGATGC
* *
1674426 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1674465 AAAAACCTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 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:1675854 original size:21 final size:21
Alignment explanation
Indices: 1675818--1675859 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
1675808 TAAAAGTTAT
1675818 TTTTAAATTAATATTTATATA
1 TTTTAAATTAATATTTATATA
1675839 TTTTATAATTAA-ATTTATATA
1 TTTTA-AATTAATATTTATATA
1675860 AAATATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTAAATTAATATTTATATA
Found at i:1675963 original size:27 final size:29
Alignment explanation
Indices: 1675911--1675966 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
1675901 ATTTAAATAA
* *
1675911 AAATATATATTTAAAATTTTTAATTTTAC
1 AAATATATATTAAAAATTATTAATTTTAC
*
1675940 AAATA-ATATTAAAAATTATTATTTTTA
1 AAATATATATTAAAAATTATTAATTTTA
1675967 AATTAATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 19 0.79
29 5 0.21
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (29 bp):
AAATATATATTAAAAATTATTAATTTTAC
Found at i:1676767 original size:13 final size:12
Alignment explanation
Indices: 1676751--1676791 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
1676741 ATATTTTATT
1676751 AAATTTAATTATA
1 AAATTTAA-TATA
1676764 AAATTT-ATAT-
1 AAATTTAATATA
1676774 AAATATTAATATA
1 AAAT-TTAATATA
1676787 AAATT
1 AAATT
1676792 ATTATTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
10 4 0.16
11 5 0.20
12 6 0.24
13 10 0.40
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
AAATTTAATATA
Found at i:1676776 original size:11 final size:11
Alignment explanation
Indices: 1676750--1676792 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
1676740 AATATTTTAT
*
1676750 TAAATTTAATTA
1 TAAAATTAA-TA
*
1676762 TAAAATTTATA
1 TAAAATTAATA
1676773 TAAATATTAATA
1 TAAA-ATTAATA
1676785 TAAAATTA
1 TAAAATTA
1676793 TTATTTAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
11 10 0.37
12 17 0.63
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TAAAATTAATA
Found at i:1676776 original size:23 final size:25
Alignment explanation
Indices: 1676731--1676791 Score: 76
Period size: 24 Copynumber: 2.6 Consensus size: 25
1676721 TTATTATTTG
*
1676731 TTAATTA-AAAATATTTTATTAAAT-
1 TTAATTATAAAAT-TTATATTAAATA
1676755 TTAATTATAAAATTTATA-TAAATA
1 TTAATTATAAAATTTATATTAAATA
1676779 TTAA-TATAAAATT
1 TTAATTATAAAATT
1676792 ATTATTTAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
23 14 0.41
24 15 0.44
25 5 0.15
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
TTAATTATAAAATTTATATTAAATA
Found at i:1678616 original size:21 final size:20
Alignment explanation
Indices: 1678586--1678638 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 20
1678576 TTAAATAATA
1678586 ATTT-AAATTTAAATAAATTT
1 ATTTAAAATTTAAA-AAATTT
* *
1678606 ATTTAAAATTTCAAAATTTT
1 ATTTAAAATTTAAAAAATTT
1678626 ATTTTAAAATTTA
1 A-TTTAAAATTTA
1678639 TTTTATATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 10 0.36
21 18 0.64
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTTAAAATTTAAAAAATTT
Found at i:1680758 original size:26 final size:25
Alignment explanation
Indices: 1680703--1680768 Score: 71
Period size: 25 Copynumber: 2.6 Consensus size: 25
1680693 ATATTTAAGA
*
1680703 TTTA-AATATAATTTATTTTTTAAT
1 TTTATAATATAAATTATTTTTTAAT
* *
1680727 TATATAATATAAATTATTTTTATATT
1 TTTATAATATAAATTATTTTT-TAAT
*
1680753 TTTATATTATATAATT
1 TTTATAATATA-AATT
1680769 TATATAATGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
24 3 0.09
25 15 0.44
26 12 0.35
27 4 0.12
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (25 bp):
TTTATAATATAAATTATTTTTTAAT
Found at i:1681618 original size:21 final size:21
Alignment explanation
Indices: 1681589--1681652 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
1681579 ATATATATTT
1681589 TTAT-TATTATATAA-AAACAA
1 TTATATATTATATAATAAA-AA
*
1681609 TTATATATTATATAATATAAA
1 TTATATATTATATAATAAAAA
* *
1681630 TAATATATTATATTATAAAAA
1 TTATATATTATATAATAAAAA
1681651 TT
1 TT
1681653 TTAAATATAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
20 4 0.11
21 31 0.84
22 2 0.05
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (21 bp):
TTATATATTATATAATAAAAA
Found at i:1681711 original size:9 final size:9
Alignment explanation
Indices: 1681699--1681760 Score: 55
Period size: 9 Copynumber: 7.3 Consensus size: 9
1681689 AAAAATAAAC
1681699 TAAATTAAT
1 TAAATTAAT
*
1681708 TAAATAAAT
1 TAAATTAAT
1681717 T-AATT--T
1 TAAATTAAT
1681723 TAAA--AAT
1 TAAATTAAT
1681730 T-AATTAAAT
1 TAAATT-AAT
1681739 TAAATTAAT
1 TAAATTAAT
1681748 TAAATTTAAT
1 TAAA-TTAAT
1681758 TAA
1 TAA
1681761 TTTTAAAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 15
0.72 0.03 0.25
Matches are distributed among these distances:
6 4 0.09
7 4 0.09
8 3 0.07
9 20 0.47
10 12 0.28
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
TAAATTAAT
Found at i:1681711 original size:14 final size:13
Alignment explanation
Indices: 1681694--1681762 Score: 77
Period size: 14 Copynumber: 5.1 Consensus size: 13
1681684 AAAATAAAAA
1681694 TAAACTAAATTAAT
1 TAAA-TAAATTAAT
1681708 TAAATAAATTAATT
1 TAAATAAATTAA-T
*
1681722 TTAA-AAATTAAT
1 TAAATAAATTAAT
1681734 TAAATTAAATTAAT
1 TAAA-TAAATTAAT
*
1681748 TAAATTTAATTAAT
1 TAAA-TAAATTAAT
1681762 T
1 T
1681763 TTAAAAATTA
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
12 4 0.08
13 15 0.31
14 30 0.61
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (13 bp):
TAAATAAATTAAT
Found at i:1681759 original size:41 final size:40
Alignment explanation
Indices: 1681680--1681775 Score: 138
Period size: 41 Copynumber: 2.4 Consensus size: 40
1681670 TCAAATCAAA
*
1681680 TTTAAAAATAAAAATAAACTAAATTAATTAAATAAATTAAT
1 TTTAAAAAT-TAAATAAACTAAATTAATTAAATAAATTAAT
* * *
1681721 TTTAAAAATTAATTAAATTAAATTAATTAAATTTAATTAAT
1 TTTAAAAATTAAATAAACTAAATTAATTAAA-TAAATTAAT
1681762 TTTAAAAATTAAAT
1 TTTAAAAATTAAAT
1681776 CGATTTAACT
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
40 19 0.39
41 30 0.61
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (40 bp):
TTTAAAAATTAAATAAACTAAATTAATTAAATAAATTAAT
Found at i:1681775 original size:5 final size:5
Alignment explanation
Indices: 1681694--1681760 Score: 56
Period size: 5 Copynumber: 14.6 Consensus size: 5
1681684 AAAATAAAAA
* * *
1681694 TAAAC TAAAT T-AAT TAAA- TAAAT TAATT TTAA- -AAAT T-AAT TAAAT
1 TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT TAAAT
*
1681739 TAAAT T-AAT TAAAT TTAAT TAA
1 TAAAT TAAAT TAAAT TAAAT TAA
1681761 TTTTAAAAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
3 2 0.04
4 16 0.33
5 31 0.63
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (5 bp):
TAAAT
Found at i:1683140 original size:2 final size:2
Alignment explanation
Indices: 1683133--1683161 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1683123 TTCAACTGAA
1683133 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 A
1683162 AAGATAATTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1688204 original size:5 final size:5
Alignment explanation
Indices: 1688190--1688234 Score: 51
Period size: 5 Copynumber: 9.4 Consensus size: 5
1688180 GGTTGATAGT
*
1688190 TTAT- TTATA TTATA TT-TA -TATA TTTTA TTATA TTATAA TTATA TT
1 TTATA TTATA TTATA TTATA TTATA TTATA TTATA TTAT-A TTATA TT
1688235 TAAATATTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
3 1 0.03
4 8 0.23
5 21 0.60
6 5 0.14
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTATA
Found at i:1688222 original size:23 final size:24
Alignment explanation
Indices: 1688189--1688233 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
1688179 CGGTTGATAG
*
1688189 TTTATTTATATTATATTTATATAT
1 TTTATTTATATTATAATTATATAT
1688213 TTTA-TTATATTATAATTATAT
1 TTTATTTATATTATAATTATAT
1688234 TTAAATATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (24 bp):
TTTATTTATATTATAATTATATAT
Found at i:1688274 original size:32 final size:31
Alignment explanation
Indices: 1688233--1688306 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 31
1688223 TATAATTATA
1688233 TTTAAATATTAA-AATTTAAAATTATAAAAAT
1 TTTAAATATTAATAATTT-AAATTATAAAAAT
* *
1688264 TTTAATATATTAATAATTTATATTATATAAAT
1 TTTAA-ATATTAATAATTTAAATTATAAAAAT
1688296 TTTAAAATATT
1 TTT-AAATATT
1688307 TTTATTTATA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
31 5 0.13
32 26 0.68
33 7 0.18
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (31 bp):
TTTAAATATTAATAATTTAAATTATAAAAAT
Found at i:1688283 original size:16 final size:14
Alignment explanation
Indices: 1688232--1688306 Score: 51
Period size: 16 Copynumber: 4.8 Consensus size: 14
1688222 TTATAATTAT
1688232 ATTTAAATATTAAA
1 ATTTAAATATTAAA
*
1688246 ATTTAAAATTATAAAA
1 ATTT-AAA-TATTAAA
1688262 ATTTTAATATATTAATA
1 A-TTTAA-ATATTAA-A
*
1688279 ATTTATATTATATAAA
1 ATTTA-AATAT-TAAA
*
1688295 TTTTAAAATATT
1 ATTT-AAATATT
1688307 TTTATTTATA
Statistics
Matches: 48, Mismatches: 5, Indels: 15
0.71 0.07 0.22
Matches are distributed among these distances:
14 4 0.08
15 4 0.08
16 29 0.60
17 11 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATTTAAATATTAAA
Found at i:1688324 original size:26 final size:26
Alignment explanation
Indices: 1688280--1688351 Score: 67
Period size: 26 Copynumber: 2.7 Consensus size: 26
1688270 ATATTAATAA
* *
1688280 TTTATATTATATAAATTTTAAAATATT
1 TTTAT-TTATATTATTTTTAAAATATT
* *
1688307 TTTATTTATATTATTTTT-ATATTTT
1 TTTATTTATATTATTTTTAAAATATT
1688332 TAATTATTT-TATTATTTTTA
1 T--TTATTTATATTATTTTTA
1688352 TTTATGTCTA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
25 6 0.16
26 21 0.55
27 11 0.29
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (26 bp):
TTTATTTATATTATTTTTAAAATATT
Found at i:1688332 original size:23 final size:24
Alignment explanation
Indices: 1688302--1688354 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
1688292 AAATTTTAAA
*
1688302 ATATTTTTATTTATATTATT-TTT
1 ATATTTTTAATTATATTATTATTT
*
1688325 ATATTTTTAATTATTTTATTATTT
1 ATATTTTTAATTATATTATTATTT
*
1688349 TTATTT
1 ATATTT
1688355 ATGTCTAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 18 0.69
24 8 0.31
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (24 bp):
ATATTTTTAATTATATTATTATTT
Found at i:1688339 original size:18 final size:19
Alignment explanation
Indices: 1688311--1688356 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
1688301 AATATTTTTA
1688311 TTTATATTATTTTTA-TATT
1 TTTA-ATTATTTTTATTATT
1688330 TTTAATTA-TTTTATTATT
1 TTTAATTATTTTTATTATT
*
1688348 TTTATTTAT
1 TTTAATTAT
1688357 GTCTAATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
17 5 0.21
18 15 0.62
19 4 0.17
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTAATTATTTTTATTATT
Found at i:1688544 original size:18 final size:18
Alignment explanation
Indices: 1688484--1688545 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 18
1688474 TAAGTTAAAT
1688484 TTTAAATAAATATTTTTTA
1 TTTAAA-AAATATTTTTTA
* **
1688503 -TCAAAAATGATATTTAATA
1 TTTAAAAA--ATATTTTTTA
*
1688522 ATTAAAAAATATTTTTTA
1 TTTAAAAAATATTTTTTA
1688540 TTTAAA
1 TTTAAA
1688546 TTTAATTATA
Statistics
Matches: 33, Mismatches: 7, Indels: 7
0.70 0.15 0.15
Matches are distributed among these distances:
17 2 0.06
18 17 0.52
19 8 0.24
20 6 0.18
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (18 bp):
TTTAAAAAATATTTTTTA
Found at i:1688558 original size:37 final size:36
Alignment explanation
Indices: 1688485--1688577 Score: 91
Period size: 37 Copynumber: 2.6 Consensus size: 36
1688475 AAGTTAAATT
**
1688485 TTAAATAAATATTTTTTATCAAAAATGATATTTAATAA
1 TTAAA-AAATATTTTTTATTTAAAATGATATTTAAT-A
* *
1688523 TTAAAAAATATTTTTTATTTAAATTTA-ATTATAATA
1 TTAAAAAATATTTTTTATTTAAAATGATATT-TAATA
* *
1688559 -TAAAATATATTTTTAATTT
1 TTAAAAAATATTTTTTATTT
1688578 TTTTATTAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
35 17 0.35
36 4 0.08
37 22 0.46
38 5 0.10
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (36 bp):
TTAAAAAATATTTTTTATTTAAAATGATATTTAATA
Found at i:1688788 original size:18 final size:20
Alignment explanation
Indices: 1688747--1688788 Score: 52
Period size: 18 Copynumber: 2.2 Consensus size: 20
1688737 AAATTTAATT
*
1688747 ATAAAATATATAATATTAAT
1 ATAAAATATATAATATTAAA
*
1688767 ATAAAATA-AT-ATTTTAAA
1 ATAAAATATATAATATTAAA
1688785 ATAA
1 ATAA
1688789 TAAAATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 10 0.50
19 2 0.10
20 8 0.40
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
ATAAAATATATAATATTAAA
Found at i:1689171 original size:35 final size:35
Alignment explanation
Indices: 1689132--1689199 Score: 86
Period size: 35 Copynumber: 1.9 Consensus size: 35
1689122 CAAAGTATAC
*
1689132 AAATATAAATTA-ATT-TAAAATTTTATTAATTAAAT
1 AAATAT-AATTATATTATAAAA-TTTAATAATTAAAT
*
1689167 AAATATAATTATATTATTAAATTTAATAATTAA
1 AAATATAATTATATTATAAAATTTAATAATTAA
1689200 TTCATTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
34 5 0.17
35 20 0.69
36 4 0.14
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (35 bp):
AAATATAATTATATTATAAAATTTAATAATTAAAT
Found at i:1689195 original size:21 final size:22
Alignment explanation
Indices: 1689134--1689208 Score: 68
Period size: 21 Copynumber: 3.5 Consensus size: 22
1689124 AAGTATACAA
*
1689134 ATATAAATT-AATTTAA-AATT
1 ATATTAATTAAATTTAATAATT
* **
1689154 TTATTAATTAAATAAATATAATT
1 ATATTAATTAAATTTA-ATAATT
1689177 ATATT-ATTAAATTTAATAATT
1 ATATTAATTAAATTTAATAATT
*
1689198 A-ATTCATTAAA
1 ATATTAATTAAA
1689209 ATTATCAATC
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
20 10 0.23
21 17 0.39
22 9 0.20
23 8 0.18
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATTAATTAAATTTAATAATT
Found at i:1689632 original size:18 final size:19
Alignment explanation
Indices: 1689605--1689640 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1689595 TTGTTGTTGT
1689605 TTTTTAATTATAAAATTAA
1 TTTTTAATTATAAAATTAA
*
1689624 TTTTT-ATTATTAAATTA
1 TTTTTAATTATAAAATTA
1689641 TTATACAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTTTAATTATAAAATTAA
Found at i:1690558 original size:16 final size:16
Alignment explanation
Indices: 1690537--1690572 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
1690527 GTTTAGCGAG
1690537 AGTTTTACAGGGTTAT
1 AGTTTTACAGGGTTAT
*
1690553 AGTTTTACAGGTTTAT
1 AGTTTTACAGGGTTAT
1690569 AGTT
1 AGTT
1690573 AAAAATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.25, C:0.06, G:0.22, T:0.47
Consensus pattern (16 bp):
AGTTTTACAGGGTTAT
Found at i:1692469 original size:18 final size:18
Alignment explanation
Indices: 1692446--1692480 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1692436 CTCAGATTCG
1692446 GGTGTGGGTTTCAGATAC
1 GGTGTGGGTTTCAGATAC
1692464 GGTGTGGGTTTCAGATA
1 GGTGTGGGTTTCAGATA
1692481 TGGTATGTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.09, G:0.40, T:0.34
Consensus pattern (18 bp):
GGTGTGGGTTTCAGATAC
Found at i:1692492 original size:18 final size:18
Alignment explanation
Indices: 1692450--1692492 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
1692440 GATTCGGGTG
*
1692450 TGGGTTTCAGATACGGTG
1 TGGGTTTCAGATACGGTA
*
1692468 TGGGTTTCAGATATGGTA
1 TGGGTTTCAGATACGGTA
*
1692486 TGTGTTT
1 TGGGTTT
1692493 AACATGAGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.16, C:0.07, G:0.35, T:0.42
Consensus pattern (18 bp):
TGGGTTTCAGATACGGTA
Found at i:1693739 original size:2 final size:2
Alignment explanation
Indices: 1693732--1693766 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
1693722 ATAATTATGA
1693732 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
1693767 ACCTAAGTGA
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:1697983 original size:21 final size:20
Alignment explanation
Indices: 1697946--1697984 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1697936 ATATACCCAA
* *
1697946 GAAAAAAACTATTAAATAGT
1 GAAAAAAAATATAAAATAGT
1697966 GAAAAAAAATACTAAAATA
1 GAAAAAAAATA-TAAAATA
1697985 TCACTAACAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 10 0.62
21 6 0.38
ACGTcount: A:0.67, C:0.05, G:0.08, T:0.21
Consensus pattern (20 bp):
GAAAAAAAATATAAAATAGT
Found at i:1699064 original size:24 final size:25
Alignment explanation
Indices: 1699037--1699098 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 25
1699027 AACATGTAGG
*
1699037 TCACCATCACT-CTCCACTTCTGCC
1 TCACCATCACTCCTCCACTTCAGCC
* *
1699061 TCACCAT-GCTCCTCCACTTCAGCT
1 TCACCATCACTCCTCCACTTCAGCC
*
1699085 TCACCCTCAC-CCTC
1 TCACCATCACTCCTC
1699099 AGGCTCCATT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
23 2 0.06
24 28 0.90
25 1 0.03
ACGTcount: A:0.16, C:0.52, G:0.05, T:0.27
Consensus pattern (25 bp):
TCACCATCACTCCTCCACTTCAGCC
Found at i:1700032 original size:2 final size:2
Alignment explanation
Indices: 1700027--1700062 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1700017 TAGCCTTTGT
1700027 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1700063 CCCCCGTGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:1700171 original size:2 final size:2
Alignment explanation
Indices: 1700166--1700192 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1700156 TTTTTTTTTC
1700166 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1700193 CCTTACTGCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1700749 original size:10 final size:10
Alignment explanation
Indices: 1700711--1700746 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
1700701 ATATATAAAA
1700711 AATTAAATAT
1 AATTAAATAT
1700721 AATTAAATAT
1 AATTAAATAT
*
1700731 ATATTATATAT
1 A-ATTAAATAT
1700742 AATTA
1 AATTA
1700747 TATTTGATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 15 0.62
11 9 0.38
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
AATTAAATAT
Found at i:1700796 original size:162 final size:164
Alignment explanation
Indices: 1700610--1700915 Score: 456
Period size: 162 Copynumber: 1.9 Consensus size: 164
1700600 GTTTGCTTAG
* * * *
1700610 AAAAAGTTGTATTATTTTAATTTTTTAT-TTTTTAAAAATTTTTATATTCAAAAAATAATAAAAC
1 AAAAAATTATATTATTTTAATTTTTTATATTTTT-AAAATATTTATACTCAAAAAATAATAAAAC
* * *
1700674 ATAAACATAAAAAATATAATTTTTTAAATATA-TAAAAAATTAAATATAATTAAATATATATT-A
65 ATAAACATAAAAAATAAAACTTTTTAAATATATTAAAAAATTAAAAATAATTAAATATATATTAA
1700737 TATATAATTATATTTGATATTCATATTTAAATTTA
130 TATATAATTATATTTGATATTCATATTTAAATTTA
* * * **
1700772 AAAAAATTATATTATTTTAATTTTTTATATTTTTAAAATATTTATACTCGATATATAATAAATTA
1 AAAAAATTATATTATTTTAATTTTTTATATTTTTAAAATATTTATACTCAAAAAATAATAAAACA
* *
1700837 TAAATATAAAAAATAAAACTTTTTAAATATATTAAAAAGTTAAAAATAATTAAATATATATTAAT
66 TAAACATAAAAAATAAAACTTTTTAAATATATTAAAAAATTAAAAATAATTAAATATATATTAAT
1700902 ATATAATTATATTT
131 ATATAATTATATTT
1700916 TATAATATTT
Statistics
Matches: 127, Mismatches: 14, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
162 78 0.61
163 33 0.26
164 16 0.13
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (164 bp):
AAAAAATTATATTATTTTAATTTTTTATATTTTTAAAATATTTATACTCAAAAAATAATAAAACA
TAAACATAAAAAATAAAACTTTTTAAATATATTAAAAAATTAAAAATAATTAAATATATATTAAT
ATATAATTATATTTGATATTCATATTTAAATTTA
Found at i:1704164 original size:11 final size:11
Alignment explanation
Indices: 1704120--1704167 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
1704110 TAAATTTAAT
1704120 TATAAAAATAAA
1 TATAAAAAT-AA
1704132 TAATAAAAATAA
1 T-ATAAAAATAA
***
1704144 TATTTTAATAA
1 TATAAAAATAA
1704155 TATAAAAATAA
1 TATAAAAATAA
1704166 TA
1 TA
1704168 AAATGAATTT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
11 17 0.59
12 4 0.14
13 8 0.28
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
TATAAAAATAA
Found at i:1704610 original size:26 final size:25
Alignment explanation
Indices: 1704553--1704639 Score: 86
Period size: 28 Copynumber: 3.4 Consensus size: 25
1704543 AGCTACCAAT
* * *
1704553 TTTGACAAAC-AACAAGCCACCATT
1 TTTGACAAACAAAAAAACCACCATA
*
1704577 TTTTACAAACAAAAATAACCACCATA
1 TTTGACAAACAAAAA-AACCACCATA
*
1704603 TTTGACAAATACAAAGGAAACCACCATA
1 TTTGAC-AA-ACAAA-AAAACCACCATA
1704631 TTTGACAAA
1 TTTGACAAA
1704640 TACAAAGGGT
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
24 9 0.17
25 3 0.06
26 14 0.27
27 4 0.08
28 21 0.40
29 1 0.02
ACGTcount: A:0.48, C:0.23, G:0.07, T:0.22
Consensus pattern (25 bp):
TTTGACAAACAAAAAAACCACCATA
Found at i:1704616 original size:28 final size:28
Alignment explanation
Indices: 1704569--1704646 Score: 99
Period size: 28 Copynumber: 2.9 Consensus size: 28
1704559 AAACAACAAG
* *
1704569 CCACCATTTTTTAC-AA-ACAAA-AATAA
1 CCACCATATTTGACAAATACAAAGAA-AA
*
1704595 CCACCATATTTGACAAATACAAAGGAAA
1 CCACCATATTTGACAAATACAAAGAAAA
1704623 CCACCATATTTGACAAATACAAAG
1 CCACCATATTTGACAAATACAAAG
1704647 GGTGGCATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
26 12 0.26
27 2 0.04
28 31 0.67
29 1 0.02
ACGTcount: A:0.49, C:0.23, G:0.06, T:0.22
Consensus pattern (28 bp):
CCACCATATTTGACAAATACAAAGAAAA
Found at i:1704647 original size:28 final size:28
Alignment explanation
Indices: 1704593--1704647 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
1704583 AAACAAAAAT
1704593 AACCACCATATTTGACAAATACAAAGGA
1 AACCACCATATTTGACAAATACAAAGGA
1704621 AACCACCATATTTGACAAATACAAAGG
1 AACCACCATATTTGACAAATACAAAGG
1704648 GTGGCATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.49, C:0.22, G:0.11, T:0.18
Consensus pattern (28 bp):
AACCACCATATTTGACAAATACAAAGGA
Found at i:1706386 original size:21 final size:22
Alignment explanation
Indices: 1706360--1706405 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
1706350 ATCTGTTGAA
* *
1706360 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGTGGAGTACT
1706381 ACTCCACCTGCTGTGGAGTACT
1 ACTCCACCTGCTGTGGAGTACT
1706403 ACT
1 ACT
1706406 TGTCTGAACA
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:0.20, C:0.28, G:0.20, T:0.33
Consensus pattern (22 bp):
ACTCCACCTGCTGTGGAGTACT
Found at i:1708952 original size:24 final size:24
Alignment explanation
Indices: 1708925--1708970 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1708915 AATAAAAATT
1708925 AGTCACCAGTTTTGACAAACAACA
1 AGTCACCAGTTTTGACAAACAACA
* * *
1708949 AGTCATCATTTTTTACAAACAA
1 AGTCACCAGTTTTGACAAACAA
1708971 AAATAACCAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.41, C:0.22, G:0.09, T:0.28
Consensus pattern (24 bp):
AGTCACCAGTTTTGACAAACAACA
Found at i:1708998 original size:28 final size:28
Alignment explanation
Indices: 1708967--1709029 Score: 92
Period size: 28 Copynumber: 2.2 Consensus size: 28
1708957 TTTTTTACAA
1708967 ACAAA-AATAACCACCATATTTGACAAAT
1 ACAAAGAA-AACCACCATATTTGACAAAT
* *
1708995 ACAAAGAAAACTACCATATTTGATAAAT
1 ACAAAGAAAACCACCATATTTGACAAAT
1709023 ACAAAGA
1 ACAAAGA
1709030 GTAATATTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 30 0.94
29 2 0.06
ACGTcount: A:0.56, C:0.17, G:0.06, T:0.21
Consensus pattern (28 bp):
ACAAAGAAAACCACCATATTTGACAAAT
Found at i:1710707 original size:27 final size:28
Alignment explanation
Indices: 1710660--1710717 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
1710650 TTTAGTGATA
*
1710660 ATTTAAATTTTTTTAAAAAA-TAATTTT
1 ATTTAAATTTATTTAAAAAATTAATTTT
* *
1710687 ATTTAAATTTAATTT-ATAAATTTATTTT
1 ATTTAAATTT-ATTTAAAAAATTAATTTT
1710715 ATT
1 ATT
1710718 ATTTTAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 14 0.54
28 12 0.46
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (28 bp):
ATTTAAATTTATTTAAAAAATTAATTTT
Found at i:1710714 original size:28 final size:27
Alignment explanation
Indices: 1710660--1710717 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 27
1710650 TTTAGTGATA
*
1710660 ATTTAAATTTTTTTAAAAAATAATTTT
1 ATTTAAATTTATTTAAAAAATAATTTT
* * *
1710687 ATTTAAATTTAATTTATAAATTTATTTT
1 ATTTAAATTT-ATTTAAAAAATAATTTT
1710715 ATT
1 ATT
1710718 ATTTTAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 10 0.38
28 16 0.62
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (27 bp):
ATTTAAATTTATTTAAAAAATAATTTT
Found at i:1712352 original size:2 final size:2
Alignment explanation
Indices: 1712345--1712374 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1712335 ATGCCAACAT
*
1712345 TA TA TA TA TA TA TA TA TA TA TA TA TC TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1712375 GGTACTCATG
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:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1713248 original size:23 final size:23
Alignment explanation
Indices: 1713207--1713255 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 23
1713197 AGTTTTAATG
1713207 TTATGTTTTTTTTTAAATTATCTT
1 TTATGTTTTTTTTTAAATTAT-TT
1713231 TTAT-TTTTTATTTT-AATTATTT
1 TTATGTTTTT-TTTTAAATTATTT
1713253 TTA
1 TTA
1713256 ATTTAAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.21
23 11 0.46
24 8 0.33
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (23 bp):
TTATGTTTTTTTTTAAATTATTT
Found at i:1713265 original size:17 final size:17
Alignment explanation
Indices: 1713231--1713282 Score: 54
Period size: 16 Copynumber: 3.1 Consensus size: 17
1713221 AAATTATCTT
* *
1713231 TTATTTTTTATTT-TAA
1 TTATTTTTAATTTAAAA
1713247 TTATTTTTAATTTAAAA
1 TTATTTTTAATTTAAAA
*
1713264 TTA-TTTAAATTTTAAAA
1 TTATTTTTAA-TTTAAAA
1713281 TT
1 TT
1713283 GTTGACACGT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
16 17 0.55
17 14 0.45
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (17 bp):
TTATTTTTAATTTAAAA
Found at i:1713887 original size:41 final size:41
Alignment explanation
Indices: 1713837--1713926 Score: 144
Period size: 41 Copynumber: 2.2 Consensus size: 41
1713827 CCTATAGCTT
** * *
1713837 GAATGGCTGGAACCTGTGAAAGGACGAGAACCCAATAGCCC
1 GAATGGCTGGAACCTAAGAAAGAACGAGAACCCAATAACCC
1713878 GAATGGCTGGAACCTAAGAAAGAACGAGAACCCAATAACCC
1 GAATGGCTGGAACCTAAGAAAGAACGAGAACCCAATAACCC
1713919 GAATGGCT
1 GAATGGCT
1713927 TGATGAGAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.38, C:0.23, G:0.27, T:0.12
Consensus pattern (41 bp):
GAATGGCTGGAACCTAAGAAAGAACGAGAACCCAATAACCC
Found at i:1714076 original size:23 final size:25
Alignment explanation
Indices: 1714031--1714077 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 25
1714021 TTTATTTTTT
**
1714031 ATTTTTTAAAAGTATATTTAATATA
1 ATTTTTTAAAAGTATATAAAATATA
1714056 ATTTTTT-AAA-TATATAAAATAT
1 ATTTTTTAAAAGTATATAAAATAT
1714078 TTTAAAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 10 0.50
24 3 0.15
25 7 0.35
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (25 bp):
ATTTTTTAAAAGTATATAAAATATA
Found at i:1714082 original size:18 final size:18
Alignment explanation
Indices: 1714059--1714097 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
1714049 TAATATAATT
* *
1714059 TTTTAAATATATAAAATA
1 TTTTAAAAATAAAAAATA
1714077 TTTTAAAAATAAAAAATA
1 TTTTAAAAATAAAAAATA
1714095 TTT
1 TTT
1714098 ATATCAAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TTTTAAAAATAAAAAATA
Found at i:1714847 original size:5 final size:5
Alignment explanation
Indices: 1714837--1714901 Score: 64
Period size: 5 Copynumber: 13.2 Consensus size: 5
1714827 AATTTATCAC
* *
1714837 TATAT TATAT TATAT TATAT TATAT TATAT T-T-T TATGAT TAAAAT TAAAT
1 TATAT TATAT TATAT TATAT TATAT TATAT TATAT TAT-AT T-ATAT TATAT
*
1714887 T-TAT TGTAT TATAT T
1 TATAT TATAT TATAT T
1714902 TAATTCAAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
3 2 0.04
4 5 0.10
5 39 0.75
6 5 0.10
7 1 0.02
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.58
Consensus pattern (5 bp):
TATAT
Found at i:1716651 original size:2 final size:2
Alignment explanation
Indices: 1716646--1716673 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1716636 CTTAAGTAGA
1716646 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
1716674 GTGGATTTTT
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:1718166 original size:20 final size:19
Alignment explanation
Indices: 1718126--1718171 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
1718116 AATTTTTTTT
*
1718126 ATTTAAATTTAATTTATAA
1 ATTTAAATTTAATTTAAAA
*
1718145 ATTTAAATTATTATTTAAAA
1 ATTTAAATT-TAATTTAAAA
*
1718165 ATATAAA
1 ATTTAAA
1718172 AAATTTATCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATTTAAATTTAATTTAAAA
Found at i:1718616 original size:18 final size:19
Alignment explanation
Indices: 1718593--1718629 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
1718583 AAGAAAAAAA
1718593 TTATTTTTATTTT-ATTTT
1 TTATTTTTATTTTGATTTT
1718611 TTATTTTTATTTTGATTTT
1 TTATTTTTATTTTGATTTT
1718630 GCTTTTGCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (19 bp):
TTATTTTTATTTTGATTTT
Found at i:1724109 original size:2 final size:2
Alignment explanation
Indices: 1724102--1724134 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1724092 TGGACAGGTC
1724102 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1724135 ATGTACACAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:1726820 original size:6 final size:6
Alignment explanation
Indices: 1726782--1726876 Score: 67
Period size: 6 Copynumber: 16.0 Consensus size: 6
1726772 AAATTTTTAT
* *
1726782 AATATA AATTATTA ACATATCA AA-ATT AATATA AATATA AA-ATA TATA-A
1 AATATA AA-TA-TA A-ATAT-A AATATA AATATA AATATA AATATA AATATA
* *
1726831 AATATA ATTAT- AATA-A AATAAA ATATATA AATAT- AATATA AATATA
1 AATATA AATATA AATATA AATATA A-ATATA AATATA AATATA AATATA
1726877 TAAATTACGT
Statistics
Matches: 71, Mismatches: 7, Indels: 22
0.71 0.07 0.22
Matches are distributed among these distances:
5 22 0.31
6 32 0.45
7 9 0.13
8 7 0.10
9 1 0.01
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (6 bp):
AATATA
Found at i:1726828 original size:27 final size:28
Alignment explanation
Indices: 1726779--1726881 Score: 108
Period size: 27 Copynumber: 3.7 Consensus size: 28
1726769 TTAAAATTTT
* *
1726779 TATAATATAAAT-TATTAACATATCAAAA
1 TATAATATAAATATATAAATATAT-AAAA
1726807 T-TAATATAAATATA-AAATATATAAAA
1 TATAATATAAATATATAAATATATAAAA
*
1726833 TATAAT-TATAATAAAATAAA-ATATATAAA
1 TATAATATA-AAT-ATATAAATATATA-AAA
1726862 TATAATATAAATATATAAAT
1 TATAATATAAATATATAAAT
1726882 TACGTATGTT
Statistics
Matches: 63, Mismatches: 4, Indels: 15
0.77 0.05 0.18
Matches are distributed among these distances:
26 7 0.11
27 23 0.37
28 16 0.25
29 15 0.24
30 2 0.03
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (28 bp):
TATAATATAAATATATAAATATATAAAA
Found at i:1726830 original size:9 final size:9
Alignment explanation
Indices: 1726816--1726880 Score: 60
Period size: 9 Copynumber: 6.8 Consensus size: 9
1726806 ATTAATATAA
1726816 ATATAAAAT
1 ATATAAAAT
1726825 ATATAAAAT
1 ATATAAAAT
*
1726834 ATAATTATAAT
1 AT-A-TAAAAT
*
1726845 AAAATAAAAT
1 -ATATAAAAT
1726855 ATAT-AAAT
1 ATATAAAAT
1726863 ATAATATAAAT
1 AT-ATA-AAAT
1726874 ATATAAA
1 ATATAAA
1726881 TTACGTATGT
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
8 6 0.13
9 18 0.39
10 9 0.20
11 12 0.26
12 1 0.02
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (9 bp):
ATATAAAAT
Found at i:1726835 original size:49 final size:42
Alignment explanation
Indices: 1726782--1726883 Score: 100
Period size: 43 Copynumber: 2.3 Consensus size: 42
1726772 AAATTTTTAT
1726782 AATATAAATTAT-TAACATATCAAAATTAATATAAATATAAAATATATAA
1 AATATAAATTATATAA-A-AT-AAAA-T-ATATAAATAT--AATATA-AA
1726831 AATAT-AATTATAATAAAATAAAATATATAAATATAATATAAA
1 AATATAAATTAT-ATAAAATAAAATATATAAATATAATATAAA
*
1726873 TATATAAATTA
1 AATATAAATTA
1726884 CGTATGTTAC
Statistics
Matches: 49, Mismatches: 1, Indels: 12
0.79 0.02 0.19
Matches are distributed among these distances:
42 6 0.12
43 11 0.22
45 10 0.20
46 1 0.02
47 4 0.08
48 8 0.16
49 6 0.12
50 3 0.06
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (42 bp):
AATATAAATTATATAAAATAAAATATATAAATATAATATAAA
Found at i:1726842 original size:15 final size:15
Alignment explanation
Indices: 1726810--1726881 Score: 73
Period size: 13 Copynumber: 5.0 Consensus size: 15
1726800 ATCAAAATTA
1726810 ATAT-AAATATAAAAT
1 ATATAAAATAT-AAAT
*
1726825 ATATAAAATATAATT
1 ATATAAAATATAAAT
1726840 ATAATAAAATA-AAAT
1 AT-ATAAAATATAAAT
1726855 ATAT-AAATAT-AAT
1 ATATAAAATATAAAT
*
1726868 ATA-AATATATAAAT
1 ATATAAAATATAAAT
1726882 TACGTATGTT
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
13 16 0.33
14 5 0.10
15 14 0.29
16 14 0.29
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
ATATAAAATATAAAT
Found at i:1727549 original size:26 final size:27
Alignment explanation
Indices: 1727520--1727574 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
1727510 TGAACGTGGC
* *
1727520 AATTTTTTAGATATATTT-AAAATTTT
1 AATTATTTAGATAAATTTAAAAATTTT
**
1727546 AATTATTTATTTAAATTTAAAAATTTT
1 AATTATTTAGATAAATTTAAAAATTTT
1727573 AA
1 AA
1727575 ATTAAAATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 14 0.58
27 10 0.42
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (27 bp):
AATTATTTAGATAAATTTAAAAATTTT
Found at i:1728523 original size:4 final size:4
Alignment explanation
Indices: 1728508--1728538 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
1728498 ATTGATTTTT
1728508 TTAA TT-A TTAA TTAA TTAA TTAA TTAA TTAA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA
1728539 ATGAATCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
TTAA
Found at i:1728790 original size:12 final size:12
Alignment explanation
Indices: 1728775--1728809 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
1728765 TCTCAAGATA
*
1728775 TATTAAAATATT
1 TATTAAAAAATT
1728787 TATTAAAAAATT
1 TATTAAAAAATT
*
1728799 AATTAAAAAAT
1 TATTAAAAAAT
1728810 AAATATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
TATTAAAAAATT
Found at i:1729028 original size:4 final size:4
Alignment explanation
Indices: 1729019--1729046 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
1729009 ATTTAAACAT
1729019 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1729047 ATTTGTGCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:1729229 original size:15 final size:15
Alignment explanation
Indices: 1729206--1729239 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
1729196 GTTGATTGAA
*
1729206 GGATTTTTATTAAAG
1 GGATATTTATTAAAG
1729221 GGATATTTATTAAAG
1 GGATATTTATTAAAG
1729236 GGAT
1 GGAT
1729240 TTTGCTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.35, C:0.00, G:0.24, T:0.41
Consensus pattern (15 bp):
GGATATTTATTAAAG
Found at i:1729816 original size:2 final size:2
Alignment explanation
Indices: 1729809--1729838 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1729799 TTGTTATTTC
1729809 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
1729839 CCTGTCAGAA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1733682 original size:2 final size:2
Alignment explanation
Indices: 1733677--1733717 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1733667 ATAAATTGTC
1733677 AT AT AT 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 AT AT AT A
1733718 AAAGATGATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1738992 original size:21 final size:21
Alignment explanation
Indices: 1738942--1738993 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
1738932 ATATTCAACT
1738942 TAAATATATTTAATTTAAAAA
1 TAAATATATTTAATTTAAAAA
*
1738963 TATATATATTTATATTT-AAAA
1 TAAATATATTTA-ATTTAAAAA
*
1738984 TAAAAATATT
1 TAAATATATT
1738994 GATAAGTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TAAATATATTTAATTTAAAAA
Found at i:1739109 original size:17 final size:18
Alignment explanation
Indices: 1739051--1739127 Score: 63
Period size: 17 Copynumber: 4.3 Consensus size: 18
1739041 AATATATTTT
*
1739051 TTAAATTAAATATTTTTAATA
1 TTAAA-TAAATA-ATTTAA-A
1739072 TTAAA-AAA-AATTTAAA
1 TTAAATAAATAATTTAAA
1739088 CTTAAATAAATAA-TTAAA
1 -TTAAATAAATAATTTAAA
* *
1739106 TT-AATAAATATTTTTAA
1 TTAAATAAATAATTTAAA
1739123 TTAAA
1 TTAAA
1739128 AATATAAATA
Statistics
Matches: 48, Mismatches: 3, Indels: 13
0.75 0.05 0.20
Matches are distributed among these distances:
16 9 0.19
17 18 0.38
18 11 0.23
19 5 0.10
21 5 0.10
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (18 bp):
TTAAATAAATAATTTAAA
Found at i:1739136 original size:30 final size:30
Alignment explanation
Indices: 1739089--1739146 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 30
1739079 AAATTTAAAC
1739089 TTAAATAAATAATTAAATTAATA-AATATTT
1 TTAAATAAATAATTAAA-TAATATAATATTT
*
1739119 TTAATTAAA-AATATAAATAATATAATAT
1 TTAAATAAATAAT-TAAATAATATAATAT
1739147 AAACATAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
29 8 0.32
30 17 0.68
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (30 bp):
TTAAATAAATAATTAAATAATATAATATTT
Found at i:1739337 original size:2 final size:2
Alignment explanation
Indices: 1739332--1739378 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
1739322 TCTCTCAAAG
1739332 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
1739374 TA TA T
1 TA TA T
1739379 TTTAAGGAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1746556 original size:26 final size:25
Alignment explanation
Indices: 1746490--1746556 Score: 64
Period size: 26 Copynumber: 2.6 Consensus size: 25
1746480 CTAAAAAATT
* *
1746490 AAAATTATTATT-TAAAATTTAATTA
1 AAAATT-TTATTATTAAATTTAATAA
* *
1746515 AATATTTTAATAATTAAATTTAAATAA
1 AAAATTTT-ATTATTAAATTT-AATAA
1746542 AAAATTTTATTATTA
1 AAAATTTTATTATTA
1746557 TATAGTAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
24 2 0.06
25 7 0.21
26 13 0.39
27 11 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
AAAATTTTATTATTAAATTTAATAA
Found at i:1746760 original size:25 final size:25
Alignment explanation
Indices: 1746727--1746782 Score: 62
Period size: 24 Copynumber: 2.2 Consensus size: 25
1746717 ACTTAATTAT
1746727 TATTT-TTATTAATTTTT-TTAAAAA
1 TATTTATTA-TAATTTTTATTAAAAA
* *
1746751 TATTTATTATATTTTTTATTAATAA
1 TATTTATTATAATTTTTATTAAAAA
1746776 TAATTTA
1 T-ATTTA
1746783 ATTAATGTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
24 12 0.44
25 10 0.37
26 5 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
TATTTATTATAATTTTTATTAAAAA
Found at i:1746774 original size:22 final size:22
Alignment explanation
Indices: 1746723--1746774 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
1746713 TTGCACTTAA
*
1746723 TTATT-ATTTTTATTAATTTTT
1 TTATTAATATTTATTAATTTTT
**
1746744 TTAAAAATATTTATT-ATATTTT
1 TTATTAATATTTATTAAT-TTTT
1746766 TTATTAATA
1 TTATTAATA
1746775 ATAATTTAAT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (22 bp):
TTATTAATATTTATTAATTTTT
Found at i:1747029 original size:26 final size:28
Alignment explanation
Indices: 1746998--1747049 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
1746988 TTTTTATAAA
1746998 TTTAAA-TTA-TTAT-TTAATAATAAATG
1 TTTAAATTTATTTATATTAAT-ATAAATG
1747024 TTTAAATTTATTTATATTAATATAAA
1 TTTAAATTTATTTATATTAATATAAA
1747050 AAATAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 6 0.26
27 3 0.13
28 9 0.39
29 5 0.22
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (28 bp):
TTTAAATTTATTTATATTAATATAAATG
Found at i:1747068 original size:20 final size:21
Alignment explanation
Indices: 1747040--1747078 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
1747030 TTTATTTATA
1747040 TTAATATAAAAAATAAAAAAC
1 TTAATATAAAAAATAAAAAAC
*
1747061 TTAA-ATAAAAATTAAAAA
1 TTAATATAAAAAATAAAAA
1747079 TATCAAATTA
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:0.72, C:0.03, G:0.00, T:0.26
Consensus pattern (21 bp):
TTAATATAAAAAATAAAAAAC
Found at i:1747329 original size:17 final size:19
Alignment explanation
Indices: 1747303--1747363 Score: 65
Period size: 18 Copynumber: 3.3 Consensus size: 19
1747293 TGTTTATAGA
*
1747303 TATTAATTAA-AA-TTTTT
1 TATTATTTAATAAGTTTTT
1747320 TATTATTTAATAAGTTTTT
1 TATTATTTAATAAGTTTTT
*
1747339 TA-TATTTAATATATTATTTT
1 TATTATTTAATA-AGT-TTTT
1747359 TATTA
1 TATTA
1747364 AATATAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
17 9 0.24
18 11 0.30
19 9 0.24
20 6 0.16
21 2 0.05
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
TATTATTTAATAAGTTTTT
Found at i:1747330 original size:21 final size:19
Alignment explanation
Indices: 1747305--1747348 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
1747295 TTTATAGATA
1747305 TTAATTAAAATTTTTTATTAT
1 TTAATT-AAATTTTTTA-TAT
*
1747326 TTAA-TAAGTTTTTTATAT
1 TTAATTAAATTTTTTATAT
1747344 TTAAT
1 TTAAT
1747349 ATATTATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 7 0.33
19 9 0.43
20 1 0.05
21 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (19 bp):
TTAATTAAATTTTTTATAT
Found at i:1747362 original size:18 final size:18
Alignment explanation
Indices: 1747316--1747369 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 18
1747306 TAATTAAAAT
1747316 TTTTTATTATTTAATA-AG
1 TTTTT-TTATTTAATATAG
1747334 TTTTTTATATTTAATATA-
1 TTTTTT-TATTTAATATAG
*
1747352 TTATTTTTATTAAATATA
1 TT-TTTTTATTTAATATA
1747370 AAAATAATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
17 1 0.03
18 26 0.81
19 5 0.16
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTTTTTATTTAATATAG
Found at i:1747550 original size:24 final size:24
Alignment explanation
Indices: 1747517--1747583 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
1747507 AATAATATTA
* * * *
1747517 TATATATAAATATTTTGTATTAAT
1 TATATTTAAATATATTATATCAAT
1747541 TATATTTAAATATATTATATCAAT
1 TATATTTAAATATATTATATCAAT
* *
1747565 TTTA-TTAAATAAATTATAT
1 TATATTTAAATATATTATAT
1747584 TCCTATTATA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
23 14 0.38
24 23 0.62
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (24 bp):
TATATTTAAATATATTATATCAAT
Found at i:1747992 original size:13 final size:13
Alignment explanation
Indices: 1747974--1747998 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1747964 AACTAAATTC
1747974 AATTTTAAATTTA
1 AATTTTAAATTTA
1747987 AATTTTAAATTT
1 AATTTTAAATTT
1747999 TTTTAAATCA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
AATTTTAAATTTA
Found at i:1752499 original size:8 final size:8
Alignment explanation
Indices: 1752474--1752661 Score: 69
Period size: 8 Copynumber: 23.6 Consensus size: 8
1752464 TCTATATTTT
1752474 TAAATATAA
1 TAAATAT-A
1752483 TATAATATA
1 TA-AATATA
1752492 TAAATATA
1 TAAATATA
1752500 T---TATA
1 TAAATATA
* *
1752505 AAAAAATA
1 TAAATATA
*
1752513 -AAAAATA
1 TAAATATA
* *
1752520 AAAAAATA
1 TAAATATA
*
1752528 TAAATACGA
1 TAAATA-TA
1752537 TACGAATATA
1 TA--AATATA
1752547 TAAATATA
1 TAAATATA
*
1752555 TAAATATT
1 TAAATATA
*
1752563 TATATAATA
1 TAAAT-ATA
1752572 TAAAT-TA
1 TAAATATA
1752579 TTAAA-ATA
1 -TAAATATA
*
1752587 TTAAAATTTA
1 -T-AAATATA
*
1752597 CAAATATA
1 TAAATATA
*
1752605 TAACATCT-
1 TAA-ATATA
1752613 TAAATATA
1 TAAATATA
*
1752621 -ATAATAAA
1 TA-AATATA
1752629 TAAA-ATA
1 TAAATATA
1752636 TATAA-ATA
1 TA-AATATA
1752644 -AAATA-A
1 TAAATATA
1752650 -AAATATA
1 TAAATATA
1752657 TAAAT
1 TAAAT
1752662 TCAGGAGAGA
Statistics
Matches: 140, Mismatches: 18, Indels: 43
0.70 0.09 0.21
Matches are distributed among these distances:
5 4 0.03
6 8 0.06
7 20 0.14
8 73 0.52
9 21 0.15
10 10 0.07
11 4 0.03
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.34
Consensus pattern (8 bp):
TAAATATA
Found at i:1752642 original size:13 final size:12
Alignment explanation
Indices: 1752613--1752654 Score: 59
Period size: 13 Copynumber: 3.5 Consensus size: 12
1752603 TATAACATCT
*
1752613 TAAATATAATAA
1 TAAATAAAATAA
1752625 TAAATAAAATATA
1 TAAATAAAATA-A
1752638 TAAATAAAATAA
1 TAAATAAAATAA
1752650 -AAATA
1 TAAATA
1752655 TATAAATTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 5 0.18
12 11 0.39
13 12 0.43
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (12 bp):
TAAATAAAATAA
Found at i:1752661 original size:19 final size:17
Alignment explanation
Indices: 1752614--1752661 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 17
1752604 ATAACATCTT
1752614 AAATATA-ATAATAAATA
1 AAATATATA-AATAAATA
1752631 AAATATATAAATAAAATAA
1 AAATATATAAAT-AAAT-A
1752650 AAATATATAAAT
1 AAATATATAAAT
1752662 TCAGGAGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.36
18 5 0.18
19 13 0.46
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAATATATAAATAAATA
Found at i:1753167 original size:14 final size:14
Alignment explanation
Indices: 1753148--1753180 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1753138 ATTAAAAAAT
1753148 TATTTTTAT-ATTAA
1 TATTTTTATAATT-A
1753162 TATTTTTATAATTA
1 TATTTTTATAATTA
1753176 TATTT
1 TATTT
1753181 AAATAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 15 0.83
15 3 0.17
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (14 bp):
TATTTTTATAATTA
Found at i:1753176 original size:26 final size:26
Alignment explanation
Indices: 1753145--1753198 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
1753135 AATATTAAAA
* * *
1753145 AATTATTTTTATATTAATATTT-TTAT
1 AATTATATTTA-AATAAAATTTATTAT
1753171 AATTATATTTAAATAAAATTTATTAT
1 AATTATATTTAAATAAAATTTATTAT
1753197 AA
1 AA
1753199 ATAATAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 8 0.33
26 16 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
AATTATATTTAAATAAAATTTATTAT
Found at i:1753216 original size:17 final size:17
Alignment explanation
Indices: 1753169--1753217 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 17
1753159 TAATATTTTT
*
1753169 ATAATTATATTTAAATA
1 ATAATTTTATTTAAATA
1753186 A-AA-TTTATTATAAATA
1 ATAATTTTATT-TAAATA
*
1753202 ATAATTTTAATTAAAT
1 ATAATTTTATTTAAAT
1753218 TATATCAAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
15 5 0.19
16 9 0.33
17 8 0.30
18 5 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATAATTTTATTTAAATA
Found at i:1753218 original size:28 final size:25
Alignment explanation
Indices: 1753151--1753218 Score: 64
Period size: 28 Copynumber: 2.5 Consensus size: 25
1753141 AAAAAATTAT
*
1753151 TTTTATATTAATATTTTTATAATTATA
1 TTTTA-ATTAA-ATTTTTATAATAATA
* *
1753178 TTTAAATAAAATTTATTATAAATAATAA
1 TTTTAATTAAATTT-TTAT-AATAAT-A
1753206 TTTTAATTAAATT
1 TTTTAATTAAATT
1753219 ATATCAAACC
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
25 4 0.12
26 8 0.24
27 9 0.27
28 12 0.36
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
TTTTAATTAAATTTTTATAATAATA
Found at i:1753714 original size:30 final size:31
Alignment explanation
Indices: 1753655--1753723 Score: 83
Period size: 30 Copynumber: 2.4 Consensus size: 31
1753645 AATGATAAAT
***
1753655 TCATATATT-TAAATTATGTTTACGTTATTA
1 TCATATATTATAAATTATGTTTAAAATATTA
1753685 TCATATATTAT-AATTATGTTTAAAATATTA
1 TCATATATTATAAATTATGTTTAAAATATTA
1753715 T-ATAT-TTAT
1 TCATATATTAT
1753724 TATATATTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 4 0.11
29 4 0.11
30 26 0.74
31 1 0.03
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (31 bp):
TCATATATTATAAATTATGTTTAAAATATTA
Found at i:1753737 original size:13 final size:12
Alignment explanation
Indices: 1753709--1753741 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
1753699 TATGTTTAAA
1753709 ATATTATATATT
1 ATATTATATATT
1753721 -TATTATATATTT
1 ATATTATATA-TT
1753733 ATATTATAT
1 ATATTATAT
1753742 TCGTATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 9 0.47
12 2 0.11
13 8 0.42
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (12 bp):
ATATTATATATT
Found at i:1756665 original size:19 final size:20
Alignment explanation
Indices: 1756641--1756681 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
1756631 TATATATTAA
1756641 TAATA-TTAAAATAATTTTT
1 TAATATTTAAAATAATTTTT
*
1756660 TAATATTTTAAATAATTTTT
1 TAATATTTAAAATAATTTTT
1756680 TA
1 TA
1756682 TGTATTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TAATATTTAAAATAATTTTT
Found at i:1757211 original size:11 final size:11
Alignment explanation
Indices: 1757178--1757223 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
1757168 AATAAGTAAT
1757178 AATATTAA-AA
1 AATATTAATAA
* *
1757188 AA-ATTATTTA
1 AATATTAATAA
1757198 AATATTAATAA
1 AATATTAATAA
1757209 AATATTAATATA
1 AATATTAATA-A
1757221 AAT
1 AAT
1757224 GTGATGTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
9 4 0.14
10 5 0.17
11 16 0.55
12 4 0.14
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
AATATTAATAA
Found at i:1757222 original size:23 final size:20
Alignment explanation
Indices: 1757178--1757223 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 20
1757168 AATAAGTAAT
*
1757178 AATATTAAAAAAATTATTTA
1 AATATTAAAAAAATTATATA
1757198 AATATTAATAAAATATTAATATA
1 AATATTAA-AAAA-ATT-ATATA
1757221 AAT
1 AAT
1757224 GTGATGTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 8 0.36
21 4 0.18
22 3 0.14
23 7 0.32
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AATATTAAAAAAATTATATA
Found at i:1757377 original size:16 final size:17
Alignment explanation
Indices: 1757345--1757389 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
1757335 TATTTTTAAA
1757345 TAATTTTTTAATATTAC
1 TAATTTTTTAATATTAC
*
1757362 TAATTTTTTTAT-TTAC
1 TAATTTTTTAATATTAC
*
1757378 TATAATTTTTAA
1 TA-ATTTTTTAA
1757390 AAAATAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 6 0.25
17 18 0.75
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (17 bp):
TAATTTTTTAATATTAC
Found at i:1757404 original size:5 final size:6
Alignment explanation
Indices: 1757389--1757413 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1757379 ATAATTTTTA
1757389 AAAAAT AAAAAT AAAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT A
1757414 TTAAAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:1758670 original size:20 final size:21
Alignment explanation
Indices: 1758634--1758672 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1758624 TTTTATTTAA
1758634 ATTTTATTATATTAAAAATTT
1 ATTTTATTATATTAAAAATTT
1758655 ATTTTATTAT-TTAAAAAT
1 ATTTTATTATATTAAAAAT
1758673 ATTAAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
ATTTTATTATATTAAAAATTT
Found at i:1759627 original size:15 final size:15
Alignment explanation
Indices: 1759586--1759629 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
1759576 TATATGTAAA
*
1759586 TATATATTTTAAAAT
1 TATAAATTTTAAAAT
1759601 TATAAATATTTAAAA-
1 TATAAAT-TTTAAAAT
1759616 TATAAAATTTTAAA
1 TAT-AAATTTTAAA
1759630 CATCAATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 15 0.58
16 11 0.42
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATAAATTTTAAAAT
Found at i:1759664 original size:23 final size:23
Alignment explanation
Indices: 1759614--1759665 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 23
1759604 AAATATTTAA
1759614 AATATAAAATTTTAAACATCAATT
1 AATA-AAAATTTTAAACATCAATT
1759638 -ATAAAAATATTTAAA-AT-AATAT
1 AATAAAAAT-TTTAAACATCAAT-T
1759660 AATAAA
1 AATAAA
1759666 TTATTATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
21 3 0.12
22 8 0.32
23 14 0.56
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (23 bp):
AATAAAAATTTTAAACATCAATT
Found at i:1760545 original size:21 final size:19
Alignment explanation
Indices: 1760507--1760549 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
1760497 ATTACGGATG
1760507 TTTAGATTAAAAATTTAAA
1 TTTAGATTAAAAATTTAAA
*
1760526 TTTAGTATTAATAAGTTTAAA
1 TTTAG-ATTAA-AAATTTAAA
1760547 TTT
1 TTT
1760550 TTATTTTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.24
20 5 0.24
21 11 0.52
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (19 bp):
TTTAGATTAAAAATTTAAA
Found at i:1761837 original size:2 final size:2
Alignment explanation
Indices: 1761830--1761854 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1761820 AAGATTGTGT
1761830 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 T
1761855 GGGTTTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1762003 original size:14 final size:15
Alignment explanation
Indices: 1761984--1762016 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
1761974 AAGAATGGCA
*
1761984 ATTTTTCTTTTTTT-
1 ATTTTTATTTTTTTC
1761998 ATTTTTATTTTTTTC
1 ATTTTTATTTTTTTC
1762013 ATTT
1 ATTT
1762017 CAAATTAACG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (15 bp):
ATTTTTATTTTTTTC
Found at i:1763152 original size:30 final size:31
Alignment explanation
Indices: 1763118--1763193 Score: 84
Period size: 30 Copynumber: 2.5 Consensus size: 31
1763108 TCATTATATT
1763118 ATTAAAATATTAATTTTATA-TATTTTTATA
1 ATTAAAATATTAATTTTATATTATTTTTATA
* * *** *
1763148 ATTAAATTTTTAAAAATATATTATTTTTATT
1 ATTAAAATATTAATTTTATATTATTTTTATA
1763179 ATT-AAATATTAATTT
1 ATTAAAATATTAATTT
1763194 AAAATGATCT
Statistics
Matches: 34, Mismatches: 11, Indels: 2
0.72 0.23 0.04
Matches are distributed among these distances:
30 22 0.65
31 12 0.35
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (31 bp):
ATTAAAATATTAATTTTATATTATTTTTATA
Found at i:1764516 original size:10 final size:10
Alignment explanation
Indices: 1764493--1764540 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
1764483 CGAATCGAAT
1764493 TTTAAATAAAA
1 TTTAAAT-AAA
*
1764504 TTTATATAAA
1 TTTAAATAAA
*
1764514 TTTAAATATA
1 TTTAAATAAA
* *
1764524 TTTAATTTAA
1 TTTAAATAAA
1764534 TTTAAAT
1 TTTAAAT
1764541 TATTATTTAA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
10 24 0.80
11 6 0.20
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
TTTAAATAAA
Found at i:1764583 original size:22 final size:21
Alignment explanation
Indices: 1764522--1764583 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 21
1764512 AATTTAAATA
*
1764522 TATTTAATTTAATTTAAATTAT
1 TATTTAATTTAA-TTATATTAT
* * *
1764544 TATTTAATAATAAATATATTTT
1 TATTTAAT-TTAATTATATTAT
1764566 TATTTAAATTTAATTATA
1 TATTT-AATTTAATTATA
1764584 AAAATATTAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
22 26 0.81
23 6 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TATTTAATTTAATTATATTAT
Found at i:1764634 original size:32 final size:32
Alignment explanation
Indices: 1764589--1764654 Score: 91
Period size: 32 Copynumber: 2.0 Consensus size: 32
1764579 TTATAAAAAT
1764589 ATTAATATAAAAAATAATATTTTAA-TAATATA
1 ATTAATATAAAAAATAAT-TTTTAACTAATATA
1764621 ATTAATA-ATAAAAATAATTTTTAACTTAATATA
1 ATTAATATA-AAAAATAATTTTTAAC-TAATATA
1764654 A
1 A
1764655 ATTTAATTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
31 7 0.23
32 16 0.52
33 8 0.26
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.41
Consensus pattern (32 bp):
ATTAATATAAAAAATAATTTTTAACTAATATA
Found at i:1764665 original size:16 final size:16
Alignment explanation
Indices: 1764512--1764676 Score: 56
Period size: 16 Copynumber: 10.1 Consensus size: 16
1764502 AATTTATATA
*
1764512 AATTTAA-ATATATTT
1 AATTTAATATAAATTT
*
1764527 AATTTAATTTAAATTAT
1 AATTTAATATAAATT-T
* *
1764544 TATTTAATAATAAATAT
1 AATTTAAT-ATAAATTT
* * *
1764561 ATTTTTATTTAAATTT
1 AATTTAATATAAATTT
*
1764577 AA-TT-ATAAAAATATT
1 AATTTAATATAAAT-TT
* *
1764592 AATATAA-A-AAATAAT
1 AATTTAATATAAAT-TT
*
1764607 ATTTTAATAATATAA-TT
1 AATTTAAT-ATA-AATTT
* * *
1764624 AATAATAAAAATAATTTTT
1 AAT--TTAATATAA-ATTT
*
1764643 AACTTAATATAAATTT
1 AATTTAATATAAATTT
1764659 AATTTAAT-TCAAATTT
1 AATTTAATAT-AAATTT
1764675 AA
1 AA
1764677 AAATAAAAAT
Statistics
Matches: 108, Mismatches: 27, Indels: 29
0.66 0.16 0.18
Matches are distributed among these distances:
14 6 0.06
15 25 0.23
16 32 0.30
17 27 0.25
18 9 0.08
19 9 0.08
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTTAATATAAATTT
Found at i:1765068 original size:9 final size:9
Alignment explanation
Indices: 1765039--1765105 Score: 55
Period size: 9 Copynumber: 7.1 Consensus size: 9
1765029 ATATAAATAA
1765039 AAATATAATAT
1 AAATAT-AT-T
1765050 AAAT-TATT
1 AAATATATT
1765058 AAATATATT
1 AAATATATT
* *
1765067 AAAAATTTT
1 AAATATATT
*
1765076 AAATATAAAT
1 AAATAT-ATT
1765086 AATATATATT
1 AA-ATATATT
*
1765096 ATATATATT
1 AAATATATT
1765105 A
1 A
1765106 TATTAATTAT
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
8 5 0.11
9 26 0.57
10 7 0.15
11 8 0.17
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (9 bp):
AAATATATT
Found at i:1765079 original size:18 final size:19
Alignment explanation
Indices: 1765039--1765083 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
1765029 ATATAAATAA
*
1765039 AAATATAATATAAATTATT
1 AAATATAATAAAAATTATT
*
1765058 AAATATATTAAAAATT-TT
1 AAATATAATAAAAATTATT
1765076 AAATATAA
1 AAATATAA
1765084 ATAATATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
AAATATAATAAAAATTATT
Found at i:1765124 original size:20 final size:18
Alignment explanation
Indices: 1765099--1765154 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 18
1765089 ATATATTATA
1765099 TATATTATATTAATTATATT
1 TATATT-TATTAA-TATATT
*
1765119 TATATTTAATATAATATTTT
1 TATATTT-AT-TAATATATT
1765139 TATATTTATTAA-ATAT
1 TATATTTATTAATATAT
1765155 GTGTTCGAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
17 3 0.09
18 3 0.09
19 3 0.09
20 20 0.62
21 3 0.09
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TATATTTATTAATATATT
Found at i:1765131 original size:15 final size:15
Alignment explanation
Indices: 1765078--1765136 Score: 54
Period size: 14 Copynumber: 4.0 Consensus size: 15
1765068 AAAATTTTAA
*
1765078 ATATAAATA-ATA-T
1 ATATTAATATATATT
1765091 ATATT-ATATATATT
1 ATATTAATATATATT
1765105 ATATTAAT-TATATTT
1 ATATTAATATATA-TT
1765120 ATATTTAATATAATATT
1 ATA-TTAATAT-ATATT
1765137 TTTATATTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
12 3 0.08
13 7 0.18
14 10 0.26
15 7 0.18
16 5 0.13
17 3 0.08
18 3 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATTAATATATATT
Found at i:1765495 original size:13 final size:14
Alignment explanation
Indices: 1765466--1765498 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1765456 TCATATATTT
*
1765466 TATTTTTTATTTAA
1 TATTTTTTAATTAA
1765480 TATTTTTTAATT-A
1 TATTTTTTAATTAA
1765493 TATTTT
1 TATTTT
1765499 AAGATGGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 7 0.39
14 11 0.61
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (14 bp):
TATTTTTTAATTAA
Found at i:1771255 original size:2 final size:2
Alignment explanation
Indices: 1771248--1771285 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
1771238 ATATTAATAA
1771248 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1771286 CGTCCAGCAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1772544 original size:2 final size:2
Alignment explanation
Indices: 1772537--1772587 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
1772527 AGGAGAAAGT
1772537 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
1772579 TA TA T- TA TA
1 TA TA TA TA TA
1772588 CCCTTTAATC
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1772637 original size:2 final size:2
Alignment explanation
Indices: 1772625--1772663 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
1772615 AGGAGAAAGT
*
1772625 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1772664 CTGAGCGAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 31 0.94
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1772646 original size:88 final size:86
Alignment explanation
Indices: 1772497--1772663 Score: 289
Period size: 88 Copynumber: 1.9 Consensus size: 86
1772487 GCAGCAGGAG
* *
1772497 ATACCGTTTAATCCATTAATCCCAGAAAGCAGGAGAAAGTTATATATATATATATATATATATAT
1 ATACCCTTTAATCCATTAATCCCAGAAAGCAGGAGAAAGTTATAAATATATATATATATATATAT
1772562 ATATATATATATATATATATATT
66 ATATA-ATAT-TATATATATATT
*
1772585 ATACCCTTTAATCCATTAATCCCAGAATGCAGGAGAAAGTTATAAATATATATATATATATATAT
1 ATACCCTTTAATCCATTAATCCCAGAAAGCAGGAGAAAGTTATAAATATATATATATATATATAT
1772650 ATATAATATTATAT
66 ATATAATATTATAT
1772664 CTGAGCGAAA
Statistics
Matches: 76, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
86 5 0.07
87 4 0.05
88 67 0.88
ACGTcount: A:0.44, C:0.10, G:0.08, T:0.38
Consensus pattern (86 bp):
ATACCCTTTAATCCATTAATCCCAGAAAGCAGGAGAAAGTTATAAATATATATATATATATATAT
ATATAATATTATATATATATT
Done.