Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008292.1 Hibiscus syriacus cultivar Beakdansim tig00110956_pilon, whole genome shotgun sequence
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: 1591938
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 7 of 8
Found at i:1265782 original size:13 final size:14
Alignment explanation
Indices: 1265766--1265823 Score: 55
Period size: 16 Copynumber: 3.9 Consensus size: 14
1265756 TTATTTTTGC
1265766 TTAATAT-TATATT
1 TTAATATATATATT
1265779 TTAATATATATATAT
1 TTAATATATATAT-T
*
1265794 ATATATATATATATAT
1 TTA-ATATATATAT-T
*
1265810 ATATATATATATAT
1 TTA-ATATATATAT
1265824 ATATATACTT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
13 7 0.17
14 5 0.12
15 3 0.07
16 26 0.63
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TTAATATATATATT
Found at i:1265789 original size:2 final size:2
Alignment explanation
Indices: 1265782--1265830 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1265772 TTATATTTTA
1265782 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1265824 AT AT AT A
1 AT AT AT A
1265831 CTTATAATAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1267006 original size:10 final size:10
Alignment explanation
Indices: 1266991--1267024 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
1266981 TTCATTTACC
1266991 ATTTATTTTT
1 ATTTATTTTT
1267001 ATTTATTTTT
1 ATTTATTTTT
* *
1267011 ATCTATTTCT
1 ATTTATTTTT
1267021 ATTT
1 ATTT
1267025 TACTAACGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.74
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:1276331 original size:1 final size:1
Alignment explanation
Indices: 1276325--1276376 Score: 59
Period size: 1 Copynumber: 52.0 Consensus size: 1
1276315 TCCTAAGTTG
* * * * *
1276325 AAAAAAAAAAACAAAACAAAAAACAAAAAACAAAAAAAAAAAAAACAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1276377 CGCTTAGGGT
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:1276340 original size:7 final size:7
Alignment explanation
Indices: 1276325--1276377 Score: 67
Period size: 7 Copynumber: 7.9 Consensus size: 7
1276315 TCCTAAGTTG
1276325 AAAAA-A
1 AAAAACA
1276331 AAAAAC-
1 AAAAACA
1276337 -AAAACA
1 AAAAACA
1276343 AAAAACA
1 AAAAACA
1276350 AAAAACAA
1 AAAAAC-A
*
1276358 AAAAAAA
1 AAAAACA
1276365 AAAAACA
1 AAAAACA
1276372 AAAAAC
1 AAAAAC
1276378 GCTTAGGGTG
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
5 5 0.12
6 5 0.12
7 25 0.61
8 6 0.15
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (7 bp):
AAAAACA
Found at i:1276352 original size:19 final size:17
Alignment explanation
Indices: 1276325--1276369 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 17
1276315 TCCTAAGTTG
1276325 AAAAAAAAAAACAAAACA
1 AAAAAAAAAAACAAAA-A
1276343 AAAAACAAAAAACAAAAA
1 AAAAA-AAAAAACAAAAA
1276361 AAAAAAAAA
1 AAAAAAAAA
1276370 CAAAAAACGC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.15
18 11 0.42
19 11 0.42
ACGTcount: A:0.91, C:0.09, G:0.00, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAACAAAAA
Found at i:1276362 original size:22 final size:23
Alignment explanation
Indices: 1276326--1276377 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
1276316 CCTAAGTTGA
* *
1276326 AAAAAAAAAACAAAACAAAAAAC
1 AAAAAACAAACAAAAAAAAAAAC
1276349 AAAAAACAAA-AAAAAAAAAAAC
1 AAAAAACAAACAAAAAAAAAAAC
1276371 AAAAAAC
1 AAAAAAC
1276378 GCTTAGGGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 18 0.67
23 9 0.33
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (23 bp):
AAAAAACAAACAAAAAAAAAAAC
Found at i:1277342 original size:105 final size:105
Alignment explanation
Indices: 1277156--1278055 Score: 1446
Period size: 105 Copynumber: 8.7 Consensus size: 105
1277146 AGGTTTTACC
1277156 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
*
1277221 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
*
1277261 CAGGGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
* *
1277326 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACGAAC-ATTTCTCAATTT
*
1277367 CTGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1277432 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
*
1277472 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1277537 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
*
1277577 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCTAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
* *
1277642 ACGAAAGGACCGATGGTTGTCAACGAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
1277682 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1277747 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
* * *
1277787 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAATGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
* * * *
1277852 ACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCCAATCT
66 ACGAAGGGACCGCTGGTTGTCAACGAAC-ATTTCTCAATTT
* * *
1277892 CAGAGCC-A----AACTTCACAACGAAGAATATTGGACTTCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
* * * *
1277952 ACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCCCAATCT
66 ACGAAGGGACCGCTGGTTGTCAACGAAC-ATTTCTCAATTT
* * * *
1277992 CAGAGCC-A----AACTTCACAACGAAGAATATTGGACTCTAGACAACGCAAGTCCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1278052 ACGA
66 ACGA
1278056 TGGATATCCA
Statistics
Matches: 768, Mismatches: 25, Indels: 9
0.96 0.03 0.01
Matches are distributed among these distances:
100 151 0.20
104 4 0.01
105 512 0.67
106 101 0.13
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACGAACATTTCTCAATTT
Found at i:1278601 original size:16 final size:16
Alignment explanation
Indices: 1278571--1278600 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1278561 ATATTTACAT
1278571 TTTATTTTTATTTTTA
1 TTTATTTTTATTTTTA
1278587 TTTA-TTTTATTTTT
1 TTTATTTTTATTTTT
1278601 TGTGTCAGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTATTTTTATTTTTA
Found at i:1279951 original size:13 final size:14
Alignment explanation
Indices: 1279935--1279976 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 14
1279925 TTATTTTTGC
1279935 TTAATAT-TATATT
1 TTAATATATATATT
1279948 TTAATATATATATAT
1 TTAATATATATAT-T
*
1279963 ATATATATATATAT
1 TTA-ATATATATAT
1279977 ATATATGTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 7 0.28
14 5 0.20
15 3 0.12
16 10 0.40
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
TTAATATATATATT
Found at i:1279958 original size:2 final size:2
Alignment explanation
Indices: 1279951--1279989 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1279941 TTATATTTTA
*
1279951 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1279990 CTTATAATAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1284513 original size:128 final size:128
Alignment explanation
Indices: 1284285--1285147 Score: 1609
Period size: 128 Copynumber: 6.7 Consensus size: 128
1284275 ACTATTAACA
* * *
1284285 TGAAGGAGCGTCCCCGGGGGCGCGTCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
*
1284350 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAAGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
*
1284413 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCTATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
*
1284478 TTATGTCACTCATGTCCCTCGGGGAAACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
*
1284541 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGTCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
*
1284606 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCATGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
* *
1284669 TGAAGGCGCGTTCCCGGGGGCGCGGCTTCTATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
*
1284734 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTATCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
1284797 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
*
1284862 TTATGTCACTCATGTTCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
*
1284925 TGAAGGCGCGTTCTCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1284990 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
1285053 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1285118 TTATGTCACTCATGTCCCTCGGGGACACTA
66 TTATGTCACTCATGTCCCTCGGGGACACTA
1285148 GATGGATTAT
Statistics
Matches: 713, Mismatches: 22, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
128 713 1.00
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.33
Consensus pattern (128 bp):
TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
Found at i:1285588 original size:34 final size:34
Alignment explanation
Indices: 1285550--1285619 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 34
1285540 AAATTTAATG
*
1285550 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * *
1285584 TTAAATTTTGAATAATATTATTTTTATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
1285618 TT
1 TT
1285620 TGAATAATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.56
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:1285639 original size:34 final size:34
Alignment explanation
Indices: 1285550--1285644 Score: 112
Period size: 28 Copynumber: 3.0 Consensus size: 34
1285540 AAATTTAATG
* * *
1285550 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTTGAATAATATAATTTTTATTTTAAAT
*
1285584 TTAAATTTTGAATAATATTATTTTTA---T---T
1 TTAAATTTTGAATAATATAATTTTTATTTTAAAT
1285612 TTAAATTTTGAATAATATAATTTTTATTTTAAA
1 TTAAATTTTGAATAATATAATTTTTATTTTAAA
1285645 AACATTTGTC
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
28 26 0.52
31 2 0.04
34 22 0.44
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.55
Consensus pattern (34 bp):
TTAAATTTTGAATAATATAATTTTTATTTTAAAT
Found at i:1286263 original size:63 final size:63
Alignment explanation
Indices: 1286164--1286295 Score: 194
Period size: 63 Copynumber: 2.1 Consensus size: 63
1286154 TATGGTATAA
* * *
1286164 AACCCTGCGGGCTAGGCATGTAACCTGGCGGGCTAGGCATGTAA-CCTGGCGAGCTAGGAATGT
1 AACCCTACGGGCTAGGAATGTAACCTGGCGGGCTAGGAATGTAACCCT-GCGAGCTAGGAATGT
* * *
1286227 AACCCTACGGGCTCGGAATGTAACCTGGCGGGCTAGGAATGTAACCCTGCGGGCTCGGAATGT
1 AACCCTACGGGCTAGGAATGTAACCTGGCGGGCTAGGAATGTAACCCTGCGAGCTAGGAATGT
1286290 AACCCT
1 AACCCT
1286296 GCAGAGATGG
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
63 59 0.95
64 3 0.05
ACGTcount: A:0.23, C:0.26, G:0.33, T:0.19
Consensus pattern (63 bp):
AACCCTACGGGCTAGGAATGTAACCTGGCGGGCTAGGAATGTAACCCTGCGAGCTAGGAATGT
Found at i:1286294 original size:21 final size:21
Alignment explanation
Indices: 1286164--1286297 Score: 166
Period size: 21 Copynumber: 6.4 Consensus size: 21
1286154 TATGGTATAA
*
1286164 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
1286185 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
*
1286206 AA-CCTGGCGAGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
* *
1286227 AACCCTACGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
1286248 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
1286269 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
1286290 AACCCTGC
1 AACCCTGC
1286298 AGAGATGGCA
Statistics
Matches: 101, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
20 6 0.06
21 89 0.88
22 6 0.06
ACGTcount: A:0.22, C:0.26, G:0.33, T:0.19
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:1286329 original size:21 final size:21
Alignment explanation
Indices: 1286303--1286344 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1286293 CCTGCAGAGA
*
1286303 TGGCATATGAACTGGTGGGCT
1 TGGCATATGAACTGGAGGGCT
*
1286324 TGGCATATGAAGTGGAGGGCT
1 TGGCATATGAACTGGAGGGCT
1286345 GGGTATGTAC
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:0.21, C:0.12, G:0.40, T:0.26
Consensus pattern (21 bp):
TGGCATATGAACTGGAGGGCT
Found at i:1288152 original size:15 final size:15
Alignment explanation
Indices: 1288118--1288155 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
1288108 TAATAAAAAA
*
1288118 AAAATAATATTTATAT
1 AAAAT-ATATTAATAT
1288134 -AAATATATTAATAT
1 AAAATATATTAATAT
1288148 AAAATATA
1 AAAATATA
1288156 ATAACTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
AAAATATATTAATAT
Found at i:1288174 original size:36 final size:34
Alignment explanation
Indices: 1288107--1288174 Score: 82
Period size: 36 Copynumber: 1.9 Consensus size: 34
1288097 ACATATTATT
* *
1288107 TTAATAAAAAAAAAATAATATTTATATAAATATA
1 TTAATAAAAAAAAAATAATATTTAAAAAAATATA
* *
1288141 TTAATATAAAATATAATAACTATTTAAAAAAATA
1 TTAATA-AAAAAAAAATAA-TATTTAAAAAAATA
1288175 CTAACATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 6 0.21
35 10 0.36
36 12 0.43
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.35
Consensus pattern (34 bp):
TTAATAAAAAAAAAATAATATTTAAAAAAATATA
Found at i:1291784 original size:35 final size:35
Alignment explanation
Indices: 1291719--1291788 Score: 106
Period size: 36 Copynumber: 2.0 Consensus size: 35
1291709 AACATCTACC
*
1291719 AAACTTTATCAAACTTTGAAAAACATTTTTCAAAG
1 AAACTTTACCAAACTTTGAAAAACATTTTTCAAAG
*
1291754 AAACATTTACCAAACTTTGAAAACCA-TTTTCAAAG
1 AAAC-TTTACCAAACTTTGAAAAACATTTTTCAAAG
1291789 TTGGTTGCCA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 13 0.41
36 19 0.59
ACGTcount: A:0.46, C:0.17, G:0.06, T:0.31
Consensus pattern (35 bp):
AAACTTTACCAAACTTTGAAAAACATTTTTCAAAG
Found at i:1296360 original size:36 final size:35
Alignment explanation
Indices: 1296313--1296408 Score: 156
Period size: 35 Copynumber: 2.7 Consensus size: 35
1296303 CAAACTCTAC
*
1296313 CAAACTTTGAAAAACATTTTTCAAAGAAACATTTAA
1 CAAACTTTGAAAATCA-TTTTCAAAGAAACATTTAA
* *
1296349 CAAACTTTGAAAATCATTTTCAAAAAAACATTTAC
1 CAAACTTTGAAAATCATTTTCAAAGAAACATTTAA
1296384 CAAACTTTGAAAATCATTTTCAAAG
1 CAAACTTTGAAAATCATTTTCAAAG
1296409 TTGATTGCCG
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
35 41 0.73
36 15 0.27
ACGTcount: A:0.48, C:0.16, G:0.05, T:0.31
Consensus pattern (35 bp):
CAAACTTTGAAAATCATTTTCAAAGAAACATTTAA
Found at i:1296366 original size:21 final size:21
Alignment explanation
Indices: 1296342--1296402 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1296332 TTCAAAGAAA
1296342 CATTTAACAAACTTTGAAAAT
1 CATTTAACAAACTTTGAAAAT
*
1296363 CATTT-TCAAA-----AAAA-
1 CATTTAACAAACTTTGAAAAT
*
1296377 CATTTACCAAACTTTGAAAAT
1 CATTTAACAAACTTTGAAAAT
1296398 CATTT
1 CATTT
1296403 TCAAAGTTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 8 0.26
20 8 0.26
21 10 0.32
ACGTcount: A:0.46, C:0.16, G:0.03, T:0.34
Consensus pattern (21 bp):
CATTTAACAAACTTTGAAAAT
Found at i:1300849 original size:8 final size:8
Alignment explanation
Indices: 1300836--1300876 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
1300826 CTCATTTTCA
1300836 GAGAATTT
1 GAGAATTT
1300844 GAGAATTT
1 GAGAATTT
*
1300852 -AGAGTTT
1 GAGAATTT
*
1300859 GGGAATTT
1 GAGAATTT
1300867 GAGAATTT
1 GAGAATTT
1300875 GA
1 GA
1300877 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:1301278 original size:124 final size:127
Alignment explanation
Indices: 1300947--1301560 Score: 945
Period size: 124 Copynumber: 4.9 Consensus size: 127
1300937 TAATCGGAGT
* *
1300947 ACTATTCA-ATGGAAGACGCGTTCCCGGGGGCACGCCTTCCATTATTTCGTCAGAGAATATGTTA
1 ACTATTCACAT-GAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
*
1301011 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCATTACCTATTATTTC
65 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGA-ATATCAGTACCTATTATTTC
* * * * *
1301075 TC-AGGTGACATGAAAGCGCGTTCCC-GGGG-GCGCCTTCCATTATTTTGTCAGAGAATATGTTA
1 ACTA-TTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTA
1301137 TCATTGCCCTATTATGTCACTCATGTCCCTC-GGGACACTAG-ATAT-AGTACCTATTATTTC
65 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGAATATCAGTACCTATTATTTC
*
1301197 ACTATTCACATGAAGGTGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
*
1301262 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGATACTAGATATATCAGTACCTA-T-TTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGA-ATATCAGTACCTATTATTTC
1301323 ACTATTCACATGAA-G-GCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
*
1301386 CATTGCCCTATTATGTCACTTATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGA-ATATCAGTACCTATTATTTC
*
1301449 ACTATTCACATGAAGGCGCGTTCCC----ACGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
*
1301510 CATTTCCCTATTATGTCACTCATGTCCCTC-GGGACACTAGATATATCAGTA
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGA-ATATCAGTA
1301561 AATCAGGTAA
Statistics
Matches: 453, Mismatches: 20, Indels: 31
0.90 0.04 0.06
Matches are distributed among these distances:
122 32 0.07
123 30 0.07
124 228 0.50
125 21 0.05
126 98 0.22
127 11 0.02
128 31 0.07
129 2 0.00
ACGTcount: A:0.23, C:0.25, G:0.19, T:0.33
Consensus pattern (127 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGAATATCAGTACCTATTATTTC
Found at i:1301987 original size:33 final size:31
Alignment explanation
Indices: 1301950--1302054 Score: 111
Period size: 33 Copynumber: 3.2 Consensus size: 31
1301940 ATTAAGTTAA
*
1301950 ATTTTATGTTAAATTTCGAATACTATAATTTAT
1 ATTTTAT-TTAAATTT-GAATAATATAATTTAT
* *
1301983 ATTTTAAATTTAAATTTGAATAATATTATTTTTT
1 ATTTT--ATTTAAATTTGAATAATA-TAATTTAT
* *
1302017 ATTTTATTTTAATTTTGAATAATATAATTTGT
1 ATTTTA-TTTAAATTTGAATAATATAATTTAT
1302049 ATTTTA
1 ATTTTA
1302055 AAAACATTTA
Statistics
Matches: 62, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
32 13 0.21
33 28 0.45
34 19 0.31
35 2 0.03
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (31 bp):
ATTTTATTTAAATTTGAATAATATAATTTAT
Found at i:1302652 original size:21 final size:21
Alignment explanation
Indices: 1302564--1302657 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
1302554 TATGGTATAA
*
1302564 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
*
1302585 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
1302606 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
1302627 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
1302648 AACCCTGCGG
1 AACCCTGCGG
1302658 AGATGGCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 3 0.04
21 63 0.91
22 3 0.04
ACGTcount: A:0.20, C:0.27, G:0.35, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:1307445 original size:47 final size:48
Alignment explanation
Indices: 1307353--1307488 Score: 238
Period size: 47 Copynumber: 2.9 Consensus size: 48
1307343 AAGGAAATGC
1307353 GAGGCAGTAGAAAGTCCCTGGCTGCTTTGAAAAACTGTTGGTTTGTCG
1 GAGGCAGTAGAAAGTCCCTGGCTGCTTTGAAAAACTGTTGGTTTGTCG
*
1307401 GAGGCAGTAGAAAGTCCCTGGATG-TTTGAAAAACTGTTGGTTTGTCG
1 GAGGCAGTAGAAAGTCCCTGGCTGCTTTGAAAAACTGTTGGTTTGTCG
* *
1307448 GAGGCAGTGGTAAGTCCCTGGCTGCTTTGAAAAACTGTTGG
1 GAGGCAGTAGAAAGTCCCTGGCTGCTTTGAAAAACTGTTGG
1307489 AAAGTATTCT
Statistics
Matches: 83, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
47 44 0.53
48 39 0.47
ACGTcount: A:0.24, C:0.15, G:0.32, T:0.29
Consensus pattern (48 bp):
GAGGCAGTAGAAAGTCCCTGGCTGCTTTGAAAAACTGTTGGTTTGTCG
Found at i:1318257 original size:15 final size:16
Alignment explanation
Indices: 1318239--1318271 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1318229 TTCCCCCAGG
1318239 TTAAATT-TTAAAAAA
1 TTAAATTATTAAAAAA
1318254 TTAAATTAATTAAAAAA
1 TTAAATT-ATTAAAAAA
1318271 T
1 T
1318272 AATAATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
TTAAATTATTAAAAAA
Found at i:1319396 original size:17 final size:18
Alignment explanation
Indices: 1319376--1319414 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
1319366 TCTAAAATAT
* *
1319376 TTAAAAATAGA-AAAAGA
1 TTAAAAACAGATAAAAAA
1319393 TTAAAAACAGATAAAAAA
1 TTAAAAACAGATAAAAAA
1319411 TTAA
1 TTAA
1319415 TTCAAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.69, C:0.03, G:0.08, T:0.21
Consensus pattern (18 bp):
TTAAAAACAGATAAAAAA
Found at i:1321317 original size:35 final size:35
Alignment explanation
Indices: 1321262--1321371 Score: 130
Period size: 35 Copynumber: 3.1 Consensus size: 35
1321252 TCTAAACCTT
* * * * *
1321262 AAATTGAAGTATTTTAGAATTTGGGGTTTAAAATT
1 AAATTAAATTATTTTGGAATTTAGGGTTTAAAATG
* *
1321297 TAATTAAATTATTTTGGAATTTAGGGTTTAGAATG
1 AAATTAAATTATTTTGGAATTTAGGGTTTAAAATG
* * *
1321332 AAATTAAATTACTTTGGAAATTAGGGTTTAGAATG
1 AAATTAAATTATTTTGGAATTTAGGGTTTAAAATG
1321367 AAATT
1 AAATT
1321372 GAGGGTTGTT
Statistics
Matches: 65, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
35 65 1.00
ACGTcount: A:0.38, C:0.01, G:0.19, T:0.42
Consensus pattern (35 bp):
AAATTAAATTATTTTGGAATTTAGGGTTTAAAATG
Found at i:1327810 original size:23 final size:22
Alignment explanation
Indices: 1327784--1327831 Score: 53
Period size: 23 Copynumber: 2.1 Consensus size: 22
1327774 ATATTTCAAT
1327784 ATAA-AAAATATTAATAAAATAAA
1 ATAATAAAATA-T-ATAAAATAAA
*
1327807 ATAATTTAAATATATAAAATAAA
1 ATAA-TAAAATATATAAAATAAA
1327830 AT
1 AT
1327832 TACAATTTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
23 16 0.73
24 1 0.05
25 5 0.23
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
ATAATAAAATATATAAAATAAA
Found at i:1327815 original size:18 final size:19
Alignment explanation
Indices: 1327784--1327833 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
1327774 ATATTTCAAT
1327784 ATAAAA-AATATT-AATAAA
1 ATAAAATAATATTAAAT-AA
*
1327802 ATAAAATAAT-TTAAATAT
1 ATAAAATAATATTAAATAA
*
1327820 ATAAAATAAAATTA
1 ATAAAATAATATTA
1327834 CAATTTAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 18 0.67
19 9 0.33
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
ATAAAATAATATTAAATAA
Found at i:1329451 original size:39 final size:39
Alignment explanation
Indices: 1329397--1329478 Score: 164
Period size: 39 Copynumber: 2.1 Consensus size: 39
1329387 GCCTCCGGGG
1329397 TCCTCATACAGTAATTCAACACTGTAAGGGAATTCCATA
1 TCCTCATACAGTAATTCAACACTGTAAGGGAATTCCATA
1329436 TCCTCATACAGTAATTCAACACTGTAAGGGAATTCCATA
1 TCCTCATACAGTAATTCAACACTGTAAGGGAATTCCATA
1329475 TCCT
1 TCCT
1329479 TTTGTTTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 43 1.00
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.29
Consensus pattern (39 bp):
TCCTCATACAGTAATTCAACACTGTAAGGGAATTCCATA
Found at i:1333271 original size:2 final size:2
Alignment explanation
Indices: 1333264--1333323 Score: 111
Period size: 2 Copynumber: 30.0 Consensus size: 2
1333254 AGCACGTTTC
*
1333264 AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1333306 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
1333324 GATAAGATTT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1334178 original size:59 final size:60
Alignment explanation
Indices: 1334091--1334221 Score: 142
Period size: 59 Copynumber: 2.2 Consensus size: 60
1334081 GGGTAAAACA
* * * *
1334091 TACAAATTG-TCATTCGATTATAAAATGTTGTTTTATTGAGT-CATTTGACCATCAGAAGT
1 TACAAAATGATCATTCGACTATAAAATGTTGATTTATTGAGTGCA-TTGACCATCAAAAGT
* ** * * *
1334150 TA-TAAATGATCATTCGACTATATGATGTTGATTTGTTGAGTGCATTGACTATTAAAAGT
1 TACAAAATGATCATTCGACTATAAAATGTTGATTTATTGAGTGCATTGACCATCAAAAGT
1334209 TACAAAATGATCA
1 TACAAAATGATCA
1334222 CTTAACTATT
Statistics
Matches: 58, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
58 4 0.07
59 43 0.74
60 11 0.19
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (60 bp):
TACAAAATGATCATTCGACTATAAAATGTTGATTTATTGAGTGCATTGACCATCAAAAGT
Found at i:1336321 original size:18 final size:18
Alignment explanation
Indices: 1336293--1336337 Score: 81
Period size: 18 Copynumber: 2.4 Consensus size: 18
1336283 ACGCAGACTG
1336293 GTTTATCTTTTAAAATGGT
1 GTTT-TCTTTTAAAATGGT
1336312 GTTTTCTTTTAAAATGGT
1 GTTTTCTTTTAAAATGGT
1336330 GTTTTCTT
1 GTTTTCTT
1336338 AAAAACTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 22 0.85
19 4 0.15
ACGTcount: A:0.20, C:0.07, G:0.16, T:0.58
Consensus pattern (18 bp):
GTTTTCTTTTAAAATGGT
Found at i:1337393 original size:16 final size:16
Alignment explanation
Indices: 1337372--1337402 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1337362 TACATTTCCA
1337372 AATCATGCATTAAAAC
1 AATCATGCATTAAAAC
*
1337388 AATCATTCATTAAAA
1 AATCATGCATTAAAA
1337403 TAAGGATTTC
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:0.52, C:0.16, G:0.03, T:0.29
Consensus pattern (16 bp):
AATCATGCATTAAAAC
Found at i:1341992 original size:37 final size:37
Alignment explanation
Indices: 1341867--1342577 Score: 225
Period size: 36 Copynumber: 19.4 Consensus size: 37
1341857 AAGCAAAGAT
* * * * *
1341867 TTTATCTCGCTTGAGATAGTTTCATTTGAAACAAAAA
1 TTTATCTCACTTGAGATAATTTCACTCGAAACAACAA
** ** ** *
1341904 CTTTATCTCACTTGAGATTGTTTTTCTTAAAACAA-GA
1 -TTTATCTCACTTGAGATAATTTCACTCGAAACAACAA
* * * *
1341941 TTCATCTCGCTTGAGACAATTTCAATCGAAACAACAA
1 TTTATCTCACTTGAGATAATTTCACTCGAAACAACAA
** ** ** *
1341978 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAA-AC
1 TTTATCTCACTTGAGATAATTTCACTCGAAACAACAA
* * * *
1342014 TTTTTCTCTCTTGAGA-AAGTTTCACTCGAAATAGCAA
1 TTTATCTCACTTGAGATAA-TTTCACTCGAAACAACAA
** ** ** *
1342051 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAA-AC
1 TTTATCTCACTTGAGATAATTTCACTCGAAACAACAA
* ** * *
1342087 TTTTTCTCGTTTGAGA-AAGTTTCACTCGAAATAGCAA
1 TTTATCTCACTTGAGATAA-TTTCACTCGAAACAACAA
* ** ** *
1342124 TTTATCTCACTTGAGATTATTTTTCTTAAAACAA-AC
1 TTTATCTCACTTGAGATAATTTCACTCGAAACAACAA
* * * **
1342160 TTCATCTCGCTTGAGACAGGTTCACTCGAAACAACAA
1 TTTATCTCACTTGAGATAATTTCACTCGAAACAACAA
* ** ** *
1342197 TTTATCTCACTTGAGATTATTTTTCTTAAAACAA-AC
1 TTTATCTCACTTGAGATAATTTCACTCGAAACAACAA
* * * * * *
1342233 TTTTTCTCGCTTAAGA-AAGTTTCACTCAAAATAGCAA
1 TTTATCTCACTTGAGATAA-TTTCACTCGAAACAACAA
** ** **
1342270 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAATC--
1 TTTATCTCACTTGAGATAATTTCACTCGAAACAA-CAA
* ** * * *
1342306 TTTTTCTCGTTTGAGA-AAGTTTCACTAGAAATAGCAA
1 TTTATCTCACTTGAGATAA-TTTCACTCGAAACAACAA
** ** ** *
1342343 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAA-AC
1 TTTATCTCACTTGAGATAATTTCACTCGAAACAACAA
* * * * * *
1342379 TTTTTTTCGCTTAAGA-AAGTTTCACTCGAAATATCAA
1 TTTATCTCACTTGAGATAA-TTTCACTCGAAACAACAA
* ** ** ** *
1342416 TTTATCACACTTGAGATTGTTT-TTTTTAAACAA-AC
1 TTTATCTCACTTGAGATAATTTCACTCGAAACAACAA
* * * *
1342451 TTTTTCTCGCTTGAGA-AAGTTTTCACTCGAAATAGCAA
1 TTTATCTCACTTGAGATAA--TTTCACTCGAAACAACAA
* ** ** *
1342489 TTTATCTCACTTGAGATTATTTTTCTTAAAACAA-AC
1 TTTATCTCACTTGAGATAATTTCACTCGAAACAACAA
* * * *
1342525 TTTTTCTCGCTTGAGA-AACTTTCACTCGAAATAGCAA
1 TTTATCTCACTTGAGATAA-TTTCACTCGAAACAACAA
1342562 TTTATCTCACTTGAGA
1 TTTATCTCACTTGAGA
1342578 CTGTTTTTCT
Statistics
Matches: 447, Mismatches: 200, Indels: 53
0.64 0.29 0.08
Matches are distributed among these distances:
35 17 0.04
36 196 0.44
37 188 0.42
38 45 0.10
39 1 0.00
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.40
Consensus pattern (37 bp):
TTTATCTCACTTGAGATAATTTCACTCGAAACAACAA
Found at i:1342003 original size:73 final size:73
Alignment explanation
Indices: 1341866--1342888 Score: 1494
Period size: 73 Copynumber: 14.0 Consensus size: 73
1341856 GAAGCAAAGA
* * * * **
1341866 TTTTATCTCGCTTGAGATAGTTTCATTTGAAACAAAAACTTTATCTCACTTGAGATTGTTTTTCT
1 TTTT-TCTCGCTTGAGAAAGTTTCACTCGAAATAGCAA-TTTATCTCACTTGAGATTGTTTTTCT
1341931 TAAAACAAGA-
64 TAAAACAA-AC
** * * *
1341941 TTCATCTCGCTTGAGACAA-TTTCAATCGAAACAACAATTTATCTCACTTGAGATTGTTTTTCTT
1 TTTTTCTCGCTTGAGA-AAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTT
1342005 AAAACAAAC
65 AAAACAAAC
*
1342014 TTTTTCTCTCTTGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTA
1 TTTTTCTCGCTTGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTA
1342079 AAACAAAC
66 AAACAAAC
* *
1342087 TTTTTCTCGTTTGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTATTTTTCTTA
1 TTTTTCTCGCTTGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTA
1342152 AAACAAAC
66 AAACAAAC
** * * * * *
1342160 TTCATCTCGCTTGAGACAGGTTCACTCGAAACAACAATTTATCTCACTTGAGATTATTTTTCTTA
1 TTTTTCTCGCTTGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTA
1342225 AAACAAAC
66 AAACAAAC
* *
1342233 TTTTTCTCGCTTAAGAAAGTTTCACTCAAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTA
1 TTTTTCTCGCTTGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTA
*
1342298 AAACAATC
66 AAACAAAC
* *
1342306 TTTTTCTCGTTTGAGAAAGTTTCACTAGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTA
1 TTTTTCTCGCTTGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTA
1342371 AAACAAAC
66 AAACAAAC
* * * * *
1342379 TTTTTTTCGCTTAAGAAAGTTTCACTCGAAATATCAATTTATCACACTTGAGATTGTTTTT-TTT
1 TTTTTCTCGCTTGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTA
1342443 AAACAAAC
66 AAACAAAC
*
1342451 TTTTTCTCGCTTGAGAAAGTTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTATTTTTCTT
1 TTTTTCTCGCTTGAGAAAG-TTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTT
1342516 AAAACAAAC
65 AAAACAAAC
* *
1342525 TTTTTCTCGCTTGAGAAACTTTCACTCGAAATAGCAATTTATCTCACTTGAGACTGTTTTTCTTA
1 TTTTTCTCGCTTGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTA
* **
1342590 AAATAATT
66 AAACAAAC
* * *
1342598 TTTTTCTCACTTGAGAAAGTTTCACTCGAAATAGCAAGTTATCTCACTTAAGATTGTTTTTCTTA
1 TTTTTCTCGCTTGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTA
1342663 AAACAAAC
66 AAACAAAC
* * * * *
1342671 TTTTTCTCGCTTGAGAAAGGTTCACTCGAAATAGTAATTTATCTAACTTGATATTTTTTTTTTCT
1 TTTTTCTCGCTTGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGA--TTGTTTTTCT
*
1342736 TAAAACAAAT
64 TAAAACAAAC
* * *
1342746 TTTTTCTCGTTTGAGAAAGTTTCACTTGAAATAGTAATTTATCTCACTTGAGATTGTTTTTCTTA
1 TTTTTCTCGCTTGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTA
1342811 AAACAAAC
66 AAACAAAC
* * *
1342819 TTTTTCTCGCTTAATAAAGTTTCACTAGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTA
1 TTTTTCTCGCTTGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTA
1342884 AAACA
66 AAACA
1342889 TTTCCAGAAA
Statistics
Matches: 856, Mismatches: 85, Indels: 16
0.89 0.09 0.02
Matches are distributed among these distances:
72 30 0.04
73 702 0.82
74 55 0.06
75 69 0.08
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.41
Consensus pattern (73 bp):
TTTTTCTCGCTTGAGAAAGTTTCACTCGAAATAGCAATTTATCTCACTTGAGATTGTTTTTCTTA
AAACAAAC
Found at i:1342630 original size:36 final size:36
Alignment explanation
Indices: 1341945--1342871 Score: 259
Period size: 37 Copynumber: 25.3 Consensus size: 36
1341935 ACAAGATTCA
* * * *
1341945 TCTCGCTTGAGACAA-TTTCAATCGAAACAACAATTTA
1 TCTCACTTGAGA-AAGTTTCACTCGAAA-TACAATTTT
** ** *
1341982 TCTCACTTGAGATTGTTTTTCT-TAAA-ACAAACTTTT
1 TCTCACTTGAGAAAGTTTCACTCGAAATAC-AA-TTTT
* *
1342018 TCTCTCTTGAGAAAGTTTCACTCGAAATAGCAATTTA
1 TCTCACTTGAGAAAGTTTCACTCGAAATA-CAATTTT
** ** *
1342055 TCTCACTTGAGATTGTTTTTCT-TAAA-ACAAACTTTT
1 TCTCACTTGAGAAAGTTTCACTCGAAATAC-AA-TTTT
** *
1342091 TCTCGTTTGAGAAAGTTTCACTCGAAATAGCAATTTA
1 TCTCACTTGAGAAAGTTTCACTCGAAATA-CAATTTT
* ** * **
1342128 TCTCACTTGAGATTA-TTTTTCT-TAAA-ACAAACTTCA
1 TCTCACTTGAGA-AAGTTTCACTCGAAATAC-AA-TTTT
* * * * *
1342164 TCTCGCTTGAGACAGGTTCACTCGAAACAACAATTTA
1 TCTCACTTGAGAAAGTTTCACTCGAAA-TACAATTTT
* ** *
1342201 TCTCACTTGAGATTA-TTTTTCT-TAAA-ACAAACTTTT
1 TCTCACTTGAGA-AAGTTTCACTCGAAATAC-AA-TTTT
* * * *
1342237 TCTCGCTTAAGAAAGTTTCACTCAAAATAGCAATTTA
1 TCTCACTTGAGAAAGTTTCACTCGAAATA-CAATTTT
** ** *
1342274 TCTCACTTGAGATTGTTTTTCT-TAAA-ACAATCTTTT
1 TCTCACTTGAGAAAGTTTCACTCGAAATACAA--TTTT
** * *
1342310 TCTCGTTTGAGAAAGTTTCACTAGAAATAGCAATTTA
1 TCTCACTTGAGAAAGTTTCACTCGAAATA-CAATTTT
** ** *
1342347 TCTCACTTGAGATTGTTTTTCT-TAAA-ACAAACTTTT
1 TCTCACTTGAGAAAGTTTCACTCGAAATAC-AA-TTTT
* * * *
1342383 TTTCGCTTAAGAAAGTTTCACTCGAAATATCAATTTA
1 TCTCACTTGAGAAAGTTTCACTCGAAATA-CAATTTT
* ** ** ** *
1342420 TCACACTTGAGATTGTTT-TTTTTAAACA-AACTTTT
1 TCTCACTTGAGAAAGTTTCACTCGAAATACAA-TTTT
* *
1342455 TCTCGCTTGAGAAAGTTTTCACTCGAAATAGCAATTTA
1 TCTCACTTGAGAAAG-TTTCACTCGAAATA-CAATTTT
* ** *
1342493 TCTCACTTGAGATTA-TTTTTCT-TAAA-ACAAACTTTT
1 TCTCACTTGAGA-AAGTTTCACTCGAAATAC-AA-TTTT
* * *
1342529 TCTCGCTTGAGAAACTTTCACTCGAAATAGCAATTTA
1 TCTCACTTGAGAAAGTTTCACTCGAAATA-CAATTTT
** ** ** *
1342566 TCTCACTTGAGACTGTTTTTCTTAAAATA-ATTTTTT
1 TCTCACTTGAGAAAGTTTCACTCGAAATACA-ATTTT
* *
1342602 TCTCACTTGAGAAAGTTTCACTCGAAATAGCAAGTTA
1 TCTCACTTGAGAAAGTTTCACTCGAAATA-CAATTTT
* ** ** *
1342639 TCTCACTTAAGATTGTTTTTCT-TAAA-ACAAACTTTT
1 TCTCACTTGAGAAAGTTTCACTCGAAATAC-AA-TTTT
* * * *
1342675 TCTCGCTTGAGAAAGGTTCACTCGAAATAGTAATTTA
1 TCTCACTTGAGAAAGTTTCACTCGAAATA-CAATTTT
* * *** *** *
1342712 TCTAACTTGATATTTTTTTTTTCTTAAA-ACAAATTTTT
1 TCTCACTTGAGAAAGTTTCACTC-GAAATAC-AA-TTTT
** * * *
1342750 TCTCGTTTGAGAAAGTTTCACTTGAAATAGTAATTTA
1 TCTCACTTGAGAAAGTTTCACTCGAAATA-CAATTTT
** ** *
1342787 TCTCACTTGAGATTGTTTTTCT-TAAA-ACAAACTTTT
1 TCTCACTTGAGAAAGTTTCACTCGAAATAC-AA-TTTT
* * * * *
1342823 TCTCGCTTAATAAAGTTTCACTAGAAATAGCAATTTA
1 TCTCACTTGAGAAAGTTTCACTCGAAATA-CAATTTT
1342860 TCTCACTTGAGA
1 TCTCACTTGAGA
1342872 TTGTTTTTCT
Statistics
Matches: 615, Mismatches: 210, Indels: 130
0.64 0.22 0.14
Matches are distributed among these distances:
34 14 0.02
35 41 0.07
36 227 0.37
37 257 0.42
38 62 0.10
39 14 0.02
ACGTcount: A:0.31, C:0.17, G:0.11, T:0.41
Consensus pattern (36 bp):
TCTCACTTGAGAAAGTTTCACTCGAAATACAATTTT
Found at i:1343127 original size:125 final size:123
Alignment explanation
Indices: 1342885--1343202 Score: 382
Period size: 125 Copynumber: 2.6 Consensus size: 123
1342875 TTTTTCTTAA
*
1342885 AACATTTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATG
1 AACATTTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAAAAGAAGTTCATAATG
* * *
1342950 AGAAGAACTTGTTCAGCCTTTTGCTCGACTCTATCGCAGAAGGAGATAGATCAGCATC
66 AGAAGAACTTGTTCAACCTTTTGCTAGACTCTATCACAGAAGGAGATAGATCAGCATC
*
1343008 AACATTTCCAGAGAATGAGTTCATAATGAGAAGAACTCATTTGAAGAGGAAAAAGAAGTTCATAA
1 AACATTTCCAGA-AA-GAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAAAAGAAGTTCATAA
* * * * *
1343073 TGAGAAGAACTTGTTCAACCTTTTGCTAGATTCTGTCATAGAATGAG---G-T--GGATC
64 TGAGAAGAACTTGTTCAACCTTTTGCTAGACTCTATCACAGAAGGAGATAGATCAGCATC
* * * * * **
1343127 ATCATTCCCAGTTAAAGAGTTCATAATGAGAAGAACTCTTCCGAAG-TGAGCGAA-AAGTTCATA
1 AACATTTCCAG--AAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGA-AAAAGAAGTTCATA
1343190 ATGAGAAGAACTT
63 ATGAGAAGAACTT
1343203 ATATCTTAGA
Statistics
Matches: 172, Mismatches: 18, Indels: 15
0.84 0.09 0.07
Matches are distributed among these distances:
118 24 0.14
119 42 0.24
120 2 0.01
121 2 0.01
122 1 0.01
123 12 0.07
124 2 0.01
125 87 0.51
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.25
Consensus pattern (123 bp):
AACATTTCCAGAAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAAAAGAAGTTCATAATG
AGAAGAACTTGTTCAACCTTTTGCTAGACTCTATCACAGAAGGAGATAGATCAGCATC
Found at i:1345633 original size:243 final size:243
Alignment explanation
Indices: 1345205--1345695 Score: 901
Period size: 243 Copynumber: 2.0 Consensus size: 243
1345195 CACTTATTTT
* *
1345205 CCGTCCAAGAAATATTCGTTCCCGGACGAAAACCGGTTACGAAAGATATATATAATAATAGATCC
1 CCGTCCAAGAAACATTCGTGCCCGGACGAAAACCGGTTACGAAAGATATATATAATAATAGATCC
1345270 AACTTTGGACCACAAAAAGAATATAAACTATTGAAAGACCATCGACAAACCGAATATCAAGTTCG
66 AACTTTGGACCACAAAAAGAATATAAACTATTGAAAGACCATCGACAAACCGAATATCAAGTTCG
1345335 AGCGACATGAGAAACTATTCACGAACACAACCACTTATCTTAATCAAATTCGAGGGCCCAAAGCA
131 AGCGACATGAGAAACTATTCACGAACACAACCACTTATCTTAATCAAATTCGAGGGCCCAAAGCA
*
1345400 GATTATCATCAAGATAATAAATAATTGTCATATTGATCAGTCGATACA
196 GATTATCATCAAGATAATAAATAATTGTCATATTGATAAGTCGATACA
1345448 CCGTCCAAGAAACATTCGTGCCCGGACGAAAACCGGTTACGAAAGATATATATAATAATAGATCC
1 CCGTCCAAGAAACATTCGTGCCCGGACGAAAACCGGTTACGAAAGATATATATAATAATAGATCC
* * * *
1345513 GACTTTGGACCACAAAAAGGATGTAAACTATTGAAAGACCGTCGACAAACCGAATATCAAGTTCG
66 AACTTTGGACCACAAAAAGAATATAAACTATTGAAAGACCATCGACAAACCGAATATCAAGTTCG
* *
1345578 AGCGACATGGGAAACTATTCACGAACACAACCACTTATCTTAATCAAATTCGAGGGTCCAAAGCA
131 AGCGACATGAGAAACTATTCACGAACACAACCACTTATCTTAATCAAATTCGAGGGCCCAAAGCA
1345643 GATTATCATCAAGATAATAAATAATTGTCATATTGATAAGTCGATACA
196 GATTATCATCAAGATAATAAATAATTGTCATATTGATAAGTCGATACA
1345691 CCGTC
1 CCGTC
1345696 AAATCAAATC
Statistics
Matches: 239, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
243 239 1.00
ACGTcount: A:0.40, C:0.21, G:0.16, T:0.23
Consensus pattern (243 bp):
CCGTCCAAGAAACATTCGTGCCCGGACGAAAACCGGTTACGAAAGATATATATAATAATAGATCC
AACTTTGGACCACAAAAAGAATATAAACTATTGAAAGACCATCGACAAACCGAATATCAAGTTCG
AGCGACATGAGAAACTATTCACGAACACAACCACTTATCTTAATCAAATTCGAGGGCCCAAAGCA
GATTATCATCAAGATAATAAATAATTGTCATATTGATAAGTCGATACA
Found at i:1345860 original size:11 final size:12
Alignment explanation
Indices: 1345832--1345858 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1345822 AAAGTTATTA
1345832 AAAATAAAAAAT
1 AAAATAAAAAAT
1345844 AAAATAAAAAAT
1 AAAATAAAAAAT
1345856 AAA
1 AAA
1345859 TATATATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAATAAAAAAT
Found at i:1350569 original size:21 final size:22
Alignment explanation
Indices: 1350543--1350584 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1350533 GGCTGAAGCA
1350543 ATGAGGA-CTGCAGCCTTTGTG
1 ATGAGGATCTGCAGCCTTTGTG
* *
1350564 ATGAGGATTTGCATCCTTTGT
1 ATGAGGATCTGCAGCCTTTGT
1350585 TATCAACAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.19, C:0.17, G:0.29, T:0.36
Consensus pattern (22 bp):
ATGAGGATCTGCAGCCTTTGTG
Found at i:1352760 original size:29 final size:29
Alignment explanation
Indices: 1352726--1352781 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
1352716 TCTAAATTAA
1352726 TTTGATGACATTGCTTACATCAATTTAGT
1 TTTGATGACATTGCTTACATCAATTTAGT
*
1352755 TTTGATGTCATTGCTTACATCAATTTA
1 TTTGATGACATTGCTTACATCAATTTA
1352782 ATTAGGTGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.27, C:0.14, G:0.12, T:0.46
Consensus pattern (29 bp):
TTTGATGACATTGCTTACATCAATTTAGT
Found at i:1353693 original size:20 final size:19
Alignment explanation
Indices: 1353670--1353716 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1353660 CGATATACCA
1353670 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
* *
1353690 GGTATCAAAATGATAAAACT
1 GGTA-AAAAATGATAAAACC
1353710 GGTAAAA
1 GGTAAAA
1353717 CGTTACCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.53, C:0.09, G:0.17, T:0.21
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:1353873 original size:20 final size:19
Alignment explanation
Indices: 1353850--1353896 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1353840 CGATATAACA
*
1353850 GGTAAAAATATGATAAAACT
1 GGTAAAAA-ATGATAAAACC
*
1353870 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
1353890 GGTAAAA
1 GGTAAAA
1353897 CGATACCAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.53, C:0.09, G:0.17, T:0.21
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:1353876 original size:180 final size:182
Alignment explanation
Indices: 1353458--1353929 Score: 696
Period size: 180 Copynumber: 2.6 Consensus size: 182
1353448 GATCCAAATT
* * * * **
1353458 AAAAATGTGTCGATCCAAAACGATATAACATGTAAAACTATGACAAAACCGGTATTGAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * * * *
1353523 AAACCGGTAAAGCGCTACCGAATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTTC
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
*
1353588 GTGAATTTAAAAGAGAAGCAATTTTAAATCCTATAAAGTGTCGATACTTTTA
131 GTGAATTTAAAAGAGAAGCAATTTTAAAGCCTATAAAGTGTCGATACTTTTA
*
1353640 AAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * *
1353705 AAACTGGTAAAACGTTACCGGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
* * ** *
1353769 GTGAATTTAAAAGAGAAGTAGTTTTAGCGCCTATAATGTGTCGATAC-TTTA
131 GTGAATTTAAAAGAGAAGCAATTTTAAAGCCTATAAAGTGTCGATACTTTTA
* * *
1353820 AAAAATATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACTGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
*
1353885 AAACCGGTAAAACGATACCAGATATATTGAAAGTGTCGATACTTT
66 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
1353930 TGTAAGTACG
Statistics
Matches: 262, Mismatches: 28, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
180 107 0.41
181 59 0.23
182 96 0.37
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (182 bp):
AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAGAGAAGCAATTTTAAAGCCTATAAAGTGTCGATACTTTTA
Found at i:1354661 original size:200 final size:200
Alignment explanation
Indices: 1353962--1354642 Score: 1166
Period size: 200 Copynumber: 3.4 Consensus size: 200
1353952 TCGACACTTT
*
1353962 TGTAATAGGTAATTTTTCAATCTAATCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAA
1 TGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAA
*
1354027 ATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAGCAGGG
66 ATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGG
* *
1354092 TGCAACAATAAAATGTCGATCCATATATAAAAAGTGTCGATCCGATAAACATCGAAACCCATAAG
131 TGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAAACCCATAAG
1354157 TATAA
196 TATAA
* *
1354162 TGTAATAGGTAATTTTTTAATCTAACCGGTACAAGTATATCGGTTTTATGAGAGAATAGGTCTAA
1 TGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAA
* * *
1354227 ATAATGTATCGATACTTTTGTAGTTTGTGTCGATATTTTTGGTCTAAAATGAATGGCAAACAGGG
66 ATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGG
* *
1354292 TGCAACAATAAAGTGTCGATCCATTTATAAAAAGTGTCGATCCCATAAACATCGAAACCTATAAG
131 TGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAAACCCATAAG
1354357 TATAA
196 TATAA
1354362 TGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAA
1 TGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAA
*
1354427 ATAATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGG
66 ATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGG
* * *
1354492 TGTAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAAACCCAAAAG
131 TGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAAACCCATAAG
1354557 TATAA
196 TATAA
* * * * *
1354562 TGTATTAGGTAATTTTTCAATCTAACCGGTATAAGTATACCGGTTTTATGGGAGAATTGGTATAT
1 TGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTA-
1354627 AAT-ATGTATCGACACT
65 AATAATGTATCGACACT
1354643 GTTTAATGTT
Statistics
Matches: 452, Mismatches: 28, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
200 449 0.99
201 3 0.01
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Consensus pattern (200 bp):
TGTAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAA
ATAATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGG
TGCAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAAACCCATAAG
TATAA
Found at i:1356094 original size:12 final size:12
Alignment explanation
Indices: 1356077--1356141 Score: 78
Period size: 12 Copynumber: 5.4 Consensus size: 12
1356067 GGTCAATAAA
1356077 GATGAAGATGAC
1 GATGAAGATGAC
1356089 GATGAAGATGAC
1 GATGAAGATGAC
1356101 GATGAA-ACTGAC
1 GATGAAGA-TGAC
* *
1356113 GATGATGATGAT
1 GATGAAGATGAC
* *
1356125 GATGATGATGAT
1 GATGAAGATGAC
1356137 GATGA
1 GATGA
1356142 TGATCTAAAC
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
11 1 0.02
12 47 0.96
13 1 0.02
ACGTcount: A:0.38, C:0.06, G:0.32, T:0.23
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:1356121 original size:3 final size:3
Alignment explanation
Indices: 1356077--1356145 Score: 68
Period size: 3 Copynumber: 23.0 Consensus size: 3
1356067 GGTCAATAAA
* * * * * *
1356077 GAT GAA GAT GAC GAT GAA GAT GAC GAT GA- AACT GAC GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA-T GAT GAT GAT GAT
1356122 GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT
1356146 CTAAACAAGT
Statistics
Matches: 52, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
2 1 0.02
3 50 0.96
4 1 0.02
ACGTcount: A:0.38, C:0.06, G:0.32, T:0.25
Consensus pattern (3 bp):
GAT
Found at i:1357706 original size:183 final size:183
Alignment explanation
Indices: 1357355--1357939 Score: 1030
Period size: 183 Copynumber: 3.2 Consensus size: 183
1357345 CAAAGTTTTC
*
1357355 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTTT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
* * *
1357420 CAAAAAGTGTCG--ATTGAAAAAACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAA
66 CAAAAAGTGTCGACATT---TACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAA
* *
1357483 TATAATCGGTATAAATATACCGGTTTTATGAGCGAATAGGTATACAACCTATATCG
128 TATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
1357539 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
1357604 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
* * *
1357669 AACCGCTATAAATATATCGGTTTTATGAGCGAATAGGTCTACAACCTATATTG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
1357722 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
1357787 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
*
1357852 AACCGGTATAAATATACCGGTTTTATGAGTGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
1357905 ACACTTTTTAATTTTGTGTCGGTACTTTATGTCCA
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCA
1357940 AAATTATAAT
Statistics
Matches: 385, Mismatches: 14, Indels: 5
0.95 0.03 0.01
Matches are distributed among these distances:
183 306 0.79
184 76 0.20
186 3 0.01
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (183 bp):
ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATAT
AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
Found at i:1358034 original size:120 final size:120
Alignment explanation
Indices: 1357821--1358059 Score: 415
Period size: 120 Copynumber: 2.0 Consensus size: 120
1357811 CGGAACCCAG
*
1357821 AATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGTGAAT
1 AATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAAT
*
1357886 AGGTCTACAACCTATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGTCCAA
66 AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAA
* * * *
1357941 AATTATAATGTACTAGATACTTTTGTAATATAACCGGTATAAGTATACCGGTTTTATTAGCGAAT
1 AATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAAT
*
1358006 AGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCA
66 AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCA
1358060 GAATGGAAGA
Statistics
Matches: 112, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
120 112 1.00
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.39
Consensus pattern (120 bp):
AATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAAT
AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAA
Found at i:1358191 original size:303 final size:303
Alignment explanation
Indices: 1357638--1358228 Score: 1083
Period size: 303 Copynumber: 2.0 Consensus size: 303
1357628 CGGAACCCAG
*
1357638 AATTATAATGTAATAGATAATTTTGTAATATAACCGCTATAAATATATCGGTTTTATGAGCGAAT
1 AATTATAATGTAATAGATAATTTTGTAATATAACCGCTATAAATATACCGGTTTTATGAGCGAAT
*
1357703 AGGTCTACAACCTATATTGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAA
66 AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAA
1357768 AAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTA
131 AAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTA
*
1357833 ATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGTGAATAGGTCTACAACC
196 ATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACC
*
1357898 TATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGTCCAA
261 TATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAA
* * * * *
1357941 AATTATAATGTACTAGATACTTTTGTAATATAACCGGTATAAGTATACCGGTTTTATTAGCGAAT
1 AATTATAATGTAATAGATAATTTTGTAATATAACCGCTATAAATATACCGGTTTTATGAGCGAAT
*
1358006 AGGTCTACAACCTATGTCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAA
66 AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAA
1358071 AAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTA
131 AAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTA
*
1358136 ATAGATAATTTTGTAATATAACCGGTATAAATATACTGGTTTTATGAGCGAATAGGTCTACAACC
196 ATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACC
1358201 TATATCGACACTTTTTAATATTGTGTCG
261 TATATCGACACTTTTTAATATTGTGTCG
1358229 CTAATTTTAA
Statistics
Matches: 277, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
303 277 1.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (303 bp):
AATTATAATGTAATAGATAATTTTGTAATATAACCGCTATAAATATACCGGTTTTATGAGCGAAT
AGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAA
AAATGTGTCGATACCTTGTCAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTA
ATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACC
TATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCAA
Found at i:1360276 original size:16 final size:16
Alignment explanation
Indices: 1360238--1360276 Score: 60
Period size: 18 Copynumber: 2.3 Consensus size: 16
1360228 AAAATATGTC
1360238 AATATAAGCGCTACCT
1 AATATAAGCGCTACCT
1360254 ATTATATAAGCGCTACCT
1 A--ATATAAGCGCTACCT
1360272 AATAT
1 AATAT
1360277 GTTATTGTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
16 5 0.24
18 16 0.76
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.31
Consensus pattern (16 bp):
AATATAAGCGCTACCT
Found at i:1360368 original size:23 final size:23
Alignment explanation
Indices: 1360318--1360362 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1360308 TACTTATTTT
* *
1360318 ATTATATAAGCGCTATCTATTAC
1 ATTATATAAGCGCTACCTAATAC
*
1360341 ATTATATAAGCGTTACCTAATA
1 ATTATATAAGCGCTACCTAATA
1360363 TGTTATTGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (23 bp):
ATTATATAAGCGCTACCTAATAC
Found at i:1364713 original size:18 final size:18
Alignment explanation
Indices: 1364690--1364724 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1364680 TTCCATCCGG
*
1364690 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
1364708 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
1364725 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:1369939 original size:18 final size:18
Alignment explanation
Indices: 1369916--1369950 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1369906 TTCCATCCGG
*
1369916 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
1369934 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
1369951 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:1372214 original size:16 final size:16
Alignment explanation
Indices: 1372193--1372235 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
1372183 GGGGTGTGAC
1372193 AAAAAAGATATTAATT
1 AAAAAAGATATTAATT
1372209 AAAAAA-ATAATTAATT
1 AAAAAAGAT-ATTAATT
1372225 -AAAAAGATATT
1 AAAAAAGATATT
1372236 TTTCTTCAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 10 0.40
16 15 0.60
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (16 bp):
AAAAAAGATATTAATT
Found at i:1373768 original size:18 final size:18
Alignment explanation
Indices: 1373747--1373818 Score: 101
Period size: 18 Copynumber: 4.1 Consensus size: 18
1373737 ACTTATAATT
*
1373747 TGTCCCGAAGGACCACTT
1 TGTCCCGAAGGACCACTA
*
1373765 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
*
1373783 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
*
1373801 TGT-CCGAAGAACCACTA
1 TGTCCCGAAGGACCACTA
1373818 T
1 T
1373819 CCATATGTCT
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
17 13 0.26
18 37 0.74
ACGTcount: A:0.28, C:0.32, G:0.18, T:0.22
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1375227 original size:20 final size:20
Alignment explanation
Indices: 1375202--1375271 Score: 67
Period size: 20 Copynumber: 3.7 Consensus size: 20
1375192 CGTTTCAAAG
1375202 ATGGTATCGATACCGTCCTT
1 ATGGTATCGATACCGTCCTT
*
1375222 ATGGTATCGGTACC--CC-T
1 ATGGTATCGATACCGTCCTT
* *
1375239 -TGGTATCGATACTGTTCTT
1 ATGGTATCGATACCGTCCTT
* *
1375258 AAGGTATTGATACC
1 ATGGTATCGATACC
1375272 TCATGAATGC
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
16 11 0.28
17 1 0.03
18 3 0.08
19 1 0.03
20 23 0.59
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (20 bp):
ATGGTATCGATACCGTCCTT
Found at i:1379396 original size:18 final size:18
Alignment explanation
Indices: 1379373--1379434 Score: 72
Period size: 18 Copynumber: 3.5 Consensus size: 18
1379363 AACTAATTTG
1379373 ATGATGTTTGACATGGAA
1 ATGATGTTTGACATGGAA
* ****
1379391 ATGATGTTT-ACTTCTCG
1 ATGATGTTTGACATGGAA
1379408 ATGATGTTTGACATGGAA
1 ATGATGTTTGACATGGAA
1379426 ATGATGTTT
1 ATGATGTTT
1379435 ACTTCTCGCT
Statistics
Matches: 33, Mismatches: 10, Indels: 2
0.73 0.22 0.04
Matches are distributed among these distances:
17 12 0.36
18 21 0.64
ACGTcount: A:0.27, C:0.08, G:0.24, T:0.40
Consensus pattern (18 bp):
ATGATGTTTGACATGGAA
Found at i:1379418 original size:35 final size:35
Alignment explanation
Indices: 1379372--1379442 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
1379362 CAACTAATTT
1379372 GATGATGTTTGACATGGAAATGATGTTTACTTCTC
1 GATGATGTTTGACATGGAAATGATGTTTACTTCTC
1379407 GATGATGTTTGACATGGAAATGATGTTTACTTCTC
1 GATGATGTTTGACATGGAAATGATGTTTACTTCTC
1379442 G
1 G
1379443 CTTGTGATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.25, C:0.11, G:0.24, T:0.39
Consensus pattern (35 bp):
GATGATGTTTGACATGGAAATGATGTTTACTTCTC
Found at i:1382071 original size:15 final size:16
Alignment explanation
Indices: 1382051--1382083 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1382041 TCATTCACTG
*
1382051 ATTCTACTG-TTCTAT
1 ATTCTAATGCTTCTAT
1382066 ATTCTAATGCTTCTAT
1 ATTCTAATGCTTCTAT
1382082 AT
1 AT
1382084 CTCCTGAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.24, C:0.18, G:0.06, T:0.52
Consensus pattern (16 bp):
ATTCTAATGCTTCTAT
Found at i:1397703 original size:34 final size:33
Alignment explanation
Indices: 1397639--1397742 Score: 102
Period size: 34 Copynumber: 2.9 Consensus size: 33
1397629 TATGGAATAT
* * *
1397639 TTAGTGCCCTGTGATTGCACCATATGTGCGATACA
1 TTAGTGCCCTATGATTGCA-CGTA-GTGCGACACA
1397674 TTAGTG-CCTATGATTGCATCGTAGATGCGACACA
1 TTAGTGCCCTATGATTGCA-CGTAG-TGCGACACA
1397708 TTCAGTGCACCCTATGATTGCACGTAGGTGCGACA
1 TT-AGTG--CCCTATGATTGCACGTA-GTGCGACA
1397743 TATTCAATGC
Statistics
Matches: 59, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
33 1 0.02
34 24 0.41
35 10 0.17
37 11 0.19
38 13 0.22
ACGTcount: A:0.24, C:0.23, G:0.24, T:0.29
Consensus pattern (33 bp):
TTAGTGCCCTATGATTGCACGTAGTGCGACACA
Found at i:1398780 original size:19 final size:19
Alignment explanation
Indices: 1398758--1399077 Score: 344
Period size: 19 Copynumber: 18.4 Consensus size: 19
1398748 CGGAAAATAC
*
1398758 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1398777 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
1398791 AATCGCAATGCGGAAATG-A
1 AATCGCAATGC-GAAATGAA
*
1398810 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1398824 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1398843 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
*
1398861 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1398875 AATCGCAATGCGAAATGAAA
1 AATCGCAATGCGAAATG-AA
1398895 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1398914 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1398933 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
1398947 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
1398966 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1398985 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
1398999 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1399018 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
1399032 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1399051 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1399070 AATCGCAA
1 AATCGCAA
1399078 CGAGATAATC
Statistics
Matches: 257, Mismatches: 10, Indels: 68
0.77 0.03 0.20
Matches are distributed among these distances:
13 2 0.01
14 54 0.21
16 25 0.10
17 18 0.07
18 11 0.04
19 126 0.49
20 21 0.08
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1398829 original size:14 final size:15
Alignment explanation
Indices: 1398810--1398887 Score: 52
Period size: 14 Copynumber: 4.8 Consensus size: 15
1398800 GCGGAAATGA
1398810 AATCGCAA-CGAGAG
1 AATCGCAAGCGAGAG
*
1398824 AATCGCAATGCGAAATGAA
1 AATCGCAA-GCG--A-GAG
*
1398843 AATCGCAATGCGAAATG
1 AATCGCAA-GCGAGA-G
1398860 AAATCGCAA-CGAGAG
1 -AATCGCAAGCGAGAG
1398875 AATCGCAATGCGA
1 AATCGCAA-GCGA
1398888 AATGAAAAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 16
0.72 0.06 0.23
Matches are distributed among these distances:
14 16 0.31
15 1 0.02
16 10 0.20
17 1 0.02
18 9 0.18
19 14 0.27
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (15 bp):
AATCGCAAGCGAGAG
Found at i:1398842 original size:52 final size:52
Alignment explanation
Indices: 1398786--1399099 Score: 387
Period size: 52 Copynumber: 6.0 Consensus size: 52
1398776 AAATCCCAAC
1398786 ATGAAAATCGCAATGCGGAAATG-AAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1398838 ATGAAAATCGCAATGCGAAATG-AAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* * * *
1398889 ATGAAAAATCGCAATGCGAAATGAAAATCGCAATGCGA-AAT-GAAAAT-CGCA
1 ATG-AAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-CAATGCGAA
* * *
1398940 ACGACAGAATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAAAATCGCAA--CGAA
1 ATGA-A-AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
*
1398997 A-G--AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
1399046 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1399098 AT
1 AT
1399100 TATAAATTGC
Statistics
Matches: 230, Mismatches: 15, Indels: 34
0.82 0.05 0.12
Matches are distributed among these distances:
47 9 0.04
48 1 0.00
49 5 0.02
50 4 0.02
51 45 0.20
52 140 0.61
53 12 0.05
54 1 0.00
56 1 0.00
57 6 0.03
58 5 0.02
59 1 0.00
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:1398856 original size:85 final size:83
Alignment explanation
Indices: 1398758--1399099 Score: 384
Period size: 85 Copynumber: 4.0 Consensus size: 83
1398748 CGGAAAATAC
1398758 AATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGGAAATG-AAATCGCAACGAG
1 AATCGCAACGCGAAATG-AAATCCCAA-ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAG
1398822 AGAATCGCAATGCGAAATGAA
63 AGAATCGCAATGCGAAATGAA
* * *
1398843 AATCGCAATGCGAAATGAAATCGCAACGA-GAGAATCGCAATGCGAAATGAAAAATCGCAATGCG
1 AATCGCAACGCGAAATGAAATCCCAA--ATGAAAATCGCAATGCGAAATG-AAAATCGCAA--CG
*
1398907 AAATGAAAATCGCAATGCGAAATGAA
61 --A-GAGAATCGCAATGCGAAATGAA
* * * * *
1398933 AATCGCAACGAC-AGAATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAAAATCGCAACGAA
1 AATCGCAACG-CGA-AAT-GAAATCCCAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAG
1398997 AGAATCGCAATGCGAAATGAA
63 AGAATCGCAATGCGAAATGAA
** * * *
1399018 AATCGCAACGAAAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGA
1 AATCGCAACGCGA-AAT-GAAATCCCAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGA
*
1399083 TAATCGCAATGCGAAAT
64 GAATCGCAATGCGAAAT
1399100 TATAAATTGC
Statistics
Matches: 226, Mismatches: 18, Indels: 26
0.84 0.07 0.10
Matches are distributed among these distances:
83 6 0.03
84 21 0.09
85 123 0.54
86 1 0.00
87 2 0.01
88 2 0.01
89 1 0.00
90 42 0.19
91 22 0.10
92 6 0.03
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.14
Consensus pattern (83 bp):
AATCGCAACGCGAAATGAAATCCCAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
ATCGCAATGCGAAATGAA
Found at i:1399004 original size:14 final size:14
Alignment explanation
Indices: 1398985--1399039 Score: 65
Period size: 14 Copynumber: 3.6 Consensus size: 14
1398975 GCGAAATGAA
1398985 AATCGCAACGAAAG
1 AATCGCAACGAAAG
1398999 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
1399016 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1399032 AATCGCAA
1 AATCGCAA
1399040 TGCGAAATGA
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 16 0.44
16 6 0.17
17 6 0.17
19 8 0.22
ACGTcount: A:0.49, C:0.20, G:0.20, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1399052 original size:33 final size:33
Alignment explanation
Indices: 1398758--1399058 Score: 262
Period size: 33 Copynumber: 8.8 Consensus size: 33
1398748 CGGAAAATAC
* *
1398758 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA-
1 AATCGCAATGCGAAATGAAAATCGCAACGA--AAG
*
1398791 AATCGCAATGCGGAAATG-AAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGAAAG
1398824 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATG
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAAA-G
* * * * *
1398860 AAATCGCAACGAGAGAATCG-CAATGCGAAATGAAA-
1 -AATCGCAATGCGA-AAT-GAAAAT-CGCAACGAAAG
1398895 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATG
1 AATCGCAATGCGAAATGAAAATCGCAA--CGAAA-G
* *
1398931 AAAATCGCAA--CGACA-G--AATCGCAATGCGAAATTAA
1 --AATCGCAATGCGAAATGAAAATCGCAA--CG-AA--AG
1398966 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1398999 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1399032 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
1399059 TGCGAAATGA
Statistics
Matches: 224, Mismatches: 18, Indels: 52
0.76 0.06 0.18
Matches are distributed among these distances:
32 12 0.05
33 126 0.56
34 24 0.11
35 11 0.05
36 9 0.04
37 15 0.07
38 22 0.10
39 5 0.02
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAAAG
Found at i:1399211 original size:19 final size:19
Alignment explanation
Indices: 1399105--1399203 Score: 145
Period size: 19 Copynumber: 5.4 Consensus size: 19
1399095 GAAATTATAA
1399105 ATTGCGATTTTCATTTCCGC
1 ATTGCGATTTTCATTT-CGC
1399125 ATTGCGATTTTCATTTCGC
1 ATTGCGATTTTCATTTCGC
*
1399144 ATTGCGA--TTC-TCTCG-
1 ATTGCGATTTTCATTTCGC
1399159 -TTGCGATTTTCATTTCGC
1 ATTGCGATTTTCATTTCGC
1399177 ATTGCGATTTTCATTTCGC
1 ATTGCGATTTTCATTTCGC
1399196 ATTGCGAT
1 ATTGCGAT
1399204 AGTCATTTTT
Statistics
Matches: 72, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.50
20 16 0.22
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.45
Consensus pattern (19 bp):
ATTGCGATTTTCATTTCGC
Found at i:1399329 original size:14 final size:14
Alignment explanation
Indices: 1399310--1399346 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1399300 CATCAATTAC
1399310 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1399324 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1399338 ACAAATCAA
1 ACAAATCAA
1399347 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1401187 original size:14 final size:14
Alignment explanation
Indices: 1401168--1401224 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1401158 GCGAAATGAA
*
1401168 AATCGCAACGACAG
1 AATCGCAACGAAAG
1401182 AATCGCAATACGAAATG
1 AATCGC-A-ACGAAA-G
1401199 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1401215 AATCGCAACG
1 AATCGCAACG
1401225 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
15 1 0.03
16 6 0.16
17 7 0.19
18 1 0.03
19 6 0.16
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1401196 original size:33 final size:33
Alignment explanation
Indices: 1401149--1401240 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
1401139 GCGAAACCAA
*
1401149 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
**
1401182 AATCGCAATACGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1401215 AATCGCAACGCGAAATG-AAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1401241 TGCGATTTTG
Statistics
Matches: 54, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
32 9 0.17
33 45 0.83
ACGTcount: A:0.48, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:1401206 original size:19 final size:19
Alignment explanation
Indices: 1401112--1401240 Score: 100
Period size: 19 Copynumber: 7.3 Consensus size: 19
1401102 TAGTTTACTT
*
1401112 TCGCAACACGAAACTTAAAA
1 TCGCAACACGAAA-TGAAAA
* **
1401132 TCGCAACGCGAAACCAAAA
1 TCGCAACACGAAATGAAAA
*
1401151 TCGCAACGCGAAATGAAAA
1 TCGCAACACGAAATGAAAA
*
1401170 TCGC-A-ACGACA-G--AA
1 TCGCAACACGAAATGAAAA
*
1401184 TCGCAATACGAAATGAAAA
1 TCGCAACACGAAATGAAAA
1401203 TCGC-A-ACGAAA-G--AA
1 TCGCAACACGAAATGAAAA
*
1401217 TCGCAACGCGAAATG-AAA
1 TCGCAACACGAAATGAAAA
1401235 TCGCAA
1 TCGCAA
1401241 TGCGATTTTG
Statistics
Matches: 91, Mismatches: 9, Indels: 20
0.76 0.08 0.17
Matches are distributed among these distances:
14 12 0.13
15 2 0.02
16 12 0.13
17 12 0.13
18 10 0.11
19 31 0.34
20 12 0.13
ACGTcount: A:0.47, C:0.24, G:0.18, T:0.11
Consensus pattern (19 bp):
TCGCAACACGAAATGAAAA
Found at i:1401263 original size:19 final size:19
Alignment explanation
Indices: 1401241--1401369 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1401231 GAAATCGCAA
1401241 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1401260 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
1401274 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1401293 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
1401307 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1401326 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1401345 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
1401365 TGCGA
1 TGCGA
1401370 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:1401283 original size:33 final size:33
Alignment explanation
Indices: 1401241--1401332 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
1401231 GAAATCGCAA
1401241 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
1401274 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
1401307 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
1401333 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:1403234 original size:19 final size:18
Alignment explanation
Indices: 1403210--1403307 Score: 86
Period size: 19 Copynumber: 5.7 Consensus size: 18
1403200 TCGCAACGAG
1403210 AATCGCAACGCGAGATGA
1 AATCGCAACGCGAGATGA
1403228 CAATCGCAA--CGAGA-G-
1 -AATCGCAACGCGAGATGA
*
1403243 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAGATG-A
1403262 AATCGCAA--CGAGA-G-
1 AATCGCAACGCGAGATGA
*
1403276 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAGATG-A
*
1403295 AATCGCAATGCGA
1 AATCGCAACGCGA
1403308 TTTGGTTTCG
Statistics
Matches: 65, Mismatches: 4, Indels: 20
0.73 0.04 0.22
Matches are distributed among these distances:
14 16 0.25
16 10 0.15
17 11 0.17
19 28 0.43
ACGTcount: A:0.43, C:0.22, G:0.24, T:0.10
Consensus pattern (18 bp):
AATCGCAACGCGAGATGA
Found at i:1403248 original size:14 final size:14
Alignment explanation
Indices: 1403198--1403285 Score: 63
Period size: 14 Copynumber: 5.7 Consensus size: 14
1403188 TTGAAATGAA
1403198 AATCGCAAC--GAG
1 AATCGCAACGAGAG
1403210 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
1403227 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
1403243 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1403262 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1403276 AATCGCAACG
1 AATCGCAACG
1403286 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 22
0.72 0.02 0.26
Matches are distributed among these distances:
12 8 0.13
14 21 0.34
15 1 0.02
16 5 0.08
17 8 0.13
18 1 0.02
19 18 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1403249 original size:33 final size:33
Alignment explanation
Indices: 1403190--1403302 Score: 194
Period size: 33 Copynumber: 3.5 Consensus size: 33
1403180 TCTTTTGGTT
1403190 GAAATGAAAATCGCAAC--GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
1403221 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1403254 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1403287 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1403303 TGCGATTTGG
Statistics
Matches: 76, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
31 15 0.20
33 61 0.80
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1403337 original size:14 final size:14
Alignment explanation
Indices: 1403318--1403372 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1403308 TTTGGTTTCG
1403318 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1403332 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1403351 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1403365 CGTTGCGA
1 CGTTGCGA
1403373 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1403380 original size:33 final size:33
Alignment explanation
Indices: 1403313--1403394 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
1403303 TGCGATTTGG
***
1403313 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1403346 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
1403379 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
1403395 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:1403399 original size:20 final size:20
Alignment explanation
Indices: 1403325--1403413 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
1403315 TCGCGTTGCG
1403325 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
1403345 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
1403358 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
1403378 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
1403398 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
1403414 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:1403534 original size:33 final size:33
Alignment explanation
Indices: 1403492--1403562 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1403482 AATACTAACT
*
1403492 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
1403525 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
1403558 TGAAA
1 TGAAA
1403563 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:1403796 original size:22 final size:22
Alignment explanation
Indices: 1403744--1403798 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1403734 TGGTTGTGAG
**
1403744 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
1403766 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
1403788 GGATTTCTTCG
1 GGATTTCTTCG
1403799 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:1403969 original size:20 final size:20
Alignment explanation
Indices: 1403944--1404136 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
1403934 CTTTAAATAT
1403944 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1403964 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1403986 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1404005 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
1404025 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
1404045 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1404065 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1404085 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1404105 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1404125 CGCGTTGCGATT
1 CGCGTTGCGATT
1404137 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1404131 original size:60 final size:60
Alignment explanation
Indices: 1403944--1404136 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
1403934 CTTTAAATAT
**
1403944 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
1404005 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
1404065 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
1404125 CGCGTTGCGATT
1 CGCGTTGCGATT
1404137 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:1404217 original size:20 final size:20
Alignment explanation
Indices: 1404192--1404243 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1404182 AAGAATCGCG
*
1404192 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
1404212 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
1404232 TTGCGATTCTGG
1 TTGCGATTCTGG
1404244 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:1406803 original size:64 final size:64
Alignment explanation
Indices: 1406729--1406872 Score: 261
Period size: 64 Copynumber: 2.2 Consensus size: 64
1406719 TATTTCTTTA
* * *
1406729 AATCAATCACTCATCTCTTATCTTGAGATTTATATATATAAAAACAAATCACTCCCCTGTATTC
1 AATCAATCACTTATCTCTTATCTTGAAATATATATATATAAAAACAAATCACTCCCCTGTATTC
1406793 AATCAATCACTTATCTCTTATCTTGAAATATATATATATAAAAACAAATCACTCCCCTGTATTC
1 AATCAATCACTTATCTCTTATCTTGAAATATATATATATAAAAACAAATCACTCCCCTGTATTC
1406857 AATCAATCACTTATCT
1 AATCAATCACTTATCT
1406873 TAGCTTTATA
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
64 77 1.00
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.36
Consensus pattern (64 bp):
AATCAATCACTTATCTCTTATCTTGAAATATATATATATAAAAACAAATCACTCCCCTGTATTC
Found at i:1407214 original size:38 final size:35
Alignment explanation
Indices: 1407118--1407235 Score: 128
Period size: 36 Copynumber: 3.2 Consensus size: 35
1407108 TGGAATATTT
* * * *
1407118 AGTGCCCTGTGATTGCACCATATGTGCGATACATTT
1 AGTGCCCTATGATTGCACCGTA-GTGCGACACATTC
*
1407154 AGTGCCCTATGATTGCATCGTAGATGCGACACATTC
1 AGTGCCCTATGATTGCACCGTAG-TGCGACACATTC
*
1407190 AGTGCACCCTATGATTGCACCGTAGGTGCGACATATTC
1 AGTG--CCCTATGATTGCACCGTA-GTGCGACACATTC
*
1407228 AATGCCCT
1 AGTGCCCT
1407236 GTGAATGTAC
Statistics
Matches: 70, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
35 1 0.01
36 37 0.53
38 31 0.44
39 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.29
Consensus pattern (35 bp):
AGTGCCCTATGATTGCACCGTAGTGCGACACATTC
Found at i:1411031 original size:43 final size:43
Alignment explanation
Indices: 1410978--1411105 Score: 229
Period size: 43 Copynumber: 3.0 Consensus size: 43
1410968 ATCCCTAATC
*
1410978 ATGTTAGTCTACATGTTTATCGACAAATGATACCTTTTATGAT
1 ATGTTAGTCTACATGTTTGTCGACAAATGATACCTTTTATGAT
* *
1411021 ATGTTCGTCTACATGTTTGTCGAAAAATGATACCTTTTATGAT
1 ATGTTAGTCTACATGTTTGTCGACAAATGATACCTTTTATGAT
1411064 ATGTTAGTCTACATGTTTGTCGACAAATGATACCTTTTATGA
1 ATGTTAGTCTACATGTTTGTCGACAAATGATACCTTTTATGA
1411106 AGGCATGTAA
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 80 1.00
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (43 bp):
ATGTTAGTCTACATGTTTGTCGACAAATGATACCTTTTATGAT
Found at i:1411505 original size:10 final size:10
Alignment explanation
Indices: 1411483--1411521 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
1411473 AAAATATATT
1411483 TTCATTTATG
1 TTCATTTATG
* *
1411493 TTCCTTTACG
1 TTCATTTATG
*
1411503 TTCGTTTATG
1 TTCATTTATG
1411513 TTCATTTAT
1 TTCATTTAT
1411522 TATGTTCGTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.15, C:0.15, G:0.10, T:0.59
Consensus pattern (10 bp):
TTCATTTATG
Found at i:1411560 original size:10 final size:10
Alignment explanation
Indices: 1411487--1411566 Score: 52
Period size: 10 Copynumber: 7.4 Consensus size: 10
1411477 TATATTTTCA
*
1411487 TTTATGTTCC
1 TTTATGTTCG
*
1411497 TTTACGTTCG
1 TTTATGTTCG
*
1411507 TTTATGTTCATT
1 TTTATGTTC--G
1411519 TATTATGTTCG
1 T-TTATGTTCG
* *
1411530 TTTACGTTTG
1 TTTATGTTCG
1411540 TTTATTGTGTTCG
1 TTTA---TGTTCG
*
1411553 TTTATGTTAG
1 TTTATGTTCG
1411563 TTTA
1 TTTA
1411567 CATCTGTTCG
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
10 36 0.67
11 1 0.02
12 1 0.02
13 16 0.30
ACGTcount: A:0.14, C:0.10, G:0.16, T:0.60
Consensus pattern (10 bp):
TTTATGTTCG
Found at i:1411598 original size:24 final size:23
Alignment explanation
Indices: 1411502--1411605 Score: 109
Period size: 23 Copynumber: 4.4 Consensus size: 23
1411492 GTTCCTTTAC
** *
1411502 GTTCGTTTATGTTCATTTATTAT
1 GTTCGTTTATGTTTGTTTATTGT
*
1411525 GTTCGTTTACGTTTGTTTATTGT
1 GTTCGTTTATGTTTGTTTATTGT
* * *
1411548 GTTCGTTTATGTTAGTTTACATCT
1 GTTCGTTTATGTTTGTTTA-TTGT
* *
1411572 GTTCGTTTGTGTTTGTTCATTTGT
1 GTTCGTTTATGTTTGTTTA-TTGT
1411596 GTTCGTTTAT
1 GTTCGTTTAT
1411606 CATTTAAATG
Statistics
Matches: 65, Mismatches: 15, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
23 36 0.55
24 29 0.45
ACGTcount: A:0.12, C:0.10, G:0.19, T:0.60
Consensus pattern (23 bp):
GTTCGTTTATGTTTGTTTATTGT
Found at i:1413246 original size:14 final size:14
Alignment explanation
Indices: 1413228--1413265 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
1413218 TCTGTCTATA
*
1413228 TGCAGAGATTT-TT
1 TGCAGGGATTTATT
1413241 TCGCAGGGATTTATT
1 T-GCAGGGATTTATT
1413256 TGCAGGGATT
1 TGCAGGGATT
1413266 ACTTCTCATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 1 0.05
14 18 0.82
15 3 0.14
ACGTcount: A:0.21, C:0.11, G:0.29, T:0.39
Consensus pattern (14 bp):
TGCAGGGATTTATT
Found at i:1415051 original size:18 final size:18
Alignment explanation
Indices: 1415030--1415067 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1415020 TTACCATGTA
1415030 AAGAAAATTACTTTTTAT
1 AAGAAAATTACTTTTTAT
1415048 AAGAAAATTACTTTTTAT
1 AAGAAAATTACTTTTTAT
1415066 AA
1 AA
1415068 CCCTAATTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (18 bp):
AAGAAAATTACTTTTTAT
Found at i:1419735 original size:6 final size:6
Alignment explanation
Indices: 1419724--1419754 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
1419714 ATTATTTTGA
1419724 CACGAC CACGAC CACGAC CACGAC CACGAC C
1 CACGAC CACGAC CACGAC CACGAC CACGAC C
1419755 CGAGACGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.52, G:0.16, T:0.00
Consensus pattern (6 bp):
CACGAC
Found at i:1420269 original size:6 final size:6
Alignment explanation
Indices: 1420258--1420293 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
1420248 TCTCGTCTCG
1420258 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1420294 ACGTTTCTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.00, C:0.17, G:0.50, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:1420445 original size:42 final size:42
Alignment explanation
Indices: 1420383--1420571 Score: 310
Period size: 42 Copynumber: 4.5 Consensus size: 42
1420373 TGCGATTTTG
1420383 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* *
1420425 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
1420467 GACTATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
1420509 GACTATAGCAACGAATTTGG-A-AAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1420549 GACTATCGCAACGTGAATTTGGA
1 GACTATCGCAAC--GAATTTGGA
1420572 CTATCGCAAT
Statistics
Matches: 136, Mismatches: 8, Indels: 5
0.91 0.05 0.03
Matches are distributed among these distances:
40 29 0.21
41 1 0.01
42 106 0.78
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:1420556 original size:21 final size:21
Alignment explanation
Indices: 1420380--1420586 Score: 160
Period size: 21 Copynumber: 10.0 Consensus size: 21
1420370 CGTTGCGATT
*
1420380 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
*
1420399 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
1420422 TTCGACTATCGCAA--CGAAC
1 TTGGACTATCGCAACGCGAAC
*
1420441 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
*
1420464 TTGGACTATCGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
* *
1420483 TTGGAATAAATCGCAATGCGAAC
1 TTGGACT--ATCGCAACGCGAAC
* * *
1420506 TTCGACTATAGCAA--CGAAT
1 TTGGACTATCGCAACGCGAAC
**
1420525 TTGGAAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGCGAAC
* * *
1420546 TTCGACTATCGCAACGTGAAT
1 TTGGACTATCGCAACGCGAAC
*
1420567 TTGGACTATCGCAATGCGAA
1 TTGGACTATCGCAACGCGAA
1420587 TATGTAAATC
Statistics
Matches: 147, Mismatches: 27, Indels: 26
0.74 0.14 0.13
Matches are distributed among these distances:
19 40 0.27
21 78 0.53
23 29 0.20
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (21 bp):
TTGGACTATCGCAACGCGAAC
Found at i:1422794 original size:21 final size:21
Alignment explanation
Indices: 1422770--1422986 Score: 141
Period size: 21 Copynumber: 10.4 Consensus size: 21
1422760 GAATAAATCA
1422770 CAACGCGAACTTTGACTATCG
1 CAACGCGAACTTTGACTATCG
*
1422791 CAA--CGAA-TTTGGAATAAATCG
1 CAACGCGAACTTT-GACT--ATCG
*
1422812 CAACGCGAACTTCGACTATCG
1 CAACGCGAACTTTGACTATCG
* *
1422833 CAA--CGAACTTGGAATAAATCG
1 CAACGCGAACTTTGACT--ATCG
*
1422854 CAACGCGAACTTGGACTATCG
1 CAACGCGAACTTTGACTATCG
*
1422875 CAA--CGAA-TTTGGAATAAATCG
1 CAACGCGAACTTT-GACT--ATCG
* * *
1422896 CAATGCGAACTTCGACTATAG
1 CAACGCGAACTTTGACTATCG
**
1422917 CAA--CGAA-TTTGGAAAATCG
1 CAACGCGAACTTT-GACTATCG
*
1422936 CAACGCGAACTTCGACTATCG
1 CAACGCGAACTTTGACTATCG
* *
1422957 CAACGTGAACTTGGACTATCG
1 CAACGCGAACTTTGACTATCG
*
1422978 CAATGCGAA
1 CAACGCGAA
1422987 TATGTAAATC
Statistics
Matches: 154, Mismatches: 22, Indels: 40
0.71 0.10 0.19
Matches are distributed among these distances:
18 7 0.05
19 36 0.23
21 80 0.52
22 2 0.01
23 25 0.16
24 4 0.03
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (21 bp):
CAACGCGAACTTTGACTATCG
Found at i:1422971 original size:42 final size:42
Alignment explanation
Indices: 1422747--1422961 Score: 362
Period size: 42 Copynumber: 5.2 Consensus size: 42
1422737 CCACCAGTCG
* *
1422747 CGCAACGAATTTGGAATAAATCACAACGCGAACTTTGACTAT
1 CGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTAT
1422789 CGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTAT
1 CGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTAT
* *
1422831 CGCAACGAACTTGGAATAAATCGCAACGCGAACTTGGACTAT
1 CGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTAT
*
1422873 CGCAACGAATTTGGAATAAATCGCAATGCGAACTTCGACTAT
1 CGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTAT
*
1422915 AGCAACGAATTTGG-A-AAATCGCAACGCGAACTTCGACTAT
1 CGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTAT
1422955 CGCAACG
1 CGCAACG
1422962 TGAACTTGGA
Statistics
Matches: 163, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
40 30 0.18
41 1 0.01
42 132 0.81
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (42 bp):
CGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTAT
Found at i:1422971 original size:84 final size:84
Alignment explanation
Indices: 1422748--1422986 Score: 360
Period size: 84 Copynumber: 2.9 Consensus size: 84
1422738 CACCAGTCGC
* *
1422748 GCAACGAATTTGGAATAAATCACAACGCGAACTTTGACTATCGCAACGAATTTGGAATAAATCGC
1 GCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCGC
* *
1422813 AACGCGAACTTCGACTATC
66 AATGCGAACTTCGACTATA
* *
1422832 GCAACGAACTTGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAAATCGC
1 GCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCGC
1422897 AATGCGAACTTCGACTATA
66 AATGCGAACTTCGACTATA
* *
1422916 GCAACGAATTTGG-A-AAATCGCAACGCGAACTTCGACTATCGCAACGTGAACTTGGACT--ATC
1 GCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAAC--GAATTTGGAATAAATC
1422977 GCAATGCGAA
64 GCAATGCGAA
1422987 TATGTAAATC
Statistics
Matches: 144, Mismatches: 9, Indels: 6
0.91 0.06 0.04
Matches are distributed among these distances:
82 43 0.30
83 1 0.01
84 100 0.69
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (84 bp):
GCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATAAATCGC
AATGCGAACTTCGACTATA
Found at i:1430559 original size:21 final size:19
Alignment explanation
Indices: 1430523--1430566 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 19
1430513 CAAAAACCCT
1430523 AAAAGATATATTTAAAATTA
1 AAAAGATATATTTAAAA-TA
1430543 AAAAGATA-ATTCCTAAAATA
1 AAAAGATATATT--TAAAATA
1430563 AAAA
1 AAAA
1430567 TAAAATAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 3 0.14
20 14 0.64
21 5 0.23
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.27
Consensus pattern (19 bp):
AAAAGATATATTTAAAATA
Found at i:1433501 original size:14 final size:15
Alignment explanation
Indices: 1433472--1433503 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
1433462 AAATAATTAA
1433472 AATAATATATTTTAT
1 AATAATATATTTTAT
1433487 AATAATATA-TTTAT
1 AATAATATATTTTAT
1433501 AAT
1 AAT
1433504 TATTAATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AATAATATATTTTAT
Found at i:1435530 original size:5 final size:5
Alignment explanation
Indices: 1435511--1435554 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
1435501 GTCCGTCCGT
* * * *
1435511 CTCGT CTCGG CTCGG CTCGG CACGG CACGG CACGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
1435555 TGGTCGTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.07, C:0.41, G:0.36, T:0.16
Consensus pattern (5 bp):
CTCGG
Found at i:1435563 original size:6 final size:6
Alignment explanation
Indices: 1435552--1435630 Score: 131
Period size: 6 Copynumber: 13.2 Consensus size: 6
1435542 ACGGCTCGGC
* * *
1435552 TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGAGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1435600 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1435631 AATACGTGTC
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 71 1.00
ACGTcount: A:0.04, C:0.16, G:0.49, T:0.30
Consensus pattern (6 bp):
TCGTGG
Found at i:1435931 original size:22 final size:22
Alignment explanation
Indices: 1435906--1435960 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
1435896 TCAGGAGTTA
* *
1435906 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
1435928 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
1435950 CGGGAGTTATA
1 CAGGAGTTATA
1435961 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:1441504 original size:5 final size:5
Alignment explanation
Indices: 1441485--1441528 Score: 52
Period size: 5 Copynumber: 8.8 Consensus size: 5
1441475 GTCCGTCCGT
* * * *
1441485 CTCGT CTCGG CTCGG CTCGG CACGG CACGG CACGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
1441529 TGGTCGTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 36 1.00
ACGTcount: A:0.07, C:0.41, G:0.36, T:0.16
Consensus pattern (5 bp):
CTCGG
Found at i:1441537 original size:6 final size:6
Alignment explanation
Indices: 1441526--1441598 Score: 128
Period size: 6 Copynumber: 12.2 Consensus size: 6
1441516 ACGGCTCGGC
* *
1441526 TCGTGG TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
1441574 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
1441599 AATACGTGTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 65 1.00
ACGTcount: A:0.03, C:0.16, G:0.49, T:0.32
Consensus pattern (6 bp):
TCGTGG
Found at i:1441897 original size:22 final size:22
Alignment explanation
Indices: 1441872--1441926 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
1441862 TCAGGAGTTA
* *
1441872 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
1441894 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
1441916 CGGGAGTTATA
1 CAGGAGTTATA
1441927 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:1446516 original size:2 final size:2
Alignment explanation
Indices: 1446511--1446542 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
1446501 TATATTTGTG
1446511 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1446543 CAAGGCTTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1448565 original size:545 final size:545
Alignment explanation
Indices: 1447529--1448609 Score: 2135
Period size: 545 Copynumber: 2.0 Consensus size: 545
1447519 AAGGTTTTGC
*
1447529 AACAGTTAATAACCTTATTTATTATTATAAAAAATGTTGTTTTAAAAGAACAGATTGAGATAGGT
1 AACAGTAAATAACCTTATTTATTATTATAAAAAATGTTGTTTTAAAAGAACAGATTGAGATAGGT
1447594 TCTTCCACTGAGATCTAATATATGATAAATACCACATCTTAATAAGGAGATAGTTTTGTGTCACC
66 TCTTCCACTGAGATCTAATATATGATAAATACCACATCTTAATAAGGAGATAGTTTTGTGTCACC
1447659 TTACATCCTTACAAAATTATTGAGAAGAGATATTAAATAAATGCAAGAATATTGTTTATGATTCC
131 TTACATCCTTACAAAATTATTGAGAAGAGATATTAAATAAATGCAAGAATATTGTTTATGATTCC
1447724 TTTATTGATGTGAAGGATATTATATTGATCTCATTAATGAGTGTCCTTGACTCAATAATATGACC
196 TTTATTGATGTGAAGGATATTATATTGATCTCATTAATGAGTGTCCTTGACTCAATAATATGACC
1447789 ACAGTTTCTGTGCCTAGAGCTCCTTTCACCGGACAGGAGCTCATCAAACTTGATTTCTATAATGT
261 ACAGTTTCTGTGCCTAGAGCTCCTTTCACCGGACAGGAGCTCATCAAACTTGATTTCTATAATGT
1447854 TGAAAATACGCATATGACAAATAGTTGGCAGCATGGAAATCAAACTTGAAATTAAAAAAATACAG
326 TGAAAATACGCATATGACAAATAGTTGGCAGCATGGAAATCAAACTTGAAATTAAAAAAATACAG
1447919 CTATGGAAAATTGAAGAGTATTGTAGAAGCATATGAGTTACTTAGCAACAAAAGACTTTGAAAAG
391 CTATGGAAAATTGAAGAGTATTGTAGAAGCATATGAGTTACTTAGCAACAAAAGACTTTGAAAAG
1447984 TCAAAGGAAATCCTCCAGTAAGGAATTGTAAGGCGGCATGAAGAATGTAGAATCAACTATACGCC
456 TCAAAGGAAATCCTCCAGTAAGGAATTGTAAGGCGGCATGAAGAATGTAGAATCAACTATACGCC
1448049 TGTTTAATTAGCTTATTTATTATTA
521 TGTTTAATTAGCTTATTTATTATTA
1448074 AACAGTAAATAACCTTATTTATTATTATAAAAAATGTTGTTTTAAAAGAACAGATTGAGATAGGT
1 AACAGTAAATAACCTTATTTATTATTATAAAAAATGTTGTTTTAAAAGAACAGATTGAGATAGGT
*
1448139 TCTTCCACTGAGATCTAATATATGATAAATACCACATCTTAATAAGGAGATGGTTTTGTGTCACC
66 TCTTCCACTGAGATCTAATATATGATAAATACCACATCTTAATAAGGAGATAGTTTTGTGTCACC
1448204 TTACATCCTTACAAAATTATTGAGAAGAGATATTAAATAAATGCAAGAATATTGTTTATGATTCC
131 TTACATCCTTACAAAATTATTGAGAAGAGATATTAAATAAATGCAAGAATATTGTTTATGATTCC
1448269 TTTATTGATGTGAAGGATATTATATTGATCTCATTAATGAGTGTCCTTGACTCAATAATATGACC
196 TTTATTGATGTGAAGGATATTATATTGATCTCATTAATGAGTGTCCTTGACTCAATAATATGACC
1448334 ACAGTTTCTGTGCCTAGAGCTCCTTTCACCGGACAGGAGCTCATCAAACTTGATTTCTATAATGT
261 ACAGTTTCTGTGCCTAGAGCTCCTTTCACCGGACAGGAGCTCATCAAACTTGATTTCTATAATGT
*
1448399 TGAAAATATGCATATGACAAATAGTTGGCAGCATGGAAATCAAACTTGAAATTAAAAAAATACAG
326 TGAAAATACGCATATGACAAATAGTTGGCAGCATGGAAATCAAACTTGAAATTAAAAAAATACAG
1448464 CTATGGAAAATTGAAGAGTATTGTAGAAGCATATGAGTTACTTAGCAACAAAAGACTTTGAAAAG
391 CTATGGAAAATTGAAGAGTATTGTAGAAGCATATGAGTTACTTAGCAACAAAAGACTTTGAAAAG
1448529 TCAAAGGAAATCCTCCAGTAAGGAATTGTAAGGCGGCATGAAGAATGTAGAATCAACTATACGCC
456 TCAAAGGAAATCCTCCAGTAAGGAATTGTAAGGCGGCATGAAGAATGTAGAATCAACTATACGCC
1448594 TGTTTAATTAGCTTAT
521 TGTTTAATTAGCTTAT
1448610 AAATGTATGA
Statistics
Matches: 533, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
545 533 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.32
Consensus pattern (545 bp):
AACAGTAAATAACCTTATTTATTATTATAAAAAATGTTGTTTTAAAAGAACAGATTGAGATAGGT
TCTTCCACTGAGATCTAATATATGATAAATACCACATCTTAATAAGGAGATAGTTTTGTGTCACC
TTACATCCTTACAAAATTATTGAGAAGAGATATTAAATAAATGCAAGAATATTGTTTATGATTCC
TTTATTGATGTGAAGGATATTATATTGATCTCATTAATGAGTGTCCTTGACTCAATAATATGACC
ACAGTTTCTGTGCCTAGAGCTCCTTTCACCGGACAGGAGCTCATCAAACTTGATTTCTATAATGT
TGAAAATACGCATATGACAAATAGTTGGCAGCATGGAAATCAAACTTGAAATTAAAAAAATACAG
CTATGGAAAATTGAAGAGTATTGTAGAAGCATATGAGTTACTTAGCAACAAAAGACTTTGAAAAG
TCAAAGGAAATCCTCCAGTAAGGAATTGTAAGGCGGCATGAAGAATGTAGAATCAACTATACGCC
TGTTTAATTAGCTTATTTATTATTA
Found at i:1455294 original size:2 final size:2
Alignment explanation
Indices: 1455287--1455316 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1455277 GAGTTGTTAC
1455287 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1455317 AACCTGACGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1459922 original size:11 final size:11
Alignment explanation
Indices: 1459904--1459980 Score: 82
Period size: 11 Copynumber: 7.0 Consensus size: 11
1459894 GTTCATGAAT
1459904 ATGTTTGTTTA
1 ATGTTTGTTTA
*
1459915 ACGTTTGTTTA
1 ATGTTTGTTTA
**
1459926 ATGTTCATTTA
1 ATGTTTGTTTA
*
1459937 ACGTTTGTTTA
1 ATGTTTGTTTA
**
1459948 ATGTTCATTTA
1 ATGTTTGTTTA
*
1459959 ATGTTCGTTTA
1 ATGTTTGTTTA
*
1459970 GTGTTTGTTTA
1 ATGTTTGTTTA
1459981 TCATTTGTTT
Statistics
Matches: 53, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 53 1.00
ACGTcount: A:0.19, C:0.06, G:0.17, T:0.57
Consensus pattern (11 bp):
ATGTTTGTTTA
Found at i:1459946 original size:33 final size:33
Alignment explanation
Indices: 1459906--1459991 Score: 100
Period size: 33 Copynumber: 2.6 Consensus size: 33
1459896 TCATGAATAT
1459906 GTTTGTTTAACGTTTGTTTAATGTTCATTTAAC
1 GTTTGTTTAACGTTTGTTTAATGTTCATTTAAC
* ** * **
1459939 GTTTGTTTAATGTTCATTTAATGTTCGTTTAGT
1 GTTTGTTTAACGTTTGTTTAATGTTCATTTAAC
* *
1459972 GTTTGTTTATCATTTGTTTA
1 GTTTGTTTAACGTTTGTTTA
1459992 TATATTCAAT
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.19, C:0.07, G:0.16, T:0.58
Consensus pattern (33 bp):
GTTTGTTTAACGTTTGTTTAATGTTCATTTAAC
Found at i:1459980 original size:22 final size:22
Alignment explanation
Indices: 1459911--1459974 Score: 101
Period size: 22 Copynumber: 2.9 Consensus size: 22
1459901 AATATGTTTG
1459911 TTTAACGTTTGTTTAATGTTCA
1 TTTAACGTTTGTTTAATGTTCA
1459933 TTTAACGTTTGTTTAATGTTCA
1 TTTAACGTTTGTTTAATGTTCA
* * *
1459955 TTTAATGTTCGTTTAGTGTT
1 TTTAACGTTTGTTTAATGTT
1459975 TGTTTATCAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.20, C:0.08, G:0.16, T:0.56
Consensus pattern (22 bp):
TTTAACGTTTGTTTAATGTTCA
Found at i:1461983 original size:24 final size:25
Alignment explanation
Indices: 1461945--1461995 Score: 86
Period size: 24 Copynumber: 2.1 Consensus size: 25
1461935 TGTTCTTATG
1461945 ACACATTTTTCTCTGCTCTTGTGGC
1 ACACATTTTTCTCTGCTCTTGTGGC
*
1461970 ACACA-TTTTCTCTGTTCTTGTGGC
1 ACACATTTTTCTCTGCTCTTGTGGC
1461994 AC
1 AC
1461996 GATCTTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 20 0.80
25 5 0.20
ACGTcount: A:0.14, C:0.27, G:0.16, T:0.43
Consensus pattern (25 bp):
ACACATTTTTCTCTGCTCTTGTGGC
Found at i:1463405 original size:22 final size:22
Alignment explanation
Indices: 1463362--1463409 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
1463352 AAAACCATAT
1463362 TAATTAAGTTAGAATTTCATTAA
1 TAATTAAGTTAGAATTTCATT-A
* * *
1463385 TAATT-AGTTATATTTTTATTA
1 TAATTAAGTTAGAATTTCATTA
1463406 TAAT
1 TAAT
1463410 AATTTTATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 5 0.23
22 12 0.55
23 5 0.23
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (22 bp):
TAATTAAGTTAGAATTTCATTA
Done.