Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032245.1 Gossypioides kirkii chromosome KI_2_4
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: 41238926
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 6100 characters in sequence are not A, C, G, or T
File 5 of 132
Found at i:1205301 original size:29 final size:28
Alignment explanation
Indices: 1205269--1205325 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
1205259 TTGAAATTTG
* * * *
1205269 AAAATTATAGAGATTGAATTCTTATAATT
1 AAAAGTATAAAGATTAAATT-TTAAAATT
1205298 AAAAGTATAAAGATTAAATTTTAAAATT
1 AAAAGTATAAAGATTAAATTTTAAAATT
1205326 TTGAAAAGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 7 0.29
29 17 0.71
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.39
Consensus pattern (28 bp):
AAAAGTATAAAGATTAAATTTTAAAATT
Found at i:1205684 original size:22 final size:22
Alignment explanation
Indices: 1205653--1205701 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
1205643 AAATTAAATT
* *
1205653 ATATATATTT-TTTATTATAAAA
1 ATATAAATTTATTAATT-TAAAA
*
1205675 ATATAAATTTATTAATTTAATA
1 ATATAAATTTATTAATTTAAAA
1205697 ATATA
1 ATATA
1205702 TATCTTTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
ATATAAATTTATTAATTTAAAA
Found at i:1206877 original size:13 final size:13
Alignment explanation
Indices: 1206861--1206894 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1206851 TATTATAAAA
1206861 AAATATTTTTTAT
1 AAATATTTTTTAT
*
1206874 AAATAATTTTTAT
1 AAATATTTTTTAT
1206887 AAAT-TTTT
1 AAATATTTT
1206895 GGGGCTGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 3 0.16
13 16 0.84
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
AAATATTTTTTAT
Found at i:1208027 original size:36 final size:36
Alignment explanation
Indices: 1207987--1208059 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
1207977 GGATGAAAAG
1207987 AAAAAATAATTTTCTTTCCATTTTTCCAACTCTCCT
1 AAAAAATAATTTTCTTTCCATTTTTCCAACTCTCCT
1208023 AAAAAATAATTTTCTTTCCATTTTTCCAACTCTCCT
1 AAAAAATAATTTTCTTTCCATTTTTCCAACTCTCCT
1208059 A
1 A
1208060 CCAATCACAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.32, C:0.25, G:0.00, T:0.44
Consensus pattern (36 bp):
AAAAAATAATTTTCTTTCCATTTTTCCAACTCTCCT
Found at i:1208142 original size:15 final size:15
Alignment explanation
Indices: 1208092--1208143 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
1208082 AAAAAATATG
*
1208092 TTTTCCATCCTTCTAA
1 TTTT-CATCCTTCCAA
*
1208108 TTTTCTTCCCTT-CAA
1 TTTTCAT-CCTTCCAA
1208123 TTTTCATCCTTCCAA
1 TTTTCATCCTTCCAA
*
1208138 ATTTCA
1 TTTTCA
1208144 ATAGTTAGGT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
14 4 0.13
15 18 0.60
16 8 0.27
ACGTcount: A:0.19, C:0.31, G:0.00, T:0.50
Consensus pattern (15 bp):
TTTTCATCCTTCCAA
Found at i:1210410 original size:7 final size:7
Alignment explanation
Indices: 1210398--1210426 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
1210388 CCTCAATATA
1210398 ATATTTG
1 ATATTTG
1210405 ATATTTG
1 ATATTTG
1210412 ATATTTG
1 ATATTTG
1210419 AT-TTTG
1 ATATTTG
1210425 AT
1 AT
1210427 TTTAATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.59
Consensus pattern (7 bp):
ATATTTG
Found at i:1210417 original size:14 final size:13
Alignment explanation
Indices: 1210398--1210435 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
1210388 CCTCAATATA
1210398 ATATTTGATATTTG
1 ATATTTGAT-TTTG
1210412 ATATTTGATTTTG
1 ATATTTGATTTTG
*
1210425 AT-TTTAATTTT
1 ATATTTGATTTT
1210436 TAACTTGGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 8 0.35
13 6 0.26
14 9 0.39
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.63
Consensus pattern (13 bp):
ATATTTGATTTTG
Found at i:1211883 original size:49 final size:49
Alignment explanation
Indices: 1211750--1211866 Score: 225
Period size: 49 Copynumber: 2.4 Consensus size: 49
1211740 AACTTAATGA
1211750 GTAAACATTTATTAAAACGGCGCAATTTTACCTTTTAACTTTAGAAAAT
1 GTAAACATTTATTAAAACGGCGCAATTTTACCTTTTAACTTTAGAAAAT
1211799 GTAAACATTTATTAAAACGGCGCAATTTTACCTTTTAACTTTAGAAAAT
1 GTAAACATTTATTAAAACGGCGCAATTTTACCTTTTAACTTTAGAAAAT
*
1211848 GTAAACATTTATCAAAACG
1 GTAAACATTTATTAAAACG
1211867 ACGTAGTTTT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
49 67 1.00
ACGTcount: A:0.40, C:0.15, G:0.10, T:0.35
Consensus pattern (49 bp):
GTAAACATTTATTAAAACGGCGCAATTTTACCTTTTAACTTTAGAAAAT
Found at i:1212400 original size:20 final size:20
Alignment explanation
Indices: 1212371--1212412 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
1212361 TTACAATCAT
1212371 TTCTAATGCCATTATCGATA
1 TTCTAATGCCATTATCGATA
*
1212391 TTCTAGTGCCATTATCGATA
1 TTCTAATGCCATTATCGATA
1212411 TT
1 TT
1212413 GATTACAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.26, C:0.19, G:0.12, T:0.43
Consensus pattern (20 bp):
TTCTAATGCCATTATCGATA
Found at i:1214475 original size:16 final size:16
Alignment explanation
Indices: 1214437--1214485 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
1214427 ATCCTTTAAA
1214437 AATAATAAAAATTTGATTT
1 AATAAT-AAAA-TT-ATTT
1214456 AATAAT-AAATTATTT
1 AATAATAAAATTATTT
1214471 AAATAATAAAATTAT
1 -AATAATAAAATTAT
1214486 ATTTTTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 4 0.14
16 8 0.29
17 10 0.36
19 6 0.21
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (16 bp):
AATAATAAAATTATTT
Found at i:1214488 original size:19 final size:18
Alignment explanation
Indices: 1214436--1214489 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 18
1214426 GATCCTTTAA
1214436 AAATAATAAAAATTTGATTT
1 AAATAAT-AAAATTT-ATTT
1214456 -AATAAT-AAA-TTATTT
1 AAATAATAAAATTTATTT
1214471 AAATAATAAAATTATATTT
1 AAATAATAAAATT-TATTT
1214490 TTTTTACCGT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
15 4 0.13
16 8 0.27
17 6 0.20
18 1 0.03
19 11 0.37
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
AAATAATAAAATTTATTT
Found at i:1215826 original size:27 final size:24
Alignment explanation
Indices: 1215777--1215823 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
1215767 ATCCTGTGAA
1215777 ACCCTAACTACTACTCGAATTTTC
1 ACCCTAACTACTACTCGAATTTTC
1215801 ACCCTAACTACTACTCGAATTTT
1 ACCCTAACTACTACTCGAATTTT
1215824 TTTTTTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.30, C:0.32, G:0.04, T:0.34
Consensus pattern (24 bp):
ACCCTAACTACTACTCGAATTTTC
Found at i:1215951 original size:52 final size:51
Alignment explanation
Indices: 1215894--1216000 Score: 171
Period size: 51 Copynumber: 2.1 Consensus size: 51
1215884 TGTGGCATGT
* *
1215894 AAATGGACCCCTGCAA-TAACCCTTTTTCAGTAAAATAAAGAAATCCCGACCA
1 AAATGGACCCCTG-AAGGAACCCTTTTTCAAT-AAATAAAGAAATCCCGACCA
1215946 AAATGGACCCCTGAAGGAACCCTTTTTCAATAAATAAAGAAATCCCGACCA
1 AAATGGACCCCTGAAGGAACCCTTTTTCAATAAATAAAGAAATCCCGACCA
1215997 AAAT
1 AAAT
1216001 TCACAAGAAG
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
51 26 0.50
52 26 0.50
ACGTcount: A:0.42, C:0.25, G:0.12, T:0.21
Consensus pattern (51 bp):
AAATGGACCCCTGAAGGAACCCTTTTTCAATAAATAAAGAAATCCCGACCA
Found at i:1216319 original size:36 final size:36
Alignment explanation
Indices: 1216278--1216378 Score: 141
Period size: 38 Copynumber: 2.8 Consensus size: 36
1216268 ATTAAAATTA
1216278 TTATTAAAATAATAAAATTACATTTTATGAGATAAG
1 TTATTAAAATAATAAAATTACATTTTATGAGATAAG
1216314 TTATTAAAA-AGATAAAAAATTACATTTTATGAGATAAG
1 TTATTAAAATA-AT--AAAATTACATTTTATGAGATAAG
* * *
1216352 CTGTTAAAATGATAAAATTACATTTTA
1 TTATTAAAATAATAAAATTACATTTTA
1216379 ACTAATAAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
35 1 0.02
36 25 0.43
38 32 0.55
ACGTcount: A:0.50, C:0.04, G:0.09, T:0.38
Consensus pattern (36 bp):
TTATTAAAATAATAAAATTACATTTTATGAGATAAG
Found at i:1216535 original size:24 final size:24
Alignment explanation
Indices: 1216507--1216552 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
1216497 TTAAATTTTA
*
1216507 AAATTTTAAAAAATAATAATAATT
1 AAATTTTAAAAAATAAAAATAATT
*
1216531 AAATTTTTAAAAATAAAAATAA
1 AAATTTTAAAAAATAAAAATAA
1216553 AAGACTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (24 bp):
AAATTTTAAAAAATAAAAATAATT
Found at i:1223482 original size:257 final size:259
Alignment explanation
Indices: 1223022--1223506 Score: 758
Period size: 257 Copynumber: 1.9 Consensus size: 259
1223012 ATAAGCATAT
* *
1223022 TCCATATAGAATTCAAGATCATTACAACAACTATGATTCTATTATTAACCAGACCGATCCAAAAT
1 TCCATATAGAATTCAAGATCATTACAACAACTATGATTCTATCATTAACCAGACCGATCCAAAAC
* * *
1223087 CACTGAAATTAAGAACAATAAAAAAAAGGAATTCAAGCAAGCAAACGATTCGGCGCATGCTTTTT
66 CACTGAAACTAAG-ACAAGAAAAAAAAGGAATTCAAGCAAGCAAAAGATTCGGCGCATGCTTTTT
*
1223152 AAACAAACAATTCAAGTAATATTTAAACATGATAATCATGCAAGTAATTAGGGTACCTAAACAGA
130 AAACAAACAATTCAAGTAATATTTAAACATGATAATCATGCAAGTAAGTAGGGTACCTAAACAGA
*
1223217 GATCGAGAAGAAGATCCGGCATCGTCTCGCAGTTTTTCCCTTGGTTTTTCTTTCGGCGCCACCGA
195 GATCGAGAAGAAGATCCAGCATCGTCTCGCAGTTTTTCCCTTGGTTTTTCTTTCGGCGCCACCGA
* * * *
1223282 TCCATATAGAATTCAAGATCATTGCAACTATTATGATTCTATCATTAACCAGACCGATTCAAAAC
1 TCCATATAGAATTCAAGATCATTACAACAACTATGATTCTATCATTAACCAGACCGATCCAAAAC
* ** * * *
1223347 CACTTAAACTAAG-GGAGGAAATAAA-GAGTTCAAGCAAGCAAAAGATTCGGCGCATGCTTTTTA
66 CACTGAAACTAAGACAAGAAAAAAAAGGAATTCAAGCAAGCAAAAGATTCGGCGCATGCTTTTTA
* * *
1223410 AACAAACAATTCGAGTAATATTTAAACATGATAATTATGCATGTAAGTAGGGTACCTAAACAGAG
131 AACAAACAATTCAAGTAATATTTAAACATGATAATCATGCAAGTAAGTAGGGTACCTAAACAGAG
*
1223475 GTCGAGAAGAAGATCCAGCATCGTCTCGCAGT
196 ATCGAGAAGAAGATCCAGCATCGTCTCGCAGT
1223507 AATATTTAAA
Statistics
Matches: 204, Mismatches: 21, Indels: 3
0.89 0.09 0.01
Matches are distributed among these distances:
257 127 0.62
258 7 0.03
260 70 0.34
ACGTcount: A:0.39, C:0.19, G:0.16, T:0.26
Consensus pattern (259 bp):
TCCATATAGAATTCAAGATCATTACAACAACTATGATTCTATCATTAACCAGACCGATCCAAAAC
CACTGAAACTAAGACAAGAAAAAAAAGGAATTCAAGCAAGCAAAAGATTCGGCGCATGCTTTTTA
AACAAACAATTCAAGTAATATTTAAACATGATAATCATGCAAGTAAGTAGGGTACCTAAACAGAG
ATCGAGAAGAAGATCCAGCATCGTCTCGCAGTTTTTCCCTTGGTTTTTCTTTCGGCGCCACCGA
Found at i:1223558 original size:81 final size:81
Alignment explanation
Indices: 1223423--1223587 Score: 303
Period size: 81 Copynumber: 2.0 Consensus size: 81
1223413 AAACAATTCG
* *
1223423 AGTAATATTTAAACATGATAATTATGCATGTAAGTAGGGTACCTAAACAGAGGTCGAGAAGAAGA
1 AGTAATATTTAAACATGATAATTATGCAAGTAAGTAGGGCACCTAAACAGAGGTCGAGAAGAAGA
1223488 TCCAGCATCGTCTCGC
66 TCCAGCATCGTCTCGC
*
1223504 AGTAATATTTAAACATGATAATTATGCAAGTAATTAGGGCACCTAAACAGAGGTCGAGAAGAAGA
1 AGTAATATTTAAACATGATAATTATGCAAGTAAGTAGGGCACCTAAACAGAGGTCGAGAAGAAGA
1223569 TCCAGCATCGTCTCGC
66 TCCAGCATCGTCTCGC
1223585 AGT
1 AGT
1223588 TTTTCCCTCG
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
81 81 1.00
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (81 bp):
AGTAATATTTAAACATGATAATTATGCAAGTAAGTAGGGCACCTAAACAGAGGTCGAGAAGAAGA
TCCAGCATCGTCTCGC
Found at i:1228409 original size:4 final size:4
Alignment explanation
Indices: 1228400--1228433 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
1228390 CATTGCTTTT
*
1228400 CTTG CTTG CTTG CTTT CTTG CTTG CTTG CATTG C
1 CTTG CTTG CTTG CTTG CTTG CTTG CTTG C-TTG C
1228434 CCATATTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.03, C:0.26, G:0.21, T:0.50
Consensus pattern (4 bp):
CTTG
Found at i:1228418 original size:16 final size:17
Alignment explanation
Indices: 1228392--1228428 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
1228382 TATAATATCA
1228392 TTGCTTTTCTTGCTTGC
1 TTGCTTTTCTTGCTTGC
1228409 TTGC-TTTCTTGCTTGC
1 TTGCTTTTCTTGCTTGC
1228425 TTGC
1 TTGC
1228429 ATTGCCCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.00, C:0.24, G:0.19, T:0.57
Consensus pattern (17 bp):
TTGCTTTTCTTGCTTGC
Found at i:1234196 original size:33 final size:33
Alignment explanation
Indices: 1234146--1234215 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
1234136 CCTGGAAATC
* *
1234146 ATGGGGATGTTAAAGGATTCAAAATGCATGGAA
1 ATGGGGATCTTAAAGGATTCAAAATCCATGGAA
* * *
1234179 ATGGGGATCTTAGAGGATTTAGAATCCATGGAA
1 ATGGGGATCTTAAAGGATTCAAAATCCATGGAA
1234212 ATGG
1 ATGG
1234216 AAACATTGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.36, C:0.07, G:0.31, T:0.26
Consensus pattern (33 bp):
ATGGGGATCTTAAAGGATTCAAAATCCATGGAA
Found at i:1243561 original size:36 final size:37
Alignment explanation
Indices: 1243493--1243564 Score: 101
Period size: 39 Copynumber: 1.9 Consensus size: 37
1243483 TATCTGAAGG
1243493 TGGTAATGATTGTTGCTTAGGAGGAGGAGGTGGTGAATT
1 TGGTAATGATTGTTGCTT--GAGGAGGAGGTGGTGAATT
* *
1243532 TGGTGATGATTGTTGCTT-AGGAGGTGGTGGTGA
1 TGGTAATGATTGTTGCTTGAGGAGGAGGTGGTGA
1243565 TGGTGACGGT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
36 14 0.45
39 17 0.55
ACGTcount: A:0.19, C:0.03, G:0.43, T:0.35
Consensus pattern (37 bp):
TGGTAATGATTGTTGCTTGAGGAGGAGGTGGTGAATT
Found at i:1244216 original size:10 final size:10
Alignment explanation
Indices: 1244201--1244231 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
1244191 ACTCCATTCT
1244201 CTTTCATCAA
1 CTTTCATCAA
1244211 CTTTCATCAA
1 CTTTCATCAA
1244221 CTTTCATCAA
1 CTTTCATCAA
1244231 C
1 C
1244232 AAAAACAAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.29, C:0.32, G:0.00, T:0.39
Consensus pattern (10 bp):
CTTTCATCAA
Found at i:1248313 original size:31 final size:34
Alignment explanation
Indices: 1248268--1248335 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
1248258 TAATTTGTTT
1248268 ATAAATAAAAA-ATATA-TTTTGATATGTTAATA
1 ATAAATAAAAATATATATTTTTGATATGTTAATA
1248300 ATAAATAAAAATATATATTTTTGATATGTTAATA
1 ATAAATAAAAATATATATTTTTGATATGTTAATA
1248334 AT
1 AT
1248336 TTAAAATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 11 0.32
33 5 0.15
34 18 0.53
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (34 bp):
ATAAATAAAAATATATATTTTTGATATGTTAATA
Found at i:1248342 original size:31 final size:32
Alignment explanation
Indices: 1248273--1248349 Score: 95
Period size: 34 Copynumber: 2.4 Consensus size: 32
1248263 TGTTTATAAA
*
1248273 TAAAAAATATA-TTTTGATATGTTAATAATAAAT
1 TAAAATATATATTTTTGATATGTTAATAAT--AT
*
1248306 AAAAATATATATTTTTGATATGTTAATAAT-T
1 TAAAATATATATTTTTGATATGTTAATAATAT
*
1248337 TAAAATAAATATT
1 TAAAATATATATT
1248350 GTAAAAATCT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
31 12 0.31
33 9 0.23
34 18 0.46
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (32 bp):
TAAAATATATATTTTTGATATGTTAATAATAT
Found at i:1252349 original size:14 final size:14
Alignment explanation
Indices: 1252330--1252369 Score: 53
Period size: 15 Copynumber: 2.8 Consensus size: 14
1252320 AAGTTGTATA
1252330 TTTAATTTTTGAAT
1 TTTAATTTTTGAAT
* *
1252344 TTTAATTTGGTGATT
1 TTTAATTT-TTGAAT
1252359 TTTAATTTTTG
1 TTTAATTTTTG
1252370 TACTTTTTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
14 10 0.45
15 12 0.55
ACGTcount: A:0.23, C:0.00, G:0.12, T:0.65
Consensus pattern (14 bp):
TTTAATTTTTGAAT
Found at i:1266456 original size:31 final size:31
Alignment explanation
Indices: 1266415--1266474 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
1266405 CTAGTGGCTC
1266415 AAATAAAAACTTTCAAATAATTCAGTGACTT
1 AAATAAAAACTTTCAAATAATTCAGTGACTT
*
1266446 AAATGAAAACTTTCAAATAATTCAGTGAC
1 AAATAAAAACTTTCAAATAATTCAGTGAC
1266475 CATTTTATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.48, C:0.13, G:0.08, T:0.30
Consensus pattern (31 bp):
AAATAAAAACTTTCAAATAATTCAGTGACTT
Found at i:1266876 original size:16 final size:18
Alignment explanation
Indices: 1266857--1266890 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
1266847 TAAATTTTTA
1266857 TTTTAAA-AATAA-ATAT
1 TTTTAAAGAATAATATAT
1266873 TTTTAAAGAATAATATAT
1 TTTTAAAGAATAATATAT
1266891 ACATGATATC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 5 0.31
18 4 0.25
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (18 bp):
TTTTAAAGAATAATATAT
Found at i:1275234 original size:28 final size:28
Alignment explanation
Indices: 1275203--1275265 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
1275193 TTTTGACCTA
*
1275203 AAAAAATTACTATTCAATTCTAACACCC
1 AAAAAATTAATATTCAATTCTAACACCC
* * *
1275231 AAAAAAATAATATTTAATTCTAACCCCC
1 AAAAAATTAATATTCAATTCTAACACCC
1275259 AAAAAAT
1 AAAAAAT
1275266 AATTCTTCGC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.27
Consensus pattern (28 bp):
AAAAAATTAATATTCAATTCTAACACCC
Found at i:1277320 original size:39 final size:38
Alignment explanation
Indices: 1277277--1277356 Score: 108
Period size: 39 Copynumber: 2.1 Consensus size: 38
1277267 GTGATCCATG
*
1277277 TTACACAAAACATTA-CAAGATTTGTAATAATTTGTGTAA
1 TTACACAAAACATTAGCAAGA--AGTAATAATTTGTGTAA
*
1277316 TTACACAAAACATTATGGAAGAAGTAATAATTTGTGTAA
1 TTACACAAAACATTA-GCAAGAAGTAATAATTTGTGTAA
1277355 TT
1 TT
1277357 GCGTAATTAC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
39 33 0.89
41 4 0.11
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (38 bp):
TTACACAAAACATTAGCAAGAAGTAATAATTTGTGTAA
Found at i:1285016 original size:30 final size:29
Alignment explanation
Indices: 1284980--1285084 Score: 83
Period size: 30 Copynumber: 3.6 Consensus size: 29
1284970 TTATTATTAT
*
1284980 ATTTGGTACCTGAACTTAACACTTTTTTTA
1 ATTTGGTACCTAAACTT-ACACTTTTTTTA
*
1285010 ATTTGGTACCTAAACTT----TTTTTTACCCA
1 ATTTGGTACCTAAACTTACACTTTTTT---TA
* * *
1285038 AATTGGTACCTGAACTTGACACTTTTCTTA
1 ATTTGGTACCTAAACTT-ACACTTTTTTTA
*
1285068 ATTTGATACCTAAACTT
1 ATTTGGTACCTAAACTT
1285085 TTTTGGACCC
Statistics
Matches: 58, Mismatches: 9, Indels: 16
0.70 0.11 0.19
Matches are distributed among these distances:
25 6 0.10
28 16 0.28
30 31 0.53
33 5 0.09
ACGTcount: A:0.28, C:0.19, G:0.10, T:0.44
Consensus pattern (29 bp):
ATTTGGTACCTAAACTTACACTTTTTTTA
Found at i:1285072 original size:58 final size:58
Alignment explanation
Indices: 1284982--1285146 Score: 226
Period size: 58 Copynumber: 2.9 Consensus size: 58
1284972 ATTATTATAT
* * * *
1284982 TTGGTACCTGAACTTAACACTTTTTTTAATTTGGTACCTAAACTTTTTTTTACCCAAA
1 TTGGTACCTGAACTTGACACTTTTCTTAATTTGATACCTAAACTTTTTTTGACCCAAA
* *
1285040 TTGGTACCTGAACTTGACACTTTTCTTAATTTGATACCTAAACTTTTTTGGACCCAAC
1 TTGGTACCTGAACTTGACACTTTTCTTAATTTGATACCTAAACTTTTTTTGACCCAAA
* * *
1285098 TTGGTACTTGAACTTGACAGTTTTTCCTAATTTGATACCT-AA-TTTTTTT
1 TTGGTACCTGAACTTGACA-CTTTTCTTAATTTGATACCTAAACTTTTTTT
1285147 AAAGTCAATT
Statistics
Matches: 96, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
57 6 0.06
58 72 0.75
59 18 0.19
ACGTcount: A:0.25, C:0.19, G:0.11, T:0.45
Consensus pattern (58 bp):
TTGGTACCTGAACTTGACACTTTTCTTAATTTGATACCTAAACTTTTTTTGACCCAAA
Found at i:1286756 original size:28 final size:27
Alignment explanation
Indices: 1286723--1286814 Score: 78
Period size: 28 Copynumber: 3.3 Consensus size: 27
1286713 GTTTTAGGTT
*
1286723 CCTTAAAATTTGAAAAAAAAATTAGATC
1 CCTTAAAATTTGAAAAAAAAATT-GAGC
* * *
1286751 TCTTAAAAGTTGGTAAAAAAAATTGAGC
1 CCTTAAAA-TTTGAAAAAAAAATTGAGC
** *
1286779 CCTTAAAAGCT-AAAAAAAAATTCGGGC
1 CCTTAAAATTTGAAAAAAAAATT-GAGC
1286806 CCTTTAAAA
1 CC-TTAAAA
1286815 GTTGTTCAAA
Statistics
Matches: 51, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
26 10 0.20
27 5 0.10
28 23 0.45
29 13 0.25
ACGTcount: A:0.49, C:0.13, G:0.12, T:0.26
Consensus pattern (27 bp):
CCTTAAAATTTGAAAAAAAAATTGAGC
Found at i:1288753 original size:23 final size:22
Alignment explanation
Indices: 1288730--1288788 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 22
1288720 GTATTGTATA
*
1288730 AAAAATATATATTATAAATTAT
1 AAAAATATATATTATAAAATAT
* *
1288752 AACAA-AT-TATTAAAAAATATT
1 AAAAATATATATTATAAAATA-T
*
1288773 AAAAATACATATTATA
1 AAAAATATATATTATA
1288789 GTGTTAAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 5
0.72 0.15 0.13
Matches are distributed among these distances:
20 10 0.36
21 7 0.25
22 5 0.18
23 6 0.21
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (22 bp):
AAAAATATATATTATAAAATAT
Found at i:1297089 original size:43 final size:43
Alignment explanation
Indices: 1297028--1297114 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 43
1297018 AAAGTGCTAT
*
1297028 CCAACAGTTTTGGTTGATTCACGTAATGACTCGAATCGAAAAG
1 CCAACAGTTTTGGTTGATTCACGTAATGACTCGAATCAAAAAG
*
1297071 CCAACAGTTTTGGTTGATTCACGTACTGACTCGAATCAAAAAG
1 CCAACAGTTTTGGTTGATTCACGTAATGACTCGAATCAAAAAG
1297114 C
1 C
1297115 TTGAGCCTTG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.28
Consensus pattern (43 bp):
CCAACAGTTTTGGTTGATTCACGTAATGACTCGAATCAAAAAG
Found at i:1299243 original size:31 final size:29
Alignment explanation
Indices: 1299207--1299284 Score: 120
Period size: 31 Copynumber: 2.6 Consensus size: 29
1299197 TTTTGGGTCC
*
1299207 AATTTGGTACTCAAACTTGACACTTTTTTCT
1 AATTTGGTACTTAAACTTGACA-TTTTTT-T
1299238 AATTTGGTACTTAAACTTGACATTTTTTT
1 AATTTGGTACTTAAACTTGACATTTTTTT
*
1299267 AAGTTGGTACTTAAACTT
1 AATTTGGTACTTAAACTT
1299285 TTTGGGGTCC
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
29 18 0.40
30 6 0.13
31 21 0.47
ACGTcount: A:0.28, C:0.14, G:0.12, T:0.46
Consensus pattern (29 bp):
AATTTGGTACTTAAACTTGACATTTTTTT
Found at i:1299273 original size:29 final size:31
Alignment explanation
Indices: 1299210--1299284 Score: 118
Period size: 29 Copynumber: 2.5 Consensus size: 31
1299200 TGGGTCCAAT
* *
1299210 TTGGTACTCAAACTTGACACTTTTTTCTAAT
1 TTGGTACTTAAACTTGACACTTTTTTCTAAG
1299241 TTGGTACTTAAACTTGACA-TTTTTT-TAAG
1 TTGGTACTTAAACTTGACACTTTTTTCTAAG
1299270 TTGGTACTTAAACTT
1 TTGGTACTTAAACTT
1299285 TTTGGGGTCC
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
29 18 0.43
30 6 0.14
31 18 0.43
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.47
Consensus pattern (31 bp):
TTGGTACTTAAACTTGACACTTTTTTCTAAG
Found at i:1299312 original size:88 final size:89
Alignment explanation
Indices: 1299168--1299335 Score: 239
Period size: 88 Copynumber: 1.9 Consensus size: 89
1299158 TGAACTTGAC
* * *
1299168 ACATTTTCTTAATTTAGTACCTAAATTTTTTTTGGGTCCAATTTGGTACTCAAACTTGACACTTT
1 ACATTTTCTTAAGTTAGTACCTAAATCTTTTTGGGGTCCAATTTGGTACTCAAACTTGACACTTT
*
1299233 TTTCTAATTTGGTACTTAAACTTG
66 TTTCTAATTTAGTACTTAAACTTG
* * * ** *
1299257 ACATTTTTTTAAGTTGGTACTTAAA-CTTTTTGGGGTCCAATTTGGTACTTGAACTTGACTCTTT
1 ACATTTTCTTAAGTTAGTACCTAAATCTTTTTGGGGTCCAATTTGGTACTCAAACTTGACACTTT
1299321 TTTCTAATTTAGTAC
66 TTTCTAATTTAGTAC
1299336 GTAATTTTTT
Statistics
Matches: 69, Mismatches: 10, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
88 48 0.70
89 21 0.30
ACGTcount: A:0.24, C:0.15, G:0.13, T:0.48
Consensus pattern (89 bp):
ACATTTTCTTAAGTTAGTACCTAAATCTTTTTGGGGTCCAATTTGGTACTCAAACTTGACACTTT
TTTCTAATTTAGTACTTAAACTTG
Found at i:1299552 original size:13 final size:13
Alignment explanation
Indices: 1299534--1299558 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1299524 AATTAAAAAA
1299534 AAATATCAAATTT
1 AAATATCAAATTT
1299547 AAATATCAAATT
1 AAATATCAAATT
1299559 AAAAATAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (13 bp):
AAATATCAAATTT
Found at i:1299555 original size:31 final size:31
Alignment explanation
Indices: 1299519--1299634 Score: 141
Period size: 31 Copynumber: 3.9 Consensus size: 31
1299509 AAACCTTAGG
1299519 TATCAAATTAAAAAAAAATATCAAATTTAAA
1 TATCAAATTAAAAAAAAATATCAAATTTAAA
* * *
1299550 TATCAAATTAAAAATAAATGTCAAGTTTAAA
1 TATCAAATTAAAAAAAAATATCAAATTTAAA
* * *
1299581 TATCAAATT-GAATAAAA-A--AAATTTAGA
1 TATCAAATTAAAAAAAAATATCAAATTTAAA
*
1299608 TATCAAATTAATAAAAAATATCAAATT
1 TATCAAATTAAAAAAAAATATCAAATT
1299635 CAGATGCCAA
Statistics
Matches: 69, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
27 16 0.23
28 5 0.07
29 1 0.01
30 5 0.07
31 42 0.61
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.31
Consensus pattern (31 bp):
TATCAAATTAAAAAAAAATATCAAATTTAAA
Found at i:1307324 original size:29 final size:29
Alignment explanation
Indices: 1307287--1307347 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
1307277 CCATTTTTAA
*
1307287 AGGAGCTAAAAT-TAAATTATAAACTTTTG
1 AGGAGCTAAAATGTAAATTACAAA-TTTTG
* *
1307316 AGGATCTAAAATGTAATTTACAAATTTTG
1 AGGAGCTAAAATGTAAATTACAAATTTTG
1307345 AGG
1 AGG
1307348 CAAAGGCTCC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 19 0.68
30 9 0.32
ACGTcount: A:0.43, C:0.07, G:0.16, T:0.34
Consensus pattern (29 bp):
AGGAGCTAAAATGTAAATTACAAATTTTG
Found at i:1311019 original size:30 final size:30
Alignment explanation
Indices: 1310971--1311052 Score: 103
Period size: 30 Copynumber: 2.7 Consensus size: 30
1310961 ATGAGGGATC
* * *
1310971 TAATAAAAATTTTTAAAAATTTTAGA-GACT
1 TAATGAAAATTTTCAAAAATTTTAAATG-CT
* *
1311001 TGATGAGAATTTTCAAAAATTTTAAATGCT
1 TAATGAAAATTTTCAAAAATTTTAAATGCT
1311031 TAATGAAAATTTTCAAAAATTT
1 TAATGAAAATTTTCAAAAATTT
1311053 GGGAGCCAAG
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 43 0.98
31 1 0.02
ACGTcount: A:0.46, C:0.05, G:0.09, T:0.40
Consensus pattern (30 bp):
TAATGAAAATTTTCAAAAATTTTAAATGCT
Found at i:1323630 original size:22 final size:22
Alignment explanation
Indices: 1323605--1323648 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1323595 AGTACGTTAG
1323605 ATCAAAGAACAAATTGATCTTC
1 ATCAAAGAACAAATTGATCTTC
1323627 ATCAAAGAACAAATTGATCTTC
1 ATCAAAGAACAAATTGATCTTC
1323649 CTGTTAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.45, C:0.18, G:0.09, T:0.27
Consensus pattern (22 bp):
ATCAAAGAACAAATTGATCTTC
Found at i:1331777 original size:12 final size:11
Alignment explanation
Indices: 1331739--1331779 Score: 50
Period size: 12 Copynumber: 3.7 Consensus size: 11
1331729 TTGAATTAAA
1331739 TTTTTAAT-AT
1 TTTTTAATAAT
1331749 TTTTT-ATAATT
1 TTTTTAATAA-T
1331760 TTTTTAATAAT
1 TTTTTAATAAT
1331771 TTATTTAAT
1 TT-TTTAAT
1331780 CGAATCGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
9 2 0.07
10 6 0.22
11 9 0.33
12 10 0.37
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTTTAATAAT
Found at i:1331779 original size:21 final size:21
Alignment explanation
Indices: 1331739--1331779 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1331729 TTGAATTAAA
*
1331739 TTTTTAATATTTTTTATAATT
1 TTTTTAATATTTATTATAATT
1331760 TTTTTAATAATTTATT-TAAT
1 TTTTTAAT-ATTTATTATAAT
1331780 CGAATCGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTTTAATATTTATTATAATT
Found at i:1344458 original size:23 final size:23
Alignment explanation
Indices: 1344428--1344472 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
1344418 CGAAACCAAC
1344428 CATTGAATCATAATTTTAAAATT
1 CATTGAATCATAATTTTAAAATT
1344451 CATTGAATCATAATTTTAAAAT
1 CATTGAATCATAATTTTAAAAT
1344473 CTTATAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.42
Consensus pattern (23 bp):
CATTGAATCATAATTTTAAAATT
Found at i:1348484 original size:30 final size:30
Alignment explanation
Indices: 1348450--1348511 Score: 115
Period size: 30 Copynumber: 2.1 Consensus size: 30
1348440 AAAGGATTTA
1348450 AGTTCAAATTTTGAAGATGATATTGTTAAG
1 AGTTCAAATTTTGAAGATGATATTGTTAAG
*
1348480 AGTTCAAATTTTGGAGATGATATTGTTAAG
1 AGTTCAAATTTTGAAGATGATATTGTTAAG
1348510 AG
1 AG
1348512 GAACAGCTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.35, C:0.03, G:0.23, T:0.39
Consensus pattern (30 bp):
AGTTCAAATTTTGAAGATGATATTGTTAAG
Found at i:1348585 original size:16 final size:17
Alignment explanation
Indices: 1348558--1348605 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
1348548 AACATGAATA
*
1348558 ATATAAAAAATATAAAT
1 ATATTAAAAATATAAAT
*
1348575 ATATT-AAAATAT-TAT
1 ATATTAAAAATATAAAT
*
1348590 ATTTTAAAAATATAAA
1 ATATTAAAAATATAAA
1348606 CTTAACATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 6 0.24
16 14 0.56
17 5 0.20
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATATTAAAAATATAAAT
Found at i:1360742 original size:10 final size:10
Alignment explanation
Indices: 1360727--1360752 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1360717 AACCAAATTG
1360727 AAAAAAAACA
1 AAAAAAAACA
1360737 AAAAAAAACA
1 AAAAAAAACA
1360747 AAAAAA
1 AAAAAA
1360753 CCCTACTACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:1360982 original size:11 final size:11
Alignment explanation
Indices: 1360966--1360990 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1360956 AAAAGACTGA
1360966 AATTTCAAGAG
1 AATTTCAAGAG
1360977 AATTTCAAGAG
1 AATTTCAAGAG
1360988 AAT
1 AAT
1360991 GACTGAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.48, C:0.08, G:0.16, T:0.28
Consensus pattern (11 bp):
AATTTCAAGAG
Found at i:1364425 original size:12 final size:12
Alignment explanation
Indices: 1364397--1364428 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
1364387 GGGCTCATAG
*
1364397 TCGGGCTCATTC
1 TCGGACTCATTC
1364409 TCGGACTCATTC
1 TCGGACTCATTC
1364421 TCGGACTC
1 TCGGACTC
1364429 TCTTCCCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.12, C:0.34, G:0.22, T:0.31
Consensus pattern (12 bp):
TCGGACTCATTC
Found at i:1368030 original size:21 final size:21
Alignment explanation
Indices: 1368006--1368046 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1367996 CAACTAATTC
1368006 GATTTAATTCAAAAATTTTAT
1 GATTTAATTCAAAAATTTTAT
* * *
1368027 GATTTCATTTATAAATTTTA
1 GATTTAATTCAAAAATTTTA
1368047 AATATTTTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.39, C:0.05, G:0.05, T:0.51
Consensus pattern (21 bp):
GATTTAATTCAAAAATTTTAT
Found at i:1373227 original size:14 final size:15
Alignment explanation
Indices: 1373198--1373231 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
1373188 TTGTACTATA
1373198 TTTAA-CCTTTTCGT
1 TTTAATCCTTTTCGT
1373212 TTTAATCCTTTT-GT
1 TTTAATCCTTTTCGT
1373226 TTTAAT
1 TTTAAT
1373232 TTCGCATAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.18, C:0.15, G:0.06, T:0.62
Consensus pattern (15 bp):
TTTAATCCTTTTCGT
Found at i:1373598 original size:18 final size:18
Alignment explanation
Indices: 1373575--1373612 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
1373565 GCAATCTTAC
1373575 CAAAATAGTGAATGTTGT
1 CAAAATAGTGAATGTTGT
1373593 CAAAATAGTGAATGTTGT
1 CAAAATAGTGAATGTTGT
1373611 CA
1 CA
1373613 TAACTTCATA
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:0.39, C:0.08, G:0.21, T:0.32
Consensus pattern (18 bp):
CAAAATAGTGAATGTTGT
Found at i:1377566 original size:4 final size:4
Alignment explanation
Indices: 1377557--1377588 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
1377547 TTCATCATTT
*
1377557 TGTA TGTA TGTA TGTA TGTA TGTA TGCA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1377589 ATCATCAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.25, C:0.03, G:0.25, T:0.47
Consensus pattern (4 bp):
TGTA
Found at i:1380337 original size:39 final size:39
Alignment explanation
Indices: 1380234--1380366 Score: 250
Period size: 39 Copynumber: 3.4 Consensus size: 39
1380224 GGGAACGATT
1380234 TCAATCTAGCAAAGGCCTTGGTCAAGGAGATACTTTGAG
1 TCAATCTAGCAAAGGCCTTGGTCAAGGAGATACTTTGAG
1380273 TCAATCTAGC-AAGGCCTTGGTCAAGGAGATACTTTGAG
1 TCAATCTAGCAAAGGCCTTGGTCAAGGAGATACTTTGAG
1380311 TCAATCTAGCAAAGGCCTTGGTCAAGGAGATACTTTGAG
1 TCAATCTAGCAAAGGCCTTGGTCAAGGAGATACTTTGAG
*
1380350 TCAATCTAGCAATGGCC
1 TCAATCTAGCAAAGGCC
1380367 CCTGTACGTT
Statistics
Matches: 92, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
38 38 0.41
39 54 0.59
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.26
Consensus pattern (39 bp):
TCAATCTAGCAAAGGCCTTGGTCAAGGAGATACTTTGAG
Found at i:1382839 original size:43 final size:43
Alignment explanation
Indices: 1382791--1382878 Score: 149
Period size: 43 Copynumber: 2.0 Consensus size: 43
1382781 TCATTTACAC
**
1382791 GTAAACCTTCCAAATTTTGTTAAATCAAATTATAATAATGAAA
1 GTAAACCTTCCAAAAATTGTTAAATCAAATTATAATAATGAAA
*
1382834 GTAAACCTTTCAAAAATTGTTAAATCAAATTATAATAATGAAA
1 GTAAACCTTCCAAAAATTGTTAAATCAAATTATAATAATGAAA
1382877 GT
1 GT
1382879 CATTTCTTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.48, C:0.10, G:0.08, T:0.34
Consensus pattern (43 bp):
GTAAACCTTCCAAAAATTGTTAAATCAAATTATAATAATGAAA
Found at i:1383625 original size:6 final size:6
Alignment explanation
Indices: 1383614--1383644 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
1383604 CAATGGCCTA
1383614 TGGCAG TGGCAG TGGCAG TGGCAG TGGCAG T
1 TGGCAG TGGCAG TGGCAG TGGCAG TGGCAG T
1383645 ACTGGTGATG
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:0.16, C:0.16, G:0.48, T:0.19
Consensus pattern (6 bp):
TGGCAG
Found at i:1385559 original size:3 final size:3
Alignment explanation
Indices: 1385551--1385586 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
1385541 ATTTTATTAA
1385551 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1385587 TTGATGACAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:1387099 original size:17 final size:17
Alignment explanation
Indices: 1387072--1387112 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
1387062 TATAAAAGAT
1387072 ATTTAATATTTTAGATTA
1 ATTT-ATATTTTAGATTA
*
1387090 ATTTATATTTTATATTA
1 ATTTATATTTTAGATTA
*
1387107 AATTAT
1 ATTTAT
1387113 TTAAATATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (17 bp):
ATTTATATTTTAGATTA
Found at i:1394261 original size:14 final size:15
Alignment explanation
Indices: 1394235--1394280 Score: 60
Period size: 14 Copynumber: 3.2 Consensus size: 15
1394225 TTTATACCAA
*
1394235 TAACTCAAATAAATC
1 TAACCCAAATAAATC
1394250 TAACCC-AATAAAT-
1 TAACCCAAATAAATC
*
1394263 TAACCCAAATTAATC
1 TAACCCAAATAAATC
1394278 TAA
1 TAA
1394281 ATATTAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 6 0.22
14 13 0.48
15 8 0.30
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (15 bp):
TAACCCAAATAAATC
Found at i:1396714 original size:18 final size:18
Alignment explanation
Indices: 1396686--1397398 Score: 252
Period size: 18 Copynumber: 41.9 Consensus size: 18
1396676 TATCAGCTTG
1396686 ATTATAATTATTTAATTAT
1 ATTA-AATTATTTAATTAT
*
1396705 ATTAAATTATTTAATCAT
1 ATTAAATTATTTAATTAT
*
1396723 GTTTAATTATGTATTTAATTAT
1 -ATTAA--AT-TATTTAATTAT
* **
1396745 A--AACACTA-TCGATTA-
1 ATTAA-ATTATTTAATTAT
*
1396760 ATTAAA-TATTTAAGTTAAAAG
1 ATTAAATTATTTAA-TT---AT
*
1396781 ATTTAATTATTTAATTAT
1 ATTAAATTATTTAATTAT
* **
1396799 ATTAAAGTAAATAATTAT
1 ATTAAATTATTTAATTAT
1396817 ATTAAATTA---AA-TAT
1 ATTAAATTATTTAATTAT
1396831 -TT-AATTATTTAATTAT
1 ATTAAATTATTTAATTAT
* ** *
1396847 ATTAAAGTAAATAAGTAT
1 ATTAAATTATTTAATTAT
* **
1396865 ATT-AA-T-TTAAAAGAT
1 ATTAAATTATTTAATTAT
1396880 A-T-AATTATTTAATTAT
1 ATTAAATTATTTAATTAT
* **
1396896 ATTAAACTAAATAATTAT
1 ATTAAATTATTTAATTAT
*
1396914 ATTAAATTATTTAATCAT
1 ATTAAATTATTTAATTAT
*
1396932 GTTTAATTATGTATTTAATTAT
1 -ATTAA--AT-TATTTAATTAT
* **
1396954 A--AACACTA-TCGATTA-
1 ATTAA-ATTATTTAATTAT
*
1396969 ATTAAA-TATTTAAGTTAAAAG
1 ATTAAATTATTTAA-TT---AT
*
1396990 ATTTAATTATTTAATTAT
1 ATTAAATTATTTAATTAT
* ** *
1397008 ATTAAAGTAAATGATTAT
1 ATTAAATTATTTAATTAT
* *
1397026 ATTAAGTTA---AA--AG
1 ATTAAATTATTTAATTAT
*
1397039 ATTTAATTATTTAATTAT
1 ATTAAATTATTTAATTAT
* **
1397057 ATTAAAGTAAATAATTAT
1 ATTAAATTATTTAATTAT
*
1397075 ATTAAATTA---AA-GAT
1 ATTAAATTATTTAATTAT
1397089 -TT-AATTATTTAATTAT
1 ATTAAATTATTTAATTAT
* **
1397105 ATTAAAGTAAATAATTAT
1 ATTAAATTATTTAATTAT
1397123 ATTAAATTA---AA-TAT
1 ATTAAATTATTTAATTAT
1397137 -TT-AATTATTTAATTAT
1 ATTAAATTATTTAATTAT
**
1397153 ATTAAATTAAATAATTAT
1 ATTAAATTATTTAATTAT
*
1397171 ATT--A--ATTTAA--AG
1 ATTAAATTATTTAATTAT
*
1397183 ATTTAATTATTTAATTAT
1 ATTAAATTATTTAATTAT
* **
1397201 ATTAAAGTAAATAATTAT
1 ATTAAATTATTTAATTAT
*
1397219 ATTAAGTTA---AA--AT
1 ATTAAATTATTTAATTAT
*
1397232 ATTTAATTATTTAATTAT
1 ATTAAATTATTTAATTAT
* **
1397250 ATTAAAGTAACTAATTAT
1 ATTAAATTATTTAATTAT
* *
1397268 ATTAAGTTA---AA--AG
1 ATTAAATTATTTAATTAT
*
1397281 ATTTAATTATTTAATTAT
1 ATTAAATTATTTAATTAT
**
1397299 ATTAAATTAAATAATTAT
1 ATTAAATTATTTAATTAT
1397317 ATTAAATTA---AA-TAT
1 ATTAAATTATTTAATTAT
1397331 -TT-AATTATTTAATTAT
1 ATTAAATTATTTAATTAT
** **
1397347 ATTAAGGTAAATAATTAT
1 ATTAAATTATTTAATTAT
*
1397365 ATTAAAAT-TTTAATTAT
1 ATTAAATTATTTAATTAT
*
1397382 ATTTAATTATTTAATTA
1 ATTAAATTATTTAATTA
1397399 ATAAAAACAG
Statistics
Matches: 511, Mismatches: 107, Indels: 153
0.66 0.14 0.20
Matches are distributed among these distances:
12 24 0.05
13 33 0.06
14 19 0.04
15 33 0.06
16 48 0.09
17 36 0.07
18 248 0.49
19 16 0.03
20 2 0.00
21 18 0.04
22 34 0.07
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (18 bp):
ATTAAATTATTTAATTAT
Found at i:1396839 original size:48 final size:48
Alignment explanation
Indices: 1396777--1396922 Score: 238
Period size: 48 Copynumber: 3.0 Consensus size: 48
1396767 ATTTAAGTTA
1396777 AAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATT
1 AAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATT
* * *
1396825 AAATATTTAATTATTTAATTATATTAAAGTAAATAAGTATATTAATTT
1 AAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATT
* *
1396873 AAAAGATATAATTATTTAATTATATTAAACTAAATAATTATATTAAATT
1 -AAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATT
1396922 A
1 A
1396923 TTTAATCATG
Statistics
Matches: 89, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
48 46 0.52
49 43 0.48
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (48 bp):
AAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATT
Found at i:1396907 original size:49 final size:49
Alignment explanation
Indices: 1396769--1396918 Score: 239
Period size: 49 Copynumber: 3.1 Consensus size: 49
1396759 AATTAAATAT
1396769 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
* * *
1396818 TTAAATT-AAATATTTAATTATTTAATTATATTAAAGTAAATAAGTATA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
* * *
1396866 TTAATTTAAAAGATATAATTATTTAATTATATTAAACTAAATAATTATA
1 TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
1396915 TTAA
1 TTAA
1396919 ATTATTTAAT
Statistics
Matches: 92, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
48 45 0.49
49 47 0.51
ACGTcount: A:0.50, C:0.01, G:0.04, T:0.45
Consensus pattern (49 bp):
TTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATA
Found at i:1397096 original size:209 final size:210
Alignment explanation
Indices: 1396698--1397325 Score: 986
Period size: 209 Copynumber: 3.1 Consensus size: 210
1396688 TATAATTATT
1396698 TAATTATATTAAATTATTTAATCATGTTTAATTATGTATTTAATTATAAACACTATCGATTAATT
1 TAATTATATTAAATTATTTAATCATGTTTAATTATGTATTTAATTATAAACACTATCGATTAATT
*
1396763 AAATATTTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATT-AA
66 AAATATTTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAA
* * *
1396827 ATATTTAATTATTTAATTATATTAAAGTAAATAAGTATATTAATTTAAAAGATATAATTATTTAA
131 ATATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATTAAAAGATTTAATTATTTAA
1396892 TTATATTAAACTAAA
196 TTATATTAAACTAAA
1396907 TAATTATATTAAATTATTTAATCATGTTTAATTATGTATTTAATTATAAACACTATCGATTAATT
1 TAATTATATTAAATTATTTAATCATGTTTAATTATGTATTTAATTATAAACACTATCGATTAATT
*
1396972 AAATATTTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATATTAAGTTAAA
66 AAATATTTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAA
*
1397037 AGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATT-AAAGATTTAATTATTTAA
131 ATATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATTAAAAGATTTAATTATTTAA
*
1397101 TTATATTAAAGTAAA
196 TTATATTAAACTAAA
* * * * *
1397116 TAATTATATTAAATTA---AAT-A--TTTAATTATTTAATT-A-TATTAA-A-T-T-AAATAATT
1 TAATTATATTAAATTATTTAATCATGTTTAATTATGTATTTAATTATAAACACTATCGATTAATT
*
1397169 --ATA-TTAA-TTTAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAA
66 AAATATTTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAA
* *
1397230 ATATTTAATTATTTAATTATATTAAAGTAACTAATTATATTAAGTTAAAAGATTTAATTATTTAA
131 ATATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATTAAAAGATTTAATTATTTAA
*
1397295 TTATATTAAATTAAA
196 TTATATTAAACTAAA
1397310 TAATTATATTAAATTA
1 TAATTATATTAAATTA
1397326 AATATTTAAT
Statistics
Matches: 399, Mismatches: 18, Indels: 19
0.92 0.04 0.04
Matches are distributed among these distances:
193 95 0.24
194 52 0.13
195 3 0.01
197 6 0.02
198 1 0.00
199 1 0.00
200 1 0.00
201 5 0.01
202 1 0.00
203 13 0.03
205 1 0.00
206 3 0.01
209 172 0.43
210 45 0.11
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (210 bp):
TAATTATATTAAATTATTTAATCATGTTTAATTATGTATTTAATTATAAACACTATCGATTAATT
AAATATTTAAGTTAAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTTAAA
ATATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATTAAAAGATTTAATTATTTAA
TTATATTAAACTAAA
Found at i:1397106 original size:48 final size:48
Alignment explanation
Indices: 1396986--1397398 Score: 637
Period size: 48 Copynumber: 8.4 Consensus size: 48
1396976 ATTTAAGTTA
* *
1396986 AAAGATTTAATTATTTAATTATATTAAAGTAAATGATTATATTAAGTT
1 AAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATT
1397034 AAAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATT
1 -AAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATT
1397083 AAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATT
1 AAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATT
* * *
1397131 AAATATTTAATTATTTAATTATATTAAATTAAATAATTATATTAATTT
1 AAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATT
*
1397179 AAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAGTT
1 AAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATT
* * *
1397227 AAAATATTTAATTATTTAATTATATTAAAGTAACTAATTATATTAAGTT
1 -AAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATT
*
1397276 AAAAGATTTAATTATTTAATTATATTAAATTAAATAATTATATTAAATT
1 -AAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATT
* *
1397325 AAATATTTAATTATTTAATTATATTAAGGTAAATAATTATATTAAAATTTT
1 AAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATT-AAA--TT
*
1397376 AATTATATTTAATTATTTAATTA
1 AA--AGATTTAATTATTTAATTA
1397399 ATAAAAACAG
Statistics
Matches: 341, Mismatches: 17, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
48 178 0.52
49 140 0.41
51 4 0.01
53 19 0.06
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (48 bp):
AAAGATTTAATTATTTAATTATATTAAAGTAAATAATTATATTAAATT
Found at i:1397358 original size:30 final size:31
Alignment explanation
Indices: 1397044--1397368 Score: 155
Period size: 30 Copynumber: 10.1 Consensus size: 31
1397034 AAAAGATTTA
1397044 ATTATTTAATTATATTAAAGTAAATAATTAT
1 ATTATTTAATTATATTAAAGTAAATAATTAT
* * * * **
1397075 ATTAAATTAA--AGATTTAATTATTTAATTAT
1 ATT-ATTTAATTATATTAAAGTAAATAATTAT
* * *
1397105 ATTAAAGTAAATAATTATATTAAATTAAATATTTA-
1 ATT--A-T--TTAATTATATTAAAGTAAATAATTAT
*
1397140 ATTATTTAATTATATTAAATTAAATAATTAT
1 ATTATTTAATTATATTAAAGTAAATAATTAT
* * * **
1397171 ATTAATTTAA--AGATTTAATTATTTAATTAT
1 ATT-ATTTAATTATATTAAAGTAAATAATTAT
* *
1397201 ATTAAAGTAAATAATTATATT-AAGTTAAAATATTTA-
1 ATT--A-T--TTAATTATATTAAAG-T-AAATAATTAT
*
1397237 ATTATTTAATTATATTAAAGTAACTAATTAT
1 ATTATTTAATTATATTAAAGTAAATAATTAT
* * * * * **
1397268 ATTAAGTTAA-AAGATTTAATTATTTAATTAT
1 ATT-ATTTAATTATATTAAAGTAAATAATTAT
* *
1397299 ATTAAATTAAATAATTATATTAAATTAAATATTTA-
1 ATT--ATT---TAATTATATTAAAGTAAATAATTAT
*
1397334 ATTATTTAATTATATTAAGGTAAATAATTAT
1 ATTATTTAATTATATTAAAGTAAATAATTAT
1397365 ATTA
1 ATTA
1397369 AAATTTTAAT
Statistics
Matches: 223, Mismatches: 45, Indels: 52
0.70 0.14 0.16
Matches are distributed among these distances:
30 88 0.39
31 46 0.21
32 24 0.11
33 5 0.02
34 7 0.03
35 11 0.05
36 36 0.16
37 6 0.03
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (31 bp):
ATTATTTAATTATATTAAAGTAAATAATTAT
Found at i:1397368 original size:5 final size:4
Alignment explanation
Indices: 1397041--1397400 Score: 100
Period size: 4 Copynumber: 83.2 Consensus size: 4
1397031 GTTAAAAGAT
* * * ** *
1397041 TTAA TTAT TTAA TTATA TTAAA GTAA ATAA TTATA TTAAA TTAA AGAT
1 TTAA TTAA TTAA TTA-A TT-AA TTAA TTAA TTA-A TT-AA TTAA TTAA
* * * * *
1397089 TTAA TTAT TTAA TTATA TTAAA GTAA ATAA TTATA TTAAA TTAA ATAT
1 TTAA TTAA TTAA TTA-A TT-AA TTAA TTAA TTA-A TT-AA TTAA TTAA
* * ** *
1397137 TTAA TTAT TTAA TTATA TTAAA TTAA ATAA TTATA TTAA TTTAA AGAT
1 TTAA TTAA TTAA TTA-A TT-AA TTAA TTAA TTA-A TTAA -TTAA TTAA
* * * * *
1397185 TTAA TTAT TTAA TTATA TTAAA GTAA ATAA TTATA TTAA GTTAAA ATAT
1 TTAA TTAA TTAA TTA-A TT-AA TTAA TTAA TTA-A TTAA -TT-AA TTAA
* * * *
1397234 TTAA TTAT TTAA TTATA TTAAA GTAA CTAA TTATA TTAA GTTAA -AAGA
1 TTAA TTAA TTAA TTA-A TT-AA TTAA TTAA TTA-A TTAA -TTAA TTA-A
* * * *
1397282 TTTAA TTAT TTAA TTATA TTAAA TTAA ATAA TTATA TTAAA TTAA ATAT
1 -TTAA TTAA TTAA TTA-A TT-AA TTAA TTAA TTA-A TT-AA TTAA TTAA
* * *
1397331 TTAA TTAT TTAA TTATA TTAA GGTAA ATAA TTATA TTAA --AA TT-- TTAA
1 TTAA TTAA TTAA TTA-A TTAA -TTAA TTAA TTA-A TTAA TTAA TTAA TTAA
*
1397378 TTATA TTTAA TTAT TTAA TTAA T
1 TTA-A -TTAA TTAA TTAA TTAA T
1397401 AAAAACAGCC
Statistics
Matches: 258, Mismatches: 61, Indels: 74
0.66 0.16 0.19
Matches are distributed among these distances:
2 4 0.02
3 1 0.00
4 151 0.59
5 87 0.34
6 15 0.06
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (4 bp):
TTAA
Found at i:1397399 original size:48 final size:45
Alignment explanation
Indices: 1396965--1397403 Score: 206
Period size: 49 Copynumber: 9.2 Consensus size: 45
1396955 AACACTATCG
* * *
1396965 ATTAATTAAATATTTA-AGTTAAAAGATTTAATTATTTAATTATATTAA
1 ATTAAGTAAATAATTATA-TTAAAA-TTTTAATTATTTAATTAT-TT-A
* * * * *
1397013 AGTAAATGATTATATTA-AGTTAAAAGATTTAATTATTTAATTATATTAA
1 ATTAAGTAAATA-ATTATA-TTAAAA-TTTTAATTATTTAATTAT-TT-A
* * * *
1397062 AGTAAATAATTATATTAAATTAAAGA-TTTAATTATTTAATTA--T-
1 ATTAAGTAAATA-ATTATATTAAA-ATTTTAATTATTTAATTATTTA
1397105 ATTAAAGTAAATAATTATATTAAATTAAATATTTAATTATTTAATTATATTAA
1 ATT-AAGTAAATAATTATATT--A--AAAT-TTTAATTATTTAATTAT-TT-A
* *
1397158 ATTAAATAATTATATTA-ATTTAAAGA-TTTAATTATTTAATTATATTAA
1 ATTAAGTAAATA-ATTATA-TTAAA-ATTTTAATTATTTAATTAT-TT-A
* * *
1397206 AGTAAATAATTATATTA-AGTTAAAATATTTAATTATTTAATTATATTAA
1 ATTAAGTAAATA-ATTATA-TTAAAAT-TTTAATTATTTAATTAT-TT-A
* * * *
1397255 AGTAACTAATTATATTA-AGTTAAAAGATTTAATTATTTAATTATATTAA
1 ATTAAGTAAATA-ATTATA-TTAAAA-TTTTAATTATTTAATTAT-TT-A
* * *
1397304 ATTAAATAATTATATTAAATT-AAATATTTAATTATTTAATTA--T-
1 ATTAAGTAAATA-ATTATATTAAAAT-TTTAATTATTTAATTATTTA
1397347 ATTAAGGTAAATAATTATATTAAAATTTTAATTATATTTAATTATTTA
1 ATTAA-GTAAATAATTATATTAAAATTTTAA-T-TATTTAATTATTTA
1397395 ATTAA-TAAA
1 ATTAAGTAAA
1397404 AACAGCCCAA
Statistics
Matches: 339, Mismatches: 22, Indels: 62
0.80 0.05 0.15
Matches are distributed among these distances:
43 26 0.08
44 17 0.05
45 13 0.04
46 5 0.01
47 4 0.01
48 108 0.32
49 143 0.42
50 4 0.01
51 2 0.01
52 8 0.02
53 9 0.03
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (45 bp):
ATTAAGTAAATAATTATATTAAAATTTTAATTATTTAATTATTTA
Found at i:1403025 original size:66 final size:66
Alignment explanation
Indices: 1402919--1403066 Score: 208
Period size: 66 Copynumber: 2.2 Consensus size: 66
1402909 CAAATTGCTC
*
1402919 AACTTAAAGAGGAGGCTGCAACGAGAGAAGCAGAGGCTCAAAAAAAATATGATGAACTCCATC-T
1 AACTTAAAGAGGAGGCTGCAACGAGAGAAGCAGAGGCTCAAAAAAAATATGAAGAACTCCA-CAT
1402983 AA
65 AA
* ** * *
1402985 AACTTAAAGAGGAGGTTGCAGTGAGAGAAGTAGAGTCTCAAAAAAAATATGAAGAACTCCACATA
1 AACTTAAAGAGGAGGCTGCAACGAGAGAAGCAGAGGCTCAAAAAAAATATGAAGAACTCCACATA
*
1403050 C
66 A
*
1403051 AACTTAAAGTGGAGGC
1 AACTTAAAGAGGAGGC
1403067 AACAGCGAGG
Statistics
Matches: 72, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
65 1 0.01
66 71 0.99
ACGTcount: A:0.45, C:0.15, G:0.24, T:0.17
Consensus pattern (66 bp):
AACTTAAAGAGGAGGCTGCAACGAGAGAAGCAGAGGCTCAAAAAAAATATGAAGAACTCCACATA
A
Found at i:1403087 original size:21 final size:21
Alignment explanation
Indices: 1403061--1403103 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1403051 AACTTAAAGT
1403061 GGAGGCAACAGCGAGGCAAGC
1 GGAGGCAACAGCGAGGCAAGC
* * *
1403082 GGAGGCAGCAGTGGGGCAAGC
1 GGAGGCAACAGCGAGGCAAGC
1403103 G
1 G
1403104 AAGGAAGCAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.21, G:0.49, T:0.02
Consensus pattern (21 bp):
GGAGGCAACAGCGAGGCAAGC
Found at i:1403462 original size:43 final size:41
Alignment explanation
Indices: 1403429--1403551 Score: 192
Period size: 43 Copynumber: 2.9 Consensus size: 41
1403419 CGCTTTATCC
1403429 AAAAGCGTCGCTAAAGAACATGGCCTTCAGCGGCGCTTGTGG
1 AAAAGCG-CGCTAAAGAACATGGCCTTCAGCGGCGCTTGTGG
1403471 AGAAAGCGCCGCTAAAGAACATGGCCTTCAGCGGCGCTTGTGG
1 A-AAAGCG-CGCTAAAGAACATGGCCTTCAGCGGCGCTTGTGG
**
1403514 GTAAGCGCTGCTAAAGAACATGGCCTTCAGCGGCGCTT
1 AAAAGCGC-GCTAAAGAACATGGCCTTCAGCGGCGCTT
1403552 ATGGGTAAGC
Statistics
Matches: 76, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
41 1 0.01
42 35 0.46
43 40 0.53
ACGTcount: A:0.25, C:0.25, G:0.31, T:0.19
Consensus pattern (41 bp):
AAAAGCGCGCTAAAGAACATGGCCTTCAGCGGCGCTTGTGG
Found at i:1403533 original size:42 final size:42
Alignment explanation
Indices: 1403431--1403568 Score: 231
Period size: 42 Copynumber: 3.3 Consensus size: 42
1403421 CTTTATCCAA
* *
1403431 AAGCGTCGCTAAAGAACATGGCCTTCAGCGGCGCTTGTGGAGA
1 AAGCGCCGCTAAAGAACATGGCCTTCAGCGGCGCTTGTGG-GT
1403474 AAGCGCCGCTAAAGAACATGGCCTTCAGCGGCGCTTGTGGGT
1 AAGCGCCGCTAAAGAACATGGCCTTCAGCGGCGCTTGTGGGT
* *
1403516 AAGCGCTGCTAAAGAACATGGCCTTCAGCGGCGCTTATGGGT
1 AAGCGCCGCTAAAGAACATGGCCTTCAGCGGCGCTTGTGGGT
1403558 AAGCGCCGCTA
1 AAGCGCCGCTA
1403569 TTTTTTGCGG
Statistics
Matches: 90, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
42 51 0.57
43 39 0.43
ACGTcount: A:0.24, C:0.25, G:0.32, T:0.19
Consensus pattern (42 bp):
AAGCGCCGCTAAAGAACATGGCCTTCAGCGGCGCTTGTGGGT
Found at i:1409461 original size:2 final size:2
Alignment explanation
Indices: 1409454--1409493 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1409444 TATCTTAAGC
1409454 TA TA TA TA 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 TA TA TA TA
1409494 GAAAGAAAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1415291 original size:20 final size:19
Alignment explanation
Indices: 1415253--1415291 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
1415243 ATAAATGCTG
**
1415253 CAAAATGAATTTATTAAAT
1 CAAAATGAATTTAAAAAAT
1415272 CAAAATGAAATTTAAAAAAT
1 CAAAATG-AATTTAAAAAAT
1415292 ATATAAAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.31
Consensus pattern (19 bp):
CAAAATGAATTTAAAAAAT
Found at i:1418006 original size:92 final size:91
Alignment explanation
Indices: 1417855--1418122 Score: 310
Period size: 92 Copynumber: 2.9 Consensus size: 91
1417845 GATGGGGTTG
* * * * *
1417855 TTTTCCCTATGATGATGCGGATAGTGTTTTTTTTTTATCCGCATCTTTCATGTTTGTTTTACTAC
1 TTTTTCCTATGATGATGCTGATAAT-TTTTTTTTTTATCGGCATCTTTCATGTTTGTTTTACTAT
* *
1417920 TTATATTTGGGTTGTTTTGGTTTGTTT
65 TTATATTCGGGTTGTTTTGATTTGTTT
*
1417947 TTCTTTCCTATGATGATGCTGATAATTTTTTTTTTTATCGGCATCTTTCATATTTGTTTTACTAT
1 TT-TTTCCTATGATGATGCTGATAATTTTTTTTTTTATCGGCATCTTTCATGTTTGTTTTACTAT
*
1418012 TTATGTTCGGGTTGTTTTGATTTGTTT
65 TTATATTCGGGTTGTTTTGATTTGTTT
** * * **
1418039 TTTTTTTTACGATG-T-CATTGATAA-TGTTTTTTTTATCGGCATCTTTCATGTCAGTTTTACTA
1 TTTTTCCTATGATGATGC--TGATAATTTTTTTTTTTATCGGCATCTTTCATGTTTGTTTTACTA
* *
1418101 TTTATGTTCAGAG-TGTTTTGAT
64 TTTATATTC-GGGTTGTTTTGAT
1418123 CTGTATGTTG
Statistics
Matches: 155, Mismatches: 17, Indels: 10
0.85 0.09 0.05
Matches are distributed among these distances:
89 1 0.01
90 53 0.34
91 17 0.11
92 64 0.41
93 20 0.13
ACGTcount: A:0.16, C:0.11, G:0.16, T:0.57
Consensus pattern (91 bp):
TTTTTCCTATGATGATGCTGATAATTTTTTTTTTTATCGGCATCTTTCATGTTTGTTTTACTATT
TATATTCGGGTTGTTTTGATTTGTTT
Found at i:1419089 original size:56 final size:57
Alignment explanation
Indices: 1418979--1419090 Score: 145
Period size: 56 Copynumber: 2.0 Consensus size: 57
1418969 ATGCTGAAAT
* * * *
1418979 GCATTTGAAGAAAGTTTTATGATATTTTTTTTATGCTCACAAGGTGGGACCAATCAAG
1 GCATTTGAAGAAAGTTATATGATA-TTATTTTATGATCACAACGTGGGACCAATCAAG
** *
1419037 GCATTTGAAGATGGTTATATGATA-TATTTTATGATGACAACGTGGGACCAATCA
1 GCATTTGAAGAAAGTTATATGATATTATTTTATGATCACAACGTGGGACCAATCA
1419091 CTGGTTCATG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
56 26 0.55
58 21 0.45
ACGTcount: A:0.32, C:0.12, G:0.21, T:0.35
Consensus pattern (57 bp):
GCATTTGAAGAAAGTTATATGATATTATTTTATGATCACAACGTGGGACCAATCAAG
Found at i:1431332 original size:16 final size:18
Alignment explanation
Indices: 1431293--1431326 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1431283 TTAGTTTATA
1431293 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
1431310 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
1431327 AATTTAAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:1432157 original size:19 final size:19
Alignment explanation
Indices: 1432121--1432156 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
1432111 TTAGTATAAT
*
1432121 ATTTGGTACTTGAATTTTA
1 ATTTGGTACCTGAATTTTA
1432140 ATTTGGTACCT-AATTTT
1 ATTTGGTACCTGAATTTT
1432157 TTTTGTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.25, C:0.08, G:0.14, T:0.53
Consensus pattern (19 bp):
ATTTGGTACCTGAATTTTA
Found at i:1433826 original size:28 final size:28
Alignment explanation
Indices: 1433760--1433838 Score: 88
Period size: 28 Copynumber: 2.8 Consensus size: 28
1433750 GAATAAATAA
*
1433760 AAAATTTTAGGACTTAAATGGATATGTG
1 AAAATTTTATGACTTAAATGGATATGTG
* * * *
1433788 -AAGTTGGTATGAATTAAATTGATATGTG
1 AAAATT-TTATGACTTAAATGGATATGTG
1433816 AAAATTTTATGACTTAAACTGGA
1 AAAATTTTATGACTTAAA-TGGA
1433839 AAGAAAAATC
Statistics
Matches: 39, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
27 4 0.10
28 28 0.72
29 7 0.18
ACGTcount: A:0.39, C:0.04, G:0.20, T:0.37
Consensus pattern (28 bp):
AAAATTTTATGACTTAAATGGATATGTG
Found at i:1434403 original size:49 final size:49
Alignment explanation
Indices: 1434331--1434429 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 49
1434321 TGAAGTATAT
*
1434331 GTGATTATAATTGTTCCGACAACAATTATGGCATCCCATAGCTCGAAAC
1 GTGATTATAATTGTTCCGACAACAATTATGACATCCCATAGCTCGAAAC
1434380 GTGATTATAATTGTTCCGACAACAATTATGACATCCCATAGCTCGAAAC
1 GTGATTATAATTGTTCCGACAACAATTATGACATCCCATAGCTCGAAAC
1434429 G
1 G
1434430 ATCGAGTCGA
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.28
Consensus pattern (49 bp):
GTGATTATAATTGTTCCGACAACAATTATGACATCCCATAGCTCGAAAC
Found at i:1434767 original size:14 final size:14
Alignment explanation
Indices: 1434748--1434782 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
1434738 CATGTGTTTA
1434748 TTTTTTAAAAATAT
1 TTTTTTAAAAATAT
1434762 TTTTTTAAAAATAT
1 TTTTTTAAAAATAT
1434776 TTTTTTA
1 TTTTTTA
1434783 TATCTCTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTTTTAAAAATAT
Found at i:1441792 original size:14 final size:14
Alignment explanation
Indices: 1441773--1441802 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1441763 GAACGATGAC
1441773 GTTAACCAAAATAT
1 GTTAACCAAAATAT
1441787 GTTAACCAAAATAT
1 GTTAACCAAAATAT
1441801 GT
1 GT
1441803 GAATAACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.47, C:0.13, G:0.10, T:0.30
Consensus pattern (14 bp):
GTTAACCAAAATAT
Found at i:1442295 original size:30 final size:31
Alignment explanation
Indices: 1442230--1442298 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
1442220 CTAATTTCAA
1442230 TGACTGTTTTGTCACTTTTCGATAACGTTAG
1 TGACTGTTTTGTCACTTTTCGATAACGTTAG
1442261 TGACTGTTTTGTCACATTTTC-A-AA-GTTGAG
1 TGACTGTTTTGTCAC-TTTTCGATAACGTT-AG
1442291 TGACTGTT
1 TGACTGTT
1442299 GTGTTAAATG
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
29 3 0.08
30 12 0.33
31 16 0.44
32 5 0.14
ACGTcount: A:0.20, C:0.14, G:0.20, T:0.45
Consensus pattern (31 bp):
TGACTGTTTTGTCACTTTTCGATAACGTTAG
Found at i:1443619 original size:17 final size:17
Alignment explanation
Indices: 1443591--1443624 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1443581 AAATTTTTAA
1443591 TTTAATAATTTTAGAATT
1 TTTAATAATTTTA-AATT
1443609 TTTAA-AATTTTAAATT
1 TTTAATAATTTTAAATT
1443625 AATAAATGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 7 0.44
18 5 0.31
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
TTTAATAATTTTAAATT
Found at i:1448614 original size:20 final size:20
Alignment explanation
Indices: 1448591--1448629 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1448581 ATTTAAAAAA
*
1448591 ATAAAAATTTTGGAATTTTT
1 ATAAAAATTTTGAAATTTTT
*
1448611 ATAAACATTTTGAAATTTT
1 ATAAAAATTTTGAAATTTT
1448630 GAAAATTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.49
Consensus pattern (20 bp):
ATAAAAATTTTGAAATTTTT
Found at i:1451904 original size:23 final size:23
Alignment explanation
Indices: 1451874--1452022 Score: 144
Period size: 23 Copynumber: 6.5 Consensus size: 23
1451864 ACACTAGCGC
*
1451874 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGTTTAGCACTGTGT-GT
*
1451897 GCTCTCTGATTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
* * *
1451920 GCTCTCTGATTAGTACTTTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
*
1451943 ACTCTCTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
*
1451966 GCTCTCTGTTGCCTAGCACT-TATGT
1 GCTCTCTGTT---TAGCACTGTGTGT
* *
1451991 GCTCTCTG-TTAGTACTTTG-GT
1 GCTCTCTGTTTAGCACTGTGTGT
*
1452012 ACTCTCTGTTT
1 GCTCTCTGTTT
1452023 GTTCCGTATA
Statistics
Matches: 107, Mismatches: 13, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
21 15 0.14
22 3 0.03
23 66 0.62
24 4 0.04
25 12 0.11
26 7 0.07
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.44
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTGTGTGT
Found at i:1452014 original size:69 final size:69
Alignment explanation
Indices: 1451875--1452022 Score: 205
Period size: 69 Copynumber: 2.1 Consensus size: 69
1451865 CACTAGCGCG
*
1451875 CTCTCTGTTTAGCACGTCTCGTGCTCTCTGATTAGCACTGTGTGTGCTCTCTGATTAGTACTTTG
1 CTCTCTGTTTAGCACGTCTCGTGCTCTCTGATTAGCACTGTATGTGCTCTCTGATTAGTACTTTG
1451940 TGTA
66 TGTA
* *
1451944 CTCTCTGTTTAGCACTGTGT-GTGCTCTCTGTTGCCTAGCACT-TATGTGCTCTCTG-TTAGTAC
1 CTCTCTGTTTAGCAC-GTCTCGTGCTCTCTGAT---TAGCACTGTATGTGCTCTCTGATTAGTAC
1452006 TTTG-GTA
62 TTTGTGTA
1452013 CTCTCTGTTT
1 CTCTCTGTTT
1452023 GTTCCGTATA
Statistics
Matches: 72, Mismatches: 3, Indels: 8
0.87 0.04 0.10
Matches are distributed among these distances:
69 39 0.54
70 14 0.19
71 12 0.17
72 7 0.10
ACGTcount: A:0.11, C:0.24, G:0.21, T:0.44
Consensus pattern (69 bp):
CTCTCTGTTTAGCACGTCTCGTGCTCTCTGATTAGCACTGTATGTGCTCTCTGATTAGTACTTTG
TGTA
Found at i:1453366 original size:23 final size:23
Alignment explanation
Indices: 1453340--1453505 Score: 150
Period size: 23 Copynumber: 7.4 Consensus size: 23
1453330 AGTGCTGGGC
1453340 AACAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
1453363 AACAGAGAGTACACAAA--G-T-
1 AACAGAGAGCACACAAAGTGCTA
*
1453382 -AC--TGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* *
1453402 ATCAGAGAGCACACGAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* * *
1453425 ATCGGAGAGCACACACAGTGCTAA
1 AACAGAGAGCACACAAAGTGCT-A
* *
1453449 TAACAGAGAGCACGA-GACGTGCTA
1 -AACAGAGAGCAC-ACAAAGTGCTA
*
1453473 AACAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
1453496 ATCAGAGAGC
1 AACAGAGAGC
1453506 GCGCTAGTGT
Statistics
Matches: 114, Mismatches: 18, Indels: 22
0.74 0.12 0.14
Matches are distributed among these distances:
16 10 0.09
18 3 0.03
19 1 0.01
20 1 0.01
21 2 0.02
22 1 0.01
23 78 0.68
24 2 0.02
25 15 0.13
26 1 0.01
ACGTcount: A:0.42, C:0.22, G:0.24, T:0.11
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTGCTA
Found at i:1453400 original size:39 final size:39
Alignment explanation
Indices: 1453346--1453420 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
1453336 GGGCAACAGA
*
1453346 GAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
* *
1453385 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGT
1453421 GCTAATCGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (39 bp):
GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
Found at i:1453459 original size:48 final size:46
Alignment explanation
Indices: 1453385--1453505 Score: 172
Period size: 48 Copynumber: 2.6 Consensus size: 46
1453375 ACAAAGTACT
* * *
1453385 GAGCACACAAAGTGCTAATCAGAGAGCAC-ACGAAGTGCTAATCGGA
1 GAGCACACACAGTGCTAATCAGAGAGCACGA-GAAGTGCTAAACAGA
*
1453431 GAGCACACACAGTGCTAATAACAGAGAGCACGAGACGTGCTAAACAGA
1 GAGCACACACAGTGCTAAT--CAGAGAGCACGAGAAGTGCTAAACAGA
1453479 GAGCACACACAGTGCTAATCAGAGAGC
1 GAGCACACACAGTGCTAATCAGAGAGC
1453506 GCGCTAGTGT
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
46 26 0.38
48 41 0.60
49 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.26, T:0.12
Consensus pattern (46 bp):
GAGCACACACAGTGCTAATCAGAGAGCACGAGAAGTGCTAAACAGA
Found at i:1458030 original size:20 final size:19
Alignment explanation
Indices: 1457991--1458030 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
1457981 TGTATTTATA
*
1457991 TAAAATTTATCAAAATTAT
1 TAAAATTTATCAAAAATAT
*
1458010 TAAAATTTAATGAAAAATAT
1 TAAAATTT-ATCAAAAATAT
1458030 T
1 T
1458031 TATAAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (19 bp):
TAAAATTTATCAAAAATAT
Found at i:1458067 original size:20 final size:21
Alignment explanation
Indices: 1458022--1458072 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
1458012 AAATTTAATG
**
1458022 AAAAATATTTATAAAAAATTGT
1 AAAAAT-TTTATAAAAAATCAT
1458044 -AAAATTTTAT-AAAAATCAT
1 AAAAATTTTATAAAAAATCAT
1458063 AAAAATTTTA
1 AAAAATTTTA
1458073 GCAATTGATC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
19 7 0.27
20 14 0.54
21 5 0.19
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
AAAAATTTTATAAAAAATCAT
Found at i:1458244 original size:20 final size:19
Alignment explanation
Indices: 1458219--1458290 Score: 67
Period size: 20 Copynumber: 3.7 Consensus size: 19
1458209 GTACGATAGC
1458219 ATTTTATAATTTTTTCACGA
1 ATTTTATAATTTTTT-ACGA
1458239 ATTTTAT-ATTTATTTAC-A
1 ATTTTATAATTT-TTTACGA
* *
1458257 TTTTTATAAGTTTCTTACGA
1 ATTTTATAA-TTTTTTACGA
*
1458277 ATTTATAAAATTTT
1 ATTT-TATAATTTT
1458291 ATAATTTTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
18 7 0.17
19 11 0.26
20 20 0.48
21 4 0.10
ACGTcount: A:0.32, C:0.07, G:0.04, T:0.57
Consensus pattern (19 bp):
ATTTTATAATTTTTTACGA
Found at i:1459843 original size:19 final size:20
Alignment explanation
Indices: 1459819--1459860 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
1459809 GGTGGTTAGT
*
1459819 ATTAGTTAAGTCAGTTGG-C
1 ATTAGTTAAGGCAGTTGGTC
*
1459838 ATTAGTTGAGGCAGTTGGTC
1 ATTAGTTAAGGCAGTTGGTC
1459858 ATT
1 ATT
1459861 TTCTGTATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.24, C:0.10, G:0.29, T:0.38
Consensus pattern (20 bp):
ATTAGTTAAGGCAGTTGGTC
Found at i:1463061 original size:3 final size:3
Alignment explanation
Indices: 1463053--1463096 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
1463043 AGTTAGGTTT
1463053 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1463097 GAGGTAAGGG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:1465424 original size:4 final size:4
Alignment explanation
Indices: 1465410--1465440 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
1465400 TATGACTTGT
1465410 ATTA ATT- ATTA ATTA ATTA ATTA ATTA ATTA
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA
1465441 GTTTTTTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 23 0.88
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
ATTA
Found at i:1470389 original size:22 final size:22
Alignment explanation
Indices: 1470364--1470407 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1470354 AATACTCTTC
1470364 AAGA-ATACTTCAAG-ACTCAAGA
1 AAGAGATA-TTCAAGCA-TCAAGA
1470386 AAGAGATATTCAAGCATCAAGA
1 AAGAGATATTCAAGCATCAAGA
1470408 TCAAGAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.50, C:0.16, G:0.16, T:0.18
Consensus pattern (22 bp):
AAGAGATATTCAAGCATCAAGA
Found at i:1473169 original size:55 final size:55
Alignment explanation
Indices: 1473104--1473214 Score: 222
Period size: 55 Copynumber: 2.0 Consensus size: 55
1473094 AATTTGACAC
1473104 TGGTATTGCTCTAGTGCTTAACACGGTGCCAATGATTGTTTTATTGGTTTTACTT
1 TGGTATTGCTCTAGTGCTTAACACGGTGCCAATGATTGTTTTATTGGTTTTACTT
1473159 TGGTATTGCTCTAGTGCTTAACACGGTGCCAATGATTGTTTTATTGGTTTTACTT
1 TGGTATTGCTCTAGTGCTTAACACGGTGCCAATGATTGTTTTATTGGTTTTACTT
1473214 T
1 T
1473215 TTGCACAGGC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.18, C:0.14, G:0.22, T:0.46
Consensus pattern (55 bp):
TGGTATTGCTCTAGTGCTTAACACGGTGCCAATGATTGTTTTATTGGTTTTACTT
Found at i:1483574 original size:2 final size:2
Alignment explanation
Indices: 1483567--1483593 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1483557 AGCTCTTTGT
1483567 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1483594 GGGGTGGCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1485206 original size:6 final size:6
Alignment explanation
Indices: 1485195--1485226 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
1485185 AAAGTAAACG
1485195 TGATTT TGATTT TGATTT TGATTT TGATTT TG
1 TGATTT TGATTT TGATTT TGATTT TGATTT TG
1485227 GTTTCGATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.16, C:0.00, G:0.19, T:0.66
Consensus pattern (6 bp):
TGATTT
Found at i:1485235 original size:18 final size:18
Alignment explanation
Indices: 1485196--1485235 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
1485186 AAGTAAACGT
*
1485196 GATTTTGATTTTGATTTT
1 GATTTTGATTTTGATTTC
*
1485214 GATTTTGATTTTGGTTTC
1 GATTTTGATTTTGATTTC
1485232 GATT
1 GATT
1485236 ACAAAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.15, C:0.03, G:0.20, T:0.62
Consensus pattern (18 bp):
GATTTTGATTTTGATTTC
Found at i:1485818 original size:16 final size:16
Alignment explanation
Indices: 1485797--1485829 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1485787 TACCTTTTTG
*
1485797 TTTTAAAATTATATTA
1 TTTTAAAATAATATTA
1485813 TTTTAAAATAATATTA
1 TTTTAAAATAATATTA
1485829 T
1 T
1485830 AATATTGTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTTAAAATAATATTA
Found at i:1495855 original size:12 final size:12
Alignment explanation
Indices: 1495840--1495864 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1495830 GAAATCCCAT
1495840 TTAAAATAGAAA
1 TTAAAATAGAAA
1495852 TTAAAATAGAAA
1 TTAAAATAGAAA
1495864 T
1 T
1495865 ACAACACAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (12 bp):
TTAAAATAGAAA
Found at i:1496879 original size:2 final size:2
Alignment explanation
Indices: 1496872--1496896 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1496862 TCAACACTTC
1496872 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1496897 CAAGACAACC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1505726 original size:22 final size:22
Alignment explanation
Indices: 1505685--1505725 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1505675 GTAATAAGTG
1505685 ATTATATGAATGGAGTTTTTGA
1 ATTATATGAATGGAGTTTTTGA
*
1505707 ATTA-ATGAATGGGGTTTTT
1 ATTATATGAATGGAGTTTTT
1505726 TATATGCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.46
Consensus pattern (22 bp):
ATTATATGAATGGAGTTTTTGA
Found at i:1507878 original size:46 final size:46
Alignment explanation
Indices: 1507818--1507924 Score: 110
Period size: 47 Copynumber: 2.3 Consensus size: 46
1507808 ATGAACCCCG
* * *
1507818 AATCATGAACCTTGAAC-TCAAACTCGAATCTAAACCTTGAACCTTA
1 AATCCTGAA-CTTGAACTTCAAACCCGAACCTAAACCTTGAACCTTA
* * * *
1507864 AATCCTGAAGCTTGAACTTCGAACCCGAACCTGAACTTTGAATCTTA
1 AATCCTGAA-CTTGAACTTCAAACCCGAACCTAAACCTTGAACCTTA
1507911 AA-CCTTGAACTTGA
1 AATCC-TGAACTTGA
1507925 GTTCAGGGTT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
46 22 0.43
47 29 0.57
ACGTcount: A:0.36, C:0.25, G:0.12, T:0.27
Consensus pattern (46 bp):
AATCCTGAACTTGAACTTCAAACCCGAACCTAAACCTTGAACCTTA
Found at i:1507956 original size:20 final size:20
Alignment explanation
Indices: 1507933--1507971 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1507923 GAGTTCAGGG
*
1507933 TTTGGGTTCATGGTTCGAGA
1 TTTGGGTTCAGGGTTCGAGA
1507953 TTTGGGTTCAGGGTTCGAG
1 TTTGGGTTCAGGGTTCGAG
1507972 TTCAAAGTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.10, G:0.38, T:0.38
Consensus pattern (20 bp):
TTTGGGTTCAGGGTTCGAGA
Found at i:1508000 original size:7 final size:7
Alignment explanation
Indices: 1507990--1508069 Score: 60
Period size: 7 Copynumber: 11.3 Consensus size: 7
1507980 TCAAAGATCG
1507990 GGTTTGA
1 GGTTTGA
1507997 GGTTT-A
1 GGTTTGA
1508003 GGTTTGA
1 GGTTTGA
1508010 GGTTT-A
1 GGTTTGA
*
1508016 GATTTGA
1 GGTTTGA
1508023 GGTTT-A
1 GGTTTGA
1508029 GGGTTTGA
1 -GGTTTGA
1508037 GGATATTTGA
1 GG---TTTGA
*
1508047 GGTTCGA
1 GGTTTGA
*
1508054 -GTTTTA
1 GGTTTGA
1508060 GAGTTTGA
1 G-GTTTGA
1508068 GG
1 GG
1508070 ATCAAGATTT
Statistics
Matches: 58, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
6 16 0.28
7 28 0.48
8 7 0.12
10 7 0.12
ACGTcount: A:0.19, C:0.01, G:0.38, T:0.42
Consensus pattern (7 bp):
GGTTTGA
Found at i:1508008 original size:13 final size:13
Alignment explanation
Indices: 1507990--1508038 Score: 80
Period size: 13 Copynumber: 3.7 Consensus size: 13
1507980 TCAAAGATCG
1507990 GGTTTGAGGTTTA
1 GGTTTGAGGTTTA
1508003 GGTTTGAGGTTTA
1 GGTTTGAGGTTTA
*
1508016 GATTTGAGGTTTA
1 GGTTTGAGGTTTA
1508029 GGGTTTGAGG
1 -GGTTTGAGG
1508039 ATATTTGAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
13 25 0.76
14 8 0.24
ACGTcount: A:0.16, C:0.00, G:0.41, T:0.43
Consensus pattern (13 bp):
GGTTTGAGGTTTA
Found at i:1509668 original size:7 final size:7
Alignment explanation
Indices: 1509656--1509680 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1509646 AGTTACAAGA
1509656 AAATTTT
1 AAATTTT
1509663 AAATTTT
1 AAATTTT
1509670 AAATTTT
1 AAATTTT
1509677 AAAT
1 AAAT
1509681 AATTTAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
AAATTTT
Found at i:1510830 original size:7 final size:7
Alignment explanation
Indices: 1510818--1510895 Score: 65
Period size: 7 Copynumber: 11.4 Consensus size: 7
1510808 CTCGAATTTA
1510818 AACCTTG
1 AACCTTG
1510825 AACCTTG
1 AACCTTG
*
1510832 AACCTTA
1 AACCTTG
1510839 AATCC-TG
1 AA-CCTTG
*
1510846 AAGCTTG
1 AACCTTG
*
1510853 AA-CTCCG
1 AACCT-TG
*
1510860 AA-CTCG
1 AACCTTG
1510866 AACC-TG
1 AACCTTG
1510872 AACCTTG
1 AACCTTG
*
1510879 AACCTTA
1 AACCTTG
1510886 AACCTTG
1 AACCTTG
1510893 AAC
1 AAC
1510896 TTGGGTTCAG
Statistics
Matches: 59, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
6 12 0.20
7 45 0.76
8 2 0.03
ACGTcount: A:0.33, C:0.29, G:0.13, T:0.24
Consensus pattern (7 bp):
AACCTTG
Found at i:1516524 original size:18 final size:19
Alignment explanation
Indices: 1516479--1516525 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
1516469 CCTCTCAATT
1516479 AAAA-TTATAAAATATTCA
1 AAAATTTATAAAATATTCA
* *
1516497 AAACATTTATAGAA-ATTCC
1 AAA-ATTTATAAAATATTCA
1516516 AAAATTTATA
1 AAAATTTATA
1516526 TATTTTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 10 0.40
19 8 0.32
20 7 0.28
ACGTcount: A:0.55, C:0.09, G:0.02, T:0.34
Consensus pattern (19 bp):
AAAATTTATAAAATATTCA
Found at i:1518513 original size:19 final size:18
Alignment explanation
Indices: 1518491--1518534 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
1518481 TGTTTTATAG
*
1518491 AAAATAATTTGATCAACGA
1 AAAATAACTTG-TCAACGA
* *
1518510 AAAATGACTTGTCGACGA
1 AAAATAACTTGTCAACGA
1518528 AAAATAA
1 AAAATAA
1518535 ATTTTTTTAC
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 12 0.57
19 9 0.43
ACGTcount: A:0.52, C:0.11, G:0.14, T:0.23
Consensus pattern (18 bp):
AAAATAACTTGTCAACGA
Found at i:1523258 original size:3 final size:3
Alignment explanation
Indices: 1523250--1523333 Score: 168
Period size: 3 Copynumber: 28.0 Consensus size: 3
1523240 ATGCAACAGC
1523250 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1523298 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1523334 TAACGACATT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 81 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:1523905 original size:12 final size:12
Alignment explanation
Indices: 1523890--1523914 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1523880 AAAATTCCAT
1523890 TTAAAATAGAAA
1 TTAAAATAGAAA
1523902 TTAAAATAGAAA
1 TTAAAATAGAAA
1523914 T
1 T
1523915 ACAACACAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.64, C:0.00, G:0.08, T:0.28
Consensus pattern (12 bp):
TTAAAATAGAAA
Found at i:1530030 original size:23 final size:23
Alignment explanation
Indices: 1530001--1530070 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
1529991 TTTGAAAAAG
*
1530001 TAATAAGCGATGGATTCGTGCGA
1 TAATAAGCAATGGATTCGTGCGA
* * *
1530024 TAATAAGCAATGGGTTCGTCCAA
1 TAATAAGCAATGGATTCGTGCGA
*
1530047 TAATAAGCAATGGAGTCGTGCGA
1 TAATAAGCAATGGATTCGTGCGA
1530070 T
1 T
1530071 CTCGTGATAT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.33, C:0.14, G:0.27, T:0.26
Consensus pattern (23 bp):
TAATAAGCAATGGATTCGTGCGA
Found at i:1543273 original size:23 final size:23
Alignment explanation
Indices: 1543244--1543313 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
1543234 TTTGAAAAAG
*
1543244 TAATAAGCGATGGATTCGTGCGA
1 TAATAAGCAATGGATTCGTGCGA
* * *
1543267 TAATAAGCAATGGGTTCGTCCAA
1 TAATAAGCAATGGATTCGTGCGA
*
1543290 TAATAAGCAATGGAGTCGTGCGA
1 TAATAAGCAATGGATTCGTGCGA
1543313 T
1 T
1543314 CTCGTGATAT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.33, C:0.14, G:0.27, T:0.26
Consensus pattern (23 bp):
TAATAAGCAATGGATTCGTGCGA
Found at i:1556364 original size:12 final size:12
Alignment explanation
Indices: 1556347--1556371 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1556337 ATTGTGTTGT
1556347 ATTTCTATTTTA
1 ATTTCTATTTTA
1556359 ATTTCTATTTTA
1 ATTTCTATTTTA
1556371 A
1 A
1556372 ATGGAATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (12 bp):
ATTTCTATTTTA
Found at i:1556937 original size:3 final size:3
Alignment explanation
Indices: 1556929--1556997 Score: 138
Period size: 3 Copynumber: 23.0 Consensus size: 3
1556919 AATGTCGTTA
1556929 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1556977 TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT
1556998 GCTGTTGCAT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:1563184 original size:23 final size:23
Alignment explanation
Indices: 1563156--1563222 Score: 107
Period size: 23 Copynumber: 2.9 Consensus size: 23
1563146 TTTGAAAAAG
1563156 TAATAAGCAATGGATTCGTGCAA
1 TAATAAGCAATGGATTCGTGCAA
* *
1563179 TAATAAGCAATGGGTTCGTCCAA
1 TAATAAGCAATGGATTCGTGCAA
*
1563202 TAATAAGCAATGGAGTCGTGC
1 TAATAAGCAATGGATTCGTGC
1563223 GATCTCGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.25
Consensus pattern (23 bp):
TAATAAGCAATGGATTCGTGCAA
Done.