Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold187
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: 2169796
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 45208 characters in sequence are not A, C, G, or T
File 10 of 13
Found at i:1481896 original size:82 final size:82
Alignment explanation
Indices: 1481743--1481923 Score: 188
Period size: 82 Copynumber: 2.2 Consensus size: 82
1481733 TTTTCATCTT
* * * * * * * *
1481743 TGGGGATACTCCAACCCCACGATCTCTGAGGGGATACTCCAATCCTGTTTTTCCTTTTAAAATGC
1 TGGGAATACTCCAACCCCACCATCTCTAAAGGGATACTCCAACCCTGTTTTTACTTCTAAAATAC
*
1481808 CGTATTTTTTTTGTCTC
66 CATATTTTTTTTGTCTC
* * * * *
1481825 TGGGAATACTTCAACCCCACCATCTCTAAAGGGATAGTCTAACCCTGTTTTTACTTCTAAAGTAT
1 TGGGAATACTCCAACCCCACCATCTCTAAAGGGATACTCCAACCCTGTTTTTACTTCTAAAATAC
**
1481890 CATA--TTTTTCATCTC
66 CATATTTTTTTTGTCTC
1481905 TAGGG-ATACTCCAACCCCA
1 T-GGGAATACTCCAACCCCA
1481924 ATCATCTTCG
Statistics
Matches: 81, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
80 23 0.28
81 3 0.04
82 55 0.68
ACGTcount: A:0.24, C:0.27, G:0.14, T:0.35
Consensus pattern (82 bp):
TGGGAATACTCCAACCCCACCATCTCTAAAGGGATACTCCAACCCTGTTTTTACTTCTAAAATAC
CATATTTTTTTTGTCTC
Found at i:1485586 original size:43 final size:44
Alignment explanation
Indices: 1485524--1485612 Score: 135
Period size: 43 Copynumber: 2.0 Consensus size: 44
1485514 TTGTTGAATT
* *
1485524 ATTTGAAAATTGTAGGGCAATCGGTTGCAAGTGAATTTTT-AAA
1 ATTTGAAAATTGTAAGGCAATCAGTTGCAAGTGAATTTTTCAAA
* *
1485567 ATTTGAAAATTGTAAGGCAATCAGTTGTAAGTGGATTTTTCAAA
1 ATTTGAAAATTGTAAGGCAATCAGTTGCAAGTGAATTTTTCAAA
1485611 AT
1 AT
1485613 AAAGAAAGAT
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
43 36 0.88
44 5 0.12
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (44 bp):
ATTTGAAAATTGTAAGGCAATCAGTTGCAAGTGAATTTTTCAAA
Found at i:1488806 original size:25 final size:25
Alignment explanation
Indices: 1488777--1488826 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1488767 ACAGAAACAC
1488777 TTAAATTTTTCGTAGTATTATCATT
1 TTAAATTTTTCGTAGTATTATCATT
1488802 TTAAATTTTTCGTAGTATTATCATT
1 TTAAATTTTTCGTAGTATTATCATT
1488827 AAAAGTAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.08, G:0.08, T:0.56
Consensus pattern (25 bp):
TTAAATTTTTCGTAGTATTATCATT
Found at i:1495341 original size:144 final size:144
Alignment explanation
Indices: 1495081--1495360 Score: 335
Period size: 144 Copynumber: 1.9 Consensus size: 144
1495071 TTGTTCTTAG
* *
1495081 AAGAATAGTTTTGTTGGTTAAATAAATTAAAGAACATATTTGTTTAATGTTTATGAATAAGTTCA
1 AAGAATAATTTTGTTGGTTAAATAAATTAAAGAACATATTTGTTTAATGTTTAAGAATAAGTTCA
* * * * *
1495146 TTTAACTTAAACTGATAGAGTCTGAACACACCCGATTTTAAACTAATCAAGCTCGAACGTTATTT
66 TTTAACTTAAACTAATAGAGTCTGAACACACCCAATTTTAAACTAACCAAGCTCGAACATAATTT
1495211 TAAAAAGGGTTAAA
131 TAAAAAGGGTTAAA
* ** * ** * *
1495225 AAGAATAATTTTTTTGGTTACGTAATTTAAAGATTATATTTGTTTATTGTTTAAGAATAAGTTTA
1 AAGAATAATTTTGTTGGTTAAATAAATTAAAGAACATATTTGTTTAATGTTTAAGAATAAGTTCA
* * * * ***** *
1495290 TTTAATTTAAACTAATCGAGTTTGAAGATGTTTAATTTTAAACTAACCAAGCTTGAACATAATTT
66 TTTAACTTAAACTAATAGAGTCTGAACACACCCAATTTTAAACTAACCAAGCTCGAACATAATTT
1495355 TAAAAA
131 TAAAAA
1495361 TCTTTAATAA
Statistics
Matches: 111, Mismatches: 25, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
144 111 1.00
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.39
Consensus pattern (144 bp):
AAGAATAATTTTGTTGGTTAAATAAATTAAAGAACATATTTGTTTAATGTTTAAGAATAAGTTCA
TTTAACTTAAACTAATAGAGTCTGAACACACCCAATTTTAAACTAACCAAGCTCGAACATAATTT
TAAAAAGGGTTAAA
Found at i:1496471 original size:13 final size:13
Alignment explanation
Indices: 1496450--1496479 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1496440 CAATACATGG
*
1496450 TACATTGTATCGA
1 TACAATGTATCGA
1496463 TACAATGTATCGA
1 TACAATGTATCGA
1496476 TACA
1 TACA
1496480 TGATGAATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
TACAATGTATCGA
Found at i:1496479 original size:33 final size:33
Alignment explanation
Indices: 1496435--1496499 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
1496425 TACCACTGTT
*
1496435 TGTATCAATACATGGT-ACATTGTATCGATACAA
1 TGTATCAATACATGATGA-ATTGTATCGATACAA
* *
1496468 TGTATCGATACATGATGAATTGTATTGATACA
1 TGTATCAATACATGATGAATTGTATCGATACA
1496500 TTACGTCTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.35, C:0.12, G:0.17, T:0.35
Consensus pattern (33 bp):
TGTATCAATACATGATGAATTGTATCGATACAA
Found at i:1504096 original size:1 final size:1
Alignment explanation
Indices: 1504090--1504181 Score: 76
Period size: 1 Copynumber: 92.0 Consensus size: 1
1504080 AAATCTTCAC
* * ** * * * **
1504090 TTTTTTTTTTGTTTTTTTTTTTTCTTTTTCCTTTTTTTTGTTTTGTTTTTTTTTTCTTTTTCCTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
1504155 TTTTTTGTTTTGTTTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1504182 CCAATTGCCA
Statistics
Matches: 71, Mismatches: 20, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 71 1.00
ACGTcount: A:0.00, C:0.08, G:0.05, T:0.87
Consensus pattern (1 bp):
T
Found at i:1504139 original size:32 final size:32
Alignment explanation
Indices: 1504089--1504183 Score: 160
Period size: 32 Copynumber: 3.0 Consensus size: 32
1504079 CAAATCTTCA
1504089 CTTTTTTTT-TTGTT-TTTTTTTTTTCTTTTTC
1 CTTTTTTTTGTT-TTGTTTTTTTTTTCTTTTTC
1504120 CTTTTTTTTGTTTTGTTTTTTTTTTCTTTTTC
1 CTTTTTTTTGTTTTGTTTTTTTTTTCTTTTTC
1504152 CTTTTTTTTGTTTTG-TTTTTTTTTCTTTTTC
1 CTTTTTTTTGTTTTGTTTTTTTTTTCTTTTTC
1504183 C
1 C
1504184 AATTGCCATG
Statistics
Matches: 62, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
31 28 0.45
32 34 0.55
ACGTcount: A:0.00, C:0.11, G:0.05, T:0.84
Consensus pattern (32 bp):
CTTTTTTTTGTTTTGTTTTTTTTTTCTTTTTC
Found at i:1513002 original size:20 final size:20
Alignment explanation
Indices: 1512979--1513050 Score: 144
Period size: 20 Copynumber: 3.6 Consensus size: 20
1512969 CATTTTTCAA
1512979 TGTATCGATACAAAGAATAT
1 TGTATCGATACAAAGAATAT
1512999 TGTATCGATACAAAGAATAT
1 TGTATCGATACAAAGAATAT
1513019 TGTATCGATACAAAGAATAT
1 TGTATCGATACAAAGAATAT
1513039 TGTATCGATACA
1 TGTATCGATACA
1513051 TTATATCAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (20 bp):
TGTATCGATACAAAGAATAT
Found at i:1513004 original size:40 final size:39
Alignment explanation
Indices: 1512959--1513053 Score: 127
Period size: 40 Copynumber: 2.4 Consensus size: 39
1512949 ATTTTCAGAA
**
1512959 TGTATCGATACATTTTTCAATGTATCGATACAAAGAATAT
1 TGTATCGATACATTAAT-AATGTATCGATACAAAGAATAT
** *
1512999 TGTATCGATACAAAGAATATTGTATCGATACAAAGAATAT
1 TGTATCGATAC-ATTAATAATGTATCGATACAAAGAATAT
1513039 TGTATCGATACATTA
1 TGTATCGATACATTA
1513054 TATCAATATA
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
39 2 0.04
40 43 0.91
41 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.35
Consensus pattern (39 bp):
TGTATCGATACATTAATAATGTATCGATACAAAGAATAT
Found at i:1515578 original size:19 final size:20
Alignment explanation
Indices: 1515554--1515599 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 20
1515544 GATACAATGA
**
1515554 ATCGATACATGTTC-ATTGT
1 ATCGATACATGGACAATTGT
1515573 ATCGATACATGGACAATTGT
1 ATCGATACATGGACAATTGT
1515593 ATCGATA
1 ATCGATA
1515600 AATGAAACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (20 bp):
ATCGATACATGGACAATTGT
Found at i:1516891 original size:20 final size:20
Alignment explanation
Indices: 1516849--1516887 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1516839 CGTGTGAATG
* *
1516849 TATCGATACAATTTTTGATA
1 TATCGATACAATATTTGAAA
1516869 TATCGATAC-ATATTTGAAA
1 TATCGATACAATATTTGAAA
1516888 ATATAGTCGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.41
Consensus pattern (20 bp):
TATCGATACAATATTTGAAA
Found at i:1516943 original size:20 final size:20
Alignment explanation
Indices: 1516918--1516969 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
1516908 TACAAGCCAA
**
1516918 TGTATCGATACAATTTTTTG
1 TGTATCGATACAATACTTTG
1516938 TGTATCGATAC-ATACTTTG
1 TGTATCGATACAATACTTTG
*
1516957 TGTATAGATACAA
1 TGTATCGATACAA
1516970 GTTTGGCTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (20 bp):
TGTATCGATACAATACTTTG
Found at i:1519081 original size:20 final size:20
Alignment explanation
Indices: 1519056--1519110 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
1519046 TGGGGACTGC
1519056 CCGGTTGTGACCTGGGAGTG
1 CCGGTTGTGACCTGGGAGTG
1519076 CCGGTTGTGACCTGGGAGTG
1 CCGGTTGTGACCTGGGAGTG
* *
1519096 CCGGTCGCGACCTGG
1 CCGGTTGTGACCTGG
1519111 TGGTACTGCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.09, C:0.25, G:0.44, T:0.22
Consensus pattern (20 bp):
CCGGTTGTGACCTGGGAGTG
Found at i:1519579 original size:13 final size:13
Alignment explanation
Indices: 1519561--1519586 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1519551 ACATTTTTCT
1519561 TTGTATCGATACA
1 TTGTATCGATACA
1519574 TTGTATCGATACA
1 TTGTATCGATACA
1519587 AAGAAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1522148 original size:33 final size:33
Alignment explanation
Indices: 1522111--1522177 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1522101 TTCAACGATT
1522111 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1522144 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1522177 T
1 T
1522178 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1522149 original size:13 final size:13
Alignment explanation
Indices: 1522131--1522155 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1522121 CATAAAATGT
1522131 TGTATCGATACAA
1 TGTATCGATACAA
1522144 TGTATCGATACA
1 TGTATCGATACA
1522156 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1522239 original size:13 final size:13
Alignment explanation
Indices: 1522221--1522245 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1522211 ATTACTCACA
1522221 TGTATCGATACAT
1 TGTATCGATACAT
1522234 TGTATCGATACA
1 TGTATCGATACA
1522246 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1522328 original size:51 final size:52
Alignment explanation
Indices: 1522254--1522380 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
1522244 CACTGATCTT
*
1522254 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACA-TTTTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1522304 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1522356 TGTATCGATACATGCAGGCAAATTT
1 TGTATCGATACATGCAGGCAAATTT
1522381 TCATATTTCG
Statistics
Matches: 74, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
50 19 0.26
51 24 0.32
52 31 0.42
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
Found at i:1529436 original size:13 final size:13
Alignment explanation
Indices: 1529418--1529443 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1529408 CAATTTTTTG
1529418 TGTATCGATACAT
1 TGTATCGATACAT
1529431 TGTATCGATACAT
1 TGTATCGATACAT
1529444 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1529460 original size:32 final size:33
Alignment explanation
Indices: 1529398--1529461 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
1529388 TACAAGCCAA
** *
1529398 TGTATCGATACAATTTTTTGTGTATCGATACAT
1 TGTATCGATACAATACTTTGTGTATAGATACAT
1529431 TGTATCGATAC-ATACTTTGTGTATAGATACA
1 TGTATCGATACAATACTTTGTGTATAGATACA
1529462 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.30, C:0.12, G:0.16, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTGTGTATAGATACAT
Found at i:1533692 original size:17 final size:16
Alignment explanation
Indices: 1533659--1533707 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
1533649 AGACGCTTAT
*
1533659 TTTATATGAAAATTTTA
1 TTTATATTAAAA-TTTA
1533676 TTTATATTAAAGATTTA
1 TTTATATTAAA-ATTTA
*
1533693 CTT-TATTAAAATTTA
1 TTTATATTAAAATTTA
1533708 AAAATTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 5 0.17
16 7 0.24
17 16 0.55
18 1 0.03
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (16 bp):
TTTATATTAAAATTTA
Found at i:1533739 original size:30 final size:30
Alignment explanation
Indices: 1533705--1533775 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
1533695 TTATTAAAAT
* **
1533705 TTAAAAATTAAATATTTATTTTGATATATA-
1 TTAAAAATTAAAAATTTATTTAAATATA-AG
*
1533735 TTAAAACTTAAAAATTTATTTAAATATAAG
1 TTAAAAATTAAAAATTTATTTAAATATAAG
1533765 TTAAAAATTAA
1 TTAAAAATTAA
1533776 TTTTAATATA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
29 1 0.03
30 34 0.97
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (30 bp):
TTAAAAATTAAAAATTTATTTAAATATAAG
Found at i:1533772 original size:23 final size:23
Alignment explanation
Indices: 1533742--1533786 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1533732 ATATTAAAAC
*
1533742 TTAAAAATTTATTTAAATATAAG
1 TTAAAAATTAATTTAAATATAAG
*
1533765 TTAAAAATTAATTTTAATATAA
1 TTAAAAATTAATTTAAATATAA
1533787 TAACAGTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (23 bp):
TTAAAAATTAATTTAAATATAAG
Found at i:1542350 original size:17 final size:16
Alignment explanation
Indices: 1542328--1542371 Score: 63
Period size: 17 Copynumber: 2.7 Consensus size: 16
1542318 TGGGCTATTC
1542328 TAAACTTGAATTCATTT
1 TAAACTTGAATTCA-TT
1542345 TAAACTTGAA-TCATT
1 TAAACTTGAATTCATT
1542360 TAAAGCTTGAAT
1 TAAA-CTTGAAT
1542372 ATTTTCAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.24
16 9 0.36
17 10 0.40
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (16 bp):
TAAACTTGAATTCATT
Found at i:1542360 original size:16 final size:16
Alignment explanation
Indices: 1542328--1542376 Score: 66
Period size: 16 Copynumber: 3.1 Consensus size: 16
1542318 TGGGCTATTC
1542328 TAAACTTGAATTCATTT
1 TAAACTTGAA-TCATTT
1542345 TAAACTTGAATCA-TT
1 TAAACTTGAATCATTT
1542360 TAAAGCTTGAAT-ATTT
1 TAAA-CTTGAATCATTT
1542376 T
1 T
1542377 CAAATTCAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.23
16 13 0.43
17 10 0.33
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.45
Consensus pattern (16 bp):
TAAACTTGAATCATTT
Found at i:1547914 original size:40 final size:34
Alignment explanation
Indices: 1547839--1547919 Score: 83
Period size: 34 Copynumber: 2.2 Consensus size: 34
1547829 AGAGGTAAGT
*
1547839 AAAA-TAAATTTGAATTTAAAAATTTATTTGAAA
1 AAAATTAAGTTTGAATTTAAAAATTTATTTGAAA
*
1547872 AAATTTAAGTTTGAATTTGAATTAAATTTGATTTGATTAA
1 AAAATTAAGTTTGAATTT-AA--AAATTT-ATTTGA--AA
1547912 AAAATTAA
1 AAAATTAA
1547920 AAATTCGAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
33 3 0.08
34 12 0.32
35 2 0.05
37 6 0.16
38 6 0.16
40 9 0.24
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.42
Consensus pattern (34 bp):
AAAATTAAGTTTGAATTTAAAAATTTATTTGAAA
Found at i:1549204 original size:20 final size:18
Alignment explanation
Indices: 1549171--1549229 Score: 77
Period size: 18 Copynumber: 3.2 Consensus size: 18
1549161 AATTATTTAA
1549171 AAATTAATTTTATATAAT
1 AAATTAATTTTATATAAT
1549189 AAATTAATTTTATAT-AT
1 AAATTAATTTTATATAAT
1549206 AAATATAGATTTTA-ATAAAT
1 AAAT-TA-ATTTTATAT-AAT
1549226 AAAT
1 AAAT
1549230 ATATTAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.16
18 19 0.51
19 6 0.16
20 6 0.16
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
AAATTAATTTTATATAAT
Found at i:1549760 original size:16 final size:17
Alignment explanation
Indices: 1549739--1549799 Score: 61
Period size: 16 Copynumber: 3.5 Consensus size: 17
1549729 ATAAAGTAAG
1549739 ATATAAATATAA-AATA
1 ATATAAATATAATAATA
*
1549755 ATATAAATATAATATTAA
1 ATATAAATATAATAAT-A
* *
1549773 TATATAAATTTAATTCATA
1 -ATATAAATATAA-TAATA
1549792 ATATAAAT
1 ATATAAAT
1549800 TATATATTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
16 12 0.32
17 2 0.05
18 9 0.24
19 12 0.32
20 2 0.05
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (17 bp):
ATATAAATATAATAATA
Found at i:1549805 original size:56 final size:54
Alignment explanation
Indices: 1549745--1549850 Score: 124
Period size: 56 Copynumber: 1.9 Consensus size: 54
1549735 TAAGATATAA
* *
1549745 ATATAAAATAATA-TAAATATAATATTAATATATAAATTTAATTCATAATATAAATT
1 ATATAAAATAAAATTAAA-ATAATATTAAAAT-TAAATTT-ATTCATAATATAAATT
** * *
1549801 ATATATTATAAAATTAAAATAATATTAAAATTTAATTTATTCATATTATA
1 ATATAAAATAAAATTAAAATAATATTAAAATTAAATTTATTCATAATATA
1549851 TTTATATCCA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
54 11 0.26
55 6 0.14
56 22 0.51
57 4 0.09
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (54 bp):
ATATAAAATAAAATTAAAATAATATTAAAATTAAATTTATTCATAATATAAATT
Found at i:1549893 original size:15 final size:16
Alignment explanation
Indices: 1549873--1549902 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1549863 ATATATCTTC
1549873 ATAATAAAA-ATAAAA
1 ATAATAAAACATAAAA
1549888 ATAATAAAACATAAA
1 ATAATAAAACATAAA
1549903 TCTAATGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (16 bp):
ATAATAAAACATAAAA
Found at i:1550032 original size:2 final size:2
Alignment explanation
Indices: 1550025--1550052 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1550015 CATGATTGTG
1550025 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1550053 TCATAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1550162 original size:20 final size:21
Alignment explanation
Indices: 1550127--1550194 Score: 59
Period size: 20 Copynumber: 3.3 Consensus size: 21
1550117 AATTATACAT
* *
1550127 AAATATAATTTTAAAA-AATA
1 AAATATAATATAAAAATAATA
1550147 AAATATAATATAAAAATAATA
1 AAATATAATATAAAAATAATA
** * *
1550168 TTATCATAATATTAATAT-ATA
1 AAAT-ATAATATAAAAATAATA
1550189 AAATAT
1 AAATAT
1550195 CAAAATCTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
20 16 0.42
21 11 0.29
22 11 0.29
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (21 bp):
AAATATAATATAAAAATAATA
Found at i:1550317 original size:24 final size:24
Alignment explanation
Indices: 1550288--1550340 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
1550278 ATATAGATAT
* *
1550288 ATAAA-TTATTAAAATTTATTTAAA
1 ATAAATTTATAAAAATTTATAT-AA
1550312 ATAAATTTATAAAAATTTATATAA
1 ATAAATTTATAAAAATTTATATAA
1550336 ATAAA
1 ATAAA
1550341 CAGTAATATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
24 12 0.46
25 14 0.54
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
ATAAATTTATAAAAATTTATATAA
Found at i:1550645 original size:29 final size:32
Alignment explanation
Indices: 1550587--1550645 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
1550577 TTAAAAAATT
*
1550587 TAATAAATAATAATATATTAATTATTATTTTA
1 TAATAAATAATAATATATTAATTATAATTTTA
1550619 TAATAAA-AATAATAT-TTAATTA-AATTT
1 TAATAAATAATAATATATTAATTATAATTT
1550646 AAAAAATTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 4 0.15
30 7 0.27
31 8 0.31
32 7 0.27
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (32 bp):
TAATAAATAATAATATATTAATTATAATTTTA
Found at i:1550650 original size:67 final size:70
Alignment explanation
Indices: 1550567--1550697 Score: 205
Period size: 70 Copynumber: 1.9 Consensus size: 70
1550557 TTTTTATAAA
* *
1550567 TTAATTAAATTTAAAAAATTTA-ATAAAT-AA-TAATATATTAATTATTATTTTATAATAAAAAT
1 TTAATTAAATTTAAAAAATTTACATAAATAAATTAAAATATTAATTATTATTTTAAAATAAAAAT
1550629 AATAT
66 AATAT
* *
1550634 TTAATTAAATTTAAAAAATTTACATTAATAAATTAAAATATTAATTATTTTTTTAAAATAAAAA
1 TTAATTAAATTTAAAAAATTTACATAAATAAATTAAAATATTAATTATTATTTTAAAATAAAAA
1550698 ATTAAATTAA
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
67 22 0.39
68 5 0.09
69 2 0.04
70 28 0.49
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.44
Consensus pattern (70 bp):
TTAATTAAATTTAAAAAATTTACATAAATAAATTAAAATATTAATTATTATTTTAAAATAAAAAT
AATAT
Found at i:1550680 original size:20 final size:22
Alignment explanation
Indices: 1550624--1550680 Score: 55
Period size: 22 Copynumber: 2.6 Consensus size: 22
1550614 TTTTATAATA
* *
1550624 AAAATAATATTTAATTAAATTT
1 AAAATATTAATTAATTAAATTT
*
1550646 AAAAAATTTACATTAA-TAAA-TT
1 AAAATA-TTA-ATTAATTAAATTT
1550668 AAAATATTAATTA
1 AAAATATTAATTA
1550681 TTTTTTTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
20 4 0.14
21 3 0.10
22 12 0.41
23 6 0.21
24 4 0.14
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAATATTAATTAATTAAATTT
Found at i:1551238 original size:89 final size:88
Alignment explanation
Indices: 1551059--1551231 Score: 201
Period size: 89 Copynumber: 2.0 Consensus size: 88
1551049 TGTACATGTA
* * * *
1551059 TTATTTTTATTAAAATTAATTAATATTGTATATGTATTATTACTTTTTATTTATAAAATATTTTT
1 TTATTTTTATTAAAATTAATTAATATTGTATATGTATTATTA-TTTTAATTGATAAAATATCTTA
* * *
1551124 AATTTATTTATAAATTATACAAAT
65 AATTTATTTACAAATAATAAAAAT
*
1551148 TTATTTTTATTAAAATTAATTAATATTGTATATGTATTATT-TTTATAATTGAT-AGA-A-CTTA
1 TTATTTTTATTAAAATTAATTAATATTGTATATGTATTATTATTT-TAATTGATAAAATATCTTA
*
1551209 AATTTATGTTAGCCAATAATAAA
65 AATTTAT-TTA-CAAATAATAAA
1551232 TTAATTTTTT
Statistics
Matches: 72, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
85 9 0.12
86 4 0.06
87 12 0.17
88 6 0.08
89 41 0.57
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.53
Consensus pattern (88 bp):
TTATTTTTATTAAAATTAATTAATATTGTATATGTATTATTATTTTAATTGATAAAATATCTTAA
ATTTATTTACAAATAATAAAAAT
Found at i:1554083 original size:15 final size:16
Alignment explanation
Indices: 1554063--1554097 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1554053 TTATTATGTT
1554063 TTTTAAAATAAAAAA-
1 TTTTAAAATAAAAAAG
*
1554078 TTTTAAATTAAAAAAG
1 TTTTAAAATAAAAAAG
1554094 TTTT
1 TTTT
1554098 TTGTTATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 14 0.78
16 4 0.22
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (16 bp):
TTTTAAAATAAAAAAG
Found at i:1554105 original size:122 final size:122
Alignment explanation
Indices: 1553872--1554107 Score: 318
Period size: 122 Copynumber: 1.9 Consensus size: 122
1553862 TATTATTTTT
*
1553872 AATAAAAATAATAATTAATTAACTTTAAAAAAATTTATATTAACAAATTAAAATATTAATTATTT
1 AATAAAAATAATAATTAATTAACTTTAAAAAAATTTACATTAACAAATTAAAATATTAATTATTT
**
1553937 TTTTAAAATAAAAAATTTAATAAAAATAAGAAGGGTTTATTATTATAATTTTTAATAA
66 TTTTAAAATAAAAAATTT-ATAAAAATAAGAAAAGTTTATTATTATAATTTTTAATAA
* * *
1553995 AATAAAAATAATATTTAATTAAGTTT-AAAAAATTTACATTAACAAATTCAAATATTAATTATTA
1 AATAAAAATAATAATTAATTAACTTTAAAAAAATTTACATTAACAAATTAAAATATT-A--ATTA
* * *
1554059 TGTTTTTTAAAATAAAAAATTT-T-AAATTAA-AAAAGTTTTTTGTTATAAT
63 T-TTTTTTAAAATAAAAAATTTATAAAAATAAGAAAAGTTTATTATTATAAT
1554108 AATATTTTTT
Statistics
Matches: 100, Mismatches: 9, Indels: 9
0.85 0.08 0.08
Matches are distributed among these distances:
122 43 0.43
123 31 0.31
124 1 0.01
125 5 0.05
126 20 0.20
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (122 bp):
AATAAAAATAATAATTAATTAACTTTAAAAAAATTTACATTAACAAATTAAAATATTAATTATTT
TTTTAAAATAAAAAATTTATAAAAATAAGAAAAGTTTATTATTATAATTTTTAATAA
Found at i:1554439 original size:23 final size:23
Alignment explanation
Indices: 1554392--1554454 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
1554382 TTATTTGAAT
**
1554392 AATGATAATTTTTTTTGTTTCTTA
1 AATGAT-ATTTTTTTAATTTCTTA
*
1554416 AATGATATTTTTTTAATTTGTTA
1 AATGATATTTTTTTAATTTCTTA
*
1554439 ATAT-AAATTTTTTTAA
1 A-ATGATATTTTTTTAA
1554455 ATTTAATTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
23 26 0.76
24 8 0.24
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.60
Consensus pattern (23 bp):
AATGATATTTTTTTAATTTCTTA
Found at i:1554531 original size:34 final size:35
Alignment explanation
Indices: 1554472--1554548 Score: 106
Period size: 35 Copynumber: 2.3 Consensus size: 35
1554462 TAACTATCAT
1554472 TTTTTA-TTTTATTAAAAAATAATAATAATAAATA
1 TTTTTATTTTTATTAAAAAATAATAATAATAAATA
*
1554506 CTTTTTATTTTTA-TAAAAAAT-ATAATAATTAATA
1 -TTTTTATTTTTATTAAAAAATAATAATAATAAATA
*
1554540 TTTTAATTT
1 TTTTTATTT
1554549 GTTAATGTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
33 8 0.21
34 12 0.31
35 14 0.36
36 5 0.13
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (35 bp):
TTTTTATTTTTATTAAAAAATAATAATAATAAATA
Found at i:1554586 original size:112 final size:115
Alignment explanation
Indices: 1554426--1554826 Score: 388
Period size: 119 Copynumber: 3.4 Consensus size: 115
1554416 AATGATATTT
* * * * *
1554426 TTTTAATTTGTTAATATAAATTTTTTTAAATTTAATTAACTATCATTTTTTATTTTATTAAAAAA
1 TTTTAATTTATTAATATAAATTTTTTTAAAATTAATTAAATATTATTTTTAATTTTATTAAAAAA
* *
1554491 TAATAATAATAAATACTTTTT-A-TTTTTATAAAAAATATAATAATTAATA
66 TAATAATAATAAATACTTTTTAATTTTTTATTATAAATA-AATAATTAATA
* * *
1554540 TTTTAATTTGTTAATGT-AA-TTTTTTAAACTTAATTAAATATTATTTTTAATTTTATTAAAAAA
1 TTTTAATTTATTAATATAAATTTTTTTAAAATTAATTAAATATTATTTTTAATTTTATTAAAAAA
** *
1554603 TAATAATAATAAACCCTTTTTAATTTAATTTTTTATTTTTAAA-AAAT-ATATAATA
66 TAATAATAATAAA---TACTT--TTTAATTTTTTA-TTATAAATAAATAAT-TAATA
*
1554658 GTTTAATTTATTAATAT-AATTTTTTTAAAAAAATTAATTAAATATTATTTTTAATTTTATTAAA
1 TTTTAATTTATTAATATAAATTTTTTT---AAAATTAATTAAATATTATTTTTAATTTTATTAAA
** ** *
1554722 AAATAATAATAA-ATGCTTTTTAATTTAATTTTTTATTTTTAAA-AAATAATTAATA
63 AAATAATAATAATA-AATACTT--TTTAATTTTTTA-TTATAAATAAATAATTAATA
* * * * *
1554777 TATTAATTTATTATTGTAAATTATTTTAAAGTTAATTAAATATTATTTTT
1 TTTTAATTTATTAATATAAATTTTTTTAAAATTAATTAAATATTATTTTT
1554827 TATTAAAAAT
Statistics
Matches: 249, Mismatches: 22, Indels: 29
0.83 0.07 0.10
Matches are distributed among these distances:
112 53 0.21
113 2 0.01
114 16 0.06
115 3 0.01
117 27 0.11
118 25 0.10
119 62 0.25
120 14 0.06
121 1 0.00
122 46 0.18
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (115 bp):
TTTTAATTTATTAATATAAATTTTTTTAAAATTAATTAAATATTATTTTTAATTTTATTAAAAAA
TAATAATAATAAATACTTTTTAATTTTTTATTATAAATAAATAATTAATA
Found at i:1554756 original size:119 final size:117
Alignment explanation
Indices: 1554529--1554826 Score: 415
Period size: 119 Copynumber: 2.5 Consensus size: 117
1554519 TAAAAAATAT
* *
1554529 AATAATTAATATTTTAATTTGTTAATGTAA-TTTTTTAAACTTAATTAAATATTATTTTTAATTT
1 AATAATTAATA-TTTAATTTATTAATGTAATTTTTTTAAAATTAATTAAATATTATTTTTAATTT
1554593 TATTAAAAAATAATAATAATAAACCCTTTTTAATTTAATTTTTTATTTTTAAAA
65 TATT-AAAAATAATAATAATAAACCCTTTTTAATTTAATTTTTTATTTTTAAAA
*
1554647 AAT-ATATAATAGTTTAATTTATTAATATAATTTTTTTAAAAAAATTAATTAAATATTATTTTTA
1 AATAAT-TAATA-TTTAATTTATTAATGTAATTTTTTT---AAAATTAATTAAATATTATTTTTA
**
1554711 ATTTTATT-AAAA-AATAATAATAAATGCTTTTTAATTTAATTTTTTATTTTTAAAA
61 ATTTTATTAAAAATAATAATAATAAACCCTTTTTAATTTAATTTTTTATTTTTAAAA
* * *
1554766 AATAATTAATATATTAATTTATTATTGTAAATTATTTTAAAGTTAATTAAATATTATTTTT
1 AATAATTAATAT-TTAATTTATTAATGT-AATTTTTTTAAAATTAATTAAATATTATTTTT
1554827 TATTAAAAAT
Statistics
Matches: 162, Mismatches: 10, Indels: 17
0.86 0.05 0.09
Matches are distributed among these distances:
117 24 0.15
118 25 0.15
119 68 0.42
120 14 0.09
122 31 0.19
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (117 bp):
AATAATTAATATTTAATTTATTAATGTAATTTTTTTAAAATTAATTAAATATTATTTTTAATTTT
ATTAAAAATAATAATAATAAACCCTTTTTAATTTAATTTTTTATTTTTAAAA
Found at i:1554770 original size:40 final size:40
Alignment explanation
Indices: 1554607--1554771 Score: 98
Period size: 40 Copynumber: 4.2 Consensus size: 40
1554597 AAAAAATAAT
** *
1554607 AATAATAAACCCTTTTTAATTTAATTTTTTATTTTTAAAA
1 AATAATAAATGCTTTTTAATTTAATTTTTTATTTTAAAAA
* *
1554647 AAT-ATATAATAG-TTTAATTTA-TTAATATAATTT-TTTTAAAAA
1 AATAATA-AAT-GCTTT--TTAATTTAAT-T-TTTTATTTTAAAAA
* * *
1554689 AATTAATTAAAT-ATTATT--TTTAA--TTTTA-TTAAAAAA
1 AA-TAA-TAAATGCTTTTTAATTTAATTTTTTATTTTAAAAA
*
1554725 TAATAATAAATGCTTTTTAATTTAATTTTTTATTTTTAAAA
1 -AATAATAAATGCTTTTTAATTTAATTTTTTATTTTAAAAA
1554766 AATAAT
1 AATAAT
1554772 TAATATATTA
Statistics
Matches: 94, Mismatches: 12, Indels: 38
0.65 0.08 0.26
Matches are distributed among these distances:
35 5 0.05
36 17 0.18
37 2 0.02
38 5 0.05
39 3 0.03
40 23 0.24
41 13 0.14
42 14 0.15
43 6 0.06
44 4 0.04
45 2 0.02
ACGTcount: A:0.45, C:0.02, G:0.01, T:0.52
Consensus pattern (40 bp):
AATAATAAATGCTTTTTAATTTAATTTTTTATTTTAAAAA
Found at i:1554990 original size:14 final size:14
Alignment explanation
Indices: 1554971--1555036 Score: 62
Period size: 14 Copynumber: 4.8 Consensus size: 14
1554961 CGTATTCGTA
1554971 AAAAAATTTTATTT
1 AAAAAATTTTATTT
*
1554985 AAAAAAATTTATTT
1 AAAAAATTTTATTT
* *
1554999 ACAAAATTTAATTT
1 AAAAAATTTTATTT
** * *
1555013 TTAATATTTTA-AT
1 AAAAAATTTTATTT
1555026 AAAAAATTTTA
1 AAAAAATTTTA
1555037 AATTATTAAA
Statistics
Matches: 40, Mismatches: 12, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
13 9 0.22
14 31 0.77
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (14 bp):
AAAAAATTTTATTT
Found at i:1555004 original size:13 final size:14
Alignment explanation
Indices: 1554969--1555008 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
1554959 AACGTATTCG
1554969 TAAAAAAATTTTATT
1 TAAAAAAA-TTTATT
1554984 TAAAAAAATTTATT
1 TAAAAAAATTTATT
*
1554998 T-ACAAAATTTA
1 TAAAAAAATTTA
1555009 ATTTTTAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 9 0.38
14 7 0.29
15 8 0.33
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (14 bp):
TAAAAAAATTTATT
Found at i:1556251 original size:21 final size:21
Alignment explanation
Indices: 1556210--1556251 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
1556200 ATACCAAATT
* *
1556210 AATTATTAAAATTTATTTAAA
1 AATTATTAAAATTAATATAAA
1556231 AATTATTAATAA-TAATATAAA
1 AATTATTAA-AATTAATATAAA
1556252 TTTAAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AATTATTAAAATTAATATAAA
Found at i:1556635 original size:55 final size:55
Alignment explanation
Indices: 1556551--1556660 Score: 202
Period size: 55 Copynumber: 2.0 Consensus size: 55
1556541 ATCCATTGTA
*
1556551 GTGTAGAAGTCATGCTAGTTGGGGAATAATTGTCAAGCTATCTTTTTAAGTCATG
1 GTGTAGAAGTCATGCTAGTTGGGGAATAATTGTCAAGCTATCCTTTTAAGTCATG
*
1556606 GTGTAGAAGTCATGCTGGTTGGGGAATAATTGTCAAGCTATCCTTTTAAGTCATG
1 GTGTAGAAGTCATGCTAGTTGGGGAATAATTGTCAAGCTATCCTTTTAAGTCATG
1556661 CTCATGTGCT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.35
Consensus pattern (55 bp):
GTGTAGAAGTCATGCTAGTTGGGGAATAATTGTCAAGCTATCCTTTTAAGTCATG
Found at i:1556717 original size:13 final size:14
Alignment explanation
Indices: 1556694--1556737 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 14
1556684 TTTAGAAATT
1556694 TTTTTATTTATATA
1 TTTTTATTTATATA
1556708 TTTTTATTATATTTATA
1 TTTTTATT-TA--TATA
1556725 TTTTTATGTTATA
1 TTTTTAT-TTATA
1556738 ATTATGTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 8 0.31
15 4 0.15
17 13 0.50
18 1 0.04
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (14 bp):
TTTTTATTTATATA
Found at i:1556717 original size:17 final size:17
Alignment explanation
Indices: 1556691--1556731 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
1556681 AGATTTAGAA
1556691 ATTTTT-TTAT-TTATAT
1 ATTTTTATTATATT-TAT
1556707 ATTTTTATTATATTTAT
1 ATTTTTATTATATTTAT
1556724 ATTTTTAT
1 ATTTTTAT
1556732 GTTATAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.26
17 15 0.65
18 2 0.09
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
ATTTTTATTATATTTAT
Found at i:1560215 original size:31 final size:31
Alignment explanation
Indices: 1560179--1560242 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
1560169 TTCAAATATA
*
1560179 AAAAATAAATCAAA-GTAATTTAAAAACATCT
1 AAAAATAAATCAAATCTAA-TTAAAAACATCT
* *
1560210 AAAAATTAATTAAATCTAATTAAAAACATCT
1 AAAAATAAATCAAATCTAATTAAAAACATCT
1560241 AA
1 AA
1560243 GACTTGGCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 26 0.90
32 3 0.10
ACGTcount: A:0.61, C:0.09, G:0.02, T:0.28
Consensus pattern (31 bp):
AAAAATAAATCAAATCTAATTAAAAACATCT
Found at i:1563634 original size:56 final size:56
Alignment explanation
Indices: 1563538--1563927 Score: 387
Period size: 56 Copynumber: 7.0 Consensus size: 56
1563528 ACCTAGCATT
* * * *
1563538 GAAAGCCTAAGAGTAGCTAGTAGGTTTCGCT-TCAGTTGAAATTGGTACCAAAATGA
1 GAAAGCCTAAAAGTAGCTAGTAGGTTTAGCTCT-AGTTGAAATTGGCACCCAAATGA
* * *
1563594 GAAAGCCTAAAAGTAGCTTGTAGGATTAGCTCTAGATGAAATTGGCACCCAAATGA
1 GAAAGCCTAAAAGTAGCTAGTAGGTTTAGCTCTAGTTGAAATTGGCACCCAAATGA
* *
1563650 GAAAACCTTAAAA-TAGCTAGTAGGTTTAG-TCTTAGTTGAAATTGGCACCTAAATGA
1 GAAAGCC-TAAAAGTAGCTAGTAGGTTTAGCTC-TAGTTGAAATTGGCACCCAAATGA
* * * * *
1563706 GAAAGCCCAATAGTAGCTACTAGGTTTAGCTTTAGTTGAAATTGGCACCCAAATAA
1 GAAAGCCTAAAAGTAGCTAGTAGGTTTAGCTCTAGTTGAAATTGGCACCCAAATGA
* * ** * *
1563762 G-AAGACCCAAGAGTAATTAGTAGGTTTATCTTTAGTTGAAATTGGCACCCAAATGA
1 GAAAG-CCTAAAAGTAGCTAGTAGGTTTAGCTCTAGTTGAAATTGGCACCCAAATGA
* * * * * * *
1563818 GAAAACCTTATAA-TAGCTAGTAGGTTTAG-TCTGAATTAAAATTAGCACCTAAATAA
1 GAAAGCC-TAAAAGTAGCTAGTAGGTTTAGCTCT-AGTTGAAATTGGCACCCAAATGA
* * * * * *
1563874 AAAAGCCTAATAGTAGCTACTAGGTTTCGCTTTAGTTGAAATTGGAACCCAAAT
1 GAAAGCCTAAAAGTAGCTAGTAGGTTTAGCTCTAGTTGAAATTGGCACCCAAAT
1563928 ATGAAGATCC
Statistics
Matches: 273, Mismatches: 50, Indels: 22
0.79 0.14 0.06
Matches are distributed among these distances:
55 13 0.05
56 247 0.90
57 13 0.05
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.28
Consensus pattern (56 bp):
GAAAGCCTAAAAGTAGCTAGTAGGTTTAGCTCTAGTTGAAATTGGCACCCAAATGA
Found at i:1563816 original size:168 final size:167
Alignment explanation
Indices: 1563538--1563973 Score: 595
Period size: 168 Copynumber: 2.6 Consensus size: 167
1563528 ACCTAGCATT
* * * * * * *
1563538 GAAAGCCTAAGAGTAGCTAGTAGGTTTCGCTTCAGTTGAAATTGGTACCAAAATGAGAA-AGCCT
1 GAAAGCCTAATAGTAGCTACTAGGTTTCGCTTTAGTTGAAATTGGAACCCAAATAAGAAGA-CCC
* * * * *
1563602 AAAAGTAGCTTGTAGGATTAGCTCTAGATGAAATTGGCACCCAAATGAGAAAACCTTAAAATAGC
65 AAGAGTA-ATTGTAGGTTTAGCTTTAGTTGAAATTGGCACCCAAATGAGAAAACCTTAAAATAGC
* * * * *
1563667 TAGTAGGTTTAGTCTTAGTTGAAATTGGCACCTAAATGA
129 TAGTAGGTTTAGTCTGAATTAAAATTAGCACCTAAATAA
* * *
1563706 GAAAGCCCAATAGTAGCTACTAGGTTTAGCTTTAGTTGAAATTGGCACCCAAATAAGAAGACCCA
1 GAAAGCCTAATAGTAGCTACTAGGTTTCGCTTTAGTTGAAATTGGAACCCAAATAAGAAGACCCA
* *
1563771 AGAGTAATTAGTAGGTTTATCTTTAGTTGAAATTGGCACCCAAATGAGAAAACCTTATAATAGCT
66 AGAGTAATT-GTAGGTTTAGCTTTAGTTGAAATTGGCACCCAAATGAGAAAACCTTAAAATAGCT
1563836 AGTAGGTTTAGTCTGAATTAAAATTAGCACCTAAATAA
130 AGTAGGTTTAGTCTGAATTAAAATTAGCACCTAAATAA
* * *
1563874 AAAAGCCTAATAGTAGCTACTAGGTTTCGCTTTAGTTGAAATTGGAACCCAAATATGAAGATCCA
1 GAAAGCCTAATAGTAGCTACTAGGTTTCGCTTTAGTTGAAATTGGAACCCAAATAAGAAGACCCA
*
1563939 AGAGTAATTGGTAGGTTTAGCTTTAGTTGACATTG
66 AGAGTAATT-GTAGGTTTAGCTTTAGTTGAAATTG
1563974 AAACCTAAAT
Statistics
Matches: 236, Mismatches: 30, Indels: 4
0.87 0.11 0.01
Matches are distributed among these distances:
167 2 0.01
168 233 0.99
169 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (167 bp):
GAAAGCCTAATAGTAGCTACTAGGTTTCGCTTTAGTTGAAATTGGAACCCAAATAAGAAGACCCA
AGAGTAATTGTAGGTTTAGCTTTAGTTGAAATTGGCACCCAAATGAGAAAACCTTAAAATAGCTA
GTAGGTTTAGTCTGAATTAAAATTAGCACCTAAATAA
Found at i:1563928 original size:56 final size:56
Alignment explanation
Indices: 1563539--1563973 Score: 362
Period size: 56 Copynumber: 7.8 Consensus size: 56
1563529 CCTAGCATTG
* * * * * * *
1563539 AAAGCCTAAGAGTAGCTAGTAGGTTTCGCTTCAGTTGAAATTGGTACCAAAATGAG
1 AAAGCCTAATAGTAGCTAGTAGGTTTAGCTTTAGTTGAAATTGGCACCCAAATAAA
* * * * * *
1563595 AAAGCCTAAAAGTAGCTTGTAGGATTAGCTCTAGATGAAATTGGCACCCAAATGAGA
1 AAAGCCTAATAGTAGCTAGTAGGTTTAGCTTTAGTTGAAATTGGCACCCAAAT-AAA
* * * *
1563652 AAA-CCTTAA-AATAGCTAGTAGGTTTAG-TCTTAGTTGAAATTGGCACCTAAATGAG
1 AAAGCC-TAATAGTAGCTAGTAGGTTTAGCT-TTAGTTGAAATTGGCACCCAAATAAA
* *
1563707 AAAGCCCAATAGTAGCTACTAGGTTTAGCTTTAGTTGAAATTGGCACCCAAAT-AA
1 AAAGCCTAATAGTAGCTAGTAGGTTTAGCTTTAGTTGAAATTGGCACCCAAATAAA
* * * ** * *
1563762 GAAGACCCAAGAGTAATTAGTAGGTTTATCTTTAGTTGAAATTGGCACCCAAATGAGA
1 AAAG-CCTAATAGTAGCTAGTAGGTTTAGCTTTAGTTGAAATTGGCACCCAAAT-AAA
* * * * * * *
1563820 AAA-CCTTATAATAGCTAGTAGGTTTAG-TCTGAATTAAAATTAGCACCTAAATAAA
1 AAAGCCTAATAGTAGCTAGTAGGTTTAGCT-TTAGTTGAAATTGGCACCCAAATAAA
* * * *
1563875 AAAGCCTAATAGTAGCTACTAGGTTTCGCTTTAGTTGAAATTGGAACCCAAATATGA
1 AAAGCCTAATAGTAGCTAGTAGGTTTAGCTTTAGTTGAAATTGGCACCCAAATA-AA
* * * ** * *
1563932 AGATCC-AAGAGTAATTGGTAGGTTTAGCTTTAGTTGACATTG
1 AAAGCCTAATAGTAGCTAGTAGGTTTAGCTTTAGTTGAAATTG
1563974 AAACCTAAAT
Statistics
Matches: 299, Mismatches: 67, Indels: 26
0.76 0.17 0.07
Matches are distributed among these distances:
55 16 0.05
56 267 0.89
57 13 0.04
58 3 0.01
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (56 bp):
AAAGCCTAATAGTAGCTAGTAGGTTTAGCTTTAGTTGAAATTGGCACCCAAATAAA
Found at i:1564845 original size:20 final size:20
Alignment explanation
Indices: 1564820--1564892 Score: 96
Period size: 20 Copynumber: 3.6 Consensus size: 20
1564810 TACAATAAAC
1564820 ATGTATCGATACAAAGCAAT
1 ATGTATCGATACAAAGCAAT
*
1564840 ATGTATCGATACATATAG--GT
1 ATGTATCGATACA-A-AGCAAT
*
1564860 CTGTATCGATACAAAGCAAT
1 ATGTATCGATACAAAGCAAT
1564880 ATGTATCGATACA
1 ATGTATCGATACA
1564893 TATAGGTCTG
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
18 2 0.04
19 1 0.02
20 39 0.87
21 1 0.02
22 2 0.04
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.29
Consensus pattern (20 bp):
ATGTATCGATACAAAGCAAT
Found at i:1564869 original size:40 final size:40
Alignment explanation
Indices: 1564821--1564911 Score: 182
Period size: 40 Copynumber: 2.3 Consensus size: 40
1564811 ACAATAAACA
1564821 TGTATCGATACAAAGCAATATGTATCGATACATATAGGTC
1 TGTATCGATACAAAGCAATATGTATCGATACATATAGGTC
1564861 TGTATCGATACAAAGCAATATGTATCGATACATATAGGTC
1 TGTATCGATACAAAGCAATATGTATCGATACATATAGGTC
1564901 TGTATCGATAC
1 TGTATCGATAC
1564912 TTTCAAGGGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (40 bp):
TGTATCGATACAAAGCAATATGTATCGATACATATAGGTC
Found at i:1564904 original size:20 final size:20
Alignment explanation
Indices: 1564841--1564911 Score: 92
Period size: 20 Copynumber: 3.5 Consensus size: 20
1564831 CAAAGCAATA
1564841 TGTATCGATACATATAGGTC
1 TGTATCGATACATATAGGTC
* *
1564861 TGTATCGATACA-A-AGCAATA
1 TGTATCGATACATATAG--GTC
1564881 TGTATCGATACATATAGGTC
1 TGTATCGATACATATAGGTC
1564901 TGTATCGATAC
1 TGTATCGATAC
1564912 TTTCAAGGGT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
18 2 0.05
19 1 0.02
20 37 0.86
21 1 0.02
22 2 0.05
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.32
Consensus pattern (20 bp):
TGTATCGATACATATAGGTC
Found at i:1565654 original size:27 final size:27
Alignment explanation
Indices: 1565610--1565669 Score: 77
Period size: 26 Copynumber: 2.2 Consensus size: 27
1565600 TTTGTTATCT
* *
1565610 CCCTTTTTATTTTAAAAAATATATTTCC
1 CCCTTTTTAGTTTAAAAAATA-ATCTCC
*
1565638 CCCTTTTT-GTTTCAAAAATAATCTCC
1 CCCTTTTTAGTTTAAAAAATAATCTCC
1565664 CCCTTT
1 CCCTTT
1565670 ATAAAGCAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 11 0.38
27 10 0.34
28 8 0.28
ACGTcount: A:0.27, C:0.25, G:0.02, T:0.47
Consensus pattern (27 bp):
CCCTTTTTAGTTTAAAAAATAATCTCC
Found at i:1568738 original size:20 final size:20
Alignment explanation
Indices: 1568710--1568784 Score: 96
Period size: 20 Copynumber: 3.8 Consensus size: 20
1568700 TTTTACTCAG
*
1568710 ATGTATCGATATATTTTTCA
1 ATGTATCGATACATTTTTCA
* * * *
1568730 ATATATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
1568750 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
1568770 ATGTATCGATACATT
1 ATGTATCGATACATT
1568785 CTGTCTTTTT
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.41
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1574834 original size:12 final size:12
Alignment explanation
Indices: 1574817--1574841 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1574807 AACTTTATCA
1574817 TCATCATCATCT
1 TCATCATCATCT
1574829 TCATCATCATCT
1 TCATCATCATCT
1574841 T
1 T
1574842 TGATGGTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.32, G:0.00, T:0.44
Consensus pattern (12 bp):
TCATCATCATCT
Found at i:1581975 original size:16 final size:16
Alignment explanation
Indices: 1581954--1581984 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1581944 ATTTATTTTT
1581954 AGAAGTTGCCAAACTG
1 AGAAGTTGCCAAACTG
1581970 AGAAGTTGCCAAACT
1 AGAAGTTGCCAAACT
1581985 AAGTTCACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.39, C:0.19, G:0.23, T:0.19
Consensus pattern (16 bp):
AGAAGTTGCCAAACTG
Found at i:1585664 original size:25 final size:25
Alignment explanation
Indices: 1585636--1585694 Score: 100
Period size: 25 Copynumber: 2.4 Consensus size: 25
1585626 TTATGTCATA
*
1585636 AAAATTTCGTATAGGAAAGAAAGAG
1 AAAATTTCATATAGGAAAGAAAGAG
*
1585661 AAAATTTCATATTGGAAAGAAAGAG
1 AAAATTTCATATAGGAAAGAAAGAG
1585686 AAAATTTCA
1 AAAATTTCA
1585695 AAAATGAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.53, C:0.05, G:0.19, T:0.24
Consensus pattern (25 bp):
AAAATTTCATATAGGAAAGAAAGAG
Found at i:1586292 original size:102 final size:102
Alignment explanation
Indices: 1586116--1586324 Score: 321
Period size: 102 Copynumber: 2.0 Consensus size: 102
1586106 GAACACTGGA
* * *
1586116 ATTGCGATTTTGCACATGCAGGAACAAAGGGTTATCAAAATATGACCAAATAGGTCTTAAAAGGC
1 ATTGCGATTTTGCACACGCACGAACAAAGGGTTATCAAAATACGACCAAATAGGTCTTAAAAGGC
* * * *
1586181 CTGGTTCACATAAATAAAGTCCACTCCTACTGAGATG
66 CTAGTTCACATAAAGAAAGTCCACTCCCACTGAAATG
*
1586218 ATTGCGATTTTGCACACGCACGAAC-AAGCGGTTATCAAAATACGACCAAATATGTCTTAAAAGG
1 ATTGCGATTTTGCACACGCACGAACAAAG-GGTTATCAAAATACGACCAAATAGGTCTTAAAAGG
*
1586282 CCTAGTTCACATAAAGGAAGTCCACTCCCACTGAAATG
65 CCTAGTTCACATAAAGAAAGTCCACTCCCACTGAAATG
1586320 ATTGC
1 ATTGC
1586325 CCAGTTCTTA
Statistics
Matches: 97, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
101 3 0.03
102 94 0.97
ACGTcount: A:0.36, C:0.21, G:0.19, T:0.24
Consensus pattern (102 bp):
ATTGCGATTTTGCACACGCACGAACAAAGGGTTATCAAAATACGACCAAATAGGTCTTAAAAGGC
CTAGTTCACATAAAGAAAGTCCACTCCCACTGAAATG
Found at i:1591620 original size:19 final size:21
Alignment explanation
Indices: 1591582--1591620 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1591572 GTAGCCTTGA
*
1591582 CCATGCATTTTTTACTATGTT
1 CCATGCATTTTTAACTATGTT
1591603 CCATGCA-TTTTAAC-ATGT
1 CCATGCATTTTTAACTATGT
1591621 CCAACATCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 6 0.35
21 7 0.41
ACGTcount: A:0.23, C:0.21, G:0.10, T:0.46
Consensus pattern (21 bp):
CCATGCATTTTTAACTATGTT
Found at i:1602828 original size:13 final size:13
Alignment explanation
Indices: 1602810--1602848 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
1602800 CACACTCAGA
1602810 TGTATCGATACAT
1 TGTATCGATACAT
1602823 TGTATCGATACAT
1 TGTATCGATACAT
1602836 TGTATCGATACAT
1 TGTATCGATACAT
1602849 GATCATTGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1602857 original size:19 final size:18
Alignment explanation
Indices: 1602832--1602894 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 18
1602822 TTGTATCGAT
1602832 ACATTGTATCGATACATG
1 ACATTGTATCGATACATG
1602850 ATCATTGTATCGATACATAG
1 A-CATTGTATCGATACAT-G
1602870 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
*
1602889 AGATTG
1 ACATTG
1602895 GCAGTAGCTA
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
18 5 0.12
19 19 0.46
20 17 0.41
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.33
Consensus pattern (18 bp):
ACATTGTATCGATACATG
Found at i:1602935 original size:43 final size:43
Alignment explanation
Indices: 1602874--1602974 Score: 202
Period size: 43 Copynumber: 2.3 Consensus size: 43
1602864 ACATAGACAA
1602874 TTGTATCGATACATGAGATTGGCAGTAGCTACCCTACCACTGT
1 TTGTATCGATACATGAGATTGGCAGTAGCTACCCTACCACTGT
1602917 TTGTATCGATACATGAGATTGGCAGTAGCTACCCTACCACTGT
1 TTGTATCGATACATGAGATTGGCAGTAGCTACCCTACCACTGT
1602960 TTGTATCGATACATG
1 TTGTATCGATACATG
1602975 GTACAATGTA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 58 1.00
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.32
Consensus pattern (43 bp):
TTGTATCGATACATGAGATTGGCAGTAGCTACCCTACCACTGT
Found at i:1602986 original size:20 final size:20
Alignment explanation
Indices: 1602961--1603013 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
1602951 TACCACTGTT
*
1602961 TGTATCGATACATGGT-ACAA
1 TGTATCGATACATGATGA-AA
*
1602981 TGTATCGATACATGATGAAT
1 TGTATCGATACATGATGAAA
1603001 TGTATCGATACAT
1 TGTATCGATACAT
1603014 TGCTTGTAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (20 bp):
TGTATCGATACATGATGAAA
Found at i:1610080 original size:13 final size:13
Alignment explanation
Indices: 1610062--1610087 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1610052 CAATTTTTTG
1610062 TGTATCGATACAT
1 TGTATCGATACAT
1610075 TGTATCGATACAT
1 TGTATCGATACAT
1610088 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1610826 original size:21 final size:21
Alignment explanation
Indices: 1610785--1610828 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1610775 CTCTCTTTTA
* *
1610785 TCTCCCCCATTTATTAATAAT
1 TCTCCCCCATTAATCAATAAT
1610806 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCATTAATCAA-TAAT
1610827 TC
1 TC
1610829 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.27, C:0.32, G:0.02, T:0.39
Consensus pattern (21 bp):
TCTCCCCCATTAATCAATAAT
Found at i:1612653 original size:13 final size:13
Alignment explanation
Indices: 1612635--1612673 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1612625 ATAATCACCC
*
1612635 TGTATCGATACAG
1 TGTATCGATACAA
1612648 TGTATCGATACAA
1 TGTATCGATACAA
1612661 TGTATCGATACAA
1 TGTATCGATACAA
1612674 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1612684 original size:20 final size:20
Alignment explanation
Indices: 1612659--1612697 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1612649 GTATCGATAC
1612659 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
1612679 AATGTATCGATACATAGAA
1 AATGTATCGATACAAAGAA
1612698 TTTCCAGATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.10, G:0.15, T:0.23
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:1614770 original size:15 final size:15
Alignment explanation
Indices: 1614750--1614780 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1614740 ATTTCGTTTG
*
1614750 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1614765 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1614780 G
1 G
1614781 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1616613 original size:21 final size:21
Alignment explanation
Indices: 1616584--1616628 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1616574 AAGTTTTCAT
*
1616584 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1616604 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1616626 TTT
1 TTT
1616629 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1618864 original size:13 final size:13
Alignment explanation
Indices: 1618846--1618871 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1618836 CAATTTTTTG
1618846 TGTATCGATACAT
1 TGTATCGATACAT
1618859 TGTATCGATACAT
1 TGTATCGATACAT
1618872 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1621671 original size:19 final size:20
Alignment explanation
Indices: 1621628--1621681 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 20
1621618 CACACTCAGA
* *
1621628 TGTATCGATACATTATGCTT
1 TGTATCGATACATGATGCAT
*
1621648 TGTATCGATACATGGT-CAT
1 TGTATCGATACATGATGCAT
*
1621667 TGTATCAATACATGA
1 TGTATCGATACATGA
1621682 GATTGGCAGT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.52
20 14 0.48
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.39
Consensus pattern (20 bp):
TGTATCGATACATGATGCAT
Found at i:1621746 original size:13 final size:13
Alignment explanation
Indices: 1621725--1621777 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
1621715 CGATACATGG
*
1621725 TACAATGTATCGA
1 TACATTGTATCGA
1621738 TACATTGTATCGA
1 TACATTGTATCGA
1621751 TACA-TG-AT-G-
1 TACATTGTATCGA
1621760 -A-ATTGTATCGA
1 TACATTGTATCGA
1621771 TACATTG
1 TACATTG
1621778 CTTGTAACGG
Statistics
Matches: 33, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
7 1 0.03
8 3 0.09
9 2 0.06
10 2 0.06
11 2 0.06
12 3 0.09
13 20 0.61
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.36
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:1621751 original size:33 final size:33
Alignment explanation
Indices: 1621709--1621777 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
1621699 CTACCACTGT
*
1621709 TTGTATCGATACATGGT-ACAATGTATCGATACA
1 TTGTATCGATACATGATGA-AATGTATCGATACA
*
1621742 TTGTATCGATACATGATGAATTGTATCGATACA
1 TTGTATCGATACATGATGAAATGTATCGATACA
1621775 TTG
1 TTG
1621778 CTTGTAACGG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.36
Consensus pattern (33 bp):
TTGTATCGATACATGATGAAATGTATCGATACA
Found at i:1624231 original size:10 final size:10
Alignment explanation
Indices: 1624216--1624297 Score: 85
Period size: 10 Copynumber: 8.0 Consensus size: 10
1624206 GTCCTTATAC
1624216 CAAAAAAAAA
1 CAAAAAAAAA
1624226 C-AAAAAAAA
1 CAAAAAAAAA
1624235 CAAAAAAAAA
1 CAAAAAAAAA
**
1624245 CAAAAAACCA
1 CAAAAAAAAA
*
1624255 GAAAAAAACAA
1 CAAAAAAA-AA
*
1624266 AAAACAAAAAA
1 CAAA-AAAAAA
*
1624277 CAAAAATAAA
1 CAAAAAAAAA
1624287 CAAGAAAAAAA
1 CAA-AAAAAAA
1624298 TAGCAAAAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
9 9 0.15
10 31 0.53
11 15 0.25
12 4 0.07
ACGTcount: A:0.84, C:0.12, G:0.02, T:0.01
Consensus pattern (10 bp):
CAAAAAAAAA
Found at i:1624232 original size:7 final size:7
Alignment explanation
Indices: 1624220--1624282 Score: 67
Period size: 7 Copynumber: 8.7 Consensus size: 7
1624210 TTATACCAAA
1624220 AAAAAAC
1 AAAAAAC
1624227 AAAAAA-
1 AAAAAAC
*
1624233 AACAAA-
1 AAAAAAC
1624239 AAAAAAC
1 AAAAAAC
1624246 AAAAAACC
1 AAAAAA-C
1624254 AGAAAAAAAC
1 ---AAAAAAC
1624264 AAAAAAC
1 AAAAAAC
1624271 AAAAAAC
1 AAAAAAC
1624278 AAAAA
1 AAAAA
1624283 TAAACAAGAA
Statistics
Matches: 49, Mismatches: 2, Indels: 10
0.80 0.03 0.16
Matches are distributed among these distances:
6 10 0.20
7 31 0.63
8 1 0.02
10 1 0.02
11 6 0.12
ACGTcount: A:0.86, C:0.13, G:0.02, T:0.00
Consensus pattern (7 bp):
AAAAAAC
Found at i:1624304 original size:24 final size:23
Alignment explanation
Indices: 1624220--1624308 Score: 90
Period size: 24 Copynumber: 3.6 Consensus size: 23
1624210 TTATACCAAA
1624220 AAAAAACAAAAAAAACAAAAAAAAAC
1 AAAAAACAAAAAAAAC---AAAAAAC
1624246 AAAAAACCAGAAAAAAACAAAAAAC
1 AAAAAA-CA-AAAAAAACAAAAAAC
1624271 AAAAAACAAAAATAAACAAGAAAA-
1 AAAAAACAAAAA-AAACAA-AAAAC
* *
1624295 AAATAGCAAAAAAA
1 AAAAAACAAAAAAA
1624309 CAGAAAAGGG
Statistics
Matches: 57, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
23 6 0.11
24 18 0.32
25 17 0.30
26 6 0.11
27 2 0.04
28 8 0.14
ACGTcount: A:0.83, C:0.11, G:0.03, T:0.02
Consensus pattern (23 bp):
AAAAAACAAAAAAAACAAAAAAC
Found at i:1624308 original size:1 final size:1
Alignment explanation
Indices: 1624217--1624297 Score: 54
Period size: 1 Copynumber: 81.0 Consensus size: 1
1624207 TCCTTATACC
* * * ** * * * *
1624217 AAAAAAAAACAAAAAAAACAAAAAAAAACAAAAAACCAGAAAAAAACAAAAAACAAAAAACAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
1624282 ATAAACAAGAAAAAAA
1 AAAAAAAAAAAAAAAA
1624298 TAGCAAAAAA
Statistics
Matches: 58, Mismatches: 22, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
1 58 1.00
ACGTcount: A:0.85, C:0.11, G:0.02, T:0.01
Consensus pattern (1 bp):
A
Found at i:1624315 original size:10 final size:9
Alignment explanation
Indices: 1624218--1624296 Score: 78
Period size: 9 Copynumber: 8.9 Consensus size: 9
1624208 CCTTATACCA
1624218 AAAAAAAAC
1 AAAAAAAAC
1624227 AAAAAAAAC
1 AAAAAAAAC
1624236 AAAAAAAA-
1 AAAAAAAAC
*
1624244 ACAAAAAACC
1 A-AAAAAAAC
1624254 AGAAAAAAAC
1 A-AAAAAAAC
1624264 --AAAAAAC
1 AAAAAAAAC
1624271 --AAAAAAC
1 AAAAAAAAC
1624278 AAAAATAAAC
1 AAAAA-AAAC
1624288 AAGAAAAAA
1 AA-AAAAAA
1624297 ATAGCAAAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 11
0.81 0.04 0.15
Matches are distributed among these distances:
7 14 0.23
8 1 0.02
9 26 0.43
10 17 0.28
11 3 0.05
ACGTcount: A:0.85, C:0.11, G:0.03, T:0.01
Consensus pattern (9 bp):
AAAAAAAAC
Found at i:1625680 original size:30 final size:28
Alignment explanation
Indices: 1625520--1626166 Score: 559
Period size: 28 Copynumber: 22.1 Consensus size: 28
1625510 GTTAATCTCT
*
1625520 TTTCAAAGCCCATAAGTCAGTGGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
1625548 TTTCAAAGCCCACAAGTCAGTGGCATTCT
1 TTTCAAAGCCCACAAGTCAGTGGCA-TCC
*
1625577 TTTCAAAGCCCACAAGTCAGTGACATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
1625605 TTTCAAAGCCTACAAGTCAGTGGCAT-C
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
1625632 TCTTCAAAAGACCACAAGTCGGTGGCGTCC
1 T-TTC-AAAGCCCACAAGTCAGTGGCATCC
** *
1625662 TTTCAAAGCCCACACAAGTTGGTGGCAACTCT
1 TTTCAAAG-CC-CACAAGTCAGTGGC-A-TCC
*
1625694 TTTCAGAGCCCACAAGTCAGTGGCAT-C
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
*
1625721 TCTTCAAAAGCCCACAAGTCAGTGGCACCC
1 T-TTC-AAAGCCCACAAGTCAGTGGCATCC
* *
1625751 TTTCAAAGCCCATACAAGTCGGTGGCAATTCT
1 TTTCAAAGCCC--ACAAGTCAGTGGC-A-TCC
* *
1625783 TTTCAAAGCCCATAAGTTAGTGGCATACCC
1 TTTCAAAGCCCACAAGTCAGTGGCAT--CC
*
1625813 TTTCAAAGCCCACAAGTCAGTGGCACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* * *
1625841 TTTCAAAGCCCACACAAGTCGGTGGTAACTCT
1 TTTCAAAG-CC-CACAAGTCAGTGG-CA-TCC
*
1625873 TTTCAAAGCCCACAAGTTAGTGGCAT-C
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
** * *
1625900 TCTTCAAAAAACCACAAGTCTGTGGCGTACCC
1 T-TTC-AAAGCCCACAAGTCAGTGGC--ATCC
* *
1625932 TTTCAAAGCCCACACAAATCAGTGGCACCC
1 TTTCAAAG-CC-CACAAGTCAGTGGCATCC
* * * *
1625962 TTCCAAAGCCCATAAGTCAGTGACACCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
1625990 TTTCAAAGCCCACAAGACAGTGGCA-CAT
1 TTTCAAAGCCCACAAGTCAGTGGCATC-C
* *
1626018 TTTCAAATCCCACAAGTCAGTAGCATCC
1 TTTCAAAGCCCACAAGTCAGTGGCATCC
* *
1626046 TTTCAAAGCCCATAAGTCAATGGCA-CTC
1 TTTCAAAGCCCACAAGTCAGTGGCATC-C
* *
1626074 TTTCAAAGCCTACAAGTCAGTGGCACTCT
1 TTTCAAAGCCCACAAGTCAGTGGCA-TCC
* * *
1626103 TTTCAAAGCCCACACGAGTCGGTGGTAACTCT
1 TTTCAAAGCCCACA--AGTCAGTGG-CA-TCC
*
1626135 TTTCAAAGCCCACACAAGTTAGTGGCA-CC
1 TTTCAAAG-CC-CACAAGTCAGTGGCATCC
1626164 TTT
1 TTT
1626167 TTCTTTAAAA
Statistics
Matches: 506, Mismatches: 75, Indels: 75
0.77 0.11 0.11
Matches are distributed among these distances:
27 6 0.01
28 185 0.37
29 112 0.22
30 113 0.22
31 20 0.04
32 64 0.13
33 2 0.00
34 4 0.01
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (28 bp):
TTTCAAAGCCCACAAGTCAGTGGCATCC
Found at i:1625719 original size:89 final size:89
Alignment explanation
Indices: 1625516--1626148 Score: 679
Period size: 89 Copynumber: 7.2 Consensus size: 89
1625506 GAACGTTAAT
* *
1625516 CTCTTTTCAAAGCCCATAAGTCAGTGGCATC-CTTTCAAAGCCCACAAGTCAGTGGCATTCTTTT
1 CTCTTTTCAAAGCCCACAAGTCAGTGGCATCTCTTTCAAAGCCCACAAGTCAGTGGCA-TCCTTT
* *
1625580 CAAAG-CC-CACAAGTCAGTGAC-A
65 CAAAGCCCACACAAGTCGGTGGCAA
* * * * *
1625602 -TCCTTTCAAAGCCTACAAGTCAGTGGCATCTC-TTCAAAAGACCACAAGTCGGTGGCGTCCTTT
1 CTCTTTTCAAAGCCCACAAGTCAGTGGCATCTCTTTC-AAAGCCCACAAGTCAGTGGCATCCTTT
*
1625665 CAAAGCCCACACAAGTTGGTGGCAA
65 CAAAGCCCACACAAGTCGGTGGCAA
* *
1625690 CTCTTTTCAGAGCCCACAAGTCAGTGGCATCTC-TTCAAAAGCCCACAAGTCAGTGGCACCCTTT
1 CTCTTTTCAAAGCCCACAAGTCAGTGGCATCTCTTTC-AAAGCCCACAAGTCAGTGGCATCCTTT
*
1625754 CAAAGCCCATACAAGTCGGTGGCAA
65 CAAAGCCCACACAAGTCGGTGGCAA
* * * * *
1625779 TTCTTTTCAAAGCCCATAAGTTAGTGGCATACCCTTTCAAAGCCCACAAGTCAGTGGCACCCTTT
1 CTCTTTTCAAAGCCCACAAGTCAGTGGCAT-CTCTTTCAAAGCCCACAAGTCAGTGGCATCCTTT
*
1625844 CAAAGCCCACACAAGTCGGTGGTAA
65 CAAAGCCCACACAAGTCGGTGGCAA
* ** * *
1625869 CTCTTTTCAAAGCCCACAAGTTAGTGGCATCTC-TTCAAAAAACCACAAGTCTGTGGCGTACCCT
1 CTCTTTTCAAAGCCCACAAGTCAGTGGCATCTCTTTC-AAAGCCCACAAGTCAGTGGC--ATCCT
* *
1625933 TTCAAAGCCCACACAAATCAGTGGC-A
63 TTCAAAGCCCACACAAGTCGGTGGCAA
* * * * * * *
1625959 C-CCTTCCAAAGCCCATAAGTCAGTGACA-CCCTTTCAAAGCCCACAAGACAGTGGCA-CATTTT
1 CTCTTTTCAAAGCCCACAAGTCAGTGGCATCTCTTTCAAAGCCCACAAGTCAGTGGCATC-CTTT
* * *
1626021 CAAA-TCC-CACAAGTCAGTAGC-A
65 CAAAGCCCACACAAGTCGGTGGCAA
* * * * *
1626043 -TCCTTTCAAAGCCCATAAGTCAATGGCA-CTCTTTCAAAGCCTACAAGTCAGTGGCACTCTTTT
1 CTCTTTTCAAAGCCCACAAGTCAGTGGCATCTCTTTCAAAGCCCACAAGTCAGTGGCA-TCCTTT
* *
1626106 CAAAGCCCACACGAGTCGGTGGTAA
65 CAAAGCCCACACAAGTCGGTGGCAA
1626131 CTCTTTTCAAAGCCCACA
1 CTCTTTTCAAAGCCCACA
1626149 CAAGTTAGTG
Statistics
Matches: 465, Mismatches: 62, Indels: 37
0.82 0.11 0.07
Matches are distributed among these distances:
84 62 0.13
85 51 0.11
86 32 0.07
87 21 0.05
88 23 0.05
89 164 0.35
90 82 0.18
91 30 0.06
ACGTcount: A:0.30, C:0.30, G:0.17, T:0.23
Consensus pattern (89 bp):
CTCTTTTCAAAGCCCACAAGTCAGTGGCATCTCTTTCAAAGCCCACAAGTCAGTGGCATCCTTTC
AAAGCCCACACAAGTCGGTGGCAA
Found at i:1626299 original size:45 final size:47
Alignment explanation
Indices: 1626229--1626338 Score: 134
Period size: 49 Copynumber: 2.3 Consensus size: 47
1626219 CTGTCTGACA
* * * *
1626229 TCGCTAGCATTGAATCAGCATATTGG-CACCTTT-ATTAGCCCAATG
1 TCGCTGGCCTTGAATTAGCACATTGGCCACCTTTCATTAGCCCAATG
* *
1626274 TCGCTGGCCTTGAATTAGCACATTGGTCCACTTTTCCCTTAGCCCAATG
1 TCGCTGGCCTTGAATTAGCACATTGG-CCACCTTT-CATTAGCCCAATG
1626323 TCGCTGGCCTTGAATT
1 TCGCTGGCCTTGAATT
1626339 GGCATATAGG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
45 22 0.40
47 6 0.11
49 27 0.49
ACGTcount: A:0.21, C:0.27, G:0.19, T:0.33
Consensus pattern (47 bp):
TCGCTGGCCTTGAATTAGCACATTGGCCACCTTTCATTAGCCCAATG
Found at i:1627067 original size:20 final size:20
Alignment explanation
Indices: 1627044--1627118 Score: 87
Period size: 20 Copynumber: 3.8 Consensus size: 20
1627034 AACTACCCAG
* *
1627044 ATGTATAGATATATTTTTCA
1 ATGTATCGATACATTTTTCA
* * *
1627064 ATGTATCGATACATGTATGA
1 ATGTATCGATACATTTTTCA
*
1627084 ATGTATCGATACATTCTTCA
1 ATGTATCGATACATTTTTCA
*
1627104 ATGCATCGATACATT
1 ATGTATCGATACATT
1627119 CTGTCTTGAT
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCA
Found at i:1627256 original size:59 final size:59
Alignment explanation
Indices: 1627163--1627282 Score: 208
Period size: 59 Copynumber: 2.0 Consensus size: 59
1627153 TAATGTATCG
1627163 ATACATCTAGTTAAAATTAAGTATTTCGAACCATTTTCAACCTTAGCTTATAGG-ACCCA
1 ATACATCTAGTTAAAATTAAGTATTTCGAACCATTTTCAACCTTAGCTTAT-GGCACCCA
1627222 ATACATCTAGTTAAAATTAAGTATTTC-AAGCCATTTTCAACCTTAGCTTATGGCACCCA
1 ATACATCTAGTTAAAATTAAGTATTTCGAA-CCATTTTCAACCTTAGCTTATGGCACCCA
1627281 AT
1 AT
1627283 GTCTAGTATG
Statistics
Matches: 59, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
58 4 0.07
59 55 0.93
ACGTcount: A:0.35, C:0.21, G:0.10, T:0.34
Consensus pattern (59 bp):
ATACATCTAGTTAAAATTAAGTATTTCGAACCATTTTCAACCTTAGCTTATGGCACCCA
Found at i:1630014 original size:13 final size:13
Alignment explanation
Indices: 1629996--1630020 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1629986 CATAAAGTGT
1629996 TGTATCGATACAA
1 TGTATCGATACAA
1630009 TGTATCGATACA
1 TGTATCGATACA
1630021 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1630018 original size:33 final size:33
Alignment explanation
Indices: 1629976--1630042 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1629966 TTCAACGATT
1629976 TGTATCGATACATAAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
*** *
1630009 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAGTGTTGTATCGATACAA
1630042 T
1 T
1630043 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCGATACAA
Found at i:1634986 original size:78 final size:78
Alignment explanation
Indices: 1634846--1635082 Score: 257
Period size: 78 Copynumber: 3.0 Consensus size: 78
1634836 TGGGAAGCTG
* * *
1634846 TGTTGAAACATGTCCACTAAGGGTATTTAGGTAATACTACTTTAAAATTGAGTCCCTT-GGATTA
1 TGTTGAAACATGTCCATTAAGGGTATTTAGGTAATACTACTTTAAAATTCAGT-CTTTAGGATTA
*
1634910 TGTGAGAACCTTCA
65 TGTGAGAACTTTCA
* *
1634924 TGTTAAAACATGTCCGTTAAGGGTATTTAGGTAATACTACTTTAAAATTCAGTCTTTAGGATTAT
1 TGTTGAAACATGTCCATTAAGGGTATTTAGGTAATACTACTTTAAAATTCAGTCTTTAGGATTAT
* *
1634989 AT-AGAAACTTTCG
66 GTGAG-AACTTTCA
* * * * * * * *
1635002 TGTCGAAACATATTCATTTAGAGTATTTATGTAATACTACCTTAAAA-TCGAGT-TCTTAGGATC
1 TGTTGAAACATGTCCATTAAGGGTATTTAGGTAATACTACTTTAAAATTC-AGTCT-TTAGGATT
*
1635065 ATGTGGGAACTTTCA
64 ATGTGAGAACTTTCA
1635080 TGT
1 TGT
1635083 CAATATATAT
Statistics
Matches: 133, Mismatches: 21, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
77 8 0.06
78 124 0.93
79 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.37
Consensus pattern (78 bp):
TGTTGAAACATGTCCATTAAGGGTATTTAGGTAATACTACTTTAAAATTCAGTCTTTAGGATTAT
GTGAGAACTTTCA
Found at i:1637185 original size:22 final size:20
Alignment explanation
Indices: 1637131--1637209 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 20
1637121 AGTGCCAAGG
*
1637131 AAATGTATCGATACATTACT
1 AAATGTATCAATACATTACT
*
1637151 AAATGTATTAATACA-TACGT
1 AAATGTATCAATACATTAC-T
* *
1637171 AAAATTGTATCAATATATTTCT
1 -AAA-TGTATCAATACATTACT
* *
1637193 CATTGTATCAATACATT
1 AAATGTATCAATACATT
1637210 CTGGGTTTTT
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
19 3 0.06
20 27 0.57
21 4 0.09
22 11 0.23
23 2 0.04
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.39
Consensus pattern (20 bp):
AAATGTATCAATACATTACT
Found at i:1646035 original size:20 final size:20
Alignment explanation
Indices: 1645965--1646035 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
1645955 CCCAGATGAT
* *
1645965 TCGATGCATTTTTCAATGTA
1 TCGATACATTCTTCAATGTA
* *
1645985 TC-ATACATGT-ATAAATGTA
1 TCGATACAT-TCTTCAATGTA
1646004 TCGATACATTCTTCAATGTA
1 TCGATACATTCTTCAATGTA
1646024 TCGATACATTCT
1 TCGATACATTCT
1646036 ATCTTTTTAC
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
19 15 0.35
20 28 0.65
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.41
Consensus pattern (20 bp):
TCGATACATTCTTCAATGTA
Found at i:1648393 original size:97 final size:97
Alignment explanation
Indices: 1648238--1648581 Score: 508
Period size: 97 Copynumber: 3.5 Consensus size: 97
1648228 AATTTTATTT
* * * * *
1648238 ATCGGGGATACTCCAACCCTATTCCTCCGAGGGGACACTCCAACCCCGTTTTTAAACACATCAAA
1 ATCGGGGACACTTCAACCCCATTCCTCCGAGGGGATACTCCAACCCCGCTTTTAAACACATCAAA
1648303 GTTTAAATCTTATTCTCACTTAAATTGTCATC
66 GTTTAAATCTTATTCTCACTTAAATTGTCATC
* * *
1648335 ATCGAGGACACTTCAACCCCATTCCTTCGGGGGGATACTCCAACCCCGCTTTTAAACACATCAAA
1 ATCGGGGACACTTCAACCCCATTCCTCCGAGGGGATACTCCAACCCCGCTTTTAAACACATCAAA
*
1648400 GTTTAAATCTTATTCTCACTTAAATTGTCACC
66 GTTTAAATCTTATTCTCACTTAAATTGTCATC
* * * * * **
1648432 ATCGGGGACACTTCAACGCCATTCCTCCGAGAGAATACTCCAATCTCGCTTTTAAATGCATCAAA
1 ATCGGGGACACTTCAACCCCATTCCTCCGAGGGGATACTCCAACCCCGCTTTTAAACACATCAAA
1648497 GTTTAAATCTTATTCTCACTTAAATTGTCATC
66 GTTTAAATCTTATTCTCACTTAAATTGTCATC
* * * *
1648529 ATCGGGGACACTCCAACCCAATTCCTCCAAGGGGATACTCCAACCCCGTTTTT
1 ATCGGGGACACTTCAACCCCATTCCTCCGAGGGGATACTCCAACCCCGCTTTT
1648582 CAATTAAAAA
Statistics
Matches: 218, Mismatches: 29, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
97 218 1.00
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.29
Consensus pattern (97 bp):
ATCGGGGACACTTCAACCCCATTCCTCCGAGGGGATACTCCAACCCCGCTTTTAAACACATCAAA
GTTTAAATCTTATTCTCACTTAAATTGTCATC
Found at i:1656131 original size:52 final size:52
Alignment explanation
Indices: 1656061--1656181 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
1656051 GAAAATTTAT
*
1656061 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
1656113 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
1656165 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
1656182 AAGATCAGTG
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:1656194 original size:52 final size:51
Alignment explanation
Indices: 1656061--1656201 Score: 212
Period size: 52 Copynumber: 2.7 Consensus size: 51
1656051 GAAAATTTAT
1656061 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
* *
1656113 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGCAAATTTGC
*
1656165 CTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
1656202 ATGTATCGAT
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.33
Consensus pattern (51 bp):
CTGCATGTATCGATACATTAATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:1656208 original size:13 final size:13
Alignment explanation
Indices: 1656190--1656214 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1656180 CAAAGATCAG
1656190 TGTATCGATACAA
1 TGTATCGATACAA
1656203 TGTATCGATACA
1 TGTATCGATACA
1656215 TGTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1656297 original size:13 final size:13
Alignment explanation
Indices: 1656279--1656303 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1656269 CAAAAAAATA
1656279 TGTATCGATACAT
1 TGTATCGATACAT
1656292 TGTATCGATACA
1 TGTATCGATACA
1656304 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1656299 original size:33 final size:33
Alignment explanation
Indices: 1656257--1656323 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1656247 AGTAGCTTAA
1656257 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1656290 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1656323 A
1 A
1656324 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1657346 original size:22 final size:21
Alignment explanation
Indices: 1657321--1657388 Score: 52
Period size: 22 Copynumber: 3.1 Consensus size: 21
1657311 ATGCTGATTC
1657321 AAGGCCAGCTATATTGGACTTA
1 AAGGCCAGCTA-ATTGGACTTA
* *
1657343 AAGG--TGCTAATGTGCTGA-TTC
1 AAGGCCAGCTAAT-TG--GACTTA
1657364 AAGGCCAGCTACATTGGACTTA
1 AAGGCCAGCTA-ATTGGACTTA
1657386 AAG
1 AAG
1657389 ATGAAGATGC
Statistics
Matches: 35, Mismatches: 4, Indels: 14
0.66 0.08 0.26
Matches are distributed among these distances:
19 2 0.06
20 6 0.17
21 8 0.23
22 11 0.31
23 6 0.17
24 2 0.06
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (21 bp):
AAGGCCAGCTAATTGGACTTA
Found at i:1657635 original size:101 final size:100
Alignment explanation
Indices: 1657434--1658585 Score: 1663
Period size: 101 Copynumber: 11.4 Consensus size: 100
1657424 TATTGGACTT
* * * * *
1657434 AAAGCTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATACGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
1657499 TGATTCAAGGCCAGCGATATTGGACTTAAAGAT-G
66 TGATTCAAGGCCAGCTATATTGGACTTAAAGATGG
* *
1657533 -AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGCCAATA
1657597 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G
63 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGG
* * *
1657634 -AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
1657698 TGATTCAAGGCCAGCGATATTGGACTTAAAGAT-G
66 TGATTCAAGGCCAGCTATATTGGACTTAAAGATGG
* *
1657732 -AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGCCAATA
1657796 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G
63 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGG
* *
1657833 -AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGCCAATA
* *
1657897 TGCTGATTCAAGGCCAGCTATATTGGGCTTAAAGATGAA
63 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG-G
* *
1657936 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGC
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
* *
1658001 TGAGTCAAGGCCAGCTACATTGGACTTAAAGATGG
66 TGATTCAAGGCCAGCTATATTGGACTTAAAGATGG
* * *
1658036 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAAGATGAAGGTGCCAATGTG
1 -AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATG
* *
1658101 CTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGG
65 CTGATTCAAGGCCAGCTATATTGGACTTAAAGATGG
* * *
1658137 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAAGATGAAGGTGCCAATGTG
1 -AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATG
* *
1658202 CTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGG
65 CTGATTCAAGGCCAGCTATATTGGACTTAAAGATGG
* * *
1658238 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAAGATGAAGGTGCCAATGTG
1 -AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATG
* *
1658303 CTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGG
65 CTGATTCAAGGCCAGCTATATTGGACTTAAAGATGG
* * *
1658339 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAAGATGAAGGTGCCAATGTG
1 -AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATG
* *
1658404 CTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGG
65 CTGATTCAAGGCCAGCTATATTGGACTTAAAGATGG
* * *
1658440 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAAGATGAAGGTGCCAATGTG
1 -AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATG
* *
1658505 CTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGG
65 CTGATTCAAGGCCAGCTATATTGGACTTAAAGATGG
* *
1658541 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
1 -AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTA
1658586 GAGGGGTTGC
Statistics
Matches: 1024, Mismatches: 19, Indels: 18
0.97 0.02 0.02
Matches are distributed among these distances:
98 142 0.14
99 2 0.00
100 1 0.00
101 833 0.81
103 1 0.00
104 45 0.04
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.24
Consensus pattern (100 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
TGATTCAAGGCCAGCTATATTGGACTTAAAGATGG
Found at i:1658033 original size:202 final size:200
Alignment explanation
Indices: 1657246--1658585 Score: 1846
Period size: 202 Copynumber: 6.7 Consensus size: 200
1657236 AAGATGAGAA
* * *
1657246 AAAGGATGCCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAAT
1 AAAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGCCAAT
* *
1657311 ATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T--AAAGGTGCTAATGTGCTGATTCAAGG
62 ATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAAAGGTGCCAATATGCTGATTCAAGG
* * * * *
1657368 CCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-
127 CCAGCTATATTGGACTTAAAGATGAAGGTGCCAATATGCTGAGTCAAGGCCAGCTACATTGGACT
1657432 T-----T--
192 TAAAGATGG
* * * *
1657434 AAAGCTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATACGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
* * *
1657499 TGATTCAAGGCCAGCGATATTGGACTTAAAGATG--AAGGTGCCAATGTGCTGAGTCAAGGCCAG
66 TGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAAAGGTGCCAATATGCTGATTCAAGGCCAG
* * *
1657562 CTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
131 CTATATTGGACTTAAAGAT-G--AAGGTGCCAATATGCTGAGTCAAGGCCAGCTACATTGGACTT
1657627 AAAGAT-G
193 AAAGATGG
* *
1657634 -AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
* * *
1657698 TGATTCAAGGCCAGCGATATTGGACTTAAAGATG--AAGGTGCCAATGTGCTGAGTCAAGGCCAG
66 TGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAAAGGTGCCAATATGCTGATTCAAGGCCAG
* * *
1657761 CTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
131 CTATATTGGACTTAAAGAT-G--AAGGTGCCAATATGCTGAGTCAAGGCCAGCTACATTGGACTT
1657826 AAAGAT-G
193 AAAGATGG
*
1657833 -AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATA
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGCCAATA
*
1657897 TGCTGATTCAAGGCCAGCTATATTGGGCTTAAAGATGAAAAAGGTGCCAATATGCTGATTCAAGG
63 TGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATG-AAAAGGTGCCAATATGCTGATTCAAGG
*
1657962 CCAGCTATATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACT
127 CCAGCTATATTGGACTTAAAGATGAAGGTGCCAATATGCTGAGTCAAGGCCAGCTACATTGGACT
1658027 TAAAGATGG
192 TAAAGATGG
* * * *
1658036 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAAGATGAAGGTGCCAATGTG
1 -AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATG
* *
1658101 CTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCC
65 CTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-GAAAAGGTGCCAATATGCTGATTCAAGGCC
* *
1658166 AGCTATATTGGGCTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTA
129 AGCTATATTGGACTTAAAGATGAAGGTGCCAATATGCTGAGTCAAGGCCAGCTACATTGGACTTA
1658231 AAGATGG
194 AAGATGG
* * * *
1658238 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAAGATGAAGGTGCCAATGTG
1 -AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATG
* *
1658303 CTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCC
65 CTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-GAAAAGGTGCCAATATGCTGATTCAAGGCC
* *
1658368 AGCTATATTGGGCTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTA
129 AGCTATATTGGACTTAAAGATGAAGGTGCCAATATGCTGAGTCAAGGCCAGCTACATTGGACTTA
1658433 AAGATGG
194 AAGATGG
* * * *
1658440 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAAGATGAAGGTGCCAATGTG
1 -AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATG
* *
1658505 CTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCC
65 CTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-GAAAAGGTGCCAATATGCTGATTCAAGGCC
*
1658570 AGCTATATTGGGCTTA
129 AGCTATATTGGACTTA
1658586 GAGGGGTTGC
Statistics
Matches: 1093, Mismatches: 32, Indels: 40
0.94 0.03 0.03
Matches are distributed among these distances:
184 36 0.03
185 1 0.00
186 1 0.00
187 41 0.04
188 4 0.00
190 47 0.04
191 1 0.00
193 38 0.03
194 1 0.00
199 246 0.23
200 1 0.00
202 583 0.53
203 2 0.00
204 2 0.00
205 89 0.08
ACGTcount: A:0.32, C:0.17, G:0.27, T:0.24
Consensus pattern (200 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
TGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAAAGGTGCCAATATGCTGATTCAAGGCCAG
CTATATTGGACTTAAAGATGAAGGTGCCAATATGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
GATGG
Found at i:1658194 original size:303 final size:302
Alignment explanation
Indices: 1657197--1658585 Score: 1880
Period size: 303 Copynumber: 4.6 Consensus size: 302
1657187 GTGATAAAGA
* * * * * * * * *
1657197 TGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGATGCCAACGTG
1 TGCCAATATGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG-G-AAAAGG-TGCCAATGTG
* *
1657262 CTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCC
63 CTGATTCAAGGCCAGCTACATTGGACTTAAAGATGG-AAAGGTGCCAATATGCTGATTCAAGGCC
* * *
1657327 AGCTATATTGGAC-T-----T--AAAGGTGCTAATGTGCTGATTCAAGGCCAGCTACATTGGACT
127 AGCTATATTGGACTTAAAGATGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACT
* * *
1657384 TAAAGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T-----T-AAAGCTGC
192 TAAAGATGAAGATGCCAATATGCTGAGTCAAGGCCAGCGACATTGGACTTAAAGATGAAAGGTGC
* *
1657442 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
257 CAATATGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGG
* * * *
1657488 TGCCAATACGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAT-G--AAGGTGCCAATGTGCTG
1 TGCCAATATGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATGTGCTG
*
1657550 AGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGC
66 ATTCAAGGCCAGCTACATTGGACTTAAAGATGG-AAAGGTGCCAATATGCTGATTCAAGGCCAGC
* * *
1657615 TATATTGGACTTAAAGATG--AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAA
130 TATATTGGACTTAAAGATGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAA
* *
1657678 AGATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATG-AAGGTGCCAA
195 AGATGAAGATGCCAATATGCTGAGTCAAGGCCAGCGACATTGGACTTAAAGATGAAAGGTGCCAA
*
1657742 TGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGG
260 TATGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGG
* *
1657788 TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT-G--AAGGTGCCAATGTGCTG
1 TGCCAATATGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATGTGCTG
*
1657850 AGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGC
66 ATTCAAGGCCAGCTACATTGGACTTAAAGATGG-AAAGGTGCCAATATGCTGATTCAAGGCCAGC
*
1657915 TATATTGGGCTTAAAGATGAAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
130 TATATTGGACTTAAAGATG-AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
* * *
1657980 AAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGC
194 AAGATGAAGATGCCAATATGCTGAGTCAAGGCCAGCGACATTGGACTTAAAGAT-G-AAAGGTGC
* * *
1658045 CAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAAGATGAAGG
257 CAATATGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGG
* *
1658091 TGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTG
1 TGCCAATATGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATGTGCTG
* * * *
1658156 ATTCAAGGCCAGCTATATTGGGCTTAAAGAT-G-AAGGTGCCAATGTGCTGAGTCAAGGCCAGCT
66 ATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAGGTGCCAATATGCTGATTCAAGGCCAGCT
* *
1658219 ACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAA
131 ATATTGGACTTAAAGAT-GAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAA
* * *
1658284 AGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCC
195 AGATGAAGATGCCAATATGCTGAGTCAAGGCCAGCGACATTGGACTTAAAGAT-G-AAAGGTGCC
* * *
1658349 AATATGCTGATTCAAGGCCAGCTATATTGGGCTTAAAGATGAAGG
258 AATATGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGG
* *
1658394 TGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTG
1 TGCCAATATGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATGTGCTG
* * * *
1658459 ATTCAAGGCCAGCTATATTGGGCTTAAAGAT-G-AAGGTGCCAATGTGCTGAGTCAAGGCCAGCT
66 ATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAGGTGCCAATATGCTGATTCAAGGCCAGCT
* *
1658522 ACATTGGACTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTA
131 ATATTGGACTTAAAGAT-GAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
1658586 GAGGGGTTGC
Statistics
Matches: 1030, Mismatches: 41, Indels: 42
0.93 0.04 0.04
Matches are distributed among these distances:
285 84 0.08
286 5 0.00
289 1 0.00
291 126 0.12
292 1 0.00
297 48 0.05
298 1 0.00
300 146 0.14
303 525 0.51
304 3 0.00
305 2 0.00
306 88 0.09
ACGTcount: A:0.32, C:0.17, G:0.26, T:0.24
Consensus pattern (302 bp):
TGCCAATATGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAGGTGCCAATGTGCTG
ATTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAGGTGCCAATATGCTGATTCAAGGCCAGCT
ATATTGGACTTAAAGATGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAA
GATGAAGATGCCAATATGCTGAGTCAAGGCCAGCGACATTGGACTTAAAGATGAAAGGTGCCAAT
ATGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGG
Found at i:1658686 original size:32 final size:33
Alignment explanation
Indices: 1658590--1658682 Score: 163
Period size: 33 Copynumber: 2.8 Consensus size: 33
1658580 GGCTTAGAGG
1658590 GGTTGCCACCGACTTGTGTGGGCTTTGGAAGAA
1 GGTTGCCACCGACTTGTGTGGGCTTTGGAAGAA
1658623 GGTTGCCACCGACTTGTGTGGGCTTTAGGAAG-A
1 GGTTGCCACCGACTTGTGTGGGCTTT-GGAAGAA
1658656 -GTTGCCACCGACTTGTGTGGGCTTTGG
1 GGTTGCCACCGACTTGTGTGGGCTTTGG
1658683 GAAGGAAAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
31 2 0.03
32 25 0.42
33 27 0.46
34 5 0.08
ACGTcount: A:0.15, C:0.19, G:0.37, T:0.29
Consensus pattern (33 bp):
GGTTGCCACCGACTTGTGTGGGCTTTGGAAGAA
Found at i:1658760 original size:34 final size:35
Alignment explanation
Indices: 1658684--1659260 Score: 294
Period size: 34 Copynumber: 15.9 Consensus size: 35
1658674 GGGCTTTGGG
*
1658684 AAGGAAAAA-AGATGCCACGGAGTTGTGGAC-TTAA
1 AAGGAAAAAGAG-TGCCACGGAGTTGTGGGCTTTAA
1658718 AAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1658754 AA-GAAAAA-AGTGCCACGGAGTTGTGGGCTTTGAA
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AA
1658788 AAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
*
1658824 ACGGAAAAAG-GTGCCACGGAGTTGTGGGCTTTAAA
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AA
* ** * ***
1658859 AAGGGAAAGAGAGTGCCACAAAGTCGTAGGTGCCACAGA
1 AA-GGAAAAAGAGTGCCACGGAGTTGT-GG-GCTTTA-A
** * ** * * **** **
1658898 GTTGTGGGCTTTAAAAGA---AAAAGGTGCCACGGAG-TTGTGGGCT
1 ----AAGG---AAAAAGAGTGCCACGGAGTTGTGG-GCTT-T---AA
** * * **
1658941 TTGAAAAGGAAAAAAGAATGCCACAAAGTTGTGGGCTTTAA
1 AAGGAAA------AAGAGTGCCACGGAGTTGTGGGCTTTAA
*
1658982 AA-GAAGAAG-GTGCCACGGAGTTGTGGGCTTTGAA
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AA
* * *
1659016 AA-GAAGAAG-GTTGCCACCGACTTGTGTGGGCTTTAGGA
1 AAGGAAAAAGAG-TGCCACGGA-GT-TGTGGGCTTTA--A
* * *
1659054 AGGGAGAAAGA-TGCCACGGAGTTGTGGAC-TTAA
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1659087 AAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1659123 AA-GAAAAAG-GTGCCACGGAGTTGTGGGCTTTGAA
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AA
*
1659157 AAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAA
1 AA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
* *
1659193 ACA-GAAAAAG-GTGCCACAGAGTTATGGGCTTTGAA
1 A-AGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AA
* * *
1659228 AA-GAAGAAAGAATGCCACGAAGTTGTGGACTTT
1 AAGGAA-AAAGAGTGCCACGGAGTTGTGGGCTTT
1659261 GAGACAAAAT
Statistics
Matches: 421, Mismatches: 69, Indels: 104
0.71 0.12 0.18
Matches are distributed among these distances:
33 66 0.16
34 93 0.22
35 77 0.18
36 67 0.16
37 68 0.16
38 13 0.03
39 10 0.02
40 2 0.00
41 3 0.01
42 9 0.02
44 2 0.00
45 11 0.03
ACGTcount: A:0.34, C:0.12, G:0.33, T:0.20
Consensus pattern (35 bp):
AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
Found at i:1658762 original size:70 final size:70
Alignment explanation
Indices: 1658687--1658877 Score: 305
Period size: 71 Copynumber: 2.7 Consensus size: 70
1658677 CTTTGGGAAG
*
1658687 GAAAAAAGATGCCACGGAGTTGTGGAC-TT-AAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCT
1 GAAAAAAG-TGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCT
1658750 TTAAAA
65 TTAAAA
*
1658756 GAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
1 GAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
*
1658821 TAAACG
66 TAAA-A
* *
1658827 GAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAGAGAGTGCCAC
1 GAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAAAGAGTGCCAC
1658878 AAAGTCGTAG
Statistics
Matches: 114, Mismatches: 5, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
68 17 0.15
69 10 0.09
70 39 0.34
71 48 0.42
ACGTcount: A:0.35, C:0.13, G:0.34, T:0.18
Consensus pattern (70 bp):
GAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
TAAAA
Found at i:1658948 original size:87 final size:88
Alignment explanation
Indices: 1658800--1658969 Score: 279
Period size: 87 Copynumber: 1.9 Consensus size: 88
1658790 GGGAAAAAGA
* * *
1658800 GTGCCACGGAGTTGTGGGCTTTAAACGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGGA
1 GTGCCACAGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGAA
* *
1658865 AAGAGAGTGCCACAAAGTCGTAG
66 AAAAGAATGCCACAAAGTCGTAG
*
1658888 GTGCCACAGAGTTGTGGGCTTTAAA-AGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAA
1 GTGCCACAGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGAA
1658952 AAAAGAATGCCACAAAGT
66 AAAAGAATGCCACAAAGT
1658970 TGTGGGCTTT
Statistics
Matches: 76, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
87 52 0.68
88 24 0.32
ACGTcount: A:0.34, C:0.14, G:0.33, T:0.19
Consensus pattern (88 bp):
GTGCCACAGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGAA
AAAAGAATGCCACAAAGTCGTAG
Found at i:1659002 original size:70 final size:70
Alignment explanation
Indices: 1658889--1659260 Score: 439
Period size: 70 Copynumber: 5.3 Consensus size: 70
1658879 AAGTCGTAGG
*
1658889 TGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAA
1 TGCCACAAAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAA
1658954 AAGAA
66 AAGAA
* *
1658959 TGCCACAAAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAA-G-AAG
1 TGCCACAAAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAA
**
1659022 AAGGT
66 AAGAA
* ** * * * *
1659027 TGCCACCGACTTGTGTGGGCTTTAGGAAGGGAGAAAGATGCCACGGAGTTGTGGAC-TT-AAAAG
1 TGCCA-CAAAGT-TGTGGGCTTTA--AA-AGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAG
* *
1659090 GGAAAAAGAG
61 GAAAAAAGAA
** *
1659100 TGCCACGGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAA
1 TGCCACAAAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAA
*
1659165 AAGAG
66 AAGAA
* * * *
1659170 TGCCACAGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACAGAGTTATGGGCTTTGAAAA-GAAG
1 TGCCACAAAGTTGTGGGCTTTAAA-AGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAA
1659234 AAAGAA
65 AAAGAA
* *
1659240 TGCCACGAAGTTGTGGACTTT
1 TGCCACAAAGTTGTGGGCTTT
1659261 GAGACAAAAT
Statistics
Matches: 260, Mismatches: 32, Indels: 20
0.83 0.10 0.06
Matches are distributed among these distances:
68 33 0.13
69 8 0.03
70 131 0.50
71 48 0.18
72 8 0.03
73 32 0.12
ACGTcount: A:0.34, C:0.13, G:0.33, T:0.21
Consensus pattern (70 bp):
TGCCACAAAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAA
AAGAA
Found at i:1659185 original size:141 final size:137
Alignment explanation
Indices: 1658886--1659260 Score: 468
Period size: 141 Copynumber: 2.7 Consensus size: 137
1658876 ACAAAGTCGT
* *
1658886 AGGTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGA
1 AGGTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGATGCCACGGAGTTGTGGACTTTGAAAAGGA
*
1658951 AAAAAGAATGCCACAAAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAA
66 AAAAAGAATGCCACAAAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAA
*
1659016 AAGAAGA
131 AAGAAAA
* * * *
1659023 AGGTTGCCACCGACTTGTGTGGGCTTTAGGAAGGGAGAAAGATGCCACGGAGTTGTGGAC-TT-A
1 AGG-TGCCACAGA-GT-TGTGGGCTTTA--AA-AGAAAAAGATGCCACGGAGTTGTGGACTTTGA
* * **
1659086 AAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGC
60 AAAGGAAAAAAGAATGCCACAAAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGC
1659151 TTTGAAAAGGGAAAA
125 TTTGAAAA--GAAAA
* * * *
1659166 AGAGTGCCACAGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACAGAGTTATGGGCTTTGAAAA-
1 AG-GTGCCACAGAGTTGTGGGCTTTAAA-AGAAAAAGATGCCACGGAGTTGTGGACTTTGAAAAG
* * *
1659230 GAAGAAAGAATGCCACGAAGTTGTGGACTTT
64 GAAAAAAGAATGCCACAAAGTTGTGGGCTTT
1659261 GAGACAAAAT
Statistics
Matches: 201, Mismatches: 26, Indels: 19
0.82 0.11 0.08
Matches are distributed among these distances:
137 3 0.01
138 8 0.04
139 24 0.12
140 39 0.19
141 84 0.42
142 5 0.02
143 37 0.18
144 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.33, T:0.21
Consensus pattern (137 bp):
AGGTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGATGCCACGGAGTTGTGGACTTTGAAAAGGA
AAAAAGAATGCCACAAAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAA
AAGAAAA
Found at i:1660235 original size:1 final size:1
Alignment explanation
Indices: 1660224--1660262 Score: 51
Period size: 1 Copynumber: 39.0 Consensus size: 1
1660214 TGAAAAGGGG
* * *
1660224 TTTTTTCTTTTTTTTTTTTTTTGTTTGTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1660263 GAAGAGTAGG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.03, G:0.05, T:0.92
Consensus pattern (1 bp):
T
Found at i:1660254 original size:17 final size:16
Alignment explanation
Indices: 1660224--1660263 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 16
1660214 TGAAAAGGGG
*
1660224 TTTTTTCTTTTTTTTT
1 TTTTTTGTTTTTTTTT
1660240 TTTTTTGTTTGTTTTTT
1 TTTTTTGTTT-TTTTTT
1660257 TTTTTTG
1 TTTTTTG
1660264 AAGAGTAGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.00, C:0.03, G:0.07, T:0.90
Consensus pattern (16 bp):
TTTTTTGTTTTTTTTT
Found at i:1667621 original size:20 final size:19
Alignment explanation
Indices: 1667576--1667628 Score: 81
Period size: 19 Copynumber: 2.7 Consensus size: 19
1667566 ATTTGCCTGC
1667576 ATGTATCGATACATTATAA
1 ATGTATCGATACATTATAA
1667595 ATGTATCGATACATT-TAA
1 ATGTATCGATACATTATAA
1667613 TAGTGTATCGATACAT
1 -A-TGTATCGATACAT
1667629 CTGGGCAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
18 3 0.09
19 16 0.50
20 13 0.41
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (19 bp):
ATGTATCGATACATTATAA
Found at i:1667640 original size:71 final size:72
Alignment explanation
Indices: 1667524--1667680 Score: 298
Period size: 71 Copynumber: 2.2 Consensus size: 72
1667514 ATTTATCTGC
1667524 ATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACA
1 ATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACA
1667589 TTATA-A
66 TTATATA
1667595 ATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACA
1 ATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACA
*
1667660 TTTTATA
66 TTATATA
1667667 ATGTATCGATACAT
1 ATGTATCGATACAT
1667681 CTGGGCAAAT
Statistics
Matches: 84, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
71 69 0.82
72 15 0.18
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (72 bp):
ATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACA
TTATATA
Found at i:1667673 original size:52 final size:52
Alignment explanation
Indices: 1667595--1667711 Score: 216
Period size: 52 Copynumber: 2.2 Consensus size: 52
1667585 TACATTATAA
*
1667595 ATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGCCTGC
1 ATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCCTGC
*
1667647 ATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCCTGC
1 ATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCCTGC
1667699 ATGTATCGATACA
1 ATGTATCGATACA
1667712 AAGATCAGTG
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 63 1.00
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (52 bp):
ATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCCTGC
Found at i:1667724 original size:52 final size:52
Alignment explanation
Indices: 1667595--1667731 Score: 197
Period size: 52 Copynumber: 2.6 Consensus size: 52
1667585 TACATTATAA
*
1667595 ATGTATCGATACATTTA-ATAGTGTATCGATACATCTGGGCAAATTTGCCTGC
1 ATGTATCGATACA-TAAGATAGTGTATCGATACATCTGGGCAAATTTGCCTGC
*** *
1667647 ATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCCTGC
1 ATGTATCGATACATAAGATAGTGTATCGATACATCTGGGCAAATTTGCCTGC
1667699 ATGTATCGATACA-AAGATCAGTGTATCGATACA
1 ATGTATCGATACATAAGAT-AGTGTATCGATACA
1667732 ATGTATCGAT
Statistics
Matches: 77, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
51 4 0.05
52 73 0.95
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (52 bp):
ATGTATCGATACATAAGATAGTGTATCGATACATCTGGGCAAATTTGCCTGC
Found at i:1667738 original size:13 final size:13
Alignment explanation
Indices: 1667720--1667744 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1667710 CAAAGATCAG
1667720 TGTATCGATACAA
1 TGTATCGATACAA
1667733 TGTATCGATACA
1 TGTATCGATACA
1667745 TGTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1667827 original size:13 final size:13
Alignment explanation
Indices: 1667809--1667833 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1667799 CAAAAAAATA
1667809 TGTATCGATACAT
1 TGTATCGATACAT
1667822 TGTATCGATACA
1 TGTATCGATACA
1667834 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1667829 original size:33 final size:33
Alignment explanation
Indices: 1667787--1667853 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1667777 AGTAGCTTAA
1667787 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1667820 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1667853 A
1 A
1667854 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1668256 original size:20 final size:20
Alignment explanation
Indices: 1668209--1668283 Score: 80
Period size: 20 Copynumber: 3.8 Consensus size: 20
1668199 AAAAAGACAT
*
1668209 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
1668228 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
1668249 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
1668269 AATGTATCGATACAT
1 AATGTATCGATACAT
1668284 CAGGGTATGA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 43 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Done.