Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold511
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: 1668812
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 11 of 12
Found at i:1466086 original size:27 final size:26
Alignment explanation
Indices: 1466033--1466088 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
1466023 TAAATTCAAA
*
1466033 AATGGGGTTGGAGCATCTCCTCAGAAT
1 AATGGGGTTGGAG-ATATCCTCAGAAT
1466060 AATGGGGTTGGAG-TATCCTCGATGAAT
1 AATGGGGTTGGAGATATCCTC-A-GAAT
1466087 AA
1 AA
1466089 AATTTGGTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 6 0.23
26 1 0.04
27 19 0.73
ACGTcount: A:0.29, C:0.14, G:0.30, T:0.27
Consensus pattern (26 bp):
AATGGGGTTGGAGATATCCTCAGAAT
Found at i:1468341 original size:19 final size:19
Alignment explanation
Indices: 1468313--1468396 Score: 72
Period size: 19 Copynumber: 4.6 Consensus size: 19
1468303 GCAATATGTA
1468313 TATCGATACAAAACTTATG
1 TATCGATACAAAACTTATG
*
1468332 TATTGATAC---A--T-TG
1 TATCGATACAAAACTTATG
1468345 TATCGATACAAAACTTATG
1 TATCGATACAAAACTTATG
** *
1468364 TATCGATACATTTACTGTTTG
1 TATCGATACA-AAACT-TATG
1468385 TATCGATACAAA
1 TATCGATACAAA
1468397 TGGTAGAAAT
Statistics
Matches: 50, Mismatches: 7, Indels: 15
0.69 0.10 0.21
Matches are distributed among these distances:
13 10 0.20
14 1 0.02
16 2 0.04
18 1 0.02
19 20 0.40
20 3 0.06
21 13 0.26
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (19 bp):
TATCGATACAAAACTTATG
Found at i:1468352 original size:32 final size:32
Alignment explanation
Indices: 1468313--1468375 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1468303 GCAATATGTA
*
1468313 TATCGATACAAAACTTATGTATTGATACATTG
1 TATCGATACAAAACTTATGTATCGATACATTG
1468345 TATCGATACAAAACTTATGTATCGATACATT
1 TATCGATACAAAACTTATGTATCGATACATT
1468376 TACTGTTTGT
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:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (32 bp):
TATCGATACAAAACTTATGTATCGATACATTG
Found at i:1473137 original size:20 final size:20
Alignment explanation
Indices: 1473112--1473168 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
1473102 GTAAAAAGAT
*
1473112 AGAATGTATCGATATATTGA
1 AGAATGTATCGATACATTGA
1473132 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
*
1473152 AAAATGTATCGATACAT
1 AGAATGTATCGATACAT
1473169 CTAGGTAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.42, C:0.09, G:0.18, T:0.32
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:1473968 original size:3 final size:3
Alignment explanation
Indices: 1473954--1474002 Score: 84
Period size: 3 Copynumber: 17.0 Consensus size: 3
1473944 AAATATTTAT
1473954 TTA TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1474000 TTA
1 TTA
1474003 AAAATTTTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 4 0.09
3 40 0.91
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:1476059 original size:20 final size:19
Alignment explanation
Indices: 1475984--1476061 Score: 59
Period size: 20 Copynumber: 3.8 Consensus size: 19
1475974 AAAAACCTAG
* *
1475984 AATGTATCGATACAATGAGA
1 AATGTATCGATACATTGA-T
1476004 AATGTATCGATACAATT-AT
1 AATGTATCGATAC-ATTGAT
* *
1476023 AAGCATGCATTGATACATTGACT
1 -A--ATGTATCGATACATTGA-T
1476046 AATGTATCGATACATT
1 AATGTATCGATACATT
1476062 TCCCTGGCAG
Statistics
Matches: 46, Mismatches: 6, Indels: 12
0.72 0.09 0.19
Matches are distributed among these distances:
20 28 0.61
21 5 0.11
22 12 0.26
23 1 0.02
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (19 bp):
AATGTATCGATACATTGAT
Found at i:1476106 original size:59 final size:59
Alignment explanation
Indices: 1476031--1476159 Score: 222
Period size: 59 Copynumber: 2.2 Consensus size: 59
1476021 ATAAGCATGC
* *
1476031 ATTGATACATTGACTAATGTATCGATACATTTCCCTGGCAGTATGCAGGATGGTTTTGT
1 ATTGATACATTAACTAATGTATCGATACATTTCCCTAGCAGTATGCAGGATGGTTTTGT
*
1476090 ATTGATACATTAACTAATGTATCGATACATTTCCCTAGCAGTATGCAGGGTGGTTTTGT
1 ATTGATACATTAACTAATGTATCGATACATTTCCCTAGCAGTATGCAGGATGGTTTTGT
*
1476149 ATCGATACATT
1 ATTGATACATT
1476160 TTAGGCATGT
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
59 66 1.00
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (59 bp):
ATTGATACATTAACTAATGTATCGATACATTTCCCTAGCAGTATGCAGGATGGTTTTGT
Found at i:1476208 original size:20 final size:19
Alignment explanation
Indices: 1476166--1476236 Score: 106
Period size: 20 Copynumber: 3.6 Consensus size: 19
1476156 CATTTTAGGC
1476166 ATGTATCGATACATTCATT
1 ATGTATCGATACATTCATT
1476185 ATGTATCGATACATTCATTT
1 ATGTATCGATACATTCA-TT
1476205 ATGTATCGATACATTCACTT
1 ATGTATCGATACATTCA-TT
*
1476225 ATTGTATTGATA
1 A-TGTATCGATA
1476237 AAAATCATAG
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
19 17 0.35
20 22 0.46
21 9 0.19
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.44
Consensus pattern (19 bp):
ATGTATCGATACATTCATT
Found at i:1480581 original size:52 final size:52
Alignment explanation
Indices: 1480433--1480561 Score: 222
Period size: 52 Copynumber: 2.5 Consensus size: 52
1480423 CGAAATATGA
* *
1480433 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATTGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
* *
1480485 AAATTTGCCTGTATGTATCGATACATTTTATAGTGTATCGATACATCTAGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
1480537 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1480562 AAGATCAGTG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTAGGC
Found at i:1480588 original size:13 final size:13
Alignment explanation
Indices: 1480570--1480594 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1480560 CAAAGATCAG
1480570 TGTATCGATACAA
1 TGTATCGATACAA
1480583 TGTATCGATACA
1 TGTATCGATACA
1480595 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:1480673 original size:19 final size:19
Alignment explanation
Indices: 1480649--1480698 Score: 91
Period size: 19 Copynumber: 2.6 Consensus size: 19
1480639 TGATACATTA
1480649 TATCGATACAAAACTTATG
1 TATCGATACAAAACTTATG
*
1480668 TATCGATACAACACTTATG
1 TATCGATACAAAACTTATG
1480687 TATCGATACAAA
1 TATCGATACAAA
1480699 TCGTTGAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.42, C:0.18, G:0.10, T:0.30
Consensus pattern (19 bp):
TATCGATACAAAACTTATG
Found at i:1481100 original size:7 final size:7
Alignment explanation
Indices: 1481090--1481128 Score: 55
Period size: 7 Copynumber: 5.7 Consensus size: 7
1481080 TTCATCCGGA
1481090 CTTTTTT
1 CTTTTTT
1481097 CTTTTTT
1 CTTTTTT
1481104 CTTTTTT
1 CTTTTTT
1481111 CTTCTTTT
1 CTT-TTTT
1481119 -TTTTTT
1 CTTTTTT
1481125 -TTTT
1 CTTTT
1481129 GACTTTTTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
6 8 0.26
7 19 0.61
8 4 0.13
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (7 bp):
CTTTTTT
Found at i:1481136 original size:17 final size:17
Alignment explanation
Indices: 1481091--1481126 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
1481081 TCATCCGGAC
1481091 TTTT-TTCTTTTTTCTT
1 TTTTCTTCTTTTTTCTT
1481107 TTTTCTTCTTTTTT-TT
1 TTTTCTTCTTTTTTCTT
1481123 TTTT
1 TTTT
1481127 TTGACTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (17 bp):
TTTTCTTCTTTTTTCTT
Found at i:1481146 original size:28 final size:27
Alignment explanation
Indices: 1481122--1481217 Score: 93
Period size: 28 Copynumber: 3.4 Consensus size: 27
1481112 TTCTTTTTTT
1481122 TTTTTTTGACTTTTTGATTGATTTTGA
1 TTTTTTTGACTTTTTGATTGATTTTGA
** *
1481149 TTTTTTAAACTTTTTTTATTGATTTTGA
1 TTTTTTTGAC-TTTTTGATTGATTTTGA
* * *
1481177 TTTTTTTCATTTAATTTGATTTGATTTTTTA
1 TTTTTTTGACTT--TTTGA-TTGA-TTTTGA
1481208 TTTTTTTGAC
1 TTTTTTTGAC
1481218 ATAAGATGTC
Statistics
Matches: 54, Mismatches: 10, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
27 10 0.19
28 23 0.43
29 4 0.07
30 4 0.07
31 13 0.24
ACGTcount: A:0.18, C:0.04, G:0.09, T:0.69
Consensus pattern (27 bp):
TTTTTTTGACTTTTTGATTGATTTTGA
Found at i:1481181 original size:19 final size:19
Alignment explanation
Indices: 1481159--1481198 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
1481149 TTTTTTAAAC
*
1481159 TTTTTTT-ATTGATTTTGA
1 TTTTTTTCATTGAATTTGA
*
1481177 TTTTTTTCATTTAATTTGA
1 TTTTTTTCATTGAATTTGA
1481196 TTT
1 TTT
1481199 GATTTTTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.17, C:0.03, G:0.07, T:0.72
Consensus pattern (19 bp):
TTTTTTTCATTGAATTTGA
Found at i:1483082 original size:51 final size:52
Alignment explanation
Indices: 1483009--1483127 Score: 177
Period size: 51 Copynumber: 2.3 Consensus size: 52
1482999 TCTAGAAAGA
* *
1483009 AAATGTATCGATACATTTTTCATTGTATCGATAAATTCTAGG-TTTTGACCC
1 AAATGTATCGATACATTATTCATTATATCGATAAATTCTAGGTTTTTGACCC
* * * *
1483060 AAATATATCAATACATTATTCATTATATTGATACATTCTAGGTTTTTGACCC
1 AAATGTATCGATACATTATTCATTATATCGATAAATTCTAGGTTTTTGACCC
1483112 AAATGTATCGATACAT
1 AAATGTATCGATACAT
1483128 GTAGGCTATT
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
51 36 0.61
52 23 0.39
ACGTcount: A:0.34, C:0.15, G:0.11, T:0.40
Consensus pattern (52 bp):
AAATGTATCGATACATTATTCATTATATCGATAAATTCTAGGTTTTTGACCC
Found at i:1483142 original size:51 final size:50
Alignment explanation
Indices: 1483038--1483146 Score: 123
Period size: 52 Copynumber: 2.2 Consensus size: 50
1483028 TCATTGTATC
* **
1483038 GATAAATTCTAGGTTTTGACCCAAATATATCAATACATTATTCATTATATT
1 GATACATTCTAGGTTTTGACCCAAATATATCAATACATTAGGCA-TATATT
* * *
1483089 GATACATTCTAGGTTTTTGACCCAAATGTATCGATACATGTAGGC-TATTTT
1 GATACATTCTAGG-TTTTGACCCAAATATATCAATACAT-TAGGCATATATT
1483140 GAT-CATT
1 GATACATT
1483147 TCGTGACATT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
50 4 0.08
51 20 0.40
52 23 0.46
53 3 0.06
ACGTcount: A:0.32, C:0.15, G:0.13, T:0.40
Consensus pattern (50 bp):
GATACATTCTAGGTTTTGACCCAAATATATCAATACATTAGGCATATATT
Found at i:1485417 original size:80 final size:80
Alignment explanation
Indices: 1485197--1485597 Score: 405
Period size: 81 Copynumber: 5.0 Consensus size: 80
1485187 TAAATTTCTC
* * * ***
1485197 TTTCCAAAAATATCAAATTTTTAACTATCGAGGATACTCCAACCCCATCATTTTCGACAAGATAC
1 TTTCC-AAAATATTAAATTTTTCACCATCGAGGATACTCCAACCCCATCATTTTCGAGGGGATAC
1485262 TCCAACCCCGTTTTTA
65 TCCAACCCCGTTTTTA
* ** * * * *
1485278 CTTCCAAAGGCATTGAATTTTTCACCATCGGGGATACTCCAAACCTATCATTTTCGAGGGGATAC
1 TTTCCAAA-ATATTAAATTTTTCACCATCGAGGATACTCCAACCCCATCATTTTCGAGGGGATAC
* *
1485343 TCCAACCTCATTTTTA
65 TCCAACCCCGTTTTTA
* * **
1485359 TTTCCAAAATATTGAATTTTTCACCATCGAGGATACTCTAACCTTATCA-TTTCTGAGGGGATAC
1 TTTCCAAAATATTAAATTTTTCACCATCGAGGATACTCCAACCCCATCATTTTC-GAGGGGATAC
* *
1485423 TCCAACACTGTTTTTA
65 TCCAACCCCGTTTTTA
* * * * * *
1485439 CTTCCAAAACTATCAAAATTTTCACCATTGGGGATACTCCAACCCCATCATTTTTGAGGGGATAC
1 TTTCCAAAA-TATTAAATTTTTCACCATCGAGGATACTCCAACCCCATCATTTTCGAGGGGATAC
1485504 TCCAACCCCGTTTTTA
65 TCCAACCCCGTTTTTA
* * * * * *
1485520 TTTCTAAAATATTAAAATTTTT-ATC-TC-AGGGATACTCCAAGCCCACCATCTCCGAGGGGATA
1 TTTCCAAAATATT-AAATTTTTCACCATCGA-GGATACTCCAACCCCATCATTTTCGAGGGGATA
* *
1485582 CTTCAACCCCGATTTT
64 CTCCAACCCCGTTTTT
1485598 CACCAAAATT
Statistics
Matches: 262, Mismatches: 52, Indels: 14
0.80 0.16 0.04
Matches are distributed among these distances:
79 47 0.18
80 73 0.28
81 139 0.53
82 3 0.01
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (80 bp):
TTTCCAAAATATTAAATTTTTCACCATCGAGGATACTCCAACCCCATCATTTTCGAGGGGATACT
CCAACCCCGTTTTTA
Found at i:1485474 original size:161 final size:161
Alignment explanation
Indices: 1485197--1485542 Score: 435
Period size: 161 Copynumber: 2.1 Consensus size: 161
1485187 TAAATTTCTC
* *
1485197 TTTCCAAAAATATCAAATTTTTAACTATCGAGGATACTCCAACCCCATCATTTTCGACAAGATAC
1 TTTCC-AAAATATTAAATTTTTAACCATCGAGGATACTCCAACCCCATCATTTTCGACAAGATAC
* * ** * *
1485262 TCCAACCCCGTTTTTACTTCCAAAGGCATTGAATTTTTCACCATCGGGGATACTCCAAACCTATC
65 TCCAACACCGTTTTTACTTCCAAAGACATCAAAATTTTCACCATCGGGGATACTCCAAACCCATC
*
1485327 ATTTTCGAGGGGATACTCCAACCTCATTTTTA
130 ATTTTCGAGGGGATACTCCAACCCCATTTTTA
* * * ** ***
1485359 TTTCCAAAATATTGAATTTTTCACCATCGAGGATACTCTAACCTTATCA-TTTCTGAGGGGATAC
1 TTTCCAAAATATTAAATTTTTAACCATCGAGGATACTCCAACCCCATCATTTTC-GACAAGATAC
* * *
1485423 TCCAACACTGTTTTTACTTCCAAA-ACTATCAAAATTTTCACCATTGGGGATACTCCAACCCCAT
65 TCCAACACCGTTTTTACTTCCAAAGAC-ATCAAAATTTTCACCATCGGGGATACTCCAAACCCAT
* *
1485487 CATTTTTGAGGGGATACTCCAACCCCGTTTTTA
129 CATTTTCGAGGGGATACTCCAACCCCATTTTTA
*
1485520 TTTCTAAAATATTAAAATTTTTA
1 TTTCCAAAATATT-AAATTTTTA
1485543 TCTCAGGGAT
Statistics
Matches: 156, Mismatches: 25, Indels: 6
0.83 0.13 0.03
Matches are distributed among these distances:
160 5 0.03
161 139 0.89
162 12 0.08
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.34
Consensus pattern (161 bp):
TTTCCAAAATATTAAATTTTTAACCATCGAGGATACTCCAACCCCATCATTTTCGACAAGATACT
CCAACACCGTTTTTACTTCCAAAGACATCAAAATTTTCACCATCGGGGATACTCCAAACCCATCA
TTTTCGAGGGGATACTCCAACCCCATTTTTA
Found at i:1487459 original size:13 final size:13
Alignment explanation
Indices: 1487441--1487467 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1487431 CATTACTCAA
1487441 TGTATCGATACAT
1 TGTATCGATACAT
1487454 TGTATCGATACAT
1 TGTATCGATACAT
1487467 T
1 T
1487468 TGAACTTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1494473 original size:8 final size:9
Alignment explanation
Indices: 1494460--1494484 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1494450 AAAAATGATG
1494460 AAAAAAACA
1 AAAAAAACA
1494469 AAAAAAACA
1 AAAAAAACA
1494478 AAAAAAA
1 AAAAAAA
1494485 ACACAGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (9 bp):
AAAAAAACA
Found at i:1494473 original size:10 final size:10
Alignment explanation
Indices: 1494460--1494497 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
1494450 AAAAATGATG
1494460 AAAAAAAC-A
1 AAAAAAACAA
1494469 AAAAAAACAA
1 AAAAAAACAA
1494479 AAAAAAACACA
1 AAAAAAACA-A
1494490 GAAAAAAA
1 -AAAAAAA
1494498 AGTGCAAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 8 0.31
10 10 0.38
11 1 0.04
12 7 0.27
ACGTcount: A:0.87, C:0.11, G:0.03, T:0.00
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:1495856 original size:35 final size:34
Alignment explanation
Indices: 1495701--1495869 Score: 126
Period size: 34 Copynumber: 5.2 Consensus size: 34
1495691 TCTTCAAATA
** *
1495701 CCTTCTTAAAGTCCATGACTCAGTGGCATCTTT-T
1 CCTT-TTAAAGTCCACAACTCCGTGGCATCTTTCT
* *
1495735 -C-TTCAAAGTCCACAACTCCGTGGCACCTTT-T
1 CCTTTTAAAGTCCACAACTCCGTGGCATCTTTCT
* * *
1495766 TCTTTTCAAAGCCCATAACTCCGTGGCA------T
1 CCTTTT-AAAGTCCACAACTCCGTGGCATCTTTCT
** *
1495795 CCTTTTAAAGTCCACAACTCTTTGGCACTCTTTTT
1 CCTTTTAAAGTCCACAACTCCGTGGCA-TCTTTCT
1495830 CCCTTTT-AAGTCCACAACTCCGTGGCATCTTTCT
1 -CCTTTTAAAGTCCACAACTCCGTGGCATCTTTCT
1495864 CCTTTT
1 CCTTTT
1495870 CAAAAGCCCA
Statistics
Matches: 108, Mismatches: 16, Indels: 23
0.73 0.11 0.16
Matches are distributed among these distances:
28 17 0.16
29 6 0.06
31 24 0.22
32 2 0.02
33 9 0.08
34 25 0.23
35 19 0.18
36 6 0.06
ACGTcount: A:0.20, C:0.31, G:0.12, T:0.37
Consensus pattern (34 bp):
CCTTTTAAAGTCCACAACTCCGTGGCATCTTTCT
Found at i:1495857 original size:63 final size:61
Alignment explanation
Indices: 1495739--1495858 Score: 161
Period size: 63 Copynumber: 1.9 Consensus size: 61
1495729 TCTTTTCTTC
*
1495739 AAAGTCCACAACTCCGTGGCACCTTTTTCTTTTCAAAGCCCATAACTCCGTGGCATCCTTTT
1 AAAGTCCACAACTCCGTGGCACCTTTTTCTTTT-AAAGCCCACAACTCCGTGGCATCCTTTT
** *
1495801 AAAGTCCACAACTCTTTGGCACTCTTTTTCCCTTTT-AAGTCCACAACTCCGTGGCATC
1 AAAGTCCACAACTCCGTGGCAC-CTTTTT--CTTTTAAAGCCCACAACTCCGTGGCATC
1495859 TTTCTCCTTT
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
62 20 0.39
63 26 0.51
65 5 0.10
ACGTcount: A:0.23, C:0.33, G:0.12, T:0.33
Consensus pattern (61 bp):
AAAGTCCACAACTCCGTGGCACCTTTTTCTTTTAAAGCCCACAACTCCGTGGCATCCTTTT
Found at i:1495961 original size:49 final size:48
Alignment explanation
Indices: 1495890--1496129 Score: 241
Period size: 43 Copynumber: 5.2 Consensus size: 48
1495880 CACAAGTTGG
* * **
1495890 TGGCATCTTCT-TTTAAGCCCAATATCGCTGGCCTTGAATCAATATAT
1 TGGCACCTTCTCTTTAAGACCAATATCGCTGGCCTTGAATCAGCATAT
* *
1495937 TGGCACCTTCATCTTTAAGACCAATGTCGCTGGCCTTGAATCAGCACAT
1 TGGCACCTTC-TCTTTAAGACCAATATCGCTGGCCTTGAATCAGCATAT
* *
1495986 TGGCA----C-CTTTAAGTCCAATATCGCTGGCCTTGAATCAGCATGT
1 TGGCACCTTCTCTTTAAGACCAATATCGCTGGCCTTGAATCAGCATAT
* * * * *
1496029 TGGCACTTTTGTCTTTAAGACTAATGTCCCTGGCCTTGAATCAGCATAT
1 TGGCAC-CTTCTCTTTAAGACCAATATCGCTGGCCTTGAATCAGCATAT
* *
1496078 TGGCA----C-CTTTAAGTCCAATATCGCTAGCCTTGAATCAGCATAT
1 TGGCACCTTCTCTTTAAGACCAATATCGCTGGCCTTGAATCAGCATAT
*
1496121 TGGCGCCTT
1 TGGCACCTT
1496130 TGTCATCTTT
Statistics
Matches: 158, Mismatches: 23, Indels: 24
0.77 0.11 0.12
Matches are distributed among these distances:
43 74 0.47
45 1 0.01
47 9 0.06
48 1 0.01
49 73 0.46
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (48 bp):
TGGCACCTTCTCTTTAAGACCAATATCGCTGGCCTTGAATCAGCATAT
Found at i:1496062 original size:92 final size:92
Alignment explanation
Indices: 1495901--1496133 Score: 358
Period size: 92 Copynumber: 2.5 Consensus size: 92
1495891 GGCATCTTCT
* ** ** *
1495901 TTTAAGCCCAATATCGCTGGCCTTGAATCAATATATTGGCACCTTCATCTTTAAGACCAATGTCG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATGTCC
1495966 CTGGCCTTGAATCAGCACATTGGCACC
66 CTGGCCTTGAATCAGCACATTGGCACC
* * *
1495993 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATGTTGGCACTTTTGTCTTTAAGACTAATGTCC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATGTCC
*
1496058 CTGGCCTTGAATCAGCATATTGGCACC
66 CTGGCCTTGAATCAGCACATTGGCACC
* *
1496085 TTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCGCCTTTGTC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTC
1496134 ATCTTTAAGT
Statistics
Matches: 127, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
92 127 1.00
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.32
Consensus pattern (92 bp):
TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCTTTAAGACCAATGTCC
CTGGCCTTGAATCAGCACATTGGCACC
Found at i:1496086 original size:21 final size:21
Alignment explanation
Indices: 1496062--1496129 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
1496052 ATGTCCCTGG
1496062 CCTTGAATCAGCATATTGGCA
1 CCTTGAATCAGCATATTGGCA
* *
1496083 CCTTTAAGTC--CA-ATATCGCTA
1 CCTTGAA-TCAGCATAT-TGGC-A
*
1496104 GCCTTGAATCAGCATATTGGCG
1 -CCTTGAATCAGCATATTGGCA
1496126 CCTT
1 CCTT
1496130 TGTCATCTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 14
0.65 0.09 0.26
Matches are distributed among these distances:
19 2 0.06
20 5 0.14
21 13 0.37
22 8 0.23
23 5 0.14
24 2 0.06
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.31
Consensus pattern (21 bp):
CCTTGAATCAGCATATTGGCA
Found at i:1496461 original size:20 final size:20
Alignment explanation
Indices: 1496438--1496488 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
1496428 AATTCAAAGA
1496438 ATCGATACATGTTGCAATGT
1 ATCGATACATGTTGCAATGT
1496458 ATCGATACATGTTGCAATGT
1 ATCGATACATGTTGCAATGT
1496478 ATCGATACATG
1 ATCGATACATG
1496489 AAAAAGATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.33
Consensus pattern (20 bp):
ATCGATACATGTTGCAATGT
Found at i:1496573 original size:20 final size:19
Alignment explanation
Indices: 1496535--1496579 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
1496525 AACTTGTAAT
**
1496535 GATACACCAAGTATGTATC
1 GATACACCAAAAATGTATC
1496554 GATACACCAAAAATTGTATC
1 GATACACCAAAAA-TGTATC
1496574 GATACA
1 GATACA
1496580 TTGGCTTGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.42, C:0.20, G:0.13, T:0.24
Consensus pattern (19 bp):
GATACACCAAAAATGTATC
Found at i:1502755 original size:13 final size:13
Alignment explanation
Indices: 1502737--1502762 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1502727 ACATTTTACT
1502737 TTGTATCGATACA
1 TTGTATCGATACA
1502750 TTGTATCGATACA
1 TTGTATCGATACA
1502763 GGGTGATTAT
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:1502926 original size:20 final size:20
Alignment explanation
Indices: 1502883--1502928 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1502873 AAATCTTTTG
1502883 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
1502904 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
1502924 CAAAA
1 CAAAA
1502929 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:1505322 original size:20 final size:20
Alignment explanation
Indices: 1505277--1505327 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
1505267 GTAGCCAAAC
**
1505277 TTGTATCGATACACCAAGTA
1 TTGTATCGATACACCAAAAA
1505297 -TGTATCGATACACCAAAAA
1 TTGTATCGATACACCAAAAA
1505316 TTGTATCGATAC
1 TTGTATCGATAC
1505328 CTTGGCTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 17 0.61
20 11 0.39
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (20 bp):
TTGTATCGATACACCAAAAA
Found at i:1506138 original size:52 final size:52
Alignment explanation
Indices: 1506051--1506340 Score: 349
Period size: 52 Copynumber: 5.7 Consensus size: 52
1506041 TAAGCTTTCA
*
1506051 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTT
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTT
* * * *
1506103 AATTCCAATGTCGCTGGCCTTGAATTAGCACATTGGCACC--T-TCATCTTT
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTT
* *
1506152 AAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTT
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTT
* * *
1506204 AAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC--T-TCATCTTG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTT
* * * * *
1506253 AAGACCAGTATCGCTGGCCTTGAATCAACATATTGGCTCCTTTGTCAACTTT
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTT
** * * * *
1506305 AAACCCAATATCGTTGGCCGTGAATCAACGTATTGG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGG
1506341 TCCTTTTATC
Statistics
Matches: 202, Mismatches: 30, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
49 83 0.41
50 2 0.01
51 2 0.01
52 115 0.57
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.32
Consensus pattern (52 bp):
AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTT
Found at i:1506226 original size:101 final size:101
Alignment explanation
Indices: 1506051--1506331 Score: 436
Period size: 101 Copynumber: 2.8 Consensus size: 101
1506041 TAAGCTTTCA
*
1506051 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAATTCCAATGTCG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAATCCAATGTCG
* *
1506116 CTGGCCTTGAATTAGCACATTGGCACCTTCATCTTT
66 CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTG
* *
1506152 AAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAGTCCAATGTCG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAATCCAATGTCG
1506217 CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTG
66 CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTG
* * * * * * *
1506253 AAGACCAGTATCGCTGGCCTTGAATCAACATATTGGCTCCTTTGTCAACTTTAAACCCAATATCG
1 AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAATCCAATGTCG
* *
1506318 TTGGCCGTGAATCA
66 CTGGCCTTGAATCA
1506332 ACGTATTGGT
Statistics
Matches: 165, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
101 165 1.00
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (101 bp):
AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCGCCTTTGTCATCTTTAAATCCAATGTCG
CTGGCCTTGAATCAGCACATTGGCACCTTCATCTTG
Found at i:1507029 original size:19 final size:19
Alignment explanation
Indices: 1507001--1507050 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
1506991 ATCGATACAA
*
1507001 TGTATTGATACATAAGTGT
1 TGTATCGATACATAAGTGT
*
1507020 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAGTGT
1507039 TGTATCGATACA
1 TGTATCGATACA
1507051 ATGTATCGCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.40
Consensus pattern (19 bp):
TGTATCGATACATAAGTGT
Found at i:1515736 original size:47 final size:47
Alignment explanation
Indices: 1515673--1515800 Score: 139
Period size: 47 Copynumber: 2.7 Consensus size: 47
1515663 GCTATGCTCG
* * * * *
1515673 TGGAGTTACTGTCGGTTGCTTGTGGAAGTTGCTGCTATCGTGAAAGC
1 TGGAGTTACTGCCGGTTGCTCGTGGAAGCTGCTACGATCGTGAAAGC
* * * *
1515720 TTGAGTTCCTGCCGGTTGCTCGTGGAAGCTGCTACGGTCGTGGAAGC
1 TGGAGTTACTGCCGGTTGCTCGTGGAAGCTGCTACGATCGTGAAAGC
* * * *
1515767 TGGAGTTGCTGCTGGTTGCTCATGGCAGCTGCTA
1 TGGAGTTACTGCCGGTTGCTCGTGGAAGCTGCTA
1515801 GTAGTGGATG
Statistics
Matches: 67, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
47 67 1.00
ACGTcount: A:0.14, C:0.20, G:0.35, T:0.31
Consensus pattern (47 bp):
TGGAGTTACTGCCGGTTGCTCGTGGAAGCTGCTACGATCGTGAAAGC
Found at i:1516478 original size:20 final size:20
Alignment explanation
Indices: 1516449--1516497 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
1516439 TGATGATTTT
*
1516449 TTTTACTTTTATTTTTTCAC
1 TTTTATTTTTATTTTTTCAC
*
1516469 TTTTATTTTTATTTTTTTAC
1 TTTTATTTTTATTTTTTCAC
1516489 TTTTCATTT
1 TTTT-ATTT
1516498 CTACTTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
20 22 0.85
21 4 0.15
ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTATTTTTATTTTTTCAC
Found at i:1516492 original size:14 final size:14
Alignment explanation
Indices: 1516446--1516478 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1516436 TCATGATGAT
*
1516446 TTTTTTTACTTTTA
1 TTTTTTCACTTTTA
1516460 TTTTTTCACTTTTA
1 TTTTTTCACTTTTA
1516474 TTTTT
1 TTTTT
1516479 ATTTTTTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTTCACTTTTA
Found at i:1517172 original size:42 final size:43
Alignment explanation
Indices: 1516995--1517511 Score: 591
Period size: 42 Copynumber: 12.2 Consensus size: 43
1516985 TAAATTAGGC
* * *
1516995 AGTCTTCAAGGTCAAAGCCGACAGGCAGACTGAGGGATAGAAA
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTAAGGGATAGGAA
* * * *
1517038 AGTCTCCAAGGTCAAAGTCGACAGGCAGATTGAGGGATAAGAA
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTAAGGGATAGGAA
* * * * * * *
1517081 AGCCTCCAGGGTCAAAGTCGATAAGCAAACTTTAGGGATAGGAA
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGAC-TAAGGGATAGGAA
* *
1517125 AGTCTCCAAGGTCAAAGCCAACAGGCAAACT-AGGGATAGGAA
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTAAGGGATAGGAA
* * *
1517167 AGTCTCCAGGGTCAAAGCCGACAAGCAGACTAAGGG-TGGGAA
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTAAGGGATAGGAA
* *
1517209 AGTCTCCAATGTCAAAGCCGATAGGCAGACTAAGGG-TAGGAA
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTAAGGGATAGGAA
* * *
1517251 AGTCTCCAGGGTCAAAGCTGACAGGCAGACTGAGGGA-AGGAA
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTAAGGGATAGGAA
* * * * *
1517293 AGTCTCTAGGGTCAAAGCCGACAGGCAGACTGAGGGA-AAGAC
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTAAGGGATAGGAA
* ** * * *
1517335 AGTCTCCAGGGTCAAAGTTGATAGGAAAACTAAGGGA-AGGAA
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTAAGGGATAGGAA
* *
1517377 AGTCTCCAAGGTCAAAGCCGATAGGCAGACTAAGGGATAGAAA
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTAAGGGATAGGAA
* * * *
1517420 AGTCTCTAAGGTTAAAGCCGACAAGCAGACTAAAGG-TAGGAA
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTAAGGGATAGGAA
*
1517462 AGTCTCCAAGGTCAAAGCCAACAGGCAGACTAAGGG-TAGGAA
1 AGTCTCCAAGGTCAAAGCCGACAGGCAGACTAAGGGATAGGAA
1517504 AGTCTCCA
1 AGTCTCCA
1517512 GAAGTTTAAT
Statistics
Matches: 406, Mismatches: 64, Indels: 9
0.85 0.13 0.02
Matches are distributed among these distances:
42 269 0.66
43 102 0.25
44 35 0.09
ACGTcount: A:0.37, C:0.19, G:0.30, T:0.15
Consensus pattern (43 bp):
AGTCTCCAAGGTCAAAGCCGACAGGCAGACTAAGGGATAGGAA
Found at i:1530695 original size:47 final size:47
Alignment explanation
Indices: 1530642--1530765 Score: 133
Period size: 47 Copynumber: 2.6 Consensus size: 47
1530632 ATGCTCGTGG
* *
1530642 AGTTGCTGTCAGTTGCTCGTGGAAGCTGCTTCTACCATGGAAGCTTA
1 AGTTGCTGTCAGTTGCTCGTGGAAGCTGCTGCTACCATGGAAGCTGA
** * * ** *
1530689 AGTTGCTGTTGGTTGCTCGTGGAAGTTGCTGCTGCTGTGGAAGCTGG
1 AGTTGCTGTCAGTTGCTCGTGGAAGCTGCTGCTACCATGGAAGCTGA
* *
1530736 AGTTGCT-ACCGATTGCTCGTGGAAGCTGCT
1 AGTTGCTGTCAG-TTGCTCGTGGAAGCTGCT
1530766 ACTGGTGGAT
Statistics
Matches: 63, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
46 1 0.02
47 62 0.98
ACGTcount: A:0.15, C:0.19, G:0.33, T:0.32
Consensus pattern (47 bp):
AGTTGCTGTCAGTTGCTCGTGGAAGCTGCTGCTACCATGGAAGCTGA
Found at i:1533644 original size:19 final size:19
Alignment explanation
Indices: 1533601--1533644 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
1533591 TATTGACTGT
*
1533601 ACAAAAATAATAGAAATGA
1 ACAAAAATAATAGAAAAGA
1533620 ACAAAAATGAATA-AAAAGA
1 ACAAAAAT-AATAGAAAAGA
*
1533639 ATAAAA
1 ACAAAA
1533645 GAATAGACAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.73, C:0.05, G:0.09, T:0.14
Consensus pattern (19 bp):
ACAAAAATAATAGAAAAGA
Found at i:1535775 original size:96 final size:97
Alignment explanation
Indices: 1535574--1535778 Score: 238
Period size: 97 Copynumber: 2.1 Consensus size: 97
1535564 AAAGACAAGG
* * * *
1535574 TTGAAGTATCCCCTCAGAGGAATAGGGTTGGAGTGTCCCCGATGATGACAATTAAGGCGAAAATA
1 TTGAAGTATCCTCTCAGAAGAATAGGGTTGGAGTATCCCCAATGATGACAATTAAGGCGAAAATA
* * * *
1535639 AGATTTAAATCTTGATGAGTTTAAAAGTAGGG
66 AGACTTAAATCTTGAAGAGTTTAAAAGGAGGA
* * * * *
1535671 TTGGAGTATCCTCTCGGAAGAATGGGGTTGGAGTATCCCTAATGATGATAATTTAA-GC-AAAAT
1 TTGAAGTATCCTCTCAGAAGAATAGGGTTGGAGTATCCCCAATGATGACAA-TTAAGGCGAAAAT
1535734 AAGACTTAAATCTT-AAGAAGTTTAAAAGCGA-GA
65 AAGACTTAAATCTTGAAG-AGTTTAAAAG-GAGGA
1535767 TTGAAGTATCCT
1 TTGAAGTATCCT
1535779 TGATGGATAA
Statistics
Matches: 91, Mismatches: 14, Indels: 7
0.81 0.12 0.06
Matches are distributed among these distances:
95 2 0.02
96 40 0.44
97 45 0.49
98 4 0.04
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.28
Consensus pattern (97 bp):
TTGAAGTATCCTCTCAGAAGAATAGGGTTGGAGTATCCCCAATGATGACAATTAAGGCGAAAATA
AGACTTAAATCTTGAAGAGTTTAAAAGGAGGA
Found at i:1537268 original size:12 final size:12
Alignment explanation
Indices: 1537251--1537275 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1537241 TTTGGCTGGT
1537251 AATGTAGCTAAA
1 AATGTAGCTAAA
1537263 AATGTAGCTAAA
1 AATGTAGCTAAA
1537275 A
1 A
1537276 GAAAAAGTCC
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:0.52, C:0.08, G:0.16, T:0.24
Consensus pattern (12 bp):
AATGTAGCTAAA
Found at i:1537764 original size:51 final size:51
Alignment explanation
Indices: 1537699--1537872 Score: 199
Period size: 51 Copynumber: 3.4 Consensus size: 51
1537689 ATCGATATAT
* * * * *
1537699 TGAAGAATGTATCGATATATTTGGGTCAAAACCTAGAATGTATCTTTACAA
1 TGAAAAATGTATCGATACATTTGGGTCAAAACCCAAAATGTATCTATACAA
* * *
1537750 TGAAAAATGTATCGATACATTTGGGTTAAAAACCCATAATATAT-TATACAA
1 TGAAAAATGTATCGATACATTTGGG-TCAAAACCCAAAATGTATCTATACAA
* * * * *
1537801 TGAAAAATGTATAGATACATTTAGCTC-AAACCCAAAATGTATCGATATAA
1 TGAAAAATGTATCGATACATTTGGGTCAAAACCCAAAATGTATCTATACAA
*
1537851 TAAAAAATGTATCGATACATTT
1 TGAAAAATGTATCGATACATTT
1537873 TCTTTCCAGA
Statistics
Matches: 104, Mismatches: 17, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
49 13 0.12
50 26 0.25
51 51 0.49
52 14 0.13
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (51 bp):
TGAAAAATGTATCGATACATTTGGGTCAAAACCCAAAATGTATCTATACAA
Found at i:1540732 original size:116 final size:116
Alignment explanation
Indices: 1540537--1540756 Score: 300
Period size: 116 Copynumber: 1.9 Consensus size: 116
1540527 ATTGGCCAAC
* * * * *
1540537 ATAATTAAATAAAATAGGCGCTAAATAAATTAATTAAATATGCATGTGGGTCCTATTTTATCTAA
1 ATAATTAAATAAAATAAGCGCCAAATAAATTAATTAAATAAGCATATGGGACCTATTTTATCTAA
* ** *
1540602 TGTATACTTTTTATAAGGCTTGACCTTGAATTAAATAATTTATGACCTAAT
66 TATATACTTTTTATAAAACTTGACCTTAAATTAAATAATTTATGACCTAAT
*
1540653 ATAATTAAATGAAATAAGC-CCAAATAAATTAATTAAATAAGCA-ATGGGACCTATTTTATCTAA
1 ATAATTAAATAAAATAAGCGCCAAATAAATTAATTAAATAAGCATATGGGACCTATTTTATCT-A
* *
1540716 TATATATATTTTTTATAAAACTTGGCCTTAAATTAAATAAT
65 -ATATATACTTTTTATAAAACTTGACCTTAAATTAAATAAT
1540757 ATGCGACCTT
Statistics
Matches: 90, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
114 16 0.18
115 23 0.26
116 51 0.57
ACGTcount: A:0.42, C:0.10, G:0.10, T:0.38
Consensus pattern (116 bp):
ATAATTAAATAAAATAAGCGCCAAATAAATTAATTAAATAAGCATATGGGACCTATTTTATCTAA
TATATACTTTTTATAAAACTTGACCTTAAATTAAATAATTTATGACCTAAT
Found at i:1541160 original size:36 final size:36
Alignment explanation
Indices: 1541045--1541419 Score: 165
Period size: 36 Copynumber: 10.5 Consensus size: 36
1541035 TAAAAGTTTT
* * *
1541045 TGAAATATCATCAAGAGAGGTTTTGAAAGTTTTTAA
1 TGAAATATCCTCAAGAGAGGCTTTGGAAGTTTTTAA
* * * * * *
1541081 TGAGAA-ATCCTTAAAAAAAGCTTAGG-AGGTTTT--
1 TGA-AATATCCTCAAGAGAGGCTTTGGAAGTTTTTAA
1541114 TGAAATATCCTCAAGAGAGGCTTTGGAAGTTTTTAA
1 TGAAATATCCTCAAGAGAGGCTTTGGAAGTTTTTAA
* ** * *
1541150 TGAAACATCCTCAAGAGAGATTTTGGAATTTTTTGA
1 TGAAATATCCTCAAGAGAGGCTTTGGAAGTTTTTAA
* * * * * * **
1541186 TGGAATGTCCAT-AAAAAAGGTTTTGG-AGATTTTGT
1 TGAAATATCC-TCAAGAGAGGCTTTGGAAGTTTTTAA
* * *
1541221 TGAAATATCCTTAAGA-ATGGCTTTGGAAGTTCTTGA
1 TGAAATATCCTCAAGAGA-GGCTTTGGAAGTTTTTAA
* * * * * ** * *
1541257 TGAAATGTCCTTAAGAAACGTTTTTTAAGCTATTAA
1 TGAAATATCCTCAAGAGAGGCTTTGGAAGTTTTTAA
* * * * * * **
1541293 TGAAGTATTC-CAAAAGAAGTTTTGGAAG-TTCTGC
1 TGAAATATCCTCAAGAGAGGCTTTGGAAGTTTTTAA
*
1541327 TGAAATATCCTCGAGAGAGGCTTTGGAAGTTTTTTTAA
1 TGAAATATCCTCAAGAGAGGCTTTGGAAG--TTTTTAA
* * * * * *
1541365 TGAAATGTCCTTAAGAAAGACTTTGAAATTTTTTAA
1 TGAAATATCCTCAAGAGAGGCTTTGGAAGTTTTTAA
* * * *
1541401 TAAAACATCTTTAAGAGAG
1 TGAAATATCCTCAAGAGAG
1541420 TTTTTAGAGT
Statistics
Matches: 247, Mismatches: 78, Indels: 28
0.70 0.22 0.08
Matches are distributed among these distances:
32 2 0.01
33 18 0.07
34 18 0.07
35 56 0.23
36 124 0.50
37 4 0.02
38 25 0.10
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (36 bp):
TGAAATATCCTCAAGAGAGGCTTTGGAAGTTTTTAA
Found at i:1551326 original size:4 final size:4
Alignment explanation
Indices: 1551306--1551344 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
1551296 AAAAAAAACA
* *
1551306 AAAT AAAC AAGT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1551345 CACCTCAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.21
Consensus pattern (4 bp):
AAAT
Found at i:1553501 original size:79 final size:79
Alignment explanation
Indices: 1553401--1554027 Score: 588
Period size: 79 Copynumber: 7.9 Consensus size: 79
1553391 GATAAAATCA
* * * * * *
1553401 GGGTTGGAGTATCCTCTCAGAAATAACGGGGTTAGAGTATCCCTGATTATAAAAAATCGATGTTT
1 GGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATGGATGTTT
1553466 TAGAAATAAAGCTG
66 TAGAAATAAAGCTG
* * * * * * *
1553480 GGGTTGGAATATCCCCTCAGAAATAACAGGGTTGAAGTATCCTCGATAGTGGAAAATGGGTGTTT
1 GGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATGGATGTTT
* *
1553545 T-GAAAATAAA-ATCA
66 TAG-AAATAAAGCT-G
* * *
1553559 GGATTGGAGTATCCCCTC-GAAAATAACGGGGTTGGAGTATCCTCGATTGTGGAAAATGGATGTT
1 GGGTTGGAGTATCCCCTCAG-AAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATGGATGTT
*
1553623 TTAG-AAT-AAGGTCG
65 TTAGAAATAAAGCT-G
* * * * * * * *
1553637 AGGTTGGAGTAT-CCCTCCGGAAATAATGAGGTTAGAGTATCCCCGATTATGAAAAATTGATGTC
1 GGGTTGGAGTATCCCCT-CAGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATGGATGTT
* * *
1553701 TTAGGAATAAAACTA
65 TTAGAAATAAAGCTG
* * * ** * *
1553716 GGGTTGGAGTATCCCCTTAGAAACAACGAGGTTGGAGTATCGTCGATTGTGAAAAATAGATATTT
1 GGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATGGATGTTT
1553781 TAGAAATAAAGCTG
66 TAGAAATAAAGCTG
* ** * * * * * *
1553795 GGGTTGGAGTATCCCTTTGGAAAAAACGAGGTTAGAGTATCCCCGATGGTGGAAAATGGGTGTTT
1 GGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATGGATGTTT
* *
1553860 TAGAAATAAA-ATCA
66 TAGAAATAAAGCT-G
* * * *
1553874 GGGTTGGAGTATCCCCTC-GTAAATAACAGGGTTGGAGTATCCCCAATTGTGGAAAATTGATGTT
1 GGGTTGGAGTATCCCCTCAG-AAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATGGATGTT
* *
1553938 TTAGAAATAAGGCCG
65 TTAGAAATAAAGCTG
* * * *
1553953 AGGTTGGAATATCCCCTCAGAAATAACAGGGTTGGAGTATCCCCGATTTTGAAAAATCGG-TGTT
1 GGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAAT-GGATGTT
*
1554017 TTGGAAATAAA
65 TTAGAAATAAA
1554028 AACATCGATG
Statistics
Matches: 447, Mismatches: 86, Indels: 30
0.79 0.15 0.05
Matches are distributed among these distances:
77 6 0.01
78 61 0.14
79 370 0.83
80 10 0.02
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (79 bp):
GGGTTGGAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATGGATGTTT
TAGAAATAAAGCTG
Found at i:1553868 original size:158 final size:158
Alignment explanation
Indices: 1553392--1554028 Score: 666
Period size: 158 Copynumber: 4.0 Consensus size: 158
1553382 TATTTTGGAG
* * * * * *
1553392 ATAAAATCAGGGTTGGAGTATCCTCTCAG-AAATAACGGGGTTAGAGTATCCCTGATTATAAAAA
1 ATAAAATCAGGGTTGGAGTATCCCCT-AGAAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAA
* *
1553456 ATCGATGTTTTAGAAATAAAGCTGGGGTTGGAATATCCCCTCAGAAATAACAGGGTT-GAAGTAT
65 ATAGATGTTTTAGAAATAAAGCTGAGGTTGGAATATCCCCTCAGAAATAACAGGGTTAG-AGTAT
* * *
1553520 CCTCGATAGTGGAAAATGGGTGTTTT-GAAA
129 CCCCGATTGTGAAAAATGGGTGTTTTAG-AA
* * * * *
1553550 ATAAAATCAGGATTGGAGTATCCCCTCGAAAATAACGGGGTTGGAGTATCCTCGATTGTGGAAAA
1 ATAAAATCAGGGTTGGAGTATCCCCTAGAAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAA
* * * * *
1553615 TGGATGTTTTAG-AAT-AAGGTCGAGGTTGGAGTAT-CCCTCCGGAAATAA-TGAGGTTAGAGTA
66 TAGATGTTTTAGAAATAAAGCT-GAGGTTGGAATATCCCCT-CAGAAATAACAG-GGTTAGAGTA
* * * * *
1553676 TCCCCGATTATGAAAAATTGATGTCTTAGGA
128 TCCCCGATTGTGAAAAATGGGTGTTTTAGAA
* **
1553707 ATAAAA-CTAGGGTTGGAGTATCCCCTTAG-AAACAACGAGGTTGGAGTATCGTCGATTGTGAAA
1 ATAAAATC-AGGGTTGGAGTATCCCC-TAGAAAATAACGAGGTTGGAGTATCCCCGATTGTGAAA
* * * * ** *
1553770 AATAGATATTTTAGAAATAAAGCTGGGGTTGGAGTATCCCTTTGGAAAAAAC-GAGGTTAGAGTA
64 AATAGATGTTTTAGAAATAAAGCTGAGGTTGGAATATCCCCTCAGAAATAACAG-GGTTAGAGTA
* *
1553834 TCCCCGATGGTGGAAAATGGGTGTTTTAGAA
128 TCCCCGATTGTGAAAAATGGGTGTTTTAGAA
* * * *
1553865 ATAAAATCAGGGTTGGAGTATCCCCTCGTAAATAAC-AGGGTTGGAGTATCCCCAATTGTGGAAA
1 ATAAAATCAGGGTTGGAGTATCCCCTAGAAAATAACGA-GGTTGGAGTATCCCCGATTGTGAAAA
* * * *
1553929 ATTGATGTTTTAGAAATAAGGCCGAGGTTGGAATATCCCCTCAGAAATAACAGGGTTGGAGTATC
65 ATAGATGTTTTAGAAATAAAGCTGAGGTTGGAATATCCCCTCAGAAATAACAGGGTTAGAGTATC
* * *
1553994 CCCGATTTTGAAAAATCGGTGTTTTGGAA
130 CCCGATTGTGAAAAATGGGTGTTTTAGAA
1554023 ATAAAA
1 ATAAAA
1554029 ACATCGATGA
Statistics
Matches: 398, Mismatches: 65, Indels: 32
0.80 0.13 0.06
Matches are distributed among these distances:
156 10 0.03
157 119 0.30
158 260 0.65
159 9 0.02
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (158 bp):
ATAAAATCAGGGTTGGAGTATCCCCTAGAAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAA
TAGATGTTTTAGAAATAAAGCTGAGGTTGGAATATCCCCTCAGAAATAACAGGGTTAGAGTATCC
CCGATTGTGAAAAATGGGTGTTTTAGAA
Found at i:1556433 original size:50 final size:50
Alignment explanation
Indices: 1556379--1556494 Score: 151
Period size: 50 Copynumber: 2.3 Consensus size: 50
1556369 AAAAATGCCT
* * * *
1556379 GAATGTATTGATACATTGAGAAATGTATCGATACATCTAGGTAAAACCCA
1 GAATGTATCGATACAATGAGAAATGTATCAATACATATAGGTAAAACCCA
* * * *
1556429 GAATGTATCAATACAATGAGTAATGTATCAATACATATGGGTGAAACCCA
1 GAATGTATCGATACAATGAGAAATGTATCAATACATATAGGTAAAACCCA
*
1556479 CAATGTATCGATACAA
1 GAATGTATCGATACAA
1556495 ATTGTGAAAA
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
50 56 1.00
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (50 bp):
GAATGTATCGATACAATGAGAAATGTATCAATACATATAGGTAAAACCCA
Found at i:1568423 original size:18 final size:18
Alignment explanation
Indices: 1568400--1568436 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1568390 TTAATGGCCT
1568400 TGAAATCATAAAGGAATA
1 TGAAATCATAAAGGAATA
*
1568418 TGAAATCGTAAAGGAATA
1 TGAAATCATAAAGGAATA
1568436 T
1 T
1568437 TGCCAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.05, G:0.19, T:0.24
Consensus pattern (18 bp):
TGAAATCATAAAGGAATA
Found at i:1569518 original size:5 final size:5
Alignment explanation
Indices: 1569508--1569570 Score: 63
Period size: 5 Copynumber: 11.6 Consensus size: 5
1569498 TAGATTTTGG
* *
1569508 AATTA AATTA AATTA AATTA AATTTA AATATA AAATA AATTTGA AATTC
1 AATTA AATTA AATTA AATTA AA-TTA AAT-TA AATTA AA-TT-A AATTA
1569557 AATTA TAATTA AAT
1 AATTA -AATTA AAT
1569571 ATAATTTAGA
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
5 29 0.59
6 17 0.35
7 3 0.06
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (5 bp):
AATTA
Found at i:1569536 original size:11 final size:10
Alignment explanation
Indices: 1569508--1569570 Score: 63
Period size: 11 Copynumber: 5.8 Consensus size: 10
1569498 TAGATTTTGG
1569508 AATTAAATTA
1 AATTAAATTA
1569518 AATTAAATTA
1 AATTAAATTA
1569528 AATTTAAATATA
1 AA-TTAAAT-TA
*
1569540 AAATAAATTTGA
1 AATTAAA-TT-A
*
1569552 AATTCAATTA
1 AATTAAATTA
1569562 TAATTAAAT
1 -AATTAAAT
1569571 ATAATTTAGA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
10 13 0.30
11 20 0.45
12 11 0.25
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (10 bp):
AATTAAATTA
Found at i:1573988 original size:20 final size:20
Alignment explanation
Indices: 1573963--1574027 Score: 81
Period size: 20 Copynumber: 3.6 Consensus size: 20
1573953 ACAAGCAATA
1573963 TATCGATACAATTCATCATG
1 TATCGATACAATTCATCATG
1573983 TATCGATAC-A---AT-A--
1 TATCGATACAATTCATCATG
1573996 TATCGATACAATTCATCATG
1 TATCGATACAATTCATCATG
1574016 TATCGATACAAT
1 TATCGATACAAT
1574028 GTATCGATAC
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 9 0.24
14 1 0.03
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 1 0.03
20 21 0.55
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.34
Consensus pattern (20 bp):
TATCGATACAATTCATCATG
Found at i:1573998 original size:33 final size:33
Alignment explanation
Indices: 1573958--1574059 Score: 161
Period size: 33 Copynumber: 3.1 Consensus size: 33
1573948 CCGTTACAAG
1573958 CAATATATCGATACAATTCATCATGTATCGATA
1 CAATATATCGATACAATTCATCATGTATCGATA
1573991 CAATATATCGATACAATTCATCATGTATCGATA
1 CAATATATCGATACAATTCATCATGTATCGATA
* * *
1574024 CAATGTATCGATAC-ATTGTACCATGTATCGATA
1 CAATATATCGATACAATT-CATCATGTATCGATA
1574057 CAA
1 CAA
1574060 ACAGTGGTAG
Statistics
Matches: 65, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
32 3 0.05
33 62 0.95
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (33 bp):
CAATATATCGATACAATTCATCATGTATCGATA
Found at i:1574043 original size:13 final size:13
Alignment explanation
Indices: 1573980--1574043 Score: 68
Period size: 13 Copynumber: 5.4 Consensus size: 13
1573970 ACAATTCATC
1573980 ATGTATCGATACA
1 ATGTATCGATACA
*
1573993 ATATATCGATACA
1 ATGTATCGATACA
1574006 A--T-TC-AT-C-
1 ATGTATCGATACA
1574013 ATGTATCGATACA
1 ATGTATCGATACA
1574026 ATGTATCGATACA
1 ATGTATCGATACA
*
1574039 TTGTA
1 ATGTA
1574044 CCATGTATCG
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
7 1 0.02
8 1 0.02
9 3 0.07
10 4 0.09
11 3 0.07
12 1 0.02
13 30 0.70
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1574132 original size:19 final size:19
Alignment explanation
Indices: 1574088--1574143 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
1574078 CTGCCAATTT
**
1574088 CATGTATCGATACAATTGTC
1 CATGTATCGATACAA-TGAA
1574108 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
1574127 CATGTATCGATACAATG
1 CATGTATCGATACAATG
1574144 TATCAATACA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
19 19 0.56
20 15 0.44
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1574960 original size:16 final size:16
Alignment explanation
Indices: 1574935--1574965 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1574925 TCCATCCTCT
*
1574935 TTTTTTTTTCATTTTG
1 TTTTTCTTTCATTTTG
1574951 TTTTTCTTTCATTTT
1 TTTTTCTTTCATTTT
1574966 ATTTCTTTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.06, C:0.10, G:0.03, T:0.81
Consensus pattern (16 bp):
TTTTTCTTTCATTTTG
Found at i:1577262 original size:19 final size:20
Alignment explanation
Indices: 1577225--1577262 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1577215 TCCCATAGCT
1577225 ATGTATCGATACAATTCATA
1 ATGTATCGATACAATTCATA
1577245 ATGTATCGATAC-ATTCAT
1 ATGTATCGATACAATTCAT
1577263 TTGAAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (20 bp):
ATGTATCGATACAATTCATA
Found at i:1581305 original size:20 final size:20
Alignment explanation
Indices: 1581276--1581350 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 20
1581266 AAAAAGACAT
*
1581276 AATGTATCGATACATTGCAG
1 AATGTATCGATACATTGCAA
*
1581296 AATATATCGATACATT-CATA
1 AATGTATCGATACATTGCA-A
* * *
1581316 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTGCAA
1581336 AATGTATCGATACAT
1 AATGTATCGATACAT
1581351 CAGGGTAAAA
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
19 2 0.04
20 42 0.93
21 1 0.02
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (20 bp):
AATGTATCGATACATTGCAA
Found at i:1581344 original size:40 final size:39
Alignment explanation
Indices: 1581273--1581350 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
1581263 GGTAAAAAGA
* *
1581273 CATAATGTATCGATACATTGCAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* *
1581312 CATACATGTATCGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
1581351 CAGGGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:1581372 original size:32 final size:32
Alignment explanation
Indices: 1581336--1581454 Score: 87
Period size: 32 Copynumber: 3.5 Consensus size: 32
1581326 TATATTGAAA
1581336 AATGTATCGATACATCAGGGTAAAAATGACAT
1 AATGTATCGATACATCAGGGTAAAAATGACAT
* *** *
1581368 AATGTATTGATACATTGCAAAATATATTCATACAT-TCAT
1 AATGTATCGATACA-T-CAGGGTA-A---A-A-ATGACAT
*
1581407 ACCTGTATCGATACATCAGGGTAAAAATGACAT
1 A-ATGTATCGATACATCAGGGTAAAAATGACAT
*
1581440 AATGTATTGATACAT
1 AATGTATCGATACAT
1581455 TGCAGAATAT
Statistics
Matches: 64, Mismatches: 13, Indels: 20
0.66 0.13 0.21
Matches are distributed among these distances:
32 27 0.42
33 6 0.09
34 5 0.08
35 1 0.02
37 1 0.02
38 5 0.08
39 6 0.09
40 13 0.20
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.31
Consensus pattern (32 bp):
AATGTATCGATACATCAGGGTAAAAATGACAT
Found at i:1581401 original size:92 final size:91
Alignment explanation
Indices: 1581245--1581419 Score: 282
Period size: 92 Copynumber: 1.9 Consensus size: 91
1581235 TACATTATTC
*
1581245 AATGTATCGATACATCTAGGTAAAAAGACATAATGTATCGATACATTGCAGAATATATCGATACA
1 AATGTATCGATACATCTAGGTAAAAAGACATAATGTATCGATACATTGCAAAATATATCGATACA
1581310 TTCATACATGTATCGATATATTGAAA
66 TTCATACATGTATCGATATATTGAAA
*
1581336 AATGTATCGATACATC-AGGGTAAAAATGACATAATGTATTGATACATTGCAAAATATATTC-AT
1 AATGTATCGATACATCTA-GGTAAAAA-GACATAATGTATCGATACATTGCAAAATATA-TCGAT
*
1581399 ACATTCATACCTGTATCGATA
63 ACATTCATACATGTATCGATA
1581420 CATCAGGGTA
Statistics
Matches: 78, Mismatches: 3, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
90 1 0.01
91 24 0.31
92 51 0.65
93 2 0.03
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (91 bp):
AATGTATCGATACATCTAGGTAAAAAGACATAATGTATCGATACATTGCAAAATATATCGATACA
TTCATACATGTATCGATATATTGAAA
Found at i:1581426 original size:72 final size:72
Alignment explanation
Indices: 1581337--1581491 Score: 267
Period size: 72 Copynumber: 2.2 Consensus size: 72
1581327 ATATTGAAAA
1581337 ATGTATCGATACATCAGGGTAAAAATGACATAATGTATTGATACATTGCAAAATATATTC-ATAC
1 ATGTATCGATACATCAGGGTAAAAATGACATAATGTATTGATACATTGCAAAATATA-TCGATAC
1581401 ATTCATAC
65 ATTCATAC
* *
1581409 CTGTATCGATACATCAGGGTAAAAATGACATAATGTATTGATACATTGCAGAATATATCGATACA
1 ATGTATCGATACATCAGGGTAAAAATGACATAATGTATTGATACATTGCAAAATATATCGATACA
1581474 TTCATAC
66 TTCATAC
*
1581481 ATGTATTGATA
1 ATGTATCGATA
1581492 TATTGAAAAA
Statistics
Matches: 78, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
71 2 0.03
72 76 0.97
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (72 bp):
ATGTATCGATACATCAGGGTAAAAATGACATAATGTATTGATACATTGCAAAATATATCGATACA
TTCATAC
Found at i:1581491 original size:20 final size:19
Alignment explanation
Indices: 1581437--1581514 Score: 66
Period size: 20 Copynumber: 3.9 Consensus size: 19
1581427 GTAAAAATGA
*
1581437 CATAATGTATTGATACATT
1 CATAATGTATCGATACATT
* *
1581456 GCAGAATATATCGATACATT
1 -CATAATGTATCGATACATT
* *
1581476 CATACATGTATTGATATATT
1 CATA-ATGTATCGATACATT
* *
1581496 GAAAAATGTATCGATACAT
1 -CATAATGTATCGATACAT
1581515 CAGGGTAAAA
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
19 3 0.07
20 40 0.89
21 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.36
Consensus pattern (19 bp):
CATAATGTATCGATACATT
Found at i:1581508 original size:40 final size:39
Alignment explanation
Indices: 1581437--1581514 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
1581427 GTAAAAATGA
* *
1581437 CATAATGTATTGATACATTGCAGAATATATCGATACATT
1 CATAATGTATTGATACATTGAAAAATATATCGATACATT
* *
1581476 CATACATGTATTGATATATTGAAAAATGTATCGATACAT
1 CATA-ATGTATTGATACATTGAAAAATATATCGATACAT
1581515 CAGGGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.36
Consensus pattern (39 bp):
CATAATGTATTGATACATTGAAAAATATATCGATACATT
Found at i:1582259 original size:86 final size:85
Alignment explanation
Indices: 1582123--1582935 Score: 873
Period size: 86 Copynumber: 9.5 Consensus size: 85
1582113 ACTAACACGT
* ** * *
1582123 GTGGGCTTTGAAAAGAGTGTTACTGACTTGCGTGGGCTTTAAAAGGGTGCCACTGACTTGCGTGG
1 GTGGGCTTTGAAAGGA-TGCCACTGACTT--GTGGGCTTTGAAAGAGTGCCACTGACTT-CGTGG
*
1582188 GCTTTGAAAGAATGCCACTGACTC
62 GCTTTGAAAGAGTGCCACTGACTC
* *
1582212 GTGGGCTTTGAGAGGATGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTAAC-TCGTGGGCTT
1 GTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTCGTGGGCTT
* *
1582276 TGAAA-AGGTACCACTGGCTC
66 TGAAAGA-GTGCCACTGACTC
* * * * *
1582296 ATGGGC-TTGAAAGGGTGCCACTAACTTGTGGGCTTTGAAA-AGTGCCATTGAC-TCGTGTGCTT
1 GTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTCGTGGGCTT
1582358 TGAAA-AGGTGCCACTGACTTGC
66 TGAAAGA-GTGCCACTGAC-T-C
* * *
1582380 GTGGGCTTTAAAAGGGTGCCACTGACTTGCGTGGGCTTTGAAAGAATGCCACTGAC-TCGTGGGC
1 GTGGGCTTTGAAAGGATGCCACTGACTT--GTGGGCTTTGAAAGAGTGCCACTGACTTCGTGGGC
1582444 TTTGAAAG-GATGCCACTGACTC
64 TTTGAAAGAG-TGCCACTGACTC
* * * *
1582466 GTGGGCTTTGAAAGGATGCCACTAAATTGTGGGCTTCGCAAG-GTTGCCACTGACTT-GTGGGCT
1 GTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGAG-TGCCACTGACTTCGTGGGCT
* * *
1582529 TCGAAAGGGTGCCACTGACTT
65 TTGAAAGAGTGCCACTGACTC
* * * *
1582550 GTGGGCTTCGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGA-TTTGTGGGCTT
1 GTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTCGTGGGCTT
* * * *
1582614 TGAAAAGAGCGCCACTAATTT
66 TG-AAAGAGTGCCACTGACTC
* * * *
1582635 GTGGCCTTTGAAAAGAGTGCCACTAACTTGTGGGCTTTGAAAGGGTGCCACTGACTT-GTGGGCT
1 GTGGGCTTTGAAAGGA-TGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTCGTGGGCT
* *
1582699 TTGAAAAGAGTGCCACTGATTT
65 TTG-AAAGAGTGCCACTGACTC
* * *
1582721 GTGGGCTTTGAAAAGAGTGTCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTT-GTGGGCT
1 GTGGGCTTTGAAAGGA-TGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTCGTGGGCT
* * *
1582785 TTGAAAAGAGTGCCACTAATTT
65 TTG-AAAGAGTGCCACTGACTC
* *
1582807 GTGGGCTTTGAAAAGG-TGCCACTGATTTGTGGGCTTTGAAAAGAGTGCCACTGA-TTTGTGGGC
1 GTGGGCTTTG-AAAGGATGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTGACTTCGTGGGC
*
1582870 TTTGAAAAGAGTGCCACTGACTT
64 TTTG-AAAGAGTGCCACTGACTC
* * *
1582893 GTGGACTTTGAAAAGAGTGCCACTGATTTGTGGGCTTTGAAAG
1 GTGGGCTTTGAAAGGA-TGCCACTGACTTGTGGGCTTTGAAAG
1582936 GGATGAACAT
Statistics
Matches: 638, Mismatches: 64, Indels: 47
0.85 0.09 0.06
Matches are distributed among these distances:
82 35 0.05
83 35 0.05
84 135 0.21
85 75 0.12
86 257 0.40
87 43 0.07
88 44 0.07
89 14 0.02
ACGTcount: A:0.22, C:0.18, G:0.31, T:0.28
Consensus pattern (85 bp):
GTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTCGTGGGCTT
TGAAAGAGTGCCACTGACTC
Found at i:1582634 original size:29 final size:29
Alignment explanation
Indices: 1582076--1582934 Score: 961
Period size: 28 Copynumber: 29.9 Consensus size: 29
1582066 AAAAAAAAAT
* *
1582076 GTGCCACTAACTTGTGTAGGCTTTGAAAAAA
1 GTGCCACTGACTTGTG--GGCTTTGAAAAGA
* *
1582107 GTTGCCACTAACACGTGTGGGCTTTGAAAAGA
1 G-TGCCACT--GACTTGTGGGCTTTGAAAAGA
** *
1582139 GTGTTACTGACTTGCGTGGGCTTT-AAAAGG
1 GTGCCACTGACTT--GTGGGCTTTGAAAAGA
1582169 GTGCCACTGACTTGCGTGGGCTTTG-AAAGA
1 GTGCCACTGACTT--GTGGGCTTTGAAAAGA
* * * *
1582199 ATGCCACTGACTCGTGGGCTTTGAGAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1582228 -TGCCACTGACTTGTGGGCTTTG-AAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
1582255 GTGCCACTAACTCGTGGGCTTTGAAAAG-
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* * ** *
1582283 GTACCACTGGCTCATGGGC-TTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
1582310 GTGCCACTAACTTGTGGGCTTTG-AAA-A
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* * *
1582337 GTGCCATTGACTCGTGTGCTTTGAAAAG-
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
1582365 GTGCCACTGACTTGCGTGGGCTTT-AAAAGG
1 GTGCCACTGACTT--GTGGGCTTTGAAAAGA
1582395 GTGCCACTGACTTGCGTGGGCTTTG-AAAGA
1 GTGCCACTGACTT--GTGGGCTTTGAAAAGA
* * *
1582425 ATGCCACTGACTCGTGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
1582454 -TGCCACTGACTCGTGGGCTTTGAAAGGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* * * *
1582482 -TGCCACTAAATTGTGGGCTTCG-CAAG-
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
1582508 GTTGCCACTGACTTGTGGGCTTCG-AAAGG
1 G-TGCCACTGACTTGTGGGCTTTGAAAAGA
* *
1582537 GTGCCACTGACTTGTGGGCTTCG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
1582565 GTGCCACTGACTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
1582593 GTGCCACTGATTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* * * *
1582622 GCGCCACTAATTTGTGGCCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
1582651 GTGCCACTAACTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1582679 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
1582708 GTGCCACTGATTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
1582737 GTGTCACTGACTTGTGGGCTTTG-AAAGG
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1582765 GTGCCACTGACTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
* *
1582794 GTGCCACTAATTTGTGGGCTTTGAAAAG-
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
1582822 GTGCCACTGATTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
1582851 GTGCCACTGATTTGTGGGCTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
1582880 GTGCCACTGACTTGTGGACTTTGAAAAGA
1 GTGCCACTGACTTGTGGGCTTTGAAAAGA
*
1582909 GTGCCACTGATTTGTGGGCTTTGAAA
1 GTGCCACTGACTTGTGGGCTTTGAAA
1582935 GGGATGAACA
Statistics
Matches: 728, Mismatches: 75, Indels: 52
0.85 0.09 0.06
Matches are distributed among these distances:
26 4 0.01
27 41 0.06
28 320 0.44
29 233 0.32
30 89 0.12
31 15 0.02
32 20 0.03
34 6 0.01
ACGTcount: A:0.23, C:0.18, G:0.31, T:0.28
Consensus pattern (29 bp):
GTGCCACTGACTTGTGGGCTTTGAAAAGA
Found at i:1583962 original size:13 final size:13
Alignment explanation
Indices: 1583944--1583969 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1583934 TACACCAAGT
1583944 ATGTATCGATACA
1 ATGTATCGATACA
1583957 ATGTATCGATACA
1 ATGTATCGATACA
1583970 CCAAAAATTG
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:1583967 original size:32 final size:33
Alignment explanation
Indices: 1583926--1583989 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1583916 TAGCCAAACT
**
1583926 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACCAAAAATTGTATCGATACAA
1583958 TGTATCGATACACCAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAAATTGTATCGATACA
1583990 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACCAAAAATTGTATCGATACAA
Found at i:1586222 original size:21 final size:21
Alignment explanation
Indices: 1586189--1586238 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
1586179 TTGCAAGTTG
*
1586189 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1586211 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
1586232 AAATAAA
1 AAATAAA
1586239 AACTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1590320 original size:20 final size:20
Alignment explanation
Indices: 1590277--1590322 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1590267 AAATCTTTTG
1590277 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
1590298 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
1590318 CAAAA
1 CAAAA
1590323 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:1592705 original size:29 final size:29
Alignment explanation
Indices: 1592672--1592730 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
1592662 GCCAAACTTG
*
1592672 TATCGATACACC-AAGTATGTATCGATACA
1 TATCGATACACCAAAAT-TGTATCGATACA
1592701 TATCGATACACCAAAATTGTATCGATACA
1 TATCGATACACCAAAATTGTATCGATACA
1592730 T
1 T
1592731 TGGCTTGTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 25 0.89
30 3 0.11
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (29 bp):
TATCGATACACCAAAATTGTATCGATACA
Found at i:1594061 original size:1 final size:1
Alignment explanation
Indices: 1594057--1594122 Score: 69
Period size: 1 Copynumber: 66.0 Consensus size: 1
1594047 TTTTTTGCTA
* * * * * * *
1594057 TTTTTTCTTTTTTTTGTTTTTTTGTTTTGTTTTTTTTTGTTTTGTTTTTTTTTGTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1594122 T
1 T
1594123 GGTGTAAAGG
Statistics
Matches: 51, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.00, C:0.02, G:0.09, T:0.89
Consensus pattern (1 bp):
T
Found at i:1594069 original size:19 final size:17
Alignment explanation
Indices: 1594042--1594122 Score: 65
Period size: 19 Copynumber: 4.5 Consensus size: 17
1594032 ATCTAGACCC
*
1594042 TTCTATTTTTTGCTATTTT
1 TTCTTTTTTTTG-T-TTTT
1594061 TTCTTTTTTTTGTTTTT
1 TTCTTTTTTTTGTTTTT
* *
1594078 TTGTTTTGTTTTTTTTTGTT
1 TT-CTTT-TTTTTGTTT-TT
*
1594098 TTGTTTTTTTTTGTTTTT
1 TT-CTTTTTTTTGTTTTT
1594116 TT-TTTTT
1 TTCTTTTT
1594123 GGTGTAAAGG
Statistics
Matches: 55, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
16 5 0.09
17 6 0.11
18 8 0.15
19 27 0.49
20 9 0.16
ACGTcount: A:0.02, C:0.04, G:0.09, T:0.85
Consensus pattern (17 bp):
TTCTTTTTTTTGTTTTT
Found at i:1594076 original size:15 final size:15
Alignment explanation
Indices: 1594073--1594122 Score: 93
Period size: 15 Copynumber: 3.4 Consensus size: 15
1594063 CTTTTTTTTG
1594073 TTTTTTTGTTTTGTT
1 TTTTTTTGTTTTGTT
1594088 TTTTTTTGTTTTGTT
1 TTTTTTTGTTTTGTT
1594103 TTTTTTTGTTTT-TT
1 TTTTTTTGTTTTGTT
1594117 TTTTTT
1 TTTTTT
1594123 GGTGTAAAGG
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
14 8 0.23
15 27 0.77
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (15 bp):
TTTTTTTGTTTTGTT
Found at i:1603846 original size:13 final size:13
Alignment explanation
Indices: 1603828--1603853 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1603818 TACACCAAGT
1603828 ATGTATCGATACA
1 ATGTATCGATACA
1603841 ATGTATCGATACA
1 ATGTATCGATACA
1603854 CCAAAAATTG
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:1603851 original size:32 final size:33
Alignment explanation
Indices: 1603810--1603873 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
1603800 TAGCCAAACT
**
1603810 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACCAAAAATTGTATCGATACAA
1603842 TGTATCGATACACCAAAAATTGTATCGATACA
1 TGTATCGATACACCAAAAATTGTATCGATACA
1603874 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACCAAAAATTGTATCGATACAA
Found at i:1606105 original size:21 final size:21
Alignment explanation
Indices: 1606072--1606121 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
1606062 TTGCAAGTTG
*
1606072 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1606094 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
1606115 AAATAAA
1 AAATAAA
1606122 AACTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1610763 original size:20 final size:20
Alignment explanation
Indices: 1610734--1610900 Score: 113
Period size: 20 Copynumber: 8.8 Consensus size: 20
1610724 AAAAAGACAT
1610734 AATGTATCGATACATTGCAG
1 AATGTATCGATACATTGCAG
* *
1610754 AATATATCGATACATT-CAT
1 AATGTATCGATACATTGCAG
* * *
1610773 ACATGTATCGATATATTGAAA
1 A-ATGTATCGATACATTGCAG
1610794 AATGTATCGATACA-T-CAG
1 AATGTATCGATACATTGCAG
* * *
1610812 --GGTA---A-A-AATGACAT
1 AATGTATCGATACATTG-CAG
1610826 AATGTATCGATACATTGCAG
1 AATGTATCGATACATTGCAG
* *
1610846 AATATATCGATACATT-CAT
1 AATGTATCGATACATTGCAG
* * *
1610865 ACATGTATCGATATATTGAAA
1 A-ATGTATCGATACATTGCAG
1610886 AATGTATCGATACAT
1 AATGTATCGATACAT
1610901 CAAGGTAAAA
Statistics
Matches: 112, Mismatches: 21, Indels: 28
0.70 0.13 0.17
Matches are distributed among these distances:
11 1 0.01
12 2 0.02
13 1 0.01
14 2 0.02
16 6 0.05
18 1 0.01
19 8 0.07
20 84 0.75
21 7 0.06
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (20 bp):
AATGTATCGATACATTGCAG
Found at i:1610808 original size:32 final size:31
Alignment explanation
Indices: 1610771--1610900 Score: 74
Period size: 32 Copynumber: 4.2 Consensus size: 31
1610761 CGATACATTC
1610771 ATACATGTATCGATATATTGAAAAATGTATCG
1 ATACAT-TATCGATATATTGAAAAATGTATCG
* * * * * *
1610803 ATACATCA-GGGTAAAAATGACATAATGTATCG
1 ATACATTATCGAT-ATATTGA-AAAATGTATCG
* * * *
1610835 ATACATT-GCAGAATATATCGATACA--T-TC-
1 ATACATTATC-G-ATATATTGAAAAATGTATCG
1610863 ATACATGTATCGATATATTGAAAAATGTATCG
1 ATACAT-TATCGATATATTGAAAAATGTATCG
1610895 ATACAT
1 ATACAT
1610901 CAAGGTAAAA
Statistics
Matches: 68, Mismatches: 19, Indels: 22
0.62 0.17 0.20
Matches are distributed among these distances:
28 16 0.24
29 4 0.06
30 5 0.07
31 8 0.12
32 29 0.43
33 5 0.07
34 1 0.01
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.32
Consensus pattern (31 bp):
ATACATTATCGATATATTGAAAAATGTATCG
Found at i:1610855 original size:92 final size:91
Alignment explanation
Indices: 1610703--1610913 Score: 388
Period size: 92 Copynumber: 2.3 Consensus size: 91
1610693 TACATTATTC
1610703 AATGTATCGATACATCTAGGTAAAAA-GACATAATGTATCGATACATTGCAGAATATATCGATAC
1 AATGTATCGATACATC-AGGTAAAAATGACATAATGTATCGATACATTGCAGAATATATCGATAC
1610767 ATTCATACATGTATCGATATATTGAAA
65 ATTCATACATGTATCGATATATTGAAA
1610794 AATGTATCGATACATCAGGGTAAAAATGACATAATGTATCGATACATTGCAGAATATATCGATAC
1 AATGTATCGATACATCA-GGTAAAAATGACATAATGTATCGATACATTGCAGAATATATCGATAC
1610859 ATTCATACATGTATCGATATATTGAAA
65 ATTCATACATGTATCGATATATTGAAA
1610886 AATGTATCGATACATCAAGGTAAAAATG
1 AATGTATCGATACATC-AGGTAAAAATG
1610914 TGAATTTTCC
Statistics
Matches: 117, Mismatches: 0, Indels: 5
0.96 0.00 0.04
Matches are distributed among these distances:
90 1 0.01
91 24 0.21
92 91 0.78
93 1 0.01
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (91 bp):
AATGTATCGATACATCAGGTAAAAATGACATAATGTATCGATACATTGCAGAATATATCGATACA
TTCATACATGTATCGATATATTGAAA
Found at i:1614934 original size:52 final size:52
Alignment explanation
Indices: 1614853--1614971 Score: 220
Period size: 52 Copynumber: 2.3 Consensus size: 52
1614843 TGAAAAGTTA
*
1614853 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
1614905 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
1614957 CTGCATGTATCGATA
1 CTGCATGTATCGATA
1614972 TAAAGATCAG
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:1614986 original size:52 final size:52
Alignment explanation
Indices: 1614853--1614993 Score: 196
Period size: 52 Copynumber: 2.7 Consensus size: 52
1614843 TGAAAAGTTA
*
1614853 CTGCATGTATCGATACATTTA-ATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TAAGATAGTGTATCGATACATCTGGGCAAATTTGC
*** *
1614905 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATAAGATAGTGTATCGATACATCTGGGCAAATTTGC
*
1614957 CTGCATGTATCGATATA-AAGATCAGTGTATCGATACA
1 CTGCATGTATCGATACATAAGAT-AGTGTATCGATACA
1614994 ATGTATCGAT
Statistics
Matches: 80, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 4 0.05
52 76 0.95
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Consensus pattern (52 bp):
CTGCATGTATCGATACATAAGATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:1615000 original size:13 final size:13
Alignment explanation
Indices: 1614982--1615006 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1614972 TAAAGATCAG
1614982 TGTATCGATACAA
1 TGTATCGATACAA
1614995 TGTATCGATACA
1 TGTATCGATACA
1615007 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:1615090 original size:13 final size:13
Alignment explanation
Indices: 1615072--1615096 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1615062 CAAAAAAATA
1615072 TGTATCGATACAT
1 TGTATCGATACAT
1615085 TGTATCGATACA
1 TGTATCGATACA
1615097 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:1615092 original size:33 final size:33
Alignment explanation
Indices: 1615050--1615116 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1615040 AGTAGCTTAA
1615050 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1615083 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1615116 A
1 A
1615117 AATCATTGAA
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:1615195 original size:21 final size:21
Alignment explanation
Indices: 1615154--1615195 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1615144 GTTGGGACCT
*
1615154 TGTATCGATACATTTTAACAA
1 TGTATCGATACATTTGAACAA
*
1615175 TGTATCGATACATTTGGACAA
1 TGTATCGATACATTTGAACAA
1615196 AAATGTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.36
Consensus pattern (21 bp):
TGTATCGATACATTTGAACAA
Found at i:1616108 original size:171 final size:171
Alignment explanation
Indices: 1615916--1616307 Score: 673
Period size: 168 Copynumber: 2.3 Consensus size: 171
1615906 TTTTAGAGAT
*
1615916 GATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
1 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
*
1615981 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAGAGATGAGAAAAAGGA
66 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGA
1616046 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
131 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
* *
1616087 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT--A-ATGATGATGAGAAAA
1 GATGAAGATGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
*
1616149 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGA
66 GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGA
1616214 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
131 TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
* *
1616255 GATGGAAAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
1 GAT-GAAGA--TGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAG
1616308 GTGCCAATGT
Statistics
Matches: 208, Mismatches: 7, Indels: 9
0.93 0.03 0.04
Matches are distributed among these distances:
168 121 0.58
169 5 0.02
171 81 0.39
173 1 0.00
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.24
Consensus pattern (171 bp):
GATGAAGATGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATGAGAAAA
GTGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCCTAAAGATGAGAAAAAGGA
TGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
Found at i:1616192 original size:64 final size:62
Alignment explanation
Indices: 1616091--1616307 Score: 180
Period size: 64 Copynumber: 3.7 Consensus size: 62
1616081 CTTAAAGATG
* *
1616091 AAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAATGATGATGAGAAAAGTGATA
1 AAGATGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGA-GA-AAAAGTGATA
* * *
1616155 AAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAG-GAT-
1 AAGATGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAGAAAAAGTGATA
** * * * *
1616215 --G-T--CAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATG-G--AAA---AT-
1 AAGATGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAGAAAAAGTGATA
* *
1616265 --G-TGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
1 AAGATGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAG
1616308 GTGCCAATGT
Statistics
Matches: 133, Mismatches: 18, Indels: 16
0.80 0.11 0.10
Matches are distributed among these distances:
50 4 0.03
52 38 0.29
54 1 0.01
55 33 0.25
57 1 0.01
58 1 0.01
61 3 0.02
62 5 0.04
63 2 0.02
64 45 0.34
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.25
Consensus pattern (62 bp):
AAGATGCCAATATGCTGATTCAAGGCCAACGATATTGGACTTAAAGATGAGAAAAAGTGATA
Found at i:1616364 original size:49 final size:47
Alignment explanation
Indices: 1616211--1616447 Score: 274
Period size: 43 Copynumber: 5.1 Consensus size: 47
1616201 ATGAGAAAAA
* * *
1616211 GGATGTCAACGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGAT
1 GGATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* *
1616258 GGAAAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT-AA-A-
1 GG---A--TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
1616307 GG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
1 GGATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
* * *
1616353 GAAGATGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AA-A-
1 G--GATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
*
1616399 GG-TGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT
1 GGATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
1616445 GGA
1 GGA
1616448 AAAGGCCAGC
Statistics
Matches: 161, Mismatches: 14, Indels: 30
0.79 0.07 0.15
Matches are distributed among these distances:
43 70 0.43
44 5 0.03
45 2 0.01
46 4 0.02
47 3 0.02
48 3 0.02
49 37 0.23
50 2 0.01
51 2 0.01
52 33 0.20
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (47 bp):
GGATGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT
Found at i:1616395 original size:92 final size:93
Alignment explanation
Indices: 1616221--1616455 Score: 393
Period size: 92 Copynumber: 2.5 Consensus size: 93
1616211 GGATGTCAAC
*
1616221 GTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGCCAATATGCTGATTCAAG
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-GAAAA-GTGCCAATATGCTGATTCAAG
*
1616286 GCCAGCTATATTGGACTTAAAGGTGCCAAT
64 GCCAGCGATATTGGACTTAAAGGTGCCAAT
*
1616316 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA-TGCCAATATGCTGATTCAAGGC
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAAAGTGCCAATATGCTGATTCAAGGC
1616380 CAGCGATATTGGACTTAAAGGTGCCAAT
66 CAGCGATATTGGACTTAAAGGTGCCAAT
*
1616408 GTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGGAAAAG-GCCA
1 GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-GAAAAGTGCCA
1616456 GCTATATTGG
Statistics
Matches: 133, Mismatches: 5, Indels: 6
0.92 0.03 0.04
Matches are distributed among these distances:
92 85 0.64
93 8 0.06
94 4 0.03
95 36 0.27
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.24
Consensus pattern (93 bp):
GTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAAAGTGCCAATATGCTGATTCAAGGC
CAGCGATATTGGACTTAAAGGTGCCAAT
Found at i:1616571 original size:32 final size:33
Alignment explanation
Indices: 1616475--1616567 Score: 154
Period size: 33 Copynumber: 2.8 Consensus size: 33
1616465 GGCTTAGAGG
*
1616475 GGTTGCCACCGACTTGTGTGGGCTCTGGAAGAA
1 GGTTGCCACCGACTTGTGTGGGCTTTGGAAGAA
1616508 GGTTGCCACCGACTTGTGTGGGCTTTAGGAAG-A
1 GGTTGCCACCGACTTGTGTGGGCTTT-GGAAGAA
1616541 -GTTGCCACCGACTTGTGTGGGCTTTGG
1 GGTTGCCACCGACTTGTGTGGGCTTTGG
1616568 GAAGGAAAAA
Statistics
Matches: 58, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
31 2 0.03
32 25 0.43
33 26 0.45
34 5 0.09
ACGTcount: A:0.15, C:0.20, G:0.37, T:0.28
Consensus pattern (33 bp):
GGTTGCCACCGACTTGTGTGGGCTTTGGAAGAA
Found at i:1616645 original size:34 final size:35
Alignment explanation
Indices: 1616569--1616762 Score: 272
Period size: 35 Copynumber: 5.5 Consensus size: 35
1616559 GGGCTTTGGG
*
1616569 AAGGAAAAA-AGATGCCACGGAGTTGTGGAC-TTAA
1 AAGGAAAAAGAG-TGCCACGGAGTTGTGGGCTTTAA
1616603 AAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1616639 AA-GAAAAA-AGTGCCACGGAGTTGTGGGCTTTGAA
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AA
1616673 AAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
*
1616709 ACGGAAAAAG-GTGCCACGGAGTTGTGGGCTTTAAA
1 AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AA
*
1616744 AAGGGAAAGAGAGTGCCAC
1 AA-GGAAAAAGAGTGCCAC
1616763 AAAGTCGTAG
Statistics
Matches: 146, Mismatches: 4, Indels: 17
0.87 0.02 0.10
Matches are distributed among these distances:
33 23 0.16
34 34 0.23
35 35 0.24
36 24 0.16
37 30 0.21
ACGTcount: A:0.36, C:0.12, G:0.34, T:0.18
Consensus pattern (35 bp):
AAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
Found at i:1616647 original size:70 final size:70
Alignment explanation
Indices: 1616572--1616762 Score: 305
Period size: 71 Copynumber: 2.7 Consensus size: 70
1616562 CTTTGGGAAG
*
1616572 GAAAAAAGATGCCACGGAGTTGTGGAC-TT-AAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCT
1 GAAAAAAG-TGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCT
1616635 TTAAAA
65 TTAAAA
*
1616641 GAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
1 GAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
*
1616706 TAAACG
66 TAAA-A
* *
1616712 GAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAGAGAGTGCCAC
1 GAAAAAAGTGCCACGGAGTTGTGGGCTTTAAAAAGGGAAAAAGAGTGCCAC
1616763 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:1616808 original size:33 final size:36
Alignment explanation
Indices: 1616771--1616920 Score: 204
Period size: 33 Copynumber: 4.3 Consensus size: 36
1616761 ACAAAGTCGT
1616771 AGGTGCCACAGAGTTGTGGGCTTT-AAAA-G-AAAA
1 AGGTGCCACAGAGTTGTGGGCTTTGAAAAGGAAAAA
*
1616804 AGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAA
1 AGGTGCCACAGAGTTGTGGGCTTTGAAAAGGAAAAA
* *
1616840 AGAGTGCCACAAAGTTGTGGGCTTT-AAAA-G-AAGA
1 AG-GTGCCACAGAGTTGTGGGCTTTGAAAAGGAAAAA
*
1616874 AGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAA
1 AGGTGCCACAGAGTTGTGGGCTTTGAAAAGGAAAAA
1616910 AGAGTGCCACA
1 AG-GTGCCACA
1616921 AAGTCGTAGG
Statistics
Matches: 101, Mismatches: 8, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
33 43 0.43
34 13 0.13
35 3 0.03
36 15 0.15
37 27 0.27
ACGTcount: A:0.35, C:0.13, G:0.33, T:0.19
Consensus pattern (36 bp):
AGGTGCCACAGAGTTGTGGGCTTTGAAAAGGAAAAA
Found at i:1616833 original size:87 final size:88
Alignment explanation
Indices: 1616685--1616854 Score: 288
Period size: 87 Copynumber: 1.9 Consensus size: 88
1616675 GGGAAAAAGA
* * *
1616685 GTGCCACGGAGTTGTGGGCTTTAAACGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGGA
1 GTGCCACAGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGAA
*
1616750 AAGAGAGTGCCACAAAGTCGTAG
66 AAAAGAGTGCCACAAAGTCGTAG
*
1616773 GTGCCACAGAGTTGTGGGCTTTAAA-AGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAA
1 GTGCCACAGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGAA
1616837 AAAAGAGTGCCACAAAGT
66 AAAAGAGTGCCACAAAGT
1616855 TGTGGGCTTT
Statistics
Matches: 77, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
87 53 0.69
88 24 0.31
ACGTcount: A:0.33, C:0.14, G:0.34, T:0.19
Consensus pattern (88 bp):
GTGCCACAGAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGGAA
AAAAGAGTGCCACAAAGTCGTAG
Found at i:1616924 original size:70 final size:70
Alignment explanation
Indices: 1616773--1616919 Score: 258
Period size: 70 Copynumber: 2.1 Consensus size: 70
1616763 AAAGTCGTAG
* *
1616773 GTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAA
1 GTGCCACGGAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAA
1616838 AAAGA
66 AAAGA
**
1616843 GTGCCACAAAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAA
1 GTGCCACGGAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAA
1616908 AAAGA
66 AAAGA
1616913 GTGCCAC
1 GTGCCAC
1616920 AAAGTCGTAG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 75 1.00
ACGTcount: A:0.35, C:0.13, G:0.33, T:0.20
Consensus pattern (70 bp):
GTGCCACGGAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAA
AAAGA
Found at i:1616933 original size:157 final size:156
Alignment explanation
Indices: 1616615--1617511 Score: 1204
Period size: 157 Copynumber: 5.9 Consensus size: 156
1616605 GGGAAAAAGA
* * *
1616615 GTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
1 GTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAA
** * * *
1616680 AAAGAGTGCCACGGAGTTGTGGGCTTTAAACGGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAA
66 AAAGAGTGCCACAAAGTTGTGGGCTTTAAA-AGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAA
*
1616745 AGGGAAAGAGAGTGCCACAAAGTCGTAG
130 A-GGAAAAAGAGTGCCACAAAGTCGTAG
1616773 GTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAA
1 GTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAA
1616838 AAAGAGTGCCACAAAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAA
66 AAAGAGTGCCACAAAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAA
1616903 GGAAAAAAGAGTGCCACAAAGTCGTAG
131 GG-AAAAAGAGTGCCACAAAGTCGTAG
1616930 GTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAA
1 GTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAA
1616995 AAAGAGTGCCACAAAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAA
66 AAAGAGTGCCACAAAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAA
1617060 GGAAAAAAGAGTGCCACAAAGTCGTAG
131 GG-AAAAAGAGTGCCACAAAGTCGTAG
1617087 GTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAA
1 GTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAA
*
1617152 AAGGAGTGCCACAAAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAA
66 AAAGAGTGCCACAAAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAA
*
1617217 -GAAGAAG-GTTGCCAC-----C----
131 GGAAAAAGAG-TGCCACAAAGTCGTAG
** * * * *
1617233 --G--AC-TTG-TGTGGGCTTTAGGAAGGGAGAAAGATGCCACGGAGTTGTGGAC-TT-AAAAGG
1 GTGCCACAGAGTTGTGGGCTTTA--AA-AGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGG
* ** * *
1617290 GAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTTGA
63 AAAAAAGAGTGCCACAAAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGA
1617355 AAAGG-----GA-----A-AAA---G-A-
128 AAAGGAAAAAGAGTGCCACAAAGTCGTAG
* *
1617368 GTGCCACGGAGTTGTGGGCTTTAAACAGAAAAATGTGCCACGGAGTTGTGGGCTTTGAAAA-GAA
1 GTGCCACAGAGTTGTGGGCTTTAAA-AGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAA
* *
1617432 GAAAGAGTGCCACGAAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAA
65 AAAAGAGTGCCACAAAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAA
*
1617497 A-GAAGAAG-GTGCCAC
130 AGGAAAAAGAGTGCCAC
1617512 GGAGTTGTGG
Statistics
Matches: 672, Mismatches: 36, Indels: 71
0.86 0.05 0.09
Matches are distributed among these distances:
132 1 0.00
137 2 0.00
139 27 0.04
140 78 0.12
141 84 0.12
142 7 0.01
143 23 0.03
144 2 0.00
148 1 0.00
150 1 0.00
154 1 0.00
155 11 0.02
156 3 0.00
157 341 0.51
158 90 0.13
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.20
Consensus pattern (156 bp):
GTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAA
AAAGAGTGCCACAAAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAA
GGAAAAAGAGTGCCACAAAGTCGTAG
Found at i:1616975 original size:33 final size:36
Alignment explanation
Indices: 1616928--1617077 Score: 204
Period size: 33 Copynumber: 4.3 Consensus size: 36
1616918 ACAAAGTCGT
1616928 AGGTGCCACAGAGTTGTGGGCTTT-AAAA-G-AAAA
1 AGGTGCCACAGAGTTGTGGGCTTTGAAAAGGAAAAA
*
1616961 AGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAA
1 AGGTGCCACAGAGTTGTGGGCTTTGAAAAGGAAAAA
* *
1616997 AGAGTGCCACAAAGTTGTGGGCTTT-AAAA-G-AAGA
1 AG-GTGCCACAGAGTTGTGGGCTTTGAAAAGGAAAAA
*
1617031 AGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAA
1 AGGTGCCACAGAGTTGTGGGCTTTGAAAAGGAAAAA
1617067 AGAGTGCCACA
1 AG-GTGCCACA
1617078 AAGTCGTAGG
Statistics
Matches: 101, Mismatches: 8, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
33 43 0.43
34 13 0.13
35 3 0.03
36 15 0.15
37 27 0.27
ACGTcount: A:0.35, C:0.13, G:0.33, T:0.19
Consensus pattern (36 bp):
AGGTGCCACAGAGTTGTGGGCTTTGAAAAGGAAAAA
Found at i:1616989 original size:87 final size:87
Alignment explanation
Indices: 1616843--1617011 Score: 320
Period size: 87 Copynumber: 1.9 Consensus size: 87
1616833 GGAAAAAAGA
*
1616843 GTGCCACAAAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAA
1 GTGCCACAAAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAA
1616908 AAAGAGTGCCACAAAGTCGTAG
66 AAAGAGTGCCACAAAGTCGTAG
*
1616930 GTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAA
1 GTGCCACAAAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAA
1616995 AAAGAGTGCCACAAAGT
66 AAAGAGTGCCACAAAGT
1617012 TGTGGGCTTT
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
87 80 1.00
ACGTcount: A:0.35, C:0.14, G:0.32, T:0.20
Consensus pattern (87 bp):
GTGCCACAAAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAA
AAAGAGTGCCACAAAGTCGTAG
Found at i:1617081 original size:70 final size:68
Alignment explanation
Indices: 1616930--1617076 Score: 222
Period size: 70 Copynumber: 2.1 Consensus size: 68
1616920 AAAGTCGTAG
*
1616930 GTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAA
1 GTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAA-G-AA
1616995 AAAGA
64 AAAGA
** *
1617000 GTGCCACAAAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAA
1 GTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAA-G-AA
1617065 AAAGA
64 AAAGA
1617070 GTGCCAC
1 GTGCCAC
1617077 AAAGTCGTAG
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 75 1.00
ACGTcount: A:0.35, C:0.13, G:0.33, T:0.20
Consensus pattern (68 bp):
GTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAA
AGA
Found at i:1617091 original size:87 final size:87
Alignment explanation
Indices: 1617000--1617168 Score: 311
Period size: 87 Copynumber: 1.9 Consensus size: 87
1616990 GGAAAAAAGA
*
1617000 GTGCCACAAAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAA
1 GTGCCACAAAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAA
1617065 AAAGAGTGCCACAAAGTCGTAG
66 AAAGAGTGCCACAAAGTCGTAG
*
1617087 GTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAA
1 GTGCCACAAAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAA
*
1617152 AAGGAGTGCCACAAAGT
66 AAAGAGTGCCACAAAGT
1617169 TGTGGGCTTT
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 79 1.00
ACGTcount: A:0.34, C:0.14, G:0.33, T:0.20
Consensus pattern (87 bp):
GTGCCACAAAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAA
AAAGAGTGCCACAAAGTCGTAG
Found at i:1617200 original size:70 final size:69
Alignment explanation
Indices: 1617087--1617548 Score: 564
Period size: 70 Copynumber: 6.6 Consensus size: 69
1617077 AAAGTCGTAG
*
1617087 GTGCCACAGAGTTGTGGGCTTT-AAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAA
1 GTGCCACGGAGTTGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAA-GAA
1617151 AAAGGA
65 AAA-GA
** * *
1617157 GTGCCACAAAGTTGTGGGCTTT-AAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAG
1 GTGCCACGGAGTTGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAA
1617221 AAG-
66 AAGA
* * ** * * *
1617224 GTTGCCACCGACTTGTGTGGGCTTTAGGAAGGGAGAAAGATGCCACGGAGTTGTGGAC-TT-AAA
1 G-TGCCACGGA-GT-TGTGGGCTTT--GAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAA
1617287 AGGGAAAAAGA
61 A--GAAAAAGA
*
1617298 GTGCCACGGAGTTGTGGGCTTT-AAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGA
1 GTGCCACGGAGTTGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAA--GA
1617362 AAAAGA
64 AAAAGA
*
1617368 GTGCCACGGAGTTGTGGGCTTT-AAACAGAAAAATGTGCCACGGAGTTGTGGGCTTTGAAAAGAA
1 GTGCCACGGAGTTGTGGGCTTTGAAA-AGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAA
1617432 GAAAGA
65 -AAAGA
* * *
1617438 GTGCCACGAAGTTGTGGGCTTT-AAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAG
1 GTGCCACGGAGTTGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAA
1617502 AAG-
66 AAGA
1617505 GTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGAGTGCCAC
1 GTGCCACGGAGTTGTGGGCTTTGAAAA-G-AAAAAG-GTGCCAC
1617549 AAAGTCGTAG
Statistics
Matches: 347, Mismatches: 28, Indels: 33
0.85 0.07 0.08
Matches are distributed among these distances:
67 22 0.06
68 39 0.11
69 48 0.14
70 141 0.41
71 55 0.16
72 3 0.01
73 38 0.11
74 1 0.00
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.20
Consensus pattern (69 bp):
GTGCCACGGAGTTGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAA
AAGA
Found at i:1617222 original size:34 final size:34
Alignment explanation
Indices: 1617085--1617548 Score: 546
Period size: 34 Copynumber: 13.3 Consensus size: 34
1617075 ACAAAGTCGT
*
1617085 AGGTGCCACAGAGTTGTGGGCTTT-AAAAGAAAA
1 AGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAA
1617118 AGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAA
1 AGGTGCCACGGAGTTGTGGGCTTTGAAAA-GAAAA
** *
1617153 AGGAGTGCCACAAAGTTGTGGGCTTT-AAAAGAAGA
1 A-G-GTGCCACGGAGTTGTGGGCTTTGAAAAGAAAA
*
1617188 AGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGA
1 AGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAA
* * ** *
1617222 AGGTTGCCACCGACTTGTGTGGGCTTTAGGAAGGGAGAA
1 AGG-TGCCACGGA-GT-TGTGGGCTTT--GAAAAGAAAA
* *
1617261 AGATGCCACGGAGTTGTGGAC-TT-AAAAGGGAAAA
1 AGGTGCCACGGAGTTGTGGGCTTTGAAAA--GAAAA
1617295 AGAGTGCCACGGAGTTGTGGGCTTT-AAAAGAAAA
1 AG-GTGCCACGGAGTTGTGGGCTTTGAAAAGAAAA
*
1617329 AAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAA
1 AGGTGCCACGGAGTTGTGGGCTTTGAAAA--GAAAA
1617365 AGAGTGCCACGGAGTTGTGGGCTTT-AAACAGAAAA
1 AG-GTGCCACGGAGTTGTGGGCTTTGAAA-AGAAAA
*
1617400 ATGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAA
1 AGGTGCCACGGAGTTGTGGGCTTTGAAAAGAA-AA
* *
1617435 AGAGTGCCACGAAGTTGTGGGCTTT-AAAAGAAGA
1 AG-GTGCCACGGAGTTGTGGGCTTTGAAAAGAAAA
*
1617469 AGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGA
1 AGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAA
1617503 AGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAA
1 AGGTGCCACGGAGTTGTGGGCTTTGAAAA-G-AAAA
1617539 AGAGTGCCAC
1 AG-GTGCCAC
1617549 AAAGTCGTAG
Statistics
Matches: 376, Mismatches: 29, Indels: 48
0.83 0.06 0.11
Matches are distributed among these distances:
32 2 0.01
33 86 0.23
34 100 0.27
35 58 0.15
36 53 0.14
37 61 0.16
38 8 0.02
39 8 0.02
ACGTcount: A:0.33, C:0.12, G:0.34, T:0.20
Consensus pattern (34 bp):
AGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAAA
Found at i:1617604 original size:33 final size:36
Alignment explanation
Indices: 1617557--1617706 Score: 186
Period size: 33 Copynumber: 4.3 Consensus size: 36
1617547 ACAAAGTCGT
*
1617557 AGGTGCCATAGAGTTGTGGGCTTT-AAAA-G-AAAA
1 AGGTGCCACAGAGTTGTGGGCTTTGAAAAGGAAAAA
*
1617590 AGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAA
1 AGGTGCCACAGAGTTGTGGGCTTTGAAAAGGAAAAA
* * *
1617626 AGAGTGCCACAAAGTTGTGGG-TTTTAAAA-G-AAGA
1 AG-GTGCCACAGAGTTGTGGGCTTTGAAAAGGAAAAA
*
1617660 AGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAA
1 AGGTGCCACAGAGTTGTGGGCTTTGAAAAGGAAAAA
1617696 AGAGTGCCACA
1 AG-GTGCCACA
1617707 AACTCGTAGG
Statistics
Matches: 98, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
33 38 0.39
34 16 0.16
35 3 0.03
36 18 0.18
37 23 0.23
ACGTcount: A:0.35, C:0.11, G:0.33, T:0.21
Consensus pattern (36 bp):
AGGTGCCACAGAGTTGTGGGCTTTGAAAAGGAAAAA
Found at i:1617616 original size:87 final size:88
Alignment explanation
Indices: 1617469--1617640 Score: 310
Period size: 87 Copynumber: 2.0 Consensus size: 88
1617459 TAAAAGAAGA
* *
1617469 AGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGG
1 AGGTGCCACAGAGTTGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGG
1617534 AAAAAAGAGTGCCACAAAGTCGT
66 AAAAAAGAGTGCCACAAAGTCGT
*
1617557 AGGTGCCATAGAGTTGTGGGCTTT-AAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGG
1 AGGTGCCACAGAGTTGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGG
1617621 AAAAAAGAGTGCCACAAAGT
66 AAAAAAGAGTGCCACAAAGT
1617641 TGTGGGTTTT
Statistics
Matches: 81, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
87 59 0.73
88 22 0.27
ACGTcount: A:0.34, C:0.13, G:0.34, T:0.20
Consensus pattern (88 bp):
AGGTGCCACAGAGTTGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGG
AAAAAAGAGTGCCACAAAGTCGT
Found at i:1617672 original size:70 final size:70
Alignment explanation
Indices: 1617568--1618221 Score: 445
Period size: 70 Copynumber: 9.3 Consensus size: 70
1617558 GGTGCCATAG
*
1617568 AGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGAGTGC
1 AGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGAGTGC
*
1617633 CACAA
66 CACGA
*
1617638 AGTTGTGGGTTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGAGTGC
1 AGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGAGTGC
*
1617703 CACAA
66 CACGA
* * * * ** ** *** * * * * ***
1617708 ACTCGTAGGTGC--CACAGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAG-TTGTGGGCTT
1 AGTTGT-GG-GCTTTA-AAAGAAGAAGG--TGCCACG---GAGTTG---TGG-GCTT-T--GAAA
* * *
1617770 TGAAAAGGAAAAAAGAGTGCCACAA
51 AGGAAA-----AAAGAGTGCCACGA
* * * *
1617795 AGTTGTGGGCTTTAAAAGAAGAAGCTGCCACGGAGTTATGAGCTTTGAAAA-G-AAGAAG-GTTG
1 AGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGAG-TG
1617857 CCACCGA
65 CCA-CGA
** * * * * *
1617864 CTTGTGTGGGCTTTAGGAAGGGAGAAAGATGCCACGGAGTTGTGGAC-TT-AAAAGGGAAAAAGA
1 AGT-TGTGGGCTTTA--AAAGAAG-AAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGA
*
1617927 GTGCCACGG
62 GTGCCACGA
* * *
1617936 AGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGC
1 AGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGAGTGC
*
1618001 CACGG
66 CACGA
* *
1618006 AGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAA-GAAGAAAGAGTG
1 AGTTGTGGGCTTTAAA-AGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGAGTG
1618070 CCACGA
65 CCACGA
*
1618076 AGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAA-G-AAGAAG-GTGC
1 AGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGAGTGC
*
1618138 CACGG
66 CACGA
* * * *
1618143 AGTTGTGGGC--T-GAA-ACG--GGTGCCACGGAGTTGTGGAC-TT-AAAGATG-AAAAA-AGTG
1 AGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAA-AGGAAAAAAGAGTG
1618198 CCACGGA
65 CCAC-GA
1618205 A-TTGTGGGCTTTAAAAG
1 AGTTGTGGGCTTTAAAAG
1618222 GGTGCCACGG
Statistics
Matches: 461, Mismatches: 80, Indels: 91
0.73 0.13 0.14
Matches are distributed among these distances:
59 3 0.01
60 3 0.01
61 39 0.08
62 2 0.00
63 3 0.01
64 4 0.01
65 1 0.00
67 19 0.04
68 31 0.07
69 44 0.10
70 154 0.33
71 57 0.12
72 12 0.03
73 33 0.07
74 1 0.00
75 1 0.00
76 4 0.01
77 2 0.00
78 3 0.01
79 4 0.01
80 2 0.00
81 3 0.01
82 5 0.01
84 3 0.01
85 2 0.00
86 7 0.02
87 19 0.04
ACGTcount: A:0.33, C:0.13, G:0.33, T:0.21
Consensus pattern (70 bp):
AGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGAGTGC
CACGA
Found at i:1617688 original size:157 final size:146
Alignment explanation
Indices: 1617567--1618127 Score: 695
Period size: 157 Copynumber: 3.8 Consensus size: 146
1617557 AGGTGCCATA
1617567 GAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGAGTG
1 GAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGAGTG
* *
1617632 CCACAAAGTTGTGGGTTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAA
66 CCACGAAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAA
*
1617697 GAGTGCCACAAACTCGTAGGTGCCACA
131 GAGTGCCAC--A--CG-A---G---CT
1617724 GAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGAGTG
1 GAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGAGTG
* * * * *
1617789 CCACAAAGTTGTGGGCTTTAAAAGAAGAAGCTGCCACGGAGTTATGAGCTTTGAAAA-G-AAGAA
66 CCACGAAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAA
1617852 G-GTTGCCAC-CGA-CT
131 GAG-TGCCACACGAGCT
* * * * * *
1617866 -TG-TGTGGGCTTTAGGAAGGGAGAAAGATGCCACGGAGTTGTGGAC-TT-AAAAGGGAAAAAGA
1 GAGTTGTGGGCTTTA--AA-AGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGA
* * * *
1617927 GTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
63 GTGCCACGAAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAA
1617992 AAAGAGTG-C-CAC--G--
128 AAAGAGTGCCACACGAGCT
*
1618005 GAGTTGTGGGCTTTAAACAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAA-GAAGAAAGAGT
1 GAGTTGTGGGCTTTAAA-AGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGAGT
1618069 GCCACGAAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAG
65 GCCACGAAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAG
1618128 AAGAAGGTGC
Statistics
Matches: 360, Mismatches: 31, Indels: 43
0.83 0.07 0.10
Matches are distributed among these distances:
139 25 0.07
140 79 0.22
141 83 0.23
142 8 0.02
143 30 0.08
144 1 0.00
149 1 0.00
150 2 0.01
154 1 0.00
155 11 0.03
156 1 0.00
157 118 0.33
ACGTcount: A:0.34, C:0.12, G:0.33, T:0.21
Consensus pattern (146 bp):
GAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGAGTG
CCACGAAGTTGTGGGCTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAA
GAGTGCCACACGAGCT
Found at i:1617720 original size:87 final size:87
Alignment explanation
Indices: 1617629--1617795 Score: 307
Period size: 87 Copynumber: 1.9 Consensus size: 87
1617619 GGAAAAAAGA
* *
1617629 GTGCCACAAAGTTGTGGGTTTTAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAA
1 GTGCCACAAAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAA
1617694 AAAGAGTGCCACAAACTCGTAG
66 AAAGAGTGCCACAAACTCGTAG
*
1617716 GTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAA
1 GTGCCACAAAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAA
1617781 AAAGAGTGCCACAAA
66 AAAGAGTGCCACAAA
1617796 GTTGTGGGCT
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 77 1.00
ACGTcount: A:0.35, C:0.14, G:0.31, T:0.20
Consensus pattern (87 bp):
GTGCCACAAAGTTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAA
AAAGAGTGCCACAAACTCGTAG
Found at i:1618085 original size:211 final size:209
Alignment explanation
Indices: 1617087--1618221 Score: 1032
Period size: 211 Copynumber: 5.3 Consensus size: 209
1617077 AAAGTCGTAG
*
1617087 GTGCCACAGAGTTGTGGGCTTT-AAAA--GAAAAAG-GTGCCACGGAGTTGTGGGCTTTGAAAAG
1 GTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAA-
** *
1617148 GAAAAAGGAGTGCCACAAAGTTGTGGGCTTT-AAAAGAAG-AAGGTGCCACGGAGTTGTGGGCTT
64 GAAAAA-G-GTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAAGGTGCCACGAAGTTGTGGGCTT
* * * * * *
1617211 T-GAAAAGAAGAAGGTTGCCACCGACTTGTGTGGGCTTTAGGAAGGGAGAAAGA-TGCCACGGAG
127 TAG-AAAGAAGAAAGATGCCACGGA-GT-TGTGGGCTTTA-AAAGGGAAAAAGAGTGCCACGGAG
*
1617274 TTGTGGAC-TTAAAAGGGAAAAAGA
188 TTGTGGGCTTTAAAA--GAAAAA-A
1617298 GTGCCACGGAGTTGTGGGCTTT-AAAA--GAAAAA-AGTGCCACGGAGTTGTGGGCTTTGAAAAG
1 GTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAA-
* *
1617359 GGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAACAGAA-AAATGTGCCACGGAGTTGTGGGCT
64 -GAAAAAG-GTGCCACGGAGTTGTGGGCTTTGAAA-AGAAGAAAGGTGCCACGAAGTTGTGGGCT
* *
1617422 TT-GAAAAGAAGAAAGAGTGCCACGAAGTTGTGGGCTTTAAAA--GAAGAAG-GTGCCACGGAGT
126 TTAG-AAAGAAGAAAGA-TGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGT
* *
1617483 TGTGGGCTTTGAAAAGAAGAAG
189 TGTGGGCTTT-AAAAGAAAAAA
*
1617505 GTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGAGTGCCACAAAGTCGTAGGTGCCATAGAG
1 GTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTG-C-C--A--C------G-----GAG
*
1617570 TTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGAGTGCCA
49 TTGTGGGCTTTAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAA-GAAGAAAG-GTGCCA
* * *
1617635 CAAAGTTGTGGGTTTTA-AAAGAAG-AAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAAG
112 CGAAGTTGTGGGCTTTAGAAAGAAGAAAGATGCCACGGAGTTGTGGGCTTT-AAAAGG------G
* *
1617698 AGTGCCACAAACTCGTAGGTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAG
170 A-----A-AAA---G-A-GTGCCACGGAGTTGTGGGCTTTAAAAGAAAAAA
* **
1617749 GTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAAAGAGTGCCACAAAGTTGTGGGCTTTAAAAGA
1 GTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGA
* * * * **
1617814 AGAAGCTGCCACGGAGTTATGAGCTTTGAAAAGAAG-AAGGTTGCCACCGACTTGTGTGGGCTTT
66 AAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAAGG-TGCCA-CGAAGT-TGTGGGCTTT
* * *
1617878 AGGAAGGGAGAAAGATGCCACGGAGTTGTGGAC-TTAAAAGGGAAAAAGAGTGCCACGGAGTTGT
128 A-GAAAGAAGAAAGATGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGT
1617942 GGGCTTTAAAAGAAAAAA
192 GGGCTTTAAAAGAAAAAA
1617960 GTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAACAG
1 GTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA-AG
1618025 AAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAAGAGTGCCACGAAGTTGTGGGCTTTA
65 AAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAAG-GTGCCACGAAGTTGTGGGCTTTA
* *
1618090 -AAAGAAG-AAGGTGCCACGGAGTTGTGGGCTTTGAAAA--GAAGAAG-GTGCCACGGAGTTGTG
129 GAAAGAAGAAAGATGCCACGGAGTTGTGGGCTTT-AAAAGGGAAAAAGAGTGCCACGGAGTTGTG
***
1618150 GGC--T----GAAACGG
193 GGCTTTAAAAGAAAAAA
* * *
1618161 GTGCCACGGAGTTGTGGAC-TT--AAAGATGAAAAA-AGTGCCACGGAATTGTGGGCTTTAAAAG
1 GTGCCACGGAGTTGTGGGCTTTGAAAAG-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAG
1618222 GGTGCCACGG
Statistics
Matches: 795, Mismatches: 62, Indels: 148
0.79 0.06 0.15
Matches are distributed among these distances:
197 2 0.00
198 29 0.04
199 6 0.01
200 2 0.00
201 22 0.03
205 1 0.00
207 41 0.05
208 57 0.07
209 9 0.01
210 15 0.02
211 199 0.25
212 89 0.11
213 17 0.02
214 1 0.00
215 1 0.00
216 3 0.00
217 2 0.00
222 2 0.00
223 1 0.00
224 44 0.06
225 28 0.04
226 16 0.02
227 80 0.10
228 20 0.03
229 7 0.01
230 20 0.03
233 2 0.00
238 2 0.00
239 2 0.00
240 1 0.00
242 2 0.00
243 1 0.00
244 50 0.06
245 21 0.03
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.21
Consensus pattern (209 bp):
GTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGA
AAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAAGGTGCCACGAAGTTGTGGGCTTTAGA
AAGAAGAAAGATGCCACGGAGTTGTGGGCTTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGC
TTTAAAAGAAAAAA
Found at i:1618147 original size:34 final size:33
Alignment explanation
Indices: 1617714--1618221 Score: 528
Period size: 34 Copynumber: 14.9 Consensus size: 33
1617704 ACAAACTCGT
*
1617714 AGGTGCCACAGAGTTGTGGGCTTTAAAAGAAAA
1 AGGTGCCACGGAGTTGTGGGCTTTAAAAGAAAA
1617747 AGGTGCCACGGAGTTGTGGGCTTTGAAAAGGAAAAA
1 AGGTGCCACGGAGTTGTGGGCTTT-AAAA-G-AAAA
** *
1617783 AGAGTGCCACAAAGTTGTGGGCTTTAAAAGAAGA
1 AG-GTGCCACGGAGTTGTGGGCTTTAAAAGAAAA
* * * *
1617817 AGCTGCCACGGAGTTATGAGCTTTGAAAAGAAGA
1 AGGTGCCACGGAGTTGTGGGCTTT-AAAAGAAAA
* * * *
1617851 AGGTTGCCACCGACTTGTGTGGGCTTTAGGAAGGGAGAA
1 AGG-TGCCACGGA-GT-TGTGGGCTTTA--AA-AGAAAA
* *
1617890 AGATGCCACGGAGTTGTGGAC-TTAAAAGGGAAAA
1 AGGTGCCACGGAGTTGTGGGCTTTAAAA--GAAAA
1617924 AGAGTGCCACGGAGTTGTGGGCTTTAAAAGAAAA
1 AG-GTGCCACGGAGTTGTGGGCTTTAAAAGAAAA
*
1617958 AAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAA
1 AGGTGCCACGGAGTTGTGGGCTTT-AAAA--GAAAA
1617994 AGAGTGCCACGGAGTTGTGGGCTTTAAACAGAAAA
1 AG-GTGCCACGGAGTTGTGGGCTTTAAA-AGAAAA
1618029 AGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAA
1 AGGTGCCACGGAGTTGTGGGCTTT-AAAAGAA-AA
* *
1618064 AGAGTGCCACGAAGTTGTGGGCTTTAAAAGAAGA
1 AG-GTGCCACGGAGTTGTGGGCTTTAAAAGAAAA
*
1618098 AGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGA
1 AGGTGCCACGGAGTTGTGGGCTTT-AAAAGAAAA
*
1618132 AGGTGCCACGGAGTTGTGGGC--T----GAAAC
1 AGGTGCCACGGAGTTGTGGGCTTTAAAAGAAAA
* *
1618159 GGGTGCCACGGAGTTGTGGAC-TTAAAGATGAAAA
1 AGGTGCCACGGAGTTGTGGGCTTTAAA-A-GAAAA
* *
1618193 AAGTGCCACGGAATTGTGGGCTTTAAAAG
1 AGGTGCCACGGAGTTGTGGGCTTTAAAAG
1618222 GGTGCCACGG
Statistics
Matches: 404, Mismatches: 39, Indels: 64
0.80 0.08 0.13
Matches are distributed among these distances:
27 22 0.05
28 1 0.00
32 1 0.00
33 86 0.21
34 117 0.29
35 56 0.14
36 54 0.13
37 52 0.13
38 10 0.02
39 5 0.01
ACGTcount: A:0.33, C:0.13, G:0.34, T:0.20
Consensus pattern (33 bp):
AGGTGCCACGGAGTTGTGGGCTTTAAAAGAAAA
Found at i:1618174 original size:61 final size:62
Alignment explanation
Indices: 1618025--1618246 Score: 245
Period size: 61 Copynumber: 3.5 Consensus size: 62
1618015 CTTTAAACAG
* *
1618025 AAAAA-GGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAAGAGTGCCACGAAGTTGTGGGCTTT
1 AAAAAGGGTGCCACGGAGTTGTGGACTTTGAAAAGAAG-AAG-GTGCCACGGAGTTGTGGGC-TT
*
1618089 AAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACGGAGTTGTGGGC-
1 -AAA-AAG--GGTGCCACGGAGTTGTGGACTTTGAAAAGAAGAAGGTGCCACGGAGTTGTGGGCT
1618153 T
62 T
* * * * *
1618154 GAAACGGGTGCCACGGAGTTGTGGAC-TT-AAAGATGAAAAAAGTGCCACGGAATTGTGGGCTT
1 AAAAAGGGTGCCACGGAGTTGTGGACTTTGAAA-A-GAAGAAGGTGCCACGGAGTTGTGGGCTT
* *
1618216 TAAAAGGGTGCCACGGAATTGTGGACTTTGA
1 AAAAAGGGTGCCACGGAGTTGTGGACTTTGA
1618247 GCAGAGATTG
Statistics
Matches: 138, Mismatches: 10, Indels: 19
0.83 0.06 0.11
Matches are distributed among these distances:
59 3 0.02
60 3 0.02
61 42 0.30
62 24 0.17
63 4 0.03
64 3 0.02
65 4 0.03
66 2 0.01
67 18 0.13
68 3 0.02
69 32 0.23
ACGTcount: A:0.31, C:0.13, G:0.35, T:0.21
Consensus pattern (62 bp):
AAAAAGGGTGCCACGGAGTTGTGGACTTTGAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTT
Found at i:1618271 original size:31 final size:31
Alignment explanation
Indices: 1618236--1618302 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
1618226 CCACGGAATT
*
1618236 GTGGACTTTGAGCAGAGATTGCCACTGAGTC
1 GTGGACTTTGAGAAGAGATTGCCACTGAGTC
1618267 GTGGACTTTGAGAAGAGATTGCCACTGAGTC
1 GTGGACTTTGAGAAGAGATTGCCACTGAGTC
1618298 GTGGA
1 GTGGA
1618303 TTTTTTTATA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.24, C:0.16, G:0.34, T:0.25
Consensus pattern (31 bp):
GTGGACTTTGAGAAGAGATTGCCACTGAGTC
Found at i:1619320 original size:17 final size:17
Alignment explanation
Indices: 1619288--1619319 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1619278 GTTTTTCCTC
1619288 TTTTGTTTTCTTTTTTG
1 TTTTGTTTTCTTTTTTG
1619305 TTTTG-TTTCTTTTTT
1 TTTTGTTTTCTTTTTT
1619320 TTGGAAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.00, C:0.06, G:0.09, T:0.84
Consensus pattern (17 bp):
TTTTGTTTTCTTTTTTG
Found at i:1619595 original size:32 final size:32
Alignment explanation
Indices: 1619559--1619630 Score: 135
Period size: 32 Copynumber: 2.2 Consensus size: 32
1619549 TGCCTTTGCA
1619559 TTTTTTTTGTGTTTTTTTTTGTTTTTTTGTTT
1 TTTTTTTTGTGTTTTTTTTTGTTTTTTTGTTT
*
1619591 TTTTTTTTGTGTTTTTTTTTGTTTTTTTTTTT
1 TTTTTTTTGTGTTTTTTTTTGTTTTTTTGTTT
1619623 TTTTTTTT
1 TTTTTTTT
1619631 TTCATCACTT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (32 bp):
TTTTTTTTGTGTTTTTTTTTGTTTTTTTGTTT
Found at i:1619632 original size:12 final size:12
Alignment explanation
Indices: 1619559--1619632 Score: 95
Period size: 12 Copynumber: 6.6 Consensus size: 12
1619549 TGCCTTTGCA
*
1619559 TTTTTTTTGTGT
1 TTTTTTTTGTTT
1619571 TTTTTTTTG---
1 TTTTTTTTGTTT
1619580 -TTTTTTTGTTT
1 TTTTTTTTGTTT
*
1619591 TTTTTTTTGTGT
1 TTTTTTTTGTTT
1619603 TTTTTTTTGTTT
1 TTTTTTTTGTTT
1619615 TTTTTTTT-TTT
1 TTTTTTTTGTTT
1619626 TTTTTTT
1 TTTTTTT
1619633 CATCACTTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
8 8 0.14
11 10 0.18
12 38 0.68
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (12 bp):
TTTTTTTTGTTT
Found at i:1619643 original size:1 final size:1
Alignment explanation
Indices: 1619559--1619632 Score: 85
Period size: 1 Copynumber: 74.0 Consensus size: 1
1619549 TGCCTTTGCA
* * * * * * *
1619559 TTTTTTTTGTGTTTTTTTTTGTTTTTTTGTTTTTTTTTTTGTGTTTTTTTTTGTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1619624 TTTTTTTTT
1 TTTTTTTTT
1619633 CATCACTTTT
Statistics
Matches: 59, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 59 1.00
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (1 bp):
T
Found at i:1619643 original size:33 final size:32
Alignment explanation
Indices: 1619574--1619648 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
1619564 TTTGTGTTTT
* ***
1619574 TTTTTGTTTTTTTGTTTTTTTTTTTGTGTTTT
1 TTTTTGTTTTTTTGTTTTTTTTTTTGTATCAC
* *
1619606 TTTTTGTTTTTTTTTTTTTTTTTTTTTCATCAC
1 TTTTTGTTTTTTTGTTTTTTTTTTTGT-ATCAC
1619639 TTTTTGTTTT
1 TTTTTGTTTT
1619649 AAGGGAACTC
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
32 25 0.69
33 11 0.31
ACGTcount: A:0.03, C:0.04, G:0.08, T:0.85
Consensus pattern (32 bp):
TTTTTGTTTTTTTGTTTTTTTTTTTGTATCAC
Found at i:1626603 original size:52 final size:52
Alignment explanation
Indices: 1626522--1626640 Score: 220
Period size: 52 Copynumber: 2.3 Consensus size: 52
1626512 TGAAAAGTTA
*
1626522 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
*
1626574 CTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
1626626 CTGCATGTATCGATA
1 CTGCATGTATCGATA
1626641 TAAAGATCAG
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Done.