Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 5 of 106
Found at i:2171703 original size:26 final size:26
Alignment explanation
Indices: 2171651--2171703 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
2171641 ATAGGTAAAA
**
2171651 ATAAAAATTTTAATTTTTTTAAAATT
1 ATAAAAATTTTAATTTTTAAAAAATT
*
2171677 ATAAATATTTT-ATTTTTAAAAATATT
1 ATAAAAATTTTAATTTTTAAAAA-ATT
2171703 A
1 A
2171704 ATTTTAAAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 9 0.39
26 14 0.61
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (26 bp):
ATAAAAATTTTAATTTTTAAAAAATT
Found at i:2177651 original size:28 final size:28
Alignment explanation
Indices: 2177619--2177676 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
2177609 GCGATGGAAG
2177619 TAAGTTCGAAATAAATGACGAGATTTAC
1 TAAGTTCGAAATAAATGACGAGATTTAC
*
2177647 TAAGTTGGAAATAAATGACGAGATTTAC
1 TAAGTTCGAAATAAATGACGAGATTTAC
2177675 TA
1 TA
2177677 GTTAATTCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.43, C:0.09, G:0.19, T:0.29
Consensus pattern (28 bp):
TAAGTTCGAAATAAATGACGAGATTTAC
Found at i:2178754 original size:23 final size:22
Alignment explanation
Indices: 2178728--2178770 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
2178718 TTAATTGATA
*
2178728 TTAAATTCAAATTAAATATTTAT
1 TTAAATTCAAAATAAA-ATTTAT
*
2178751 TTAAATTTAAAATAAAATTT
1 TTAAATTCAAAATAAAATTT
2178771 GAAAACTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (22 bp):
TTAAATTCAAAATAAAATTTAT
Found at i:2179412 original size:28 final size:28
Alignment explanation
Indices: 2179381--2179437 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
2179371 AAAAATAAAC
2179381 AAACAAATAATTTATATTTAATATTTTT
1 AAACAAATAATTTATATTTAATATTTTT
2179409 AAACAAATAATTTATATTTAATATTTTT
1 AAACAAATAATTTATATTTAATATTTTT
2179437 A
1 A
2179438 CTTTTATCTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (28 bp):
AAACAAATAATTTATATTTAATATTTTT
Found at i:2179456 original size:12 final size:12
Alignment explanation
Indices: 2179439--2179476 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
2179429 ATATTTTTAC
2179439 TTTTATCTGT-AT
1 TTTTATCT-TAAT
*
2179451 TTTTATATTAAT
1 TTTTATCTTAAT
2179463 TTTTATCTTAAT
1 TTTTATCTTAAT
2179475 TT
1 TT
2179477 GTATAAAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 1 0.04
12 22 0.96
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (12 bp):
TTTTATCTTAAT
Found at i:2181966 original size:212 final size:212
Alignment explanation
Indices: 2181593--2181985 Score: 612
Period size: 212 Copynumber: 1.9 Consensus size: 212
2181583 AAGTTTAATG
* *
2181593 AATCATGATGTTCTAGATGTTTGATCAAAATAAAAAATTTTCTTGAAATGAAGAAGGCACTTTGA
1 AATCATGATGTTCTAAATGTTTAATCAAAATAAAAAATTTTCTTGAAATGAAGAAGGCACTTTGA
* * * * **
2181658 TGGGGCTAAAATTTTTGTAATTTCTAGCATCATTTTATACTTATGCTAGTAGTTGGTGAATTTTT
66 TGGGGCTAAAATTTTTGCAACTTCTAGCATCATTTTAAACTTATGCTAGTAATTGGTGAATTGAT
*
2181723 GAAAACCAGAGTATAGACATGGAAGTAATTCTAAAATAAAGTAGTTGAATGTGGTAGAGGGAAAC
131 GAAAACCAGAGCATAGACATGGAAGTAATTCTAAAATAAAGTAGTTGAATGTGGTAGAGGGAAAC
2181788 CCAAATGGTGTATTTAC
196 CCAAATGGTGTATTTAC
* *
2181805 AATCATTGATGTTCTAAATGTTTAATTAAAAT-AAAAATTTTGTTGAAATGAAGAAGGCACTTTG
1 AATCA-TGATGTTCTAAATGTTTAATCAAAATAAAAAATTTTCTTGAAATGAAGAAGGCACTTTG
* *
2181869 ATGGGGGC-AAAATTTTTTGCAACTTCTAGCATTATTTTAAACTTATGCTTGTAATTGGTGAATT
65 AT-GGGGCTAAAA-TTTTTGCAACTTCTAGCATCATTTTAAACTTATGCTAGTAATTGGTGAATT
*
2181933 GAT-AAAACCAGAGCATAGACATGGAAGTAATTCTAAAATAGAGTAGTTGAATG
128 GATGAAAACCAGAGCATAGACATGGAAGTAATTCTAAAATAAAGTAGTTGAATG
2181986 CAGTGTAGAG
Statistics
Matches: 164, Mismatches: 14, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
212 90 0.55
213 74 0.45
ACGTcount: A:0.37, C:0.09, G:0.20, T:0.35
Consensus pattern (212 bp):
AATCATGATGTTCTAAATGTTTAATCAAAATAAAAAATTTTCTTGAAATGAAGAAGGCACTTTGA
TGGGGCTAAAATTTTTGCAACTTCTAGCATCATTTTAAACTTATGCTAGTAATTGGTGAATTGAT
GAAAACCAGAGCATAGACATGGAAGTAATTCTAAAATAAAGTAGTTGAATGTGGTAGAGGGAAAC
CCAAATGGTGTATTTAC
Found at i:2193420 original size:2 final size:2
Alignment explanation
Indices: 2193413--2193447 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2193403 AGGATTAGTG
2193413 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2193448 TGGGGTTTTT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2202448 original size:4 final size:4
Alignment explanation
Indices: 2202441--2202465 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2202431 TACACAAACA
2202441 AAAG AAAG AAAG AAAG AAAG AAAG A
1 AAAG AAAG AAAG AAAG AAAG AAAG A
2202466 TTAATTAATT
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:0.24, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:2203990 original size:28 final size:28
Alignment explanation
Indices: 2203959--2204076 Score: 118
Period size: 28 Copynumber: 4.2 Consensus size: 28
2203949 ATATTAAAAA
*
2203959 AAAAAAAAAGCTGTTACAAG-CTATGTTG
1 AAAAAAAAAGTTGTTACAAGTC-ATGTTG
** *
2203987 AAAAAATATTGTTATTACAAGTCATGTTG
1 AAAAAA-AAAGTTGTTACAAGTCATGTTG
*
2204016 AAAACAAAAA-TTGTTACACGTCATGTTG
1 AAAA-AAAAAGTTGTTACAAGTCATGTTG
* *
2204044 AAAAAACAA-TTGTTACATGTCATGTT-
1 AAAAAAAAAGTTGTTACAAGTCATGTTG
2204070 AAAAAAA
1 AAAAAAA
2204077 TTTTATTGCT
Statistics
Matches: 76, Mismatches: 11, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
26 6 0.08
27 20 0.26
28 26 0.34
29 21 0.28
30 3 0.04
ACGTcount: A:0.47, C:0.10, G:0.14, T:0.30
Consensus pattern (28 bp):
AAAAAAAAAGTTGTTACAAGTCATGTTG
Found at i:2204065 original size:27 final size:27
Alignment explanation
Indices: 2203959--2204076 Score: 116
Period size: 27 Copynumber: 4.3 Consensus size: 27
2203949 ATATTAAAAA
*
2203959 AAAAAAAAAGCTGTTACAAG-CTATGTTG
1 AAAAAAAAA-TTGTTACAAGTC-ATGTTG
*
2203987 -AAAAAATATTGTTATTACAAGTCATGTTG
1 AAAAAAAAATTG---TTACAAGTCATGTTG
*
2204016 AAAACAAAAATTGTTACACGTCATGTTG
1 AAAA-AAAAATTGTTACAAGTCATGTTG
* *
2204044 AAAAAACAATTGTTACATGTCATGTT-
1 AAAAAAAAATTGTTACAAGTCATGTTG
2204070 AAAAAAA
1 AAAAAAA
2204077 TTTTATTGCT
Statistics
Matches: 77, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
26 8 0.10
27 27 0.35
28 18 0.23
29 13 0.17
30 4 0.05
31 7 0.09
ACGTcount: A:0.47, C:0.10, G:0.14, T:0.30
Consensus pattern (27 bp):
AAAAAAAAATTGTTACAAGTCATGTTG
Found at i:2204089 original size:29 final size:28
Alignment explanation
Indices: 2204052--2204131 Score: 78
Period size: 29 Copynumber: 2.9 Consensus size: 28
2204042 TGAAAAAACA
* *
2204052 ATTGTTACATGTCATGTTAAAAAAATTTT
1 ATTGCTACACGTCAT-TTAAAAAAATTTT
2204081 ATTGCTACACG-CTATATTCAAAAAAATTTT
1 ATTGCTACACGTC-AT-TT-AAAAAAATTTT
2204111 A---CTACACGTCATTTAAAAAAA
1 ATTGCTACACGTCATTTAAAAAAA
2204132 AAAACATGTT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
25 7 0.16
26 2 0.04
27 9 0.20
28 2 0.04
29 13 0.29
30 12 0.27
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.36
Consensus pattern (28 bp):
ATTGCTACACGTCATTTAAAAAAATTTT
Found at i:2207047 original size:48 final size:48
Alignment explanation
Indices: 2206973--2207090 Score: 173
Period size: 48 Copynumber: 2.5 Consensus size: 48
2206963 GAATTGCTTC
* * * *
2206973 TGCCCTTTCCATGTGCTCCTCGTGTATTTCTTCAGATTCATTTGCTGT
1 TGCCCTTTCCATGTGATCTTCTTGTATTTCTTCACATTCATTTGCTGT
*
2207021 TGCCCTTTCCATGCGATCTTCTTGTATTTCTTCACATTCATTTGCTGT
1 TGCCCTTTCCATGTGATCTTCTTGTATTTCTTCACATTCATTTGCTGT
**
2207069 TGCCAGTTCCATGTGATCTTCT
1 TGCCCTTTCCATGTGATCTTCT
2207091 GGGCACAACA
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 62 1.00
ACGTcount: A:0.12, C:0.27, G:0.15, T:0.46
Consensus pattern (48 bp):
TGCCCTTTCCATGTGATCTTCTTGTATTTCTTCACATTCATTTGCTGT
Found at i:2208675 original size:54 final size:54
Alignment explanation
Indices: 2208571--2208692 Score: 135
Period size: 54 Copynumber: 2.2 Consensus size: 54
2208561 GTGCCTCAGT
*
2208571 TTTTGGTTCTTCTTTCTTTGGCTCTACCTTGGGTTCTTCCTCCTTAGCCTCTTCC
1 TTTT-GTTCTTCTTTCTTTGGCTCTACCTTGGGTTCTTCCTCCTTAGCCTCTACC
* * *
2208626 TTTTGTTCTTCTTTCTTTGGTTC-AGCCTCT-GGTTCTTCCT-TTTGGGCCTCTACC
1 TTTTGTTCTTCTTTCTTTGGCTCTA-CCT-TGGGTTCTTCCTCCTT-AGCCTCTACC
2208680 -TTTGTTTCTTCTT
1 TTTTG-TTCTTCTT
2208693 GTTTTGATTC
Statistics
Matches: 59, Mismatches: 4, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
53 7 0.12
54 47 0.80
55 5 0.08
ACGTcount: A:0.03, C:0.28, G:0.15, T:0.54
Consensus pattern (54 bp):
TTTTGTTCTTCTTTCTTTGGCTCTACCTTGGGTTCTTCCTCCTTAGCCTCTACC
Found at i:2217561 original size:27 final size:28
Alignment explanation
Indices: 2217509--2217566 Score: 77
Period size: 27 Copynumber: 2.1 Consensus size: 28
2217499 ATACTACAAT
2217509 AAATGGTACTATTCTTCTTGACCAAA-A
1 AAATGGTACTATTCTTCTTGACCAAAGA
2217536 AAATGGTACTA-TCATTCTTGTA-CAAAGA
1 AAATGGTACTATTC-TTCTTG-ACCAAAGA
2217564 AAA
1 AAA
2217567 CTTATTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
26 2 0.07
27 21 0.75
28 5 0.18
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (28 bp):
AAATGGTACTATTCTTCTTGACCAAAGA
Found at i:2227150 original size:3 final size:3
Alignment explanation
Indices: 2227142--2227176 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2227132 CATCAAAAAA
2227142 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2227177 AAATTTATTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:2230265 original size:54 final size:54
Alignment explanation
Indices: 2230183--2230291 Score: 218
Period size: 54 Copynumber: 2.0 Consensus size: 54
2230173 TAAATTTTGG
2230183 ATATGCTTATTGAAAGCCTCCTTCTACTACCATTGGAATTTTGCGGCAGCTTGT
1 ATATGCTTATTGAAAGCCTCCTTCTACTACCATTGGAATTTTGCGGCAGCTTGT
2230237 ATATGCTTATTGAAAGCCTCCTTCTACTACCATTGGAATTTTGCGGCAGCTTGT
1 ATATGCTTATTGAAAGCCTCCTTCTACTACCATTGGAATTTTGCGGCAGCTTGT
2230291 A
1 A
2230292 ATCTAAGTAC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (54 bp):
ATATGCTTATTGAAAGCCTCCTTCTACTACCATTGGAATTTTGCGGCAGCTTGT
Found at i:2239319 original size:22 final size:19
Alignment explanation
Indices: 2239293--2239337 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 19
2239283 CATCAATATA
2239293 ATTAATTACCACTACTAATTTG
1 ATTAATTA-CA-TA-TAATTTG
*
2239315 ATTAATTATATATAATTTG
1 ATTAATTACATATAATTTG
2239334 ATTA
1 ATTA
2239338 CCTTTGCCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 11 0.50
20 2 0.09
21 1 0.05
22 8 0.36
ACGTcount: A:0.40, C:0.09, G:0.04, T:0.47
Consensus pattern (19 bp):
ATTAATTACATATAATTTG
Found at i:2258815 original size:31 final size:29
Alignment explanation
Indices: 2258776--2258848 Score: 87
Period size: 31 Copynumber: 2.5 Consensus size: 29
2258766 TTTAATGAAC
* *
2258776 ATAAAATTTTATTTG-ATTTAATATAAATAA
1 ATAAAATTTCATTTGAACTTAATA-AAA-AA
2258806 ATAAAAATTTCA-TTGAACTTAATAAAAAA
1 AT-AAAATTTCATTTGAACTTAATAAAAAA
2258835 ATAAAATTTCATTT
1 ATAAAATTTCATTT
2258849 AAATTTTTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
28 9 0.24
29 6 0.16
30 8 0.21
31 15 0.39
ACGTcount: A:0.52, C:0.04, G:0.03, T:0.41
Consensus pattern (29 bp):
ATAAAATTTCATTTGAACTTAATAAAAAA
Found at i:2288236 original size:17 final size:17
Alignment explanation
Indices: 2288216--2288275 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 17
2288206 TAAAAATATG
2288216 ATTATAATAAATATAAT
1 ATTATAATAAATATAAT
*
2288233 ATTATAAT--ATTTAAT
1 ATTATAATAAATATAAT
2288248 A-TATAAATAAA-ATAAT
1 ATTAT-AATAAATATAAT
*
2288264 AATTAAAATAAA
1 -ATTATAATAAA
2288276 AAAATTACAT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 3 0.09
15 10 0.29
16 4 0.11
17 16 0.46
18 2 0.06
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATTATAATAAATATAAT
Found at i:2288262 original size:23 final size:20
Alignment explanation
Indices: 2288236--2288280 Score: 54
Period size: 23 Copynumber: 2.1 Consensus size: 20
2288226 ATATAATATT
*
2288236 ATAATATTTAATATATAAATAAA
1 ATAATAATTAA-A-ATAAA-AAA
2288259 ATAATAATTAAAATAAAAAA
1 ATAATAATTAAAATAAAAAA
2288279 AT
1 AT
2288281 TACATTGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 5 0.24
21 5 0.24
22 1 0.05
23 10 0.48
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAATAATTAAAATAAAAAA
Found at i:2288578 original size:55 final size:57
Alignment explanation
Indices: 2288477--2288583 Score: 139
Period size: 55 Copynumber: 1.9 Consensus size: 57
2288467 TTCTTTAATA
* * *
2288477 TAATTTTTTATATTATATATTTTATTTTAATTTCTTTTACTCATATTATATAAATTT
1 TAATTTCTTATATTATATATTTTATGTTAATTTCTATTACTCATATTATATAAATTT
* *
2288534 TAATTTCTTATATT-T-TATTTTATGTTATTTTCTAATT-CTTATATTATATA
1 TAATTTCTTATATTATATATTTTATGTTAATTTCT-ATTACTCATATTATATA
2288584 TTTTATTTTA
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
55 28 0.64
56 3 0.07
57 13 0.30
ACGTcount: A:0.30, C:0.06, G:0.01, T:0.64
Consensus pattern (57 bp):
TAATTTCTTATATTATATATTTTATGTTAATTTCTATTACTCATATTATATAAATTT
Found at i:2288614 original size:38 final size:38
Alignment explanation
Indices: 2288542--2288622 Score: 92
Period size: 38 Copynumber: 2.1 Consensus size: 38
2288532 TTTAATTTCT
* *
2288542 TATATTTTATTTTATGTTATTTTCTAATTCTTATATTA
1 TATATTTTATTTTATGTTATTTTATAATTATTATATTA
*
2288580 TATATTTTATTTTAATGTT-TTTTATTTTAATTATAATATTA
1 TATATTTTATTTT-ATGTTATTTTA---TAATTATTATATTA
2288621 TA
1 TA
2288623 AAATATTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
38 17 0.47
39 5 0.14
41 14 0.39
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (38 bp):
TATATTTTATTTTATGTTATTTTATAATTATTATATTA
Found at i:2288641 original size:24 final size:23
Alignment explanation
Indices: 2288604--2288648 Score: 56
Period size: 22 Copynumber: 1.9 Consensus size: 23
2288594 ATGTTTTTTA
*
2288604 TTTTAATTATAATATTATAAAATAT
1 TTTTAATTA-AA-ATAATAAAATAT
2288629 TTTTAA-TAAAATAATAAAAT
1 TTTTAATTAAAATAATAAAAT
2288649 TGAAGGGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 9 0.47
23 2 0.11
24 2 0.11
25 6 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TTTTAATTAAAATAATAAAATAT
Found at i:2309037 original size:16 final size:15
Alignment explanation
Indices: 2309016--2309046 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
2309006 TTTAAGTAGA
2309016 TTTAAAATATATATTT
1 TTTAAAATAT-TATTT
2309032 TTTAAAATATTATTT
1 TTTAAAATATTATTT
2309047 AAAATTGATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
TTTAAAATATTATTT
Found at i:2311998 original size:2 final size:2
Alignment explanation
Indices: 2311991--2312047 Score: 78
Period size: 2 Copynumber: 28.5 Consensus size: 2
2311981 GTAATACCTT
* * * *
2311991 AC AC AC AC AC AC AC GC AC AC GC AC AC GC AC AC GC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
2312033 AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC A
2312048 TATATATATA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.44, C:0.49, G:0.07, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2312099 original size:32 final size:32
Alignment explanation
Indices: 2312063--2312129 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
2312053 ATATATATAT
2312063 ACACATATATTACAACAAGATGTGAGAGGAAA
1 ACACATATATTACAACAAGATGTGAGAGGAAA
2312095 ACACATATATTACAACAAGATGTGAGAGGAAA
1 ACACATATATTACAACAAGATGTGAGAGGAAA
2312127 ACA
1 ACA
2312130 AGATGTGAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.51, C:0.13, G:0.18, T:0.18
Consensus pattern (32 bp):
ACACATATATTACAACAAGATGTGAGAGGAAA
Found at i:2316395 original size:28 final size:28
Alignment explanation
Indices: 2316355--2316422 Score: 111
Period size: 28 Copynumber: 2.5 Consensus size: 28
2316345 ACAACATATC
2316355 TATCTAATTTTAAATTTTAAAGTTGAGT
1 TATCTAATTTTAAATTTTAAAGTTGAGT
*
2316383 TATCTAATTTTAAATTTTAAAGTTGGGT
1 TATCTAATTTTAAATTTTAAAGTTGAGT
*
2316411 TA-CTAAATTTAA
1 TATCTAATTTTAA
2316423 GATGGATAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 9 0.24
28 29 0.76
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.49
Consensus pattern (28 bp):
TATCTAATTTTAAATTTTAAAGTTGAGT
Found at i:2322087 original size:16 final size:16
Alignment explanation
Indices: 2322066--2322105 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
2322056 TAGCTATGGC
2322066 ATTGCAAGAACTATGA
1 ATTGCAAGAACTATGA
2322082 ATTGCAAGAACTATGA
1 ATTGCAAGAACTATGA
2322098 ATTGCAAG
1 ATTGCAAG
2322106 TACCTGGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.42, C:0.12, G:0.20, T:0.25
Consensus pattern (16 bp):
ATTGCAAGAACTATGA
Found at i:2327973 original size:2 final size:2
Alignment explanation
Indices: 2327923--2327954 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2327913 ACTAGTTATG
2327923 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
2327955 TAATATCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2328242 original size:2 final size:2
Alignment explanation
Indices: 2328235--2328285 Score: 54
Period size: 2 Copynumber: 27.0 Consensus size: 2
2328225 AATGTTATGA
* *
2328235 AT AT AT AT AT AT -T AT AT AT AT AT -T GT AT AA AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
2328274 AT AT AC AT AT AT
1 AT AT AT AT AT AT
2328286 TTAATTTATA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
1 3 0.07
2 38 0.93
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2328252 original size:11 final size:11
Alignment explanation
Indices: 2328236--2328278 Score: 59
Period size: 11 Copynumber: 3.7 Consensus size: 11
2328226 ATGTTATGAA
2328236 TATATATATAT
1 TATATATATAT
2328247 TATATATATATT
1 TATATATATA-T
*
2328259 GTATAAATATAT
1 -TATATATATAT
2328271 TATATATA
1 TATATATA
2328279 CATATATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 17 0.61
12 2 0.07
13 9 0.32
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (11 bp):
TATATATATAT
Found at i:2328253 original size:13 final size:13
Alignment explanation
Indices: 2328235--2328283 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
2328225 AATGTTATGA
2328235 ATATATATATATT
1 ATATATATATATT
2328248 ATATATATAT-TGT
1 ATATATATATAT-T
2328261 ATA-A-ATATATT
1 ATATATATATATT
*
2328272 ATATATACATAT
1 ATATATATATAT
2328284 ATTTAATTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
11 8 0.26
12 4 0.13
13 19 0.61
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (13 bp):
ATATATATATATT
Found at i:2328285 original size:17 final size:16
Alignment explanation
Indices: 2328235--2328311 Score: 51
Period size: 17 Copynumber: 4.9 Consensus size: 16
2328225 AATGTTATGA
2328235 ATATATATATATTAT--
1 ATATATAT-TATTATAC
*
2328250 ATATATATT-GTATA-
1 ATATATATTATTATAC
2328264 A-ATATATTATATATAC
1 ATATATATTAT-TATAC
2328280 ATATAT-TTAATTTATAC
1 ATATATATT-A-TTATAC
2328297 ATA-AGTATTATTATA
1 ATATA-TATTATTATA
2328312 ATTTATAATA
Statistics
Matches: 51, Mismatches: 2, Indels: 17
0.73 0.03 0.24
Matches are distributed among these distances:
13 10 0.20
14 2 0.04
15 12 0.24
16 9 0.18
17 15 0.29
18 3 0.06
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.49
Consensus pattern (16 bp):
ATATATATTATTATAC
Found at i:2328329 original size:22 final size:22
Alignment explanation
Indices: 2328283--2328332 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
2328273 TATATACATA
*
2328283 TATTTAATTTATACATAAGTAT
1 TATTTAATTTATACATAACTAT
2328305 TATTATAATTTATA-ATAAACT-T
1 TATT-TAATTTATACAT-AACTAT
2328327 TATTTA
1 TATTTA
2328333 CATGATTACA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 2 0.08
22 11 0.44
23 12 0.48
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (22 bp):
TATTTAATTTATACATAACTAT
Found at i:2328491 original size:25 final size:25
Alignment explanation
Indices: 2328432--2328492 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
2328422 TATAAAACAT
2328432 TATA-ACATATAAATTATATCATTA
1 TATATACATATAAATTATATCATTA
* *
2328456 -ATTNTATATATAAAGTTATAT-ATTA
1 TA-TATACATATAAA-TTATATCATTA
2328481 TATATACATATA
1 TATATACATATA
2328493 TTTAATTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
23 1 0.03
24 1 0.03
25 20 0.69
26 7 0.24
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.44
Consensus pattern (25 bp):
TATATACATATAAATTATATCATTA
Found at i:2328521 original size:23 final size:19
Alignment explanation
Indices: 2328477--2328529 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 19
2328467 AAAGTTATAT
2328477 ATTATATATACATATATTTA
1 ATTATATATA-ATATATTTA
2328497 ATTTATATATAAGTATTATTATA
1 A-TTATATATAA-TA-TATT-TA
2328520 ATTATA-ATAA
1 ATTATATATAA
2328530 ACTTTATTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
20 2 0.07
21 15 0.52
22 9 0.31
23 3 0.10
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (19 bp):
ATTATATATAATATATTTA
Found at i:2328573 original size:207 final size:205
Alignment explanation
Indices: 2328264--2328881 Score: 966
Period size: 208 Copynumber: 3.0 Consensus size: 205
2328254 ATATTGTATA
2328264 AATATATTATATATACATATATTTAATTTATACATAAGTATTATTATAATTTATAATAAACTTTA
1 AATATATTATATATACATATATTTAATTTATACATAAGTATTATTATAA-TTATAATAAACTTTA
* *
2328329 TTTACATGATTACACTTAATAACTTTATTAATTATCACTTTAGATTTTATAACATATTATTTATA
65 TTTACATGATTACACTTAATAACTTTATTAGTTATCACATTAGATTTTATAACATATTATTTATA
2328394 ATTAGTTATTATTTATACAAAACTTTGATATAAAACATTATAACATATAAATTATATCATTAATT
130 ATTAGTTATTATTTATAC-AAACTTTGATATAAAACATTATAACATATAAATTATATCATTAATT
2328459 NTATATATAAAGT
194 -TATATATAAAGT
* *
2328472 TATATATTATATATACATATATTTAATTTATATATAAGTATTATTATAATTATAATAAACTTTAT
1 AATATATTATATATACATATATTTAATTTATACATAAGTATTATTATAATTATAATAAACTTTAT
* *
2328537 TTGCATGATTACACTTAATAACTTTATTAGTTATCACATTAGATTTTATAACATATTGTTTATAA
66 TTACATGATTACACTTAATAACTTTATTAGTTATCACATTAGATTTTATAACATATTATTTATAA
* * * *
2328602 TTAATTATTATTTATACAAACTTTGATATAAAACATTTTAACATATAATTTGTATCATTAATTAT
131 TTAGTTATTATTTATACAAACTTTGATATAAAACATTATAACATATAAATTATATCATTAATT-T
2328667 ATATAATAAAGT
195 ATAT-ATAAAGT
* * * * *
2328679 AATATATTATATACACATATATTTAATTTATACATAAGTATTACTACGACTTATAATAAATTTTA
1 AATATATTATATATACATATATTTAATTTATACATAAGTATTATTA-TAATTATAATAAACTTTA
* * * *
2328744 TTTATATGATTACACTTAATAAGTTTATTAGCTATCACCTTAGATTTTATAACATATTATTTATA
65 TTTACATGATTACACTTAATAACTTTATTAGTTATCACATTAGATTTTATAACATATTATTTATA
* ** *
2328809 ATTAGTTATTATTTATACAAACTTTGATATAAAATATTATAACGCATAAGTTATATCATTAATTT
130 ATTAGTTATTATTTATACAAACTTTGATATAAAACATTATAACATATAAATTATATCATTAATTT
2328874 CATATATA
195 -ATATATA
2328882 TATATATATA
Statistics
Matches: 376, Mismatches: 31, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
206 48 0.13
207 146 0.39
208 182 0.48
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (205 bp):
AATATATTATATATACATATATTTAATTTATACATAAGTATTATTATAATTATAATAAACTTTAT
TTACATGATTACACTTAATAACTTTATTAGTTATCACATTAGATTTTATAACATATTATTTATAA
TTAGTTATTATTTATACAAACTTTGATATAAAACATTATAACATATAAATTATATCATTAATTTA
TATATAAAGT
Found at i:2332991 original size:21 final size:21
Alignment explanation
Indices: 2332965--2333017 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
2332955 TTATTTTTAT
**
2332965 TTTATATTATTTTTTTAAATA
1 TTTATATTATTAATTTAAATA
2332986 TTTATAATTGA-TAATTTAAATA
1 TTTAT-ATT-ATTAATTTAAATA
*
2333008 TTAATATTAT
1 TTTATATTAT
2333018 ATTTATAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
20 1 0.04
21 8 0.31
22 16 0.62
23 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTATATTATTAATTTAAATA
Found at i:2333049 original size:38 final size:34
Alignment explanation
Indices: 2333007--2333092 Score: 97
Period size: 31 Copynumber: 2.5 Consensus size: 34
2332997 TAATTTAAAT
2333007 ATTAATATTATATTTATAATTTAAAAGTTATTAGAATG
1 ATTAATATT-TATTT-T--TTTAAAAGTTATTAGAATG
*
2333045 ATT-A-ATTT-TTTTNTTAAAAGTTATTAGAATG
1 ATTAATATTTATTTTTTTAAAAGTTATTAGAATG
*
2333076 ATTAATTTTTATTTTTT
1 ATTAATATTTATTTTTT
2333093 AAATATTAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
31 21 0.50
32 1 0.02
33 4 0.10
34 8 0.19
35 1 0.02
36 3 0.07
37 1 0.02
38 3 0.07
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.55
Consensus pattern (34 bp):
ATTAATATTTATTTTTTTAAAAGTTATTAGAATG
Found at i:2333062 original size:31 final size:30
Alignment explanation
Indices: 2333026--2333090 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 30
2333016 ATATTTATAA
2333026 TTTAAAAGTTATTAGAATGATTAATTTTTT
1 TTTAAAAGTTATTAGAATGATTAATTTTTT
2333056 TNTTAAAAGTTATTAGAATGATTAATTTTTAT
1 T-TTAAAAGTTATTAGAATGATTAATTTTT-T
2333088 TTT
1 TTT
2333091 TTAAATATTA
Statistics
Matches: 33, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
30 1 0.03
31 30 0.91
32 2 0.06
ACGTcount: A:0.35, C:0.00, G:0.09, T:0.54
Consensus pattern (30 bp):
TTTAAAAGTTATTAGAATGATTAATTTTTT
Found at i:2341113 original size:23 final size:23
Alignment explanation
Indices: 2341087--2341132 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
2341077 ATACAATAAC
*
2341087 CTTATCCTAATATAATTAGGAAT
1 CTTATCCTAATAGAATTAGGAAT
2341110 CTTATCCTAATAGAATTAGGAAT
1 CTTATCCTAATAGAATTAGGAAT
2341133 TGTTATTCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (23 bp):
CTTATCCTAATAGAATTAGGAAT
Found at i:2343575 original size:2 final size:2
Alignment explanation
Indices: 2343568--2343627 Score: 50
Period size: 2 Copynumber: 30.5 Consensus size: 2
2343558 AAGTAATAAA
* * * * * * *
2343568 AT AT AT AT TT AT TT AT AT AT TT AT AT AT AT AC GT GT GT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2343609 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
2343628 CTTGTATAAT
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (2 bp):
AT
Found at i:2343586 original size:12 final size:12
Alignment explanation
Indices: 2343568--2343626 Score: 57
Period size: 12 Copynumber: 4.7 Consensus size: 12
2343558 AAGTAATAAA
2343568 ATATATATTTAT
1 ATATATATTTAT
*
2343580 TTATATATTTAT
1 ATATATATTTAT
2343592 ATATATACGTGTGTAT
1 ATATATA--T-T-TAT
*
2343608 -TATATATATAT
1 ATATATATTTAT
2343619 ATATATAT
1 ATATATAT
2343627 ACTTGTATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
11 3 0.08
12 24 0.62
13 1 0.03
14 1 0.03
15 7 0.18
16 3 0.08
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (12 bp):
ATATATATTTAT
Found at i:2348295 original size:29 final size:29
Alignment explanation
Indices: 2348249--2348306 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
2348239 CCTTCAGGAA
2348249 ATTAACTGCAGCAGACTGAAATCGGTTCT
1 ATTAACTGCAGCAGACTGAAATCGGTTCT
2348278 ATTAACTGCAGC-GAACTGAAATCGGTTCT
1 ATTAACTGCAGCAG-ACTGAAATCGGTTCT
2348307 TTGCTATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 1 0.04
29 27 0.96
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.28
Consensus pattern (29 bp):
ATTAACTGCAGCAGACTGAAATCGGTTCT
Found at i:2352657 original size:15 final size:15
Alignment explanation
Indices: 2352615--2352682 Score: 73
Period size: 15 Copynumber: 4.5 Consensus size: 15
2352605 CAATACAATA
* *
2352615 TGATTACAAGTAACG
1 TGATTGCAAGTAATG
* *
2352630 TGATTGTATGTAATG
1 TGATTGCAAGTAATG
*
2352645 TGATTGCAAGTAATA
1 TGATTGCAAGTAATG
* *
2352660 TGATTACAAGCAATG
1 TGATTGCAAGTAATG
2352675 TGATTGCA
1 TGATTGCA
2352683 GAGAAGATAA
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 42 1.00
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.34
Consensus pattern (15 bp):
TGATTGCAAGTAATG
Found at i:2356610 original size:24 final size:24
Alignment explanation
Indices: 2356583--2356921 Score: 412
Period size: 24 Copynumber: 14.1 Consensus size: 24
2356573 TGTTTTCACT
2356583 ATGTACAGAAACATGTGACACGTC
1 ATGTACAGAAACATGTGACACGTC
*
2356607 ATGTACAGAAATATGTGACACGTC
1 ATGTACAGAAACATGTGACACGTC
* * * * *
2356631 ATGTATAGAAATATATGACATGCC
1 ATGTACAGAAACATGTGACACGTC
* *
2356655 ATGTA-AAAGAACATGTGACACGCC
1 ATGTACAGA-AACATGTGACACGTC
*
2356679 ATATACAGAAACATGTGACACGTC
1 ATGTACAGAAACATGTGACACGTC
* *
2356703 ATGTA-AAAGAACATGTGACACGCC
1 ATGTACAGA-AACATGTGACACGTC
* *
2356727 ATATACAGAAACATGTGACACGCC
1 ATGTACAGAAACATGTGACACGTC
* * *
2356751 ATGTACAAAAACATGTAACACGCC
1 ATGTACAGAAACATGTGACACGTC
*
2356775 ATGTACAGAAATATGTGACACGTC
1 ATGTACAGAAACATGTGACACGTC
2356799 ATGTACAGAAACATGTGACACGTC
1 ATGTACAGAAACATGTGACACGTC
*
2356823 ATGTACAGAAATATGTGACACGTC
1 ATGTACAGAAACATGTGACACGTC
* * *
2356847 ATATATAGAAACATGTGACATGTC
1 ATGTACAGAAACATGTGACACGTC
* *
2356871 ATATACAAAAACATGTGACACGTC
1 ATGTACAGAAACATGTGACACGTC
* * *
2356895 ATATACAAAAACATGTGACAAGTC
1 ATGTACAGAAACATGTGACACGTC
2356919 ATG
1 ATG
2356922 GTTAGGTTGT
Statistics
Matches: 276, Mismatches: 35, Indels: 8
0.87 0.11 0.03
Matches are distributed among these distances:
23 4 0.01
24 268 0.97
25 4 0.01
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (24 bp):
ATGTACAGAAACATGTGACACGTC
Found at i:2357055 original size:58 final size:57
Alignment explanation
Indices: 2356984--2357123 Score: 162
Period size: 58 Copynumber: 2.4 Consensus size: 57
2356974 TATAAAAACA
*
2356984 TGTTACACACCATAGTT-AAAAAA-GGTTATTACACGCAATATTGGAAAAAAAATATTGT
1 TGTTACACGCCATAGTTGAAAAAATGGTTATTACACGCAATATT-G--AAAAAATATTGT
* * *
2357042 TGTTACACGCCATA-TTGAAAAAATATTGTTGTTACACGCCATATTGAAAAAATATTGT
1 TGTTACACGCCATAGTTG-AAAAA-ATGGTTATTACACGCAATATTGAAAAAATATTGT
*
2357100 TGTTACACGCTAT-GTTGAAAAAAT
1 TGTTACACGCCATAGTTGAAAAAAT
2357124 ATTGTTGCTA
Statistics
Matches: 72, Mismatches: 5, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
56 2 0.03
57 7 0.10
58 40 0.56
59 5 0.07
60 2 0.03
61 16 0.22
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (57 bp):
TGTTACACGCCATAGTTGAAAAAATGGTTATTACACGCAATATTGAAAAAATATTGT
Found at i:2357062 original size:29 final size:29
Alignment explanation
Indices: 2357012--2357164 Score: 202
Period size: 29 Copynumber: 5.2 Consensus size: 29
2357002 AAAAAGGTTA
*
2357012 TTACACGCAATATTGGAAAAAAAATATTGTTG
1 TTACACGCCATATT-G--AAAAAATATTGTTG
2357044 TTACACGCCATATTGAAAAAATATTGTTG
1 TTACACGCCATATTGAAAAAATATTGTTG
2357073 TTACACGCCATATTGAAAAAATATTGTTG
1 TTACACGCCATATTGAAAAAATATTGTTG
* *
2357102 TTACACGCTATGTTGAAAAAATATTGTTG
1 TTACACGCCATATTGAAAAAATATTGTTG
* * * *
2357131 CTACACGACATATT-CAAAAATATT-TTA
1 TTACACGCCATATTGAAAAAATATTGTTG
2357158 TTACACG
1 TTACACG
2357165 TTAATGCTAA
Statistics
Matches: 111, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
27 8 0.07
28 9 0.08
29 80 0.72
31 1 0.01
32 13 0.12
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.34
Consensus pattern (29 bp):
TTACACGCCATATTGAAAAAATATTGTTG
Found at i:2357344 original size:15 final size:15
Alignment explanation
Indices: 2357324--2357353 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
2357314 GGGAATAAAA
*
2357324 ACCAAAAATTGCAAC
1 ACCAAAAATTACAAC
2357339 ACCAAAAATTACAAC
1 ACCAAAAATTACAAC
2357354 CAAACACGCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.27, G:0.03, T:0.13
Consensus pattern (15 bp):
ACCAAAAATTACAAC
Found at i:2357549 original size:16 final size:17
Alignment explanation
Indices: 2357528--2357560 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2357518 AGAGTACAAG
*
2357528 AAAAAGATAAA-AAAAA
1 AAAAAGAGAAAGAAAAA
2357544 AAAAAGAGAAAGAAAAA
1 AAAAAGAGAAAGAAAAA
2357561 GAAGAATGAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (17 bp):
AAAAAGAGAAAGAAAAA
Found at i:2359766 original size:29 final size:29
Alignment explanation
Indices: 2359724--2359780 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
2359714 CCTTCAGGAA
2359724 ATTAACCGCAGCAGACTGAAATCGGTTCT
1 ATTAACCGCAGCAGACTGAAATCGGTTCT
*
2359753 ATTAACTGCAGCAGACTGAAATCGGTTC
1 ATTAACCGCAGCAGACTGAAATCGGTTC
2359781 CTTGCTATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.25
Consensus pattern (29 bp):
ATTAACCGCAGCAGACTGAAATCGGTTCT
Found at i:2362111 original size:627 final size:626
Alignment explanation
Indices: 2360917--2362170 Score: 2499
Period size: 627 Copynumber: 2.0 Consensus size: 626
2360907 TAACTACTCA
2360917 AATTTCATGCATATCTTTTTTTTAATAAAATATTATTTATTCTTCTTCTCTTTATCATCTTTTAT
1 AATTTCATGCATATCTTTTTTTTAATAAAATATTATTTATTCTTCTTCTCTTTATCATCTTTTAT
2360982 AGGATAGGGGTCTCATATGTCCCTCACTAAACTTTATATTTACGTACAATTATTTATATGTAATT
66 AGGATAGGGGTCTCATATGTCCCTCACTAAACTTTATATTTACGTACAATTATTTATATGTAATT
2361047 GTAACTTCACGTGATAGAAATTTTATATGTCTTTCATTAAAAATTATTTTTTAGAGAGAAAAAAG
131 GTAACTTCACGTGATAGAAATTTTATATGTCTTTCATTAAAAATTATTTTTTAGAGAGAAAAAAG
2361112 TATGATGGTTCTAGAACTACTTAAAAGTATTATGGTCACCGACAAGATTAAAAGAAATTTTTCTT
196 TATGATGGTTCTAGAACTACTTAAAAGTATTATGGTCACCGACAAGATTAAAAGAAATTTTTCTT
2361177 AATTAACCATGCATGTGTGCATGACTTATTTTATTATATATTAAAATACCCCATTTAATGATTCT
261 AATTAACCATGCATGTGTGCATGACTTATTTTATTATATATTAAAATACCCCATTTAATGATTCT
2361242 TAACAGGGGTACTTAACATTTGCCTTGCCAGTATCAGTAGCTAGCACTACTAGCACTGCTCCAGA
326 TAACAGGGGTACTTAACATTTGCCTTGCCAGTATCAGTAGCTAGCACTACTAGCACTGCTCCAGA
2361307 GCAGAGTTATTTAATATTTTATTAACCAAAAATCAAAGTTAAAGTTCTGCATTGAATAAAGTGAT
391 GCAGAGTTATTTAATATTTTATTAACCAAAAATCAAAGTTAAAGTTCTGCATTGAATAAAGTGAT
2361372 TAAAGGAAAGTAGATTCAATTGACCTTGGATCTTGCAAAATAAAAAAATCGATTTCTTTTCCAAT
456 TAAAGGAAAGTAGATTCAATTGACCTTGGATCTTGCAAAATAAAAAAATCGATTTCTTTTCCAAT
2361437 GCAAGATTCACTGAAGGACACAAAAGGAATTATGCTAGAAAGAATTACCACTAATGATCTGAGTT
521 GCAAGATTCACTGAAGGACACAAAAGGAATTATGCTAGAAAGAATTACCACTAATGATCTGAGTT
2361502 AAATATTTCAATGCATTGAAAGTAATAAAATATATATTTAT
586 AAATATTTCAATGCATTGAAAGTAATAAAATATATATTTAT
2361543 ANATTTCATGCATATCTTTTTTTTAATAAAATATTATTTATTCTTCTTCTCTTTATCATCTTTTA
1 A-ATTTCATGCATATCTTTTTTTTAATAAAATATTATTTATTCTTCTTCTCTTTATCATCTTTTA
2361608 TAGGATAGGGGTCTCATATGTCCCTCACTAAACTTTATATTTACGTACAATTATTTATATGTAAT
65 TAGGATAGGGGTCTCATATGTCCCTCACTAAACTTTATATTTACGTACAATTATTTATATGTAAT
2361673 TGTAACTTCACGTGATAGAAATTTTATATGTCTTTCATTAAAAATTATTTTTTAGAGAGAAAAAA
130 TGTAACTTCACGTGATAGAAATTTTATATGTCTTTCATTAAAAATTATTTTTTAGAGAGAAAAAA
2361738 GTATGATGGTTCTAGAACTACTTAAAAGTATTATGGTCACCGACAAGATTAAAAGAAATTTTTCT
195 GTATGATGGTTCTAGAACTACTTAAAAGTATTATGGTCACCGACAAGATTAAAAGAAATTTTTCT
2361803 TAATTAACCATGCATGTGTGCATGACTTATTTTATTATATATTAAAATACCCCATTTAATGATTC
260 TAATTAACCATGCATGTGTGCATGACTTATTTTATTATATATTAAAATACCCCATTTAATGATTC
2361868 TTAACAGGGGTACTTAACATTTGCCTTGCCAGTATCAGTAGCTAGCACTACTAGCACTGCTCCAG
325 TTAACAGGGGTACTTAACATTTGCCTTGCCAGTATCAGTAGCTAGCACTACTAGCACTGCTCCAG
2361933 AGCAGAGTTATTTAATATTTTATTAACCAAAAATCAAAGTTAAAGTTCTGCATTGAATAAAGTGA
390 AGCAGAGTTATTTAATATTTTATTAACCAAAAATCAAAGTTAAAGTTCTGCATTGAATAAAGTGA
2361998 TTAAAGGAAAGTAGATTCAATTGACCTTGGATCTTGCAAAATAAAAAAATCGATTTCTTTTCCAA
455 TTAAAGGAAAGTAGATTCAATTGACCTTGGATCTTGCAAAATAAAAAAATCGATTTCTTTTCCAA
2362063 TGCAAGATTCACTGAAGGACACAAAAGGAATTATGCTAGAAAGAATTACCACTAATGATCTGAGT
520 TGCAAGATTCACTGAAGGACACAAAAGGAATTATGCTAGAAAGAATTACCACTAATGATCTGAGT
2362128 TAAATATTTCAATGCATTGAAAGTAATAAAATATATATTTAT
585 TAAATATTTCAATGCATTGAAAGTAATAAAATATATATTTAT
2362170 A
1 A
2362171 TATATATATA
Statistics
Matches: 627, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
626 1 0.00
627 626 1.00
ACGTcount: A:0.36, C:0.14, G:0.13, T:0.37
Consensus pattern (626 bp):
AATTTCATGCATATCTTTTTTTTAATAAAATATTATTTATTCTTCTTCTCTTTATCATCTTTTAT
AGGATAGGGGTCTCATATGTCCCTCACTAAACTTTATATTTACGTACAATTATTTATATGTAATT
GTAACTTCACGTGATAGAAATTTTATATGTCTTTCATTAAAAATTATTTTTTAGAGAGAAAAAAG
TATGATGGTTCTAGAACTACTTAAAAGTATTATGGTCACCGACAAGATTAAAAGAAATTTTTCTT
AATTAACCATGCATGTGTGCATGACTTATTTTATTATATATTAAAATACCCCATTTAATGATTCT
TAACAGGGGTACTTAACATTTGCCTTGCCAGTATCAGTAGCTAGCACTACTAGCACTGCTCCAGA
GCAGAGTTATTTAATATTTTATTAACCAAAAATCAAAGTTAAAGTTCTGCATTGAATAAAGTGAT
TAAAGGAAAGTAGATTCAATTGACCTTGGATCTTGCAAAATAAAAAAATCGATTTCTTTTCCAAT
GCAAGATTCACTGAAGGACACAAAAGGAATTATGCTAGAAAGAATTACCACTAATGATCTGAGTT
AAATATTTCAATGCATTGAAAGTAATAAAATATATATTTAT
Found at i:2378878 original size:2 final size:2
Alignment explanation
Indices: 2378865--2378901 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
2378855 CCGAAGTTGC
* *
2378865 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2378902 GAGGGATACT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2386189 original size:28 final size:28
Alignment explanation
Indices: 2386141--2386226 Score: 72
Period size: 28 Copynumber: 3.0 Consensus size: 28
2386131 AAAATACAAA
2386141 TTTAATATATTTATATATTTTATTATTAATT
1 TTTAA-AT-TTTAT-TATTTTATTATTAATT
* *
2386172 TTTAAATTTTATTATTTT-TAATATCATAT
1 TTTAAATTTTATTATTTTATTAT-TAAT-T
*
2386201 TTT-ATTTTTATT-TTTTATTA-TAATT
1 TTTAAATTTTATTATTTTATTATTAATT
2386226 T
1 T
2386227 AATTTTTTTC
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
25 2 0.04
26 3 0.06
27 7 0.15
28 19 0.40
29 9 0.19
30 2 0.04
31 5 0.11
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.67
Consensus pattern (28 bp):
TTTAAATTTTATTATTTTATTATTAATT
Found at i:2392064 original size:19 final size:19
Alignment explanation
Indices: 2392042--2392085 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
2392032 ACGCGCCTTG
2392042 TTTTTTTT-TT-TTTTCCT
1 TTTTTTTTATTATTTTCCT
2392059 TCTTTTTTTATTATTTT-CT
1 T-TTTTTTTATTATTTTCCT
2392078 TTTTTTTT
1 TTTTTTTT
2392086 GGAATTTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 1 0.04
18 14 0.58
19 5 0.21
20 4 0.17
ACGTcount: A:0.05, C:0.09, G:0.00, T:0.86
Consensus pattern (19 bp):
TTTTTTTTATTATTTTCCT
Found at i:2399768 original size:104 final size:103
Alignment explanation
Indices: 2399589--2399905 Score: 456
Period size: 104 Copynumber: 3.0 Consensus size: 103
2399579 TGCTCAAATT
2399589 GAAGCAACACAGCATCAATAACTTGTTGTGCAGTCTAACACTCACCTTCTAACACAACAAGTTTT
1 GAAGCAACACAGCATCAATAACTTGTTGTGCAGTCTAACACTCACCTTCTAACACAACAAGTTTT
* *
2399654 ATGACTGCTTCGAGTTCATCCGCAAATGAATTTAAGTA
66 GTGGCTGCTTCGAGTTCATCCGCAAATGAATTTAAGTA
* *
2399692 GAAGCAACATAGCATTAATAACTTTGTTGTGCAGTCTAACACTCACCTTCTAACACAACAAGTTT
1 GAAGCAACACAGCATCAATAAC-TTGTTGTGCAGTCTAACACTCACCTTCTAACACAACAAGTTT
*
2399757 TGTGGCTGCTTCGAGTTCATCCGCAAATGAATTTAAGAA
65 TGTGGCTGCTTCGAGTTCATCCGCAAATGAATTTAAGTA
* * *
2399796 GAAGCAACAGAGCATCAATAAATTGTTGTGCAGTCTAACACTTACCTTACCTTCTAACACAATAA
1 GAAGCAACACAGCATCAATAACTTGTTGTGCAGTCTAACAC-T--C--ACCTTCTAACACAACAA
* * * *
2399861 GTTTTAG-AGCTGCTTTGAGTTCATCCACAAGTGAATTTAAGTA
61 GTTTT-GTGGCTGCTTCGAGTTCATCCGCAAATGAATTTAAGTA
2399904 GA
1 GA
2399906 GGTGTCTCAA
Statistics
Matches: 193, Mismatches: 14, Indels: 9
0.89 0.06 0.04
Matches are distributed among these distances:
103 39 0.20
104 98 0.51
106 1 0.01
108 54 0.28
109 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.16, T:0.29
Consensus pattern (103 bp):
GAAGCAACACAGCATCAATAACTTGTTGTGCAGTCTAACACTCACCTTCTAACACAACAAGTTTT
GTGGCTGCTTCGAGTTCATCCGCAAATGAATTTAAGTA
Found at i:2402381 original size:115 final size:114
Alignment explanation
Indices: 2402198--2402461 Score: 399
Period size: 115 Copynumber: 2.3 Consensus size: 114
2402188 ACCAACAAGG
*
2402198 ACAGTTTGCAATTAATGAATATA-AGACT-AGTTTTTCCATAAAAACTAACAATTCCATATTAAA
1 ACAGTTTGCAATTAATGAATATACA-ACTAATTTTTTCCATAAAAACTAACAATTCCATATTAAA
* *
2402261 AGATGGAACTATAAGAAATTTTTTTAAAAATTCACATACAAGGTGCATCA
65 AGATGGAAATATAAGAAAATTTTTTAAAAATTCACATACAAGGTGCATCA
* * * * *
2402311 ACAGTATGCAATTAATGAATAGACCACTAAATTTTTTCCATAAAAACTAACAAATT-CATGTTAT
1 ACAGTTTGCAATTAATGAATATACAACT-AATTTTTTCCATAAAAACTAAC-AATTCCATATTAA
*
2402375 AAGATGGAAATATAAGAAAATTTTTTAAAAATTCACATAGAAGGTGCATCA
64 AAGATGGAAATATAAGAAAATTTTTTAAAAATTCACATACAAGGTGCATCA
2402426 ACAGTTTGCAATTAATGAATATACAACTAATTTTTT
1 ACAGTTTGCAATTAATGAATATACAACTAATTTTTT
2402462 GCGATCCGAT
Statistics
Matches: 135, Mismatches: 12, Indels: 7
0.88 0.08 0.05
Matches are distributed among these distances:
113 24 0.18
114 8 0.06
115 99 0.73
116 4 0.03
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.33
Consensus pattern (114 bp):
ACAGTTTGCAATTAATGAATATACAACTAATTTTTTCCATAAAAACTAACAATTCCATATTAAAA
GATGGAAATATAAGAAAATTTTTTAAAAATTCACATACAAGGTGCATCA
Found at i:2405922 original size:13 final size:12
Alignment explanation
Indices: 2405905--2405945 Score: 57
Period size: 13 Copynumber: 3.3 Consensus size: 12
2405895 ATATTCATTT
2405905 AAAAAATAAATA
1 AAAAAATAAATA
2405917 TAAAAAAT-AATA
1 -AAAAAATAAATA
2405929 AAAAAGATAAATA
1 AAAAA-ATAAATA
2405942 AAAA
1 AAAA
2405946 TTAACCATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
11 5 0.19
12 6 0.23
13 15 0.58
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.17
Consensus pattern (12 bp):
AAAAAATAAATA
Found at i:2405928 original size:12 final size:12
Alignment explanation
Indices: 2405904--2405945 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
2405894 GATATTCATT
2405904 TAAAAAATAAATA
1 TAAAAAAT-AATA
2405917 TAAAAAATAATA
1 TAAAAAATAATA
2405929 -AAAAAGATAA-A
1 TAAAAA-ATAATA
2405940 TAAAAA
1 TAAAAA
2405946 TTAACCATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 6 0.22
12 13 0.48
13 8 0.30
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (12 bp):
TAAAAAATAATA
Found at i:2450439 original size:6 final size:6
Alignment explanation
Indices: 2450409--2450460 Score: 54
Period size: 6 Copynumber: 8.7 Consensus size: 6
2450399 ACCTACATCA
* *
2450409 AAAAAT AAATAAT AATAAA- ATAAAT AAAAAT AATAAT AAAAAT AAAAA-
1 AAAAAT AAA-AAT AA-AAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
2450457 AAAA
1 AAAA
2450461 TATGAATGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
5 7 0.18
6 24 0.62
7 7 0.18
8 1 0.03
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (6 bp):
AAAAAT
Found at i:2450441 original size:21 final size:22
Alignment explanation
Indices: 2450408--2450462 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
2450398 CACCTACATC
2450408 AAAAAATAAATAATAAT-AAAAT
1 AAAAAA-AAATAATAATAAAAAT
*
2450430 AAATAAAAATAATAATAAAAAT
1 AAAAAAAAATAATAATAAAAAT
2450452 AAAAAAAAATA
1 AAAAAAAAATA
2450463 TGAATGAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 10 0.33
22 20 0.67
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (22 bp):
AAAAAAAAATAATAATAAAAAT
Found at i:2450442 original size:18 final size:18
Alignment explanation
Indices: 2450409--2450456 Score: 71
Period size: 18 Copynumber: 2.6 Consensus size: 18
2450399 ACCTACATCA
2450409 AAAAATAAATAATAATAA-
1 AAAAATAAA-AATAATAAT
2450427 AATAAATAAAAATAATAAT
1 AA-AAATAAAAATAATAAT
2450446 AAAAATAAAAA
1 AAAAATAAAAA
2450457 AAAATATGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 19 0.68
19 9 0.32
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (18 bp):
AAAAATAAAAATAATAAT
Found at i:2451126 original size:51 final size:47
Alignment explanation
Indices: 2451058--2451164 Score: 124
Period size: 47 Copynumber: 2.2 Consensus size: 47
2451048 GTGGCCGACG
* * **
2451058 AAAAGGAGGAAAGGAATAGAGAGAGAGAGAGAGAGAGCACCAATCGACGCC
1 AAAAGGAGAAAAAGAATA-A-AGAGAGAG-G-GAGAAAACCAATCGACGCC
* *
2451109 AAAGGGAGAAAAAGAATAAAGAGAGAGGGAGAAAACCAATCGGCGCC
1 AAAAGGAGAAAAAGAATAAAGAGAGAGGGAGAAAACCAATCGACGCC
2451156 AAAAGGAGA
1 AAAAGGAGA
2451165 GTCGGTCGAC
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
47 24 0.49
48 1 0.02
49 8 0.16
50 1 0.02
51 15 0.31
ACGTcount: A:0.50, C:0.12, G:0.34, T:0.04
Consensus pattern (47 bp):
AAAAGGAGAAAAAGAATAAAGAGAGAGGGAGAAAACCAATCGACGCC
Found at i:2451922 original size:12 final size:12
Alignment explanation
Indices: 2451907--2451941 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
2451897 ATATATATAT
*
2451907 AAATAATAATTA
1 AAATAATAATAA
*
2451919 AAATAAAAATAA
1 AAATAATAATAA
2451931 AAATAATAATA
1 AAATAATAATA
2451942 TACCATGACA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
AAATAATAATAA
Found at i:2460859 original size:31 final size:33
Alignment explanation
Indices: 2460824--2460886 Score: 87
Period size: 31 Copynumber: 2.0 Consensus size: 33
2460814 TTTTTCTTTC
*
2460824 TCAATTAATA-TCGTGTGAAT-ATTT-TGTTTTT
1 TCAATTAACACTC-TGTGAATAATTTCTGTTTTT
2460855 TCAATTAACACTCTGTGAATAATTTCTGTTTT
1 TCAATTAACACTCTGTGAATAATTTCTGTTTT
2460887 CACGTAAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 16 0.57
32 6 0.21
33 6 0.21
ACGTcount: A:0.27, C:0.11, G:0.11, T:0.51
Consensus pattern (33 bp):
TCAATTAACACTCTGTGAATAATTTCTGTTTTT
Found at i:2460887 original size:31 final size:30
Alignment explanation
Indices: 2460816--2460888 Score: 76
Period size: 31 Copynumber: 2.4 Consensus size: 30
2460806 TTGTGGATTT
* * *
2460816 TTTCTTTCTCAATTAATATCGTGTGAATAT
1 TTTCTTTTTCAATTAACATCGTGTGAATAA
*
2460846 TTTGTTTTTTCAATTAACACTC-TGTGAATAA
1 TTT-CTTTTTCAATTAACA-TCGTGTGAATAA
2460877 TTTCTGTTTTCA
1 TTTCT-TTTTCA
2460889 CGTAAATTAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
30 4 0.11
31 29 0.83
32 2 0.06
ACGTcount: A:0.25, C:0.14, G:0.10, T:0.52
Consensus pattern (30 bp):
TTTCTTTTTCAATTAACATCGTGTGAATAA
Found at i:2461076 original size:29 final size:31
Alignment explanation
Indices: 2461043--2461110 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 31
2461033 CAGAAATTAT
*
2461043 TCATAAAATAT-AAATTAAAAAAATTT-AAA
1 TCATAAAATATCAAATGAAAAAAATTTGAAA
*
2461072 TCATAAAATATCATATGAAAAAAATTTGAAA
1 TCATAAAATATCAAATGAAAAAAATTTGAAA
*
2461103 TCCTAAAA
1 TCATAAAA
2461111 AATTATACGT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
29 11 0.32
30 13 0.38
31 10 0.29
ACGTcount: A:0.60, C:0.07, G:0.03, T:0.29
Consensus pattern (31 bp):
TCATAAAATATCAAATGAAAAAAATTTGAAA
Found at i:2462171 original size:30 final size:30
Alignment explanation
Indices: 2462111--2462172 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
2462101 GCATTTAATC
*
2462111 AAGTCTTTATATTTTTATTTTAAGTTAAAT
1 AAGTCTTTATATTTTTATTTTAAGTCAAAT
2462141 AAGTCTTTATATTTTTATTTTTAA-TCAAAT
1 AAGTCTTTATATTTTTA-TTTTAAGTCAAAT
2462171 AA
1 AA
2462173 ATATTTTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 24 0.80
31 6 0.20
ACGTcount: A:0.35, C:0.05, G:0.05, T:0.55
Consensus pattern (30 bp):
AAGTCTTTATATTTTTATTTTAAGTCAAAT
Found at i:2465240 original size:29 final size:29
Alignment explanation
Indices: 2465197--2465252 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
2465187 CATTATTTGA
2465197 ATTATAACCTCATTAAACCCAAATAAAAT
1 ATTATAACCTCATTAAACCCAAATAAAAT
*
2465226 ATTATAACCTTATTAAACCCAAATAAA
1 ATTATAACCTCATTAAACCCAAATAAA
2465253 TACTAGCCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.52, C:0.20, G:0.00, T:0.29
Consensus pattern (29 bp):
ATTATAACCTCATTAAACCCAAATAAAAT
Found at i:2473901 original size:16 final size:17
Alignment explanation
Indices: 2473877--2473914 Score: 53
Period size: 15 Copynumber: 2.3 Consensus size: 17
2473867 ATTAAATCAA
2473877 AAAATAATTTTATTAA-T
1 AAAATAA-TTTATTAAGT
2473894 AAAA-AATTTATTAAGT
1 AAAATAATTTATTAAGT
2473910 AAAAT
1 AAAAT
2473915 TATAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 8 0.42
16 7 0.37
17 4 0.21
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (17 bp):
AAAATAATTTATTAAGT
Found at i:2477603 original size:4 final size:4
Alignment explanation
Indices: 2477596--2477620 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2477586 ACAAGTAAGT
2477596 ATTA ATTA ATTA ATTA ATTA ATTA A
1 ATTA ATTA ATTA ATTA ATTA ATTA A
2477621 ATGTGATTAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
ATTA
Found at i:2482080 original size:30 final size:30
Alignment explanation
Indices: 2482017--2482106 Score: 112
Period size: 30 Copynumber: 3.1 Consensus size: 30
2482007 TCACATACTC
* * * *
2482017 TTATACTTTTATTGTG-TTCAATTAAGTTT
1 TTATATTTTTATTTTGAATCAAATAAGTTT
*
2482046 TTATATTTTTATTTTGAATCAAATAAGCTT
1 TTATATTTTTATTTTGAATCAAATAAGTTT
*
2482076 TTATATTTTTATTTTGAGTCAAA-AAGTTT
1 TTATATTTTTATTTTGAATCAAATAAGTTT
2482105 TT
1 TT
2482107 TTGACTAATG
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
29 21 0.40
30 32 0.60
ACGTcount: A:0.29, C:0.06, G:0.09, T:0.57
Consensus pattern (30 bp):
TTATATTTTTATTTTGAATCAAATAAGTTT
Found at i:2486474 original size:2 final size:2
Alignment explanation
Indices: 2486467--2486567 Score: 75
Period size: 2 Copynumber: 51.5 Consensus size: 2
2486457 CTAATTCTTG
* *
2486467 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A- AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * *
2486508 A- ACT -T TT AT -T AC GT AA ACT TT NT AT AT AT AT AT AT AT AT AT
1 AT A-T AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
*
2486549 AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT A
2486568 ATTTAACTTT
Statistics
Matches: 77, Mismatches: 16, Indels: 12
0.73 0.15 0.11
Matches are distributed among these distances:
1 4 0.05
2 73 0.95
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2494816 original size:71 final size:70
Alignment explanation
Indices: 2494654--2494791 Score: 158
Period size: 71 Copynumber: 2.0 Consensus size: 70
2494644 TAATGTATAC
**
2494654 ATAT-AAAATGTA-TTAAGAAATAAAAATAAAATATTATCTTCTGAAGAAAAAATTTAAAATAAA
1 ATATAAAAAT-TATTTAA-AAATAAAAATAAAATATTATCTTCTGAAGAAAAAATGAAAAATAAA
2494717 ATATGCA
64 ATATGCA
* * *
2494724 ATATAAGAAATTATATTAAAAATAAAAATAAAATA-TATACTTGT-AATAAGAAATGAAAAATAA
1 ATATAA-AAATTAT-TTAAAAATAAAAATAAAATATTAT-CTTCTGAAGAAAAAATGAAAAATAA
2494787 AATAT
63 AATAT
2494792 ATTTAATTAA
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
70 4 0.07
71 26 0.45
72 24 0.41
73 4 0.07
ACGTcount: A:0.61, C:0.03, G:0.07, T:0.30
Consensus pattern (70 bp):
ATATAAAAATTATTTAAAAATAAAAATAAAATATTATCTTCTGAAGAAAAAATGAAAAATAAAAT
ATGCA
Found at i:2496726 original size:105 final size:105
Alignment explanation
Indices: 2496544--2496743 Score: 382
Period size: 105 Copynumber: 1.9 Consensus size: 105
2496534 TCAGACACCA
*
2496544 GCTTTTCTTCTTTTGTTTCCCCAAGAATGGAATTTTACTTCTATCTTTATACTCTTCCAGGGGAC
1 GCTTTTCTTCCTTTGTTTCCCCAAGAATGGAATTTTACTTCTATCTTTATACTCTTCCAGGGGAC
*
2496609 TTGCATGATTTACATTGTGTTCCTTTTATATGCCTATATT
66 TTGCATGATTTACAATGTGTTCCTTTTATATGCCTATATT
2496649 GCTTTTCTTCCTTTGTTTCCCCAAGAATGGAATTTTACTTCTATCTTTATACTCTTCCAGGGGAC
1 GCTTTTCTTCCTTTGTTTCCCCAAGAATGGAATTTTACTTCTATCTTTATACTCTTCCAGGGGAC
2496714 TTGCATGATTTACAATGTGTTCCTTTTATA
66 TTGCATGATTTACAATGTGTTCCTTTTATA
2496744 CGCATACATT
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 93 1.00
ACGTcount: A:0.20, C:0.20, G:0.14, T:0.47
Consensus pattern (105 bp):
GCTTTTCTTCCTTTGTTTCCCCAAGAATGGAATTTTACTTCTATCTTTATACTCTTCCAGGGGAC
TTGCATGATTTACAATGTGTTCCTTTTATATGCCTATATT
Found at i:2496934 original size:23 final size:23
Alignment explanation
Indices: 2496890--2496942 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
2496880 TTTTTTTTAT
*
2496890 TTTTTTAAAAAATATAATAATAA
1 TTTTTTAAAAAATATAAAAATAA
*
2496913 TTTTTTAAATTAATA-AAAAATAA
1 TTTTTTAAA-AAATATAAAAATAA
*
2496936 TATTTTA
1 TTTTTTA
2496943 GTTTTTTCAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 22 0.85
24 4 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TTTTTTAAAAAATATAAAAATAA
Found at i:2498440 original size:16 final size:17
Alignment explanation
Indices: 2498411--2498443 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2498401 ATCGTTTAAG
2498411 AAATAAAAATAATTATT
1 AAATAAAAATAATTATT
2498428 AAATAAAAA-AATTATT
1 AAATAAAAATAATTATT
2498444 TTGAGGATCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAATAAAAATAATTATT
Found at i:2500404 original size:21 final size:20
Alignment explanation
Indices: 2500380--2500423 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
2500370 ATTTTTATTT
*
2500380 AAATTAAAAATACTAAATATA
1 AAATTAAAAATAATAAA-ATA
* *
2500401 AAATTATAATTAATAAAATA
1 AAATTAAAAATAATAAAATA
2500421 AAA
1 AAA
2500424 ATATTTAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (20 bp):
AAATTAAAAATAATAAAATA
Found at i:2508410 original size:2 final size:2
Alignment explanation
Indices: 2508403--2508428 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2508393 TATGGCCTTA
2508403 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
2508429 TCACGTGTAA
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:2508638 original size:44 final size:44
Alignment explanation
Indices: 2508570--2508654 Score: 143
Period size: 44 Copynumber: 1.9 Consensus size: 44
2508560 TGCCCATGAT
*
2508570 AGTGCCGCTATCACTTACCTAGCATTAGCTAAAACTACCAGTTA
1 AGTGCCGCTATCACTTACCCAGCATTAGCTAAAACTACCAGTTA
* *
2508614 AGTGCGGCTATCATTTACCCAGCATTAGCTAAAACTACCAG
1 AGTGCCGCTATCACTTACCCAGCATTAGCTAAAACTACCAG
2508655 CAATGTAGTA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.26
Consensus pattern (44 bp):
AGTGCCGCTATCACTTACCCAGCATTAGCTAAAACTACCAGTTA
Found at i:2529971 original size:2 final size:2
Alignment explanation
Indices: 2529958--2530033 Score: 143
Period size: 2 Copynumber: 38.0 Consensus size: 2
2529948 ATCTATCTTG
*
2529958 AT AT AC 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 AT AT
2530000 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
2530034 NNNNNNNNNN
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2530090 original size:2 final size:2
Alignment explanation
Indices: 2530083--2530159 Score: 154
Period size: 2 Copynumber: 38.5 Consensus size: 2
2530073 NNNNNNNNNN
2530083 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
2530125 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2530160 GTCATCCTAC
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 75 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2540695 original size:29 final size:29
Alignment explanation
Indices: 2540662--2540732 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
2540652 ATTTTTAATC
* *
2540662 ATAAAATTTTATTTAATCCAAAATAAAA-T
1 ATAAAAATTTATTTAAT-CAAAATAAAACA
* * *
2540691 ATAAAAATTTAATTGATCATAATAAAACA
1 ATAAAAATTTATTTAATCAAAATAAAACA
2540720 ATAAAAATTTATT
1 ATAAAAATTTATT
2540733 CAAAATTTTC
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 9 0.26
29 26 0.74
ACGTcount: A:0.56, C:0.06, G:0.01, T:0.37
Consensus pattern (29 bp):
ATAAAAATTTATTTAATCAAAATAAAACA
Found at i:2545665 original size:2 final size:2
Alignment explanation
Indices: 2545658--2545683 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2545648 AATATGGTGG
2545658 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
2545684 TGATTATGAC
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:2571659 original size:1 final size:1
Alignment explanation
Indices: 2571653--2571678 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
2571643 GCCAATATAC
2571653 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
2571679 TCCTTTCTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2584915 original size:18 final size:18
Alignment explanation
Indices: 2584892--2584928 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
2584882 AGTCTGCCTC
2584892 TTCTTCGCC-TCCTCCGCT
1 TTCTTCGCCAT-CTCCGCT
2584910 TTCTTCGCCATCTCCGCT
1 TTCTTCGCCATCTCCGCT
2584928 T
1 T
2584929 GCTCCTCCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.03, C:0.46, G:0.11, T:0.41
Consensus pattern (18 bp):
TTCTTCGCCATCTCCGCT
Found at i:2587112 original size:28 final size:29
Alignment explanation
Indices: 2587081--2587135 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
2587071 ATTTTAAAAA
* *
2587081 ATTCAAATGA-TATTTATTTTTTTATTAC
1 ATTCAAATAAGTATTTATATTTTTATTAC
*
2587109 ATTCAACTAAGTATTTATATTTTTATT
1 ATTCAAATAAGTATTTATATTTTTATT
2587136 TTATATTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 8 0.35
29 15 0.65
ACGTcount: A:0.33, C:0.07, G:0.04, T:0.56
Consensus pattern (29 bp):
ATTCAAATAAGTATTTATATTTTTATTAC
Found at i:2587156 original size:17 final size:17
Alignment explanation
Indices: 2587134--2587167 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
2587124 TATATTTTTA
2587134 TTTTAT-ATTAAATAATT
1 TTTTATAATT-AATAATT
2587151 TTTTATAATTAATAATT
1 TTTTATAATTAATAATT
2587168 GATTAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTTATAATTAATAATT
Found at i:2587896 original size:15 final size:15
Alignment explanation
Indices: 2587875--2587925 Score: 65
Period size: 15 Copynumber: 3.7 Consensus size: 15
2587865 TGATTAATAC
2587875 TTAATTAATTACCCA
1 TTAATTAATTACCCA
*
2587890 TTGATTAA-TA--C-
1 TTAATTAATTACCCA
2587901 TTAATTAATTACCCA
1 TTAATTAATTACCCA
2587916 TTAATTAATT
1 TTAATTAATT
2587926 GAAGTCTCAC
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
11 7 0.23
12 3 0.10
14 3 0.10
15 17 0.57
ACGTcount: A:0.39, C:0.14, G:0.02, T:0.45
Consensus pattern (15 bp):
TTAATTAATTACCCA
Found at i:2587901 original size:26 final size:26
Alignment explanation
Indices: 2587865--2587924 Score: 111
Period size: 26 Copynumber: 2.3 Consensus size: 26
2587855 TCTCAATAAC
2587865 TGATTAATACTTAATTAATTACCCAT
1 TGATTAATACTTAATTAATTACCCAT
2587891 TGATTAATACTTAATTAATTACCCAT
1 TGATTAATACTTAATTAATTACCCAT
*
2587917 TAATTAAT
1 TGATTAAT
2587925 TGAAGTCTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.40, C:0.13, G:0.03, T:0.43
Consensus pattern (26 bp):
TGATTAATACTTAATTAATTACCCAT
Found at i:2607360 original size:45 final size:45
Alignment explanation
Indices: 2607311--2607401 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 45
2607301 GAAATTTGCA
2607311 AAGAGAACATTGCAAATTTAATATTAGC-TTATTTTTAAATTTTAT
1 AAGAGAACATTGCAAATTTAATATTA-CATTATTTTTAAATTTTAT
* *
2607356 AAGAGAACGTTGTAAATTTAATATTACATTATTTTTAAATTTTAT
1 AAGAGAACATTGCAAATTTAATATTACATTATTTTTAAATTTTAT
2607401 A
1 A
2607402 TAAGGTGGAG
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
44 1 0.02
45 42 0.98
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (45 bp):
AAGAGAACATTGCAAATTTAATATTACATTATTTTTAAATTTTAT
Found at i:2609011 original size:2 final size:2
Alignment explanation
Indices: 2609006--2609042 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
2608996 TCCCTTTTAA
2609006 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT -T AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2609043 AACTTGTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
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):
AT
Found at i:2609632 original size:2 final size:2
Alignment explanation
Indices: 2609627--2609661 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2609617 ATACAACAAN
2609627 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
2609662 CACTTTAAAT
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:2622101 original size:2 final size:2
Alignment explanation
Indices: 2622079--2622116 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
2622069 GAAATCTATG
* *
2622079 AT AT TT AT AT AT -T AT AC 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 A
2622117 AAAATATTAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2622180 original size:36 final size:36
Alignment explanation
Indices: 2622131--2622199 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
2622121 TATTACATAA
* *
2622131 ATTCTAAATTTTTAAATGAAACTAATCTTTATCGTG
1 ATTCTAAAATTTTAAATGAAAATAATCTTTATCGTG
2622167 ATTCTAAAATTTTAAATGAAAATAATCTTTATC
1 ATTCTAAAATTTTAAATGAAAATAATCTTTATC
2622200 ATGAAAAGCA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.41, C:0.10, G:0.06, T:0.43
Consensus pattern (36 bp):
ATTCTAAAATTTTAAATGAAAATAATCTTTATCGTG
Found at i:2625943 original size:16 final size:17
Alignment explanation
Indices: 2625922--2625953 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2625912 TACAACTTAC
2625922 AAATAAAAA-TAAAAAT
1 AAATAAAAAGTAAAAAT
2625938 AAATAAAAAGTAAAAA
1 AAATAAAAAGTAAAAA
2625954 ATTTTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (17 bp):
AAATAAAAAGTAAAAAT
Found at i:2625977 original size:17 final size:16
Alignment explanation
Indices: 2625927--2625977 Score: 50
Period size: 17 Copynumber: 3.1 Consensus size: 16
2625917 CTTACAAATA
* *
2625927 AAAATAAAAATAAATA
1 AAAATAAAAATATATT
*
2625943 AAAAGTAAAAA-ATTTT
1 AAAA-TAAAAATATATT
2625959 AAAATAAAATATATATT
1 AAAATAAAA-ATATATT
2625976 AA
1 AA
2625978 TAATTTAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
15 5 0.18
16 11 0.39
17 12 0.43
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (16 bp):
AAAATAAAAATATATT
Found at i:2626077 original size:22 final size:22
Alignment explanation
Indices: 2626037--2626083 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
2626027 TTAAAAGACT
*
2626037 AAAAAATGAAAATACAAATAGAA
1 AAAAAAAGAAAATACAAATA-AA
*
2626060 AAAAAAAGAAACTA-AAATAAA
1 AAAAAAAGAAAATACAAATAAA
2626081 AAA
1 AAA
2626084 TCATATTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 5 0.23
23 12 0.55
ACGTcount: A:0.79, C:0.04, G:0.06, T:0.11
Consensus pattern (22 bp):
AAAAAAAGAAAATACAAATAAA
Found at i:2631305 original size:134 final size:134
Alignment explanation
Indices: 2631130--2631401 Score: 481
Period size: 134 Copynumber: 2.0 Consensus size: 134
2631120 TAAAAGTCCA
* *
2631130 ACTTTTCTTACCTCAGAGCCATGCTTTCTCACCTGCTATCTTTTGTTGATTTTAGTTTTAGGTGT
1 ACTTTTCTTACCTCAGAGCCATGCTTCCTCACCTGCTATCTTTTGTTGATTTCAGTTTTAGGTGT
*
2631195 GCCTGTGTGTGATGACATCTATTTTCATGTTCACCTGTTGTCTGTCTCCCTTATTGTTCATCTCC
66 GCCTGTGTGTGATGACATCTATTTTCATGTTCACCTGTTGTCCGTCTCCCTTATTGTTCATCTCC
2631260 TGAT
131 TGAT
* *
2631264 ACTTTTGTTACCTCAGAGCCATTCTTCCTCACCTGCTATCTTTTGTTGATTTCAGTTTTAGGTGT
1 ACTTTTCTTACCTCAGAGCCATGCTTCCTCACCTGCTATCTTTTGTTGATTTCAGTTTTAGGTGT
* *
2631329 GCCTGTGTGTGATGACATCTATTTTCATGTTCACCTTTTGTCCGTCTGCCTTATTGTTCATCTCC
66 GCCTGTGTGTGATGACATCTATTTTCATGTTCACCTGTTGTCCGTCTCCCTTATTGTTCATCTCC
2631394 TGAT
131 TGAT
2631398 ACTT
1 ACTT
2631402 GTGTCATTTT
Statistics
Matches: 131, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
134 131 1.00
ACGTcount: A:0.14, C:0.24, G:0.16, T:0.46
Consensus pattern (134 bp):
ACTTTTCTTACCTCAGAGCCATGCTTCCTCACCTGCTATCTTTTGTTGATTTCAGTTTTAGGTGT
GCCTGTGTGTGATGACATCTATTTTCATGTTCACCTGTTGTCCGTCTCCCTTATTGTTCATCTCC
TGAT
Found at i:2635161 original size:2 final size:2
Alignment explanation
Indices: 2635154--2635183 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2635144 TAAGTATTAT
2635154 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
2635184 GGTTATTCTT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2642746 original size:2 final size:2
Alignment explanation
Indices: 2642739--2642780 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
2642729 AAACCGAGGA
2642739 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2642781 GAAGGGAGAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2642892 original size:3 final size:3
Alignment explanation
Indices: 2642886--2642919 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
2642876 CACTCCTCCA
* *
2642886 AAC AAC AGC AAC ATC AAC AAC AAC AAC AAC AAC A
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC A
2642920 GTGACGATGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.32, G:0.03, T:0.03
Consensus pattern (3 bp):
AAC
Found at i:2645946 original size:2 final size:2
Alignment explanation
Indices: 2645934--2645969 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2645924 TTATTGTTCG
2645934 AC AC A- AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
2645970 NNNNNNNNNN
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.47, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2646100 original size:2 final size:2
Alignment explanation
Indices: 2646093--2646124 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2646083 NNNNNNNACA
2646093 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
2646125 GTATATGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2646157 original size:2 final size:2
Alignment explanation
Indices: 2646152--2646177 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2646142 CCAGGTACTG
2646152 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
2646178 GCATTTCCAG
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:2668034 original size:12 final size:12
Alignment explanation
Indices: 2668019--2668062 Score: 70
Period size: 12 Copynumber: 3.7 Consensus size: 12
2668009 TGATGAGGAA
2668019 GACGATGACAAT
1 GACGATGACAAT
2668031 GACGATGACAAT
1 GACGATGACAAT
* *
2668043 GATGATGACGAT
1 GACGATGACAAT
2668055 GACGATGA
1 GACGATGA
2668063 TGGCGATGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.39, C:0.14, G:0.30, T:0.18
Consensus pattern (12 bp):
GACGATGACAAT
Found at i:2668038 original size:6 final size:6
Alignment explanation
Indices: 2668019--2668062 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 6
2668009 TGATGAGGAA
* * *
2668019 GACGAT GACAAT GACGAT GACAAT GATGAT GACGAT GACGAT GA
1 GACGAT GACGAT GACGAT GACGAT GACGAT GACGAT GACGAT GA
2668063 TGGCGATGAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.39, C:0.14, G:0.30, T:0.18
Consensus pattern (6 bp):
GACGAT
Found at i:2668061 original size:15 final size:15
Alignment explanation
Indices: 2668029--2668082 Score: 54
Period size: 15 Copynumber: 3.4 Consensus size: 15
2668019 GACGATGACA
2668029 ATGACGATGACAATGATG
1 ATGACGATGAC---GATG
2668047 ATGACGATGACGATG
1 ATGACGATGACGATG
* *
2668062 ATGGCGATGAAGATG
1 ATGACGATGACGATG
*
2668077 TTGACG
1 ATGACG
2668083 GTGGTGACGA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
15 21 0.66
18 11 0.34
ACGTcount: A:0.33, C:0.11, G:0.33, T:0.22
Consensus pattern (15 bp):
ATGACGATGACGATG
Found at i:2668063 original size:18 final size:18
Alignment explanation
Indices: 2667934--2668064 Score: 81
Period size: 18 Copynumber: 7.3 Consensus size: 18
2667924 TTATTGGTAT
2667934 TGATGATGACGATGAGGACGA
1 TGATGATGACGAT---GACGA
* *
2667955 TGATGAGGAAGATGAC-A
1 TGATGATGACGATGACGA
* *
2667972 -G-TGATGATGATTACGA
1 TGATGATGACGATGACGA
* * * *
2667988 TGATGTTTATGATGA-AA
1 TGATGATGACGATGACGA
* *
2668005 TTGATGATGAGGAAGACGA
1 -TGATGATGACGATGACGA
** *
2668024 TGACAATGACGATGACAA
1 TGATGATGACGATGACGA
2668042 TGATGATGACGATGACGA
1 TGATGATGACGATGACGA
2668060 TGATG
1 TGATG
2668065 GCGATGAAGA
Statistics
Matches: 83, Mismatches: 22, Indels: 13
0.70 0.19 0.11
Matches are distributed among these distances:
15 10 0.12
16 2 0.02
17 3 0.04
18 56 0.67
19 1 0.01
21 11 0.13
ACGTcount: A:0.36, C:0.08, G:0.32, T:0.24
Consensus pattern (18 bp):
TGATGATGACGATGACGA
Found at i:2674880 original size:19 final size:19
Alignment explanation
Indices: 2674856--2674893 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
2674846 AAGATTGTAA
2674856 TTAAGGATGTGGTATGCAC
1 TTAAGGATGTGGTATGCAC
2674875 TTAAGGATGTGGTATGCAC
1 TTAAGGATGTGGTATGCAC
2674894 AAGCATAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.32, T:0.32
Consensus pattern (19 bp):
TTAAGGATGTGGTATGCAC
Found at i:2678975 original size:2 final size:2
Alignment explanation
Indices: 2678968--2678997 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2678958 ACCATGAACC
*
2678968 CT CT CT CT CT CT CT CT CT CT CT CT TT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2678998 TTTTCATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:2682684 original size:29 final size:28
Alignment explanation
Indices: 2682639--2682694 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
2682629 AAAATTTTAA
* *
2682639 AATTAAATTATTTAATTTTTA-AAAAAT
1 AATTAAATTATTGAATTATTAGAAAAAT
2682666 AATTCAAATTGATTGAATTATTAGAAAAA
1 AATT-AAATT-ATTGAATTATTAGAAAAA
2682695 ATAAAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 4 0.17
28 5 0.21
29 10 0.42
30 5 0.21
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (28 bp):
AATTAAATTATTGAATTATTAGAAAAAT
Found at i:2693168 original size:22 final size:22
Alignment explanation
Indices: 2693142--2693188 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
2693132 CGTTTATTGA
2693142 TTATTTAAAAATTTTTGATTAT
1 TTATTTAAAAATTTTTGATTAT
** * *
2693164 TTATTTATTATTTTTTGGTTAT
1 TTATTTAAAAATTTTTGATTAT
2693186 TTA
1 TTA
2693189 AATCCATGTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (22 bp):
TTATTTAAAAATTTTTGATTAT
Found at i:2707584 original size:22 final size:23
Alignment explanation
Indices: 2707549--2707592 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
2707539 CTAACTATTT
2707549 TTTTCTTTTCTTGCTTTGTGTTTG
1 TTTTCTTTTCTTGCTTT-TGTTTG
2707573 TTTT-TTTT-TTGCTTTTGTTT
1 TTTTCTTTTCTTGCTTTTGTTT
2707593 CTGTGGTTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 5 0.25
22 7 0.35
23 4 0.20
24 4 0.20
ACGTcount: A:0.00, C:0.09, G:0.14, T:0.77
Consensus pattern (23 bp):
TTTTCTTTTCTTGCTTTTGTTTG
Found at i:2707846 original size:5 final size:5
Alignment explanation
Indices: 2707836--2707864 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
2707826 CATCCCGATT
2707836 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
2707865 TTAATTTATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:2712387 original size:7 final size:7
Alignment explanation
Indices: 2712371--2712401 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
2712361 GCAACCGGAA
2712371 ACAA-CC
1 ACAATCC
2712377 ACAATCC
1 ACAATCC
2712384 ACAATCC
1 ACAATCC
2712391 ACAATCC
1 ACAATCC
2712398 ACAA
1 ACAA
2712402 ATAAAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.17
7 20 0.83
ACGTcount: A:0.48, C:0.42, G:0.00, T:0.10
Consensus pattern (7 bp):
ACAATCC
Found at i:2716618 original size:15 final size:15
Alignment explanation
Indices: 2716598--2716628 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2716588 GTCCAACTGC
2716598 CACCATCACCACCAA
1 CACCATCACCACCAA
2716613 CACCATCACCACCAA
1 CACCATCACCACCAA
2716628 C
1 C
2716629 CCAACCCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.55, G:0.00, T:0.06
Consensus pattern (15 bp):
CACCATCACCACCAA
Found at i:2717682 original size:2 final size:2
Alignment explanation
Indices: 2717667--2717714 Score: 78
Period size: 2 Copynumber: 23.5 Consensus size: 2
2717657 AAAACTTCTC
*
2717667 TA TA TA GTA AA 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
2717710 TA TA T
1 TA TA T
2717715 NNNNNNNNNN
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 41 0.95
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2718030 original size:2 final size:2
Alignment explanation
Indices: 2718023--2718062 Score: 57
Period size: 2 Copynumber: 20.5 Consensus size: 2
2718013 NNNNNNNNNN
2718023 AT AT AT AT AT AT AT AT AT AT AT AT AT AT CA- AT AT A- 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
2718063 GGAGCACAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 2 0.06
2 32 0.91
3 1 0.03
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:2719011 original size:11 final size:11
Alignment explanation
Indices: 2718997--2719026 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
2718987 CCGAATAAAA
2718997 TATTAATATTT
1 TATTAATATTT
2719008 TATTAATATTT
1 TATTAATATTT
2719019 TATTAATA
1 TATTAATA
2719027 AAATATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TATTAATATTT
Done.