Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008183.1 Hibiscus syriacus cultivar Beakdansim tig00110783_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: 2364390
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 11
Found at i:1158480 original size:20 final size:20
Alignment explanation
Indices: 1158441--1158500 Score: 97
Period size: 20 Copynumber: 3.0 Consensus size: 20
1158431 AAATCGCAAC
1158441 GCGATTTT-AGTTTT-GCGTT
1 GCGATTTTCA-TTTTCGCGTT
1158460 GCGATTTTCATTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
1158480 GCGATTTTCATTTTCGCGTT
1 GCGATTTTCATTTTCGCGTT
1158500 G
1 G
1158501 GGAATTTAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
19 12 0.31
20 27 0.69
ACGTcount: A:0.10, C:0.17, G:0.23, T:0.50
Consensus pattern (20 bp):
GCGATTTTCATTTTCGCGTT
Found at i:1158514 original size:20 final size:20
Alignment explanation
Indices: 1158444--1158514 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
1158434 TCGCAACGCG
* *
1158444 ATTTTAGTTTTGCGTTGCGA
1 ATTTAAGTTTCGCGTTGCGA
* * *
1158464 TTTTCATTTTCGCGTTGCGA
1 ATTTAAGTTTCGCGTTGCGA
* * * *
1158484 TTTTCATTTTCGCGTTGGGA
1 ATTTAAGTTTCGCGTTGCGA
1158504 ATTTAAGTTTC
1 ATTTAAGTTTC
1158515 AGAAACTACT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.14, C:0.14, G:0.21, T:0.51
Consensus pattern (20 bp):
ATTTAAGTTTCGCGTTGCGA
Found at i:1160690 original size:21 final size:20
Alignment explanation
Indices: 1160666--1160734 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 20
1160656 CCTATCGTTT
1160666 AAGAGGCCCCTCTCATCATC
1 AAGAGGCCCCTCTCATCATC
* * * *
1160686 GAAGAAGCCCCTCCCACCGTTC
1 -AAGAGGCCCCTCTCATC-ATC
*
1160708 AAGAGGCCCCTGTCATCATTC
1 AAGAGGCCCCTCTCATCA-TC
1160729 AAGAGG
1 AAGAGG
1160735 TCTCTCATGT
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
21 35 0.95
22 2 0.05
ACGTcount: A:0.26, C:0.36, G:0.20, T:0.17
Consensus pattern (20 bp):
AAGAGGCCCCTCTCATCATC
Found at i:1160699 original size:42 final size:41
Alignment explanation
Indices: 1160636--1160732 Score: 113
Period size: 42 Copynumber: 2.3 Consensus size: 41
1160626 GATACACCTA
* * * * *
1160636 TCATCATTCAAGAGGCGCCTCCTATCGTTTAAGAGGCCCCTC
1 TCATCA-TCAAGAAGCCCCTCCCACCGTTCAAGAGGCCCCTC
*
1160678 TCATCATCGAAGAAGCCCCTCCCACCGTTCAAGAGGCCCCTG
1 TCATCATC-AAGAAGCCCCTCCCACCGTTCAAGAGGCCCCTC
1160720 TCATCATTCAAGA
1 TCATCA-TCAAGA
1160733 GGTCTCTCAT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
41 2 0.04
42 43 0.91
43 2 0.04
ACGTcount: A:0.25, C:0.35, G:0.18, T:0.23
Consensus pattern (41 bp):
TCATCATCAAGAAGCCCCTCCCACCGTTCAAGAGGCCCCTC
Found at i:1162234 original size:66 final size:65
Alignment explanation
Indices: 1162075--1162250 Score: 257
Period size: 66 Copynumber: 2.6 Consensus size: 65
1162065 TGGGGTACAT
1162075 TTTTTTTGCTTGTTTAATTGAATTT-TACATTGAAAGTTGATTTGTTTAATTGATGAGGAAATAA
1 TTTTTTTGCTTGTTTAATTG-ATTTGT--A---AAAGTTGATTTGTTTAATTGATGAGGAAATAA
1162139 GAATTA
60 GAATTA
* *
1162145 -TTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATT
1 TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAA-TTGATGAGGAAATAAGAATT
1162209 A
65 A
1162210 TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTT
1 TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTT
1162251 GTTTTAAATT
Statistics
Matches: 101, Mismatches: 2, Indels: 10
0.89 0.02 0.09
Matches are distributed among these distances:
64 17 0.17
65 19 0.19
66 40 0.40
67 1 0.01
68 4 0.04
69 20 0.20
ACGTcount: A:0.28, C:0.02, G:0.17, T:0.53
Consensus pattern (65 bp):
TTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTA
Found at i:1162328 original size:19 final size:19
Alignment explanation
Indices: 1162304--1162344 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
1162294 GTTGAAGGTA
*
1162304 CAATTCGCAACGCGAAAGT
1 CAATTCACAACGCGAAAGT
1162323 CAATTCACAACGCGAAAGT
1 CAATTCACAACGCGAAAGT
1162342 CAA
1 CAA
1162345 ATTTGCATTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.41, C:0.27, G:0.17, T:0.15
Consensus pattern (19 bp):
CAATTCACAACGCGAAAGT
Found at i:1162734 original size:18 final size:18
Alignment explanation
Indices: 1162711--1162746 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
1162701 AAGCCGGTTG
1162711 TGATTGGGATTTTGATTT
1 TGATTGGGATTTTGATTT
1162729 TGATTGGGATTTTGATTT
1 TGATTGGGATTTTGATTT
1162747 CCTTTTGCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.00, G:0.28, T:0.56
Consensus pattern (18 bp):
TGATTGGGATTTTGATTT
Found at i:1165028 original size:24 final size:24
Alignment explanation
Indices: 1164994--1165067 Score: 130
Period size: 24 Copynumber: 3.1 Consensus size: 24
1164984 CCATCACATC
*
1164994 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAGTATTGACCAAG
*
1165018 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAGTATTGACCAAG
1165042 ATCAAAGTCCGAGTATTGACCAAG
1 ATCAAAGTCCGAGTATTGACCAAG
1165066 AT
1 AT
1165068 TAAATTTCGA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (24 bp):
ATCAAAGTCCGAGTATTGACCAAG
Found at i:1165085 original size:24 final size:24
Alignment explanation
Indices: 1164994--1165085 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
1164984 CCATCACATC
* * *
1164994 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
1165018 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
1165042 ATCAAAGTCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* * *
1165066 ATTAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
1165086 TAGTACTCAT
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 60 1.00
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:1166033 original size:18 final size:17
Alignment explanation
Indices: 1165985--1166033 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 17
1165975 CAAAACATTT
1165985 GTGTTGCGAATCTAAAAC
1 GTGTTGCGAAT-TAAAAC
* *
1166003 CTGTTGCGAAATTAAATTC
1 GTGTTGCG-AATTAAA-AC
1166022 GTGTTGCGAATT
1 GTGTTGCGAATT
1166034 CGAAAATCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 15 0.58
19 11 0.42
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (17 bp):
GTGTTGCGAATTAAAAC
Found at i:1166049 original size:20 final size:19
Alignment explanation
Indices: 1166024--1166071 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
1166014 TTAAATTCGT
1166024 GTTGCGAATTCGAAAATCTA
1 GTTGCGAATTCGAAAATC-A
* *
1166044 GTTGCG-ATTTGAAATTCA
1 GTTGCGAATTCGAAAATCA
1166062 GTTGCGAATT
1 GTTGCGAATT
1166072 TGACTTTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 7 0.28
19 12 0.48
20 6 0.24
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.35
Consensus pattern (19 bp):
GTTGCGAATTCGAAAATCA
Found at i:1166072 original size:19 final size:20
Alignment explanation
Indices: 1166005--1166174 Score: 102
Period size: 20 Copynumber: 8.7 Consensus size: 20
1165995 TCTAAAACCT
* *
1166005 GTTGCGAAATT-AAATTCGT
1 GTTGCGAATTTGAAATTCGA
* * *
1166024 GTTGCGAATTCGAAAATCTA
1 GTTGCGAATTTGAAATTCGA
1166044 GTTGCG-ATTTGAAATTC-A
1 GTTGCGAATTTGAAATTCGA
** * *
1166062 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGAAATTCGA
* *
1166082 GTTGCGAATTTG-ACTATCGC
1 GTTGCGAATTTGAAAT-TCGA
* *
1166102 GTTGCGAATTTG-ACTATCGT
1 GTTGCGAATTTGAAAT-TCGA
* *
1166122 GTTGCGAATTTG-ACTATCGT
1 GTTGCGAATTTGAAAT-TCGA
*
1166142 GTTGCGAATTTGACAA-TCGC
1 GTTGCGAATTTGA-AATTCGA
*
1166162 TTTGCGAATTTGA
1 GTTGCGAATTTGA
1166175 CTTTTGTGTT
Statistics
Matches: 126, Mismatches: 19, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
18 7 0.06
19 27 0.21
20 91 0.72
22 1 0.01
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.38
Consensus pattern (20 bp):
GTTGCGAATTTGAAATTCGA
Found at i:1166087 original size:20 final size:20
Alignment explanation
Indices: 1166062--1166273 Score: 254
Period size: 20 Copynumber: 10.6 Consensus size: 20
1166052 TTGAAATTCA
* *
1166062 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTATCGT
*
1166082 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTATCGT
1166102 GTTGCGAATTTGACTATCGT
1 GTTGCGAATTTGACTATCGT
1166122 GTTGCGAATTTGACTATCGT
1 GTTGCGAATTTGACTATCGT
*
1166142 GTTGCGAATTTGACAATCGCT
1 GTTGCGAATTTGACTATCG-T
* *
1166163 -TTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTATCGT
* * *
1166182 GTTGCGAATTTAACTTTTGT
1 GTTGCGAATTTGACTATCGT
*
1166202 GTTGCGGATTTGACTATCGCT
1 GTTGCGAATTTGACTATCG-T
1166223 -TTGCGAATTTGACTTAT-GT
1 GTTGCGAATTTGAC-TATCGT
1166242 GTTGCG-ATTT-ACATATTCGT
1 GTTGCGAATTTGAC-TA-TCGT
1166262 GTTGCGAATTTG
1 GTTGCGAATTTG
1166274 GAAAATCGCA
Statistics
Matches: 168, Mismatches: 15, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
18 4 0.02
19 7 0.04
20 148 0.88
21 9 0.05
ACGTcount: A:0.19, C:0.14, G:0.24, T:0.43
Consensus pattern (20 bp):
GTTGCGAATTTGACTATCGT
Found at i:1166144 original size:60 final size:59
Alignment explanation
Indices: 1166062--1166273 Score: 284
Period size: 60 Copynumber: 3.5 Consensus size: 59
1166052 TTGAAATTCA
* * *
1166062 GTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTATCGT
1 GTTGCGAATTTGACTATCGTGTTGCGAATTTGACTATCGCTTTGCGAATTTGACTAT-GT
* *
1166122 GTTGCGAATTTGACTATCGTGTTGCGAATTTGACAATCGCTTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTATCGTGTTGCGAATTTGACTATCGCTTTGCGAATTTGAC-TATGT
* * * *
1166182 GTTGCGAATTTAACTTTTGTGTTGCGGATTTGACTATCGCTTTGCGAATTTGACTTATGT
1 GTTGCGAATTTGACTATCGTGTTGCGAATTTGACTATCGCTTTGCGAATTTGAC-TATGT
1166242 GTTGCG-ATTT-ACATATTCGTGTTGCGAATTTG
1 GTTGCGAATTTGAC-TA-TCGTGTTGCGAATTTG
1166274 GAAAATCGCA
Statistics
Matches: 135, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
58 2 0.01
59 5 0.04
60 126 0.93
61 2 0.01
ACGTcount: A:0.19, C:0.14, G:0.24, T:0.43
Consensus pattern (59 bp):
GTTGCGAATTTGACTATCGTGTTGCGAATTTGACTATCGCTTTGCGAATTTGACTATGT
Found at i:1166623 original size:70 final size:72
Alignment explanation
Indices: 1166477--1166624 Score: 167
Period size: 70 Copynumber: 2.1 Consensus size: 72
1166467 ATTTTTTTAA
* * * * *
1166477 ACTTTGCATCCTTCTCATTTTCCATGTTTTTTTTAAAAATTTAAAAGTATCGATATTTGTGGAAA
1 ACTTTGCAGCCTTCTCATTTTCCA--TTTTTTTTAAAAATTGAAAAATATCGATATCTGTAGAAA
*
1166542 AATATTAAT
64 AATATCAAT
* *
1166551 ACTTTGCAGCCTTCTCATTTTTCA-TTTTTTT-AAAATTGAAAAATATCTATACTCT-TAGAAAA
1 ACTTTGCAGCCTTCTCATTTTCCATTTTTTTTAAAAATTGAAAAATATCGATA-TCTGTAGAAAA
*
1166613 ATATCGAT
65 ATATCAAT
1166621 ACTT
1 ACTT
1166625 ACTAATTATA
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
70 33 0.52
71 9 0.14
74 22 0.34
ACGTcount: A:0.33, C:0.14, G:0.08, T:0.45
Consensus pattern (72 bp):
ACTTTGCAGCCTTCTCATTTTCCATTTTTTTTAAAAATTGAAAAATATCGATATCTGTAGAAAAA
TATCAAT
Found at i:1167400 original size:71 final size:70
Alignment explanation
Indices: 1167275--1167454 Score: 288
Period size: 71 Copynumber: 2.5 Consensus size: 70
1167265 ACTCACATTA
* *
1167275 ACATTAACATTCATCCATTGATCACTGTTACTAATTAATAAACAATTAACTCTGACTATGACTCA
1 ACATT-ACATTCATCCATTGATCACTATTACTAATTAATAAACAACTAACTCTGACTATGACTCA
1167340 CAACTC
65 CAACTC
* *
1167346 ACATTGACATTCATCCATTGATCACAATTACTAATTAATAAACAACTAATTCTGACTATGACTCA
1 ACATT-ACATTCATCCATTGATCACTATTACTAATTAATAAACAACTAACTCTGACTATGACTCA
1167411 CAACTC
65 CAACTC
*
1167417 ACATTAGCATTCATCCATTGATCACTACTACTAATTAA
1 ACATTA-CATTCATCCATTGATCACTATTACTAATTAA
1167455 GAGAGTAATT
Statistics
Matches: 101, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
70 1 0.01
71 100 0.99
ACGTcount: A:0.38, C:0.24, G:0.06, T:0.32
Consensus pattern (70 bp):
ACATTACATTCATCCATTGATCACTATTACTAATTAATAAACAACTAACTCTGACTATGACTCAC
AACTC
Found at i:1175358 original size:12 final size:10
Alignment explanation
Indices: 1175316--1175356 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
1175306 TTTATCACAC
1175316 CAAATTCTCT
1 CAAATTCTCT
1175326 CAAATTCTCT
1 CAAATTCTCT
1175336 -AAATTTCTCT
1 CAAA-TTCTCT
*
1175346 CAAATACTCT
1 CAAATTCTCT
1175356 C
1 C
1175357 TCTTTTTAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 22 0.79
11 3 0.11
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:1175676 original size:111 final size:111
Alignment explanation
Indices: 1175482--1175814 Score: 603
Period size: 111 Copynumber: 3.0 Consensus size: 111
1175472 TGGAAACCAT
* *
1175482 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACGCTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* *
1175547 TATTTAATTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
*
1175593 ATATCTCGACATTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1175658 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
*
1175704 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAATAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
1175769 TAATTAGTTGATTTATTTAATGTATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
1175815 TTTTTGTAAT
Statistics
Matches: 214, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 214 1.00
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:1177746 original size:20 final size:19
Alignment explanation
Indices: 1177703--1177749 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
1177693 AATGAGATAA
* *
1177703 AAAAAGAAAATAAAAGAAG
1 AAAAAGAAAAAAAAACAAG
*
1177722 TAAAAGAAAAAATAAACAAG
1 AAAAAGAAAAAA-AAACAAG
1177742 AAAAAGAA
1 AAAAAGAA
1177750 TGAAGTAACG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.79, C:0.02, G:0.13, T:0.06
Consensus pattern (19 bp):
AAAAAGAAAAAAAAACAAG
Found at i:1177972 original size:2 final size:2
Alignment explanation
Indices: 1177965--1177997 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1177955 AGTTATATGA
1177965 AT AT AT AT 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 AT AT AT AT A
1177998 ATAACTTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1178041 original size:24 final size:24
Alignment explanation
Indices: 1178014--1178061 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1178004 TATAAACAAT
* *
1178014 GTATAAAAATAATAGTAATAATAA
1 GTATAAAAATAAAAATAATAATAA
**
1178038 GTATTTAAATAAAAATAATAATAA
1 GTATAAAAATAAAAATAATAATAA
1178062 TAGTAATAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (24 bp):
GTATAAAAATAAAAATAATAATAA
Found at i:1178674 original size:35 final size:35
Alignment explanation
Indices: 1178635--1178706 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
1178625 CTAAAAAACC
*
1178635 CTATTTTAGACTAGTATTTGAGCCCTAATCTAACT
1 CTATTTTAGACTAGTATTTGAGCCCTAATCCAACT
*
1178670 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1 CTATTTTAGACTAGTATTTGAGCCCTAATCCAACT
1178705 CT
1 CT
1178707 TCTTTGTTGG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.40
Consensus pattern (35 bp):
CTATTTTAGACTAGTATTTGAGCCCTAATCCAACT
Found at i:1179636 original size:106 final size:106
Alignment explanation
Indices: 1179451--1179662 Score: 354
Period size: 106 Copynumber: 2.0 Consensus size: 106
1179441 TGTATTGTTC
* *
1179451 CGAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGTTCTGGAACTAGGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGAAACTAGGAAATTGTTTGTTGACA
*
1179516 ATCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * *
1179557 CGAGTCCAATATCCTTCG-CTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGAC
1 CGAGTCCAATATCCTCCGTC-GTGAAGTTGAAATTGGCTCTGAAACTAGGAAATTGTTTGTTGAC
1179621 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
65 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
1179663 TAAGTGTTGA
Statistics
Matches: 99, Mismatches: 6, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
105 1 0.01
106 98 0.99
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.35
Consensus pattern (106 bp):
CGAGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGAAACTAGGAAATTGTTTGTTGACA
ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:1180122 original size:21 final size:20
Alignment explanation
Indices: 1180098--1180202 Score: 80
Period size: 21 Copynumber: 5.4 Consensus size: 20
1180088 AGAAACTGTC
1180098 TCAAGGGAGACAAAATTCGTT
1 TCAAGGGAGACAAAATT-GTT
* *
1180119 TCAAGGAAGAC-----TGTC
1 TCAAGGGAGACAAAATTGTT
*
1180134 TCAAGAGAGACAAAATTTGTT
1 TCAAGGGAGACAAAA-TTGTT
* *
1180155 TCAA--GAGAAATAAATTGTC
1 TCAAGGGAGACA-AAATTGTT
1180174 TCAAGGGAGACAAAATTTGTT
1 TCAAGGGAGACAAAA-TTGTT
1180195 TCAAGGGA
1 TCAAGGGA
1180203 AACTATCTCA
Statistics
Matches: 65, Mismatches: 9, Indels: 20
0.69 0.10 0.21
Matches are distributed among these distances:
15 11 0.17
16 1 0.02
19 13 0.20
20 6 0.09
21 34 0.52
ACGTcount: A:0.40, C:0.12, G:0.23, T:0.25
Consensus pattern (20 bp):
TCAAGGGAGACAAAATTGTT
Found at i:1180132 original size:36 final size:35
Alignment explanation
Indices: 1180078--1180232 Score: 166
Period size: 36 Copynumber: 4.2 Consensus size: 35
1180068 GCAAATTGTG
*
1180078 TTGTTTCGAGAGAAACTGTCTCAAGGGAGACAAAAT
1 TTGTTTCAAG-GAAACTGTCTCAAGGGAGACAAAAT
* *
1180114 TCGTTTCAAGGAAGACTGTCTCAAGAGAGACAAAAT
1 TTGTTTCAAGGAA-ACTGTCTCAAGGGAGACAAAAT
*
1180150 TTGTTTCAAGAGAAATAAATTGTCTCAAGGGAGACAAAAT
1 TTGTTTCAAG-G----AAACTGTCTCAAGGGAGACAAAAT
* * *
1180190 TTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAAT
1 TTGTTTCAA-GGAAACTGTCTCAAGGGAGACAAAAT
1180226 CTTGTTT
1 -TTGTTT
1180233 TAAGAAAAAT
Statistics
Matches: 101, Mismatches: 10, Indels: 15
0.80 0.08 0.12
Matches are distributed among these distances:
35 3 0.03
36 58 0.57
37 7 0.07
40 30 0.30
41 3 0.03
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (35 bp):
TTGTTTCAAGGAAACTGTCTCAAGGGAGACAAAAT
Found at i:1180196 original size:76 final size:77
Alignment explanation
Indices: 1180094--1180244 Score: 225
Period size: 76 Copynumber: 2.0 Consensus size: 77
1180084 CGAGAGAAAC
*
1180094 TGTCTCAAGGGAGACAAAATTCGTTTCAA-GGAAGACTGTCTCAAGAGAGACAAAAT-TTGTTTC
1 TGTCTCAAGGGAGACAAAATTCGTTTCAAGGGAA-ACTATCTCAAGAGAGACAAAATCTTGTTTC
*
1180157 AAGAGAAATAAAT
65 AAGAAAAATAAAT
* * * *
1180170 TGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACTATCTCAAGCGAGATAAAATCTTGTTTTA
1 TGTCTCAAGGGAGACAAAATTCGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATCTTGTTTCA
1180235 AGAAAAATAA
66 AGAAAAATAA
1180245 TCTTGAGGGA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
76 47 0.70
77 20 0.30
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (77 bp):
TGTCTCAAGGGAGACAAAATTCGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATCTTGTTTCA
AGAAAAATAAAT
Found at i:1181751 original size:28 final size:29
Alignment explanation
Indices: 1181707--1181768 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
1181697 TTTTTGTCCC
1181707 TTTTTCTTTTTGATTTT-TGTTCTTTC-TTG
1 TTTTTCTTTTTGATTTTCT-TT-TTTCTTTG
*
1181736 TTTTTC-TTTTGTTTTTCTTTTTTCTTTG
1 TTTTTCTTTTTGATTTTCTTTTTTCTTTG
1181764 TTTTT
1 TTTTT
1181769 TTGCTTCTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 4 0.13
28 19 0.63
29 7 0.23
ACGTcount: A:0.02, C:0.10, G:0.08, T:0.81
Consensus pattern (29 bp):
TTTTTCTTTTTGATTTTCTTTTTTCTTTG
Found at i:1181756 original size:17 final size:17
Alignment explanation
Indices: 1181707--1181768 Score: 61
Period size: 17 Copynumber: 3.3 Consensus size: 17
1181697 TTTTTGTCCC
*
1181707 TTTTTCTTTTTGATTTTTG
1 TTTTTCTTTTT--TCTTTG
1181726 TTCTTTCTTGTTTTTCTTTTG
1 TT-TTTC-T-TTTTTC-TTTG
1181747 TTTTTCTTTTTTCTTTG
1 TTTTTCTTTTTTCTTTG
1181764 TTTTT
1 TTTTT
1181769 TTGCTTCTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
17 9 0.24
18 6 0.16
19 3 0.08
20 9 0.24
21 7 0.18
22 4 0.11
ACGTcount: A:0.02, C:0.10, G:0.08, T:0.81
Consensus pattern (17 bp):
TTTTTCTTTTTTCTTTG
Found at i:1181776 original size:16 final size:15
Alignment explanation
Indices: 1181720--1181792 Score: 53
Period size: 16 Copynumber: 4.7 Consensus size: 15
1181710 TTCTTTTTGA
*
1181720 TTTTTGTTCTTT-CT
1 TTTTTGTTCTTTGTT
*
1181734 TGTTT-TTCTTTTGTTT
1 TTTTTGTTC-TTTG-TT
*
1181750 TTCTTTTTTCTTTGTT
1 TT-TTTGTTCTTTGTT
1181766 TTTTTGCTTCTTT-TCT
1 TTTTTG-TTCTTTGT-T
1181782 TTTTTGTTCTT
1 TTTTTGTTCTT
1181793 GATTGGATCT
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
13 3 0.06
14 7 0.15
15 9 0.19
16 19 0.40
17 7 0.15
18 3 0.06
ACGTcount: A:0.00, C:0.12, G:0.08, T:0.79
Consensus pattern (15 bp):
TTTTTGTTCTTTGTT
Found at i:1181792 original size:31 final size:30
Alignment explanation
Indices: 1181707--1181792 Score: 79
Period size: 31 Copynumber: 2.8 Consensus size: 30
1181697 TTTTTGTCCC
**
1181707 TTTTTCTTTT-TGATTTTTGTTCTTTCTTG
1 TTTTTCTTTTGTTTTTTTTGTTCTTTCTTG
* *
1181736 TTTTTCTTTTGTTTTTCTTTTTTCTTTGTT-
1 TTTTTCTTTTGTTTTT-TTTGTTCTTTCTTG
1181766 TTTTTGCTTCTT-TTCTTTTTTGTTCTT
1 TTTTT-CTT-TTGTT-TTTTTTGTTCTT
1181793 GATTGGATCT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
29 10 0.21
30 8 0.17
31 24 0.51
32 5 0.11
ACGTcount: A:0.01, C:0.12, G:0.08, T:0.79
Consensus pattern (30 bp):
TTTTTCTTTTGTTTTTTTTGTTCTTTCTTG
Found at i:1182201 original size:15 final size:15
Alignment explanation
Indices: 1182181--1182209 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1182171 CCAAGTTGTG
1182181 TCTTTAGAATAACGC
1 TCTTTAGAATAACGC
1182196 TCTTTAGAATAACG
1 TCTTTAGAATAACG
1182210 TTCAGATGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (15 bp):
TCTTTAGAATAACGC
Found at i:1183642 original size:17 final size:16
Alignment explanation
Indices: 1183620--1183653 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1183610 GTAAAACAGT
1183620 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
1183637 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
1183653 A
1 A
1183654 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:1187537 original size:23 final size:24
Alignment explanation
Indices: 1187469--1187537 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 24
1187459 AGTAAGAGAG
*
1187469 AGAGAAAAAGTAAAAGTTAACATGAA
1 AGAGAAAAA-AAAAAGTTAA-ATGAA
1187495 AGAGAAAAAAAATGAA--TAAA-GAA
1 AGAGAAAAAAAA--AAGTTAAATGAA
1187518 AGAGAAAAAAAAAAGTTAAA
1 AGAGAAAAAAAAAAGTTAAA
1187538 AATTTGGGAG
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
21 2 0.05
23 19 0.50
24 1 0.03
25 5 0.13
26 9 0.24
27 2 0.05
ACGTcount: A:0.70, C:0.01, G:0.17, T:0.12
Consensus pattern (24 bp):
AGAGAAAAAAAAAAGTTAAATGAA
Found at i:1194430 original size:24 final size:24
Alignment explanation
Indices: 1194386--1194435 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1194376 ATAAAGAACC
*
1194386 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
1194410 AAAATAAAGTTTAAACA-ACCATTA
1 AAAATAAA-CTTAAACATACCATTA
1194434 AA
1 AA
1194436 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:1198154 original size:16 final size:16
Alignment explanation
Indices: 1198117--1198157 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
1198107 AAAAATGAAG
*
1198117 AATAAA-AATAAGTAAA
1 AATAAATAA-AAGGAAA
1198133 AA-AAATAAAAGGAAA
1 AATAAATAAAAGGAAA
1198148 AATAAATAAA
1 AATAAATAAA
1198158 TAAATAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (16 bp):
AATAAATAAAAGGAAA
Found at i:1199080 original size:37 final size:37
Alignment explanation
Indices: 1199039--1199135 Score: 140
Period size: 37 Copynumber: 2.6 Consensus size: 37
1199029 GGATCATATC
* *
1199039 TTTAGGAGTTTAAATCATAGTAGAACTCTATCCTACT
1 TTTAGGAGTTTGAATCCTAGTAGAACTCTATCCTACT
* * * *
1199076 TTTAGGAGTTTGAATCCTAGCAAAATTCTATCCTATT
1 TTTAGGAGTTTGAATCCTAGTAGAACTCTATCCTACT
1199113 TTTAGGAGTTTGAATCCTAGTAG
1 TTTAGGAGTTTGAATCCTAGTAG
1199136 GACGAAAAGG
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 52 1.00
ACGTcount: A:0.30, C:0.14, G:0.16, T:0.39
Consensus pattern (37 bp):
TTTAGGAGTTTGAATCCTAGTAGAACTCTATCCTACT
Found at i:1199242 original size:27 final size:27
Alignment explanation
Indices: 1199212--1199269 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
1199202 AGCCATATAT
* *
1199212 GATGCCGCCATCGCCTTTCCATTACCA
1 GATGCCGCCATCACCTTTCAATTACCA
*
1199239 GATGCCGCCGTCACCTTTCAATTACCA
1 GATGCCGCCATCACCTTTCAATTACCA
1199266 GATG
1 GATG
1199270 TCGTCGCCGC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.21, C:0.36, G:0.17, T:0.26
Consensus pattern (27 bp):
GATGCCGCCATCACCTTTCAATTACCA
Found at i:1199586 original size:3 final size:3
Alignment explanation
Indices: 1199578--1199627 Score: 55
Period size: 3 Copynumber: 16.7 Consensus size: 3
1199568 ACCTGCTTAG
* * * **
1199578 GAC GAC GAC GAC GAT GAT GAC GAT GGT GAC GAC GAC GAC GAC GAC GAC
1 GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC
1199626 GA
1 GA
1199628 TGATGACAGC
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.24, G:0.36, T:0.08
Consensus pattern (3 bp):
GAC
Found at i:1199611 original size:12 final size:12
Alignment explanation
Indices: 1199581--1199630 Score: 64
Period size: 12 Copynumber: 4.2 Consensus size: 12
1199571 TGCTTAGGAC
1199581 GACGACGACGAT
1 GACGACGACGAT
* * *
1199593 GATGACGATGGT
1 GACGACGACGAT
*
1199605 GACGACGACGAC
1 GACGACGACGAT
1199617 GACGACGACGAT
1 GACGACGACGAT
1199629 GA
1 GA
1199631 TGACAGCGAG
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.32, C:0.22, G:0.36, T:0.10
Consensus pattern (12 bp):
GACGACGACGAT
Found at i:1213536 original size:29 final size:30
Alignment explanation
Indices: 1213503--1213585 Score: 105
Period size: 30 Copynumber: 2.8 Consensus size: 30
1213493 CCCGAAGGAC
*
1213503 CTATCCAGAGGTCACAAAGATCC-CGGCAA
1 CTATCCAGAGGTCACAAAGAACCTCGGCAA
*
1213532 CTATCCAGAGGTCATAAAGAACCTCGGCAA
1 CTATCCAGAGGTCACAAAGAACCTCGGCAA
* * * *
1213562 CTGTCCATAGGTCCCGAAGAACCT
1 CTATCCAGAGGTCACAAAGAACCT
1213586 AGGTAAACTG
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
29 21 0.46
30 25 0.54
ACGTcount: A:0.33, C:0.30, G:0.20, T:0.17
Consensus pattern (30 bp):
CTATCCAGAGGTCACAAAGAACCTCGGCAA
Found at i:1213598 original size:31 final size:31
Alignment explanation
Indices: 1213560--1213624 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
1213550 GAACCTCGGC
*
1213560 AACTGTCCATAGGTCCCG-AAGAACCTAGGTA
1 AACTGTCCATAGGTCCCGAAAG-ACATAGGTA
* *
1213591 AACTGTCCATATGTCTCGAAAGACATAGGTA
1 AACTGTCCATAGGTCCCGAAAGACATAGGTA
1213622 AAC
1 AAC
1213625 CCTCGACTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 27 0.90
32 3 0.10
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.22
Consensus pattern (31 bp):
AACTGTCCATAGGTCCCGAAAGACATAGGTA
Found at i:1214855 original size:20 final size:22
Alignment explanation
Indices: 1214830--1214887 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
1214820 TTCCCCTTGA
1214830 AGTGCATCGATGCATGC-T-AC
1 AGTGCATCGATGCATGCTTAAC
*
1214850 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATGC-TTAAC
1214873 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
1214888 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (22 bp):
AGTGCATCGATGCATGCTTAAC
Found at i:1216557 original size:31 final size:30
Alignment explanation
Indices: 1216519--1216621 Score: 113
Period size: 31 Copynumber: 3.4 Consensus size: 30
1216509 TAAAATTTAA
* *
1216519 TAATGATTTAATCATTATTAAATTTTAACTT
1 TAATGATTTAATAATTATT-AATGTTAACTT
1216550 TAATGATTTGATACTAATTATT-A-GTTAACTT
1 TAATGATTT-A-A-TAATTATTAATGTTAACTT
*
1216581 TAATGA-TTAATAATAATTAATAGTTAACTT
1 TAATGATTTAATAATTATTAAT-GTTAACTT
1216611 TAATGATTTAA
1 TAATGATTTAA
1216622 CTTTAATGAT
Statistics
Matches: 62, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
27 7 0.11
28 2 0.03
29 1 0.02
30 16 0.26
31 26 0.42
32 2 0.03
33 1 0.02
34 7 0.11
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.48
Consensus pattern (30 bp):
TAATGATTTAATAATTATTAATGTTAACTT
Found at i:1216605 original size:30 final size:30
Alignment explanation
Indices: 1216543--1216618 Score: 116
Period size: 30 Copynumber: 2.5 Consensus size: 30
1216533 TTATTAAATT
* * *
1216543 TTAACTTTAATGATTTGATACTAATTATTAG
1 TTAACTTTAATGA-TTAATAATAATTAATAG
1216574 TTAACTTTAATGATTAATAATAATTAATAG
1 TTAACTTTAATGATTAATAATAATTAATAG
1216604 TTAACTTTAATGATT
1 TTAACTTTAATGATT
1216619 TAACTTTAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
30 29 0.69
31 13 0.31
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.47
Consensus pattern (30 bp):
TTAACTTTAATGATTAATAATAATTAATAG
Found at i:1216623 original size:14 final size:14
Alignment explanation
Indices: 1216542--1216854 Score: 171
Period size: 14 Copynumber: 21.4 Consensus size: 14
1216532 ATTATTAAAT
1216542 TTTAACTTTAATGA
1 TTTAACTTTAATGA
*
1216556 TTTGATACTAATT-ATTA
1 TTT-A-ACT--TTAATGA
*
1216573 GTTAACTTTAATGA
1 TTTAACTTTAATGA
1216587 TTAATAA-TAATTAAT-A
1 TT--TAACT--TTAATGA
*
1216603 GTTAACTTTAATGA
1 TTTAACTTTAATGA
1216617 TTTAACTTTAATGA
1 TTTAACTTTAATGA
*
1216631 TTTAATACTAATT-ATTA
1 TTT-A-ACT--TTAATGA
*
1216648 GTTAACTTTAATGA
1 TTTAACTTTAATGA
*
1216662 TTTAA-TAATAATTAGTA
1 TTTAACT-TTAA-T-G-A
1216679 TTTAACTTTAATGA
1 TTTAACTTTAATGA
*
1216693 TTTATCTTTAATGA
1 TTTAACTTTAATGA
*
1216707 TTTGATACTAATT-ATTA
1 TTT-A-ACT--TTAATGA
*
1216724 GTTAACTTTAATGA
1 TTTAACTTTAATGA
* *
1216738 TTTAA-TAATAATAA
1 TTTAACT-TTAATGA
1216752 TTTAACTTTAATGA
1 TTTAACTTTAATGA
1216766 TTTAACTTTAATGA
1 TTTAACTTTAATGA
*
1216780 TTTAA-TAATT-ATAA
1 TTTAACT--TTAATGA
*
1216794 ATTAACTTTAATGA
1 TTTAACTTTAATGA
* *
1216808 TTTAA-TAATAATAA
1 TTTAACT-TTAATGA
*
1216822 TTTAACTTTAATTA
1 TTTAACTTTAATGA
*
1216836 TTTAA-TAATAATGA
1 TTTAACT-TTAATGA
1216850 TTTAA
1 TTTAA
1216855 TAATAGTAAT
Statistics
Matches: 232, Mismatches: 32, Indels: 70
0.69 0.10 0.21
Matches are distributed among these distances:
13 18 0.08
14 139 0.60
15 21 0.09
16 18 0.08
17 29 0.12
18 7 0.03
ACGTcount: A:0.41, C:0.05, G:0.06, T:0.48
Consensus pattern (14 bp):
TTTAACTTTAATGA
Found at i:1216650 original size:45 final size:44
Alignment explanation
Indices: 1216574--1216666 Score: 159
Period size: 45 Copynumber: 2.1 Consensus size: 44
1216564 TAATTATTAG
1216574 TTAACTTTAATGATTAATAATAATTAATAGTTAACTTTAATGAT
1 TTAACTTTAATGATTAATAATAATTAATAGTTAACTTTAATGAT
* *
1216618 TTAACTTTAATGATTTAATACTAATTATTAGTTAACTTTAATGAT
1 TTAACTTTAATGA-TTAATAATAATTAATAGTTAACTTTAATGAT
1216663 TTAA
1 TTAA
1216667 TAATAATTAG
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
44 13 0.28
45 33 0.72
ACGTcount: A:0.41, C:0.05, G:0.06, T:0.47
Consensus pattern (44 bp):
TTAACTTTAATGATTAATAATAATTAATAGTTAACTTTAATGAT
Found at i:1216656 original size:31 final size:31
Alignment explanation
Indices: 1216618--1216696 Score: 131
Period size: 31 Copynumber: 2.5 Consensus size: 31
1216608 CTTTAATGAT
* *
1216618 TTAACTTTAATGATTTAATACTAATTATTAG
1 TTAACTTTAATGATTTAATAATAATTAGTAG
*
1216649 TTAACTTTAATGATTTAATAATAATTAGTAT
1 TTAACTTTAATGATTTAATAATAATTAGTAG
1216680 TTAACTTTAATGATTTA
1 TTAACTTTAATGATTTA
1216697 TCTTTAATGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.39, C:0.05, G:0.06, T:0.49
Consensus pattern (31 bp):
TTAACTTTAATGATTTAATAATAATTAGTAG
Found at i:1216702 original size:45 final size:45
Alignment explanation
Indices: 1216653--1216741 Score: 142
Period size: 45 Copynumber: 2.0 Consensus size: 45
1216643 TATTAGTTAA
*
1216653 CTTTAATGATTTAATAATAATTAGTATTTAACTTTAATGATTTAT
1 CTTTAATGATTTAATAATAATTAGTAGTTAACTTTAATGATTTAT
* * *
1216698 CTTTAATGATTTGATACTAATTATTAGTTAACTTTAATGATTTA
1 CTTTAATGATTTAATAATAATTAGTAGTTAACTTTAATGATTTA
1216742 ATAATAATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.36, C:0.06, G:0.08, T:0.51
Consensus pattern (45 bp):
CTTTAATGATTTAATAATAATTAGTAGTTAACTTTAATGATTTAT
Found at i:1216757 original size:28 final size:29
Alignment explanation
Indices: 1216542--1216772 Score: 127
Period size: 31 Copynumber: 7.7 Consensus size: 29
1216532 ATTATTAAAT
* *
1216542 TTTAACTTTAATGATTTGATACTAATTATTA
1 TTTAACTTTAATGATTT-A-ACTAATAATAA
*
1216573 GTTAACTTTAATGA-TTAA-TAATAATTAA
1 TTTAACTTTAATGATTTAACTAATAA-TAA
* *
1216601 TAGTTAACTTTAATGATTTAACT-TTAATGA
1 T--TTAACTTTAATGATTTAACTAATAATAA
* * * *
1216631 TTTAATACTAATT-ATTAGTTAACT-TTAATGA
1 TTT-A-ACT--TTAATGATTTAACTAATAATAA
* * *
1216662 TTTAA-TAATAATTAGTATTTAACT-TTAATGA
1 TTTAACT-TTAA-T-G-ATTTAACTAATAATAA
* * *
1216693 TTTATCTTTAATGATTTGATACTAATTATTA
1 TTTAACTTTAATGATTT-A-ACTAATAATAA
*
1216724 GTTAACTTTAATGATTTAA-TAATAATAA
1 TTTAACTTTAATGATTTAACTAATAATAA
1216752 TTTAACTTTAATGATTTAACT
1 TTTAACTTTAATGATTTAACT
1216773 TTAATGATTT
Statistics
Matches: 161, Mismatches: 21, Indels: 38
0.73 0.10 0.17
Matches are distributed among these distances:
27 7 0.04
28 36 0.22
29 8 0.05
30 27 0.17
31 79 0.49
32 4 0.02
ACGTcount: A:0.39, C:0.06, G:0.07, T:0.48
Consensus pattern (29 bp):
TTTAACTTTAATGATTTAACTAATAATAA
Found at i:1221166 original size:84 final size:86
Alignment explanation
Indices: 1220859--1221332 Score: 681
Period size: 84 Copynumber: 5.5 Consensus size: 86
1220849 AGCGGATTAA
* *
1220859 TTACAGTTTCCCCA-GTCCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTCCCTT
1 TTACAGTTTCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTCCCTT
*
1220923 TGTTATGTGCAAGGGTAAGCC
66 TGTTGTGTGCAAGGGTAAGCC
* * *
1220944 TTACAGTTTCCCCAGGTTCCTTTGCTATATTCAAGGGTAAGCCTTACAGTTTTCCCCAGGTCCCT
1 TTACAGTTTCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAG-TTTCCCCAGGTCCCT
1221009 TTGTTGTGTGCAAGGGTAAGCC
65 TTGTTGTGTGCAAGGGTAAGCC
* * *
1221031 TTATAGTTTTCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAAGTCCCT
1 TTACAG-TTTCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTCCCT
1221096 TTGTTGTGTGCAAAGGGTAAGCC
65 TTGTTGTGTGC-AAGGGTAAGCC
*
1221119 -TACAGTTTCCCCA-G-TCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTTCCTT
1 TTACAGTTTCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTCCCTT
* * *
1221181 TGCTGTGTGCAATGGTGAGCC
66 TGTTGTGTGCAAGGGTAAGCC
* * *
1221202 TTACAGTTT-CCCAGGTTCCTTTGTTGTGTGCAAGGGTGAGCCTTACAGTTT-CCCAGGTTCCTT
1 TTACAGTTTCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTCCCTT
1221265 TGTTGTGTGCAAGGGTAAGCC
66 TGTTGTGTGCAAGGGTAAGCC
* * * * *
1221286 TTACAGTTTCCCCAGGCTCTTTTGCTATGTGAAAGGATAAGACCTTA
1 TTACAGTTTCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAG-CCTTA
1221333 TCGTTTTTGC
Statistics
Matches: 349, Mismatches: 31, Indels: 17
0.88 0.08 0.04
Matches are distributed among these distances:
83 13 0.04
84 102 0.29
85 72 0.21
86 42 0.12
87 70 0.20
88 50 0.14
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.34
Consensus pattern (86 bp):
TTACAGTTTCCCCAGGTTCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCCCCAGGTCCCTT
TGTTGTGTGCAAGGGTAAGCC
Found at i:1221230 original size:42 final size:43
Alignment explanation
Indices: 1220859--1221301 Score: 664
Period size: 43 Copynumber: 10.4 Consensus size: 43
1220849 AGCGGATTAA
1220859 TTACAGTTTCCCCA-GTCCCTTTGTTGTGTGCAAGGGTAAGCC
1 TTACAGTTTCCCCAGGTCCCTTTGTTGTGTGCAAGGGTAAGCC
*
1220901 TTACAGTTTCCCCAGGTCCCTTTGTTATGTGCAAGGGTAAGCC
1 TTACAGTTTCCCCAGGTCCCTTTGTTGTGTGCAAGGGTAAGCC
* * * * *
1220944 TTACAGTTTCCCCAGGTTCCTTTGCTATATTCAAGGGTAAGCC
1 TTACAGTTTCCCCAGGTCCCTTTGTTGTGTGCAAGGGTAAGCC
1220987 TTACAGTTTTCCCCAGGTCCCTTTGTTGTGTGCAAGGGTAAGCC
1 TTACAG-TTTCCCCAGGTCCCTTTGTTGTGTGCAAGGGTAAGCC
* *
1221031 TTATAGTTTTCCCCAGGTCCCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAG-TTTCCCCAGGTCCCTTTGTTGTGTGCAAGGGTAAGCC
*
1221075 TTACAGTTTCCCCAAGTCCCTTTGTTGTGTGCAAAGGGTAAGCC
1 TTACAGTTTCCCCAGGTCCCTTTGTTGTGTGC-AAGGGTAAGCC
*
1221119 -TACAGTTTCCCCA-GT-CCTTTGCTGTGTGCAAGGGTAAGCC
1 TTACAGTTTCCCCAGGTCCCTTTGTTGTGTGCAAGGGTAAGCC
* * * *
1221159 TTACAGTTTCCCCAGGTTCCTTTGCTGTGTGCAATGGTGAGCC
1 TTACAGTTTCCCCAGGTCCCTTTGTTGTGTGCAAGGGTAAGCC
* *
1221202 TTACAGTTT-CCCAGGTTCCTTTGTTGTGTGCAAGGGTGAGCC
1 TTACAGTTTCCCCAGGTCCCTTTGTTGTGTGCAAGGGTAAGCC
*
1221244 TTACAGTTT-CCCAGGTTCCTTTGTTGTGTGCAAGGGTAAGCC
1 TTACAGTTTCCCCAGGTCCCTTTGTTGTGTGCAAGGGTAAGCC
1221286 TTACAGTTTCCCCAGG
1 TTACAGTTTCCCCAGG
1221302 CTCTTTTGCT
Statistics
Matches: 373, Mismatches: 21, Indels: 13
0.92 0.05 0.03
Matches are distributed among these distances:
40 11 0.03
41 26 0.07
42 99 0.27
43 147 0.39
44 90 0.24
ACGTcount: A:0.17, C:0.25, G:0.24, T:0.34
Consensus pattern (43 bp):
TTACAGTTTCCCCAGGTCCCTTTGTTGTGTGCAAGGGTAAGCC
Found at i:1226313 original size:31 final size:31
Alignment explanation
Indices: 1226288--1226430 Score: 214
Period size: 31 Copynumber: 4.6 Consensus size: 31
1226278 TCCATGGATT
* *
1226288 CCAAAGAACCTAGGTAATCAGTCCATATGTC
1 CCAAAGAACATAGGTAAACAGTCCATATGTC
* *
1226319 CCGAAGAACATAAGTAAACAGTCCATATGTC
1 CCAAAGAACATAGGTAAACAGTCCATATGTC
*
1226350 CCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCAAAGAACATAGGTAAACAGTCCATATGTC
*
1226381 CCAAAGAACATAGGTAAACAGTCCATATATC
1 CCAAAGAACATAGGTAAACAGTCCATATGTC
**
1226412 CCGCAGAACATAGGTAAAC
1 CCAAAGAACATAGGTAAAC
1226431 CCTCGACCCT
Statistics
Matches: 103, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 103 1.00
ACGTcount: A:0.41, C:0.24, G:0.17, T:0.19
Consensus pattern (31 bp):
CCAAAGAACATAGGTAAACAGTCCATATGTC
Found at i:1227435 original size:21 final size:21
Alignment explanation
Indices: 1227411--1227455 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1227401 TTTTGTTCGT
* *
1227411 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1227432 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1227453 TTG
1 TTG
1227456 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1230606 original size:31 final size:31
Alignment explanation
Indices: 1230568--1230723 Score: 251
Period size: 31 Copynumber: 5.0 Consensus size: 31
1230558 TTCGAATGAC
* * *
1230568 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
1230599 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
1230630 CAGTCCATATGTCCCGAAGAATATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1230661 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
1230692 CAGTCCATATATCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1230723 C
1 C
1230724 CCTCGACCCT
Statistics
Matches: 118, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
31 117 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:1231729 original size:21 final size:21
Alignment explanation
Indices: 1231705--1231749 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1231695 TTTTGTTCGT
* *
1231705 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1231726 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1231747 TTG
1 TTG
1231750 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:1236214 original size:16 final size:16
Alignment explanation
Indices: 1236195--1236228 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1236185 CAATATACGA
1236195 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
1236211 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
1236227 AT
1 AT
1236229 TTAGATGTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:1236969 original size:130 final size:130
Alignment explanation
Indices: 1236765--1237012 Score: 433
Period size: 130 Copynumber: 1.9 Consensus size: 130
1236755 AATTTTCTTC
*
1236765 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGCTAACACATGTCAGAT
** *
1236830 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * *
1236895 TAATTAGGTGGTGACATGTGTCACCAATGACATGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGCTAACACATGTCAGAT
1236960 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
1237013 TATATAAATA
Statistics
Matches: 111, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
130 111 1.00
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.37
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:1237449 original size:35 final size:35
Alignment explanation
Indices: 1237399--1237472 Score: 121
Period size: 35 Copynumber: 2.1 Consensus size: 35
1237389 AATCTGACAT
* *
1237399 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
*
1237434 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
1237469 AATT
1 AATT
1237473 AAGGACTGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.35, C:0.01, G:0.23, T:0.41
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:1239977 original size:60 final size:61
Alignment explanation
Indices: 1239877--1240044 Score: 166
Period size: 60 Copynumber: 2.8 Consensus size: 61
1239867 TATATGTTTG
* * * ** * *
1239877 GGATGAAATTGGAATGTTCAAAAAGTTTGGA-GACCGATTTAGAATGA-AGCTCATAGTTT-G
1 GGATGAAATTAGAATATTC-AAAAGTTTAGAGGACTAATTTAGAATGATA-CTCATAATTTAA
*
1239937 GAGATGAAATTTA-AATATTCAAAAGTTTA-AGGACTAATTTAGAATGATATTCATAATTTAA
1 G-GATGAAA-TTAGAATATTCAAAAGTTTAGAGGACTAATTTAGAATGATACTCATAATTTAA
* * *
1239998 GGATGAAATTAGAATATTTAAAAGTTTAGGGGACTAATTTAAAATGA
1 GGATGAAATTAGAATATTCAAAAGTTTAGAGGACTAATTTAGAATGA
1240045 GGATATACTT
Statistics
Matches: 90, Mismatches: 11, Indels: 13
0.79 0.10 0.11
Matches are distributed among these distances:
59 4 0.04
60 53 0.59
61 31 0.34
62 2 0.02
ACGTcount: A:0.42, C:0.05, G:0.20, T:0.33
Consensus pattern (61 bp):
GGATGAAATTAGAATATTCAAAAGTTTAGAGGACTAATTTAGAATGATACTCATAATTTAA
Found at i:1240010 original size:31 final size:32
Alignment explanation
Indices: 1239951--1240044 Score: 90
Period size: 31 Copynumber: 3.0 Consensus size: 32
1239941 TGAAATTTAA
*
1239951 ATATTCAAAAGTTTAAGGACTAATTTAGAATG
1 ATATTCAAAAGTTTAAGGACTAAATTAGAATG
*
1239983 ATATTCATAA-TTTAAGGA-TGAAATTAGAAT-
1 ATATTCAAAAGTTTAAGGACT-AAATTAGAATG
* * *
1240013 AT-TT-AAAAGTTTAGGGGACTAATTTAAAATG
1 ATATTCAAAAGTTTA-AGGACTAAATTAGAATG
1240044 A
1 A
1240045 GGATATACTT
Statistics
Matches: 51, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
28 3 0.06
29 6 0.12
30 14 0.27
31 19 0.37
32 9 0.18
ACGTcount: A:0.45, C:0.04, G:0.16, T:0.35
Consensus pattern (32 bp):
ATATTCAAAAGTTTAAGGACTAAATTAGAATG
Found at i:1254747 original size:31 final size:29
Alignment explanation
Indices: 1254682--1254768 Score: 102
Period size: 31 Copynumber: 2.9 Consensus size: 29
1254672 AAACTATATA
* * *
1254682 TTTAGTACTTAAATTATTATTTTTTTTGT
1 TTTAGTACTTAAACTATCATTTTTTTCGT
1254711 TTTAGTACTTAAACTATCAGTTTTCTTTCGT
1 TTTAGTACTTAAACTATCA-TTTT-TTTCGT
* * *
1254742 TTTAGTACCTAAACTTTCATTTATTTC
1 TTTAGTACTTAAACTATCATTTTTTTC
1254769 AAAATCATAC
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
29 21 0.42
30 7 0.14
31 22 0.44
ACGTcount: A:0.24, C:0.13, G:0.07, T:0.56
Consensus pattern (29 bp):
TTTAGTACTTAAACTATCATTTTTTTCGT
Found at i:1260455 original size:30 final size:30
Alignment explanation
Indices: 1260419--1260555 Score: 92
Period size: 30 Copynumber: 4.7 Consensus size: 30
1260409 AGATGTTGCT
1260419 GCCGCTGAAGTTCCAGCTGCTGCTGCTGCC
1 GCCGCTGAAGTTCCAGCTGCTGCTGCTGCC
* * *
1260449 GCCGCTGAAGTTCCCGCTG-TAGTTCCAGCTGCA
1 GCCGCTGAAGTTCCAGCTGCT-G---CTGCTGCC
* * *
1260482 ACCTCTGATGTTCCA---GCTGCTGCT---
1 GCCGCTGAAGTTCCAGCTGCTGCTGCTGCC
* *
1260506 GCCACTGAAGTTCCAAG-TGCTGGTGCTGCC
1 GCCGCTGAAGTTCC-AGCTGCTGCTGCTGCC
*
1260536 GCCGCTGAAGTTCCAACTGC
1 GCCGCTGAAGTTCCAGCTGC
1260556 CACTCCTGTT
Statistics
Matches: 81, Mismatches: 14, Indels: 24
0.68 0.12 0.20
Matches are distributed among these distances:
24 11 0.14
25 1 0.01
27 12 0.15
29 2 0.02
30 37 0.46
31 1 0.01
33 17 0.21
ACGTcount: A:0.15, C:0.34, G:0.27, T:0.25
Consensus pattern (30 bp):
GCCGCTGAAGTTCCAGCTGCTGCTGCTGCC
Found at i:1265164 original size:46 final size:43
Alignment explanation
Indices: 1265109--1265210 Score: 159
Period size: 46 Copynumber: 2.3 Consensus size: 43
1265099 TATCACGCTG
* *
1265109 GTTATATTTTGGTCAGTTAACTATTGTTTTCAAAATCATCACTAGT
1 GTTAAATTTTGGTCAGTCAACTATTGTTTTCAAAATCAT---TAGT
1265155 GTTAAATTTTGGTCAGTCAACTATTGTTTTCAAAATCATTAGT
1 GTTAAATTTTGGTCAGTCAACTATTGTTTTCAAAATCATTAGT
1265198 GTTAAATTTTGGT
1 GTTAAATTTTGGT
1265211 TACGTTGTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
43 17 0.31
46 37 0.69
ACGTcount: A:0.28, C:0.11, G:0.15, T:0.46
Consensus pattern (43 bp):
GTTAAATTTTGGTCAGTCAACTATTGTTTTCAAAATCATTAGT
Found at i:1265238 original size:34 final size:35
Alignment explanation
Indices: 1265178--1265250 Score: 121
Period size: 34 Copynumber: 2.1 Consensus size: 35
1265168 CAGTCAACTA
1265178 TTGTTTTCAAAATCATTAGTGTTAAATTTTGGTTACG
1 TTGTTTTCAAAATC--TAGTGTTAAATTTTGGTTACG
1265215 TTGTTTTCAAAATC-AGTGTTAAATTTTGGTTACG
1 TTGTTTTCAAAATCTAGTGTTAAATTTTGGTTACG
1265249 TT
1 TT
1265251 TTGGTAACCT
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
34 22 0.61
37 14 0.39
ACGTcount: A:0.26, C:0.08, G:0.16, T:0.49
Consensus pattern (35 bp):
TTGTTTTCAAAATCTAGTGTTAAATTTTGGTTACG
Found at i:1265738 original size:20 final size:20
Alignment explanation
Indices: 1265713--1265791 Score: 122
Period size: 20 Copynumber: 4.0 Consensus size: 20
1265703 CAATGCGATA
*
1265713 CTGACTTTCGCAACGTGATT
1 CTGACTTTCGCAACGAGATT
*
1265733 CTGACTTTCGCAACGCGATT
1 CTGACTTTCGCAACGAGATT
1265753 CTGACTTTCGCAACGAGATT
1 CTGACTTTCGCAACGAGATT
* *
1265773 CTGACTATCGCAATGAGAT
1 CTGACTTTCGCAACGAGAT
1265792 AATACAAAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.30
Consensus pattern (20 bp):
CTGACTTTCGCAACGAGATT
Found at i:1266337 original size:19 final size:16
Alignment explanation
Indices: 1266296--1266354 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 16
1266286 AACGAGAAAA
1266296 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
1266312 TCG--TTGCGATTTTC
1 TCGCATTGCGATTTTC
1266326 ATTTCGCATTGCGA--TTC
1 ---TCGCATTGCGATTTTC
*
1266343 TCTCATTGCGAT
1 TCGCATTGCGAT
1266355 AATCAGTTTC
Statistics
Matches: 36, Mismatches: 1, Indels: 13
0.72 0.02 0.26
Matches are distributed among these distances:
14 21 0.58
16 3 0.08
17 6 0.17
19 6 0.17
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.44
Consensus pattern (16 bp):
TCGCATTGCGATTTTC
Found at i:1267980 original size:41 final size:42
Alignment explanation
Indices: 1267926--1268017 Score: 132
Period size: 42 Copynumber: 2.2 Consensus size: 42
1267916 CCTCTTCAAC
* *
1267926 GATGACAGTGGCCTCTTGAACG-GTGGGGGGGACTCTTGAGA
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGA
* * *
1267967 GATGATAGGGGCCTCTTGAACGATTGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGA
1268009 GATGACAGG
1 GATGACAGG
1268018 TGAGTTGGGC
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
41 20 0.45
42 24 0.55
ACGTcount: A:0.22, C:0.15, G:0.41, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGAGTGGAGGGGACTCTTGAGA
Found at i:1267997 original size:21 final size:20
Alignment explanation
Indices: 1267909--1268006 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
1267899 TGGAATGGTG
* *
1267909 GGAGGGACCTCTTCAACGAT
1 GGAGGGGCCTCTTGAACGAT
* * *
1267929 GACAGTGGCCTCTTGAACGGT
1 G-GAGGGGCCTCTTGAACGAT
* *
1267950 GGGGGGGACTCTTGAGA-GAT
1 GGAGGGGCCTCTTGA-ACGAT
*
1267970 GATAGGGGCCTCTTGAACGATT
1 G-GAGGGGCCTCTTGAACGA-T
*
1267992 GGAGGGGACTCTTGA
1 GGAGGGGCCTCTTGA
1268007 GGGATGACAG
Statistics
Matches: 58, Mismatches: 15, Indels: 9
0.71 0.18 0.11
Matches are distributed among these distances:
20 15 0.26
21 41 0.71
22 2 0.03
ACGTcount: A:0.21, C:0.18, G:0.38, T:0.22
Consensus pattern (20 bp):
GGAGGGGCCTCTTGAACGAT
Found at i:1268380 original size:20 final size:20
Alignment explanation
Indices: 1268355--1268407 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
1268345 GAATAATAGT
*
1268355 TTACTTTCACAACACGAAAC
1 TTACTTTCACAACACGAAAA
* *
1268375 TTACTTTCGCAACGCGAAAA
1 TTACTTTCACAACACGAAAA
* *
1268395 TGACTATCACAAC
1 TTACTTTCACAAC
1268408 GCGGAAATGG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.38, C:0.28, G:0.09, T:0.25
Consensus pattern (20 bp):
TTACTTTCACAACACGAAAA
Found at i:1268408 original size:20 final size:20
Alignment explanation
Indices: 1268361--1268430 Score: 68
Period size: 20 Copynumber: 3.5 Consensus size: 20
1268351 TAGTTTACTT
* * * *
1268361 TCACAACACGAAACTTACTT
1 TCACAACGCGAAAATGACTA
*
1268381 TCGCAACGCGAAAATGACTA
1 TCACAACGCGAAAATGACTA
* *
1268401 TCACAACGCGGAAATGGCTA
1 TCACAACGCGAAAATGACTA
*
1268421 TCGCAACGCG
1 TCACAACGCG
1268431 GAAACAAAAT
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.36, C:0.29, G:0.19, T:0.17
Consensus pattern (20 bp):
TCACAACGCGAAAATGACTA
Found at i:1268431 original size:20 final size:20
Alignment explanation
Indices: 1268381--1268434 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
1268371 AAACTTACTT
*
1268381 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
* *
1268401 TCACAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
1268421 TCGCAACGCGGAAA
1 TCGCAACGCGGAAA
1268435 CAAAATCGCA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.37, C:0.26, G:0.24, T:0.13
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:1268444 original size:19 final size:18
Alignment explanation
Indices: 1268420--1268479 Score: 75
Period size: 19 Copynumber: 3.2 Consensus size: 18
1268410 GGAAATGGCT
1268420 ATCGCAACGCGGAAACAAA
1 ATCGCAACGC-GAAACAAA
* *
1268439 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAA-CAAA
1268458 ATCGCAACGCGAAACACAA
1 ATCGCAACGCGAAACA-AA
1268477 ATC
1 ATC
1268480 ACATTGCGAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
18 5 0.14
19 30 0.86
ACGTcount: A:0.47, C:0.25, G:0.18, T:0.10
Consensus pattern (18 bp):
ATCGCAACGCGAAACAAA
Found at i:1268505 original size:19 final size:19
Alignment explanation
Indices: 1268483--1268565 Score: 87
Period size: 19 Copynumber: 4.3 Consensus size: 19
1268473 ACAAATCACA
1268483 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCG
* *
1268502 TTGCGATTTTCATTTCACA
1 TTGCGATTTTCATTTCGCG
*
1268521 TTGCGATTTT-GTTTCCGCG
1 TTGCGATTTTCATTT-CGCG
** *
1268540 TTGCGATAGTCATTTTCGTG
1 TTGCGATTTTCA-TTTCGCG
1268560 TTGCGA
1 TTGCGA
1268566 AAGTAAACTA
Statistics
Matches: 52, Mismatches: 9, Indels: 5
0.79 0.14 0.08
Matches are distributed among these distances:
18 3 0.06
19 37 0.71
20 9 0.17
21 3 0.06
ACGTcount: A:0.13, C:0.19, G:0.22, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCG
Found at i:1268553 original size:38 final size:38
Alignment explanation
Indices: 1268478--1268554 Score: 111
Period size: 38 Copynumber: 2.0 Consensus size: 38
1268468 GAAACACAAA
**
1268478 TCACATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCACATTGCGATTTTCATTTCGCGTTGCGATAGTCATT
*
1268516 TCACATTGCGATTTT-GTTTCCGCGTTGCGATAGTCATT
1 TCACATTGCGATTTTCATTT-CGCGTTGCGATAGTCATT
1268554 T
1 T
1268555 TCGTGTTGCG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
37 3 0.09
38 32 0.91
ACGTcount: A:0.16, C:0.21, G:0.18, T:0.45
Consensus pattern (38 bp):
TCACATTGCGATTTTCATTTCGCGTTGCGATAGTCATT
Found at i:1269121 original size:18 final size:18
Alignment explanation
Indices: 1269098--1269145 Score: 87
Period size: 18 Copynumber: 2.7 Consensus size: 18
1269088 TCGGTCGATC
1269098 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
*
1269116 AGGTGATAGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
1269134 AGGTGATGGCTC
1 AGGTGATGGCTC
1269146 CCGAAGTGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.15, C:0.12, G:0.46, T:0.27
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:1270492 original size:20 final size:20
Alignment explanation
Indices: 1270467--1270508 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1270457 ATAGTTTATT
1270467 AAAATGAAAATCGCAACACG
1 AAAATGAAAATCGCAACACG
** *
1270487 AAAATGACTATCGCAACGCG
1 AAAATGAAAATCGCAACACG
1270507 AA
1 AA
1270509 TTTGACTATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.50, C:0.21, G:0.17, T:0.12
Consensus pattern (20 bp):
AAAATGAAAATCGCAACACG
Found at i:1270514 original size:20 final size:20
Alignment explanation
Indices: 1270476--1270524 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
1270466 TAAAATGAAA
*
1270476 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
1270496 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
1270516 ATCGCAACG
1 ATCGCAACG
1270525 AGAGAATCGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:1270829 original size:22 final size:22
Alignment explanation
Indices: 1270801--1270844 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1270791 GATGGATATA
1270801 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
1270823 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
1270845 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:1271061 original size:20 final size:20
Alignment explanation
Indices: 1271038--1271104 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
1271028 ATTATCTCGA
*
1271038 TGCGAAAGTCAGTATCGCAT
1 TGCGATAGTCAGTATCGCAT
* * *
1271058 TGCGATTTTGT-ATTATCGCGT
1 TGCGA--TAGTCAGTATCGCAT
1271079 TGCGATAGTCAGTATCGCAT
1 TGCGATAGTCAGTATCGCAT
1271099 TGCGAT
1 TGCGAT
1271105 TTTCCAAATT
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
19 3 0.08
20 19 0.51
21 13 0.35
22 2 0.05
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.34
Consensus pattern (20 bp):
TGCGATAGTCAGTATCGCAT
Found at i:1271070 original size:41 final size:41
Alignment explanation
Indices: 1271010--1271107 Score: 160
Period size: 41 Copynumber: 2.4 Consensus size: 41
1271000 CGCTTTAAAA
* *
1271010 ATCGCATTGCGATTATGTATTATCTCGATGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCGATGCGAAAGTCAGT
* *
1271051 ATCGCATTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCGATGCGAAAGTCAGT
1271092 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
1271108 CCAAATTCGC
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.38
Consensus pattern (41 bp):
ATCGCATTGCGATTTTGTATTATCGCGATGCGAAAGTCAGT
Found at i:1271075 original size:21 final size:22
Alignment explanation
Indices: 1271045--1271107 Score: 78
Period size: 20 Copynumber: 3.0 Consensus size: 22
1271035 CGATGCGAAA
1271045 GTCAGTATCGCATTGCGATTTT
1 GTCAGTATCGCATTGCGATTTT
* * *
1271067 GT-ATTATCGCGTTGCGA--TA
1 GTCAGTATCGCATTGCGATTTT
1271086 GTCAGTATCGCATTGCGATTTT
1 GTCAGTATCGCATTGCGATTTT
1271108 CCAAATTCGC
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
19 3 0.09
20 13 0.41
21 13 0.41
22 3 0.09
ACGTcount: A:0.19, C:0.17, G:0.24, T:0.40
Consensus pattern (22 bp):
GTCAGTATCGCATTGCGATTTT
Found at i:1271123 original size:41 final size:41
Alignment explanation
Indices: 1271038--1271125 Score: 115
Period size: 41 Copynumber: 2.1 Consensus size: 41
1271028 ATTATCTCGA
* ** * *
1271038 TGCGAAAGTCAGTATCGCATTGCGATTTTGTATTATCGCGT
1 TGCGATAGTCAGTATCGCATTGCGATTTTCAAATATCGCAT
1271079 TGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT-TCGCAT
1 TGCGATAGTCAGTATCGCATTGCGATTTT-CAAATATCGCAT
1271120 TGCGAT
1 TGCGAT
1271126 TTACTTATTC
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
41 39 0.95
42 2 0.05
ACGTcount: A:0.23, C:0.19, G:0.23, T:0.35
Consensus pattern (41 bp):
TGCGATAGTCAGTATCGCATTGCGATTTTCAAATATCGCAT
Found at i:1271137 original size:20 final size:21
Alignment explanation
Indices: 1271093--1271144 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1271083 ATAGTCAGTA
*
1271093 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
1271114 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
1271134 TCGCATTGCGA
1 TCGCATTGCGA
1271145 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:1271165 original size:21 final size:20
Alignment explanation
Indices: 1271141--1271186 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
1271131 TATTCGCATT
1271141 GCGAATTGGGAAAATCGCAAC
1 GCGAATT-GGAAAATCGCAAC
*
1271162 GCGAAATTGGAAAATCGCATC
1 GCG-AATTGGAAAATCGCAAC
1271183 GCGA
1 GCGA
1271187 TAGTCATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 1 0.04
21 18 0.78
22 4 0.17
ACGTcount: A:0.37, C:0.20, G:0.28, T:0.15
Consensus pattern (20 bp):
GCGAATTGGAAAATCGCAAC
Found at i:1277734 original size:73 final size:73
Alignment explanation
Indices: 1277644--1277793 Score: 273
Period size: 73 Copynumber: 2.1 Consensus size: 73
1277634 AAACCTCCTA
* *
1277644 ATTATTCTAATTAAGGAATTAAACTAACCCATATAAAATTTAAGATTTTATCTAAGTCAAGAGTA
1 ATTATTCTAATTAAGGAATTAAACTAACCAATATAAAATTTAAGACTTTATCTAAGTCAAGAGTA
1277709 AATTATTT
66 AATTATTT
*
1277717 ATTATTCTAATTAAGGAATTAAACTAACCAATATAAAATTTAAGACTTTATTTAAGTCAAGAGTA
1 ATTATTCTAATTAAGGAATTAAACTAACCAATATAAAATTTAAGACTTTATCTAAGTCAAGAGTA
1277782 AATTATTT
66 AATTATTT
1277790 ATTA
1 ATTA
1277794 AAGATCTAAT
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 74 1.00
ACGTcount: A:0.45, C:0.09, G:0.08, T:0.39
Consensus pattern (73 bp):
ATTATTCTAATTAAGGAATTAAACTAACCAATATAAAATTTAAGACTTTATCTAAGTCAAGAGTA
AATTATTT
Found at i:1278308 original size:16 final size:16
Alignment explanation
Indices: 1278287--1278327 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
1278277 TCAGAGCTTC
*
1278287 TGAATCATTCAGCATT
1 TGAATCATTCAACATT
*
1278303 TGAATCATTCAATATT
1 TGAATCATTCAACATT
1278319 TGAATCATT
1 TGAATCATT
1278328 TATCGCTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (16 bp):
TGAATCATTCAACATT
Found at i:1282055 original size:10 final size:10
Alignment explanation
Indices: 1282036--1282065 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1282026 AATTTAATTC
1282036 TTAATTCTTT
1 TTAATTCTTT
*
1282046 TTAATCCTTT
1 TTAATTCTTT
1282056 TTAATTCTTT
1 TTAATTCTTT
1282066 AATTTAATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.20, C:0.13, G:0.00, T:0.67
Consensus pattern (10 bp):
TTAATTCTTT
Found at i:1282073 original size:13 final size:12
Alignment explanation
Indices: 1282036--1282083 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 12
1282026 AATTTAATTC
1282036 TTAATTCTT--T
1 TTAATTCTTAAT
*
1282046 TTAATCCTT--T
1 TTAATTCTTAAT
1282056 TTAATTCTTTAAT
1 TTAATTC-TTAAT
1282069 TTAATTCTTAAT
1 TTAATTCTTAAT
1282081 TTA
1 TTA
1282084 GATAGTAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
10 15 0.45
11 2 0.06
12 8 0.24
13 8 0.24
ACGTcount: A:0.27, C:0.10, G:0.00, T:0.62
Consensus pattern (12 bp):
TTAATTCTTAAT
Found at i:1282079 original size:20 final size:19
Alignment explanation
Indices: 1282026--1282081 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 19
1282016 AGCATTTTAG
1282026 AATTTAATTCTTAATTCTT
1 AATTTAATTCTTAATTCTT
*
1282045 --TTTAATCCTTTTTAATTCTTT
1 AATTTAA---TTCTTAATTC-TT
1282066 AATTTAATTCTTAATT
1 AATTTAATTCTTAATT
1282082 TAGATAGTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 11
0.69 0.05 0.26
Matches are distributed among these distances:
17 5 0.17
20 17 0.59
21 2 0.07
23 5 0.17
ACGTcount: A:0.29, C:0.11, G:0.00, T:0.61
Consensus pattern (19 bp):
AATTTAATTCTTAATTCTT
Found at i:1295284 original size:22 final size:22
Alignment explanation
Indices: 1295241--1295284 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1295231 GAGGTTAAAA
* *
1295241 GAAATAATGTAAATATTAAGGT
1 GAAATAATGTAAAAAATAAGGT
1295263 GAAATAAT-TAAAAAATAGAGGT
1 GAAATAATGTAAAAAATA-AGGT
1295285 TTAAAATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.55, C:0.00, G:0.18, T:0.27
Consensus pattern (22 bp):
GAAATAATGTAAAAAATAAGGT
Found at i:1296930 original size:15 final size:16
Alignment explanation
Indices: 1296907--1296940 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1296897 AATATCTTTA
1296907 AATTAATAAATT-ATT
1 AATTAATAAATTAATT
*
1296922 AATTTATAAATTAATT
1 AATTAATAAATTAATT
1296938 AAT
1 AAT
1296941 ACACCTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AATTAATAAATTAATT
Found at i:1297816 original size:379 final size:379
Alignment explanation
Indices: 1297116--1298141 Score: 1798
Period size: 379 Copynumber: 2.7 Consensus size: 379
1297106 TGGACACATG
*
1297116 CCACCCTAAGTAGAGCATACATTTGCCACTAATTAGCATTGTTGTGATGCATGGTTTAAATTAAT
1 CCACCCTAAGTAGAGCATACATTTGCCACTAATTAGCATTGTTCTGATGCATGGTTTAAATTAAT
*
1297181 GACTAACATATGATTTTATGTTAAGAAAACGAATTTATAAAATTTAAAAGATAAAAATCAATTAT
66 GACGAACATATGATTTTATGTTAAGAAAACGAATTTATAAAATTTAAAAGATAAAAATCAATTAT
1297246 CAATAAAAAATATTTAAATTAAAATTTTAAATTTTTTAAAGGATAGACACTGCACTTTCACCTTT
131 CAAT-AAAAATATTTAAATTAAAATTTTAAATTTTTTAAAGGATAGACACTGCACTTTCACCTTT
*
1297311 TATCCATCCT-TGGTGAGGACTATATACAAGAGAGTCGACATGTTTTCTTTCATAAAATTTGTTC
195 TATCCAT-CTGTGGTGAGGACTATATACAAGAGAGTTGACATGTTTTCTTTCATAAAATTTGTTC
* *
1297375 CACACTAAAAATTTTAAATTAATATTCTAGAAAATTTTTACGTGTCACCTTTTATCTGACATTAT
259 CACACTAAAATTTTTAAATTAATATTCTAGAAAATTTTTACGTGCCACCTTTTATCTGACATTAT
1297440 TTTTTAGGTGTCTAGATTATTACAATAATTAAATTTGACTATTAGGTAACACGTGC
324 TTTTTAGGTGTCTAGATTATTACAATAATTAAATTTGACTATTAGGTAACACGTGC
1297496 CCACCCTAAGTAGAGCATACATTTGCCACTAATTAGCATTGTTCTGATGCATGGTTTAAATTAAT
1 CCACCCTAAGTAGAGCATACATTTGCCACTAATTAGCATTGTTCTGATGCATGGTTTAAATTAAT
*
1297561 TACGAACATATGATTTTATGTTAAGAAAACGAATTTATAAAATTTAAAAGATAAAAATCAATTAT
66 GACGAACATATGATTTTATGTTAAGAAAACGAATTTATAAAATTTAAAAGATAAAAATCAATTAT
* *
1297626 CAATAAAAATATTTAAATTAAATTTTTAAATTTTTTAAAGGATAGACACTGCACTTACACCTTTT
131 CAATAAAAATATTTAAATTAAAATTTTAAATTTTTTAAAGGATAGACACTGCACTTTCACCTTTT
*
1297691 ATCCATATGTGGTGAGGACTATATACAAGAGAGTTGACATGTTTTCTTTCATAAAATTTGTTCCA
196 ATCCATCTGTGGTGAGGACTATATACAAGAGAGTTGACATGTTTTCTTTCATAAAATTTGTTCCA
*
1297756 CACTAAAATTTTTAAATTAATATTCTATAAAATTTTTACGTGCCACCTTTTATCTGACATTATTT
261 CACTAAAATTTTTAAATTAATATTCTAGAAAATTTTTACGTGCCACCTTTTATCTGACATTATTT
* *
1297821 TTTAGGTGTCTGGATTATTACAATAGTTAAATTTGACTATTAGGTAACACGTGC
326 TTTAGGTGTCTAGATTATTACAATAATTAAATTTGACTATTAGGTAACACGTGC
*
1297875 CCACCCTAAGTAGAGCATACATTTGCCACTAATTAGCATTGTTCTGATTCATGGTTTAAATTAAT
1 CCACCCTAAGTAGAGCATACATTTGCCACTAATTAGCATTGTTCTGATGCATGGTTTAAATTAAT
*
1297940 GACGAACATATGATTTTATGTTAAGAAAATGAATTTATAAAATTTTAAAA-ATAAAAAATCAA-T
66 GACGAACATATGATTTTATGTTAAGAAAACGAATTTATAAAA-TTTAAAAGAT-AAAAATCAATT
* *
1298003 -T--A-AAAAATATTTAAATTAAAATTTTAAATTTTTTAAAAGATACACACTGC-CATTTCACCT
129 ATCAATAAAAATATTTAAATTAAAATTTTAAATTTTTTAAAGGATAGACACTGCAC-TTTCACCT
*
1298063 TTTATCCATCCGTGGTGAGGACTATATACAAGAGAGTTGACATGTTTTCTTTCATAAAATTTGTT
193 TTTATCCATCTGTGGTGAGGACTATATACAAGAGAGTTGACATGTTTTCTTTCATAAAATTTGTT
1298128 CCACACTAAAATTT
258 CCACACTAAAATTT
1298142 AAGAAATCCT
Statistics
Matches: 621, Mismatches: 21, Indels: 13
0.95 0.03 0.02
Matches are distributed among these distances:
374 1 0.00
375 129 0.21
376 1 0.00
378 2 0.00
379 341 0.55
380 147 0.24
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (379 bp):
CCACCCTAAGTAGAGCATACATTTGCCACTAATTAGCATTGTTCTGATGCATGGTTTAAATTAAT
GACGAACATATGATTTTATGTTAAGAAAACGAATTTATAAAATTTAAAAGATAAAAATCAATTAT
CAATAAAAATATTTAAATTAAAATTTTAAATTTTTTAAAGGATAGACACTGCACTTTCACCTTTT
ATCCATCTGTGGTGAGGACTATATACAAGAGAGTTGACATGTTTTCTTTCATAAAATTTGTTCCA
CACTAAAATTTTTAAATTAATATTCTAGAAAATTTTTACGTGCCACCTTTTATCTGACATTATTT
TTTAGGTGTCTAGATTATTACAATAATTAAATTTGACTATTAGGTAACACGTGC
Found at i:1298022 original size:28 final size:29
Alignment explanation
Indices: 1297960--1298023 Score: 69
Period size: 28 Copynumber: 2.2 Consensus size: 29
1297950 TGATTTTATG
* *
1297960 TTAAGAAAATGAATTTATAAAATTTTAAAA
1 TTAA-AAAATCAATTTAAAAAATTTTAAAA
*
1297990 ATAAAAAATCAA-TTAAAAAATATTT-AAA
1 TTAAAAAATCAATTTAAAAAAT-TTTAAAA
1298018 TTAAAA
1 TTAAAA
1298024 TTTTAAATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
28 16 0.55
29 10 0.34
30 3 0.10
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.33
Consensus pattern (29 bp):
TTAAAAAATCAATTTAAAAAATTTTAAAA
Found at i:1299492 original size:23 final size:24
Alignment explanation
Indices: 1299466--1299523 Score: 84
Period size: 23 Copynumber: 2.5 Consensus size: 24
1299456 GTATAAATGT
1299466 ACCGAAGTGCCA-CGTAGAATTGC
1 ACCGAAGTGCCAGCGTAGAATTGC
*
1299489 ACCGATGTG-CAGCGTAGAATTGC
1 ACCGAAGTGCCAGCGTAGAATTGC
*
1299512 ACCGTAGTGCCA
1 ACCGAAGTGCCA
1299524 TATAAGATTG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
22 2 0.07
23 26 0.87
24 2 0.07
ACGTcount: A:0.28, C:0.26, G:0.28, T:0.19
Consensus pattern (24 bp):
ACCGAAGTGCCAGCGTAGAATTGC
Found at i:1310680 original size:60 final size:59
Alignment explanation
Indices: 1310609--1310768 Score: 178
Period size: 60 Copynumber: 2.7 Consensus size: 59
1310599 AATATGTCCT
* * * * * *
1310609 CAAAATATGACTTTTATTTTAAATTGGTCCCTATA-TTTTTAAGTATTTTAATTTCATCCC
1 CAAACTATGACTTTAATTCTAAATTGG-CCCTAAACTTTTGAA-TATTTCAATTTCATCCC
* * * *
1310669 TAAACTATGACTATCATTCTAAATTAGCCCTTAAACTTTTGAATATTTCAATTTCATCCC
1 CAAACTATGACTTTAATTCTAAATTGGCCC-TAAACTTTTGAATATTTCAATTTCATCCC
*
1310729 CAAACTATGACATTAATTCTAAATTGGCCCTCAAACTTTT
1 CAAACTATGACTTTAATTCTAAATTGGCCCT-AAACTTTT
1310769 TGCACATTCC
Statistics
Matches: 83, Mismatches: 14, Indels: 6
0.81 0.14 0.06
Matches are distributed among these distances:
59 4 0.05
60 73 0.88
61 6 0.07
ACGTcount: A:0.33, C:0.19, G:0.06, T:0.42
Consensus pattern (59 bp):
CAAACTATGACTTTAATTCTAAATTGGCCCTAAACTTTTGAATATTTCAATTTCATCCC
Found at i:1310794 original size:60 final size:60
Alignment explanation
Indices: 1310658--1310796 Score: 174
Period size: 60 Copynumber: 2.3 Consensus size: 60
1310648 TAAGTATTTT
* * * *
1310658 AATTTCATCCCTAAACTATGACTATCATTCTAAATTAGCCCTTAAACTTTTGAATATTTC
1 AATTTCATCCCTAAACTATGACTATAATTCTAAATTAGCCCTCAAACTTTTGAACATTCC
* * *
1310718 AATTTCATCCCCAAACTATGAC-ATTAATTCTAAATTGGCCCTCAAACTTTTTGCACATTCC
1 AATTTCATCCCTAAACTATGACTA-TAATTCTAAATTAGCCCTCAAAC-TTTTGAACATTCC
*
1310779 AATTTTAT-CCTAAACTAT
1 AATTTCATCCCTAAACTAT
1310797 ATAAAGGCAT
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
59 1 0.01
60 50 0.74
61 17 0.25
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.38
Consensus pattern (60 bp):
AATTTCATCCCTAAACTATGACTATAATTCTAAATTAGCCCTCAAACTTTTGAACATTCC
Found at i:1311771 original size:41 final size:40
Alignment explanation
Indices: 1311708--1311786 Score: 115
Period size: 41 Copynumber: 1.9 Consensus size: 40
1311698 TCGAGCTATG
* *
1311708 TGTTGAAAATCAATGAAAGGAAAATGGTGGCTAACAAAAT
1 TGTTGAAAATCAATGAAAGGAAAACGGTGGCCAACAAAAT
1311748 TGTTGAAAAGTC-ATGGAAAGGAAAACGGTGGCCAACAAA
1 TGTTGAAAA-TCAAT-GAAAGGAAAACGGTGGCCAACAAA
1311787 TGTTGATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
40 11 0.31
41 24 0.69
ACGTcount: A:0.46, C:0.10, G:0.25, T:0.19
Consensus pattern (40 bp):
TGTTGAAAATCAATGAAAGGAAAACGGTGGCCAACAAAAT
Found at i:1313082 original size:15 final size:15
Alignment explanation
Indices: 1313058--1313089 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1313048 TGGCAGATCC
*
1313058 AAATCCAGAATGGGA
1 AAATCAAGAATGGGA
1313073 AAATCAAGAATGGGA
1 AAATCAAGAATGGGA
1313088 AA
1 AA
1313090 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.09, G:0.25, T:0.12
Consensus pattern (15 bp):
AAATCAAGAATGGGA
Found at i:1314512 original size:21 final size:21
Alignment explanation
Indices: 1314486--1314530 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1314476 GATTTCTGGG
* *
1314486 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
1314507 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
1314528 CAA
1 CAA
1314531 ACGAACAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:1315000 original size:56 final size:55
Alignment explanation
Indices: 1314910--1315020 Score: 213
Period size: 56 Copynumber: 2.0 Consensus size: 55
1314900 TATGCATGTA
1314910 TGTATGCTTGATTATATGATTGATCTGTTCTTTTATGTGTTAGGTGATAAAGTAT
1 TGTATGCTTGATTATATGATTGATCTGTTCTTTTATGTGTTAGGTGATAAAGTAT
1314965 TGTATGCTTGATTATATGGATTGATCTGTTCTTTTATGTGTTAGGTGATAAAGTAT
1 TGTATGCTTGATTATAT-GATTGATCTGTTCTTTTATGTGTTAGGTGATAAAGTAT
1315021 AAGTGATTAC
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
55 17 0.31
56 38 0.69
ACGTcount: A:0.23, C:0.05, G:0.23, T:0.49
Consensus pattern (55 bp):
TGTATGCTTGATTATATGATTGATCTGTTCTTTTATGTGTTAGGTGATAAAGTAT
Found at i:1315195 original size:18 final size:18
Alignment explanation
Indices: 1315172--1315206 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1315162 CTAGGAGATT
1315172 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
1315190 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
1315207 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:1316290 original size:147 final size:148
Alignment explanation
Indices: 1316092--1316404 Score: 526
Period size: 147 Copynumber: 2.1 Consensus size: 148
1316082 GAGTCGAGGG
*
1316092 TCTACGCGGTCCTTCGGGATATATATATATTCTTTGGAACATGTGTGAAGTCT-GATGAGACACA
1 TCTACGCGGTCCTTCGGGA-ATATATATATTCTTTGGAACATGTGTGAAGTCTGGA-AAGACACA
*
1316156 TA-TATGATCCCTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCAT
64 TACT-TGATCCCTAGCATATGTATATGATTCGTAAGGAATTCTATGTGGTCCTTATGGACATCAT
1316220 TATATGGCACTACGGTGCAAT
128 TATATGGCACTACGGTGCAAT
*
1316241 TCTACGCGGTCCTTCGGG-ATATGTATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACATA
1 TCTACGCGGTCCTTCGGGAATATATATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACATA
*
1316305 CTTGATCCCTAGTATATGTATATGATTCGTAAGGAATTCTATGTGGTCCTTATGGACATCATTAT
66 CTTGATCCCTAGCATATGTATATGATTCGTAAGGAATTCTATGTGGTCCTTATGGACATCATTAT
1316370 ATGGCACTACGGTGCAAT
131 ATGGCACTACGGTGCAAT
1316388 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
1316405 TGCAATTATA
Statistics
Matches: 157, Mismatches: 4, Indels: 8
0.93 0.02 0.05
Matches are distributed among these distances:
146 1 0.01
147 135 0.86
148 3 0.02
149 18 0.11
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (148 bp):
TCTACGCGGTCCTTCGGGAATATATATATTCTTTGGAACATGTGTGAAGTCTGGAAAGACACATA
CTTGATCCCTAGCATATGTATATGATTCGTAAGGAATTCTATGTGGTCCTTATGGACATCATTAT
ATGGCACTACGGTGCAAT
Found at i:1316405 original size:23 final size:23
Alignment explanation
Indices: 1316372--1316416 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
1316362 ATCATTATAT
*
1316372 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTATACGC
*
1316395 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTATACG
1316417 AGCTGTGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGC
Found at i:1318822 original size:64 final size:65
Alignment explanation
Indices: 1318754--1318914 Score: 213
Period size: 64 Copynumber: 2.5 Consensus size: 65
1318744 TTGTTTGAAG
* *
1318754 GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCATTAATAAGGA-AACATCGAATGCA-ATT
1 GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGTAATAA-GACAACATCGAATACATATT
1318817 A
65 A
* * *
1318818 GTGCATCGATGCATAAGGCA-TGCATCGATGCATCCCAGTAATAATACAACATCGAATACATTTT
1 GTGCATCGATGCATAA-GTAGTGCATCGATGCATCCCAGTAATAAGACAACATCGAATACATATT
1318882 A
65 A
* *
1318883 -TGCACCGATGCATCAGTAGTGCATCGATGCAT
1 GTGCATCGATGCATAAGTAGTGCATCGATGCAT
1318915 ACCTTCATTA
Statistics
Matches: 85, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
63 3 0.04
64 77 0.91
65 5 0.06
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (65 bp):
GTGCATCGATGCATAAGTAGTGCATCGATGCATCCCAGTAATAAGACAACATCGAATACATATTA
Found at i:1319834 original size:23 final size:23
Alignment explanation
Indices: 1319800--1319862 Score: 85
Period size: 23 Copynumber: 2.7 Consensus size: 23
1319790 ATTATTATAT
1319800 GGCACTAC-GGTGCAATTCTACGC
1 GGCACT-CTGGTGCAATTCTACGC
*
1319823 GGCACTCTGGTGCAATTCTACGT
1 GGCACTCTGGTGCAATTCTACGC
1319846 GGCACT-TCGGTGCAATT
1 GGCACTCT-GGTGCAATT
1319863 ATATGAGCTG
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
22 2 0.05
23 35 0.95
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (23 bp):
GGCACTCTGGTGCAATTCTACGC
Found at i:1335002 original size:31 final size:31
Alignment explanation
Indices: 1334966--1335025 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
1334956 AACTTAAAAG
*
1334966 AGTTTTGCAATAATGAAATTTAAATAATTTT
1 AGTTTTACAATAATGAAATTTAAATAATTTT
* *
1334997 AGTTTTATAATACTGAAATTTAAATAATT
1 AGTTTTACAATAATGAAATTTAAATAATT
1335026 CATACAACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.45
Consensus pattern (31 bp):
AGTTTTACAATAATGAAATTTAAATAATTTT
Found at i:1335074 original size:22 final size:22
Alignment explanation
Indices: 1335049--1335560 Score: 686
Period size: 22 Copynumber: 23.6 Consensus size: 22
1335039 TAATAATTTT
*
1335049 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
1335071 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
1335093 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
**
1335115 TTTTAAAATAAAT-TTTCCCATA
1 TTTTAAAATAAATCAAT-CCATA
1335137 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
1335159 TTTTAAAATAAAGCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
1335181 TTTTAAAATAAGTCAATCCATA
1 TTTTAAAATAAATCAATCCATA
*
1335203 TTTTAAAA-AAATCTATCCATA
1 TTTTAAAATAAATCAATCCATA
1335224 TTTTAAAATAAA--AATTTCCATA
1 TTTTAAAATAAATCAA--TCCATA
*
1335246 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
*** *
1335268 TTTTAAAATAAATTTTTTCATA
1 TTTTAAAATAAATCAATCCATA
1335290 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
**
1335312 TTTTAAAATAAAAT-TTTCCATA
1 TTTTAAAAT-AAATCAATCCATA
*
1335334 TTTTAAAATAAATCAATTCATA
1 TTTTAAAATAAATCAATCCATA
* *** *
1335356 TTTTAAAATAATTTTTTTCATA
1 TTTTAAAATAAATCAATCCATA
1335378 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
1335400 TTTTAAAATAAAT---TCCATA
1 TTTTAAAATAAATCAATCCATA
1335419 -TTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
** *
1335440 -TTTAAAATAAAT-TTTTCATA
1 TTTTAAAATAAATCAATCCATA
*
1335460 TTTAAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
1335482 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
1335504 TTTTAAAATAAATCAATCCATA
1 TTTTAAAATAAATCAATCCATA
**
1335526 TTTTAAAATAAATCAATATATA
1 TTTTAAAATAAATCAATCCATA
1335548 TTTTAAAATAAAT
1 TTTTAAAATAAAT
1335561 TTTAAAATAG
Statistics
Matches: 433, Mismatches: 43, Indels: 28
0.86 0.09 0.06
Matches are distributed among these distances:
18 12 0.03
19 6 0.01
20 6 0.01
21 53 0.12
22 349 0.81
23 5 0.01
24 2 0.00
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTTAAAATAAATCAATCCATA
Found at i:1335577 original size:11 final size:12
Alignment explanation
Indices: 1335525--1335574 Score: 50
Period size: 12 Copynumber: 4.3 Consensus size: 12
1335515 ATCAATCCAT
1335525 ATTTTAAAATAA
1 ATTTTAAAATAA
* * *
1335537 A--TCAATATAT
1 ATTTTAAAATAA
1335547 ATTTTAAAATAA
1 ATTTTAAAATAA
*
1335559 ATTTTAAAATAG
1 ATTTTAAAATAA
1335571 ATTT
1 ATTT
1335575 AAATGATTTT
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
10 7 0.24
12 22 0.76
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (12 bp):
ATTTTAAAATAA
Found at i:1335833 original size:13 final size:13
Alignment explanation
Indices: 1335815--1335855 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
1335805 ATTGTTTTTA
1335815 TTATTATAATTAT
1 TTATTATAATTAT
*
1335828 TTATTATTATTAT
1 TTATTATAATTAT
1335841 TTA--ATAATT-T
1 TTATTATAATTAT
1335851 TTATT
1 TTATT
1335856 GATTTTCAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
10 4 0.17
11 5 0.21
13 15 0.62
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
TTATTATAATTAT
Found at i:1335860 original size:10 final size:9
Alignment explanation
Indices: 1335800--1335861 Score: 52
Period size: 9 Copynumber: 6.4 Consensus size: 9
1335790 CCATTTTTCT
*
1335800 TTTTTATTG
1 TTTTTATTA
1335809 TTTTTATTA
1 TTTTTATTA
* *
1335818 TTATAATTA
1 TTTTTATTA
1335827 TTTATTATTA
1 TTT-TTATTA
*
1335837 TTATTTAATAA
1 TT-TTT-ATTA
1335848 TTTTTATTGA
1 TTTTTATT-A
1335858 TTTT
1 TTTT
1335862 CAGACCCAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
9 19 0.45
10 17 0.40
11 6 0.14
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.69
Consensus pattern (9 bp):
TTTTTATTA
Found at i:1338982 original size:36 final size:36
Alignment explanation
Indices: 1338933--1339002 Score: 124
Period size: 36 Copynumber: 1.9 Consensus size: 36
1338923 GCTATGCACA
1338933 CAAAGATCATGTTAGATTGATACCAAAAGTATTCCC
1 CAAAGATCATGTTAGATTGATACCAAAAGTATTCCC
1338969 CAAAGAT-ATTGTTAGATTGATACCAAAAGTATTC
1 CAAAGATCA-TGTTAGATTGATACCAAAAGTATTC
1339003 GACGGTAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
35 1 0.03
36 32 0.97
ACGTcount: A:0.40, C:0.16, G:0.14, T:0.30
Consensus pattern (36 bp):
CAAAGATCATGTTAGATTGATACCAAAAGTATTCCC
Found at i:1339531 original size:43 final size:43
Alignment explanation
Indices: 1339467--1339593 Score: 184
Period size: 43 Copynumber: 3.0 Consensus size: 43
1339457 GGCTTTAGAG
* * * *
1339467 AAGTTAAGAGTGAAAACTATCCCCTATATATAAAGTTTTGTTA
1 AAGTTAGGAGTGAAAGCTATCCCCTATATGTAAAGTTTTATTA
* * *
1339510 AAGTTAGGAGTGAAAGTTATCCGCTATATGTAAAGTTTTATTG
1 AAGTTAGGAGTGAAAGCTATCCCCTATATGTAAAGTTTTATTA
1339553 AAGTTAGGAGTGAAAGCTAT-CCCTATATGTAAAGTTTTATT
1 AAGTTAGGAGTGAAAGCTATCCCCTATATGTAAAGTTTTATT
1339594 TGATGTACCG
Statistics
Matches: 75, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
42 20 0.27
43 55 0.73
ACGTcount: A:0.35, C:0.09, G:0.19, T:0.36
Consensus pattern (43 bp):
AAGTTAGGAGTGAAAGCTATCCCCTATATGTAAAGTTTTATTA
Found at i:1339686 original size:6 final size:6
Alignment explanation
Indices: 1339671--1339716 Score: 56
Period size: 6 Copynumber: 7.5 Consensus size: 6
1339661 TTCATACATA
* * *
1339671 CATTTG CATTTT CATTTTG CATTTG CATTTG CATTTA CATTCG CAT
1 CATTTG CATTTG CA-TTTG CATTTG CATTTG CATTTG CATTTG CAT
1339717 CCTTGCTTAG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
6 29 0.85
7 5 0.15
ACGTcount: A:0.20, C:0.20, G:0.11, T:0.50
Consensus pattern (6 bp):
CATTTG
Found at i:1341835 original size:72 final size:72
Alignment explanation
Indices: 1341748--1341891 Score: 245
Period size: 72 Copynumber: 2.0 Consensus size: 72
1341738 ATACAATAAA
*
1341748 GCTTAAGTTGCCCCCCTAAAGCAATTGGTTAATCGCCCC-GACTTTATGGATAATATTCAGCTAG
1 GCTTAAGTTGCCCCCCTAAAGCAATTGGTTAATAGCCCCAG-CTTTATGGATAATATTCAGCTAG
1341812 TCTGTTAT
65 TCTGTTAT
* *
1341820 GCTTGAGTTGTCCCCCTAAAGCAATTGGTTAATAGCCCCAGCTTTATGGATAATATTCAGCTAGT
1 GCTTAAGTTGCCCCCCTAAAGCAATTGGTTAATAGCCCCAGCTTTATGGATAATATTCAGCTAGT
1341885 CTGTTAT
66 CTGTTAT
1341892 ACTATTATAT
Statistics
Matches: 68, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
72 67 0.99
73 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (72 bp):
GCTTAAGTTGCCCCCCTAAAGCAATTGGTTAATAGCCCCAGCTTTATGGATAATATTCAGCTAGT
CTGTTAT
Found at i:1341991 original size:13 final size:14
Alignment explanation
Indices: 1341969--1342008 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
1341959 TTCAAATAGC
1341969 AAAAAGAAGAAAAG
1 AAAAAGAAGAAAAG
1341983 AAAAA-AAGAAAAG
1 AAAAAGAAGAAAAG
1341996 -AAAAGAGAGAAAA
1 AAAAAGA-AGAAAA
1342009 AGAGAGGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 4 0.17
13 9 0.38
14 11 0.46
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (14 bp):
AAAAAGAAGAAAAG
Found at i:1343309 original size:54 final size:53
Alignment explanation
Indices: 1343183--1343342 Score: 214
Period size: 54 Copynumber: 3.0 Consensus size: 53
1343173 AGCTTCACTG
* * * * *
1343183 GCGAACATCTGTGCAAAAACCACAGGAAATTATGAATGTGTTGTCAAA-ATTT
1 GCGAACATCTGTGCAGAAGCCACAGAAAATGATGAATGTGTTGTCAAATTTTT
* * *
1343235 GCGAACGTCTGTGCAGAAGCCACAGAAAAAGATGAATATGTTGTCAAATCTTTT
1 GCGAACATCTGTGCAGAAGCCACAGAAAATGATGAATGTGTTGTCAAAT-TTTT
*
1343289 GCGAACATCTGTACAGAAGCCACAGAAAATGATGAATGTGTTGTCAAATGTTTT
1 GCGAACATCTGTGCAGAAGCCACAGAAAATGATGAATGTGTTGTCAAAT-TTTT
1343343 ATGAACCAGT
Statistics
Matches: 93, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
52 41 0.44
54 52 0.56
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (53 bp):
GCGAACATCTGTGCAGAAGCCACAGAAAATGATGAATGTGTTGTCAAATTTTT
Found at i:1343746 original size:22 final size:22
Alignment explanation
Indices: 1343712--1343774 Score: 81
Period size: 22 Copynumber: 2.9 Consensus size: 22
1343702 ACATCTACAT
*
1343712 TCTTTAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
* *
1343734 TCTTCAAATATGATATATTCTC
1 TCTTCAAAGATGATAGATTCTC
* *
1343756 TTTTCAAAGATGAAAGATT
1 TCTTCAAAGATGATAGATT
1343775 TATAGGATTT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.35, C:0.13, G:0.11, T:0.41
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:1344810 original size:217 final size:217
Alignment explanation
Indices: 1344420--1345038 Score: 970
Period size: 217 Copynumber: 2.9 Consensus size: 217
1344410 CTATTTCCCT
*
1344420 AGATGATAAAGCCTTCGGGTTATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTA
1 AGATGATAAAGCCTTCGGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTA
*
1344485 GAAACTAAGCCTTTGGGTGTTTACTAATTATCTCAAAAGAGCTATTAAAGGAAGCTAAGCCTAAT
66 GAAACTAAGCCTTTGGGGGTTTACTAATTATCTCAAAAGAGCTATTAAAGGAAGCTAAGCCTAAT
* * * * * *
1344550 AAAGGGGTTCATTGACAACCAAGAAACTAAACCTTCGGGGTTTCTTGATTTATAAATCCTTTAGG
131 AAAGGGGTTCATTGAAAACTAAGAAACTAAGCCTTCGGGGTTTCTTGATTTGTAAGTCCTTCAGG
1344615 CCATCTGTAAGCCTTTCGAGCA
196 CCATCTGTAAGCCTTTCGAGCA
*
1344637 AGATGATAAAGCCTTCGGGTCATCCATAAGATCTTCAGTGCAGGATGTTTTCAAATGAGATTTTA
1 AGATGATAAAGCCTTCGGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTA
*
1344702 GAAACTAAGCCTTTGGGGGTTTACTAATTATCTCAAAAGAGCTATTAAAGGAAGCTAAGCCTAAC
66 GAAACTAAGCCTTTGGGGGTTTACTAATTATCTCAAAAGAGCTATTAAAGGAAGCTAAGCCTAAT
* *
1344767 AAAGGGGTTC-TTGATAACTAAGAAACTAAGCCTTCGAGGGTTTCTTGATTTGTAAGT-CTTCGG
131 AAAGGGGTTCATTGAAAACTAAGAAACTAAGCCTTCG-GGGTTTCTTGATTTGTAAGTCCTTCAG
*
1344830 GCCATCTGTAAGCCTTTCGAGTA
195 GCCATCTGTAAGCCTTTCGAGCA
* * *
1344853 AGATGATAAATCCTT-GGGTCATCCATAAGACCTTCAATGTAGGATG-TTTCAAATGAGATTTTA
1 AGATGATAAAGCCTTCGGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTA
* *
1344916 GAAACTAAGCCTTTAGGGGTTTTCT-A--ATCTCAAAAGA--T-TGTAAAGGAAGCTAAGCCTAA
66 GAAACTAAGCCTTTGGGGGTTTACTAATTATCTCAAAAGAGCTAT-TAAAGGAAGCTAAGCCTAA
*
1344975 TAAAAGGGTTCATTGAAAACTAAGAAACTAAGCCTTCGGGGGTTTCTTGATTTGTAAGTCCTTC
130 TAAAGGGGTTCATTGAAAACTAAGAAACTAAGCCTTC-GGGGTTTCTTGATTTGTAAGTCCTTC
1345039 GGGTCATTCA
Statistics
Matches: 376, Mismatches: 21, Indels: 16
0.91 0.05 0.04
Matches are distributed among these distances:
208 1 0.00
209 29 0.08
210 44 0.12
211 16 0.04
213 1 0.00
214 40 0.11
215 28 0.07
216 63 0.17
217 154 0.41
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (217 bp):
AGATGATAAAGCCTTCGGGTCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGAGATTTTA
GAAACTAAGCCTTTGGGGGTTTACTAATTATCTCAAAAGAGCTATTAAAGGAAGCTAAGCCTAAT
AAAGGGGTTCATTGAAAACTAAGAAACTAAGCCTTCGGGGTTTCTTGATTTGTAAGTCCTTCAGG
CCATCTGTAAGCCTTTCGAGCA
Found at i:1346671 original size:24 final size:24
Alignment explanation
Indices: 1346582--1346704 Score: 137
Period size: 24 Copynumber: 5.3 Consensus size: 24
1346572 GATTTTCAAT
* *
1346582 TTGAATTCTGCTATGAT--ATGAC
1 TTGAATTCTGATCTGATACATGAC
*
1346604 CTGAATTCTGATCTGATAC-TGAC
1 TTGAATTCTGATCTGATACATGAC
*
1346627 ATGAATTCTGAT-TGATACATGAC
1 TTGAATTCTGATCTGATACATGAC
*
1346650 TTGGATTCTGATCTGATACATGAC
1 TTGAATTCTGATCTGATACATGAC
* * *
1346674 TTGGATTCTGATTTGATACTTGAC
1 TTGAATTCTGATCTGATACATGAC
*
1346698 CTGAATT
1 TTGAATT
1346705 ATGTTTTGAT
Statistics
Matches: 87, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
22 20 0.23
23 29 0.33
24 38 0.44
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.39
Consensus pattern (24 bp):
TTGAATTCTGATCTGATACATGAC
Found at i:1351504 original size:20 final size:20
Alignment explanation
Indices: 1351457--1351517 Score: 68
Period size: 20 Copynumber: 2.9 Consensus size: 20
1351447 ATTCCCCTGT
1351457 GGGGGAAATCGGTTCCCCTTCAA
1 GGGGG-AATCGGTT-CCC-TCAA
*
1351480 AGGGGAATCGGTTCCCTCAA
1 GGGGGAATCGGTTCCCTCAA
* *
1351500 GGGGGGATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
1351518 TGCACCAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 19 0.56
21 3 0.09
22 8 0.24
23 4 0.12
ACGTcount: A:0.20, C:0.26, G:0.33, T:0.21
Consensus pattern (20 bp):
GGGGGAATCGGTTCCCTCAA
Done.