Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold13
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: 2744999
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.26
Warning! 506982 characters in sequence are not A, C, G, or T
File 8 of 15
Found at i:1510860 original size:52 final size:52
Alignment explanation
Indices: 1510748--1510867 Score: 170
Period size: 52 Copynumber: 2.3 Consensus size: 52
1510738 AATACATTTA
* ***
1510748 ATAGTGTATCGATACATCTGGGCAAATTTGCCTGCATGTATCGATACATTTT
1 ATAGTGTATCGATACATCTGGGAAAATTTGCCTGCATGTATCGATACATAAG
*
1510800 ATAATGTATCGATACATCTGGGAAAATTTGCCTGCATGTATCGATACA-AAG
1 ATAGTGTATCGATACATCTGGGAAAATTTGCCTGCATGTATCGATACATAAG
*
1510851 ATCAGTGTATCCATACA
1 AT-AGTGTATCGATACA
1510868 ATGTATCGAT
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
51 2 0.03
52 58 0.97
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (52 bp):
ATAGTGTATCGATACATCTGGGAAAATTTGCCTGCATGTATCGATACATAAG
Found at i:1511057 original size:70 final size:70
Alignment explanation
Indices: 1510975--1511127 Score: 306
Period size: 70 Copynumber: 2.2 Consensus size: 70
1510965 ACAACATTTT
1510975 ATGTATCGATACAAATCGTTGAAATTCAAAATTTTTGACCGTTGGGACCTTGTATCGATACATTC
1 ATGTATCGATACAAATCGTTGAAATTCAAAATTTTTGACCGTTGGGACCTTGTATCGATACATTC
1511040 TAACA
66 TAACA
1511045 ATGTATCGATACAAATCGTTGAAATTCAAAATTTTTGACCGTTGGGACCTTGTATCGATACATTC
1 ATGTATCGATACAAATCGTTGAAATTCAAAATTTTTGACCGTTGGGACCTTGTATCGATACATTC
1511110 TAACA
66 TAACA
1511115 ATGTATCGATACA
1 ATGTATCGATACA
1511128 TTTGGACAAA
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 83 1.00
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Consensus pattern (70 bp):
ATGTATCGATACAAATCGTTGAAATTCAAAATTTTTGACCGTTGGGACCTTGTATCGATACATTC
TAACA
Found at i:1512407 original size:28 final size:28
Alignment explanation
Indices: 1512326--1512407 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
1512316 TTTTGGAGAT
*
1512326 AATAACGAGGTTGGAGTGTTCCCTCG--GA
1 AATAACGAGGTTGGAGT-AT-CCTCGATGA
* * *
1512354 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGAGGTTGGAGTATCCTCGATGA
1512382 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGAGGTTGGAGTATCCTCGAT
1512408 TGTGAAAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 4 0.09
27 1 0.02
28 40 0.89
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCTCGATGA
Found at i:1512550 original size:51 final size:51
Alignment explanation
Indices: 1512390--1512560 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
1512380 GAAATAACGA
* * *
1512390 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * *
1512442 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
1512495 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
1512546 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
1512561 TCAGAAATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 39 0.40
52 16 0.16
53 32 0.33
54 10 0.10
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:1512606 original size:27 final size:28
Alignment explanation
Indices: 1512543--1512618 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
1512533 AAAATAAAGT
*
1512543 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
1512571 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
1512598 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
1512619 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:1515094 original size:20 final size:20
Alignment explanation
Indices: 1515067--1515121 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
1515057 TAAAATTTCC
*
1515067 AAATGTATCGATACAAAGAT
1 AAATGTATCGATACAAAGAA
** *
1515087 CCATGTATCGATACACAGAA
1 AAATGTATCGATACAAAGAA
1515107 AAATGTATCGATACA
1 AAATGTATCGATACA
1515122 TTTCCTTGGC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.45, C:0.16, G:0.15, T:0.24
Consensus pattern (20 bp):
AAATGTATCGATACAAAGAA
Found at i:1515165 original size:19 final size:18
Alignment explanation
Indices: 1515141--1515208 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
1515131 CAGTAGCTAA
1515141 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
1515160 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
1515175 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
1515192 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1515209 TTGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:1515181 original size:13 final size:13
Alignment explanation
Indices: 1515163--1515187 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1515153 ACAATACTTA
1515163 TGTATCGATACAT
1 TGTATCGATACAT
1515176 TGTATCGATACA
1 TGTATCGATACA
1515188 AAACTTATGT
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:1515185 original size:32 final size:32
Alignment explanation
Indices: 1515144--1515206 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1515134 TAGCTAATTA
*
1515144 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
1515176 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
1515207 AATTGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:1515270 original size:21 final size:21
Alignment explanation
Indices: 1515244--1515299 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
1515234 GTTGGGACCC
1515244 TGTATCGATACATTCCACAAA
1 TGTATCGATACATTCCACAAA
*
1515265 TGTATCGATACATTCTACAAA
1 TGTATCGATACATTCCACAAA
1515286 TGTATCGATACATT
1 TGTATCGATACATT
1515300 TAAATTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.36, C:0.20, G:0.11, T:0.34
Consensus pattern (21 bp):
TGTATCGATACATTCCACAAA
Found at i:1515324 original size:17 final size:17
Alignment explanation
Indices: 1515302--1515334 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1515292 GATACATTTA
1515302 AATTTTTTTTTTTTTTC
1 AATTTTTTTTTTTTTTC
1515319 AATTTTTTTTTTTTTT
1 AATTTTTTTTTTTTTT
1515335 TTTCAAACAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.85
Consensus pattern (17 bp):
AATTTTTTTTTTTTTTC
Found at i:1516010 original size:55 final size:53
Alignment explanation
Indices: 1515926--1516658 Score: 1070
Period size: 55 Copynumber: 13.3 Consensus size: 53
1515916 ATAAATTGTA
* * * * *
1515926 TCCTGCTCATTGAGGAGTAAAAAGTGCCACCAACTCGTGTGGGCTTTGAAAGGCG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTT-AAAGGTG
* *
1515981 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCCACTTGTGTGGGCTTTGAAAAGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTT-AAAGGTG
* *
1516036 TCCTGCTCTTTGGGGAATGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTAA-AGGTG
*
1516091 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTT-AAAGGTG
* *
1516146 TCCTGTTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTT-AAAGGTG
1516201 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTAA-AGGTG
*
1516256 TCCTGCTCTTTGGGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTAA-AGGTG
* *
1516311 TCCTGCTCGTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTT-AAAGGTG
*
1516366 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTT-AAAGGTG
*
1516421 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTGAAAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTT-AAAGGTG
1516476 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTAA-AGGTG
*
1516531 TCCTGCTCTTTGAGGACTGGAAAATGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACT-GAAAGTGCCACCAACTTGTGTGGGCTTTAA-AGGTG
1516586 TCCTGCTCTTTGAGGACTGAAAGGTGCCACCAACTTGTGTGGGCTTTAAGAGGTG
1 TCCTGCTCTTTGAGGACTGAAA-GTGCCACCAACTTGTGTGGGCTTTAA-AGGTG
1516641 TCCTGCTCTTTGAGGACT
1 TCCTGCTCTTTGAGGACT
1516659 AAAAAGCGGA
Statistics
Matches: 639, Mismatches: 27, Indels: 24
0.93 0.04 0.03
Matches are distributed among these distances:
54 21 0.03
55 602 0.94
56 16 0.03
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (53 bp):
TCCTGCTCTTTGAGGACTGAAAGTGCCACCAACTTGTGTGGGCTTTAAAGGTG
Found at i:1516221 original size:26 final size:26
Alignment explanation
Indices: 1516192--1516281 Score: 74
Period size: 26 Copynumber: 3.3 Consensus size: 26
1516182 GTGTGGGCTT
1516192 TGAAAGGTGTCCTGCTCTTTGAGGAC
1 TGAAAGGTGTCCTGCTCTTTGAGGAC
** * * *
1516218 TGAAAGGTG-CCACCAACTTGTGTGGGC
1 TGAAAGGTGTCCTGC-TCTT-TGAGGAC
* *
1516245 TTTAAGAGGTGTCCTGCTCTTTGGGGAC
1 -TGAA-AGGTGTCCTGCTCTTTGAGGAC
1516273 TGAAAGGTG
1 TGAAAGGTG
1516282 CCACCAACTT
Statistics
Matches: 47, Mismatches: 12, Indels: 10
0.68 0.17 0.14
Matches are distributed among these distances:
25 3 0.06
26 17 0.36
27 8 0.17
28 8 0.17
29 8 0.17
30 3 0.06
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29
Consensus pattern (26 bp):
TGAAAGGTGTCCTGCTCTTTGAGGAC
Found at i:1516310 original size:29 final size:29
Alignment explanation
Indices: 1516222--1516310 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 29
1516212 GAGGACTGAA
1516222 AGGTGCCACCAACTTGTGTGGGCTTTAAG
1 AGGTGCCACCAACTTGTGTGGGCTTTAAG
** * *
1516251 AGGTGTCCTGC-TCTT-TG-GGGAC-TGAA-
1 AGGTG-CCACCAACTTGTGTGGG-CTTTAAG
1516277 AGGTGCCACCAACTTGTGTGGGCTTTAAG
1 AGGTGCCACCAACTTGTGTGGGCTTTAAG
1516306 AGGTG
1 AGGTG
1516311 TCCTGCTCGT
Statistics
Matches: 45, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
25 3 0.07
26 8 0.18
27 9 0.20
28 9 0.20
29 13 0.29
30 3 0.07
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.28
Consensus pattern (29 bp):
AGGTGCCACCAACTTGTGTGGGCTTTAAG
Found at i:1516496 original size:26 final size:26
Alignment explanation
Indices: 1516467--1516611 Score: 71
Period size: 26 Copynumber: 5.3 Consensus size: 26
1516457 GTGTGGGCTT
1516467 TGAAAGGTGTCCTGCTCTTTGAGGAC
1 TGAAAGGTGTCCTGCTCTTTGAGGAC
** * * *
1516493 TGAAAGGTG-CCACCAACTTGTGTGGGC
1 TGAAAGGTGTCCTGC-TCTT-TGAGGAC
*
1516520 TTTAAGAGGTGTCCTGCTCTTTGAGGAC
1 -TGAA-AGGTGTCCTGCTCTTTGAGGAC
* ** * * *
1516548 TGGAAA-ATG-CCACCAACTTGTGTGGGC
1 T-GAAAGGTGTCCTGC-TCTT-TGAGGAC
*
1516575 TTTAAGAGGTGTCCTGCTCTTTGAGGAC
1 -TGAA-AGGTGTCCTGCTCTTTGAGGAC
1516603 TGAAAGGTG
1 TGAAAGGTG
1516612 CCACCAACTT
Statistics
Matches: 81, Mismatches: 26, Indels: 24
0.62 0.20 0.18
Matches are distributed among these distances:
25 6 0.07
26 22 0.27
27 17 0.21
28 17 0.21
29 13 0.16
30 6 0.07
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.29
Consensus pattern (26 bp):
TGAAAGGTGTCCTGCTCTTTGAGGAC
Found at i:1517666 original size:13 final size:12
Alignment explanation
Indices: 1517642--1517701 Score: 57
Period size: 12 Copynumber: 4.8 Consensus size: 12
1517632 CTTTTCTCTC
*
1517642 TTTTTCTTTGTT
1 TTTTTTTTTGTT
1517654 TTGTTTTTTTGTT
1 TT-TTTTTTTGTT
**
1517667 TTTTTTTTCCTT
1 TTTTTTTTTGTT
**
1517679 TTTTTTTTACTCT
1 TTTTTTTTTGT-T
1517692 TTTTTTTTTG
1 TTTTTTTTTG
1517702 AAGAGAAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
12 20 0.50
13 20 0.50
ACGTcount: A:0.02, C:0.08, G:0.07, T:0.83
Consensus pattern (12 bp):
TTTTTTTTTGTT
Found at i:1517682 original size:14 final size:14
Alignment explanation
Indices: 1517665--1517700 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
1517655 TGTTTTTTTG
1517665 TTTTTTTTTT-C-C
1 TTTTTTTTTTACTC
1517677 TTTTTTTTTTACTC
1 TTTTTTTTTTACTC
1517691 TTTTTTTTTT
1 TTTTTTTTTT
1517701 GAAGAGAAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 10 0.45
13 1 0.05
14 11 0.50
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTTTTTTTACTC
Found at i:1529986 original size:28 final size:28
Alignment explanation
Indices: 1529905--1529986 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
1529895 TTTTGGAGAT
*
1529905 AATAACGAGGTTGGAGTGTTCCCTCG--GA
1 AATAACGAGGTTGGAGT-AT-CCTCGATGA
* * *
1529933 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGAGGTTGGAGTATCCTCGATGA
1529961 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGAGGTTGGAGTATCCTCGAT
1529987 TGTGAAAAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
26 4 0.09
27 1 0.02
28 40 0.89
ACGTcount: A:0.27, C:0.17, G:0.32, T:0.24
Consensus pattern (28 bp):
AATAACGAGGTTGGAGTATCCTCGATGA
Found at i:1530129 original size:51 final size:51
Alignment explanation
Indices: 1529969--1530139 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
1529959 GAAATAACGA
* * *
1529969 GGTTGGAGTATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTA-TTTTGAAAATAAAATCGG
** * * * * *
1530021 AATTGGAGTATCCCCGATTAAAGGAGAAATTGGTGTTGTGAAAATAAAACCGG
1 GGTTGGAGTATCCCCGATT--ATGAAAAATTGGTATTTTGAAAATAAAATCGG
* * *
1530074 GGTTGGAGTATCCCCGATTATGAAAAATCGATATTTTGAAAATAAAGTCGG
1 GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
1530125 GGTTGGAGTATCCCC
1 GGTTGGAGTATCCCC
1530140 TCAGAAATAA
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 39 0.40
52 16 0.16
53 32 0.33
54 10 0.10
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (51 bp):
GGTTGGAGTATCCCCGATTATGAAAAATTGGTATTTTGAAAATAAAATCGG
Found at i:1530185 original size:27 final size:28
Alignment explanation
Indices: 1530122--1530197 Score: 102
Period size: 27 Copynumber: 2.8 Consensus size: 28
1530112 AAAATAAAGT
*
1530122 CGGGGTTGGAGTATCCCCTCA-GAAATAA
1 CGGGGTTGGAGTATCCCC-GATGAAATAA
*
1530150 CGGGGTTGGAGTATCCCCGATG-ATTAA
1 CGGGGTTGGAGTATCCCCGATGAAATAA
*
1530177 CGGGGTTGGAGTGTCCCCGAT
1 CGGGGTTGGAGTATCCCCGAT
1530198 TGTGAAGAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
27 25 0.57
28 19 0.43
ACGTcount: A:0.21, C:0.21, G:0.34, T:0.24
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGATGAAATAA
Found at i:1532686 original size:13 final size:13
Alignment explanation
Indices: 1532668--1532693 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1532658 ACAAAGATCC
1532668 ATGTATCGATACA
1 ATGTATCGATACA
1532681 ATGTATCGATACA
1 ATGTATCGATACA
1532694 CAGAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1532689 original size:33 final size:33
Alignment explanation
Indices: 1532647--1532713 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1532637 AAAATTTCCA
***
1532647 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
1532680 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
1532713 A
1 A
1532714 TTTCCTTGGC
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:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:1532773 original size:13 final size:13
Alignment explanation
Indices: 1532755--1532779 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1532745 ACAATACTTA
1532755 TGTATCGATACAT
1 TGTATCGATACAT
1532768 TGTATCGATACA
1 TGTATCGATACA
1532780 AAACTTATGA
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:1534157 original size:19 final size:19
Alignment explanation
Indices: 1534130--1534174 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
1534120 TAGTATGAAC
*
1534130 AAAATTAAGTATTTACAATT
1 AAAA-TAAGTATTCACAATT
*
1534150 AAAATAAGTATTCACATTT
1 AAAATAAGTATTCACAATT
1534169 AAAATA
1 AAAATA
1534175 TATTAATACA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.53, C:0.07, G:0.04, T:0.36
Consensus pattern (19 bp):
AAAATAAGTATTCACAATT
Found at i:1535097 original size:3 final size:3
Alignment explanation
Indices: 1535089--1535157 Score: 138
Period size: 3 Copynumber: 23.0 Consensus size: 3
1535079 AGTTTCGACG
1535089 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1535137 TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT
1535158 AAACATCATT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:1535267 original size:18 final size:18
Alignment explanation
Indices: 1535244--1535278 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
1535234 TCTAACATTT
1535244 GAAGGTAAGAAAATATTA
1 GAAGGTAAGAAAATATTA
1535262 GAAGGTAAGAAAATATT
1 GAAGGTAAGAAAATATT
1535279 TTTGAAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.54, C:0.00, G:0.23, T:0.23
Consensus pattern (18 bp):
GAAGGTAAGAAAATATTA
Found at i:1536083 original size:20 final size:20
Alignment explanation
Indices: 1536058--1536111 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
1536048 GTTTGAGACA
1536058 ATGTATTGATACAATTCTTC
1 ATGTATTGATACAATTCTTC
1536078 ATGTATTGATACAATTCTTC
1 ATGTATTGATACAATTCTTC
*
1536098 ATGTATCGATACAA
1 ATGTATTGATACAA
1536112 CGTGCCATGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (20 bp):
ATGTATTGATACAATTCTTC
Found at i:1536190 original size:20 final size:20
Alignment explanation
Indices: 1536165--1536215 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
1536155 AGTTTTATGT
*
1536165 ATCGATACAATTGTGGATGC
1 ATCGATACAATTATGGATGC
1536185 ATCGATACAATTATGGATGC
1 ATCGATACAATTATGGATGC
1536205 ATCGATACAAT
1 ATCGATACAAT
1536216 GTATCGATAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.29
Consensus pattern (20 bp):
ATCGATACAATTATGGATGC
Found at i:1545097 original size:19 final size:20
Alignment explanation
Indices: 1545054--1545106 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
1545044 TGCTAGTTTT
**
1545054 ATGTATCGATACAATTGTGC
1 ATGTATCGATACAATAATGC
1545074 ATGTATCGATACAATAAT-C
1 ATGTATCGATACAATAATGC
1545093 ATGTATCGATACAA
1 ATGTATCGATACAA
1545107 AGCATTATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (20 bp):
ATGTATCGATACAATAATGC
Found at i:1546050 original size:15 final size:15
Alignment explanation
Indices: 1546020--1546049 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1546010 TAGATCTTTC
1546020 TAAAATATATATTTT
1 TAAAATATATATTTT
1546035 TAAAATAT-TATTTT
1 TAAAATATATATTTT
1546049 T
1 T
1546050 TTCATGATGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TAAAATATATATTTT
Found at i:1546301 original size:3 final size:3
Alignment explanation
Indices: 1546293--1546320 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1546283 CTAAACAAAT
1546293 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1546321 ATGTCATGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:1549739 original size:12 final size:12
Alignment explanation
Indices: 1549682--1549741 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 12
1549672 GCTTATTTAT
*
1549682 TTTTTAT-TATA
1 TTTTTATATAAA
*
1549693 TGTTTATATAAA
1 TTTTTATATAAA
*
1549705 TTTTAATATATTAA
1 TTTT--TATATAAA
*
1549719 TAATTTATATAAA
1 T-TTTTATATAAA
1549732 TTTTTATATA
1 TTTTTATATA
1549742 TTTGTTTTGA
Statistics
Matches: 38, Mismatches: 7, Indels: 7
0.73 0.13 0.13
Matches are distributed among these distances:
11 6 0.16
12 14 0.37
13 8 0.21
14 8 0.21
15 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (12 bp):
TTTTTATATAAA
Found at i:1549792 original size:20 final size:20
Alignment explanation
Indices: 1549718--1549801 Score: 61
Period size: 19 Copynumber: 4.2 Consensus size: 20
1549708 TAATATATTA
* *
1549718 ATAATTTA-TATAAATTTTT
1 ATAATTTATTATTATTTTTT
*
1549737 ATATATTTGTT-TTGATTTTTT
1 ATA-ATTTATTATT-ATTTTTT
*
1549758 AT-ATTGAATTA-TATTTTTT
1 ATAATT-TATTATTATTTTTT
1549777 ATAATTTATTATTATTATTTT
1 ATAATTTATTATTATT-TTTT
1549798 -TAAT
1 ATAAT
1549802 ATCAAATTTG
Statistics
Matches: 51, Mismatches: 6, Indels: 15
0.71 0.08 0.21
Matches are distributed among these distances:
19 19 0.37
20 19 0.37
21 13 0.25
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (20 bp):
ATAATTTATTATTATTTTTT
Found at i:1550365 original size:17 final size:16
Alignment explanation
Indices: 1550343--1550374 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
1550333 ATATATTTAA
1550343 ATTTATTAAATTAAATT
1 ATTTATT-AATTAAATT
1550360 ATTTATTAATTAAAT
1 ATTTATTAATTAAAT
1550375 AATATTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTATTAATTAAATT
Found at i:1550384 original size:16 final size:16
Alignment explanation
Indices: 1550342--1550377 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1550332 AATATATTTA
1550342 AATTTATTAAATTAAAT
1 AATTTATT-AATTAAAT
*
1550359 TATTTATTAATTAAAT
1 AATTTATTAATTAAAT
1550375 AAT
1 AAT
1550378 ATTTTAAACC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AATTTATTAATTAAAT
Found at i:1551515 original size:2 final size:2
Alignment explanation
Indices: 1551508--1551568 Score: 104
Period size: 2 Copynumber: 30.5 Consensus size: 2
1551498 TTTCTTCATA
* *
1551508 AT AT AT AT GT AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1551550 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
1551569 AATGTGGCTG
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1551796 original size:4 final size:4
Alignment explanation
Indices: 1551779--1551817 Score: 51
Period size: 4 Copynumber: 9.8 Consensus size: 4
1551769 AGCCAATTTA
* * *
1551779 ATAC ATAA ATAC ATAC ATAC ATAT ATAC ATAC ATGC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1551818 TATATATATA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.51, C:0.18, G:0.03, T:0.28
Consensus pattern (4 bp):
ATAC
Found at i:1551818 original size:16 final size:16
Alignment explanation
Indices: 1551779--1551837 Score: 73
Period size: 16 Copynumber: 3.7 Consensus size: 16
1551769 AGCCAATTTA
*
1551779 ATACATAAATACATAC
1 ATACATATATACATAC
1551795 ATACATATATACATAC
1 ATACATATATACATAC
* * *
1551811 ATGCATATATATATAT
1 ATACATATATACATAC
*
1551827 ATATATATATA
1 ATACATATATA
1551838 TATATATATA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.51, C:0.12, G:0.02, T:0.36
Consensus pattern (16 bp):
ATACATATATACATAC
Found at i:1551820 original size:2 final size:2
Alignment explanation
Indices: 1551815--1551848 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1551805 ACATACATGC
1551815 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1551849 TAAGGGATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1555034 original size:13 final size:13
Alignment explanation
Indices: 1555016--1555040 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1555006 CATGGCACAT
1555016 TGTATCGATACAA
1 TGTATCGATACAA
1555029 TGTATCGATACA
1 TGTATCGATACA
1555041 TGGCATATTG
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:1555039 original size:33 final size:32
Alignment explanation
Indices: 1554996--1555093 Score: 126
Period size: 33 Copynumber: 3.0 Consensus size: 32
1554986 TAGCACTATT
*
1554996 TGTATTGATACATGGCACATTGTATCGATACAA
1 TGTATCGATACATGGCA-ATTGTATCGATACAA
1555029 TGTATCGATACATGGCATATTGTATCGATACAA
1 TGTATCGATACATGGCA-ATTGTATCGATACAA
* *
1555062 TGTATCAAAACATGATG-AATTGTATCGATACA
1 TGTATCGATACATG--GCAATTGTATCGATACA
1555094 TTGCTTCAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
33 57 0.97
34 1 0.02
35 1 0.02
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (32 bp):
TGTATCGATACATGGCAATTGTATCGATACAA
Found at i:1555054 original size:20 final size:19
Alignment explanation
Indices: 1554995--1555060 Score: 63
Period size: 20 Copynumber: 3.7 Consensus size: 19
1554985 CTAGCACTAT
*
1554995 TTGTATTGATACATGGCACA
1 TTGTATCGATACATGGCA-A
1555015 TTGTATCGAT--A---CAA
1 TTGTATCGATACATGGCAA
1555029 -TGTATCGATACATGGCATA
1 TTGTATCGATACATGGCA-A
1555048 TTGTATCGATACA
1 TTGTATCGATACA
1555061 ATGTATCAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 14
0.72 0.02 0.26
Matches are distributed among these distances:
13 9 0.24
14 1 0.03
15 3 0.08
18 3 0.08
19 1 0.03
20 21 0.55
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (19 bp):
TTGTATCGATACATGGCAA
Found at i:1566727 original size:22 final size:21
Alignment explanation
Indices: 1566702--1566745 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 21
1566692 TTTTAAATGA
1566702 TTATCAAGGGGGAGAAAATTTT
1 TTATCAAGGGGGAG-AAATTTT
1566724 TTATCAAGGGGGAGAAATTTT
1 TTATCAAGGGGGAGAAATTTT
1566745 T
1 T
1566746 AAACGAGAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 8 0.36
22 14 0.64
ACGTcount: A:0.34, C:0.05, G:0.27, T:0.34
Consensus pattern (21 bp):
TTATCAAGGGGGAGAAATTTT
Found at i:1567359 original size:19 final size:20
Alignment explanation
Indices: 1567332--1567383 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
1567322 TGTATCGATA
*
1567332 CATTATATCGATAAATGT-T
1 CATTGTATCGATAAATGTAT
* *
1567351 CATTGTATCGTTACATGTAT
1 CATTGTATCGATAAATGTAT
*
1567371 AATTGTATCGATA
1 CATTGTATCGATA
1567384 CATGAAACTG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (20 bp):
CATTGTATCGATAAATGTAT
Found at i:1567453 original size:20 final size:20
Alignment explanation
Indices: 1567430--1567495 Score: 83
Period size: 20 Copynumber: 3.6 Consensus size: 20
1567420 ATCGATACAA
1567430 TGTATCGATACATGATAAAT
1 TGTATCGATACATGATAAAT
1567450 TGTATCGATAC------AA-
1 TGTATCGATACATGATAAAT
1567463 TGTATCGATACATGATAAAT
1 TGTATCGATACATGATAAAT
1567483 TGTATCGATACAT
1 TGTATCGATACAT
1567496 TGCTTCCAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 14
0.74 0.00 0.26
Matches are distributed among these distances:
13 11 0.28
14 2 0.05
19 2 0.05
20 24 0.62
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (20 bp):
TGTATCGATACATGATAAAT
Found at i:1567458 original size:33 final size:33
Alignment explanation
Indices: 1567416--1567494 Score: 158
Period size: 33 Copynumber: 2.4 Consensus size: 33
1567406 CTACCGCTGT
1567416 TTGTATCGATACAATGTATCGATACATGATAAA
1 TTGTATCGATACAATGTATCGATACATGATAAA
1567449 TTGTATCGATACAATGTATCGATACATGATAAA
1 TTGTATCGATACAATGTATCGATACATGATAAA
1567482 TTGTATCGATACA
1 TTGTATCGATACA
1567495 TTGCTTCCAA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.34
Consensus pattern (33 bp):
TTGTATCGATACAATGTATCGATACATGATAAA
Found at i:1567492 original size:13 final size:13
Alignment explanation
Indices: 1567417--1567474 Score: 65
Period size: 13 Copynumber: 4.9 Consensus size: 13
1567407 TACCGCTGTT
1567417 TGTATCGATACAA
1 TGTATCGATACAA
1567430 TGTATCGATAC-A
1 TGTATCGATACAA
*
1567442 TG-AT--A-A-AT
1 TGTATCGATACAA
1567450 TGTATCGATACAA
1 TGTATCGATACAA
1567463 TGTATCGATACA
1 TGTATCGATACA
1567475 TGATAAATTG
Statistics
Matches: 37, Mismatches: 2, Indels: 12
0.73 0.04 0.24
Matches are distributed among these distances:
8 3 0.08
9 3 0.08
11 3 0.08
12 4 0.11
13 24 0.65
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1567497 original size:13 final size:13
Alignment explanation
Indices: 1567416--1567497 Score: 62
Period size: 13 Copynumber: 7.2 Consensus size: 13
1567406 CTACCGCTGT
1567416 TTGTATCGATACA
1 TTGTATCGATACA
*
1567429 ATGTATCGATACA
1 TTGTATCGATACA
1567442 -TG-AT--A-A-A
1 TTGTATCGATACA
1567449 TTGTATCGATACA
1 TTGTATCGATACA
*
1567462 ATGTATCGATACA
1 TTGTATCGATACA
1567475 -TG-AT--A-A-A
1 TTGTATCGATACA
1567482 TTGTATCGATACA
1 TTGTATCGATACA
1567495 TTG
1 TTG
1567498 CTTCCAACGG
Statistics
Matches: 55, Mismatches: 2, Indels: 24
0.68 0.02 0.30
Matches are distributed among these distances:
7 2 0.04
8 6 0.11
9 6 0.11
11 6 0.11
12 6 0.11
13 29 0.53
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1572177 original size:52 final size:52
Alignment explanation
Indices: 1572026--1572156 Score: 244
Period size: 52 Copynumber: 2.5 Consensus size: 52
1572016 TCTGAAATAT
1572026 GAAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGG
*
1572078 GAAAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGG
1 GAAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGG
*
1572130 GCAAATTTGCCTGCATGTATCGATACA
1 GAAAATTTGCCTGCATGTATCGATACA
1572157 AAGATCAGTG
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 77 1.00
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (52 bp):
GAAAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGG
Found at i:1572240 original size:32 final size:33
Alignment explanation
Indices: 1572196--1572261 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
1572186 AGTAGCTTAT
* *
1572196 ATTGTATTGATACAAAAC-TTATGTATTGATAC
1 ATTGTATCGATACAAAACTTTATGTATCGATAC
*
1572228 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAACTTTATGTATCGATAC
1572261 A
1 A
1572262 AGTCATTGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.53
33 14 0.47
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (33 bp):
ATTGTATCGATACAAAACTTTATGTATCGATAC
Found at i:1573214 original size:55 final size:52
Alignment explanation
Indices: 1573150--1573565 Score: 276
Period size: 43 Copynumber: 8.8 Consensus size: 52
1573140 CGATATTGGG
* *
1573150 CTTAAAGATGAGAAAAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAA
1 CTTAAAGATG-G-AAAAGG-TGCCAATATGCTGATTCAAGGCCAGCTACATTGAA
* * * *
1573205 CTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCTAGCTATATTGGA
1 CTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAA
* * *
1573257 C-T-----T---AAAGGTACCAATGTGCTGATTCAAGGCCAGCTACATTGGA
1 CTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAA
* * * *
1573300 CTTAAAGA---AGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGA
1 CTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAA
* *
1573349 C-T-----T---AAAGGTGCCAATATGTTGATTCAAGGCCAGCTACATTGGA
1 CTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAA
*
1573392 C-T-----T---AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATT-AGA
1 CTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGA-A
* * * *
1573435 CTTAAAGA---AGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGA
1 CTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAA
* *
1573484 C-T-----T---AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGA
1 CTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAA
1573527 CTTAAAGAT-G--AAGGTGCCAATATGCTGATTCAAGGCCAG
1 CTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAG
1573566 GGATATTGGG
Statistics
Matches: 303, Mismatches: 33, Indels: 56
0.77 0.08 0.14
Matches are distributed among these distances:
43 149 0.49
44 3 0.01
46 1 0.00
48 2 0.01
49 100 0.33
51 1 0.00
52 31 0.10
53 5 0.02
54 1 0.00
55 10 0.03
ACGTcount: A:0.33, C:0.18, G:0.25, T:0.25
Consensus pattern (52 bp):
CTTAAAGATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAA
Found at i:1573285 original size:43 final size:43
Alignment explanation
Indices: 1573221--1573565 Score: 420
Period size: 43 Copynumber: 7.6 Consensus size: 43
1573211 GATGGAAAAT
* *
1573221 GTGCCAATATGCTGATTCAAGGCTAGCTATATTGGACTTAAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
* *
1573264 GTACCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT-----A-AAG
* *
1573313 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
*
1573356 GTGCCAATATGTTGATTCAAGGCCAGCTACATTGGACTTAAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
* *
1573399 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTAGACTTAAAGAAGAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT-----A-AAG
* *
1573448 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
*
1573491 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAG
1 GTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT----A--AAG
1573540 GTGCCAATATGCTGATTCAAGGCCAG
1 GTGCCAATATGCTGATTCAAGGCCAG
1573566 GGATATTGGG
Statistics
Matches: 262, Mismatches: 22, Indels: 30
0.83 0.07 0.10
Matches are distributed among these distances:
43 153 0.58
44 2 0.01
47 1 0.00
48 2 0.01
49 104 0.40
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (43 bp):
GTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAG
Found at i:1573356 original size:92 final size:86
Alignment explanation
Indices: 1573221--1573565 Score: 420
Period size: 92 Copynumber: 3.8 Consensus size: 86
1573211 GATGGAAAAT
* * * *
1573221 GTGCCAATATGCTGATTCAAGGCTAGCTATATTGGACTTAAAGGTACCAATGTGCTGATTCAAGG
1 GTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTGCCAATATGCTGATTCAAGG
1573286 CCAGCTACATTGGACTTAAAGAAGAAG
66 CCAGCTACATTGGACTT-----A-AAG
* * *
1573313 GTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATATGTTGATTCAAGG
1 GTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTGCCAATATGCTGATTCAAGG
1573378 CCAGCTACATTGGACTTAAAG
66 CCAGCTACATTGGACTTAAAG
* *
1573399 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTAGACTTAAAGAAGAAGGTGCCAATATGCTGAT
1 GTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT-----A-AAGGTGCCAATATGCTGAT
* *
1573464 TCAAGGCCAGCGATATTGGACTTAAAG
60 TCAAGGCCAGCTACATTGGACTTAAAG
*
1573491 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGAT
1 GTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT----A--AAGGTGCCAATATGCTGAT
1573556 TCAAGGCCAG
60 TCAAGGCCAG
1573566 GGATATTGGG
Statistics
Matches: 231, Mismatches: 15, Indels: 14
0.89 0.06 0.05
Matches are distributed among these distances:
86 38 0.16
87 1 0.00
91 4 0.02
92 188 0.81
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (86 bp):
GTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTGCCAATATGCTGATTCAAGG
CCAGCTACATTGGACTTAAAG
Found at i:1573377 original size:21 final size:21
Alignment explanation
Indices: 1573310--1573377 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
1573300 CTTAAAGAAG
*
1573310 AAGGTGCCAATATGCTGATTC
1 AAGGTGCCAATATGTTGATTC
* *
1573331 AA-G-GCCAGCGATAT-TGGACTTA
1 AAGGTGCCA---ATATGTTGA-TTC
1573353 AAGGTGCCAATATGTTGATTC
1 AAGGTGCCAATATGTTGATTC
1573374 AAGG
1 AAGG
1573378 CCAGCTACAT
Statistics
Matches: 35, Mismatches: 5, Indels: 14
0.65 0.09 0.26
Matches are distributed among these distances:
19 4 0.11
20 1 0.03
21 14 0.40
22 11 0.31
23 1 0.03
24 4 0.11
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.26
Consensus pattern (21 bp):
AAGGTGCCAATATGTTGATTC
Found at i:1573463 original size:135 final size:135
Alignment explanation
Indices: 1573221--1573565 Score: 573
Period size: 135 Copynumber: 2.5 Consensus size: 135
1573211 GATGGAAAAT
* * *
1573221 GTGCCAATATGCTGATTCAAGGCTAGCTATATTGGACTTAAAGGTACCAATGTGCTGATTCAAGG
1 GTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGG
*
1573286 CCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACT
66 CCAGCTACATTAGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACT
1573351 TAAAG
131 TAAAG
*
1573356 GTGCCAATATGTTGATTCAAGGCCAGCTACATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGG
1 GTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGG
1573421 CCAGCTACATTAGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACT
66 CCAGCTACATTAGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACT
1573486 TAAAG
131 TAAAG
* *
1573491 GTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGAT
1 GTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTT----A--AAGGTGCCAATGTGCTGAT
1573556 TCAAGGCCAG
60 TCAAGGCCAG
1573566 GGATATTGGG
Statistics
Matches: 196, Mismatches: 8, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
135 167 0.85
139 1 0.01
141 28 0.14
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (135 bp):
GTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGG
CCAGCTACATTAGACTTAAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACT
TAAAG
Found at i:1573620 original size:32 final size:32
Alignment explanation
Indices: 1573572--1574026 Score: 622
Period size: 32 Copynumber: 14.2 Consensus size: 32
1573562 CCAGGGATAT
1573572 TGGGC-TTAGA-AGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
* *
1573602 TGGGCTTTAAAGAGGGTTGCCACCAACTTGTG
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
* * *
1573634 TGGGCTTTGGGGAGGGTTGCCACCAACTTGTG
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
*
1573666 TGGGCTTTAGA-AGGGATTGCCACCAACTTGTG
1 TGGGCTTTAGAGAGGG-TTGCCACCGACTTGTG
* * *
1573698 TGGGCTTTAGAAGAAGGTTGCCAACGACTTATG
1 TGGGCTTTAG-AGAGGGTTGCCACCGACTTGTG
* * *
1573731 TGGGCTTT-GGGAAGGGCTGCCACTGACTTGTG
1 TGGGCTTTAGAG-AGGGTTGCCACCGACTTGTG
1573763 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
*
1573795 TGGGCTTTAG-GAAAGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAG-AGGGTTGCCACCGACTTGTG
1573827 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
*
1573859 TGGGCTTT-GGGAAGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAG-AGGGTTGCCACCGACTTGTG
1573891 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
*
1573923 TGGGCTTT-GGGAAGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAG-AGGGTTGCCACCGACTTGTG
* *
1573955 TGGGATTT-GGGAAGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAG-AGGGTTGCCACCGACTTGTG
1573987 TGGGCTTT-GAGAAGGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAG-AGGGTTGCCACCGACTTGTG
1574019 TGGGCTTT
1 TGGGCTTT
1574027 TGAAAAGGGT
Statistics
Matches: 385, Mismatches: 28, Indels: 22
0.89 0.06 0.05
Matches are distributed among these distances:
30 5 0.01
31 14 0.04
32 336 0.87
33 27 0.07
34 3 0.01
ACGTcount: A:0.16, C:0.18, G:0.37, T:0.28
Consensus pattern (32 bp):
TGGGCTTTAGAGAGGGTTGCCACCGACTTGTG
Found at i:1574090 original size:34 final size:35
Alignment explanation
Indices: 1574046--1574119 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
1574036 TGCCACTAAC
* * * *
1574046 TTGTGGGCTTA-AAAGGAAAAAAAGTGCTATGGAG
1 TTGTGAGCTTACAAAAGAAAAAAAGTGCCACGGAG
*
1574080 TTGTGAGCTTACAAAAGAAAAAGAGTGCCACGGAG
1 TTGTGAGCTTACAAAAGAAAAAAAGTGCCACGGAG
1574115 TTGTG
1 TTGTG
1574120 GACTTTGGAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 10 0.29
35 24 0.71
ACGTcount: A:0.36, C:0.09, G:0.31, T:0.23
Consensus pattern (35 bp):
TTGTGAGCTTACAAAAGAAAAAAAGTGCCACGGAG
Found at i:1574147 original size:29 final size:29
Alignment explanation
Indices: 1574098--1574185 Score: 95
Period size: 30 Copynumber: 3.0 Consensus size: 29
1574088 TTACAAAAGA
* * *
1574098 AAAAGAGTGCCACGGAGTTGTGGACTTTGG
1 AAAAGA-TGCCACCGACTTGTGGGCTTTGG
*
1574128 AAAAGATGCCACCGACTTGTGGGCTTCGG
1 AAAAGATGCCACCGACTTGTGGGCTTTGG
* * *
1574157 AAAAGGGTGCCACTGATTTGTGGGCTTTG
1 AAAA-GATGCCACCGACTTGTGGGCTTTG
1574186 AAGGTTAAAG
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
29 23 0.47
30 26 0.53
ACGTcount: A:0.24, C:0.17, G:0.34, T:0.25
Consensus pattern (29 bp):
AAAAGATGCCACCGACTTGTGGGCTTTGG
Found at i:1574149 original size:128 final size:129
Alignment explanation
Indices: 1574004--1574247 Score: 330
Period size: 128 Copynumber: 1.9 Consensus size: 129
1573994 TGAGAAGGGT
**
1574004 TGCCACCGACTTGTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTAAAAGGAAAAAAA
1 TGCCACCGACTTGTGTGGGCTTCGGAAAAGGGTGCCACTAACTTGTGGGCTTAAAAGGAAAAAAA
*
1574069 GTGCTATGGAGTTGTGAGCTTACAAAAGAAAAAGAGTGCCACGGAGTTGTGGACTTTGGAAAAGA
66 GTGCCATGGAGTTGTGAGCTT-CAAAAGAAAAAGAGTGCCACGGAGTTGTGGACTTTGGAAAAGA
* * ** ** *
1574134 TGCCACCGAC-T-TGTGGGCTTCGGAAAAGGGTGCCACTGATTTGTGGGCTTTGAAGGTTAAAGA
1 TGCCACCGACTTGTGTGGGCTTCGGAAAAGGGTGCCACTAACTTGTGGGCTTAAAAGGAAAAAAA
* ** * *
1574197 GTGCCATGGAGTTGTGGGCTTGGAAGGAAAAAGAGTGCCATGGAGTTGTGG
66 GTGCCATGGAGTTGTGAGCTTCAAAAGAAAAAGAGTGCCACGGAGTTGTGG
1574248 GCTTAAAATG
Statistics
Matches: 99, Mismatches: 15, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
127 26 0.26
128 62 0.63
129 1 0.01
130 10 0.10
ACGTcount: A:0.28, C:0.14, G:0.34, T:0.25
Consensus pattern (129 bp):
TGCCACCGACTTGTGTGGGCTTCGGAAAAGGGTGCCACTAACTTGTGGGCTTAAAAGGAAAAAAA
GTGCCATGGAGTTGTGAGCTTCAAAAGAAAAAGAGTGCCACGGAGTTGTGGACTTTGGAAAAGA
Found at i:1574212 original size:34 final size:34
Alignment explanation
Indices: 1574046--1574251 Score: 144
Period size: 34 Copynumber: 6.3 Consensus size: 34
1574036 TGCCACTAAC
** * *
1574046 TTGTGGGCTTAAAAGGAAAAAAAGTGCTATGGAG
1 TTGTGGGCTTGGAAGGAAAAAGAGTGCCATGGAG
* ** * *
1574080 TTGTGAGCTTACAAAAGAAAAAGAGTGCCACGGAG
1 TTGTGGGCTT-GGAAGGAAAAAGAGTGCCATGGAG
* * ** *
1574115 TTGTGGACTT---TGG-AAAAGA-TGCCACCGAC
1 TTGTGGGCTTGGAAGGAAAAAGAGTGCCATGGAG
* * *
1574144 TTGTGGGCTT---CGG-AAAAGGGTGCCACT-GAT
1 TTGTGGGCTTGGAAGGAAAAAGAGTGCCA-TGGAG
* **
1574174 TTGTGGGCTTTGAAGGTTAAAGAGTGCCATGGAG
1 TTGTGGGCTTGGAAGGAAAAAGAGTGCCATGGAG
1574208 TTGTGGGCTTGGAAGGAAAAAGAGTGCCATGGAG
1 TTGTGGGCTTGGAAGGAAAAAGAGTGCCATGGAG
1574242 TTGTGGGCTT
1 TTGTGGGCTT
1574252 AAAATGGTGC
Statistics
Matches: 140, Mismatches: 24, Indels: 16
0.78 0.13 0.09
Matches are distributed among these distances:
29 24 0.17
30 23 0.16
31 1 0.01
33 3 0.02
34 62 0.44
35 27 0.19
ACGTcount: A:0.29, C:0.12, G:0.34, T:0.25
Consensus pattern (34 bp):
TTGTGGGCTTGGAAGGAAAAAGAGTGCCATGGAG
Found at i:1574255 original size:27 final size:26
Alignment explanation
Indices: 1574225--1574284 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 26
1574215 CTTGGAAGGA
*
1574225 AAAAGAGTGCCA-TGGAGTTGTGGGCTT
1 AAAAG-GTGCCACT-GAGTTGTGGACTT
1574252 AAAATGGTGCCACTGAGTTGTGGACTT
1 AAAA-GGTGCCACTGAGTTGTGGACTT
1574279 AAAAGG
1 AAAAGG
1574285 AAAAGAGTGC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 2 0.07
27 26 0.87
28 2 0.07
ACGTcount: A:0.30, C:0.12, G:0.33, T:0.25
Consensus pattern (26 bp):
AAAAGGTGCCACTGAGTTGTGGACTT
Found at i:1574287 original size:128 final size:127
Alignment explanation
Indices: 1574004--1574315 Score: 308
Period size: 128 Copynumber: 2.4 Consensus size: 127
1573994 TGAGAAGGGT
* ** * **
1574004 TGCCACCGACTTGTGTGGGCTTTTGAAAAGGGTGCCACTAACTTGTGGGCTTAAAAGGAAAAAAA
1 TGCCACCGAC-T-TGTGGACTTAGGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAGGAAAAAAA
*
1574069 GTGCTATGGAGTTGTGAGCTTACAAAAGAAAAAGAGTGCCACGGAGTTGTGGACTTTGGAAAAGA
64 GTGCCATGGAGTTGTGAGCTTACAAAAGAAAAAGAGTGCCACGGAGTTGTGGACTTT-GAAAAGA
* * * ** *
1574134 TGCCACCGACTTGTGGGCTTCGGAAAAGGGTGCCACTGATTTGTGGGCTTTGAAGGTTAAAGAGT
1 TGCCACCGACTTGTGGACTTAGGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAGGAAAAAAAGT
* ** * * * *
1574199 GCCATGGAGTTGTGGGCTT-GGAAGGAAAAAGAGTGCCATGGAGTTGTGGGC-TT-AAAATGG
66 GCCATGGAGTTGTGAGCTTACAAAAGAAAAAGAGTGCCACGGAGTTGTGGACTTTGAAAA-GA
* * * *
1574259 TGCCACTGAGTTGTGGACTTAAAAGGAAAAGAGTGCCAC-GTAGTTGTGGGCTTTGAA
1 TGCCACCGACTTGTGGACTT---AGGAAAAGGGTGCCACTG-ACTTGTGGGCTTTGAA
1574316 AAGAAGGTGC
Statistics
Matches: 154, Mismatches: 23, Indels: 12
0.81 0.12 0.06
Matches are distributed among these distances:
124 4 0.03
125 18 0.12
126 2 0.01
127 28 0.18
128 91 0.59
129 1 0.01
130 10 0.06
ACGTcount: A:0.28, C:0.14, G:0.33, T:0.25
Consensus pattern (127 bp):
TGCCACCGACTTGTGGACTTAGGAAAAGGGTGCCACTGACTTGTGGGCTTTGAAGGAAAAAAAGT
GCCATGGAGTTGTGAGCTTACAAAAGAAAAAGAGTGCCACGGAGTTGTGGACTTTGAAAAGA
Found at i:1574304 original size:60 final size:61
Alignment explanation
Indices: 1574197--1574311 Score: 162
Period size: 60 Copynumber: 1.9 Consensus size: 61
1574187 AGGTTAAAGA
* ** *
1574197 GTGCCATGGAGTTGTGGGCTTGGAAGGAAAAAGAGTGCCATGGAGTTGTGGGCTTAAAATG
1 GTGCCATGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAATG
*
1574258 GTGCCACT-GAGTTGTGGACTTAAAAGG-AAAAGAGTGCCACGTAGTTGTGGGCTT
1 GTGCCA-TGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
1574312 TGAAAAGAAG
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
60 25 0.52
61 22 0.46
62 1 0.02
ACGTcount: A:0.26, C:0.12, G:0.37, T:0.25
Consensus pattern (61 bp):
GTGCCATGGAGTTGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAATG
Found at i:1574329 original size:31 final size:29
Alignment explanation
Indices: 1574284--1574343 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 29
1574274 GACTTAAAAG
* * *
1574284 GAAAAGAGTGCCACGTAGTTGTGGGCTTT
1 GAAAAGAGTGCCACGGAGTCGTGGACTTT
1574313 GAAAAGAAGGTGCCACGGAGTCGTGGACTTT
1 GAAAAG-A-GTGCCACGGAGTCGTGGACTTT
1574344 AAGAAGGTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
29 6 0.23
30 1 0.04
31 19 0.73
ACGTcount: A:0.27, C:0.15, G:0.35, T:0.23
Consensus pattern (29 bp):
GAAAAGAGTGCCACGGAGTCGTGGACTTT
Found at i:1575592 original size:15 final size:15
Alignment explanation
Indices: 1575563--1575592 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1575553 CTTTTTTCTG
*
1575563 TGTTTTTTTTTGTTT
1 TGTTTTTTTGTGTTT
1575578 TGTTTTTTTGTGTTT
1 TGTTTTTTTGTGTTT
1575593 ACTTTTGACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (15 bp):
TGTTTTTTTGTGTTT
Found at i:1582583 original size:13 final size:13
Alignment explanation
Indices: 1582565--1582589 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1582555 CAAAGATCAG
1582565 TGTATCGATACAA
1 TGTATCGATACAA
1582578 TGTATCGATACA
1 TGTATCGATACA
1582590 TTTGAAATGT
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:1582667 original size:13 final size:13
Alignment explanation
Indices: 1582649--1582673 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1582639 ACAAAACTTA
1582649 TGTATCGATACAT
1 TGTATCGATACAT
1582662 TGTATCGATACA
1 TGTATCGATACA
1582674 ACACTTTATG
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:1582669 original size:32 final size:33
Alignment explanation
Indices: 1582628--1582693 Score: 116
Period size: 32 Copynumber: 2.0 Consensus size: 33
1582618 AGTAGCTTAT
1582628 ATTGTATCGATACAAAAC-TTATGTATCGATAC
1 ATTGTATCGATACAAAACTTTATGTATCGATAC
*
1582660 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAACTTTATGTATCGATAC
1582693 A
1 A
1582694 AATTGTATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 17 0.53
33 15 0.47
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (33 bp):
ATTGTATCGATACAAAACTTTATGTATCGATAC
Found at i:1590580 original size:40 final size:41
Alignment explanation
Indices: 1590511--1590601 Score: 130
Period size: 40 Copynumber: 2.2 Consensus size: 41
1590501 ATATTTTGAA
* * *
1590511 ATAAATTTGTTTTATAAAAGGGGAGATTTTGTGGTAGTTTT
1 ATAAATTTGTTTTATAAAAGAGGACATTTTGTGCTAGTTTT
1590552 ATAAATTTG-TTTATAAAAGAGGACATTTTGTGCTAGTTTT
1 ATAAATTTGTTTTATAAAAGAGGACATTTTGTGCTAGTTTT
*
1590592 GTAAAATTTG
1 AT-AAATTTG
1590602 GAGATAATAA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
40 29 0.64
41 16 0.36
ACGTcount: A:0.32, C:0.02, G:0.21, T:0.45
Consensus pattern (41 bp):
ATAAATTTGTTTTATAAAAGAGGACATTTTGTGCTAGTTTT
Found at i:1591350 original size:13 final size:13
Alignment explanation
Indices: 1591332--1591356 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1591322 ATATTACTTA
1591332 GTATCGATATATT
1 GTATCGATATATT
1591345 GTATCGATATAT
1 GTATCGATATAT
1591357 GTTCTGGGTA
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:0.08, G:0.16, T:0.44
Consensus pattern (13 bp):
GTATCGATATATT
Found at i:1591460 original size:13 final size:12
Alignment explanation
Indices: 1591423--1591480 Score: 61
Period size: 13 Copynumber: 5.0 Consensus size: 12
1591413 AACTCACTCA
*
1591423 GTATCGATATAGT
1 GTATCGATACA-T
1591436 GTATCGATACATT
1 GTATCGATACA-T
1591449 GTATCGATACAT
1 GTATCGATACAT
1591461 G-AT-GA-A-AT
1 GTATCGATACAT
1591469 GTATCGATACAT
1 GTATCGATACAT
1591481 TGAGCCCAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
8 3 0.08
9 3 0.08
10 4 0.10
11 3 0.08
12 4 0.10
13 22 0.56
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.34
Consensus pattern (12 bp):
GTATCGATACAT
Found at i:1596674 original size:52 final size:52
Alignment explanation
Indices: 1596526--1596654 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
1596516 CGAAATGTGA
1596526 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
1596578 AAATTTGCCTGTATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
1596630 AAATTTACCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1596655 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:1596681 original size:13 final size:13
Alignment explanation
Indices: 1596663--1596687 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1596653 CAAAGATCAG
1596663 TGTATCGATACAA
1 TGTATCGATACAA
1596676 TGTATCGATACA
1 TGTATCGATACA
1596688 TTTGAGTAAT
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:1596750 original size:13 final size:13
Alignment explanation
Indices: 1596732--1596815 Score: 60
Period size: 13 Copynumber: 5.5 Consensus size: 13
1596722 AGCTTCGTAG
1596732 CGATACATTGTAT
1 CGATACATTGTAT
1596745 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
1596764 CGATACATTGTAT
1 CGATACATTGTAT
1596777 CGATACAACACTTATGTAT
1 CGAT---ACA--T-TGTAT
1596796 CGATACATTGTAT
1 CGATACATTGTAT
1596809 CGATACA
1 CGATACA
1596816 ACACTTATGT
Statistics
Matches: 59, Mismatches: 0, Indels: 24
0.71 0.00 0.29
Matches are distributed among these distances:
13 26 0.44
14 1 0.02
15 2 0.03
16 8 0.14
17 2 0.03
18 1 0.02
19 19 0.32
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:1596764 original size:19 final size:18
Alignment explanation
Indices: 1596740--1596836 Score: 97
Period size: 19 Copynumber: 5.8 Consensus size: 18
1596730 AGCGATACAT
1596740 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
1596759 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
1596772 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
1596791 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
1596804 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
1596823 TGTATCGATACAAA
1 TGTATCGATACAAA
1596837 TCGTTGAAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 25
0.73 0.00 0.27
Matches are distributed among these distances:
13 22 0.33
14 2 0.03
16 4 0.06
18 3 0.05
19 35 0.53
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:1596773 original size:32 final size:32
Alignment explanation
Indices: 1596732--1596834 Score: 197
Period size: 32 Copynumber: 3.2 Consensus size: 32
1596722 AGCTTCGTAG
*
1596732 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
1596764 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
1596796 CGATACATTGTATCGATACAACACTTATGTAT
1 CGATACATTGTATCGATACAACACTTATGTAT
1596828 CGATACA
1 CGATACA
1596835 AATCGTTGAA
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
32 70 1.00
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGTAT
Found at i:1600929 original size:20 final size:20
Alignment explanation
Indices: 1600904--1600966 Score: 90
Period size: 20 Copynumber: 3.1 Consensus size: 20
1600894 TTTTTACCCA
1600904 AATGTATCGATACATTTTTC
1 AATGTATCGATACATTTTTC
* * *
1600924 AATGTATCGATACATGTATG
1 AATGTATCGATACATTTTTC
*
1600944 AATGTATCGATACATTCTTC
1 AATGTATCGATACATTTTTC
1600964 AAT
1 AAT
1600967 CTCATCGAAG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.33, C:0.14, G:0.13, T:0.40
Consensus pattern (20 bp):
AATGTATCGATACATTTTTC
Found at i:1601306 original size:10 final size:10
Alignment explanation
Indices: 1601291--1601342 Score: 77
Period size: 10 Copynumber: 5.1 Consensus size: 10
1601281 CGTCCTTCGT
1601291 ACCAAAAAAA
1 ACCAAAAAAA
1601301 ACCAAAAAAA
1 ACCAAAAAAA
*
1601311 AACAAAAAAA
1 ACCAAAAAAA
*
1601321 ACAAAAAAAA
1 ACCAAAAAAA
1601331 ACCAAACAAAA
1 ACCAAA-AAAA
1601342 A
1 A
1601343 AACAAACAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
10 32 0.86
11 5 0.14
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (10 bp):
ACCAAAAAAA
Found at i:1601309 original size:9 final size:9
Alignment explanation
Indices: 1601293--1601352 Score: 59
Period size: 9 Copynumber: 6.4 Consensus size: 9
1601283 TCCTTCGTAC
1601293 CAAAAAAAA
1 CAAAAAAAA
1601302 CCAAAAAAAAA
1 -C-AAAAAAAA
1601313 CAAAAAAAA
1 CAAAAAAAA
1601322 CAAAAAAAAA
1 C-AAAAAAAA
* *
1601332 CCAAACAAA
1 CAAAAAAAA
*
1601341 -AAAACAAA
1 CAAAAAAAA
1601349 CAAA
1 CAAA
1601353 TATAAAAAGG
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
8 7 0.16
9 18 0.41
10 11 0.25
11 8 0.18
ACGTcount: A:0.83, C:0.17, G:0.00, T:0.00
Consensus pattern (9 bp):
CAAAAAAAA
Found at i:1601330 original size:23 final size:23
Alignment explanation
Indices: 1601304--1601348 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1601294 AAAAAAAACC
1601304 AAAAA-AAAACAAAAAAAACAAAA
1 AAAAACAAAAC-AAAAAAACAAAA
*
1601327 AAAAACCAAACAAAAAAACAAA
1 AAAAACAAAACAAAAAAACAAA
1601349 CAAATATAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.87, C:0.13, G:0.00, T:0.00
Consensus pattern (23 bp):
AAAAACAAAACAAAAAAACAAAA
Found at i:1601348 original size:12 final size:12
Alignment explanation
Indices: 1601294--1601352 Score: 70
Period size: 12 Copynumber: 5.1 Consensus size: 12
1601284 CCTTCGTACC
*
1601294 AAAAA-AAACCA
1 AAAAACAAACAA
1601305 AAAAA-AAACAAA
1 AAAAACAAAC-AA
1601317 AAAAACAAA-AA
1 AAAAACAAACAA
*
1601328 AAAACCAAACAA
1 AAAAACAAACAA
1601340 AAAAACAAACAA
1 AAAAACAAACAA
1601352 A
1 A
1601353 TATAAAAAGG
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
11 19 0.45
12 20 0.48
13 3 0.07
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAACAAACAA
Found at i:1602640 original size:28 final size:28
Alignment explanation
Indices: 1602600--1602927 Score: 358
Period size: 28 Copynumber: 11.7 Consensus size: 28
1602590 CTAGAATGTT
* * * *
1602600 CATCACTTCAAAGTCCACAAGTCAATTG
1 CATCCCTTCAAAGCCCACAAGTCAGTGG
1602628 CATCCCTTCAAAGCCCACAAGTCAGTGG
1 CATCCCTTCAAAGCCCACAAGTCAGTGG
*
1602656 CATCCTTTCAAAGCCCACAAGTCAGTGG
1 CATCCCTTCAAAGCCCACAAGTCAGTGG
* *
1602684 CATCCTTTCAAAGCCCACAAGTTAGTGG
1 CATCCCTTCAAAGCCCACAAGTCAGTGG
1602712 CA-CCCTTTTCAAAGCCCACAAGTCAGTGG
1 CATCCC--TTCAAAGCCCACAAGTCAGTGG
* *
1602741 CATCCTTTCAAAGCCCACAAGTTAGTGG
1 CATCCCTTCAAAGCCCACAAGTCAGTGG
* *
1602769 CA-CCTTTTCATAGCCCACAAGTCAGTGG
1 CATCC-CTTCAAAGCCCACAAGTCAGTGG
* * *
1602797 CA-CCTTTTCATAGCCCACAAGTCAGTAG
1 CATCC-CTTCAAAGCCCACAAGTCAGTGG
** *
1602825 C-TCATTTTCAAAGCCCACAAGTCAGTGC
1 CATC-CCTTCAAAGCCCACAAGTCAGTGG
*
1602853 CATCCTTTCAAAGCCCACAAGTCAGTGG
1 CATCCCTTCAAAGCCCACAAGTCAGTGG
* *** *
1602881 CGTTTTTTCAAAGTCCACAAGTCAGTGG
1 CATCCCTTCAAAGCCCACAAGTCAGTGG
* *
1602909 CATCCTTTTAAAGCCCACA
1 CATCCCTTCAAAGCCCACA
1602928 CAAGTCGGTG
Statistics
Matches: 265, Mismatches: 28, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
27 4 0.02
28 234 0.88
29 25 0.09
30 2 0.01
ACGTcount: A:0.29, C:0.31, G:0.16, T:0.24
Consensus pattern (28 bp):
CATCCCTTCAAAGCCCACAAGTCAGTGG
Found at i:1602694 original size:56 final size:56
Alignment explanation
Indices: 1602606--1602927 Score: 434
Period size: 56 Copynumber: 5.7 Consensus size: 56
1602596 TGTTCATCAC
* * * *
1602606 TTCAAAGTCCACAAGTCAATTGCATCCCTTCAAAGCCCACAAGTCAGTGGCATCCT
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCT
* *
1602662 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCACCCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCC-T
*
1602719 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTTAGTGGCA-CCTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCC-T
* * * *
1602775 TTCATAGCCCACAAGTCAGTGGCA-CCTTTTCATAGCCCACAAGTCAGTAGC-TCATT
1 TTCAAAGCCCACAAGTCAGTGGCATCC-TTTCAAAGCCCACAAGTCAGTGGCATC-CT
* * **
1602831 TTCAAAGCCCACAAGTCAGTGCCATCCTTTCAAAGCCCACAAGTCAGTGGCGTTTT
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCT
* *
1602887 TTCAAAGTCCACAAGTCAGTGGCATCCTTTTAAAGCCCACA
1 TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACA
1602928 CAAGTCGGTG
Statistics
Matches: 241, Mismatches: 19, Indels: 12
0.89 0.07 0.04
Matches are distributed among these distances:
55 2 0.01
56 183 0.76
57 56 0.23
ACGTcount: A:0.29, C:0.31, G:0.16, T:0.24
Consensus pattern (56 bp):
TTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCCCACAAGTCAGTGGCATCCT
Found at i:1602834 original size:84 final size:84
Alignment explanation
Indices: 1602606--1602927 Score: 443
Period size: 84 Copynumber: 3.8 Consensus size: 84
1602596 TGTTCATCAC
* * * *
1602606 TTCAAAGTCCACAAGTCAATTGCATCC-CTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGC
1602670 CCACAAGTCAGTGGCATCCT
65 CCACAAGTCAGTGGCATCCT
*
1602690 TTCAAAGCCCACAAGTTAGTGGCACCCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCA-CCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGC
*
1602755 CCACAAGTTAGTGGCA-CCTT
65 CCACAAGTCAGTGGCATCC-T
* * * *
1602775 TTCATAGCCCACAAGTCAGTGGCACCTTTTCATAGCCCACAAGTCAGTAGC-TCATTTTCAAAGC
1 TTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCATC-CTTTCAAAGC
*
1602839 CCACAAGTCAGTGCCATCCT
65 CCACAAGTCAGTGGCATCCT
*** * *
1602859 TTCAAAGCCCACAAGTCAGTGGCGTTTTTTCAAAGTCCACAAGTCAGTGGCATCCTTTTAAAGCC
1 TTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCC
1602924 CACA
66 CACA
1602928 CAAGTCGGTG
Statistics
Matches: 210, Mismatches: 23, Indels: 10
0.86 0.09 0.04
Matches are distributed among these distances:
83 2 0.01
84 130 0.62
85 78 0.37
ACGTcount: A:0.29, C:0.31, G:0.16, T:0.24
Consensus pattern (84 bp):
TTCAAAGCCCACAAGTCAGTGGCACCTTTTCAAAGCCCACAAGTCAGTGGCATCCTTTCAAAGCC
CACAAGTCAGTGGCATCCT
Found at i:1602960 original size:32 final size:32
Alignment explanation
Indices: 1602917--1603006 Score: 153
Period size: 32 Copynumber: 2.8 Consensus size: 32
1602907 GGCATCCTTT
*
1602917 TAAAGCCCACACAAGTCGGTGGTAACTTTCTC
1 TAAAGCCCACACAAGTTGGTGGTAACTTTCTC
* *
1602949 TAAGGCCCACACAAGTTGGTGGCAACTTTCTC
1 TAAAGCCCACACAAGTTGGTGGTAACTTTCTC
1602981 TAAAGCCCACACAAGTTGGTGGTAAC
1 TAAAGCCCACACAAGTTGGTGGTAAC
1603007 CCTTCTAAAC
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 53 1.00
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (32 bp):
TAAAGCCCACACAAGTTGGTGGTAACTTTCTC
Found at i:1603756 original size:20 final size:20
Alignment explanation
Indices: 1603731--1603893 Score: 146
Period size: 20 Copynumber: 7.6 Consensus size: 20
1603721 TACCCAGATA
1603731 TATCGATACATTTTTCAATG
1 TATCGATACATTTTTCAATG
* * * *
1603751 TATCGATATATGTATGAATG
1 TATCGATACATTTTTCAATG
1603771 TATCGATACATTTTTCAATG
1 TATCGATACATTTTTCAATG
*
1603791 TATCGATACATTTTGTCTTTTTACACAGATA
1 TATCGATACA-------TTTTT---CA-ATG
1603822 TATCGATACATTTTTCAATG
1 TATCGATACATTTTTCAATG
* * *
1603842 TATCGATACATGTATGAATG
1 TATCGATACATTTTTCAATG
*
1603862 TATCGATACATTCTTCAATG
1 TATCGATACATTTTTCAATG
1603882 TATCGATACATT
1 TATCGATACATT
1603894 CTGTCTTTTT
Statistics
Matches: 115, Mismatches: 17, Indels: 22
0.75 0.11 0.14
Matches are distributed among these distances:
20 89 0.77
21 2 0.02
24 5 0.04
27 5 0.04
30 2 0.02
31 12 0.10
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.42
Consensus pattern (20 bp):
TATCGATACATTTTTCAATG
Found at i:1603786 original size:40 final size:40
Alignment explanation
Indices: 1603731--1603889 Score: 165
Period size: 40 Copynumber: 3.7 Consensus size: 40
1603721 TACCCAGATA
1603731 TATCGATACATTTTTCAATGTATCGATATATGTATGAATG
1 TATCGATACATTTTTCAATGTATCGATATATGTATGAATG
* ** *
1603771 TATCGATACATTTTTCAATGTATCGATACATTTTGTCTTTTTACACAGATA
1 TATCGATACATTTTTCAATGTATCGAT--A-TATG------TA-TGA-ATG
*
1603822 TATCGATACATTTTTCAATGTATCGATACATGTATGAATG
1 TATCGATACATTTTTCAATGTATCGATATATGTATGAATG
*
1603862 TATCGATACATTCTTCAATGTATCGATA
1 TATCGATACATTTTTCAATGTATCGATA
1603890 CATTCTGTCT
Statistics
Matches: 98, Mismatches: 10, Indels: 22
0.75 0.08 0.17
Matches are distributed among these distances:
40 56 0.57
41 1 0.01
42 3 0.03
43 3 0.03
48 2 0.02
49 3 0.03
50 1 0.01
51 29 0.30
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (40 bp):
TATCGATACATTTTTCAATGTATCGATATATGTATGAATG
Found at i:1603847 original size:51 final size:50
Alignment explanation
Indices: 1603768--1603943 Score: 210
Period size: 51 Copynumber: 3.7 Consensus size: 50
1603758 ATATGTATGA
1603768 ATGTATCGATACATTTTTCAATGTATCGATACATTTTGTCTTTTTACACAG
1 ATGTATCGATACATTTTTCAATGTATCGATACA-TTTGTCTTTTTACACAG
* **
1603819 ATATATCGATACATTTTTCAATGTATCGATACA--TG------TA-TGA-
1 ATGTATCGATACATTTTTCAATGTATCGATACATTTGTCTTTTTACACAG
* *
1603859 ATGTATCGATACATTCTTCAATGTATCGATACATTCTGTCTTTTTACCCAG
1 ATGTATCGATACATTTTTCAATGTATCGATACATT-TGTCTTTTTACACAG
*
1603910 ATGTATCGATACATTATTCAATGTATCGATACAT
1 ATGTATCGATACATTTTTCAATGTATCGATACAT
1603944 CTAGTTAAAT
Statistics
Matches: 106, Mismatches: 8, Indels: 22
0.78 0.06 0.16
Matches are distributed among these distances:
40 31 0.29
41 1 0.01
42 2 0.02
43 2 0.02
48 2 0.02
49 2 0.02
50 1 0.01
51 65 0.61
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.41
Consensus pattern (50 bp):
ATGTATCGATACATTTTTCAATGTATCGATACATTTGTCTTTTTACACAG
Found at i:1603872 original size:91 final size:91
Alignment explanation
Indices: 1603717--1603943 Score: 400
Period size: 91 Copynumber: 2.5 Consensus size: 91
1603707 AAAAGTCACA
*
1603717 TTTTTACCCAGATATATCGATACATTTTTCAATGTATCGATATATGTATGAATGTATCGATACAT
1 TTTTTACCCAGATATATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACAT
* *
1603782 TTTTCAATGTATCGATACATTTTGTC
66 TCTTCAATGTATCGATACATTCTGTC
*
1603808 TTTTTACACAGATATATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACAT
1 TTTTTACCCAGATATATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACAT
1603873 TCTTCAATGTATCGATACATTCTGTC
66 TCTTCAATGTATCGATACATTCTGTC
* *
1603899 TTTTTACCCAGATGTATCGATACATTATTCAATGTATCGATACAT
1 TTTTTACCCAGATATATCGATACATTTTTCAATGTATCGATACAT
1603944 CTAGTTAAAT
Statistics
Matches: 129, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
91 129 1.00
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.42
Consensus pattern (91 bp):
TTTTTACCCAGATATATCGATACATTTTTCAATGTATCGATACATGTATGAATGTATCGATACAT
TCTTCAATGTATCGATACATTCTGTC
Found at i:1605591 original size:10 final size:11
Alignment explanation
Indices: 1605576--1605604 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
1605566 CCACTAGATG
1605576 ATTTTTCAAA-
1 ATTTTTCAAAC
1605586 ATTTTTCAAAC
1 ATTTTTCAAAC
1605597 ATTTTTCA
1 ATTTTTCA
1605605 TAAAAACTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (11 bp):
ATTTTTCAAAC
Found at i:1617854 original size:24 final size:24
Alignment explanation
Indices: 1617821--1617874 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 24
1617811 TCCTTCGTAT
1617821 AAAAAAAATAAA-AAACCAAA-AAA
1 AAAAAAAATAAACAAA-CAAATAAA
1617844 AAAAAACAATAAACAAACAAATAAA
1 AAAAAA-AATAAACAAACAAATAAA
1617869 AAAAAA
1 AAAAAA
1617875 GGTCCAGATG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
23 6 0.21
24 10 0.36
25 12 0.43
ACGTcount: A:0.85, C:0.09, G:0.00, T:0.06
Consensus pattern (24 bp):
AAAAAAAATAAACAAACAAATAAA
Found at i:1619159 original size:28 final size:28
Alignment explanation
Indices: 1619120--1619615 Score: 635
Period size: 28 Copynumber: 17.5 Consensus size: 28
1619110 ACATTCTTCT
*
1619120 CTTT-AAAGCCCACAAGTCAGCGGCATC
1 CTTTCAAAGCCCACAAGTCAGTGGCATC
* *
1619147 CTTTGAAAGCCCACAAGTCAATGGCATC
1 CTTTCAAAGCCCACAAGTCAGTGGCATC
*
1619175 CTTTCAAAGCCCACAAGTCATTGGCATC
1 CTTTCAAAGCCCACAAGTCAGTGGCATC
* *
1619203 CTTTCAAAGCCCACAAGTTAGTGGCACC
1 CTTTCAAAGCCCACAAGTCAGTGGCATC
*
1619231 CTTTTCAAAGCCCACAAGTCAGTGGCACC
1 C-TTTCAAAGCCCACAAGTCAGTGGCATC
*
1619260 CTTTTCAAAGCCCATAAGTCAGTGGCATC
1 C-TTTCAAAGCCCACAAGTCAGTGGCATC
1619289 CTTTCAAAGCCCACAAGTCAGTGGCATC
1 CTTTCAAAGCCCACAAGTCAGTGGCATC
1619317 CTTTCAAAGCCCACAAGTCAGTGGCATC
1 CTTTCAAAGCCCACAAGTCAGTGGCATC
1619345 CTTTCAAAGCCCACAAGTCAGTGGCATC
1 CTTTCAAAGCCCACAAGTCAGTGGCATC
* *
1619373 CTTTCAAAACCCACAAGTCAATGGCA-C
1 CTTTCAAAGCCCACAAGTCAGTGGCATC
* **
1619400 CTTTTCATAGCCCACAAGTCAGCAGCA-C
1 C-TTTCAAAGCCCACAAGTCAGTGGCATC
*
1619428 CTTATCATAGCCCACAAGTCAGTGGCA-C
1 CTT-TCAAAGCCCACAAGTCAGTGGCATC
*
1619456 CTTTTCAAAGCCCACAAGTTAGTGGCATC
1 C-TTTCAAAGCCCACAAGTCAGTGGCATC
* *
1619485 CTTTCAAAGCCCACAAGTTAGTGCCATC
1 CTTTCAAAGCCCACAAGTCAGTGGCATC
* * *
1619513 TTTTCAAAGCCCATAAGTCAGAGGCA-C
1 CTTTCAAAGCCCACAAGTCAGTGGCATC
*
1619540 CTTCTCAAAACCCACAAGTCAGTGGCATC
1 CTT-TCAAAGCCCACAAGTCAGTGGCATC
* *
1619569 CTTAT-AAAGCCTACATAAGTCAGTGGCAAC
1 CTT-TCAAAGCC--CACAAGTCAGTGGCATC
*
1619599 TTTCTCTAAAGCCCACA
1 CTT-TC-AAAGCCCACA
1619616 CAAGTTGGTG
Statistics
Matches: 418, Mismatches: 39, Indels: 21
0.87 0.08 0.04
Matches are distributed among these distances:
27 11 0.03
28 317 0.76
29 63 0.15
30 21 0.05
32 6 0.01
ACGTcount: A:0.30, C:0.31, G:0.16, T:0.23
Consensus pattern (28 bp):
CTTTCAAAGCCCACAAGTCAGTGGCATC
Found at i:1620423 original size:20 final size:20
Alignment explanation
Indices: 1620398--1620448 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1620388 ACCCTGATGT
* *
1620398 ATCGATACATTTTTTAATGA
1 ATCGATACATTTATGAATGA
* *
1620418 ATCGATACATGTATGAATGT
1 ATCGATACATTTATGAATGA
1620438 ATCGATACATT
1 ATCGATACATT
1620449 CTATCTTTTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (20 bp):
ATCGATACATTTATGAATGA
Found at i:1620449 original size:71 final size:71
Alignment explanation
Indices: 1620362--1620498 Score: 229
Period size: 71 Copynumber: 1.9 Consensus size: 71
1620352 TACATTCTTC
* * *
1620362 AATGTATCGATACATTCTATCATTTTACCCTGATGTATCGATACATTTTTTAATGAATCGATACA
1 AATGTATCGATACATTCTATCATTTTACCCAGATGTATCGATACATTATTCAATGAATCGATACA
1620427 TGTATG
66 TGTATG
* *
1620433 AATGTATCGATACATTCTATCTTTTTACCCAGATGTATCGATACATTATTCAATGTATCGATACA
1 AATGTATCGATACATTCTATCATTTTACCCAGATGTATCGATACATTATTCAATGAATCGATACA
1620498 T
66 T
1620499 CTAATTAAAT
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
71 61 1.00
ACGTcount: A:0.31, C:0.17, G:0.12, T:0.40
Consensus pattern (71 bp):
AATGTATCGATACATTCTATCATTTTACCCAGATGTATCGATACATTATTCAATGAATCGATACA
TGTATG
Found at i:1624377 original size:16 final size:17
Alignment explanation
Indices: 1624358--1624391 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
1624348 TAGCCAAACT
1624358 TGTATCGATACAA-GTA
1 TGTATCGATACAATGTA
1624374 TGTATCGATACAATGTA
1 TGTATCGATACAATGTA
1624391 T
1 T
1624392 ACACAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (17 bp):
TGTATCGATACAATGTA
Found at i:1628441 original size:15 final size:15
Alignment explanation
Indices: 1628421--1628451 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1628411 TAAAAATGTC
*
1628421 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1628436 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1628451 C
1 C
1628452 CAAACGAAAT
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:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1630706 original size:20 final size:20
Alignment explanation
Indices: 1630663--1630708 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1630653 AAATCTTTTG
1630663 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
1630684 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
1630704 CAAAA
1 CAAAA
1630709 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:1632375 original size:20 final size:20
Alignment explanation
Indices: 1632350--1632390 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
1632340 TGATATGAAT
1632350 TACTTGATTAAGGGGGAGAA
1 TACTTGATTAAGGGGGAGAA
1632370 TACTTGATTAAGGGGGAGAA
1 TACTTGATTAAGGGGGAGAA
1632390 T
1 T
1632391 TATTAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.05, G:0.34, T:0.27
Consensus pattern (20 bp):
TACTTGATTAAGGGGGAGAA
Found at i:1633137 original size:13 final size:13
Alignment explanation
Indices: 1633119--1633144 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1633109 TACAGCAAGT
1633119 ATGTATCGATACA
1 ATGTATCGATACA
1633132 ATGTATCGATACA
1 ATGTATCGATACA
1633145 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1637631 original size:14 final size:16
Alignment explanation
Indices: 1637573--1637624 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
1637563 TCATTTAATA
*
1637573 AATTAAATAAATATAT
1 AATTATATAAATATAT
** *
1637589 TTTTATTTAAAT-T-T
1 AATTATATAAATATAT
1637603 AATTATATAAATATAT
1 AATTATATAAATATAT
1637619 AATTAT
1 AATTAT
1637625 TAATATAAAA
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
14 10 0.37
15 2 0.07
16 15 0.56
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AATTATATAAATATAT
Found at i:1637648 original size:18 final size:20
Alignment explanation
Indices: 1637605--1637648 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
1637595 TTAAATTTAA
1637605 TTATATAAATATATAATTAT
1 TTATATAAATATATAATTAT
* *
1637625 TAATATAAA-A-ATAATTTT
1 TTATATAAATATATAATTAT
1637643 TTATAT
1 TTATAT
1637649 TTTAAATAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 12 0.57
19 1 0.05
20 8 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTATATAAATATATAATTAT
Found at i:1638442 original size:169 final size:164
Alignment explanation
Indices: 1638161--1638487 Score: 447
Period size: 169 Copynumber: 2.0 Consensus size: 164
1638151 TTTTTTTCCA
* * * *
1638161 TTTTTTTCATAACTATGATCCTTTTTTATTTTCTTATGAGCTAATTATTGGAATAAAAATGTTTT
1 TTTTTTTCATAACTATGATCCCTTTTTATTTTCTTATGAGCCAATAATTGAAATAAAAATGTTTT
* * * * *
1638226 CATCATTATTTAATTAAAAAAATTCCAGATTATTTGTTCAGGCTGAATCCACTAGATTGTCCAAC
66 CATCATAATTTAATTAAAAAAATTCCACACTATTTGTTCAGGCTGAATCCACCAGATTATCCAAC
* *
1638291 TTGAGGCTGAAACCCCATGAAAAGCTTGCTTTTT
131 TGGAGGATGAAACCCCATGAAAAGCTTGCTTTTT
* *
1638325 TTTTTTTCATAATTATGATCTCCTTTTTGTTTTCTTATGAGCCAATAAATTGAAATAAAAAATGT
1 TTTTTTTCATAACTATGATC-CCTTTTTATTTTCTTATGAGCCAAT-AATTGAAAT-AAAAATGT
* *
1638390 TTTCATCATAATTTATTTAAAAAATATTACGACACTATTTGTTCAGGCTGAATCCACCAGATTAT
63 TTTCATCATAATTTAATTAAAAAA-ATT-CCACACTATTTGTTCAGGCTGAATCCACCAGATTAT
* * *
1638455 CCAACTGGGGGATGAAACCCCGTGAGAAGCTTG
126 CCAACTGGAGGATGAAACCCCATGAAAAGCTTG
1638488 TTTGTGGTGG
Statistics
Matches: 140, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
164 19 0.14
165 22 0.16
166 7 0.05
167 30 0.21
168 3 0.02
169 59 0.42
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (164 bp):
TTTTTTTCATAACTATGATCCCTTTTTATTTTCTTATGAGCCAATAATTGAAATAAAAATGTTTT
CATCATAATTTAATTAAAAAAATTCCACACTATTTGTTCAGGCTGAATCCACCAGATTATCCAAC
TGGAGGATGAAACCCCATGAAAAGCTTGCTTTTT
Found at i:1638794 original size:2 final size:2
Alignment explanation
Indices: 1638787--1638820 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
1638777 AAGCTTGTAA
1638787 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1638821 TGAGCTTTGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1639736 original size:3 final size:3
Alignment explanation
Indices: 1639723--1639751 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
1639713 AAACTAGCCT
1639723 CTC CT- CTC CTC CTC CTC CTC CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
1639752 TTCCACACAG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (3 bp):
CTC
Found at i:1642891 original size:13 final size:13
Alignment explanation
Indices: 1642858--1642888 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1642848 TACTACGATT
1642858 ATAATTAAATTAA
1 ATAATTAAATTAA
1642871 ATAATTAAATT-A
1 ATAATTAAATTAA
1642883 ATAATT
1 ATAATT
1642889 TAATAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.39
13 11 0.61
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
ATAATTAAATTAA
Found at i:1647936 original size:33 final size:33
Alignment explanation
Indices: 1647894--1647959 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
1647884 TGGCAGAAGA
*
1647894 ACAGGAACCACTTTCAGTAGTAGTGAAAAACTG
1 ACAGGAACCACTTTCAGTAGTAGGGAAAAACTG
*
1647927 ACAGGAACCACTTTCATTAGTAGGGAAAAACTG
1 ACAGGAACCACTTTCAGTAGTAGGGAAAAACTG
1647960 GTTTCAAGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.21
Consensus pattern (33 bp):
ACAGGAACCACTTTCAGTAGTAGGGAAAAACTG
Found at i:1652973 original size:33 final size:33
Alignment explanation
Indices: 1652908--1652969 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
1652898 TGGCAGAAGA
1652908 ACAGGAACCACTTTCAGTAGTAGTGGAAAACTG
1 ACAGGAACCACTTTCAGTAGTAGTGGAAAACTG
*
1652941 ACAGGAACCACTTTCATTAGTAG-GGAAAA
1 ACAGGAACCACTTTCAGTAGTAGTGGAAAA
1652970 ACTGGTTTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
32 6 0.21
33 22 0.79
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.21
Consensus pattern (33 bp):
ACAGGAACCACTTTCAGTAGTAGTGGAAAACTG
Found at i:1653440 original size:33 final size:33
Alignment explanation
Indices: 1653392--1653457 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
1653382 CTACTTGAAA
1653392 CCAGTTTTTCCCTACTAATGAAAGTGGTTCCTG
1 CCAGTTTTTCCCTACTAATGAAAGTGGTTCCTG
*
1653425 CCAG-TTTTCCACTACTACTGAAAGTGGTTCCTG
1 CCAGTTTTTCC-CTACTAATGAAAGTGGTTCCTG
1653458 TTCTTCTACC
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 6 0.19
33 25 0.81
ACGTcount: A:0.21, C:0.26, G:0.18, T:0.35
Consensus pattern (33 bp):
CCAGTTTTTCCCTACTAATGAAAGTGGTTCCTG
Found at i:1663560 original size:28 final size:28
Alignment explanation
Indices: 1663500--1663556 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
1663490 TCCTATGGTG
* * **
1663500 AATAAGGAGATGTATCAAAGATTGGGTG
1 AATAAAGAGATGTATCAAAGATCGGGAA
1663528 AATAAAGAGATGTATCAAAGA-CGGGAA
1 AATAAAGAGATGTATCAAAGATCGGGAA
1663555 AA
1 AA
1663557 ATAACATGCA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 5 0.20
28 20 0.80
ACGTcount: A:0.47, C:0.05, G:0.28, T:0.19
Consensus pattern (28 bp):
AATAAAGAGATGTATCAAAGATCGGGAA
Found at i:1663651 original size:132 final size:132
Alignment explanation
Indices: 1663414--1663656 Score: 432
Period size: 132 Copynumber: 1.8 Consensus size: 132
1663404 CTTCTAAAAG
*
1663414 AGACGGAAAAAACAACATGCAAACCAGCTCCTACACCAATTAATCCGAATCATAAACTTGGAAGA
1 AGACGGAAAAAACAACATGCAAACCAGCTCCTACACCAATTAATCCGAATCATAAACTTGGAAAA
*
1663479 GCAGAAAACGATCCTATGGTGAATAAGGAGATGTATCAAAGATTGGGTGAATAAAGAGATGTATC
66 GCAGAAAACGATCCTATGGTGAATAAAGAGATGTATCAAAGATTGGGTGAATAAAGAGATGTATC
1663544 AA
131 AA
* * *
1663546 AGACGGGAAAAATAACATGCAAACCAGCTCCTACACCAATTGATCCGAATCATAAACTTGGAAAA
1 AGACGGAAAAAACAACATGCAAACCAGCTCCTACACCAATTAATCCGAATCATAAACTTGGAAAA
*
1663611 GCAGAAAACGATCCTATGGTGAATAAAGAGATGTGTCAAAGATTGG
66 GCAGAAAACGATCCTATGGTGAATAAAGAGATGTATCAAAGATTGG
1663657 TTGGAAAGTT
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
132 105 1.00
ACGTcount: A:0.43, C:0.17, G:0.21, T:0.19
Consensus pattern (132 bp):
AGACGGAAAAAACAACATGCAAACCAGCTCCTACACCAATTAATCCGAATCATAAACTTGGAAAA
GCAGAAAACGATCCTATGGTGAATAAAGAGATGTATCAAAGATTGGGTGAATAAAGAGATGTATC
AA
Found at i:1672455 original size:23 final size:23
Alignment explanation
Indices: 1672429--1672481 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
1672419 ATTTAATTTA
1672429 ATTTATTAAAAATTTAAAAATAT
1 ATTTATTAAAAATTTAAAAATAT
** *
1672452 ATTT-TATATTAATTTTAAAATAT
1 ATTTAT-TAAAAATTTAAAAATAT
1672475 ATTTATT
1 ATTTATT
1672482 TATACATATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
22 1 0.04
23 23 0.92
24 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
ATTTATTAAAAATTTAAAAATAT
Found at i:1672592 original size:11 final size:11
Alignment explanation
Indices: 1672561--1672626 Score: 75
Period size: 11 Copynumber: 6.2 Consensus size: 11
1672551 GGTGAGAGAG
1672561 GAAAAAGAGAAA
1 GAAAAAGA-AAA
1672573 G--AAAGAAAA
1 GAAAAAGAAAA
*
1672582 GAAAGAGAAAA
1 GAAAAAGAAAA
*
1672593 GAAAAAGGAAA
1 GAAAAAGAAAA
1672604 GAAAAAGAAAA
1 GAAAAAGAAAA
*
1672615 -AAAAACAAAA
1 GAAAAAGAAAA
1672625 GA
1 GA
1672627 GGGAAGGAGG
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
9 4 0.09
10 14 0.30
11 27 0.59
12 1 0.02
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (11 bp):
GAAAAAGAAAA
Found at i:1672604 original size:22 final size:21
Alignment explanation
Indices: 1672561--1672626 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
1672551 GGTGAGAGAG
* *
1672561 GAAAAAGAGAAAGAAAGAAAA
1 GAAAAAGAAAAAAAAAGAAAA
* *
1672582 GAAAGAGAAAAGAAAAAGGAAA
1 GAAAAAGAAAA-AAAAAGAAAA
*
1672604 GAAAAAGAAAAAAAAACAAAA
1 GAAAAAGAAAAAAAAAGAAAA
1672625 GA
1 GA
1672627 GGGAAGGAGG
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
21 19 0.51
22 18 0.49
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (21 bp):
GAAAAAGAAAAAAAAAGAAAA
Found at i:1672609 original size:17 final size:17
Alignment explanation
Indices: 1672561--1672615 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
1672551 GGTGAGAGAG
1672561 GAAAAAGAGAAAG--AAA
1 GAAAAAG-GAAAGAAAAA
1672577 G-AAAA-GAAAGAGAAAA
1 GAAAAAGGAAAGA-AAAA
1672593 GAAAAAGGAAAGAAAAA
1 GAAAAAGGAAAGAAAAA
1672610 GAAAAA
1 GAAAAA
1672616 AAAACAAAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
13 5 0.15
15 4 0.12
16 5 0.15
17 14 0.41
18 6 0.18
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (17 bp):
GAAAAAGGAAAGAAAAA
Found at i:1672612 original size:6 final size:6
Alignment explanation
Indices: 1672561--1672619 Score: 52
Period size: 6 Copynumber: 9.8 Consensus size: 6
1672551 GGTGAGAGAG
* *
1672561 GAAAAA GAGAAA GAAAGAA -AAGAAA GAGAAAA GAAAAA G-GAAA GAAAAA
1 GAAAAA GAAAAA GAAA-AA GAA-AAA GA-AAAA GAAAAA GAAAAA GAAAAA
1672610 GAAAAA -AAAA
1 GAAAAA GAAAA
1672620 CAAAAGAGGG
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
5 8 0.18
6 26 0.59
7 9 0.20
8 1 0.02
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:1672774 original size:10 final size:11
Alignment explanation
Indices: 1672741--1672798 Score: 71
Period size: 11 Copynumber: 5.2 Consensus size: 11
1672731 TCATGTCGTA
*
1672741 TTTATTTTATT
1 TTTATTATATT
1672752 TTTATTATATT
1 TTTATTATATT
*
1672763 TTTATTATTTT
1 TTTATTATATT
*
1672774 TTATATTATACT
1 TT-TATTATATT
*
1672786 TGTATTATATT
1 TTTATTATATT
1672797 TT
1 TT
1672799 GTATAGTTAA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
11 31 0.79
12 8 0.21
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (11 bp):
TTTATTATATT
Found at i:1672779 original size:18 final size:17
Alignment explanation
Indices: 1672745--1672798 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
1672735 GTCGTATTTA
1672745 TTTTATTTTTATTATAT
1 TTTTATTTTTATTATAT
*
1672762 TTTTATTATTTTTTATA-
1 TTTTATT-TTTATTATAT
* * *
1672779 TTATACTTGTATTATAT
1 TTTTATTTTTATTATAT
1672796 TTT
1 TTT
1672799 GTATAGTTAA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
16 7 0.24
17 14 0.48
18 8 0.28
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.72
Consensus pattern (17 bp):
TTTTATTTTTATTATAT
Found at i:1672791 original size:23 final size:24
Alignment explanation
Indices: 1672750--1672803 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
1672740 ATTTATTTTA
* *
1672750 TTTT-TATTATATTTTTATTAT-T
1 TTTTATATTATACTTGTATTATAT
1672772 TTTTATATTATACTTGTATTATAT
1 TTTTATATTATACTTGTATTATAT
1672796 TTTGTATA
1 TTT-TATA
1672804 GTTAAAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 4 0.15
23 15 0.56
24 4 0.15
25 4 0.15
ACGTcount: A:0.26, C:0.02, G:0.04, T:0.69
Consensus pattern (24 bp):
TTTTATATTATACTTGTATTATAT
Found at i:1673631 original size:22 final size:22
Alignment explanation
Indices: 1673606--1673648 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1673596 ACATAATTTA
*
1673606 TTATAATATTTTA-ATTTTAAAT
1 TTAT-ATATTTAAGATTTTAAAT
*
1673628 TTATTTATTTAAGATTTTAAA
1 TTATATATTTAAGATTTTAAA
1673649 ATATAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (22 bp):
TTATATATTTAAGATTTTAAAT
Found at i:1675851 original size:24 final size:25
Alignment explanation
Indices: 1675804--1675870 Score: 75
Period size: 24 Copynumber: 2.6 Consensus size: 25
1675794 TGTATAGCAA
1675804 TATATATATATATATAGCTTTATTATA-C
1 TATATATATATAT-TAG--TTATTA-AGC
*
1675832 TATATATATATATTAG-TATTAAGT
1 TATATATATATATTAGTTATTAAGC
1675856 TATATATATATATTA
1 TATATATATATATTA
1675871 ATATATATTT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
23 1 0.03
24 20 0.54
27 3 0.08
28 13 0.35
ACGTcount: A:0.42, C:0.03, G:0.04, T:0.51
Consensus pattern (25 bp):
TATATATATATATTAGTTATTAAGC
Done.