Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 187 of 202
Found at i:57421092 original size:19 final size:19
Alignment explanation
Indices: 57421070--57421106 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
57421060 TAAAAATTAT
*
57421070 GAAAATTGTTTAAAATATA
1 GAAAATTATTTAAAATATA
*
57421089 GAAAATTATTTGAAATAT
1 GAAAATTATTTAAAATAT
57421107 TATAAAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (19 bp):
GAAAATTATTTAAAATATA
Found at i:57421791 original size:18 final size:19
Alignment explanation
Indices: 57421770--57421812 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
57421760 TAAAAATTGG
*
57421770 AAAATTATGGAAAA-TATT
1 AAAATTATAGAAAATTATT
*
57421788 AAAAATATAGAAAATTATT
1 AAAATTATAGAAAATTATT
57421807 AAAATT
1 AAAATT
57421813 GTTAATAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (19 bp):
AAAATTATAGAAAATTATT
Found at i:57421841 original size:19 final size:19
Alignment explanation
Indices: 57421780--57421841 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
57421770 AAAATTATGG
* *
57421780 AAAATATTAAAAATA-TAG
1 AAAATTTTAAAAATATTAT
* *
57421798 AAAATTATTAAAATTGTTAAT
1 AAAATT-TTAAAAATATT-AT
*
57421819 AAAATTTTAAAACTATTAT
1 AAAATTTTAAAAATATTAT
57421838 AAAA
1 AAAA
57421842 AGCATAAATT
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
18 5 0.14
19 13 0.37
20 10 0.29
21 7 0.20
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (19 bp):
AAAATTTTAAAAATATTAT
Found at i:57422531 original size:30 final size:29
Alignment explanation
Indices: 57422494--57422659 Score: 183
Period size: 30 Copynumber: 5.6 Consensus size: 29
57422484 TTTTTTGCAT
*
57422494 TTTGACCCCTAAACTTT-TCTAAAAATACA
1 TTTGACCCCTAAACTTTCTC-AAAATTACA
*
57422523 TATTGACCCCTAAACTTTCTCAAAACTACA
1 T-TTGACCCCTAAACTTTCTCAAAATTACA
* * * *
57422553 TTTCAACCCCTAATCTTT-TCTAAATTATA
1 TTT-GACCCCTAAACTTTCTCAAAATTACA
57422582 TTTTGACCCCTAAACTTTCTCAAAATTACA
1 -TTTGACCCCTAAACTTTCTCAAAATTACA
*
57422612 TTCTGACCCTTAAACTTTCTCAAAATTACA
1 TT-TGACCCCTAAACTTTCTCAAAATTACA
* *
57422642 CTTTGGCCCCAAAACTTT
1 -TTTGACCCCTAAACTTT
57422660 TTTTGCACTT
Statistics
Matches: 116, Mismatches: 14, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
29 25 0.22
30 87 0.75
31 4 0.03
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.36
Consensus pattern (29 bp):
TTTGACCCCTAAACTTTCTCAAAATTACA
Found at i:57422606 original size:59 final size:60
Alignment explanation
Indices: 57422498--57422613 Score: 180
Period size: 59 Copynumber: 1.9 Consensus size: 60
57422488 TTGCATTTTG
57422498 ACCCCTAAACTTTTCTAAAAATACATATTGACCCCTAAACTTTCTCAAAACTACATTTCA
1 ACCCCTAAACTTTTCTAAAAATACATATTGACCCCTAAACTTTCTCAAAACTACATTTCA
* * * * *
57422558 ACCCCTAATCTTTTCT-AAATTATATTTTGACCCCTAAACTTTCTCAAAATTACATT
1 ACCCCTAAACTTTTCTAAAAATACATATTGACCCCTAAACTTTCTCAAAACTACATT
57422614 CTGACCCTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
59 36 0.71
60 15 0.29
ACGTcount: A:0.35, C:0.27, G:0.02, T:0.36
Consensus pattern (60 bp):
ACCCCTAAACTTTTCTAAAAATACATATTGACCCCTAAACTTTCTCAAAACTACATTTCA
Found at i:57422660 original size:89 final size:89
Alignment explanation
Indices: 57422492--57422660 Score: 227
Period size: 89 Copynumber: 1.9 Consensus size: 89
57422482 ATTTTTTTGC
57422492 ATTTTGACCCCTAAACTTTTCTAAAAATACATATTGACCCCTAAACTTTCTCAAAACTACATTTC
1 ATTTTGACCCCTAAACTTTTCTAAAAATACATATTGACCCCTAAACTTTCTCAAAACTACATTTC
* *
57422557 AACCCCTAATCTTTTCTAAATTAT
66 AACCCCAAAACTTTTCTAAATTAT
* * *
57422581 ATTTTGACCCCTAAAC-TTTCTCAAAATTACAT-TCTGACCCTTAAACTTTCTCAAAATTACACT
1 ATTTTGACCCCTAAACTTTTCT-AAAAATACATAT-TGACCCCTAAACTTTCTCAAAACTACA-T
**
57422644 TT-GGCCCCAAAACTTTT
63 TTCAACCCCAAAACTTTT
57422661 TTTGCACTTA
Statistics
Matches: 70, Mismatches: 7, Indels: 6
0.84 0.08 0.07
Matches are distributed among these distances:
88 6 0.09
89 61 0.87
90 3 0.04
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.37
Consensus pattern (89 bp):
ATTTTGACCCCTAAACTTTTCTAAAAATACATATTGACCCCTAAACTTTCTCAAAACTACATTTC
AACCCCAAAACTTTTCTAAATTAT
Found at i:57423049 original size:15 final size:15
Alignment explanation
Indices: 57423014--57423057 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
57423004 ACAAAAATAA
* *
57423014 AAGAGAAAGACAAAGG
1 AAGAAAAAGA-AAAAG
57423030 AAGAAAAAGAAAAAG
1 AAGAAAAAGAAAAAG
*
57423045 AAGAAAAGGAAAA
1 AAGAAAAAGAAAA
57423058 GGGGAGGAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.73, C:0.02, G:0.25, T:0.00
Consensus pattern (15 bp):
AAGAAAAAGAAAAAG
Found at i:57423164 original size:17 final size:17
Alignment explanation
Indices: 57423142--57423174 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
57423132 GCTGAACGAG
*
57423142 GGAGAAGAAAAAAGAAA
1 GGAGAAAAAAAAAGAAA
57423159 GGAGAAAAAAAAAGAA
1 GGAGAAAAAAAAAGAA
57423175 GAAGAAAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (17 bp):
GGAGAAAAAAAAAGAAA
Found at i:57423180 original size:23 final size:23
Alignment explanation
Indices: 57423153--57423197 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
57423143 GAGAAGAAAA
*
57423153 AAGAAAGGAGAAAAAAAAAGAAG
1 AAGAAAGAAGAAAAAAAAAGAAG
**
57423176 AAGAAAGAAGAAGGAAAAAGAA
1 AAGAAAGAAGAAAAAAAAAGAA
57423198 AGGGGGAAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (23 bp):
AAGAAAGAAGAAAAAAAAAGAAG
Found at i:57423192 original size:27 final size:27
Alignment explanation
Indices: 57423144--57423199 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
57423134 TGAACGAGGG
*
57423144 AGAAGAAAAAAGAAAGGAGAAAAAAAA
1 AGAAGAAAAAAGAAAAGAGAAAAAAAA
* *
57423171 AGAAGAAGAAAGAAGAAG-GAAAAAGAA
1 AGAAGAAAAAAGAA-AAGAGAAAAAAAA
57423198 AG
1 AG
57423200 GGGGAAAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 23 0.92
28 2 0.08
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (27 bp):
AGAAGAAAAAAGAAAAGAGAAAAAAAA
Found at i:57423232 original size:13 final size:13
Alignment explanation
Indices: 57423146--57423225 Score: 56
Period size: 13 Copynumber: 6.2 Consensus size: 13
57423136 AACGAGGGAG
57423146 AAGAAAAAAGAAA
1 AAGAAAAAAGAAA
*
57423159 GGAGAAAAAA-AAA
1 -AAGAAAAAAGAAA
* *
57423172 GAAGAAGAAAGAAG
1 -AAGAAAAAAGAAA
*
57423186 AAGGAAAAAG-AA
1 AAGAAAAAAGAAA
* ***
57423198 AGGGGGAAAGAAA
1 AAGAAAAAAGAAA
57423211 AAGAAAAAAGAAA
1 AAGAAAAAAGAAA
57423224 AA
1 AA
57423226 AATAAAAAAT
Statistics
Matches: 50, Mismatches: 14, Indels: 5
0.72 0.20 0.07
Matches are distributed among these distances:
12 8 0.16
13 32 0.64
14 10 0.20
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (13 bp):
AAGAAAAAAGAAA
Found at i:57423502 original size:21 final size:21
Alignment explanation
Indices: 57423476--57423515 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
57423466 AGCAAAGAAG
57423476 AAAAAAAG-AGAAGAAAAAATA
1 AAAAAAAGAAGAA-AAAAAATA
57423497 AAAAAAAGAAGAAAAAAAA
1 AAAAAAAGAAGAAAAAAAA
57423516 GGAAAAGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.03
Consensus pattern (21 bp):
AAAAAAAGAAGAAAAAAAATA
Found at i:57423521 original size:9 final size:10
Alignment explanation
Indices: 57423473--57423513 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
57423463 CCCAGCAAAG
57423473 AAGAA-AAAA
1 AAGAAGAAAA
57423482 AGAGAAGAAAA
1 A-AGAAGAAAA
*
57423493 AATAA-AAAA
1 AAGAAGAAAA
57423502 AAGAAGAAAA
1 AAGAAGAAAA
57423512 AA
1 AA
57423514 AAGGAAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
9 9 0.33
10 13 0.48
11 5 0.19
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (10 bp):
AAGAAGAAAA
Found at i:57423521 original size:19 final size:20
Alignment explanation
Indices: 57423476--57423513 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
57423466 AGCAAAGAAG
57423476 AAAAAAAGAGAAGAAAAAAT
1 AAAAAAAGAGAAGAAAAAAT
57423496 AAAAAAA-AGAAGAAAAAA
1 AAAAAAAGAGAAGAAAAAA
57423514 AAGGAAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.03
Consensus pattern (20 bp):
AAAAAAAGAGAAGAAAAAAT
Found at i:57423521 original size:22 final size:21
Alignment explanation
Indices: 57423476--57423527 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
57423466 AGCAAAGAAG
*
57423476 AAAAAAAGAGAAGAAAAAATA
1 AAAAAAAGAGAAGAAAAAAGA
57423497 AAAAAAAGAAGAA-AAAAAAGGA
1 AAAAAAAG-AGAAGAAAAAA-GA
57423519 AAAGAAAAG
1 AAA-AAAAG
57423528 GGTTCAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 14 0.52
22 8 0.30
23 5 0.19
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (21 bp):
AAAAAAAGAGAAGAAAAAAGA
Found at i:57423694 original size:5 final size:5
Alignment explanation
Indices: 57423684--57423719 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
57423674 TATTTATATT
*
57423684 TTTAA TTTAA TTTAA TTTAA TTTTAA TTTAT TTTAA
1 TTTAA TTTAA TTTAA TTTAA -TTTAA TTTAA TTTAA
57423720 ATAATTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 23 0.82
6 5 0.18
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTTAA
Found at i:57423707 original size:21 final size:20
Alignment explanation
Indices: 57423683--57423730 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 20
57423673 GTATTTATAT
*
57423683 TTTTAATTTAATTTAATTTAA
1 TTTTAATTTAATTTAA-ATAA
*
57423704 TTTTAATTTATTTTAAATAA
1 TTTTAATTTAATTTAAATAA
57423724 TTTTAAT
1 TTTTAAT
57423731 AAATAAGGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTAATTTAATTTAAATAA
Found at i:57424030 original size:11 final size:11
Alignment explanation
Indices: 57424016--57424145 Score: 65
Period size: 11 Copynumber: 12.9 Consensus size: 11
57424006 TTTTTTTTAA
57424016 TTTTAAAATAT
1 TTTTAAAATAT
57424027 TTTTAAAATACT
1 TTTTAAAATA-T
*
57424039 TTTT-TAAT-T
1 TTTTAAAATAT
*
57424048 TTTT----TAA
1 TTTTAAAATAT
57424055 TTTTAAAATAT
1 TTTTAAAATAT
*
57424066 TTTAAAAATACTT
1 TTTTAAAATA--T
*
57424079 TTTTTAAAT-T
1 TTTTAAAATAT
57424089 TTTT---A-A-
1 TTTTAAAATAT
*
57424095 TTTTAAAATAA
1 TTTTAAAATAT
57424106 TTTTAAAATAT
1 TTTTAAAATAT
*
57424117 TTTT-TAAT-T
1 TTTTAAAATAT
*
57424126 TTTT-AAAGAT
1 TTTTAAAATAT
57424136 TTTTAAAATA
1 TTTTAAAATA
57424146 AAAATGGGCC
Statistics
Matches: 92, Mismatches: 11, Indels: 32
0.68 0.08 0.24
Matches are distributed among these distances:
6 5 0.05
7 5 0.05
9 13 0.14
10 14 0.15
11 42 0.46
12 5 0.05
13 8 0.09
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.58
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:57424059 original size:79 final size:77
Alignment explanation
Indices: 57423966--57424129 Score: 249
Period size: 79 Copynumber: 2.1 Consensus size: 77
57423956 TAATAAATAT
** * *
57423966 ATTTTTTTAATTTTAAAATATTTTTTACATAC-TTTTTAAATTTTTTTTAATTTTAAAATATTTT
1 ATTTTTTTAATTTTAAAATATTTTAAAAATACTTTTTTAAA--TTTTTTAATTTTAAAATAATTT
57424030 TAAAATACTTTTTTA
64 TAAAATA-TTTTTTA
57424045 ATTTTTTTAATTTTAAAATATTTTAAAAATACTTTTTTTAAATTTTTTAATTTTAAAATAATTTT
1 ATTTTTTTAATTTTAAAATATTTTAAAAATAC-TTTTTTAAATTTTTTAATTTTAAAATAATTTT
57424110 AAAATATTTTTTA
65 AAAATATTTTTTA
57424123 ATTTTTT
1 ATTTTTT
57424130 AAAGATTTTT
Statistics
Matches: 79, Mismatches: 4, Indels: 5
0.90 0.05 0.06
Matches are distributed among these distances:
78 14 0.18
79 57 0.72
81 8 0.10
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (77 bp):
ATTTTTTTAATTTTAAAATATTTTAAAAATACTTTTTTAAATTTTTTAATTTTAAAATAATTTTA
AAATATTTTTTA
Found at i:57424102 original size:29 final size:30
Alignment explanation
Indices: 57424064--57424145 Score: 78
Period size: 29 Copynumber: 2.8 Consensus size: 30
57424054 ATTTTAAAAT
* **
57424064 ATTTTAAAAATACTTTTTTTAA-ATTTTTTA
1 ATTTTAAAAATA-ATTTTAAAATATTTTTTA
57424094 ATTTT-AAAATAATTTTAAAATATTTTTTA
1 ATTTTAAAAATAATTTTAAAATATTTTTTA
** * *
57424123 ATTTTTTAAAGATTTTTAAAATA
1 ATTTTAAAAATAATTTTAAAATA
57424146 AAAATGGGCC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
28 6 0.14
29 19 0.43
30 19 0.43
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (30 bp):
ATTTTAAAAATAATTTTAAAATATTTTTTA
Found at i:57424138 original size:40 final size:39
Alignment explanation
Indices: 57423966--57424129 Score: 233
Period size: 40 Copynumber: 4.2 Consensus size: 39
57423956 TAATAAATAT
* * * *
57423966 ATTTTTTTAATTTTAAAATATTTTTTACATACTTTTTAA
1 ATTTTTTTAATTTTAAAATAATTTTAAAATACTTTTTTA
*
57424005 ATTTTTTTTAATTTTAAAATATTTTTAAAATACTTTTTTA
1 A-TTTTTTTAATTTTAAAATAATTTTAAAATACTTTTTTA
57424045 ATTTTTTTAATTTTAAAAT-ATTTTAAAAATACTTTTTTTA
1 ATTTTTTTAATTTTAAAATAATTTT-AAAATAC-TTTTTTA
*
57424085 AATTTTTTAATTTTAAAATAATTTTAAAATA-TTTTTTA
1 ATTTTTTTAATTTTAAAATAATTTTAAAATACTTTTTTA
57424123 ATTTTTT
1 ATTTTTT
57424130 AAAGATTTTT
Statistics
Matches: 115, Mismatches: 6, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
38 17 0.15
39 26 0.23
40 67 0.58
41 5 0.04
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (39 bp):
ATTTTTTTAATTTTAAAATAATTTTAAAATACTTTTTTA
Found at i:57424542 original size:18 final size:17
Alignment explanation
Indices: 57424527--57424893 Score: 281
Period size: 17 Copynumber: 20.4 Consensus size: 17
57424517 ACAAATTTCC
*
57424527 CGTGTTTCAAAAATTTC
1 CGTGTTTCAAAAATTTT
* *
57424544 CATGTTTTCAAAAATTTC
1 CGTG-TTTCAAAAATTTT
**
57424562 CGTGTTTCAAAAATCCT
1 CGTGTTTCAAAAATTTT
57424579 CGTGTTTTCAAAAA-TTT
1 CGTG-TTTCAAAAATTTT
57424596 CGGTGTTTCAAAAATTTT
1 C-GTGTTTCAAAAATTTT
* * *
57424614 TGTGTTTAAAAAAAAATTTC
1 CGTGTTT---CAAAAATTTT
*
57424634 CGTGTTTCAAAAATTTG
1 CGTGTTTCAAAAATTTT
57424651 CGTGTTTTCAAAAATTTTT
1 CGTG-TTTCAAAAA-TTTT
*
57424670 GCGT-TTTCAAAAAAAATTCT
1 -CGTGTTTC---AAAAATTTT
** *
57424690 ATTGTTTCAAAAATGTT
1 CGTGTTTCAAAAATTTT
* *
57424707 CGCGTTTTCAAAAATTGT
1 CGTG-TTTCAAAAATTTT
*
57424725 CGTGTTTTAAAAATTTT
1 CGTGTTTCAAAAATTTT
*
57424742 CGTGTTTTCAAAAATGTTCA
1 CGTG-TTTCAAAAAT-TT-T
*
57424762 CGT-TTTCAAAAAATTCT
1 CGTGTTTC-AAAAATTTT
*
57424779 CGTGTTTCACAAATTTT
1 CGTGTTTCAAAAATTTT
* *
57424796 TGTGTTTTCAAAAAAATTCT
1 CGTG-TTTC--AAAAATTTT
*
57424816 CGTGTTTTCAAAAAATTCT
1 CGTG-TTTC-AAAAATTTT
*
57424835 CTTGTTTCAAAAATTTT
1 CGTGTTTCAAAAATTTT
*
57424852 CGCGTTTTCAAAAATTTT
1 CGTG-TTTCAAAAATTTT
*
57424870 CGTGTTTTAAAAATTTT
1 CGTGTTTCAAAAATTTT
57424887 CGTGTTT
1 CGTGTTT
57424894 TTTTTAAAAA
Statistics
Matches: 283, Mismatches: 43, Indels: 48
0.76 0.11 0.13
Matches are distributed among these distances:
17 111 0.39
18 100 0.35
19 25 0.09
20 42 0.15
21 5 0.02
ACGTcount: A:0.31, C:0.13, G:0.12, T:0.44
Consensus pattern (17 bp):
CGTGTTTCAAAAATTTT
Found at i:57424630 original size:20 final size:21
Alignment explanation
Indices: 57424605--57424646 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
57424595 TCGGTGTTTC
**
57424605 AAAAATTTTTGTGTTT-AAAA
1 AAAAATTTCCGTGTTTCAAAA
57424625 AAAAATTTCCGTGTTTCAAAA
1 AAAAATTTCCGTGTTTCAAAA
57424646 A
1 A
57424647 TTTGCGTGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (21 bp):
AAAAATTTCCGTGTTTCAAAA
Found at i:57424801 original size:145 final size:144
Alignment explanation
Indices: 57424531--57424894 Score: 427
Period size: 145 Copynumber: 2.5 Consensus size: 144
57424521 ATTTCCCGTG
* * *
57424531 TTTCAAAAATTTCCA-TGTTTTCAAAAATTTC-CGTGTTTCAAAAATCCTCGTGTTTTCAAAAA-
1 TTTCAAAAAATTCTATTG-TTTCAAAAATTTCGCGT-TTTCAAAAATTCTCGTGTTTT-AAAAAT
* ***
57424593 TTTCG-GTGTTTCAAAAATTTTTGTGTTTAAAAAAAAATTTCCGTGTTTCAAAAATTTGCGTGTT
63 TTTCGTGT-TTTCAAAAATGTTCACGTTTAAAAAAAAATTTCCGTGTTTCAAAAATTTGCGTGTT
* *
57424657 TTC-AAAAATTTTTGCGT
127 TTCAAAAAATTCTCGCGT
*
57424674 TTTCAAAAAAAATTCTATTGTTTCAAAAATGTTCGCGTTTTCAAAAATTGTCGTGTTTTAAAAAT
1 TTTC--AAAAAATTCTATTGTTTCAAAAAT-TTCGCGTTTTCAAAAATTCTCGTGTTTTAAAAAT
** * **
57424739 TTTCGTGTTTTCAAAAATGTTCACGTTT-TCAAAAAA-TTCTCGTGTTTCACAAATTTTTGTGTT
63 TTTCGTGTTTTCAAAAATGTTCACGTTTAAAAAAAAATTTC-CGTGTTTCAAAAATTTGCGTGTT
*
57424802 TTCAAAAAAATTCTCGTGT
127 TTC-AAAAAATTCTCGCGT
* *
57424821 TTTCAAAAAATTCTCTTGTTTCAAAAATTTTCGCGTTTTCAAAAATTTTCGTGTTTTAAAAATTT
1 TTTCAAAAAATTCTATTGTTTCAAAAA-TTTCGCGTTTTCAAAAATTCTCGTGTTTTAAAAATTT
57424886 TCGTGTTTT
65 TCGTGTTTT
57424895 TTTTAAAAAT
Statistics
Matches: 192, Mismatches: 18, Indels: 20
0.83 0.08 0.09
Matches are distributed among these distances:
143 4 0.02
144 3 0.02
145 119 0.62
146 46 0.24
147 20 0.10
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.45
Consensus pattern (144 bp):
TTTCAAAAAATTCTATTGTTTCAAAAATTTCGCGTTTTCAAAAATTCTCGTGTTTTAAAAATTTT
CGTGTTTTCAAAAATGTTCACGTTTAAAAAAAAATTTCCGTGTTTCAAAAATTTGCGTGTTTTCA
AAAAATTCTCGCGT
Found at i:57424895 original size:18 final size:18
Alignment explanation
Indices: 57424527--57424894 Score: 324
Period size: 18 Copynumber: 20.4 Consensus size: 18
57424517 ACAAATTTCC
*
57424527 CGTG-TTTCAAAAATTTC
1 CGTGTTTTCAAAAATTTT
* *
57424544 CATGTTTTCAAAAATTTC
1 CGTGTTTTCAAAAATTTT
**
57424562 CGTG-TTTCAAAAATCCT
1 CGTGTTTTCAAAAATTTT
57424579 CGTGTTTTCAAAAA-TTT
1 CGTGTTTTCAAAAATTTT
57424596 CG-GTGTTTCAAAAATTTT
1 CGTGT-TTTCAAAAATTTT
* ** *
57424614 TGTGTTTAAAAAAAAATTTC
1 CGTGTTT--TCAAAAATTTT
*
57424634 CGTG-TTTCAAAAATTTG
1 CGTGTTTTCAAAAATTTT
57424651 CGTGTTTTCAAAAATTTT
1 CGTGTTTTCAAAAATTTT
* * **
57424669 TGCGTTTTCAAAAAAAATT
1 CGTGTTTTC-AAAAATTTT
* *
57424688 C-TATTGTTTCAAAAATGTT
1 CGT-GT-TTTCAAAAATTTT
* *
57424707 CGCGTTTTCAAAAATTGT
1 CGTGTTTTCAAAAATTTT
57424725 CGTGTTTT-AAAAATTTT
1 CGTGTTTTCAAAAATTTT
*
57424742 CGTGTTTTCAAAAATGTT
1 CGTGTTTTCAAAAATTTT
** *
57424760 CACGTTTTCAAAAAATTCT
1 CGTGTTTTC-AAAAATTTT
*
57424779 CGTG-TTTCACAAATTTT
1 CGTGTTTTCAAAAATTTT
* *
57424796 TGTGTTTTCAAAAAAATTCT
1 CGTGTTTTC--AAAAATTTT
*
57424816 CGTGTTTTCAAAAAATTCT
1 CGTGTTTTC-AAAAATTTT
*
57424835 CTTG-TTTCAAAAATTTT
1 CGTGTTTTCAAAAATTTT
*
57424852 CGCGTTTTCAAAAATTTT
1 CGTGTTTTCAAAAATTTT
57424870 CGTGTTTT-AAAAATTTT
1 CGTGTTTTCAAAAATTTT
57424887 CGTGTTTT
1 CGTGTTTT
57424895 TTTTAAAAAT
Statistics
Matches: 284, Mismatches: 49, Indels: 36
0.77 0.13 0.10
Matches are distributed among these distances:
16 2 0.01
17 94 0.33
18 115 0.40
19 43 0.15
20 30 0.11
ACGTcount: A:0.31, C:0.13, G:0.12, T:0.45
Consensus pattern (18 bp):
CGTGTTTTCAAAAATTTT
Found at i:57424935 original size:17 final size:17
Alignment explanation
Indices: 57424711--57424935 Score: 63
Period size: 17 Copynumber: 12.6 Consensus size: 17
57424701 AATGTTCGCG
* *
57424711 TTTTCAAAAATTGTCGT
1 TTTTCAAAAATTCTTGT
57424728 GTTTT-AAAAATT-TTCGT
1 -TTTTCAAAAATTCTT-GT
**
57424745 GTTTTCAAAAATGTTCACG-
1 -TTTTCAAAAA--TTCTTGT
*
57424764 TTTTCAAAAAATTCTCGT
1 TTTTC-AAAAATTCTTGT
* * *
57424782 GTTTCACAAATTTTTGT
1 TTTTCAAAAATTCTTGT
*
57424799 GTTTTCAAAAAAATTCTCGT
1 -TTTTC--AAAAATTCTTGT
57424819 GTTTTCAAAAAATTCTCT-T
1 -TTTTC-AAAAATTCT-TGT
* *
57424838 GTTTCAAAAATT-TTCGCG
1 TTTTCAAAAATTCTT-G-T
57424856 TTTTCAAAAATT-TTCGT
1 TTTTCAAAAATTCTT-GT
*
57424873 GTTTT-AAAAATTTTCGTGTTT
1 -TTTTCAAAAA--TTC-T-TGT
* *
57424894 TTTTTAAAAA-T-ATGT
1 TTTTCAAAAATTCTTGT
* *
57424909 GTTTCTAAAATTCTTGT
1 TTTTCAAAAATTCTTGT
57424926 TTTTCAAAAA
1 TTTTCAAAAA
57424936 AATTCCGTGT
Statistics
Matches: 158, Mismatches: 26, Indels: 47
0.68 0.11 0.20
Matches are distributed among these distances:
15 10 0.06
16 3 0.02
17 51 0.32
18 46 0.29
19 18 0.11
20 22 0.14
21 7 0.04
22 1 0.01
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.48
Consensus pattern (17 bp):
TTTTCAAAAATTCTTGT
Found at i:57424939 original size:19 final size:19
Alignment explanation
Indices: 57424915--57424972 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
57424905 ATGTGTTTCT
57424915 AAAATTCTTGTTTTTCAAA
1 AAAATTCTTGTTTTTCAAA
*
57424934 AAAATTC-CGTGTTTTCAAA
1 AAAATTCTTGT-TTTTCAAA
* * *
57424953 AAAAATATTGTGTTTCAAA
1 AAAATTCTTGTTTTTCAAA
57424972 A
1 A
57424973 TTCTTGCGTT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
18 2 0.06
19 28 0.88
20 2 0.06
ACGTcount: A:0.41, C:0.10, G:0.09, T:0.40
Consensus pattern (19 bp):
AAAATTCTTGTTTTTCAAA
Found at i:57424953 original size:18 final size:18
Alignment explanation
Indices: 57424526--57424955 Score: 187
Period size: 18 Copynumber: 23.9 Consensus size: 18
57424516 AACAAATTTC
*
57424526 CCGTG-TTTCAAAAATTT
1 CCGTGTTTTCAAAAAATT
* *
57424543 CCATGTTTTCAAAAATTT
1 CCGTGTTTTCAAAAAATT
*
57424561 CCGTG-TTTC-AAAAATC
1 CCGTGTTTTCAAAAAATT
*
57424577 CTCGTGTTTTCAAAAATTT
1 C-CGTGTTTTCAAAAAATT
* *
57424596 CGGTG-TTTCAAAAATTT
1 CCGTGTTTTCAAAAAATT
** **
57424613 TTGTGTTTAAAAAAAAATTT
1 CCGTGTTT-TCAAAAAA-TT
*
57424633 CCGTG-TTTCAAAAATTT
1 CCGTGTTTTCAAAAAATT
* *
57424650 GCGTGTTTTCAAAAATTT
1 CCGTGTTTTCAAAAAATT
** *
57424668 TTGCGTTTTCAAAAAAAATT
1 CCGTGTTTTC--AAAAAATT
**
57424688 CTAT-TGTTTC-AAAAATGT
1 CCGTGT-TTTCAAAAAAT-T
* *
57424706 TCGCGTTTTC-AAAAATT
1 CCGTGTTTTCAAAAAATT
* *
57424723 GTCGTGTTTT-AAAAATTT
1 -CCGTGTTTTCAAAAAATT
* *
57424741 TCGTGTTTTCAAAAATGTT
1 CCGTGTTTTCAAAAA-ATT
57424760 CAC--GTTTTCAAAAAATT
1 C-CGTGTTTTCAAAAAATT
* *
57424777 CTCGTG-TTTCACAAATTT
1 C-CGTGTTTTCAAAAAATT
**
57424795 TTGTGTTTTCAAAAAAATT
1 CCGTGTTTTC-AAAAAATT
57424814 CTCGTGTTTTCAAAAAATT
1 C-CGTGTTTTCAAAAAATT
* *
57424833 CTCTTG-TTTCAAAAATTT
1 C-CGTGTTTTCAAAAAATT
* * *
57424851 TCGCGTTTTCAAAAATTT
1 CCGTGTTTTCAAAAAATT
* *
57424869 TCGTGTTTT-AAAAATTT
1 CCGTGTTTTCAAAAAATT
* **
57424886 TCGTGTTTTTTTTAAAAATAT
1 CCGTG--TTTTCAAAAAAT-T
*
57424907 --GTG-TTTC-TAAAATT
1 CCGTGTTTTCAAAAAATT
*
57424921 -CTTGTTTTTCAAAAAAATT
1 CCGTG-TTTTC-AAAAAATT
57424940 CCGTGTTTTCAAAAAA
1 CCGTGTTTTCAAAAAA
57424956 AATATTGTGT
Statistics
Matches: 323, Mismatches: 56, Indels: 67
0.72 0.13 0.15
Matches are distributed among these distances:
14 1 0.00
15 7 0.02
16 9 0.03
17 75 0.23
18 141 0.44
19 55 0.17
20 34 0.11
21 1 0.00
ACGTcount: A:0.32, C:0.13, G:0.11, T:0.44
Consensus pattern (18 bp):
CCGTGTTTTCAAAAAATT
Found at i:57424966 original size:145 final size:143
Alignment explanation
Indices: 57424531--57424972 Score: 422
Period size: 145 Copynumber: 3.1 Consensus size: 143
57424521 ATTTCCCGTG
* * **
57424531 TTTCAAAAATTTCCA-TGTTTTCAAAAAT-TTC-CGTGTTTCAAAAATCCTCGTGTTTTCAAAAA
1 TTTCAAAAAATTCTATTG-TTTCAAAAATGTTCGCGT-TTTCAAAAATTGTCGTGTTTT-AAAAA
* * * *
57424593 -TTTCG-GTGTTTCAAAAATTTTTGTGTTTAAAAAAAAATT-TCCGTGTTTCAAAAATTTGCGTG
63 TTTTCGTGT-TTTCAAAAATATTCGT-TTT--CAAAAAATTCT-CGTGTTTCAAAAATTTCCGTG
* *
57424655 TTTTC--AAAAATTTTTGCGT
123 TTTTCAAAAAAATTATTGTGT
57424674 TTTCAAAAAAAATTCTATTGTTTCAAAAATGTTCGCGTTTTCAAAAATTGTCGTGTTTTAAAAAT
1 TTTC--AAAAAATTCTATTGTTTCAAAAATGTTCGCGTTTTCAAAAATTGTCGTGTTTTAAAAAT
* * **
57424739 TTTCGTGTTTTCAAAAATGTTCACGTTTTCAAAAAATTCTCGTGTTTCACAAATTTTTGTGTTTT
64 TTTCGTGTTTTCAAAAATATT--CGTTTTCAAAAAATTCTCGTGTTTCAAAAATTTCCGTGTTTT
* *
57424804 CAAAAAAATTCTCGTGT
127 CAAAAAAATTATTGTGT
* * *
57424821 TTTCAAAAAATTCTCTTGTTTCAAAAATTTTCGCGTTTTCAAAAATTTTCGTGTTTTAAAAATTT
1 TTTCAAAAAATTCTATTGTTTCAAAAATGTTCGCGTTTTCAAAAATTGTCGTGTTTTAAAAATTT
* * * * *
57424886 TCGTGTTTTTTTTAAAAATA-T-GTGTTTC-TAAAATTCTTGTTTTTCAAAAAAATTCCGTGTTT
66 TCGTG---TTTTCAAAAATATTCGT-TTTCAAAAAATTCTCGTGTTTC-AAAAATTTCCGTGTTT
*
57424948 TCAAAAAAAATATTGTG-
126 TCAAAAAAATTATTGTGT
57424965 TTTCAAAA
1 TTTCAAAA
57424973 TTCTTGCGTT
Statistics
Matches: 254, Mismatches: 28, Indels: 33
0.81 0.09 0.10
Matches are distributed among these distances:
143 4 0.02
144 24 0.09
145 148 0.58
146 42 0.17
147 24 0.09
148 12 0.05
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (143 bp):
TTTCAAAAAATTCTATTGTTTCAAAAATGTTCGCGTTTTCAAAAATTGTCGTGTTTTAAAAATTT
TCGTGTTTTCAAAAATATTCGTTTTCAAAAAATTCTCGTGTTTCAAAAATTTCCGTGTTTTCAAA
AAAATTATTGTGT
Found at i:57430685 original size:1 final size:1
Alignment explanation
Indices: 57430681--57430759 Score: 68
Period size: 1 Copynumber: 79.0 Consensus size: 1
57430671 CTAAAAATGC
* * * * * * * *
57430681 AAAAAAACAAAAAAAAAAACAAAAACAAAAACAAAAAAACAAAAAAACAAAAACAAAAAAAGAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
57430746 AGAAAAGAAAAAAA
1 AAAAAAAAAAAAAA
57430760 TTAAGATGAA
Statistics
Matches: 58, Mismatches: 20, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 58 1.00
ACGTcount: A:0.87, C:0.09, G:0.04, T:0.00
Consensus pattern (1 bp):
A
Found at i:57430691 original size:8 final size:8
Alignment explanation
Indices: 57430680--57430746 Score: 79
Period size: 8 Copynumber: 8.6 Consensus size: 8
57430670 CCTAAAAATG
57430680 CAAAAAAA
1 CAAAAAAA
57430688 CAAAAAAA
1 CAAAAAAA
57430696 -AAAACAAA
1 CAAAA-AAA
57430704 -AACAAAAA
1 CAA-AAAAA
57430712 CAAAAAAA
1 CAAAAAAA
57430720 CAAAAAAA
1 CAAAAAAA
57430728 C--AAAAA
1 CAAAAAAA
57430734 CAAAAAAA
1 CAAAAAAA
*
57430742 GAAAA
1 CAAAA
57430747 GAAAAGAAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 10
0.83 0.02 0.16
Matches are distributed among these distances:
6 6 0.11
7 4 0.08
8 39 0.74
9 4 0.08
ACGTcount: A:0.87, C:0.12, G:0.01, T:0.00
Consensus pattern (8 bp):
CAAAAAAA
Found at i:57430704 original size:28 final size:27
Alignment explanation
Indices: 57430680--57430759 Score: 101
Period size: 28 Copynumber: 3.0 Consensus size: 27
57430670 CCTAAAAATG
*
57430680 CAAAAAAACAAAA-AAAAAAACAAAAA
1 CAAAAAAAAAAAACAAAAAAACAAAAA
57430706 CAAAAACAAAAAAACAAAAAAACAAAAA
1 CAAAAA-AAAAAAACAAAAAAACAAAAA
* * *
57430734 CAAAAAAAGAAAAGAAAAGAA-AAAAA
1 CAAAAAAAAAAAACAAAAAAACAAAAA
57430760 TTAAGATGAA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
26 11 0.23
27 18 0.38
28 19 0.40
ACGTcount: A:0.86, C:0.10, G:0.04, T:0.00
Consensus pattern (27 bp):
CAAAAAAAAAAAACAAAAAAACAAAAA
Found at i:57432251 original size:79 final size:76
Alignment explanation
Indices: 57431972--57432271 Score: 413
Period size: 79 Copynumber: 3.8 Consensus size: 76
57431962 TACTATCCTA
* *
57431972 GAGGTATTTTCTAATTTCTATTTTTTCTAAAAAAATACAACTCATATTGCGAGAGGTGAGTTGAG
1 GAGGTATTTTTTAATTTCT-GTTTTTC---AAAAAT-CAACTCATATTGCGAGAGGTGAGTTGAG
*
57432037 CCTCGGGTCACACACC
61 CCTCGGGTCACACGCC
57432053 GAGGTATTTTTTAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 GAGGTATTTTTTAATTTCTGTTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
*
57432118 CGGGTCACACGCT
64 CGGGTCACACGCC
* * *
57432131 GAGGTA-TTTTTAATTTCTGTTTCTCAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCA
1 GAGGTATTTTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG
* *
57432195 GGTCATATGCC
66 GGTCACACGCC
*
57432206 GAGGTATTTCTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTCCGAGAGGTGAGTTGAGCC
1 GAGGTA-TT-TTTT-AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
57432271 T
63 T
57432272 AGACCTGTCC
Statistics
Matches: 202, Mismatches: 13, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
75 51 0.25
77 19 0.09
78 52 0.26
79 56 0.28
80 6 0.03
81 18 0.09
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (76 bp):
GAGGTATTTTTTAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCG
GGTCACACGCC
Found at i:57432470 original size:6 final size:6
Alignment explanation
Indices: 57432459--57432488 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
57432449 AAATATATAT
57432459 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
57432489 AAATACTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
TTTTTA
Found at i:57432813 original size:75 final size:73
Alignment explanation
Indices: 57432710--57433639 Score: 467
Period size: 78 Copynumber: 12.2 Consensus size: 73
57432700 GGACAGGTCT
*
57432710 AGTTGAGCCTCGGGTCACGCTGAGGTATTTTTCAATTTCTGCTTTTCAAAAATCAACTCATATTG
1 AGTTGAGCCTCGGGACACGCTGAGGTATTTTTCAATTTCTG-TTTTCAAAAATCAACTCATATTG
57432775 CGAGAGGTG
65 CGAGAGGTG
* *
57432784 AGTTGACCCTCGGGCACACGCAGAGGTATTTTTCAATTTCTGTTTTTTCAAAATAATCAACTCAT
1 AGTTGAGCCTCGGG-ACACGCTGAGGTATTTTTCAATTTCTG--TTTTC-AAA-AATCAACTCAT
*
57432849 ATTGCGAGAGATG
61 ATTGCGAGAGGTG
* *
57432862 AGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAAATTTCTGTTTTCAAAAATCAACTCATATTGC
1 AGTTGAGCCTCGGGACACGCTGAGGTATTTTTCAATTTCTGTTTTCAAAAATCAACTCATATTGC
57432927 GAGAGGTG
66 GAGAGGTG
* * * * * ** **
57432935 AGTTGAGCCTTGGGTCACATGCCGAGGTA--TTTC--TTTCAAG-TTTCTATTAT-TGCT-ATA-
1 AGTTGAGCCTCGGG--ACACGCTGAGGTATTTTTCAATTTC-TGTTTTCAAAAATCAACTCATAT
* *
57432992 -G-GTGAGTTG
63 TGCGAGAGGTG
* * * *** * * * * ****
57433001 AGCCTCGGGTCACAC-GTTTA-GGT-A-TTTTTCAATTTCTATTT-T-TCAAAAAATCAACTCAT
1 AG--TTGAG-C-CTCGGGACACGCTGAGGTATT---TTTCAATTTCTGTTTTCAAA--AA-TCA-
* * * *
57433060 ATTGCGAGA--G-GTGAGTTG
55 ACT-C-ATATTGCGAGAGGTG
* * * *
57433078 AGTCTCGAG--TC---ACACACCGAGGTATCTTTT-AATTTCTATTTTTCAAAAAAATCTACTCA
1 AGT-T-GAGCCTCGGGACACGCTGAGGTAT-TTTTCAATTTCT-GTTTTC--AAAAATCAACTCA
*
57433137 TATTACGAGAGGTG
60 TATTGCGAGAGGTG
* ** *
57433151 AGTTGAGCCTCGGGTCACATGCCAAGGTAATTCTTTTAATTTCTGTTTTTCAAATAAATCAACTC
1 AGTTGAGCCTCGGG--ACACGCTGAGGT-ATT-TTTCAATTTCTG-TTTTC-AA-AAATCAACTC
*
57433216 ATATTGCGAGTGGTG
59 ATATTGCGAGAGGTG
* *
57433231 AGTTGAGCCTCGGGTCACATC-CTGAGGTATTTTTCAGTTTCTATTTTTCAAAAAATCAACTCAT
1 AGTTGAGCCTCGGG--ACA-CGCTGAGGTATTTTTCAATTTCT-GTTTTC-AAAAATCAACTCAT
57433295 ATTGCGAGAGGTG
61 ATTGCGAGAGGTG
* * * * *
57433308 AGTTGAGCCTCGAGTCACATG-TCAAGGTATTTTTTAAATTTCTGTTTTTCAAAAAATCAACCCA
1 AGTTGAGCCTCG-G-GACACGCT-GAGGTA-TTTTTCAATTTCTG-TTTTC-AAAAATCAACTCA
*
57433372 TATTGCGAGAAGTG
60 TATTGCGAGAGGTG
* *
57433386 AGTTGAGCCTC-GGACACATGCCGAGGTATTTCTTTTAAATTTCTGTTTTTCAAAAATCAACTCA
1 AGTTGAGCCTCGGGACAC--GCTGAGGTA--T-TTTTCAATTTCTG-TTTTCAAAAATCAACTCA
57433450 TATTGCGAGAGGTG
60 TATTGCGAGAGGTG
* * *
57433464 AGTTGAGCCTTGGGTCACACGCTGAGGTATTTTTCAATTTTTGTATTTTTTTCAAAAAAATCAAT
1 AGTTGAGCCTCGGG--ACACGCTGAGGTATTTTTCAATTTCTG-----TTTTC--AAAAATCAAC
*
57433529 TCATATTGGGAGAGGTG
57 TCATATTGCGAGAGGTG
* * * * *
57433546 AGTTGAACCTCGGGTTGCAGGCCGAGATATTCTTTTCAATTTCTGTTTTTCAAAAAAATCAACTC
1 AGTTGAGCCTCGGG--ACACGCTGAGGTA-T-TTTTCAATTTCTG-TTTTC--AAAAATCAACTC
*
57433611 ATATTTCGAGAGGTG
59 ATATTGCGAGAGGTG
57433626 AGTTGAGCCTCGGG
1 AGTTGAGCCTCGGG
57433640 TCGCATGCCG
Statistics
Matches: 666, Mismatches: 113, Indels: 148
0.72 0.12 0.16
Matches are distributed among these distances:
64 1 0.00
65 1 0.00
66 9 0.01
67 2 0.00
68 3 0.00
69 10 0.02
70 5 0.01
71 24 0.04
72 9 0.01
73 54 0.08
74 22 0.03
75 45 0.07
76 21 0.03
77 93 0.14
78 154 0.23
79 40 0.06
80 109 0.16
81 4 0.01
82 47 0.07
83 1 0.00
84 12 0.02
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (73 bp):
AGTTGAGCCTCGGGACACGCTGAGGTATTTTTCAATTTCTGTTTTCAAAAATCAACTCATATTGC
GAGAGGTG
Found at i:57433024 original size:61 final size:58
Alignment explanation
Indices: 57432921--57433040 Score: 150
Period size: 61 Copynumber: 2.0 Consensus size: 58
57432911 AATCAACTCA
* *
57432921 TATTGCGAGAGGTGAGTTGAGCCTTGGGTCACATGCCGAGGTATTTCTTTCAAGTTTCTAT
1 TATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCGAGGTA-TT-TTTCAA-TTTCTAT
* * ***
57432982 TATTGCTATAGGTGAGTTGAGCCTCGGGTCACACGTTTAGGTATTTTTCAATTTCTAT
1 TATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCGAGGTATTTTTCAATTTCTAT
57433040 T
1 T
57433041 TTTCAAAAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
58 8 0.15
59 6 0.12
60 2 0.04
61 36 0.69
ACGTcount: A:0.20, C:0.16, G:0.25, T:0.39
Consensus pattern (58 bp):
TATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCGAGGTATTTTTCAATTTCTAT
Found at i:57433098 original size:138 final size:131
Alignment explanation
Indices: 57432860--57433117 Score: 363
Period size: 138 Copynumber: 1.9 Consensus size: 131
57432850 TTGCGAGAGA
57432860 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAAATTTCTGTTTTCAAAAATCAACTCATATT
1 TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAAATTTCTGTTTTCAAAAATCAACTCATATT
* * **
57432925 GCGAGAGGTGAGTTGAGCCTTGGGTCACATGCCGAGGTATTTCTTTCAAGTTTCTATTATTGCTA
66 GCGAGAGGTGAGTTGAGCCTCGAGTCACACACCGAGGTA--TCTTTCAA-TTTCTATTATTGCTA
57432990 TAGG
128 TAGG
* * * *
57432994 TGAGTTGAGCCTCGGGTCACACGTTTAGGTATTTTTCAATTTCTATTTTTCAAAAAATCAACTCA
1 TGAGTTGAGCCTCGGGT--CACGCTGAGGTATTTTTAAATTTCT-GTTTTC-AAAAATCAACTCA
* *
57433059 TATTGCGAGAGGTGAGTTGAGTCTCGAGTCACACACCGAGGTATCTTTTAATTTCTATT
62 TATTGCGAGAGGTGAGTTGAGCCTCGAGTCACACACCGAGGTATCTTTCAATTTCTATT
57433118 TTTCAAAAAA
Statistics
Matches: 110, Mismatches: 10, Indels: 7
0.87 0.08 0.06
Matches are distributed among these distances:
134 17 0.15
135 8 0.07
136 29 0.26
137 5 0.05
138 51 0.46
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (131 bp):
TGAGTTGAGCCTCGGGTCACGCTGAGGTATTTTTAAATTTCTGTTTTCAAAAATCAACTCATATT
GCGAGAGGTGAGTTGAGCCTCGAGTCACACACCGAGGTATCTTTCAATTTCTATTATTGCTATAG
G
Found at i:57433218 original size:80 final size:77
Alignment explanation
Indices: 57432982--57433651 Score: 797
Period size: 78 Copynumber: 8.5 Consensus size: 77
57432972 AAGTTTCTAT
* * * *** * *
57432982 TATTGCTATAGGTGAGTTGAGCCTCGGGTCACACGTTTAGGTATTTTTCAATTTCTATTTTTCAA
1 TATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTTTAATTTCTGTTTTTCAA
57433047 AAAATCAACTCA
66 AAAATCAACTCA
* * ** * *
57433059 TATTGCGAGAGGTGAGTTGAGTCTCGAGTCACACACCGAGGTATCTTTTAATTTCTATTTTTCAA
1 TATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTTTAATTTCTGTTTTTC-A
*
57433124 AAAAATCTACTCA
65 AAAAATCAACTCA
* *
57433137 TATTACGAGAGGTGAGTTGAGCCTCGGGTCACATGCCAAGGTAATTCTTTTAATTTCTGTTTTTC
1 TATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGT-ATT-TTTTAATTTCTGTTTTTC
57433202 AAATAAATCAACTCA
64 AAA-AAATCAACTCA
* * * *
57433217 TATTGCGAGTGGTGAGTTGAGCCTCGGGTCACAT-CCTGAGGTATTTTTCAGTTTCTATTTTTCA
1 TATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCC-GAGGTATTTTTTAATTTCTGTTTTTCA
57433281 AAAAATCAACTCA
65 AAAAATCAACTCA
* * *
57433294 TATTGCGAGAGGTGAGTTGAGCCTCGAGTCACATGTCAAGGTATTTTTTAAATTTCTGTTTTTCA
1 TATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTTT-AATTTCTGTTTTTCA
*
57433359 AAAAATCAACCCA
65 AAAAATCAACTCA
* *
57433372 TATTGCGAGAAGTGAGTTGAGCCTC-GGACACATGCCGAGGTATTTCTTTTAAATTTCTGTTTTT
1 TATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTA-TT-TTTT-AATTTCTGTTTTT
57433436 C-AAAAATCAACTCA
63 CAAAAAATCAACTCA
* * * * *
57433450 TATTGCGAGAGGTGAGTTGAGCCTTGGGTCACACGCTGAGGTATTTTTCAATTTTTGTATTTTTT
1 TATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTTTAATTTCTG----TTTT
*
57433515 TCAAAAAAATCAATTCA
62 TC-AAAAAATCAACTCA
* * ** * *
57433532 TATTGGGAGAGGTGAGTTGAACCTCGGGTTGCAGGCCGAGATATTCTTTTCAATTTCTGTTTTTC
1 TATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATT-TTTT-AATTTCTGTTTTTC
57433597 AAAAAAATCAACTCA
64 -AAAAAATCAACTCA
* *
57433612 TATTTCGAGAGGTGAGTTGAGCCTCGGGTCGCATGCCGAG
1 TATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAG
57433652 CTGTTCTCGA
Statistics
Matches: 511, Mismatches: 64, Indels: 33
0.84 0.11 0.05
Matches are distributed among these distances:
76 7 0.01
77 122 0.24
78 156 0.31
79 43 0.08
80 124 0.24
82 49 0.10
83 3 0.01
84 7 0.01
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (77 bp):
TATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTTTAATTTCTGTTTTTCAA
AAAATCAACTCA
Found at i:57433429 original size:235 final size:232
Alignment explanation
Indices: 57432982--57433638 Score: 904
Period size: 235 Copynumber: 2.8 Consensus size: 232
57432972 AAGTTTCTAT
* * * *
57432982 TATTGCTATAGGTGAGTTGAGCCTCGGGTCACACGTTTAGGTATTTTTCAATTTCTATTTTTCAA
1 TATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTTCAATTTCTATTTTTCAA
* * *
57433047 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTCGAGTCACACACCGAGGTATCTTTTAATT
66 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCACACGCCGAGGTATTTTTTAATT
* * *
57433112 TCTATTTTTCAAAAAAATCTACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCACATGCCAAG
131 TCTGTTTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTC-GGACACATGCCAAG
57433177 GTAATTCTTTTAATTTCTGTTTTTCAAATAAATCAACTCA
195 GTAATTCTTTTAATTTCTGTTTTTC-AA-AAATCAACTCA
* *
57433217 TATTGCGAGTGGTGAGTTGAGCCTCGGGTCACATC-CTGAGGTATTTTTCAGTTTCTATTTTTCA
1 TATTGCGAGAGGTGAGTTGAGCCTCGGGTCACA-CGCTGAGGTATTTTTCAATTTCTATTTTTCA
* * *
57433281 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCACATGTCAAGGTATTTTTTAAA
65 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCACACGCCGAGGTATTTTTT-AA
* * * *
57433346 TTTCTGTTTTTC-AAAAAATCAACCCATATTGCGAGAAGTGAGTTGAGCCTCGGACACATGCCGA
129 TTTCTGTTTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGACACATGCCAA
*
57433410 GGTATTTCTTTTAAATTTCTGTTTTTCAAAAATCAACTCA
194 GGTAATTCTTTT-AATTTCTGTTTTTCAAAAATCAACTCA
* *
57433450 TATTGCGAGAGGTGAGTTGAGCCTTGGGTCACACGCTGAGGTATTTTTCAATTTTTGTATTTTTT
1 TATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTTCAA--TTTCTA--TTTT
* * * * ** * *
57433515 TCAAAAAAATCAATTCATATTGGGAGAGGTGAGTTGAACCTCGGGTTGCAGGCCGAGATATTCTT
62 TC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCACACGCCGAGGTATT-TT
*
57433580 TTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTTCGAGAGGTGAGTTGAGCCTCGG
125 TT-AATTTCTGTTTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGG
57433639 GTCGCATGCC
Statistics
Matches: 373, Mismatches: 38, Indels: 17
0.87 0.09 0.04
Matches are distributed among these distances:
232 1 0.00
233 57 0.15
234 24 0.06
235 166 0.45
236 14 0.04
237 6 0.02
238 49 0.13
239 18 0.05
240 38 0.10
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.36
Consensus pattern (232 bp):
TATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATTTTTCAATTTCTATTTTTCAA
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCACACGCCGAGGTATTTTTTAATT
TCTGTTTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGACACATGCCAAGG
TAATTCTTTTAATTTCTGTTTTTCAAAAATCAACTCA
Found at i:57433869 original size:30 final size:28
Alignment explanation
Indices: 57433834--57433999 Score: 163
Period size: 30 Copynumber: 5.6 Consensus size: 28
57433824 ATTTTTGCAT
*
57433834 TTTGACCCCTAAACTTTTCTAAAAATACA
1 TTTGACCCCTAAAC-TTTCTAAAATTACA
*
57433863 TGTTGACCCCTAAACTTTCTCAAAACTACA
1 T-TTGACCCCTAAACTTTCT-AAAATTACA
* *
57433893 TTTCAACCCCTAATCTTTTCT-AAATTACA
1 TTT-GACCCCTAAAC-TTTCTAAAATTACA
*
57433922 TTTTAACCCCTAAACTTTCTTAAAATTACA
1 -TTTGACCCCTAAACTTTC-TAAAATTACA
*
57433952 TTTTGACCCTTAAACTTTCTCAAAATTACA
1 -TTTGACCCCTAAACTTTCT-AAAATTACA
* *
57433982 CTTTGGCCCCAAAACTTT
1 -TTTGACCCCTAAACTTT
57434000 TTTTGCGTTT
Statistics
Matches: 118, Mismatches: 11, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
28 4 0.03
29 27 0.23
30 82 0.69
31 5 0.04
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.37
Consensus pattern (28 bp):
TTTGACCCCTAAACTTTCTAAAATTACA
Found at i:57433952 original size:59 final size:59
Alignment explanation
Indices: 57433838--57433999 Score: 189
Period size: 59 Copynumber: 2.7 Consensus size: 59
57433828 TTGCATTTTG
* *
57433838 ACCCCTAAACTTTTCTAAAAATACATGTTGACCCCTAAACTTTCTCAAAACTACATTTCA
1 ACCCCTAAACTTTTCT-AAATTACATTTTGACCCCTAAACTTTCTCAAAACTACATTTCA
* * * * **
57433898 ACCCCTAATCTTTTCTAAATTACATTTTAACCCCTAAACTTTCTTAAAATTACATTTTG
1 ACCCCTAAACTTTTCTAAATTACATTTTGACCCCTAAACTTTCTCAAAACTACATTTCA
* * * * *
57433957 ACCCTTAAACTTTCTCAAAATTACACTTTGGCCCCAAAACTTT
1 ACCCCTAAACTTT-TCTAAATTACATTTTGACCCCTAAACTTT
57434000 TTTTGCGTTT
Statistics
Matches: 86, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
59 47 0.55
60 39 0.45
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.36
Consensus pattern (59 bp):
ACCCCTAAACTTTTCTAAATTACATTTTGACCCCTAAACTTTCTCAAAACTACATTTCA
Found at i:57434000 original size:89 final size:89
Alignment explanation
Indices: 57433831--57434000 Score: 227
Period size: 89 Copynumber: 1.9 Consensus size: 89
57433821 TTAATTTTTG
*
57433831 CATTTTGACCCCTAAACTTTTCTAAAAATACATGTTGACCCCTAAACTTTCTCAAAACTACATTT
1 CATTTTAACCCCTAAACTTTTCTAAAAATACATGTTGACCCCTAAACTTTCTCAAAACTACATTT
* *
57433896 CAACCCCTAATCTTTTCTAAATTA
66 CAACCCCAAAACTTTTCTAAATTA
* * * *
57433920 CATTTTAACCCCTAAAC-TTTCTTAAAATTACATTTTGACCCTTAAACTTTCTCAAAATTACACT
1 CATTTTAACCCCTAAACTTTTC-TAAAAATACATGTTGACCCCTAAACTTTCTCAAAACTACA-T
**
57433984 TT-GGCCCCAAAACTTTT
64 TTCAACCCCAAAACTTTT
57434001 TTTGCGTTTA
Statistics
Matches: 70, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
88 4 0.06
89 63 0.90
90 3 0.04
ACGTcount: A:0.33, C:0.26, G:0.04, T:0.37
Consensus pattern (89 bp):
CATTTTAACCCCTAAACTTTTCTAAAAATACATGTTGACCCCTAAACTTTCTCAAAACTACATTT
CAACCCCAAAACTTTTCTAAATTA
Found at i:57434516 original size:15 final size:17
Alignment explanation
Indices: 57434482--57434513 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
57434472 GCTGAACGAG
57434482 GGAGAAGAAAAAAGAAA
1 GGAGAAGAAAAAAGAAA
57434499 GGAGAA-AAAAAAGAA
1 GGAGAAGAAAAAAGAA
57434514 GGAACAAGAA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (17 bp):
GGAGAAGAAAAAAGAAA
Found at i:57434522 original size:26 final size:28
Alignment explanation
Indices: 57434484--57434545 Score: 76
Period size: 26 Copynumber: 2.3 Consensus size: 28
57434474 TGAACGAGGG
57434484 AGAAGAAAAAAGAAA-GGAGAAA-AAAA
1 AGAAGAAAAAAGAAAGGGAGAAAGAAAA
* * *
57434510 AGAAGGAACAAGAAAGGGGGAAAGAAAA
1 AGAAGAAAAAAGAAAGGGAGAAAGAAAA
57434538 AGAA-AAAA
1 AGAAGAAAA
57434546 GAAAAAAACA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 13 0.45
27 8 0.28
28 8 0.28
ACGTcount: A:0.71, C:0.02, G:0.27, T:0.00
Consensus pattern (28 bp):
AGAAGAAAAAAGAAAGGGAGAAAGAAAA
Found at i:57434816 original size:13 final size:13
Alignment explanation
Indices: 57434798--57434822 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
57434788 GGCCCAGCAA
57434798 AGAAGAAAAAAGG
1 AGAAGAAAAAAGG
57434811 AGAAGAAAAAAG
1 AGAAGAAAAAAG
57434823 AAAAATAAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (13 bp):
AGAAGAAAAAAGG
Found at i:57434841 original size:22 final size:22
Alignment explanation
Indices: 57434796--57434854 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
57434786 CCGGCCCAGC
* *
57434796 AAAGAAGAAAAAAGGAGAAGAAA
1 AAAGAA-AAAAAAGAAGAAAAAA
*
57434819 AAAGAAAAATAAGAAGAAAAAA
1 AAAGAAAAAAAAGAAGAAAAAA
*
57434841 AAGGAAAAGAAAAG
1 AAAGAAAA-AAAAG
57434855 CGTTCAATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 20 0.67
23 10 0.33
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (22 bp):
AAAGAAAAAAAAGAAGAAAAAA
Found at i:57435369 original size:17 final size:17
Alignment explanation
Indices: 57435327--57435730 Score: 274
Period size: 17 Copynumber: 22.4 Consensus size: 17
57435317 ACAAATTTCC
57435327 CGTGTTTCAAAAATTTAAT
1 CGTGTTTCAAAAATTT--T
*
57435346 TGT-TTTCAAAAATTTT
1 CGTGTTTCAAAAATTTT
* **
57435362 CGCGTTTCAAAAATCCT
1 CGTGTTTCAAAAATTTT
*
57435379 CGTGTTTTCAAAAA-TTC
1 CGTG-TTTCAAAAATTTT
57435396 CGGTGTTTCAAAAATTTT
1 C-GTGTTTCAAAAATTTT
*
57435414 CGTGTTTTCAAAATTTTTTT
1 CGTG-TTTCAAAA--ATTTT
*
57435434 GCGT-TTTCAAAAAAAATTCT
1 -CGTGTTTC---AAAAATTTT
* *
57435454 CTTATTTCAAAAATTTT
1 CGTGTTTCAAAAATTTT
* *
57435471 CGCGTTTTCAAAAATTGT
1 CGTG-TTTCAAAAATTTT
*
57435489 CGTGTTTTAAAAATTTT
1 CGTGTTTCAAAAATTTT
57435506 CGTGTTTTCAAAAATTTT
1 CGTG-TTTCAAAAATTTT
* *
57435524 CATGTTTTCAAAAAATTCT
1 CGTG-TTTC-AAAAATTTT
*
57435543 CGTGTTTCACAAATTTT
1 CGTGTTTCAAAAATTTT
* *
57435560 TGTGTTTTCAAAAAAAATTCT
1 CGTG-TTTC---AAAAATTTT
*
57435581 CGTGTTTTCAAAAAATTCT
1 CGTG-TTTC-AAAAATTTT
*
57435600 CTTGTTTCAAAAATTTT
1 CGTGTTTCAAAAATTTT
* * *
57435617 TGCTTTTTCAAAAATTGT
1 CG-TGTTTCAAAAATTTT
* *
57435635 CGTGTTTTAAAAATTAT
1 CGTGTTTCAAAAATTTT
** *
57435652 CGTGTTTTTAAAATTCT
1 CGTGTTTCAAAAATTTT
* * *
57435669 CGTATTTCAAAAGTTTC
1 CGTGTTTCAAAAATTTT
*
57435686 CGTGTTTCAAAAAAGAATTCT
1 CGTGTTTC---AAA-AATTTT
57435707 CGTGTTTCAAAAATTTT
1 CGTGTTTCAAAAATTTT
57435724 CGTGTTT
1 CGTGTTT
57435731 TTTTTAAAAA
Statistics
Matches: 306, Mismatches: 55, Indels: 50
0.74 0.13 0.12
Matches are distributed among these distances:
16 2 0.01
17 126 0.41
18 99 0.32
19 32 0.10
20 14 0.05
21 29 0.09
22 4 0.01
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.46
Consensus pattern (17 bp):
CGTGTTTCAAAAATTTT
Found at i:57435369 original size:35 final size:34
Alignment explanation
Indices: 57435330--57435730 Score: 224
Period size: 35 Copynumber: 11.1 Consensus size: 34
57435320 AATTTCCCGT
**
57435330 GTTTCAAAAATTTAATTGTTTTCAAAAATTTTCGC
1 GTTTCAAAAATTT-CGTGTTTTCAAAAATTTTCGC
* * *
57435365 GTTTCAAAAATCCTCGTGTTTTCAAAAA-TTCCGGT
1 GTTTCAAAAAT-TTCGTGTTTTCAAAAATTTTC-GC
* *
57435400 GTTTCAAAAATTTTCGTGTTTTCAAAATTTTTTTGC
1 GTTTCAAAAA-TTTCGTGTTTTCAAAA-ATTTTCGC
57435436 GTTTTCAAAAAAAATTCTC-T-TATTTCAAAAATTTTCGC
1 G-TTTC---AAAAATT-TCGTGT-TTTCAAAAATTTTCGC
*
57435474 GTTTTCAAAAATTGTCGTGTTTT-AAAAATTTTCGT
1 G-TTTCAAAAATT-TCGTGTTTTCAAAAATTTTCGC
* * *
57435509 GTTTTCAAAAATTTTCATGTTTTCAAAAAATTCTCGT
1 G-TTTCAAAAA-TTTCGTGTTTTC-AAAAATTTTCGC
* * * *
57435546 GTTTCACAAATTTTTGTGTTTTCAAAAAAAATTCTCGT
1 GTTTCA-AAAATTTCGTGTTTTC---AAAAATTTTCGC
* *
57435584 GTTTTCAAAAAATTCTCTTG-TTTCAAAAATTTTTGC
1 G-TTTC-AAAAATT-TCGTGTTTTCAAAAATTTTCGC
* * *
57435620 TTTTTCAAAAATTGTCGTGTTTT-AAAAATTATCGT
1 -GTTTCAAAAATT-TCGTGTTTTCAAAAATTTTCGC
** * * * *
57435655 GTTTTTAAAATTCTCGT-ATTTCAAAAGTTTCCGT
1 GTTTCAAAAATT-TCGTGTTTTCAAAAATTTTCGC
*
57435689 GTTTCAAAAAAGAATTCTCGTG-TTTCAAAAATTTTCGT
1 GTTTC---AAA-AATT-TCGTGTTTTCAAAAATTTTCGC
57435727 GTTT
1 GTTT
57435731 TTTTTAAAAA
Statistics
Matches: 293, Mismatches: 43, Indels: 57
0.75 0.11 0.15
Matches are distributed among these distances:
33 3 0.01
34 29 0.10
35 107 0.37
36 41 0.14
37 24 0.08
38 54 0.18
39 24 0.08
40 11 0.04
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.46
Consensus pattern (34 bp):
GTTTCAAAAATTTCGTGTTTTCAAAAATTTTCGC
Found at i:57435478 original size:92 final size:91
Alignment explanation
Indices: 57435366--57435697 Score: 290
Period size: 92 Copynumber: 3.7 Consensus size: 91
57435356 AATTTTCGCG
**
57435366 TTTCAAAAATCCTCGTGTTTTCAAAAATTCCGGTGTTTCAAAAATTTTCGTGTTTTCAAAATTTT
1 TTTCAAAAATTTTCGTGTTTTCAAAAATTCC-GTGTTTCAAAAATTTTCGTGTTTTCAAAATTTT
*
57435431 TTTGCGTTTTCAAAAAAAATTCTCTTA
65 TTTGCGTTTTCAAAAAAAATTCTCGTA
* * *
57435458 TTTCAAAAATTTTCGCGTTTTCAAAAATTGTCGTGTTTTAAAAATTTTCGTGTTTTCAAAAATTT
1 TTTCAAAAATTTTCGTGTTTTCAAAAATT-CCGTGTTTCAAAAATTTTCGTGTTTTC-AAAATTT
** *
57435523 TCAT--GTTTTC--AAAAAATTCTCGTG
64 TTTTGCGTTTTCAAAAAAAATTCTCGTA
* * * *
57435547 TTTCACAAATTTTTGTGTTTTCAAAAAAAATTCTCGTGTTTTCAAAAAATTCTCTTG-TTTCAAA
1 TTTCAAAAATTTTCGTGTTTTC---AAAAATTC-CGTG-TTTC-AAAAATTTTCGTGTTTTCAAA
* * * *
57435611 A-ATTTTTGCTTTTTC---AAAAATTGTCGTG
60 ATTTTTTTGCGTTTTCAAAAAAAATTCTCGTA
* * * * * *
57435639 TTTTAAAAATTATCGTGTTTT-TAAAATTCTCGTATTTCAAAAGTTTCCGTG-TTTCAAAA
1 TTTCAAAAATTTTCGTGTTTTCAAAAATTC-CGTGTTTCAAAAATTTTCGTGTTTTCAAAA
57435698 AAGAATTCTC
Statistics
Matches: 199, Mismatches: 31, Indels: 26
0.78 0.12 0.10
Matches are distributed among these distances:
86 17 0.09
87 4 0.02
88 11 0.06
89 31 0.16
91 9 0.05
92 94 0.47
93 22 0.11
94 11 0.06
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.46
Consensus pattern (91 bp):
TTTCAAAAATTTTCGTGTTTTCAAAAATTCCGTGTTTCAAAAATTTTCGTGTTTTCAAAATTTTT
TTGCGTTTTCAAAAAAAATTCTCGTA
Found at i:57435711 original size:21 final size:21
Alignment explanation
Indices: 57435663--57435719 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
57435653 GTGTTTTTAA
*
57435663 AATTCTCGTATTTC--AAAAG
1 AATTCTCGTGTTTCAAAAAAG
*
57435682 -TTTC-CGTGTTTCAAAAAAG
1 AATTCTCGTGTTTCAAAAAAG
57435701 AATTCTCGTGTTTCAAAAA
1 AATTCTCGTGTTTCAAAAA
57435720 TTTTCGTGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 7 0.23
18 3 0.10
19 5 0.16
20 3 0.10
21 13 0.42
ACGTcount: A:0.35, C:0.16, G:0.12, T:0.37
Consensus pattern (21 bp):
AATTCTCGTGTTTCAAAAAAG
Found at i:57435718 original size:19 final size:17
Alignment explanation
Indices: 57435327--57435791 Score: 251
Period size: 17 Copynumber: 25.8 Consensus size: 17
57435317 ACAAATTTCC
57435327 CGTGTTTCAAAAATT-T
1 CGTGTTTCAAAAATTCT
** *
57435343 AATTGTTTTCAAAAATTTT
1 -CGTG-TTTCAAAAATTCT
* *
57435362 CGCGTTTCAAAAATCCT
1 CGTGTTTCAAAAATTCT
57435379 CGTGTTTTCAAAAATTC-
1 CGTG-TTTCAAAAATTCT
*
57435396 CGGTGTTTCAAAAATTTT
1 C-GTGTTTCAAAAATTCT
* *
57435414 CGTGTTTTCAAAATTTTTTT
1 CGTG-TTTCAAAA--ATTCT
57435434 GCGT-TTTCAAAAAAAATTCT
1 -CGTGTTTC---AAAAATTCT
* * *
57435454 CTTATTTCAAAAATTTT
1 CGTGTTTCAAAAATTCT
* *
57435471 CGCGTTTTCAAAAATTGT
1 CGTG-TTTCAAAAATTCT
* *
57435489 CGTGTTTTAAAAATTTT
1 CGTGTTTCAAAAATTCT
*
57435506 CGTGTTTTCAAAAATTTT
1 CGTG-TTTCAAAAATTCT
*
57435524 CATGTTTTCAAAAAATTCT
1 CGTG-TTTC-AAAAATTCT
* *
57435543 CGTGTTTCACAAATTTT
1 CGTGTTTCAAAAATTCT
*
57435560 TGTGTTTTCAAAAAAAATTCT
1 CGTG-TTTC---AAAAATTCT
57435581 CGTGTTTTCAAAAAATTCT
1 CGTG-TTTC-AAAAATTCT
* *
57435600 CTTGTTTCAAAAATTTT
1 CGTGTTTCAAAAATTCT
* * *
57435617 TGCTTTTTCAAAAATTGT
1 CG-TGTTTCAAAAATTCT
* *
57435635 CGTGTTTTAAAAATTAT
1 CGTGTTTCAAAAATTCT
**
57435652 CGTGTTTTTAAAATTCT
1 CGTGTTTCAAAAATTCT
* *
57435669 CGTATTTCAAAAGTT-T
1 CGTGTTTCAAAAATTCT
57435685 CCGTGTTTCAAAAAAGAATTCT
1 -CGTGTTTC---AAA-AATTCT
*
57435707 CGTGTTTCAAAAATTTT
1 CGTGTTTCAAAAATTCT
*
57435724 CGTGTTTTTTTTAAAAATT-T
1 CGTG----TTTCAAAAATTCT
* *
57435744 -GTATTTCTAAAATTCT
1 CGTGTTTCAAAAATTCT
*
57435760 CGTTTTTCAAAAAAATTC-
1 CGTGTTTC--AAAAATTCT
57435778 CGTGTTTTCAAAAA
1 CGTG-TTTCAAAAA
57435792 AAATATTGTG
Statistics
Matches: 354, Mismatches: 58, Indels: 72
0.73 0.12 0.15
Matches are distributed among these distances:
15 9 0.03
16 2 0.01
17 138 0.39
18 102 0.29
19 44 0.12
20 15 0.04
21 39 0.11
22 5 0.01
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.46
Consensus pattern (17 bp):
CGTGTTTCAAAAATTCT
Found at i:57435740 original size:146 final size:143
Alignment explanation
Indices: 57435346--57435731 Score: 401
Period size: 146 Copynumber: 2.7 Consensus size: 143
57435336 AAAATTTAAT
* * * *
57435346 TGTTTTCAAAAATTTTCGCG-TTTCAAAAATCCTCGTGTTTTC-AAAAATTC-CGGTGTTTCAAA
1 TGTTTT-AAAAATTATCGTGTTTTCAAAAATTCTC-AGTTTTCAAAAAATTCTC-GTGTTTCAAA
* ** * * *
57435408 AATTTTCGTGTTTTCAAAATTTTTTTGCGTTTTCAAAAAAAATTCTCTTATTTCAAAAATTTTCG
63 AATTCTCGTGTTTTCAAAAAATTCTCGTGTTTTC--AAAAAATTCTCTTATTTCAAAAATTTTCG
57435473 CGTTTTCAAAAATTGTCG
126 CGTTTTCAAAAATTGTCG
* * *
57435491 TGTTTTAAAAATTTTCGTGTTTTCAAAAATTTTCATGTTTTCAAAAAATTCTCGTGTTTCACAAA
1 TGTTTTAAAAATTATCGTGTTTTCAAAAATTCTCA-GTTTTCAAAAAATTCTCGTGTTTCAAAAA
* * * * *
57435556 TTTTTGTGTTTTCAAAAAAAATTCTCGTGTTTTCAAAAAATTCTCTTGTTTCAAAAATTTTTGCT
65 TTCTCGTGTTTTC--AAAAAATTCTCGTGTTTTCAAAAAATTCTCTTATTTCAAAAATTTTCGCG
57435621 TTTTCAAAAATTGTCG
128 TTTTCAAAAATTGTCG
* **
57435637 TGTTTTAAAAATTATCGTGTTTT-TAAAATTCTC-GTATTTCAAAAGTTTC-CGTGTTTCAAAAA
1 TGTTTTAAAAATTATCGTGTTTTCAAAAATTCTCAGT-TTTCAAAAAATTCTCGTGTTTC---AA
*
57435699 AGAATTCTCGTG-TTTC-AAAAATTTTCGTGTTTT
62 A-AATTCTCGTGTTTTCAAAAAATTCTCGTGTTTT
57435732 TTTTAAAAAT
Statistics
Matches: 207, Mismatches: 23, Indels: 24
0.81 0.09 0.09
Matches are distributed among these distances:
143 26 0.13
144 23 0.11
145 32 0.15
146 103 0.50
147 9 0.04
148 14 0.07
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.46
Consensus pattern (143 bp):
TGTTTTAAAAATTATCGTGTTTTCAAAAATTCTCAGTTTTCAAAAAATTCTCGTGTTTCAAAAAT
TCTCGTGTTTTCAAAAAATTCTCGTGTTTTCAAAAAATTCTCTTATTTCAAAAATTTTCGCGTTT
TCAAAAATTGTCG
Found at i:57435771 original size:91 final size:93
Alignment explanation
Indices: 57435639--57435809 Score: 235
Period size: 91 Copynumber: 1.9 Consensus size: 93
57435629 AATTGTCGTG
* * **
57435639 TTTTAAAAATTATCGTGTTTTTAAAATTCTCGTATTTC-AAAAGTTTCCGTG-TTTCAAAAAAGA
1 TTTTAAAAATTATCGTATTTCTAAAATTCTCGTATTTCAAAAAAATTCCGTGTTTTCAAAAAA-A
57435702 AT-TCTCGTGTTTCAAAAATTTTCGTGTTTT
65 ATAT-T-GTGTTTCAAAAATTTTCGTGTTTT
*
57435732 TTTTAAAAATT-T-GTATTTCTAAAATTCTCGTTTTTCAAAAAAATTCCGTGTTTTCAAAAAAAA
1 TTTTAAAAATTATCGTATTTCTAAAATTCTCGTATTTCAAAAAAATTCCGTGTTTTCAAAAAAAA
57435795 TATTGTGTTTCAAAA
66 TATTGTGTTTCAAAA
57435810 TTCTTGCGTT
Statistics
Matches: 70, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
91 32 0.46
92 16 0.23
93 22 0.31
ACGTcount: A:0.34, C:0.11, G:0.10, T:0.45
Consensus pattern (93 bp):
TTTTAAAAATTATCGTATTTCTAAAATTCTCGTATTTCAAAAAAATTCCGTGTTTTCAAAAAAAA
TATTGTGTTTCAAAAATTTTCGTGTTTT
Found at i:57435790 original size:18 final size:18
Alignment explanation
Indices: 57435346--57435792 Score: 231
Period size: 18 Copynumber: 24.7 Consensus size: 18
57435336 AAAATTTAAT
*
57435346 TGTTTTCAAAAATTTTCG
1 TGTTTTCAAAAAATTTCG
* *
57435364 CG-TTTC-AAAAATCCTCG
1 TGTTTTCAAAAAAT-TTCG
*
57435381 TGTTTTC-AAAAATTCCG
1 TGTTTTCAAAAAATTTCG
*
57435398 -GTGTTTCAAAAATTTTCG
1 TGT-TTTCAAAAAATTTCG
** *
57435416 TGTTTTCAAAATTTTTTTG
1 TGTTTTCAAAA-AATTTCG
*
57435435 CGTTTTCAAAAAAAATTCTC-
1 TGTTTTC--AAAAAATT-TCG
*
57435455 T-TATTTCAAAAATTTTCG
1 TGT-TTTCAAAAAATTTCG
*
57435473 CGTTTTC-AAAAATTGTCG
1 TGTTTTCAAAAAATT-TCG
*
57435491 TGTTTT-AAAAATTTTCG
1 TGTTTTCAAAAAATTTCG
* *
57435508 TGTTTTCAAAAATTTTCA
1 TGTTTTCAAAAAATTTCG
57435526 TGTTTTCAAAAAATTCTCG
1 TGTTTTCAAAAAATT-TCG
* * *
57435545 TG-TTTCACAAATTTTTG
1 TGTTTTCAAAAAATTTCG
57435562 TGTTTTCAAAAAAAATTCTCG
1 TGTTTTC--AAAAAATT-TCG
*
57435583 TGTTTTCAAAAAATTCTCT
1 TGTTTTCAAAAAATT-TCG
* *
57435602 TG-TTTCAAAAATTTTTG
1 TGTTTTCAAAAAATTTCG
57435619 CT-TTTTC-AAAAATTGTCG
1 -TGTTTTCAAAAAATT-TCG
57435637 TGTTTT--AAAAATTATCG
1 TGTTTTCAAAAAATT-TCG
*
57435654 TGTTTT--TAAAATTCTCG
1 TGTTTTCAAAAAATT-TCG
* *
57435671 T-ATTTC-AAAAGTTTCCG
1 TGTTTTCAAAAAATTT-CG
57435688 TG-TTTCAAAAAAGAATTCTCG
1 TGTTTTC--AAAA-AATT-TCG
*
57435709 TG-TTTCAAAAATTTTCG
1 TGTTTTCAAAAAATTTCG
**
57435726 TGTTTTTTTTAAAAATTT-G
1 TG--TTTTCAAAAAATTTCG
* *
57435745 T-ATTTC-TAAAATTCTCG
1 TGTTTTCAAAAAATT-TCG
*
57435762 T-TTTTCAAAAAAATTCCG
1 TGTTTTC-AAAAAATTTCG
57435780 TGTTTTCAAAAAA
1 TGTTTTCAAAAAA
57435793 AATATTGTGT
Statistics
Matches: 337, Mismatches: 52, Indels: 80
0.72 0.11 0.17
Matches are distributed among these distances:
15 6 0.02
16 15 0.04
17 92 0.27
18 124 0.37
19 49 0.15
20 25 0.07
21 25 0.07
22 1 0.00
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.46
Consensus pattern (18 bp):
TGTTTTCAAAAAATTTCG
Found at i:57437327 original size:12 final size:12
Alignment explanation
Indices: 57437305--57437436 Score: 115
Period size: 12 Copynumber: 10.8 Consensus size: 12
57437295 TGAGTTATAC
*
57437305 ATAAATATTA-T
1 ATAATTATTATT
57437316 ATACATTATTATT
1 ATA-ATTATTATT
**
57437329 ATAATTATTAACC
1 ATAATTATT-ATT
* *
57437342 ATTATTATGGTTTT
1 ATAATTAT--TATT
57437356 AT-ATTATTATT
1 ATAATTATTATT
*
57437367 ATTATTATTATT
1 ATAATTATTATT
*
57437379 ATTATTATTATT
1 ATAATTATTATT
*
57437391 ATTATTATTATT
1 ATAATTATTATT
*
57437403 ATTATTATTATT
1 ATAATTATTATT
*
57437415 ATTATTATTATT
1 ATAATTATTATT
*
57437427 ATTATTATTA
1 ATAATTATTA
57437437 AATAAAGTAA
Statistics
Matches: 107, Mismatches: 8, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
11 8 0.07
12 79 0.74
13 17 0.16
14 2 0.02
15 1 0.01
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (12 bp):
ATAATTATTATT
Found at i:57437328 original size:3 final size:3
Alignment explanation
Indices: 57437320--57437436 Score: 166
Period size: 3 Copynumber: 39.3 Consensus size: 3
57437310 TATTATATAC
* ** * *
57437320 ATT ATT ATT ATA ATT ATT AACC ATT ATT ATG GTT -TT A-T ATT ATT
1 ATT ATT ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT
57437364 ATT ATT ATT 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 ATT ATT ATT
57437412 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
57437437 AATAAAGTAA
Statistics
Matches: 102, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
2 4 0.04
3 97 0.95
4 1 0.01
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:57437560 original size:7 final size:7
Alignment explanation
Indices: 57437548--57437572 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
57437538 AAGTATAAGA
57437548 TATTTAT
1 TATTTAT
57437555 TATTTAT
1 TATTTAT
57437562 TATTTAT
1 TATTTAT
57437569 TATT
1 TATT
57437573 AAATTAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (7 bp):
TATTTAT
Found at i:57438053 original size:3 final size:3
Alignment explanation
Indices: 57438045--57438097 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
57438035 TAAGTATAAG
57438045 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
57438093 TAT TA
1 TAT TA
57438098 AGATGAGTGG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:57442202 original size:34 final size:34
Alignment explanation
Indices: 57442159--57442226 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
57442149 CGACACTAAG
57442159 AGGATGGAGACGCTCCTGATGTGATCACGGGTAC
1 AGGATGGAGACGCTCCTGATGTGATCACGGGTAC
57442193 AGGATGGAGACGCTCCTGATGTGATCACGGGTAC
1 AGGATGGAGACGCTCCTGATGTGATCACGGGTAC
57442227 GTTCTTTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.24, C:0.21, G:0.35, T:0.21
Consensus pattern (34 bp):
AGGATGGAGACGCTCCTGATGTGATCACGGGTAC
Found at i:57443390 original size:9 final size:9
Alignment explanation
Indices: 57443373--57443409 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
57443363 TGAGTTTTCG
57443373 AATTCGAAT
1 AATTCGAAT
*
57443382 AACTCGAAT
1 AATTCGAAT
57443391 AATTCGAAT
1 AATTCGAAT
57443400 AATTCGAAT
1 AATTCGAAT
57443409 A
1 A
57443410 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:57445643 original size:10 final size:9
Alignment explanation
Indices: 57445614--57445639 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
57445604 ATTTTATATT
57445614 AATATTTTA
1 AATATTTTA
57445623 AATATTTTA
1 AATATTTTA
57445632 AATATTTT
1 AATATTTT
57445640 TAAAAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (9 bp):
AATATTTTA
Found at i:57462808 original size:46 final size:46
Alignment explanation
Indices: 57462696--57463070 Score: 615
Period size: 46 Copynumber: 8.1 Consensus size: 46
57462686 ATAAAACAGT
*
57462696 TTGGGCAGCATTTAAGCATCAAAATTGGACAGCATATATGTAACAAA
1 TTGGGCAGCATTTATGCATCAAAATTGGACAGCAT-TATGTAACAAA
* **
57462743 TTGGGCAGCATTTAAGCATCAAAATTTTACAGCATTATGTAACAAA
1 TTGGGCAGCATTTATGCATCAAAATTGGACAGCATTATGTAACAAA
*
57462789 TTGGGCAGCTTTTATGCATCAAAATTGGACAGCATTATGTAACAAA
1 TTGGGCAGCATTTATGCATCAAAATTGGACAGCATTATGTAACAAA
*
57462835 TTGGGCAGCTTTTATGCATCAAAATTGGACAGCATTATGTAACAAA
1 TTGGGCAGCATTTATGCATCAAAATTGGACAGCATTATGTAACAAA
* *
57462881 TTGGGCAGCTTTTATGCATCAAAATTGGACAGCATATATGTAATAAA
1 TTGGGCAGCATTTATGCATCAAAATTGGACAGCAT-TATGTAACAAA
*
57462928 TTGGGCAGCATTTAAGCATCAAAATTGGACAGCATTATGTAACAAA
1 TTGGGCAGCATTTATGCATCAAAATTGGACAGCATTATGTAACAAA
*
57462974 TTGGGCAGCTTTTATGCATCAAAATTGGACAGCATTATGTAACAAA
1 TTGGGCAGCATTTATGCATCAAAATTGGACAGCATTATGTAACAAA
* *
57463020 TTCGGCAGCATTTATGCATCAAAATTGGACAGCATATATGTAATAAA
1 TTGGGCAGCATTTATGCATCAAAATTGGACAGCAT-TATGTAACAAA
57463067 TTGG
1 TTGG
57463071 TTCAACTCAT
Statistics
Matches: 310, Mismatches: 16, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
46 221 0.71
47 89 0.29
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (46 bp):
TTGGGCAGCATTTATGCATCAAAATTGGACAGCATTATGTAACAAA
Found at i:57462921 original size:139 final size:139
Alignment explanation
Indices: 57462696--57463070 Score: 644
Period size: 139 Copynumber: 2.7 Consensus size: 139
57462686 ATAAAACAGT
* * *
57462696 TTGGGCAGCATTTAAGCATCAAAATTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCA
1 TTGGGCAGCTTTTATGCATCAAAATTGGACAGCAT-TATGTAACAAATTGGGCAGCATTTATGCA
** * * *
57462761 TCAAAATTTTACAGCAT-TATGTAACAAATTGGGCAGCTTTTATGCATCAAAATTGGACAGCATT
65 TCAAAATTGGACAGCATATATGTAATAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGCATT
57462825 ATGTAACAAA
130 ATGTAACAAA
*
57462835 TTGGGCAGCTTTTATGCATCAAAATTGGACAGCATTATGTAACAAATTGGGCAGCTTTTATGCAT
1 TTGGGCAGCTTTTATGCATCAAAATTGGACAGCATTATGTAACAAATTGGGCAGCATTTATGCAT
57462900 CAAAATTGGACAGCATATATGTAATAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGCATTA
66 CAAAATTGGACAGCATATATGTAATAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGCATTA
57462965 TGTAACAAA
131 TGTAACAAA
*
57462974 TTGGGCAGCTTTTATGCATCAAAATTGGACAGCATTATGTAACAAATTCGGCAGCATTTATGCAT
1 TTGGGCAGCTTTTATGCATCAAAATTGGACAGCATTATGTAACAAATTGGGCAGCATTTATGCAT
57463039 CAAAATTGGACAGCATATATGTAATAAATTGG
66 CAAAATTGGACAGCATATATGTAATAAATTGG
57463071 TTCAACTCAT
Statistics
Matches: 224, Mismatches: 11, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
138 42 0.19
139 182 0.81
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (139 bp):
TTGGGCAGCTTTTATGCATCAAAATTGGACAGCATTATGTAACAAATTGGGCAGCATTTATGCAT
CAAAATTGGACAGCATATATGTAATAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGCATTA
TGTAACAAA
Found at i:57462967 original size:185 final size:186
Alignment explanation
Indices: 57462673--57463070 Score: 672
Period size: 185 Copynumber: 2.1 Consensus size: 186
57462663 ATTCATGAAT
* ** **
57462673 TTGGTCAGCATATATAAAACAGTTTGGGCAGCATTTAAGCATCAAAATTGGACAGCATATATGTA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGCATATATGTA
**
57462738 ACAAATTGGGCAGCATTTAAGCATCAAAATTTTACAGCATTATGTAACAAATTGGGCAGCTTTTA
66 ACAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGCATTATGTAACAAATTGGGCAGCTTTTA
* *
57462803 TGCATCAAAATTGGACAGCATTATGTAACAAATTGGGCAGCTTTTATGCATCAAAA
131 TGCATCAAAATTGGACAGCATTATGTAACAAATTCGGCAGCATTTATGCATCAAAA
* *
57462859 TTGGACAGCAT-TATGTAACAAATTGGGCAGCTTTTATGCATCAAAATTGGACAGCATATATGTA
1 TTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGCATATATGTA
*
57462923 ATAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGCATTATGTAACAAATTGGGCAGCTTTTA
66 ACAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGCATTATGTAACAAATTGGGCAGCTTTTA
57462988 TGCATCAAAATTGGACAGCATTATGTAACAAATTCGGCAGCATTTATGCATCAAAA
131 TGCATCAAAATTGGACAGCATTATGTAACAAATTCGGCAGCATTTATGCATCAAAA
*
57463044 TTGGACAGCATATATGTAATAAATTGG
1 TTGGACAGCATATATGTAACAAATTGG
57463071 TTCAACTCAT
Statistics
Matches: 198, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
185 174 0.88
186 24 0.12
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.30
Consensus pattern (186 bp):
TTGGACAGCATATATGTAACAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGCATATATGTA
ACAAATTGGGCAGCATTTAAGCATCAAAATTGGACAGCATTATGTAACAAATTGGGCAGCTTTTA
TGCATCAAAATTGGACAGCATTATGTAACAAATTCGGCAGCATTTATGCATCAAAA
Found at i:57463994 original size:43 final size:43
Alignment explanation
Indices: 57463895--57464023 Score: 156
Period size: 43 Copynumber: 3.0 Consensus size: 43
57463885 AACTCGTACA
* *
57463895 ATGCCAACGTCCCAGACGTGGTCTTACATGTAATCACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACATATCG
* **
57463938 ATGCC-ACTATCCCAGACAAGGTCTTACACGTAAACACA-AGTCG
1 ATGCCAAC-GTCCCAGACGTGGTCTTACACGTAAACACATA-TCG
*
57463981 ATGCCAACGTCCCACACGTGGTCTTACACG-ATAACACATATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACACGTA-AACACATATCG
57464024 GAAATCCTAT
Statistics
Matches: 72, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
42 4 0.06
43 65 0.90
44 3 0.04
ACGTcount: A:0.31, C:0.30, G:0.17, T:0.22
Consensus pattern (43 bp):
ATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACATATCG
Found at i:57464850 original size:18 final size:18
Alignment explanation
Indices: 57464827--57464865 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
57464817 GTGCCGAAAC
57464827 CTTAACAAGCATGGATGA
1 CTTAACAAGCATGGATGA
57464845 CTTAACAAGCATGGATGA
1 CTTAACAAGCATGGATGA
57464863 CTT
1 CTT
57464866 CTTTCTTTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.26
Consensus pattern (18 bp):
CTTAACAAGCATGGATGA
Found at i:57467816 original size:16 final size:15
Alignment explanation
Indices: 57467797--57467840 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
57467787 AATAATTTTT
57467797 TAAATTATTTCTAATC
1 TAAATTATTTCT-ATC
*
57467813 TAAATTATTTGCTATT
1 TAAATTATTT-CTATC
*
57467829 TAAATAATTTCT
1 TAAATTATTTCT
57467841 GCAGTACTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 21 0.84
17 2 0.08
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.52
Consensus pattern (15 bp):
TAAATTATTTCTATC
Found at i:57469567 original size:24 final size:23
Alignment explanation
Indices: 57469527--57469576 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
57469517 GAAAATGAGC
*
57469527 TTTAAATAACTAATATA-AATTGA
1 TTTAAATAAATAATATAGAA-TGA
*
57469550 TTTAAAGTAAATAGTATAGAATGA
1 TTTAAA-TAAATAATATAGAATGA
57469574 TTT
1 TTT
57469577 TAAAATAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 6 0.26
24 15 0.65
25 2 0.09
ACGTcount: A:0.48, C:0.02, G:0.10, T:0.40
Consensus pattern (23 bp):
TTTAAATAAATAATATAGAATGA
Found at i:57478835 original size:19 final size:19
Alignment explanation
Indices: 57478798--57478835 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
57478788 CTAATTAAGT
*
57478798 TTTAATTAGATGAATTTAG
1 TTTAATTAGATGAAATTAG
57478817 TTTAATTAAGA-GAAATTAG
1 TTTAATT-AGATGAAATTAG
57478836 GAAAAAGGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (19 bp):
TTTAATTAGATGAAATTAG
Found at i:57479014 original size:5 final size:5
Alignment explanation
Indices: 57479004--57479045 Score: 84
Period size: 5 Copynumber: 8.4 Consensus size: 5
57478994 AATAAATAAG
57479004 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT AT
57479046 AACTAAAGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATTAT
Found at i:57479413 original size:18 final size:17
Alignment explanation
Indices: 57479362--57479415 Score: 56
Period size: 19 Copynumber: 3.1 Consensus size: 17
57479352 AATATGTAAA
57479362 TTAAAAAA-ATAAAAAT
1 TTAAAAAATATAAAAAT
* *
57479378 TTTAAAATTATGAAAAAAT
1 TTAAAAAATAT--AAAAAT
57479397 TTAAAAAATATAGAAAAT
1 TTAAAAAATATA-AAAAT
57479415 T
1 T
57479416 ATTAAAATTG
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
16 6 0.20
17 3 0.10
18 6 0.20
19 15 0.50
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (17 bp):
TTAAAAAATATAAAAAT
Found at i:57479444 original size:30 final size:28
Alignment explanation
Indices: 57479372--57479450 Score: 79
Period size: 30 Copynumber: 2.8 Consensus size: 28
57479362 TTAAAAAAAT
*
57479372 AAAAAT-TTTAAAATTATGAAAAAATTTA
1 AAAAATATTTAAAATTAT-TAAAAATTTA
** *
57479400 AAAAATATAGAAAATTATTAAAATTGTTA
1 AAAAATATTTAAAATTATTAAAAAT-TTA
*
57479429 ATAAAATATTTAAAATAATTAA
1 A-AAAATATTTAAAATTATTAA
57479451 GTTAGTATCA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
28 11 0.27
29 13 0.32
30 17 0.41
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (28 bp):
AAAAATATTTAAAATTATTAAAAATTTA
Found at i:57481933 original size:28 final size:27
Alignment explanation
Indices: 57481863--57481955 Score: 80
Period size: 29 Copynumber: 3.3 Consensus size: 27
57481853 ATATAAAAGT
57481863 ACAAAAAAAATAT-AAATTATTAAAAA
1 ACAAAAAAAATATGAAATTATTAAAAA
*
57481889 ACTCCAAAAAAACATATGTAATTATTAAAATA
1 A---CAAAAAAA-ATATGAAATTATTAAAA-A
* **
57481921 ACAAAAAGAATATGCAAATTACAAAAAA
1 ACAAAAAAAATATG-AAATTATTAAAAA
*
57481949 ATAAAAA
1 ACAAAAA
57481956 TTTTAAAATT
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
26 1 0.02
28 12 0.22
29 24 0.44
30 4 0.07
31 11 0.20
32 2 0.04
ACGTcount: A:0.67, C:0.09, G:0.03, T:0.22
Consensus pattern (27 bp):
ACAAAAAAAATATGAAATTATTAAAAA
Found at i:57481979 original size:19 final size:20
Alignment explanation
Indices: 57481951--57481992 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
57481941 ACAAAAAAAT
* *
57481951 AAAAATTTTAAAATTAT-GA
1 AAAAAATTTAAAAATATGGA
57481970 AAAAAATTTAAAAATATGGA
1 AAAAAATTTAAAAATATGGA
57481990 AAA
1 AAA
57481993 TTATTAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (20 bp):
AAAAAATTTAAAAATATGGA
Found at i:57482014 original size:38 final size:38
Alignment explanation
Indices: 57481952--57482025 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 38
57481942 CAAAAAAATA
57481952 AAAATTTTAAAATTATGAAAAAAATTTA-AAAATATGG
1 AAAATTTTAAAATTATGAAAAAAATTTACAAAATATGG
* * *
57481989 AAAATTATTAAAATTGTTAATAAAATTTACAAAATAT
1 AAAATT-TTAAAATTATGAAAAAAATTTACAAAATAT
57482026 TATAAAAAGC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
37 6 0.19
38 19 0.59
39 7 0.22
ACGTcount: A:0.58, C:0.01, G:0.05, T:0.35
Consensus pattern (38 bp):
AAAATTTTAAAATTATGAAAAAAATTTACAAAATATGG
Found at i:57486298 original size:18 final size:21
Alignment explanation
Indices: 57486275--57486314 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
57486265 ATTTCAAAAC
57486275 TTAAG-TATT-TTA-AAATAA
1 TTAAGTTATTATTATAAATAA
57486293 TTAAGTTATTATTATAAATAA
1 TTAAGTTATTATTATAAATAA
57486314 T
1 T
57486315 GACATTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.26
19 4 0.21
20 3 0.16
21 7 0.37
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (21 bp):
TTAAGTTATTATTATAAATAA
Found at i:57487282 original size:21 final size:21
Alignment explanation
Indices: 57487169--57487290 Score: 66
Period size: 20 Copynumber: 6.1 Consensus size: 21
57487159 AATTACAAAA
* *
57487169 AATAAAAAATTTAAAATTATG
1 AATAAAATATTTAAAATTATT
57487190 AA-AAAATATTTAAAA--A-T
1 AATAAAATATTTAAAATTATT
*
57487207 -ATAGAAATCA-TTAAAATTGTT
1 AATA-AAAT-ATTTAAAATTATT
*
57487228 AAT-AAA-ATTTACAAAATATT
1 AATAAAATATTTA-AAATTATT
** *
57487248 -ATAAAA-AGCATAAAATTGTT
1 AATAAAATA-TTTAAAATTATT
*
57487268 AATAAAATATTTAAAATAATT
1 AATAAAATATTTAAAATTATT
57487289 AA
1 AA
57487291 GTTAGTATCA
Statistics
Matches: 75, Mismatches: 13, Indels: 26
0.66 0.11 0.23
Matches are distributed among these distances:
16 1 0.01
17 1 0.01
18 12 0.16
19 6 0.08
20 31 0.41
21 21 0.28
22 3 0.04
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (21 bp):
AATAAAATATTTAAAATTATT
Found at i:57487284 original size:40 final size:40
Alignment explanation
Indices: 57487179--57487285 Score: 123
Period size: 40 Copynumber: 2.7 Consensus size: 40
57487169 AATAAAAAAT
* * * *
57487179 TTAAAATTATGAA-AAAATATTTAAAA-ATATAGAAATCA
1 TTAAAATTGTTAATAAAATATTTAAAATATATAAAAAGCA
*
57487217 TTAAAATTGTTAATAAAAT-TTACAAAATATTATAAAAAGCA
1 TTAAAATTGTTAATAAAATATT-TAAAATA-TATAAAAAGCA
57487258 -TAAAATTGTTAATAAAATATTTAAAATA
1 TTAAAATTGTTAATAAAATATTTAAAATA
57487286 ATTAAGTTAG
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
38 13 0.22
39 9 0.16
40 25 0.43
41 11 0.19
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.35
Consensus pattern (40 bp):
TTAAAATTGTTAATAAAATATTTAAAATATATAAAAAGCA
Found at i:57487481 original size:19 final size:20
Alignment explanation
Indices: 57487459--57487500 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
57487449 AAGTATATGT
57487459 AAATTA-CAAAAAAAATTTA
1 AAATTATCAAAAAAAATTTA
* *
57487478 AAATTATGAAAAAATATTTA
1 AAATTATCAAAAAAAATTTA
57487498 AAA
1 AAA
57487501 ATATAGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (20 bp):
AAATTATCAAAAAAAATTTA
Found at i:57487489 original size:20 final size:21
Alignment explanation
Indices: 57487466--57487510 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
57487456 TGTAAATTAC
*
57487466 AAAAAAAATTTAAAATTAT-G
1 AAAAAAAATTTAAAAATATAG
*
57487486 AAAAAATATTTAAAAATATAG
1 AAAAAAAATTTAAAAATATAG
57487507 AAAA
1 AAAA
57487511 TTATTAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (21 bp):
AAAAAAAATTTAAAAATATAG
Found at i:57488167 original size:18 final size:18
Alignment explanation
Indices: 57488119--57488260 Score: 117
Period size: 18 Copynumber: 7.9 Consensus size: 18
57488109 GATGAAGAAC
* *
57488119 GAGAATGAGAATGTGAGT
1 GAGAGTGAGAATGAGAGT
* * *
57488137 GTGAGTGAAAATGAGAAT
1 GAGAGTGAGAATGAGAGT
*
57488155 GAGAGCGAGAATGAGAGT
1 GAGAGTGAGAATGAGAGT
**
57488173 GTA-AGTGAGGGTGAGAGT
1 G-AGAGTGAGAATGAGAGT
**
57488191 GTA-AGTGAGGGTGAGAGT
1 G-AGAGTGAGAATGAGAGT
*
57488209 GAGATTGAGAATGAGAGT
1 GAGAGTGAGAATGAGAGT
* *
57488227 GTGAGTGAAAATGAGAGT
1 GAGAGTGAGAATGAGAGT
* *
57488245 GTGAGCGAGAATGAGA
1 GAGAGTGAGAATGAGA
57488261 ATGAAAGTCA
Statistics
Matches: 102, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
17 1 0.01
18 100 0.98
19 1 0.01
ACGTcount: A:0.37, C:0.01, G:0.42, T:0.20
Consensus pattern (18 bp):
GAGAGTGAGAATGAGAGT
Found at i:57488173 original size:36 final size:36
Alignment explanation
Indices: 57488114--57488264 Score: 133
Period size: 36 Copynumber: 4.2 Consensus size: 36
57488104 ATGGAGATGA
* * * *
57488114 AGAACGAGAATGAGAATGTGAGTGTGAGTGAAAATG
1 AGAATGAGAGTGAGAATGAGAGTGTGAGTGAGAATG
* * **
57488150 AGAATGAGAGCGAGAATGAGAGTGTAAGTGAGGGTG
1 AGAATGAGAGTGAGAATGAGAGTGTGAGTGAGAATG
* ** * *
57488186 AGAGTGTA-AGTGAGGGTGAGAGTGAGATTGAGAATG
1 AGAATG-AGAGTGAGAATGAGAGTGTGAGTGAGAATG
* * * *
57488222 AGAGTGTGAGTGAAAATGAGAGTGTGAGCGAGAATG
1 AGAATGAGAGTGAGAATGAGAGTGTGAGTGAGAATG
57488258 AGAATGA
1 AGAATGA
57488265 AAGTCACGAC
Statistics
Matches: 87, Mismatches: 26, Indels: 4
0.74 0.22 0.03
Matches are distributed among these distances:
36 86 0.99
37 1 0.01
ACGTcount: A:0.38, C:0.02, G:0.41, T:0.19
Consensus pattern (36 bp):
AGAATGAGAGTGAGAATGAGAGTGTGAGTGAGAATG
Found at i:57488264 original size:6 final size:6
Alignment explanation
Indices: 57488119--57488260 Score: 81
Period size: 6 Copynumber: 23.7 Consensus size: 6
57488109 GATGAAGAAC
* * * * * * * * *
57488119 GAGAAT GAGAAT GTGAGT GTGAGT GAAAAT GAGAAT GAGAGC GAGAAT
1 GAGAGT GAGAGT GAGAGT GAGAGT GAGAGT GAGAGT GAGAGT GAGAGT
* * *
57488167 GAGAGT GTA-AGT GAGGGT GAGAGT GTA-AGT GAGGGT GAGAGT GAGATT
1 GAGAGT G-AGAGT GAGAGT GAGAGT G-AGAGT GAGAGT GAGAGT GAGAGT
* * * * * * *
57488215 GAGAAT GAGAGT GTGAGT GAAAAT GAGAGT GTGAGC GAGAAT GAGA
1 GAGAGT GAGAGT GAGAGT GAGAGT GAGAGT GAGAGT GAGAGT GAGA
57488261 ATGAAAGTCA
Statistics
Matches: 103, Mismatches: 29, Indels: 8
0.74 0.21 0.06
Matches are distributed among these distances:
5 2 0.02
6 99 0.96
7 2 0.02
ACGTcount: A:0.37, C:0.01, G:0.42, T:0.20
Consensus pattern (6 bp):
GAGAGT
Found at i:57491741 original size:3 final size:3
Alignment explanation
Indices: 57491733--57491782 Score: 73
Period size: 3 Copynumber: 16.3 Consensus size: 3
57491723 ACAAATTTTA
* *
57491733 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT ATAT CAT TGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT
57491779 TAT T
1 TAT T
57491783 CTCATTATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:57492092 original size:2 final size:2
Alignment explanation
Indices: 57492081--57492114 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
57492071 GCACATTTTT
*
57492081 TA TA TG TA TA TA T- 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
57492115 TTGTATAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:57497388 original size:9 final size:10
Alignment explanation
Indices: 57497376--57497450 Score: 50
Period size: 10 Copynumber: 7.4 Consensus size: 10
57497366 GAAAAATATT
57497376 AAAATTATAA
1 AAAATTATAA
*
57497386 AAAA-TATTTA
1 AAAATTA-TAA
57497396 AAAA-TATAA
1 AAAATTATAA
*
57497405 AAAATTAT-T
1 AAAATTATAA
*
57497414 AAAATTGTTAA
1 AAAATT-ATAA
57497425 TAAAATT-TAA
1 -AAAATTATAA
57497435 AAACTATTATAA
1 AAA--ATTATAA
57497447 AAAA
1 AAAA
57497451 GCATAAAATT
Statistics
Matches: 52, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
9 17 0.33
10 20 0.38
11 3 0.06
12 12 0.23
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.33
Consensus pattern (10 bp):
AAAATTATAA
Found at i:57497388 original size:18 final size:18
Alignment explanation
Indices: 57497362--57497419 Score: 80
Period size: 19 Copynumber: 3.1 Consensus size: 18
57497352 TTAAGTAATC
*
57497362 TTATGAAAAATATTAAAA
1 TTATAAAAAATATTAAAA
57497380 TTATAAAAAATATTTAAAA
1 TTATAAAAAATA-TTAAAA
*
57497399 ATATAAAAAATTATTAAAA
1 TTATAAAAAA-TATTAAAA
57497418 TT
1 TT
57497420 GTTAATAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
18 11 0.31
19 22 0.63
20 2 0.06
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (18 bp):
TTATAAAAAATATTAAAA
Found at i:57497431 original size:21 final size:21
Alignment explanation
Indices: 57497405--57497480 Score: 59
Period size: 21 Copynumber: 3.7 Consensus size: 21
57497395 AAAAATATAA
57497405 AAAATTATTAAAATTGTTAAT
1 AAAATTATTAAAATTGTTAAT
* * * *
57497426 AAAATT-TAAAAACTATTATAA
1 AAAATTATTAAAATTGTTA-AT
**
57497447 AAAAGCA-TAAAATTGTTAAT
1 AAAATTATTAAAATTGTTAAT
57497467 AAAA-TATTTAAAAT
1 AAAATTA-TTAAAAT
57497481 AATTAAGTTA
Statistics
Matches: 40, Mismatches: 11, Indels: 8
0.68 0.19 0.14
Matches are distributed among these distances:
19 1 0.03
20 14 0.35
21 25 0.62
ACGTcount: A:0.58, C:0.03, G:0.04, T:0.36
Consensus pattern (21 bp):
AAAATTATTAAAATTGTTAAT
Found at i:57501513 original size:9 final size:9
Alignment explanation
Indices: 57501401--57501523 Score: 62
Period size: 9 Copynumber: 13.4 Consensus size: 9
57501391 TTTTATATTA
57501401 AAAATA-AT
1 AAAATATAT
57501409 ACAAATA-AT
1 A-AAATATAT
57501418 ACAAATATAT
1 A-AAATATAT
57501428 ACAAAT-TA-
1 A-AAATATAT
57501436 AAAATAT-T
1 AAAATATAT
*
57501444 ATAAATTTAT
1 A-AAATATAT
57501454 AAAAGTATAT
1 AAAA-TATAT
* *
57501464 AAAAGTACAA
1 AAAA-TATAT
57501474 AAAATATA-
1 AAAATATAT
*
57501482 AAAACATATT
1 AAAATATA-T
*
57501492 ATAAATGAAAT
1 A-AAAT-ATAT
57501503 AAAATATAT
1 AAAATATAT
*
57501512 AAATTAT-T
1 AAAATATAT
57501520 AAAA
1 AAAA
57501524 ATTGTCAAAA
Statistics
Matches: 93, Mismatches: 11, Indels: 22
0.74 0.09 0.17
Matches are distributed among these distances:
7 4 0.04
8 15 0.16
9 36 0.39
10 31 0.33
11 5 0.05
12 2 0.02
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.29
Consensus pattern (9 bp):
AAAATATAT
Found at i:57509325 original size:22 final size:22
Alignment explanation
Indices: 57509284--57509326 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
57509274 AAAATAATAA
57509284 AATACTTATAACGTTTTTATGTC
1 AATACTTATAAC-TTTTTATGTC
57509307 AATACTTATATA-TTTTTATG
1 AATACTTATA-ACTTTTTATG
57509327 AATTAAATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 8 0.42
23 10 0.53
24 1 0.05
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.51
Consensus pattern (22 bp):
AATACTTATAACTTTTTATGTC
Found at i:57514595 original size:17 final size:17
Alignment explanation
Indices: 57514567--57514600 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
57514557 AGGTCATACC
57514567 ATTTTATATTTATATAAT
1 ATTTTATATTTAT-TAAT
57514585 ATTTT-TATTTATTAAT
1 ATTTTATATTTATTAAT
57514601 TACTTCATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 7 0.44
18 5 0.31
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
ATTTTATATTTATTAAT
Found at i:57517302 original size:174 final size:174
Alignment explanation
Indices: 57517012--57517361 Score: 700
Period size: 174 Copynumber: 2.0 Consensus size: 174
57517002 TGGCGATGGC
57517012 TATACAACTTGAAATTTCTTGGTGTGTCATTTGGACAAGAGGAAGGGTCATCGAAGATAAGCGGA
1 TATACAACTTGAAATTTCTTGGTGTGTCATTTGGACAAGAGGAAGGGTCATCGAAGATAAGCGGA
57517077 ATCCTATTCATTGGGAGTTTAAACCAAAATCATGGATGATATCAACACCTTGTGGAAATTGCTAC
66 ATCCTATTCATTGGGAGTTTAAACCAAAATCATGGATGATATCAACACCTTGTGGAAATTGCTAC
57517142 AGAAATTGTACAATGAAAACGGGATACAACCAAACTGATAGTTT
131 AGAAATTGTACAATGAAAACGGGATACAACCAAACTGATAGTTT
57517186 TATACAACTTGAAATTTCTTGGTGTGTCATTTGGACAAGAGGAAGGGTCATCGAAGATAAGCGGA
1 TATACAACTTGAAATTTCTTGGTGTGTCATTTGGACAAGAGGAAGGGTCATCGAAGATAAGCGGA
57517251 ATCCTATTCATTGGGAGTTTAAACCAAAATCATGGATGATATCAACACCTTGTGGAAATTGCTAC
66 ATCCTATTCATTGGGAGTTTAAACCAAAATCATGGATGATATCAACACCTTGTGGAAATTGCTAC
57517316 AGAAATTGTACAATGAAAACGGGATACAACCAAACTGATAGTTT
131 AGAAATTGTACAATGAAAACGGGATACAACCAAACTGATAGTTT
57517360 TA
1 TA
57517362 GCTTCTCATC
Statistics
Matches: 176, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
174 176 1.00
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (174 bp):
TATACAACTTGAAATTTCTTGGTGTGTCATTTGGACAAGAGGAAGGGTCATCGAAGATAAGCGGA
ATCCTATTCATTGGGAGTTTAAACCAAAATCATGGATGATATCAACACCTTGTGGAAATTGCTAC
AGAAATTGTACAATGAAAACGGGATACAACCAAACTGATAGTTT
Found at i:57517384 original size:23 final size:23
Alignment explanation
Indices: 57517352--57517397 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
57517342 CAACCAAACT
*
57517352 GATAGTTTTAGCTTCTCATCTGG
1 GATAGCTTTAGCTTCTCATCTGG
57517375 GATAGCTTTAGCTTCTCATCTGG
1 GATAGCTTTAGCTTCTCATCTGG
57517398 TACTTGATTT
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:0.17, C:0.20, G:0.22, T:0.41
Consensus pattern (23 bp):
GATAGCTTTAGCTTCTCATCTGG
Found at i:57522192 original size:16 final size:17
Alignment explanation
Indices: 57522161--57522193 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
57522151 CATGTTGGAT
*
57522161 ACATATCCATATCCAAG
1 ACATATCCATAACCAAG
57522178 ACATA-CCATAACCAAG
1 ACATATCCATAACCAAG
57522194 TAACATTGTA
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:0.45, C:0.30, G:0.06, T:0.18
Consensus pattern (17 bp):
ACATATCCATAACCAAG
Found at i:57525203 original size:7 final size:7
Alignment explanation
Indices: 57525191--57525217 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
57525181 TTTTCAACAA
57525191 ATTTAAT
1 ATTTAAT
57525198 ATTTAAT
1 ATTTAAT
57525205 ATTTAAT
1 ATTTAAT
57525212 ATTTAA
1 ATTTAA
57525218 CAATGTTATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (7 bp):
ATTTAAT
Found at i:57530309 original size:24 final size:24
Alignment explanation
Indices: 57530282--57530329 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
57530272 AAATTAGAAA
57530282 AACAAAAAGGCTTAATTTTTAACT
1 AACAAAAAGGCTTAATTTTTAACT
57530306 AACAAAAAGGCTTAATTTTTAACT
1 AACAAAAAGGCTTAATTTTTAACT
57530330 TTTTTTAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.12, G:0.08, T:0.33
Consensus pattern (24 bp):
AACAAAAAGGCTTAATTTTTAACT
Found at i:57532171 original size:16 final size:17
Alignment explanation
Indices: 57532138--57532179 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
57532128 ATTTTTATTA
*
57532138 AATTATATT-TAATAAT
1 AATTATATTAAAATAAT
57532154 AATTATATTAAAAT-AT
1 AATTATATTAAAATAAT
*
57532170 AATTAAATTA
1 AATTATATTA
57532180 TTTTTATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 20 0.87
17 3 0.13
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AATTATATTAAAATAAT
Found at i:57532188 original size:60 final size:61
Alignment explanation
Indices: 57532115--57532232 Score: 193
Period size: 60 Copynumber: 2.0 Consensus size: 61
57532105 ATTTTCTAAT
57532115 ATTATATTATATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAA
1 ATTATATTATATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAA
* * * *
57532176 ATTAT-TTTTATTATTTTTATTAAATTATGTTTAATAATAATTTTATTAAAATTTAAT
1 ATTATATTATATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAAT
57532233 AACAATAATC
Statistics
Matches: 53, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
60 48 0.91
61 5 0.09
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (61 bp):
ATTATATTATATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAA
Found at i:57532356 original size:16 final size:15
Alignment explanation
Indices: 57532335--57532376 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
57532325 ATTAAATTAC
57532335 TTATTACAATTATATT
1 TTATTACAATT-TATT
57532351 TTATTACAACTTTATT
1 TTATTACAA-TTTATT
*
57532367 CTATTACAAT
1 TTATTACAAT
57532377 GGACCGAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 1 0.04
16 21 0.88
17 2 0.08
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.52
Consensus pattern (15 bp):
TTATTACAATTTATT
Found at i:57538694 original size:16 final size:16
Alignment explanation
Indices: 57538669--57538706 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
57538659 TGATAGGAAT
57538669 GAAAGAAAAGAAAGAA
1 GAAAGAAAAGAAAGAA
*
57538685 GAAAGGAAAGAAAGAA
1 GAAAGAAAAGAAAGAA
57538701 GAAAGA
1 GAAAGA
57538707 GATGGGTAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (16 bp):
GAAAGAAAAGAAAGAA
Found at i:57539280 original size:19 final size:18
Alignment explanation
Indices: 57539228--57539289 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 18
57539218 TTTTATTAAC
*
57539228 AATTTTAA-TTATTTTCT
1 AATTTTAATTTTTTTTCT
*
57539245 ATATTTTAAAATATTTTTTCAT
1 A-ATTTT--AATTTTTTTTC-T
*
57539267 AATTTTAATTTTTTTTGT
1 AATTTTAATTTTTTTTCT
57539285 AATTT
1 AATTT
57539290 ACATATAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
17 1 0.03
18 11 0.31
19 9 0.25
20 2 0.06
21 11 0.31
22 2 0.06
ACGTcount: A:0.31, C:0.03, G:0.02, T:0.65
Consensus pattern (18 bp):
AATTTTAATTTTTTTTCT
Found at i:57539302 original size:39 final size:39
Alignment explanation
Indices: 57539228--57539302 Score: 89
Period size: 39 Copynumber: 1.9 Consensus size: 39
57539218 TTTTATTAAC
* *
57539228 AATTTTAATTATTTTCTATATTTTAAAATATTTTTTCAT
1 AATTTTAATTATTTTCTATAATTTAAAATAATTTTTCAT
* * *
57539267 AATTTTAATT-TTTTTTGTAATTTACATATAATTTTT
1 AATTTTAATTATTTTCTATAATTTA-AAATAATTTTT
57539303 GTTATTTTAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
38 11 0.37
39 19 0.63
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.63
Consensus pattern (39 bp):
AATTTTAATTATTTTCTATAATTTAAAATAATTTTTCAT
Found at i:57539428 original size:16 final size:17
Alignment explanation
Indices: 57539397--57539439 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
57539387 TTGTACTTTC
57539397 ATATAT-TTTATAAATTT
1 ATATATATTT-TAAATTT
57539414 ATA-ATATTTTAAATTT
1 ATATATATTTTAAATTT
*
57539430 GTATATATTT
1 ATATATATTT
57539440 GTATTATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (17 bp):
ATATATATTTTAAATTT
Found at i:57539439 original size:26 final size:25
Alignment explanation
Indices: 57539401--57539449 Score: 62
Period size: 26 Copynumber: 1.9 Consensus size: 25
57539391 ACTTTCATAT
57539401 ATTTTATAAATTTATAATATTTTAA
1 ATTTTATAAATTTATAATATTTTAA
* * *
57539426 ATTTGTATATATTTGTATTATTTT
1 ATTT-TATAAATTTATAATATTTT
57539450 TAATATAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 4 0.20
26 16 0.80
ACGTcount: A:0.35, C:0.00, G:0.04, T:0.61
Consensus pattern (25 bp):
ATTTTATAAATTTATAATATTTTAA
Found at i:57540505 original size:10 final size:10
Alignment explanation
Indices: 57540468--57540595 Score: 66
Period size: 9 Copynumber: 13.9 Consensus size: 10
57540458 TTTTTAATAA
57540468 TTTATATA-T
1 TTTATATATT
*
57540477 TTTATTTCATT
1 TTTATAT-ATT
*
57540488 TATA-ATATGT
1 TTTATATAT-T
57540498 TTT-TATATT
1 TTTATATATT
* * *
57540507 TTTTTGTACT
1 TTTATATATT
57540517 TTTATATATT
1 TTTATATATT
*
57540527 TTTATAAATT
1 TTTATATATT
*
57540537 TATA-ATA-T
1 TTTATATATT
57540545 TTT-TA-ATT
1 TTTATATATT
*
57540553 TGTATATA-T
1 TTTATATATT
*
57540562 TTTAT-T-GT
1 TTTATATATT
57540570 TTT-TATATT
1 TTTATATATT
57540579 TTTAT-TATT
1 TTTATATATT
57540588 TTTA-ATAT
1 TTTATATAT
57540596 AAAATATCAT
Statistics
Matches: 89, Mismatches: 16, Indels: 28
0.67 0.12 0.21
Matches are distributed among these distances:
7 2 0.02
8 13 0.15
9 36 0.40
10 34 0.38
11 4 0.04
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.67
Consensus pattern (10 bp):
TTTATATATT
Found at i:57540552 original size:16 final size:17
Alignment explanation
Indices: 57540517--57540564 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
57540507 TTTTTGTACT
57540517 TTTATATAT-TTTTATAAA
1 TTTATATATATTTT-T-AA
57540535 TTTATA-ATATTTTTAA
1 TTTATATATATTTTTAA
*
57540551 TTTGTATATATTTT
1 TTTATATATATTTT
57540565 ATTGTTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 7 0.26
17 10 0.37
18 10 0.37
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (17 bp):
TTTATATATATTTTTAA
Found at i:57540563 original size:26 final size:26
Alignment explanation
Indices: 57540497--57540595 Score: 85
Period size: 26 Copynumber: 3.7 Consensus size: 26
57540487 TTATAATATG
* **
57540497 TTTTTATATTTTTTTGTACTTTTATATA
1 TTTTTATATATTTTAATA-TTTT-TATA
*
57540525 TTTTTATAAATTTATAATATTTTTA-A
1 TTTTTATATATTT-TAATATTTTTATA
* * *
57540551 TTTGTATATATTTTATTGTTTTTATA
1 TTTTTATATATTTTAATATTTTTATA
57540577 TTTTTAT-TATTTTTAATAT
1 TTTTTATATA-TTTTAATAT
57540596 AAAATATCAT
Statistics
Matches: 57, Mismatches: 11, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
25 11 0.19
26 26 0.46
27 2 0.04
28 15 0.26
29 3 0.05
ACGTcount: A:0.27, C:0.01, G:0.03, T:0.69
Consensus pattern (26 bp):
TTTTTATATATTTTAATATTTTTATA
Found at i:57540576 original size:16 final size:17
Alignment explanation
Indices: 57540497--57540591 Score: 77
Period size: 19 Copynumber: 5.4 Consensus size: 17
57540487 TTATAATATG
*
57540497 TTTTTATATTTTTTTGTA
1 TTTTTATATTTTTAT-TA
*
57540515 CTTTTATATATTTTTATAAA
1 -TTTT-TATATTTTTAT-TA
*
57540535 TTTATAATATTTTTA--A
1 TTT-TTATATTTTTATTA
* *
57540551 TTTGTATATATTTTATTG
1 TTTTTATAT-TTTTATTA
57540569 TTTTTATATTTTTATTA
1 TTTTTATATTTTTATTA
57540586 TTTTTA
1 TTTTTA
57540592 ATATAAAATA
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
15 4 0.06
16 9 0.15
17 13 0.21
18 8 0.13
19 16 0.26
20 12 0.19
ACGTcount: A:0.26, C:0.01, G:0.03, T:0.69
Consensus pattern (17 bp):
TTTTTATATTTTTATTA
Found at i:57540581 original size:17 final size:18
Alignment explanation
Indices: 57540497--57540595 Score: 73
Period size: 18 Copynumber: 5.6 Consensus size: 18
57540487 TTATAATATG
*
57540497 TTTTTATAT-TTTTTTGTA
1 TTTTTATATATTTTAT-TA
*
57540515 CTTTTATATATTTT-TATA
1 TTTTTATATATTTTAT-TA
** *
57540533 AATTTATAATATTTT-TAA
1 TTTTTAT-ATATTTTATTA
* *
57540551 TTTGTATATATTTTATTG
1 TTTTTATATATTTTATTA
57540569 TTTTTATAT-TTTTATTA
1 TTTTTATATATTTTATTA
57540586 TTTTTA-ATAT
1 TTTTTATATAT
57540596 AAAATATCAT
Statistics
Matches: 65, Mismatches: 12, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
16 2 0.03
17 21 0.32
18 30 0.46
19 12 0.18
ACGTcount: A:0.27, C:0.01, G:0.03, T:0.69
Consensus pattern (18 bp):
TTTTTATATATTTTATTA
Found at i:57540590 original size:9 final size:9
Alignment explanation
Indices: 57540497--57540591 Score: 56
Period size: 10 Copynumber: 10.7 Consensus size: 9
57540487 TTATAATATG
57540497 TTTTTA-TA
1 TTTTTATTA
*
57540505 TTTTTTTGTA
1 TTTTTAT-TA
*
57540515 CTTTTATATA
1 TTTTTAT-TA
*
57540525 TTTTTATAAA
1 TTTTTAT-TA
* *
57540535 TTTATAATA
1 TTTTTATTA
57540544 TTTTTA--A
1 TTTTTATTA
*
57540551 TTTGTA-TA
1 TTTTTATTA
*
57540559 TATTTTATTG
1 T-TTTTATTA
57540569 TTTTTA-TA
1 TTTTTATTA
57540577 TTTTTATTA
1 TTTTTATTA
57540586 TTTTTA
1 TTTTTA
57540592 ATATAAAATA
Statistics
Matches: 67, Mismatches: 14, Indels: 11
0.73 0.15 0.12
Matches are distributed among these distances:
7 6 0.09
8 14 0.21
9 23 0.34
10 24 0.36
ACGTcount: A:0.26, C:0.01, G:0.03, T:0.69
Consensus pattern (9 bp):
TTTTTATTA
Found at i:57540596 original size:36 final size:37
Alignment explanation
Indices: 57540492--57540596 Score: 101
Period size: 36 Copynumber: 2.9 Consensus size: 37
57540482 TTCATTTATA
* *
57540492 ATATGTTTTTATATTTTTTTGTACTTTTATATATTTTT
1 ATATGTTTTTATATTTTTAT-TATTTTTATATATTTTT
** * *
57540530 ATAAATTTATAATATTTTTA--ATTTGTATATA-TTTT
1 ATATGTTT-TTATATTTTTATTATTTTTATATATTTTT
57540565 AT-TGTTTTTATATTTTTATTATTTTTAATATA
1 ATATGTTTTTATATTTTTATTATTTTT-ATATA
57540597 AAATATCATA
Statistics
Matches: 53, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
33 10 0.19
34 3 0.06
35 11 0.21
36 14 0.26
38 6 0.11
39 9 0.17
ACGTcount: A:0.29, C:0.01, G:0.04, T:0.67
Consensus pattern (37 bp):
ATATGTTTTTATATTTTTATTATTTTTATATATTTTT
Found at i:57545979 original size:18 final size:18
Alignment explanation
Indices: 57545956--57546094 Score: 107
Period size: 18 Copynumber: 7.7 Consensus size: 18
57545946 ATCTCATTCC
* *
57545956 CATTCTCGCTCACACTCT
1 CATTCTCACTCTCACTCT
* *
57545974 CATTCTCACTCACACTGT
1 CATTCTCACTCTCACTCT
*
57545992 CATTCTCAATCTCACTCT
1 CATTCTCACTCTCACTCT
* * *
57546010 CACTCTCACCCTCACTCA
1 CATTCTCACTCTCACTCT
* * **
57546028 CACTCTCATTCTCAAACT
1 CATTCTCACTCTCACTCT
* * *
57546046 CATTCTCGCTCTTATTCT
1 CATTCTCACTCTCACTCT
* *
57546064 CATTCTCACTCACACTCA
1 CATTCTCACTCTCACTCT
* *
57546082 CACTCTCATTCTC
1 CATTCTCACTCTC
57546095 GTTTTTCATC
Statistics
Matches: 93, Mismatches: 28, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 93 1.00
ACGTcount: A:0.21, C:0.42, G:0.02, T:0.35
Consensus pattern (18 bp):
CATTCTCACTCTCACTCT
Found at i:57545996 original size:42 final size:42
Alignment explanation
Indices: 57545947--57546095 Score: 136
Period size: 42 Copynumber: 3.4 Consensus size: 42
57545937 GGATGCTGAA
*
57545947 TCTCATTCCCATTCTCGCTCACACTCTCATTCTCACTCACAC
1 TCTCATTCCCATTCTCGCTCTCACTCTCATTCTCACTCACAC
* * * * **
57545989 TGTCATTCTCAATCTCACTCTCACTCTCACCCTCACTCACAC
1 TCTCATTCCCATTCTCGCTCTCACTCTCATTCTCACTCACAC
* *
57546031 TCTCATTCTCAAACTCATTCTCGCTCTTATTCTCATTCTCACTCACAC
1 TCTCA-T-TC---C-CATTCTCGCTCTCACTCTCATTCTCACTCACAC
* * *
57546079 TCACACTCTCATTCTCG
1 TCTCATTCCCATTCTCG
57546096 TTTTTCATCT
Statistics
Matches: 83, Mismatches: 18, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
42 47 0.57
43 1 0.01
44 2 0.02
46 2 0.02
48 31 0.37
ACGTcount: A:0.20, C:0.42, G:0.03, T:0.35
Consensus pattern (42 bp):
TCTCATTCCCATTCTCGCTCTCACTCTCATTCTCACTCACAC
Found at i:57545998 original size:24 final size:24
Alignment explanation
Indices: 57545971--57546094 Score: 107
Period size: 24 Copynumber: 5.4 Consensus size: 24
57545961 TCGCTCACAC
*
57545971 TCTCATTCTCACTCACACTGTCAT
1 TCTCATTCTCACTCACACTCTCAT
* *
57545995 TCTCAATCTCACTCTCACTCTCA-
1 TCTCATTCTCACTCACACTCTCAT
57546018 -C-C---CTCACTCACACTCTCAT
1 TCTCATTCTCACTCACACTCTCAT
** * * * *
57546037 TCTCAAACTCATTCTCGCTCTTAT
1 TCTCATTCTCACTCACACTCTCAT
* *
57546061 TCTCATTCTCACTCACACTCACAC
1 TCTCATTCTCACTCACACTCTCAT
57546085 TCTCATTCTC
1 TCTCATTCTC
57546095 GTTTTTCATC
Statistics
Matches: 78, Mismatches: 16, Indels: 12
0.74 0.15 0.11
Matches are distributed among these distances:
18 15 0.19
20 1 0.01
21 2 0.03
22 1 0.01
24 59 0.76
ACGTcount: A:0.21, C:0.42, G:0.02, T:0.35
Consensus pattern (24 bp):
TCTCATTCTCACTCACACTCTCAT
Found at i:57546004 original size:6 final size:6
Alignment explanation
Indices: 57545968--57546094 Score: 92
Period size: 6 Copynumber: 21.2 Consensus size: 6
57545958 TTCTCGCTCA
* * * * *
57545968 CACTCT CATTCT CACTCA CACTGT CATTCT CAATCT CACTCT CACTCT
1 CACTCT CACTCT CACTCT CACTCT CACTCT CACTCT CACTCT CACTCT
* * * ** * * * *
57546016 CACCCT CACTCA CACTCT CATTCT CAAACT CATTCT CGCTCT TATTCT
1 CACTCT CACTCT CACTCT CACTCT CACTCT CACTCT CACTCT CACTCT
* * * *
57546064 CATTCT CACTCA CACTCA CACTCT CATTCT C
1 CACTCT CACTCT CACTCT CACTCT CACTCT C
57546095 GTTTTTCATC
Statistics
Matches: 93, Mismatches: 28, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
6 93 1.00
ACGTcount: A:0.21, C:0.43, G:0.02, T:0.35
Consensus pattern (6 bp):
CACTCT
Found at i:57546423 original size:5 final size:5
Alignment explanation
Indices: 57546413--57546438 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
57546403 GAAAGCAGTA
57546413 TTCTT TTCTT TTCTT TTCTT TTCTT T
1 TTCTT TTCTT TTCTT TTCTT TTCTT T
57546439 GCAAACAAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTCTT
Found at i:57546892 original size:9 final size:9
Alignment explanation
Indices: 57546871--57547005 Score: 57
Period size: 9 Copynumber: 14.4 Consensus size: 9
57546861 TTTTGGCAAT
57546871 TTTTA-ATA
1 TTTTATATA
*
57546879 ATTTATATA
1 TTTTATATA
*
57546888 TTTTATTTCA
1 TTTTATAT-A
*
57546898 TTTATAATATGT
1 TTT-T-ATAT-A
*
57546910 TTTTATATT
1 TTTTATATA
* *
57546919 TTTTTTGTA
1 TTTTATATA
57546928 CTTTTATATA
1 -TTTTATATA
57546938 TTTT-TATAA
1 TTTTATAT-A
*
57546947 ATTTATAATA
1 TTTTAT-ATA
57546957 TTTTA-A-A
1 TTTTATATA
57546964 TTTGTATATA
1 TTT-TATATA
57546974 TTTGTAT-TA
1 TTT-TATATA
57546983 TTTGTAT-TA
1 TTT-TATATA
*
57546992 TTTTTTATTA
1 TTTTATA-TA
57547002 TTTT
1 TTTT
57547006 TAATATAAAA
Statistics
Matches: 100, Mismatches: 14, Indels: 24
0.72 0.10 0.17
Matches are distributed among these distances:
7 4 0.04
8 12 0.12
9 39 0.39
10 35 0.35
11 4 0.04
12 6 0.06
ACGTcount: A:0.29, C:0.01, G:0.04, T:0.66
Consensus pattern (9 bp):
TTTTATATA
Found at i:57546951 original size:18 final size:17
Alignment explanation
Indices: 57546930--57546976 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
57546920 TTTTTGTACT
*
57546930 TTTATATATTTTTATAAA
1 TTTATATATATTT-TAAA
57546948 TTTATA-ATATTTTAAA
1 TTTATATATATTTTAAA
*
57546964 TTTGTATATATTT
1 TTTATATATATTT
57546977 GTATTATTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 9 0.35
17 11 0.42
18 6 0.23
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (17 bp):
TTTATATATATTTTAAA
Found at i:57546987 original size:19 final size:19
Alignment explanation
Indices: 57546963--57547004 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
57546953 AATATTTTAA
57546963 ATTTGTA-TATATTTGTATT
1 ATTTGTATTAT-TTTGTATT
*
57546982 ATTTGTATTATTTTTTATT
1 ATTTGTATTATTTTGTATT
57547001 ATTT
1 ATTT
57547005 TTAATATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 18 0.86
20 3 0.14
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (19 bp):
ATTTGTATTATTTTGTATT
Found at i:57547007 original size:9 final size:9
Alignment explanation
Indices: 57546963--57547004 Score: 57
Period size: 10 Copynumber: 4.4 Consensus size: 9
57546953 AATATTTTAA
57546963 ATTTGTATAT
1 ATTTGTAT-T
57546973 ATTTGTATT
1 ATTTGTATT
57546982 ATTTGTATT
1 ATTTGTATT
*
57546991 ATTTTTTATT
1 A-TTTGTATT
57547001 ATTT
1 ATTT
57547005 TTAATATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
9 14 0.47
10 16 0.53
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (9 bp):
ATTTGTATT
Done.