Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold24
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: 3006277
ACGTcount: A:0.30, C:0.13, G:0.13, T:0.30
Warning! 383161 characters in sequence are not A, C, G, or T
File 13 of 19
Found at i:1987166 original size:14 final size:14
Alignment explanation
Indices: 1987133--1987173 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
1987123 TTAATTTAAT
*
1987133 TAATTTTTATAAT-
1 TAATTTTTAAAATA
1987146 T-ATTTTTAAAATA
1 TAATTTTTAAAATA
*
1987159 TAATTTTTAATATA
1 TAATTTTTAAAATA
1987173 T
1 T
1987174 TTAAAATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 10 0.42
13 2 0.08
14 12 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TAATTTTTAAAATA
Found at i:1987176 original size:23 final size:23
Alignment explanation
Indices: 1987150--1987193 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1987140 TATAATTATT
*
1987150 TTTAAAATATAATTTTTAATATA
1 TTTAAAATATAAATTTTAATATA
*
1987173 TTTAAAATTTAAATTTTAATA
1 TTTAAAATATAAATTTTAATA
1987194 GTTATAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTAAAATATAAATTTTAATATA
Found at i:1987187 original size:24 final size:24
Alignment explanation
Indices: 1987132--1987193 Score: 65
Period size: 23 Copynumber: 2.6 Consensus size: 24
1987122 TTTAATTTAA
* *
1987132 TTAATTTTTATAATTATTTTTAAAAT
1 TTAAATTTT-TAA-TATATTTAAAAT
*
1987158 AT-AATTTTTAATATATTTAAAAT
1 TTAAATTTTTAATATATTTAAAAT
1987181 TTAAA-TTTTAATA
1 TTAAATTTTTAATA
1987194 GTTATAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
23 20 0.65
24 5 0.16
25 5 0.16
26 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (24 bp):
TTAAATTTTTAATATATTTAAAAT
Found at i:1987437 original size:2 final size:2
Alignment explanation
Indices: 1987430--1987473 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1987420 AGTGTTTGGG
1987430 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1987472 CT
1 CT
1987474 AAATTGATGA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:1988442 original size:17 final size:19
Alignment explanation
Indices: 1988383--1988449 Score: 66
Period size: 17 Copynumber: 3.5 Consensus size: 19
1988373 ATATATATAT
* *
1988383 ATATATATATCATTATTTAAA
1 ATATAAATATAATTA-TT-AA
*
1988404 ATTTAAATATAATTATTAA
1 ATATAAATATAATTATTAA
*
1988423 ATATAAATAT-A-TATTTA
1 ATATAAATATAATTATTAA
1988440 ATATAAATAT
1 ATATAAATAT
1988450 TTTTATTTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
17 15 0.37
18 1 0.02
19 11 0.27
20 2 0.05
21 12 0.29
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (19 bp):
ATATAAATATAATTATTAA
Found at i:1988520 original size:40 final size:41
Alignment explanation
Indices: 1988437--1988528 Score: 111
Period size: 40 Copynumber: 2.3 Consensus size: 41
1988427 AAATATATAT
* * *
1988437 TTAATATAAAT-ATTTTTATTTTTTATATATTTTAAAAAAA
1 TTAAAATAAATAATATTTATATTTTATATATTTTAAAAAAA
1988477 TTAAAA-AAATAATATTTATATTTT-TATA-TTTAAAAATATA
1 TTAAAATAAATAATATTTATATTTTATATATTTTAAAAA-A-A
1988517 TTAAAATAAATA
1 TTAAAATAAATA
1988529 TTTAAAAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
38 8 0.18
39 9 0.20
40 23 0.51
41 5 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (41 bp):
TTAAAATAAATAATATTTATATTTTATATATTTTAAAAAAA
Found at i:1988548 original size:24 final size:24
Alignment explanation
Indices: 1988502--1988550 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
1988492 TTATATTTTT
**
1988502 ATATTTAAAAATATATTAAAATAA
1 ATATTTAAAAATATAAAAAAATAA
1988526 ATATTTAAAAA-ATAAAAATAATAA
1 ATATTTAAAAATATAAAAA-AATAA
1988550 A
1 A
1988551 AATATATTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (24 bp):
ATATTTAAAAATATAAAAAAATAA
Found at i:1988981 original size:3 final size:3
Alignment explanation
Indices: 1988973--1989006 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
1988963 TTAATATCTC
*
1988973 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTT TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1989007 GTCCATTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.29, T:0.71
Consensus pattern (3 bp):
TTG
Found at i:1991124 original size:16 final size:16
Alignment explanation
Indices: 1991068--1991129 Score: 61
Period size: 16 Copynumber: 3.9 Consensus size: 16
1991058 TATTAATGTG
* *
1991068 AATTATTTTGAATTCA
1 AATTATTTTAAATTAA
* * * *
1991084 TATCATTTAAAATTTA
1 AATTATTTTAAATTAA
1991100 AATTATTTTAAATTAA
1 AATTATTTTAAATTAA
*
1991116 AATTATTTTTAATT
1 AATTATTTTAAATT
1991130 TTTATTCATT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (16 bp):
AATTATTTTAAATTAA
Found at i:1993786 original size:3 final size:3
Alignment explanation
Indices: 1993778--1993816 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1993768 GTTCTGCATA
1993778 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1993817 TTTACCCTGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1994335 original size:3 final size:3
Alignment explanation
Indices: 1994327--1994357 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1994317 GTATTGTAAA
1994327 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1994358 GGTTTTATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:1996189 original size:20 final size:20
Alignment explanation
Indices: 1996166--1996204 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1996156 TTATGTAAAT
1996166 TTAAATTT-AAATATAAATAA
1 TTAAATTTGAAAT-TAAATAA
1996186 TTAAATTTGAAATTAAATA
1 TTAAATTTGAAATTAAATA
1996205 TAAAAATGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (20 bp):
TTAAATTTGAAATTAAATAA
Found at i:1996454 original size:2 final size:2
Alignment explanation
Indices: 1996447--1996475 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1996437 ACTGACTGGG
1996447 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1996476 CAGCTGACAG
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1998579 original size:21 final size:21
Alignment explanation
Indices: 1998532--1998579 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
1998522 ATAGAAATCA
1998532 TTATTT-TTTTTCTTCTACTT
1 TTATTTCTTTTTCTTCTACTT
* *
1998552 TCT-TTTCTTTTTCTTTTCCTT
1 T-TATTTCTTTTTCTTCTACTT
1998573 TTATTTC
1 TTATTTC
1998580 ATGCCCCCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
20 5 0.22
21 18 0.78
ACGTcount: A:0.06, C:0.19, G:0.00, T:0.75
Consensus pattern (21 bp):
TTATTTCTTTTTCTTCTACTT
Found at i:1999276 original size:17 final size:16
Alignment explanation
Indices: 1999254--1999296 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
1999244 AACTTAAATT
*
1999254 AATAAATTTTATATTTA
1 AATAAATTTTA-ATATA
*
1999271 AATAAAATTTAATATA
1 AATAAATTTTAATATA
1999287 AATTAAATTT
1 AA-TAAATTT
1999297 ATTGAAAAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 6 0.27
17 16 0.73
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATAAATTTTAATATA
Found at i:1999288 original size:16 final size:17
Alignment explanation
Indices: 1999254--1999298 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
1999244 AACTTAAATT
* *
1999254 AATAAATTTTATATTTA
1 AATAAAATTTATATATA
1999271 AATAAAATTTA-ATATA
1 AATAAAATTTATATATA
*
1999287 AATTAAATTTAT
1 AATAAAATTTAT
1999299 TGAAAAGAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 14 0.58
17 10 0.42
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AATAAAATTTATATATA
Found at i:1999719 original size:25 final size:27
Alignment explanation
Indices: 1999679--1999736 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
1999669 AAAAATATTA
*
1999679 AAAAAATTATTTATAAGA-TTTAAATT
1 AAAAAATTATTGATAAGATTTTAAATT
* *
1999705 TAAAAATT-TTGATAATATTTTAAATT
1 AAAAAATTATTGATAAGATTTTAAATT
1999731 AAAAAA
1 AAAAAA
1999737 CTAGTTATCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 7 0.26
26 20 0.74
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (27 bp):
AAAAAATTATTGATAAGATTTTAAATT
Found at i:1999882 original size:7 final size:7
Alignment explanation
Indices: 1999870--1999914 Score: 54
Period size: 7 Copynumber: 6.1 Consensus size: 7
1999860 CGTTGAAATA
1999870 AATTTTT
1 AATTTTT
1999877 AATTTTT
1 AATTTTT
*
1999884 AATTAAATT
1 AATT--TTT
1999893 AATTTTT
1 AATTTTT
*
1999900 AATATTT
1 AATTTTT
1999907 AATTTTT
1 AATTTTT
1999914 A
1 A
1999915 TTTAAATAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
7 26 0.81
9 6 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (7 bp):
AATTTTT
Found at i:1999891 original size:23 final size:23
Alignment explanation
Indices: 1999865--1999910 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1999855 TTTTACGTTG
*
1999865 AAATAAATTTTTAATTTTTAATT
1 AAATAAATTTTTAATATTTAATT
*
1999888 AAATTAATTTTTAATATTTAATT
1 AAATAAATTTTTAATATTTAATT
1999911 TTTATTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
AAATAAATTTTTAATATTTAATT
Found at i:1999896 original size:16 final size:16
Alignment explanation
Indices: 1999875--1999941 Score: 77
Period size: 16 Copynumber: 4.3 Consensus size: 16
1999865 AAATAAATTT
1999875 TTAATTTTTAATTAAA
1 TTAATTTTTAATTAAA
*
1999891 TTAATTTTTAA-T-AT
1 TTAATTTTTAATTAAA
*
1999905 TTAATTTTTATTTAAA
1 TTAATTTTTAATTAAA
*
1999921 -TAAATTTTAACTTAAA
1 TTAATTTTTAA-TTAAA
1999937 TTAAT
1 TTAAT
1999942 AATTTTAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
14 11 0.27
15 10 0.24
16 17 0.41
17 3 0.07
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (16 bp):
TTAATTTTTAATTAAA
Found at i:1999972 original size:46 final size:45
Alignment explanation
Indices: 1999880--1999972 Score: 102
Period size: 46 Copynumber: 2.0 Consensus size: 45
1999870 AATTTTTAAT
* **
1999880 TTTTAATTAAATTAATTTTTAATATTTAATTTTTATTTAAATAAA
1 TTTTAATTAAATTAATTTTTAATATATAATTTTTAAATAAATAAA
1999925 TTTTAACTTAAATTAATAATTTTAA-ATAT-ATTATTTAAATAAA-AAA
1 TTTTAA-TTAAATTAAT--TTTTAATATATAATT-TTTAAATAAATAAA
1999971 TT
1 TT
1999973 ATTTAAATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
45 6 0.15
46 18 0.44
47 11 0.27
48 6 0.15
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (45 bp):
TTTTAATTAAATTAATTTTTAATATATAATTTTTAAATAAATAAA
Found at i:1999975 original size:16 final size:16
Alignment explanation
Indices: 1999954--1999984 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1999944 TTTTAAATAT
1999954 ATTATTTAAATAAAAA
1 ATTATTTAAATAAAAA
1999970 ATTATTTAAATAAAA
1 ATTATTTAAATAAAA
1999985 TTATAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTATTTAAATAAAAA
Found at i:2003254 original size:12 final size:12
Alignment explanation
Indices: 2003221--2003259 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
2003211 AATATTTTGG
2003221 ATATAAT-TATA
1 ATATAATATATA
2003232 ATAT-A-ATATA
1 ATATAATATATA
2003242 ATATAATATATA
1 ATATAATATATA
2003254 ATATAA
1 ATATAA
2003260 ATTATTAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.36
11 5 0.20
12 11 0.44
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
ATATAATATATA
Found at i:2003259 original size:5 final size:5
Alignment explanation
Indices: 2003221--2003251 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
2003211 AATATTTTGG
2003221 ATATA ATTATA ATATA ATATA ATATA ATATA
1 ATATA A-TATA ATATA ATATA ATATA ATATA
2003252 TAATATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:2004199 original size:28 final size:28
Alignment explanation
Indices: 2004139--2004193 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
2004129 TATTTAAATT
2004139 TAATTATAAATATAAAAATAATATTTTA
1 TAATTATAAATATAAAAATAATATTTTA
2004167 TAATTAATAAATA-ATAAAAT-ATATTTT
1 TAATT-ATAAATATA-AAAATAATATTTT
2004194 TAAATTCAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
28 13 0.52
29 12 0.48
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
TAATTATAAATATAAAAATAATATTTTA
Found at i:2015517 original size:174 final size:174
Alignment explanation
Indices: 2015227--2015560 Score: 506
Period size: 174 Copynumber: 1.9 Consensus size: 174
2015217 AAATTTACCG
* * *
2015227 TTCAGTATCATCTTCAGTAGGACTGGAGTTTCCCTGAAGAAATTCATCACGGTAAATTAAAGGAG
1 TTCAGTATCATCTCCAATAGAACTGGAGTTTCCCTGAAGAAATTCATCACGGTAAATTAAAGGAG
* * * *
2015292 GAGACCTTATTCTTTTAGAAACTGGAGGCCCAACATTTCTTACTGCAGGAGAAGGATCATTGTGT
66 GAGACCTCATTCTTTTAGAAACCGGAGGCCCAACATTTCTCACTGCAGGAGAAGGATCATTGTGC
*
2015357 GCAGAAGGCAAGGATCTAGGACGAATTAGTGCTGGAGTTTTCCC
131 ACAGAAGGCAAGGATCTAGGACGAATTAGTGCTGGAGTTTTCCC
* * *
2015401 TTCAGTATCATCTCCAATAGAACTGGAGTTTTCCTGAAGGAATTCATCATGGTAAATTAAAGGAG
1 TTCAGTATCATCTCCAATAGAACTGGAGTTTCCCTGAAGAAATTCATCACGGTAAATTAAAGGAG
* * **
2015466 GAGACCTCGTTCTTTTAGAAACCGGAGGTCCAAGGTTTCTCACTGCAGGAGAAGGATCATTGTGC
66 GAGACCTCATTCTTTTAGAAACCGGAGGCCCAACATTTCTCACTGCAGGAGAAGGATCATTGTGC
* * *
2015531 ACATAAGGCAAGGATCTCGGATGAATTAGT
131 ACAGAAGGCAAGGATCTAGGACGAATTAGT
2015561 ACATCAGAGC
Statistics
Matches: 142, Mismatches: 18, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
174 142 1.00
ACGTcount: A:0.30, C:0.18, G:0.25, T:0.28
Consensus pattern (174 bp):
TTCAGTATCATCTCCAATAGAACTGGAGTTTCCCTGAAGAAATTCATCACGGTAAATTAAAGGAG
GAGACCTCATTCTTTTAGAAACCGGAGGCCCAACATTTCTCACTGCAGGAGAAGGATCATTGTGC
ACAGAAGGCAAGGATCTAGGACGAATTAGTGCTGGAGTTTTCCC
Found at i:2019094 original size:18 final size:18
Alignment explanation
Indices: 2019073--2019129 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
2019063 TATAATATAA
2019073 TATAATTATATAAATTTT
1 TATAATTATATAAATTTT
2019091 TATATATTA-AT-AA--TT
1 TATA-ATTATATAAATTTT
2019106 TAT-ATTATATAAATTTT
1 TATAATTATATAAATTTT
*
2019123 AATAATT
1 TATAATT
2019130 GTAATTCAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 12
0.71 0.02 0.27
Matches are distributed among these distances:
13 4 0.12
14 2 0.06
15 7 0.22
17 6 0.19
18 9 0.28
19 4 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TATAATTATATAAATTTT
Found at i:2019831 original size:83 final size:82
Alignment explanation
Indices: 2019718--2019880 Score: 245
Period size: 83 Copynumber: 2.0 Consensus size: 82
2019708 AGTTGGTTGG
* * * * * * *
2019718 GTTGACTTTGTCTCAAAAGTTCAGATTGACTGTTAAATTTGTTGATTGCTTTAGTTTTTTTTTTT
1 GTTGACTTTCTCTAAAAAGATCAGACTGACTGTTAAATTTGTTGATTACTTTAGTTTTTTTCTTC
*
2019783 TTTTTTAATTTCTTATTA
66 TTTTTT-ATTCCTTATTA
2019801 GTTGACTTTCTCTAAAAAGATCAGACTGACTGTTAAATTTGTTGATTACTTTAGTTTTTTTCTTC
1 GTTGACTTTCTCTAAAAAGATCAGACTGACTGTTAAATTTGTTGATTACTTTAGTTTTTTTCTTC
2019866 TTTTTTATTCCTTAT
66 TTTTTTATTCCTTAT
2019881 CTGACATCTT
Statistics
Matches: 72, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
82 8 0.11
83 64 0.89
ACGTcount: A:0.21, C:0.11, G:0.12, T:0.55
Consensus pattern (82 bp):
GTTGACTTTCTCTAAAAAGATCAGACTGACTGTTAAATTTGTTGATTACTTTAGTTTTTTTCTTC
TTTTTTATTCCTTATTA
Found at i:2023445 original size:13 final size:13
Alignment explanation
Indices: 2023427--2023453 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2023417 AAATTAATTA
2023427 AATTATAATTTAT
1 AATTATAATTTAT
2023440 AATTATAATTTAT
1 AATTATAATTTAT
2023453 A
1 A
2023454 TATTTTTAGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AATTATAATTTAT
Found at i:2024302 original size:4 final size:4
Alignment explanation
Indices: 2024293--2024317 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2024283 TAAAACACAA
2024293 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
2024318 CACCGAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:2024374 original size:5 final size:5
Alignment explanation
Indices: 2024364--2024397 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
2024354 GTACAATGCA
2024364 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
2024398 AATAGCTCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:2027446 original size:12 final size:12
Alignment explanation
Indices: 2027429--2027453 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2027419 AAGTGTTGGA
2027429 TCTAAAACTTTT
1 TCTAAAACTTTT
2027441 TCTAAAACTTTT
1 TCTAAAACTTTT
2027453 T
1 T
2027454 GCATGGCAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.52
Consensus pattern (12 bp):
TCTAAAACTTTT
Found at i:2028136 original size:15 final size:16
Alignment explanation
Indices: 2028112--2028141 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2028102 CAGGCTAGAT
2028112 GGCAACAGGAAGAAAA
1 GGCAACAGGAAGAAAA
2028128 GGCAA-AGGAAGAAA
1 GGCAACAGGAAGAAA
2028142 TACTTACTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.57, C:0.10, G:0.33, T:0.00
Consensus pattern (16 bp):
GGCAACAGGAAGAAAA
Found at i:2032545 original size:23 final size:23
Alignment explanation
Indices: 2032496--2032545 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
2032486 TTCAAAATGT
*
2032496 AAAT-TTTAAAACTATAAATATT
1 AAATATTTAAAACTATAAATATC
* * *
2032518 TAATATTTAAAATTTTAAATATC
1 AAATATTTAAAACTATAAATATC
2032541 AAATA
1 AAATA
2032546 AATAAAATAA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
22 3 0.14
23 19 0.86
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (23 bp):
AAATATTTAAAACTATAAATATC
Found at i:2035222 original size:12 final size:12
Alignment explanation
Indices: 2035205--2035230 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2035195 ATCCTAAGCT
2035205 TTCAAGTATTTA
1 TTCAAGTATTTA
2035217 TTCAAGTATTTA
1 TTCAAGTATTTA
2035229 TT
1 TT
2035231 ATTTTATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.54
Consensus pattern (12 bp):
TTCAAGTATTTA
Found at i:2035824 original size:28 final size:28
Alignment explanation
Indices: 2035762--2035830 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 28
2035752 ATTTAGATAC
*
2035762 ATTTATATATTCATATCATATTTATTTTAT
1 ATTTA-ATATT-ATATCATATTTATTATAT
* *
2035792 TTTTAATATTATATCGTATTTA-TATAT
1 ATTTAATATTATATCATATTTATTATAT
2035819 AATTTAAT-TTAT
1 -ATTTAATATTAT
2035831 TTTTATATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
27 8 0.24
28 17 0.50
29 5 0.15
30 4 0.12
ACGTcount: A:0.35, C:0.04, G:0.01, T:0.59
Consensus pattern (28 bp):
ATTTAATATTATATCATATTTATTATAT
Found at i:2035864 original size:39 final size:39
Alignment explanation
Indices: 2035774--2035861 Score: 101
Period size: 39 Copynumber: 2.3 Consensus size: 39
2035764 TTATATATTC
* *
2035774 ATATCATATTTATTTTATTTTTAATATTATATCGTATTT
1 ATATCATATTTAATTTATTTTTAATATTATATCGTAATT
*
2035813 ATAT-ATAATTTAATTTATTTTT-ATATTTTCATC-TAATT
1 ATATCAT-ATTTAATTTATTTTTAATATTAT-ATCGTAATT
*
2035851 ATATCACATTT
1 ATATCATATTT
2035862 TAAATCGATA
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
38 20 0.48
39 22 0.52
ACGTcount: A:0.33, C:0.07, G:0.01, T:0.59
Consensus pattern (39 bp):
ATATCATATTTAATTTATTTTTAATATTATATCGTAATT
Found at i:2037837 original size:32 final size:34
Alignment explanation
Indices: 2037801--2037875 Score: 88
Period size: 32 Copynumber: 2.3 Consensus size: 34
2037791 TATTGATTTA
2037801 AAATTTTAAAAAAATAAAAAT-A-TTTAATGATT
1 AAATTTTAAAAAAATAAAAATCACTTTAATGATT
2037833 AAA-TTT--AAAAATAAAAATCATCTTTAATGATT
1 AAATTTTAAAAAAATAAAAATCA-CTTTAATGATT
**
2037865 ATTTTTTAAAA
1 AAATTTTAAAA
2037876 TTATATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
29 12 0.34
30 1 0.03
31 3 0.09
32 14 0.40
33 3 0.09
35 2 0.06
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (34 bp):
AAATTTTAAAAAAATAAAAATCACTTTAATGATT
Found at i:2037884 original size:13 final size:13
Alignment explanation
Indices: 2037862--2037908 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
2037852 ATCTTTAATG
*
2037862 ATTATTTTTTAAA
1 ATTATATTTTAAA
*
2037875 ATTATATTTTTAA
1 ATTATATTTTAAA
2037888 A--ATATTTTAAA
1 ATTATATTTTAAA
*
2037899 AATATATTTT
1 ATTATATTTT
2037909 TTTCATGCTC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 10 0.34
13 19 0.66
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
ATTATATTTTAAA
Found at i:2039342 original size:27 final size:26
Alignment explanation
Indices: 2039295--2039352 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
2039285 GACTATATTT
**
2039295 AATAT-AT-TTTTAAAAGTAAATATAA
1 AATATAATATTTTAAAAAAAAAT-TAA
*
2039320 GATATAATATTTTAAAAAAAAATTAA
1 AATATAATATTTTAAAAAAAAATTAA
2039346 AATATAA
1 AATATAA
2039353 AATATTATGT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 4 0.15
26 11 0.41
27 12 0.44
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.36
Consensus pattern (26 bp):
AATATAATATTTTAAAAAAAAATTAA
Found at i:2042251 original size:21 final size:20
Alignment explanation
Indices: 2042226--2042265 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
2042216 TTTACTATCA
*
2042226 TTATATTATTAAAATATTATT
1 TTATATTAATAAAAT-TTATT
2042247 TTATATTAATAAAATTTAT
1 TTATATTAATAAAATTTAT
2042266 AATTAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTATATTAATAAAATTTATT
Found at i:2043459 original size:29 final size:28
Alignment explanation
Indices: 2043447--2043502 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
2043437 ATCAAATGAT
*
2043447 AAATA-AAAATTTATTTGAATATAATAA
1 AAATATAAAATTTATTTAAATATAATAA
2043474 AAATATAAAATTTATTTTAAA-A-AATAA
1 AAATATAAAATTTA-TTTAAATATAATAA
2043501 AA
1 AA
2043503 TAATTCAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 12 0.46
28 9 0.35
29 5 0.19
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (28 bp):
AAATATAAAATTTATTTAAATATAATAA
Found at i:2048973 original size:25 final size:24
Alignment explanation
Indices: 2048940--2048986 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
2048930 CTCGAATTAC
2048940 ATTAGATAATATTAAATAAGATACG
1 ATTAGATAATA-TAAATAAGATACG
* *
2048965 ATTATATAATATAAATATGATA
1 ATTAGATAATATAAATAAGATA
2048987 TAAAAATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.53, C:0.02, G:0.09, T:0.36
Consensus pattern (24 bp):
ATTAGATAATATAAATAAGATACG
Found at i:2049415 original size:24 final size:23
Alignment explanation
Indices: 2049373--2049417 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
2049363 CTTTCAACGT
*
2049373 TTTAAAAATAATTATATTATTAA
1 TTTAAAAATAATTAAATTATTAA
*
2049396 TTTAAAATTTAATTAAATTATT
1 TTTAAAA-ATAATTAAATTATT
2049418 TATATAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 7 0.37
24 12 0.63
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TTTAAAAATAATTAAATTATTAA
Found at i:2049625 original size:15 final size:16
Alignment explanation
Indices: 2049605--2049645 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
2049595 AAATAATTTA
2049605 TTTAATTTAA-TAAAT
1 TTTAATTTAATTAAAT
*
2049620 TTTAATTAAATTAAAT
1 TTTAATTTAATTAAAT
*
2049636 TTAAATTTAA
1 TTTAATTTAA
2049646 ATTTTTTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TTTAATTTAATTAAAT
Found at i:2049714 original size:22 final size:22
Alignment explanation
Indices: 2049666--2049714 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
2049656 TTGATTCATA
2049666 TTAA-ATTATTATTTAATAAAT
1 TTAATATTATTATTTAATAAAT
**
2049687 AAAATATTATT-TTTATATAAAT
1 TTAATATTATTATTTA-ATAAAT
2049709 TTAATA
1 TTAATA
2049715 ATAAAAAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TTAATATTATTATTTAATAAAT
Found at i:2050269 original size:16 final size:17
Alignment explanation
Indices: 2050238--2050285 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
2050228 AGATATGATT
2050238 ATATAAAATA-AATATG
1 ATATAAAATATAATATG
*
2050254 AT-TGAAATATAATATG
1 ATATAAAATATAATATG
*
2050270 ATATAAAAAATAATAT
1 ATATAAAATATAATAT
2050286 AAATTTAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 6 0.22
16 10 0.37
17 11 0.41
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.33
Consensus pattern (17 bp):
ATATAAAATATAATATG
Found at i:2050302 original size:34 final size:35
Alignment explanation
Indices: 2050216--2050302 Score: 90
Period size: 34 Copynumber: 2.5 Consensus size: 35
2050206 AATATAATTG
* * *
2050216 ATAATTTTATATAGATATGATTATATAAAATAAAT
1 ATAATTTAATATAAATATGATTATAAAAAATAAAT
* *
2050251 ATGATTGAA-ATATAATATGA-TATAAAAAAT-AAT
1 ATAATTTAATATA-AATATGATTATAAAAAATAAAT
2050284 ATAAATTTAATATAAATAT
1 AT-AATTTAATATAAATAT
2050303 ATGAACGTGT
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
33 5 0.12
34 22 0.52
35 15 0.36
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (35 bp):
ATAATTTAATATAAATATGATTATAAAAAATAAAT
Found at i:2051629 original size:11 final size:12
Alignment explanation
Indices: 2051609--2051633 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2051599 TACTTCAAAA
2051609 TTTTCTTTTTTT
1 TTTTCTTTTTTT
2051621 TTTTCTTTTTTT
1 TTTTCTTTTTTT
2051633 T
1 T
2051634 AATTTCAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TTTTCTTTTTTT
Found at i:2052847 original size:2 final size:2
Alignment explanation
Indices: 2052840--2052873 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2052830 CATCATCTTT
2052840 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
2052874 AAAATGTCAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2057688 original size:17 final size:17
Alignment explanation
Indices: 2057662--2057695 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2057652 AAAATTGATT
*
2057662 ATAATCATATTGAACAC
1 ATAATCATATTCAACAC
*
2057679 ATAATTATATTCAACAC
1 ATAATCATATTCAACAC
2057696 TAAAACCCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.18, G:0.03, T:0.32
Consensus pattern (17 bp):
ATAATCATATTCAACAC
Found at i:2059440 original size:2 final size:2
Alignment explanation
Indices: 2059433--2059474 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
2059423 CTTAGTTTAA
* *
2059433 AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2059475 TGAGTTGAGG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2062332 original size:24 final size:24
Alignment explanation
Indices: 2062277--2062333 Score: 71
Period size: 25 Copynumber: 2.4 Consensus size: 24
2062267 TGTTTATTTA
*
2062277 TTTTTTT-AATGCAAAAATAAAAT
1 TTTTTTTAAATCCAAAAATAAAAT
* *
2062300 TTTAATTTAAATCCAAAAATAAACT
1 TTT-TTTTAAATCCAAAAATAAAAT
2062325 TTTTTTTAA
1 TTTTTTTAA
2062334 TTTGAACTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
23 3 0.11
24 8 0.29
25 17 0.61
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.46
Consensus pattern (24 bp):
TTTTTTTAAATCCAAAAATAAAAT
Found at i:2065246 original size:4 final size:4
Alignment explanation
Indices: 2065239--2065273 Score: 70
Period size: 4 Copynumber: 8.8 Consensus size: 4
2065229 AATAAATAAA
2065239 TATT TATT TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TATT TATT TAT
2065274 AAAGAGTCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:2066911 original size:16 final size:16
Alignment explanation
Indices: 2066890--2066920 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2066880 AAAAGAATCG
2066890 AACACTATGGGATTCA
1 AACACTATGGGATTCA
2066906 AACACTATGGGATTC
1 AACACTATGGGATTC
2066921 GAACCCTCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.26
Consensus pattern (16 bp):
AACACTATGGGATTCA
Found at i:2068763 original size:21 final size:21
Alignment explanation
Indices: 2068737--2068783 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2068727 TATTTATTTT
** *
2068737 TATATAAAAATTTACTTAATA
1 TATATAAAAATAAAATTAATA
*
2068758 TATATAAATATAAAATTAATA
1 TATATAAAAATAAAATTAATA
2068779 TATAT
1 TATAT
2068784 TATATAATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
TATATAAAAATAAAATTAATA
Found at i:2070984 original size:11 final size:11
Alignment explanation
Indices: 2070970--2071017 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
2070960 GTTTATATTT
*
2070970 TATTTATATCA
1 TATTTAAATCA
2070981 TATTTTAAAT-A
1 TA-TTTAAATCA
* *
2070992 TTTTTATATCA
1 TATTTAAATCA
2071003 TATTTAAATCA
1 TATTTAAATCA
2071014 TATT
1 TATT
2071018 ATTACGTTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
10 6 0.20
11 18 0.60
12 6 0.20
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (11 bp):
TATTTAAATCA
Found at i:2071020 original size:27 final size:27
Alignment explanation
Indices: 2070998--2071054 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
2070988 AATATTTTTA
2070998 TATCATATTTAAATCATATTATTACGT
1 TATCATATTTAAATCATATTATTACGT
*
2071025 TATCATATTTAAATCATATTATTATGT
1 TATCATATTTAAATCATATTATTACGT
2071052 TAT
1 TAT
2071055 GTTTAATATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.37, C:0.09, G:0.04, T:0.51
Consensus pattern (27 bp):
TATCATATTTAAATCATATTATTACGT
Found at i:2072389 original size:102 final size:102
Alignment explanation
Indices: 2072213--2072510 Score: 366
Period size: 102 Copynumber: 2.9 Consensus size: 102
2072203 CAAACTCCCA
* *
2072213 GTGAAGGAACTT-TTGTTTCTGTGGAGTCTATTTCCATATTGGAGACATCAGCACTTACAACCCT
1 GTGAAGGAACTTCTT-TTTCTGTGGGGTCTATTTCCATATCGGAGACATCAGCACTTACAACCCT
*
2072277 AGGCTGCTGAGAAGCTTCAGCATAATCTTCCAGTTGGG
65 AGGCTGCTGAGAAGCCTCAGCATAATCTTCCAGTTGGG
* * ***
2072315 GTGAAGGAACTTCTTTTTCTGTGGGGTCTATTTCCATATCGGATACAT-TGTCACTTACAATTTT
1 GTGAAGGAACTTCTTTTTCTGTGGGGTCTATTTCCATATCGGAGACATCAG-CACTTACAACCCT
* *
2072379 AGGCTGCTGAGAAGCCTCAGCATGATCTTCCGGTTGGG
65 AGGCTGCTGAGAAGCCTCAGCATAATCTTCCAGTTGGG
* * * * * * *** * *
2072417 GTGAAGGAACCTCTTTTTCTGAGGGGTCTATTTCCATATTGAAAACATCAGCATTTTGGAGCTTA
1 GTGAAGGAACTTCTTTTTCTGTGGGGTCTATTTCCATATCGGAGACATCAGCACTTACAACCCTA
*
2072482 GGCTGCTGAGAAGCCTCAGCATGATCTTC
66 GGCTGCTGAGAAGCCTCAGCATAATCTTC
2072511 AGATTGGAGC
Statistics
Matches: 171, Mismatches: 22, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
101 1 0.01
102 167 0.98
103 3 0.02
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (102 bp):
GTGAAGGAACTTCTTTTTCTGTGGGGTCTATTTCCATATCGGAGACATCAGCACTTACAACCCTA
GGCTGCTGAGAAGCCTCAGCATAATCTTCCAGTTGGG
Found at i:2073496 original size:159 final size:159
Alignment explanation
Indices: 2072562--2073475 Score: 1256
Period size: 159 Copynumber: 5.7 Consensus size: 159
2072552 CGGGATTAGC
* *
2072562 AGATTCATCAGAGATGACTTGTGACAATGATGGTCCTTCCTCTGTGGGATTAGATTCCACATTGC
1 AGATTCATCAGAGATGACTTGTGACAAGGATGGTCC-T--TCTGTGGGATTTGATTCCACATTGC
* * * * * *
2072627 AGACCTCAACAAGATTAACCTCAAACCTCTGAACAAGCTCTTGATCATCAGAATTGCCGGACTGC
63 AGGCCTCAACAAGATCAACCTCAGACCTCTGAACAAGCTCTTTATCATCAGAATTGCCAGATTGC
* * *
2072692 AGTGAAGATGCCGGTTTAAGCTCTGGATTCGT
128 AGTGAAGATGCCAGTGTAAGCTCTGGATTGGT
* * * *
2072724 AGATTGATCAGAGAAT-ACCTGTGACAAGGATGATCCTTCTTTGGGATTTGATTCCACATTGCAG
1 AGATTCATCAGAG-ATGACTTGTGACAAGGATGGTCCTTCTGTGGGATTTGATTCCACATTGCAG
*
2072788 GCCTCAACAAGATCAACCTCAGACCTCTGAACAAGCTCTTTCTCATCAGAATTGCCAGATTGCAG
65 GCCTCAACAAGATCAACCTCAGACCTCTGAACAAGCTCTTTATCATCAGAATTGCCAGATTGCAG
* * * *
2072853 TGTATG-TGGCTGTGTAAGCTCTGGATTAGT
130 TG-AAGATGCCAGTGTAAGCTCTGGATTGGT
* * * * *
2072883 AGATTCATGAGAGATGACTTCTGACAAGGATTGTCCTCCTGTGGGATTTGATTCCACATTGCAGA
1 AGATTCATCAGAGATGACTTGTGACAAGGATGGTCCTTCTGTGGGATTTGATTCCACATTGCAGG
* * * *
2072948 CCTCAACAAGACCACCCTCAGACCTTTGAACTAGCTCTTTATCATCAGAATTGCCAGATTGCAGT
66 CCTCAACAAGATCAACCTCAGACCTCTGAACAAGCTCTTTATCATCAGAATTGCCAGATTGCAGT
* * * * *
2073013 GAAGAAGCCTGTGTAAGTTCAGGACTGGT
131 GAAGATGCCAGTGTAAGCTCTGGATTGGT
* * *
2073042 AGATTCATCAGGGATGACTTGTGACGAGGATGGTCCTTCTGAGGGATTTGATTCCACATTGCAGG
1 AGATTCATCAGAGATGACTTGTGACAAGGATGGTCCTTCTGTGGGATTTGATTCCACATTGCAGG
* * *
2073107 CCTCAAAAAGATCAACCTCGGACCTCTGAACAAGCTCTTTACCATCAGAATTGCCAGATTGCAGT
66 CCTCAACAAGATCAACCTCAGACCTCTGAACAAGCTCTTTATCATCAGAATTGCCAGATTGCAGT
2073172 GAAGATGCCAGTGTAAGCTCTGGATTGGT
131 GAAGATGCCAGTGTAAGCTCTGGATTGGT
* * * ** *
2073201 AGATTCATTAGCGATGGCTTGTGATGAGGATGGTCCCTCTGTGGGATTTGATTCCACATTGCAGG
1 AGATTCATCAGAGATGACTTGTGACAAGGATGGTCCTTCTGTGGGATTTGATTCCACATTGCAGG
*
2073266 CCTCAACAAGATCAACCTCAGACCTCTGAACAAGCTCTTTATCATCAGAATTGTCAGATTGCAGT
66 CCTCAACAAGATCAACCTCAGACCTCTGAACAAGCTCTTTATCATCAGAATTGCCAGATTGCAGT
* * *
2073331 AAAGATGCCAGCGTAAGCTCTAGATTGGT
131 GAAGATGCCAGTGTAAGCTCTGGATTGGT
* *
2073360 AGATTCATCAGAGATGGCTTGTGATAAGGATGGTCCTTCTGTGGGATTTGATTCCACATTGCAGG
1 AGATTCATCAGAGATGACTTGTGACAAGGATGGTCCTTCTGTGGGATTTGATTCCACATTGCAGG
* * * * *
2073425 CCCCAACATGACCAACCTCAGACCTCTGAGCAAGCTCTTTATTATCAGAAT
66 CCTCAACAAGATCAACCTCAGACCTCTGAACAAGCTCTTTATCATCAGAAT
2073476 CATTAGATTG
Statistics
Matches: 667, Mismatches: 81, Indels: 11
0.88 0.11 0.01
Matches are distributed among these distances:
158 4 0.01
159 629 0.94
160 2 0.00
161 1 0.00
162 29 0.04
163 2 0.00
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Consensus pattern (159 bp):
AGATTCATCAGAGATGACTTGTGACAAGGATGGTCCTTCTGTGGGATTTGATTCCACATTGCAGG
CCTCAACAAGATCAACCTCAGACCTCTGAACAAGCTCTTTATCATCAGAATTGCCAGATTGCAGT
GAAGATGCCAGTGTAAGCTCTGGATTGGT
Found at i:2074771 original size:72 final size:72
Alignment explanation
Indices: 2074563--2074773 Score: 244
Period size: 72 Copynumber: 2.9 Consensus size: 72
2074553 ATTTCAAAGT
* * *
2074563 AGGCTCTGCTTCA-ACTTCAGAATTATTCTCAACCATACCAAGTGCCTCCACCATGCCTGACAAA
1 AGGCTCTGATTCACA-TTCAGAATTATTCTCAACCATAGCAAGTGCATCCACCATGCCTGAC---
*
2074627 TTATCCGGACA
62 TTAACCGGACA
* * * * ** *
2074638 AGGCTCTGATTTACATTCAGAATTATTCTCAGCCATAGCAGGTGCATTCACTGTGCTTGACTTAA
1 AGGCTCTGATTCACATTCAGAATTATTCTCAACCATAGCAAGTGCATCCACCATGCCTGACTTAA
*
2074703 CCGGCCA
66 CCGGACA
** *
2074710 AGGCTCTGATTCACATTCAGAATTATTCTCAACCATAGCAAGTGTGTCCTCCATGCCTGACTTA
1 AGGCTCTGATTCACATTCAGAATTATTCTCAACCATAGCAAGTGCATCCACCATGCCTGACTTA
2074774 TCTGGACATG
Statistics
Matches: 113, Mismatches: 22, Indels: 5
0.81 0.16 0.04
Matches are distributed among these distances:
72 63 0.56
75 49 0.43
76 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.16, T:0.29
Consensus pattern (72 bp):
AGGCTCTGATTCACATTCAGAATTATTCTCAACCATAGCAAGTGCATCCACCATGCCTGACTTAA
CCGGACA
Found at i:2091537 original size:22 final size:23
Alignment explanation
Indices: 2091493--2091538 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
2091483 TTTAATTTAA
2091493 TTATTTTTAAATAAATTTAAATT
1 TTATTTTTAAATAAATTTAAATT
2091516 TTATTATTT-AATAAA-TTAAATT
1 TTATT-TTTAAATAAATTTAAATT
2091538 T
1 T
2091539 AAATATTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 8 0.36
23 11 0.50
24 3 0.14
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TTATTTTTAAATAAATTTAAATT
Found at i:2091545 original size:22 final size:22
Alignment explanation
Indices: 2091502--2091569 Score: 68
Period size: 22 Copynumber: 3.0 Consensus size: 22
2091492 ATTATTTTTA
* *
2091502 AATAAATTTAAATTTTATTATTT
1 AATAAA-TTAAATTTAAATATTT
2091525 AATAAATTAAATTTAAATATTT
1 AATAAATTAAATTTAAATATTT
*
2091547 --TAATATTTAATTTAAATAATTT
1 AATAA-ATTAAATTTAAAT-ATTT
2091569 A
1 A
2091570 TAAGTTTAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
20 3 0.08
21 12 0.31
22 18 0.46
23 6 0.15
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AATAAATTAAATTTAAATATTT
Found at i:2091568 original size:30 final size:30
Alignment explanation
Indices: 2091498--2091579 Score: 91
Period size: 30 Copynumber: 2.8 Consensus size: 30
2091488 TTTAATTATT
*
2091498 TTTAAATAAATTT-AAATTTTATTATTTAA
1 TTTAAATAAATTTAAAATTTTAATATTTAA
2091527 --TAAATTAAATTTAAATATTTTAATATTTAA
1 TTTAAA-TAAATTTAAA-ATTTTAATATTTAA
* *
2091557 TTTAAAT-AATTTATAAGTTTAAT
1 TTTAAATAAATTTAAAATTTTAAT
2091580 TAAGTTATTT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
27 4 0.09
28 7 0.16
29 9 0.20
30 20 0.44
31 1 0.02
32 4 0.09
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (30 bp):
TTTAAATAAATTTAAAATTTTAATATTTAA
Found at i:2091657 original size:32 final size:30
Alignment explanation
Indices: 2091593--2091657 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 30
2091583 GTTATTTTGT
*
2091593 TTTTAATTAATATTAAAAAAATTAATTTAA
1 TTTTAATTAATATTAAAAAAATTAATTAAA
*
2091623 TTTTAACTTAAGTTTTAAAATAAA-TAATTAAA
1 TTTTAA-TTAA-TATTAAAA-AAATTAATTAAA
2091655 TTT
1 TTT
2091658 GAGATTAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 6 0.20
31 4 0.13
32 17 0.57
33 3 0.10
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (30 bp):
TTTTAATTAATATTAAAAAAATTAATTAAA
Found at i:2092191 original size:11 final size:11
Alignment explanation
Indices: 2092175--2092240 Score: 54
Period size: 11 Copynumber: 6.4 Consensus size: 11
2092165 TATATATAAA
2092175 ATAATAAAAAT
1 ATAATAAAAAT
2092186 ATAATATAAAAT
1 ATAATA-AAAAT
2092198 AT-ATAAATAAT
1 ATAATAAA-AAT
2092209 AT-AT--AAAT
1 ATAATAAAAAT
*
2092217 AT-ATTAAAAT
1 ATAATAAAAAT
*
2092227 -TAATATAAAT
1 ATAATAAAAAT
2092237 ATAA
1 ATAA
2092241 ATTATGATAT
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
8 7 0.15
9 2 0.04
10 12 0.26
11 19 0.40
12 7 0.15
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
ATAATAAAAAT
Found at i:2092205 original size:20 final size:20
Alignment explanation
Indices: 2092163--2092271 Score: 75
Period size: 20 Copynumber: 5.2 Consensus size: 20
2092153 TTAATAATTT
*
2092163 TATATATATAAAATAATAAAAA
1 TATA-ATATAAAAT-ATATAAA
2092185 TATAATATAAAATATAT-AA
1 TATAATATAAAATATATAAA
2092204 -ATAATATATAAATATATTAAA
1 TATAATATA-AAATATA-TAAA
*
2092225 -ATTAATAT-AAATATA-AAT
1 TA-TAATATAAAATATATAAA
2092243 TATGATATATAAAACTCTATATAAA
1 TAT-A-ATATAAAA---TATATAAA
2092268 TATA
1 TATA
2092272 TCATTCAAAT
Statistics
Matches: 72, Mismatches: 3, Indels: 22
0.74 0.03 0.23
Matches are distributed among these distances:
18 11 0.15
19 11 0.15
20 15 0.21
21 15 0.21
22 10 0.14
24 5 0.07
25 5 0.07
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.37
Consensus pattern (20 bp):
TATAATATAAAATATATAAA
Found at i:2092233 original size:31 final size:29
Alignment explanation
Indices: 2092166--2092241 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 29
2092156 ATAATTTTAT
2092166 ATATATAAAATAATAAAAATATAATATAAA
1 ATATAT-AAATAATAAAAATATAATATAAA
2092196 ATATATAAATAATATATAAATAT-AT-TAAA
1 ATATATAAATAATA-A-AAATATAATATAAA
2092225 ATTAATATAAAT-ATAAA
1 A-T-ATATAAATAATAAA
2092242 TTATGATATA
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
28 1 0.02
29 14 0.33
30 13 0.31
31 14 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (29 bp):
ATATATAAATAATAAAAATATAATATAAA
Found at i:2092251 original size:40 final size:39
Alignment explanation
Indices: 2092162--2092256 Score: 104
Period size: 40 Copynumber: 2.4 Consensus size: 39
2092152 TTTAATAATT
*
2092162 TTATATATATAAAATAATAAAAATATAATATAAAATATA
1 TTATATATATAAAATAATAAAAATATAATATAAAATAAA
* *
2092201 -TAAATAATATATAAATATATTAAAAT-TAATATAAATATAAA
1 TTATAT-ATATA-AAATA-ATAAAAATATAATATAAA-ATAAA
2092242 TTATGATATATAAAA
1 TTAT-ATATATAAAA
2092257 CTCTATATAA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
38 4 0.09
39 5 0.11
40 14 0.30
41 14 0.30
42 7 0.15
43 2 0.04
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (39 bp):
TTATATATATAAAATAATAAAAATATAATATAAAATAAA
Found at i:2092560 original size:11 final size:11
Alignment explanation
Indices: 2092534--2092584 Score: 52
Period size: 11 Copynumber: 4.5 Consensus size: 11
2092524 TCATGCTAAA
2092534 AATATTAAATAT
1 AATA-TAAATAT
2092546 -ATATAAATAT
1 AATATAAATAT
*
2092556 AATATAAAAATT
1 AATATAAATA-T
2092568 AAT-TATAATAT
1 AATATA-AATAT
2092579 AATATA
1 AATATA
2092585 TTAATATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
10 7 0.21
11 17 0.52
12 9 0.27
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
AATATAAATAT
Found at i:2092561 original size:5 final size:5
Alignment explanation
Indices: 2092541--2092612 Score: 50
Period size: 5 Copynumber: 15.4 Consensus size: 5
2092531 AAAAATATTA
2092541 AATAT -ATAT AAATAT AATAT AA-A- AAT-T AATTAT AATAT AATAT -AT-T
1 AATAT AATAT -AATAT AATAT AATAT AATAT AA-TAT AATAT AATAT AATAT
** *
2092587 AATAT TTTAA AAT-T AATAT AATAT AA
1 AATAT AATAT AATAT AATAT AATAT AA
2092613 ATTATTAATT
Statistics
Matches: 52, Mismatches: 6, Indels: 18
0.68 0.08 0.24
Matches are distributed among these distances:
3 3 0.06
4 14 0.27
5 28 0.54
6 7 0.13
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
AATAT
Found at i:2092576 original size:18 final size:17
Alignment explanation
Indices: 2092551--2092651 Score: 86
Period size: 18 Copynumber: 6.0 Consensus size: 17
2092541 AATATATATA
2092551 AATATAATATAAAAATT
1 AATATAATATAAAAATT
*
2092568 AATTATAATATAATATATT
1 AA-TATAATATAA-AAATT
*
2092587 AATAT--T-TTAAAATT
1 AATATAATATAAAAATT
*
2092601 AATATAATATAAATTATT
1 AATATAATATAAA-AATT
2092619 AAT-T-ATATAAAAATT
1 AATATAATATAAAAATT
* *
2092634 TATATAAATATATAAATT
1 AATAT-AATATAAAAATT
2092652 CTTAAATTTA
Statistics
Matches: 67, Mismatches: 8, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
14 9 0.13
15 7 0.10
16 10 0.15
17 6 0.09
18 29 0.43
19 6 0.09
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AATATAATATAAAAATT
Found at i:2092632 original size:33 final size:33
Alignment explanation
Indices: 2092557--2092645 Score: 110
Period size: 33 Copynumber: 2.7 Consensus size: 33
2092547 TATAAATATA
2092557 ATATAAAAATTAATTATAATAT-AATATATTAAT
1 ATATAAAAATTAA-TATAATATAAATATATTAAT
* *
2092590 ATTTTAAAATTAATATAATATAAAT-TATTAATT
1 ATATAAAAATTAATATAATATAAATATATTAA-T
*
2092623 ATATAAAAATTTATATAAATATA
1 ATATAAAAATTAATAT-AATATA
2092646 TAAATTCTTA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
32 14 0.29
33 28 0.58
34 6 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (33 bp):
ATATAAAAATTAATATAATATAAATATATTAAT
Found at i:2092862 original size:18 final size:19
Alignment explanation
Indices: 2092818--2092876 Score: 68
Period size: 18 Copynumber: 3.2 Consensus size: 19
2092808 ATTTAAATTT
2092818 ATTTATAAATATTAATATAA
1 ATTTA-AAATATTAATATAA
**
2092838 AAATAAAAT-TTAATATAA
1 ATTTAAAATATTAATATAA
*
2092856 ATTT-AAATAATAATATAA
1 ATTTAAAATATTAATATAA
2092874 ATT
1 ATT
2092877 ATTAGATTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
17 4 0.12
18 22 0.67
19 4 0.12
20 3 0.09
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTTAAAATATTAATATAA
Found at i:2093460 original size:17 final size:16
Alignment explanation
Indices: 2093427--2093475 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
2093417 TTAAATAAAA
* *
2093427 TTATTTTTTTGATATT
1 TTATTTTTTTTAAATT
2093443 TTAATTTTTTTTAAATT
1 TT-ATTTTTTTTAAATT
2093460 TTATTATATTTTTAAA
1 TTATT-T-TTTTTAAA
2093476 AATTAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 5 0.18
17 15 0.54
18 8 0.29
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (16 bp):
TTATTTTTTTTAAATT
Found at i:2093865 original size:33 final size:32
Alignment explanation
Indices: 2093825--2093891 Score: 80
Period size: 32 Copynumber: 2.0 Consensus size: 32
2093815 ACATTATTTA
* *
2093825 AATATAAATATAAAAATATAATTTTTTAAATATAT
1 AATA-AAAT-TAAAAATATAA-ATGTTAAATATAT
*
2093860 AATAAAATTAAAAATTTAAATGTTAAATATAT
1 AATAAAATTAAAAATATAAATGTTAAATATAT
2093892 TTATAATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
32 11 0.38
33 10 0.34
34 4 0.14
35 4 0.14
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (32 bp):
AATAAAATTAAAAATATAAATGTTAAATATAT
Found at i:2094617 original size:18 final size:17
Alignment explanation
Indices: 2094576--2094650 Score: 55
Period size: 18 Copynumber: 4.2 Consensus size: 17
2094566 AAATCTGATC
2094576 TATATTTTATATATTTA
1 TATATTTTATATATTTA
* *
2094593 TACTATTTTTTATTATTTT
1 TA-TATTTTATA-TATTTA
*
2094612 TATATTATAATCATATTTA
1 TATATT-TTAT-ATATTTA
*
2094631 -A-ATTATTATATATTCA
1 TATATT-TTATATATTTA
2094647 TATA
1 TATA
2094651 AATTTTATTA
Statistics
Matches: 45, Mismatches: 7, Indels: 11
0.71 0.11 0.17
Matches are distributed among these distances:
16 6 0.13
17 10 0.22
18 14 0.31
19 14 0.31
20 1 0.02
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (17 bp):
TATATTTTATATATTTA
Found at i:2097647 original size:21 final size:18
Alignment explanation
Indices: 2097611--2097658 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 18
2097601 AGTTTGGCTT
2097611 TTTAATTTTTTTATAAAA
1 TTTAATTTTTTTATAAAA
2097629 TTTAATTATTTATTAATAAAA
1 TTTAATT-TTT-TT-ATAAAA
*
2097650 ATT-ATTTTT
1 TTTAATTTTT
2097659 ACATTAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 7 0.27
19 6 0.23
20 5 0.19
21 8 0.31
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
TTTAATTTTTTTATAAAA
Found at i:2097672 original size:31 final size:30
Alignment explanation
Indices: 2097637--2097702 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
2097627 AATTTAATTA
2097637 TTTATT-AATAAAAATTATTTTTACATTAAAT
1 TTTATTAAATAAAAATTA-TTTTA-ATTAAAT
* *
2097668 TTTATTAAATAATAATTATTTTATTTAAAT
1 TTTATTAAATAAAAATTATTTTAATTAAAT
2097698 TTTAT
1 TTTAT
2097703 ATTTAAAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
30 11 0.34
31 11 0.34
32 10 0.31
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (30 bp):
TTTATTAAATAAAAATTATTTTAATTAAAT
Found at i:2097747 original size:21 final size:22
Alignment explanation
Indices: 2097714--2097770 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 22
2097704 TTTAAAATAA
2097714 AATATA-AATTTTAAATGA-GTT
1 AATATATAA-TTTAAATGACGTT
* *
2097735 AATATATAATTT-AATTACTTT
1 AATATATAATTTAAATGACGTT
*
2097756 AATATATAAATTAAA
1 AATATATAATTTAAA
2097771 AATAAAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
20 4 0.13
21 22 0.73
22 4 0.13
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.44
Consensus pattern (22 bp):
AATATATAATTTAAATGACGTT
Found at i:2098448 original size:22 final size:22
Alignment explanation
Indices: 2098423--2098477 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
2098413 TTATTTTAAA
*
2098423 AATATTAAAATATTATTAT-ATT
1 AATATTTAAATATT-TTATAATT
*
2098445 AATATTTATATATTTTATAATT
1 AATATTTAAATATTTTATAATT
2098467 AA-ATTTAAATA
1 AATATTTAAATA
2098478 AAAATATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 12 0.41
22 17 0.59
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
AATATTTAAATATTTTATAATT
Found at i:2098832 original size:5 final size:5
Alignment explanation
Indices: 2098822--2098852 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
2098812 GAATCAAATA
*
2098822 AATTT AATTT AATTT AAATT AATTT AATTT A
1 AATTT AATTT AATTT AATTT AATTT AATTT A
2098853 TAAATATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (5 bp):
AATTT
Found at i:2098845 original size:15 final size:16
Alignment explanation
Indices: 2098820--2098852 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
2098810 AAGAATCAAA
2098820 TAAATTTAATTTAATT
1 TAAATTTAATTTAATT
2098836 TAAA-TTAATTTAATT
1 TAAATTTAATTTAATT
2098851 TA
1 TA
2098853 TAAATATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TAAATTTAATTTAATT
Found at i:2103656 original size:2 final size:2
Alignment explanation
Indices: 2103649--2103679 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2103639 AGCAAGTGTA
2103649 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2103680 AAGATTAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2105573 original size:11 final size:11
Alignment explanation
Indices: 2105539--2105573 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
2105529 AATATGATAC
*
2105539 AATATGAAAAT
1 AATATAAAAAT
*
2105550 AATATAAATAT
1 AATATAAAAAT
2105561 AATATAAAAAT
1 AATATAAAAAT
2105572 AA
1 AA
2105574 AAATATCTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (11 bp):
AATATAAAAAT
Found at i:2106463 original size:3 final size:3
Alignment explanation
Indices: 2106455--2106483 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2106445 ACTATAAGAA
2106455 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2106484 AGGGGAGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2107878 original size:62 final size:62
Alignment explanation
Indices: 2107806--2107938 Score: 146
Period size: 62 Copynumber: 2.1 Consensus size: 62
2107796 TGATTAATAA
* *
2107806 TTAAATAATTTTTTAATTAATCGATATTTATAAATATT-AATTAAAA-ATTATTTAATTAT-TAT
1 TTAAA-AATTTTATAATTAAT--ATA-TTATAAATATTAAATTAAAATAATATTTAATTATATAT
2107868 T
62 T
* *** *
2107869 TTAAAAATTTTATATTTAATATATTATTTTTATTAAATTAAAATAATATTTAATTATATTTT
1 TTAAAAATTTTATAATTAATATATTATAAATATTAAATTAAAATAATATTTAATTATATATT
2107931 TTAAAAAT
1 TTAAAAAT
2107939 ATAACTTTAA
Statistics
Matches: 60, Mismatches: 7, Indels: 7
0.81 0.09 0.09
Matches are distributed among these distances:
59 8 0.13
60 11 0.18
61 12 0.20
62 24 0.40
63 5 0.08
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.53
Consensus pattern (62 bp):
TTAAAAATTTTATAATTAATATATTATAAATATTAAATTAAAATAATATTTAATTATATATT
Found at i:2108605 original size:28 final size:28
Alignment explanation
Indices: 2108527--2108607 Score: 71
Period size: 28 Copynumber: 2.9 Consensus size: 28
2108517 AAAAAATCTC
*
2108527 TATATTAT-ATATTT-TTAATTGAATATT
1 TATATTATAAT-TTTATTAATTAAATATT
* * *
2108554 TA-A-AAAAATTTTAATTTATATAAATATT
1 TATATTATAATTTT-ATTAAT-TAAATATT
2108582 TATATTATAATTTTATTAATTAAATA
1 TATATTATAATTTTATTAATTAAATA
2108608 AATATTTTAT
Statistics
Matches: 41, Mismatches: 7, Indels: 11
0.69 0.12 0.19
Matches are distributed among these distances:
25 4 0.10
26 3 0.07
27 6 0.15
28 15 0.37
29 6 0.15
30 7 0.17
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (28 bp):
TATATTATAATTTTATTAATTAAATATT
Found at i:2109486 original size:19 final size:19
Alignment explanation
Indices: 2109452--2109499 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
2109442 AAAATTAATT
2109452 AAAATAT-AATACGATAAA
1 AAAATATAAATACGATAAA
* *
2109470 AAAATATAAATATGATATA
1 AAAATATAAATACGATAAA
*
2109489 AATATATAAAT
1 AAAATATAAAT
2109500 GTATTAAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 7 0.27
19 19 0.73
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (19 bp):
AAAATATAAATACGATAAA
Found at i:2109807 original size:16 final size:16
Alignment explanation
Indices: 2109783--2109833 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
2109773 TTGAACAATA
*
2109783 ATTTAATTATTTATAT
1 ATTTTATTATTTATAT
*
2109799 ATTTTATTATATTTAAATT
1 ATTTTA-T-TATTTATA-T
2109818 ATTTTA-TATTTATAT
1 ATTTTATTATTTATAT
2109833 A
1 A
2109834 AATTTAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
15 2 0.07
16 12 0.41
17 1 0.03
18 7 0.24
19 7 0.24
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
ATTTTATTATTTATAT
Found at i:2109813 original size:9 final size:8
Alignment explanation
Indices: 2109790--2109890 Score: 52
Period size: 8 Copynumber: 12.1 Consensus size: 8
2109780 ATAATTTAAT
2109790 TATTTATA
1 TATTTATA
2109798 TATTTTATTA
1 TA-TTTA-TA
*
2109808 TATTTAAA
1 TATTTATA
2109816 TTATTT-TA
1 -TATTTATA
2109824 TATTTATA
1 TATTTATA
2109832 TAAATTTA-A
1 T--ATTTATA
2109841 TATGTTATAA
1 TAT-TTAT-A
2109851 TTCATTT-TA
1 -T-ATTTATA
2109860 TA-TTA-A
1 TATTTATA
*
2109866 T-TTTAAAA
1 TATTT-ATA
2109874 TATTTATA
1 TATTTATA
2109882 TATTTATA
1 TATTTATA
2109890 T
1 T
2109891 CTTATTCATT
Statistics
Matches: 74, Mismatches: 3, Indels: 32
0.68 0.03 0.29
Matches are distributed among these distances:
6 6 0.08
7 9 0.12
8 24 0.32
9 19 0.26
10 11 0.15
11 3 0.04
12 2 0.03
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (8 bp):
TATTTATA
Found at i:2109813 original size:26 final size:26
Alignment explanation
Indices: 2109782--2109890 Score: 89
Period size: 26 Copynumber: 4.0 Consensus size: 26
2109772 TTTGAACAAT
2109782 AATTTAATTATTTATATATTT-TATTA
1 AATTTAATTATTTATATATTTATA-TA
*
2109808 TATTTAAATTATTT-TATATTTATATA
1 AATTT-AATTATTTATATATTTATATA
2109834 AATTTAA-TATGTTATAATTCATTTTATATTA
1 AATTTAATTAT-TTAT-A-T-A-TTTATA-TA
* *
2109865 ATTTTAAAATATTTATATATTTATAT
1 AATTT-AATTATTTATATATTTATAT
2109891 CTTATTCATT
Statistics
Matches: 69, Mismatches: 3, Indels: 21
0.74 0.03 0.23
Matches are distributed among these distances:
24 3 0.04
25 4 0.06
26 18 0.26
27 12 0.17
28 7 0.10
29 2 0.03
30 7 0.10
31 7 0.10
32 6 0.09
33 3 0.04
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (26 bp):
AATTTAATTATTTATATATTTATATA
Found at i:2109837 original size:20 final size:19
Alignment explanation
Indices: 2109798--2109837 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
2109788 ATTATTTATA
*
2109798 TATTTTATTATATTTAAAT
1 TATTTTATTATATATAAAT
*
2109817 TATTTTATATTTATATAAAT
1 TATTTTAT-TATATATAAAT
2109837 T
1 T
2109838 TAATATGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTTTATTATATATAAAT
Found at i:2109849 original size:52 final size:58
Alignment explanation
Indices: 2109782--2109890 Score: 135
Period size: 57 Copynumber: 2.0 Consensus size: 58
2109772 TTTGAACAAT
*
2109782 AATTTAATTATTTAT-A-T-A-TTT-TATT-ATATTTAAATTATTT-TATATTTATATA
1 AATTTAATTATTTATAATTCATTTTATATTAAT-TTTAAAATATTTATATATTTATATA
2109834 AATTTAA-TATGTTATAATTCATTTTATATTAATTTTAAAATATTTATATATTTATAT
1 AATTTAATTAT-TTATAATTCATTTTATATTAATTTTAAAATATTTATATATTTATAT
2109891 CTTATTCATT
Statistics
Matches: 48, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
51 3 0.06
52 11 0.23
53 1 0.02
54 1 0.02
55 1 0.02
56 3 0.06
57 15 0.31
58 13 0.27
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (58 bp):
AATTTAATTATTTATAATTCATTTTATATTAATTTTAAAATATTTATATATTTATATA
Found at i:2109863 original size:36 final size:33
Alignment explanation
Indices: 2109790--2109863 Score: 87
Period size: 34 Copynumber: 2.1 Consensus size: 33
2109780 ATAATTTAAT
*
2109790 TATTTATATATTTTATTATATTTAAATTATTTTA
1 TATTTATATAATTTA-TATATTTAAATTATTTTA
2109824 TATTTATATAAATTTA-ATATGTTATAATTCATTTTA
1 TATTTATAT-AATTTATATAT-TTA-AATT-ATTTTA
2109860 TATT
1 TATT
2109864 AATTTTAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
33 4 0.11
34 12 0.34
35 9 0.26
36 10 0.29
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (33 bp):
TATTTATATAATTTATATATTTAAATTATTTTA
Found at i:2110549 original size:26 final size:26
Alignment explanation
Indices: 2110520--2110569 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
2110510 ATTTTTATAT
2110520 TTTTACAATAATTTTAAA-TAAAATTA
1 TTTTACAATAA-TTTAAATTAAAATTA
**
2110546 TTTTTTAATAATTTAAATTAAAAT
1 TTTTACAATAATTTAAATTAAAAT
2110570 AAACCCAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 6 0.29
26 15 0.71
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (26 bp):
TTTTACAATAATTTAAATTAAAATTA
Found at i:2110780 original size:33 final size:33
Alignment explanation
Indices: 2110743--2110808 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 33
2110733 TACCGTGACC
*
2110743 ATTGATTTTATTCGGATTCAAAGTAAATATCTT
1 ATTGATTTTATTCGGATTCAAAATAAATATCTT
2110776 ATTGATTTTATTCGGATTCAAAATAAATATCTT
1 ATTGATTTTATTCGGATTCAAAATAAATATCTT
2110809 TTTAACTGCT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.11, T:0.45
Consensus pattern (33 bp):
ATTGATTTTATTCGGATTCAAAATAAATATCTT
Found at i:2111200 original size:24 final size:24
Alignment explanation
Indices: 2111155--2111200 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
2111145 TTAAAAATCA
*
2111155 AATTGAACCAAATACATTTAATTG
1 AATTGAACCAAATACATATAATTG
*
2111179 AATTGAACCTAAATTCA-ATAAT
1 AATTGAACC-AAATACATATAAT
2111201 AATAATAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 13 0.68
25 6 0.32
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.33
Consensus pattern (24 bp):
AATTGAACCAAATACATATAATTG
Found at i:2111504 original size:17 final size:17
Alignment explanation
Indices: 2111482--2111536 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 17
2111472 AATTTAAGAT
2111482 ATTTTATATTTATATAA
1 ATTTTATATTTATATAA
*
2111499 ATTTTAAAATGTTA-AT-A
1 ATTTT-ATAT-TTATATAA
2111516 A-TTTATA-TTATATAA
1 ATTTTATATTTATATAA
2111531 ATTTTA
1 ATTTTA
2111537 AAATATATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 11
0.70 0.05 0.25
Matches are distributed among these distances:
13 3 0.10
14 2 0.06
15 4 0.13
16 7 0.23
17 7 0.23
18 5 0.16
19 3 0.10
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
ATTTTATATTTATATAA
Found at i:2112200 original size:2 final size:2
Alignment explanation
Indices: 2112193--2112218 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2112183 CCAAAAGTTA
2112193 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
2112219 GCATTCTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2115951 original size:30 final size:29
Alignment explanation
Indices: 2115899--2115968 Score: 77
Period size: 30 Copynumber: 2.4 Consensus size: 29
2115889 TTCGAGTATG
*
2115899 TTTTATTATTTAATTAATTTAAATATTTA
1 TTTTATTATTTAATTAAGTTAAATATTTA
* * *
2115928 TTTTATTTATTTATTTTAGTTAAATTTTTA
1 TTTTA-TTATTTAATTAAGTTAAATATTTA
* *
2115958 ATTTAATATTT
1 TTTTATTATTT
2115969 TTTAAAAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 10 0.29
30 24 0.71
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (29 bp):
TTTTATTATTTAATTAAGTTAAATATTTA
Found at i:2116198 original size:18 final size:17
Alignment explanation
Indices: 2116175--2116210 Score: 63
Period size: 18 Copynumber: 2.1 Consensus size: 17
2116165 GACTAAATTA
2116175 ATATTTAATAAACTATTT
1 ATATTTAATAAA-TATTT
2116193 ATATTTAATAAATATTT
1 ATATTTAATAAATATTT
2116210 A
1 A
2116211 AAATATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
ATATTTAATAAATATTT
Found at i:2116209 original size:11 final size:11
Alignment explanation
Indices: 2116193--2116226 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
2116183 TAAACTATTT
2116193 ATATTTAATAA
1 ATATTTAATAA
2116204 ATATTTAA-AA
1 ATATTTAATAA
2116214 TATATTTAATAA
1 -ATATTTAATAA
2116226 A
1 A
2116227 ATATAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
10 2 0.10
11 17 0.81
12 2 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
ATATTTAATAA
Found at i:2117182 original size:15 final size:16
Alignment explanation
Indices: 2117153--2117182 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2117143 TATTAAAAAT
2117153 ATATATTTTAAAATTA
1 ATATATTTTAAAATTA
2117169 ATAT-TTTTAAAATT
1 ATATATTTTAAAATT
2117183 TTATAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATATATTTTAAAATTA
Found at i:2118055 original size:9 final size:10
Alignment explanation
Indices: 2118030--2118073 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
2118020 ATATAATGAA
2118030 AAAAAATTTT
1 AAAAAATTTT
2118040 AAAAAATTTT
1 AAAAAATTTT
* **
2118050 ATAAATAGATT
1 A-AAAAATTTT
2118061 AAAAAATTTT
1 AAAAAATTTT
2118071 AAA
1 AAA
2118074 TGCTTTATTT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
10 20 0.74
11 7 0.26
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.36
Consensus pattern (10 bp):
AAAAAATTTT
Found at i:2118366 original size:17 final size:18
Alignment explanation
Indices: 2118346--2118385 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
2118336 ATGATATATT
2118346 TAAAAAGATTAA-TTAAA
1 TAAAAAGATTAATTTAAA
*
2118363 TAAAAATATTAATTTAAA
1 TAAAAAGATTAATTTAAA
2118381 -AAAAA
1 TAAAAA
2118386 AAAGTAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (18 bp):
TAAAAAGATTAATTTAAA
Found at i:2118833 original size:44 final size:44
Alignment explanation
Indices: 2118783--2118871 Score: 144
Period size: 44 Copynumber: 2.0 Consensus size: 44
2118773 CAAACAAAAC
2118783 TTTTATAAATTTAGATCAATTTGACT-CGAATTATGATTTATTAA
1 TTTTATAAATTTAGATCAATTTGA-TACGAATTATGATTTATTAA
* *
2118827 TTTTATAAATTTGGATCAGTTTGATACGAATTATGATTTATTAA
1 TTTTATAAATTTAGATCAATTTGATACGAATTATGATTTATTAA
2118871 T
1 T
2118872 AAAACTATAT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
43 1 0.02
44 41 0.98
ACGTcount: A:0.35, C:0.06, G:0.11, T:0.48
Consensus pattern (44 bp):
TTTTATAAATTTAGATCAATTTGATACGAATTATGATTTATTAA
Found at i:2123509 original size:15 final size:16
Alignment explanation
Indices: 2123473--2123512 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
2123463 TTTAATATTT
*
2123473 ATAAAATTTTTAATTAA
1 ATAAAA-TTATAATTAA
2123490 ATAAAATTATAATT-A
1 ATAAAATTATAATTAA
2123505 ATAAAATT
1 ATAAAATT
2123513 TATTTTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.41
16 7 0.32
17 6 0.27
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAAAATTATAATTAA
Found at i:2123515 original size:16 final size:17
Alignment explanation
Indices: 2123473--2123515 Score: 63
Period size: 16 Copynumber: 2.6 Consensus size: 17
2123463 TTTAATATTT
*
2123473 ATAAAATTTTTAATTAA
1 ATAAAATTTATAATTAA
2123490 ATAAAA-TTATAATT-A
1 ATAAAATTTATAATTAA
2123505 ATAAAATTTAT
1 ATAAAATTTAT
2123516 TTTAAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 7 0.29
16 11 0.46
17 6 0.25
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAAAATTTATAATTAA
Found at i:2123781 original size:24 final size:23
Alignment explanation
Indices: 2123754--2123806 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 23
2123744 ACATGAATAT
*
2123754 AATATAAATATACAAATATATTAA
1 AATATAAATAAACAAATA-ATTAA
* *
2123778 AATATAGATAAACTAATAATTAA
1 AATATAAATAAACAAATAATTAA
*
2123801 CATATA
1 AATATA
2123807 GAAATTTATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 10 0.40
24 15 0.60
ACGTcount: A:0.60, C:0.06, G:0.02, T:0.32
Consensus pattern (23 bp):
AATATAAATAAACAAATAATTAA
Found at i:2124489 original size:11 final size:11
Alignment explanation
Indices: 2124442--2124489 Score: 53
Period size: 11 Copynumber: 4.2 Consensus size: 11
2124432 AAATATACAA
2124442 AATATAAAAAT
1 AATATAAAAAT
*
2124453 ATGACATAAAAAT
1 A--ATATAAAAAT
2124466 AAT-TAAAACAT
1 AATATAAAA-AT
2124477 AATATAAAAAT
1 AATATAAAAAT
2124488 AA
1 AA
2124490 ATGATTCGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
10 5 0.16
11 11 0.35
12 5 0.16
13 10 0.32
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.25
Consensus pattern (11 bp):
AATATAAAAAT
Found at i:2124649 original size:26 final size:27
Alignment explanation
Indices: 2124599--2124651 Score: 76
Period size: 25 Copynumber: 2.0 Consensus size: 27
2124589 ATATTAATTT
2124599 TTTCTTTTATTTCTCTCTCTCTTTTTC
1 TTTCTTTTATTTCTCTCTCTCTTTTTC
2124626 TTTC-TTTATTT-T-TCATCTCTTTTTC
1 TTTCTTTTATTTCTCTC-TCTCTTTTTC
2124651 T
1 T
2124652 ATGATATGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
24 2 0.08
25 12 0.48
26 7 0.28
27 4 0.16
ACGTcount: A:0.06, C:0.23, G:0.00, T:0.72
Consensus pattern (27 bp):
TTTCTTTTATTTCTCTCTCTCTTTTTC
Found at i:2124816 original size:22 final size:23
Alignment explanation
Indices: 2124784--2124827 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
2124774 TATATTTAAA
*
2124784 ATATAACATAAAAATA-ATATGC
1 ATATAAAATAAAAATATATATGC
*
2124806 ATATAAAATAAATATATATATG
1 ATATAAAATAAAAATATATATG
2124828 TAAAAATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.32
Consensus pattern (23 bp):
ATATAAAATAAAAATATATATGC
Found at i:2124886 original size:21 final size:21
Alignment explanation
Indices: 2124834--2124910 Score: 72
Period size: 21 Copynumber: 3.8 Consensus size: 21
2124824 TATGTAAAAA
*
2124834 TATATAAAAATA-AAAATAAAT
1 TATATAAAAATATAAAA-AATT
*
2124855 TAT-T-AATATATAAAAAATT
1 TATATAAAAATATAAAAAATT
*
2124874 TATATAAAAATAT-AATAATT
1 TATATAAAAATATAAAAAATT
*
2124894 TAAATAAAAAATATAAA
1 TATAT-AAAAATATAAA
2124911 TACTAATATA
Statistics
Matches: 46, Mismatches: 5, Indels: 9
0.77 0.08 0.15
Matches are distributed among these distances:
19 11 0.24
20 16 0.35
21 17 0.37
22 2 0.04
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (21 bp):
TATATAAAAATATAAAAAATT
Found at i:2124919 original size:33 final size:32
Alignment explanation
Indices: 2124806--2124926 Score: 84
Period size: 33 Copynumber: 3.7 Consensus size: 32
2124796 AATAATATGC
* * * *
2124806 ATATAAA-ATAAATATATATATGTAAA-AATAT
1 ATATAAATAAAAATATATA-ATTTAAATAAAAA
* * * *
2124837 ATAAAAATAAAAATAAATTATTAATATATAAAAA
1 ATATAAATAAAAATATATAATT--TAAATAAAAA
* *
2124871 ATTTATATAAAAATATAATAATTTAAATAAAAA
1 ATATAAATAAAAATAT-ATAATTTAAATAAAAA
**
2124904 ATATAAATACTAATATATAATTT
1 ATATAAATAAAAATATATAATTT
2124927 TTTATCTTTT
Statistics
Matches: 67, Mismatches: 18, Indels: 9
0.71 0.19 0.10
Matches are distributed among these distances:
31 8 0.12
32 15 0.22
33 24 0.36
34 15 0.22
35 5 0.07
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.36
Consensus pattern (32 bp):
ATATAAATAAAAATATATAATTTAAATAAAAA
Found at i:2127018 original size:2 final size:2
Alignment explanation
Indices: 2127011--2127056 Score: 56
Period size: 2 Copynumber: 23.0 Consensus size: 2
2127001 GGCAAATGTA
* * * *
2127011 AT AT AT AT AT AT AT AC AT AG AT AG AT AG AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2127053 AT AT
1 AT AT
2127057 GCATGTAGTT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (2 bp):
AT
Found at i:2129251 original size:3 final size:3
Alignment explanation
Indices: 2129243--2129271 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
2129233 ATATTCAATG
2129243 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2129272 CCCGCCTCGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2130070 original size:16 final size:16
Alignment explanation
Indices: 2130049--2130126 Score: 61
Period size: 17 Copynumber: 4.8 Consensus size: 16
2130039 TTAAAATAAT
*
2130049 ATTTTAAATTTATTAA
1 ATTTTAAATATATTAA
* *
2130065 ATTTTATATAATATAAA
1 ATTTTAAAT-ATATTAA
*
2130082 ATATT-AATATATTAA
1 ATTTTAAATATATTAA
*
2130097 ATTTTATAA-AAATATATA
1 ATTTTA-AATATAT-TA-A
2130115 ATTTTAAATATA
1 ATTTTAAATATA
2130127 ATTATAAAAT
Statistics
Matches: 47, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
15 10 0.21
16 13 0.28
17 15 0.32
18 9 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTTTAAATATATTAA
Found at i:2130135 original size:27 final size:26
Alignment explanation
Indices: 2130062--2130174 Score: 99
Period size: 27 Copynumber: 4.3 Consensus size: 26
2130052 TTAAATTTAT
*
2130062 TAAATTT-TATATAATATAAAATAT-
1 TAAATTTAAATATAATATAAAATATA
* *
2130086 TAATATATTAAATTTTATA-AAAATATA
1 TAA-AT-TTAAATATAATATAAAATATA
*
2130113 TAATTTTAAATATAATTATAAAATATA
1 TAAATTTAAATATAA-TATAAAATATA
* *
2130140 AAAATATAACATA-AATATATAAATATA
1 TAAATTTAA-ATATAATATA-AAATATA
2130167 TAAATTTA
1 TAAATTTA
2130175 TTATTAATTA
Statistics
Matches: 70, Mismatches: 11, Indels: 13
0.74 0.12 0.14
Matches are distributed among these distances:
24 3 0.04
25 10 0.14
26 16 0.23
27 38 0.54
28 3 0.04
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.42
Consensus pattern (26 bp):
TAAATTTAAATATAATATAAAATATA
Found at i:2130145 original size:21 final size:21
Alignment explanation
Indices: 2130120--2130169 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
2130110 ATATAATTTT
*
2130120 AAATATAATTATAAA-ATATAA
1 AAATATAA-CATAAATATATAA
2130141 AAATATAACATAAATATATAA
1 AAATATAACATAAATATATAA
*
2130162 ATATATAA
1 AAATATAA
2130170 ATTTATTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
20 5 0.19
21 21 0.81
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (21 bp):
AAATATAACATAAATATATAA
Done.