Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001574.1 Hibiscus syriacus cultivar Beakdansim tig00003126_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: 1705968
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 6 of 7
Found at i:1114577 original size:22 final size:22
Alignment explanation
Indices: 1114549--1114596 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1114539 TCATCTCTCA
*
1114549 TTTTTTTCTCTTTTACTTT-TAT
1 TTTTTTTATCTTTTA-TTTATAT
*
1114571 TTTTTTTATTTTTTATTTATAT
1 TTTTTTTATCTTTTATTTATAT
1114593 TTTT
1 TTTT
1114597 CTATTTTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 3 0.13
22 20 0.87
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.81
Consensus pattern (22 bp):
TTTTTTTATCTTTTATTTATAT
Found at i:1114583 original size:21 final size:21
Alignment explanation
Indices: 1114548--1114610 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 21
1114538 ATCATCTCTC
*
1114548 ATTTTTTTCTCTTTTACTTTTAT
1 ATTTTTTTAT-TTTT-CTTTTAT
1114571 -TTTTTTTATTTTT-TATTTAT
1 ATTTTTTTATTTTTCT-TTTAT
*
1114591 ATTTTTCTATTTTTTCTTTT
1 ATTTTTTTA-TTTTTCTTTT
1114611 TCTGATAGCC
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
19 1 0.03
20 5 0.15
21 11 0.32
22 16 0.47
23 1 0.03
ACGTcount: A:0.13, C:0.08, G:0.00, T:0.79
Consensus pattern (21 bp):
ATTTTTTTATTTTTCTTTTAT
Found at i:1114589 original size:20 final size:21
Alignment explanation
Indices: 1114566--1114605 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1114556 CTCTTTTACT
*
1114566 TTTAT-TTTTTTTATTTTTTA
1 TTTATATTTTTCTATTTTTTA
1114586 TTTATATTTTTCTATTTTTT
1 TTTATATTTTTCTATTTTTT
1114606 CTTTTTCTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (21 bp):
TTTATATTTTTCTATTTTTTA
Found at i:1117428 original size:46 final size:46
Alignment explanation
Indices: 1117327--1117645 Score: 431
Period size: 46 Copynumber: 7.1 Consensus size: 46
1117317 GCATGTCCAA
* * *
1117327 TATTTTACCAATACACTTACTATTT-ATTTCATAAGCTCGTAAGCT
1 TATTTTACCAATATACTTACCATTTAATTCCATAAGCTCGTAAGCT
**
1117372 TATTTTACCAATATACTTACCATTTAATAACATAAGCTCGTAAGCT
1 TATTTTACCAATATACTTACCATTTAATTCCATAAGCTCGTAAGCT
* * * *
1117418 TATTTAACCAATATACTTACCAATTAATACCATAAGCTTGTAAGCT
1 TATTTTACCAATATACTTACCATTTAATTCCATAAGCTCGTAAGCT
*
1117464 TATTTTACC-AT-TACTTACCATTTAA-TCGTATAAGCTCGTAAGCT
1 TATTTTACCAATATACTTACCATTTAATTC-CATAAGCTCGTAAGCT
*
1117508 TATTTTACC-ATATACTTACCATTT-GTTCCATAAGCTCGTAAGCT
1 TATTTTACCAATATACTTACCATTTAATTCCATAAGCTCGTAAGCT
* *
1117552 TATTTTACCAATATACTTACCATTTAATTGCATAAGCTCATAAGCT
1 TATTTTACCAATATACTTACCATTTAATTCCATAAGCTCGTAAGCT
* *
1117598 TATTTTACC-ATATACTTGCCA-TT-ATTTCATAAGCTCGTAAGCT
1 TATTTTACCAATATACTTACCATTTAATTCCATAAGCTCGTAAGCT
1117641 TATTT
1 TATTT
1117646 GCATGTTTAC
Statistics
Matches: 247, Mismatches: 21, Indels: 14
0.88 0.07 0.05
Matches are distributed among these distances:
43 24 0.10
44 64 0.26
45 65 0.26
46 94 0.38
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (46 bp):
TATTTTACCAATATACTTACCATTTAATTCCATAAGCTCGTAAGCT
Found at i:1117502 original size:90 final size:89
Alignment explanation
Indices: 1117327--1117645 Score: 444
Period size: 90 Copynumber: 3.5 Consensus size: 89
1117317 GCATGTCCAA
* * *
1117327 TATTTTACCAATACACTTACTATTTATTTCATAAGCTCGTAAGCTTATTTTACCAATATACTTAC
1 TATTTTACC-ATATACTTACCA-TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTAC
*
1117392 CATTTAATAACATAAGCTCGTAAGCT
64 CATTTAATAGCATAAGCTCGTAAGCT
* * *
1117418 TATTTAACCAATATACTTACCAATTAATACCATAAGCTTGTAAGCTTATTTTACC-AT-TACTTA
1 TATTTTACC-ATATACTTACC-ATT-ATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTA
* *
1117481 CCATTTAATCGTATAAGCTCGTAAGCT
63 CCATTTAATAGCATAAGCTCGTAAGCT
*
1117508 TATTTTACCATATACTTACCATTTGTTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACC
1 TATTTTACCATATACTTACCA-TTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACC
* *
1117573 ATTTAATTGCATAAGCTCATAAGCT
65 ATTTAATAGCATAAGCTCGTAAGCT
* *
1117598 TATTTTACCATATACTTGCCATTATTTCATAAGCTCGTAAGCTTATTT
1 TATTTTACCATATACTTACCATTATTCCATAAGCTCGTAAGCTTATTT
1117646 GCATGTTTAC
Statistics
Matches: 204, Mismatches: 19, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
88 27 0.13
89 40 0.20
90 88 0.43
91 22 0.11
92 27 0.13
ACGTcount: A:0.32, C:0.20, G:0.08, T:0.40
Consensus pattern (89 bp):
TATTTTACCATATACTTACCATTATTCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCA
TTTAATAGCATAAGCTCGTAAGCT
Found at i:1120094 original size:7 final size:7
Alignment explanation
Indices: 1120080--1120203 Score: 85
Period size: 7 Copynumber: 16.9 Consensus size: 7
1120070 ATGGGTCAGC
1120080 AATAATA
1 AATAATA
*
1120087 ACTAATA
1 AATAATA
1120094 AATAATA
1 AATAATA
*
1120101 GTAATGATA
1 --AATAATA
1120110 AATAAT-
1 AATAATA
1120116 AATAAT-
1 AATAATA
1120122 AATAATA
1 AATAATA
1120129 AATAAATA
1 AAT-AATA
1120137 AATAATA
1 AATAATA
1120144 GTAATATATA
1 --AATA-ATA
1120154 TAAT-ATA
1 -AATAATA
1120161 ATATAAT-
1 A-ATAATA
1120168 AATAATA
1 AATAATA
**
1120175 CGTAATA
1 AATAATA
1120182 AATAATA
1 AATAATA
1120189 ATACTAATA
1 A-A-TAATA
*
1120198 TATAAT
1 AATAAT
1120204 GATATATAAT
Statistics
Matches: 96, Mismatches: 9, Indels: 24
0.74 0.07 0.19
Matches are distributed among these distances:
6 18 0.19
7 45 0.47
8 11 0.11
9 19 0.20
10 3 0.03
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.33
Consensus pattern (7 bp):
AATAATA
Found at i:1120113 original size:13 final size:13
Alignment explanation
Indices: 1120080--1120217 Score: 87
Period size: 13 Copynumber: 10.8 Consensus size: 13
1120070 ATGGGTCAGC
1120080 AATAATAACTAATA
1 AATAATAA-TAATA
*
1120094 AATAATAGTAAT-
1 AATAATAATAATA
*
1120106 GAT-A-AATAAT-
1 AATAATAATAATA
1120116 AATAATAATAATA
1 AATAATAATAATA
1120129 AATAAATAAATAAT-
1 AAT-AAT-AATAATA
*
1120143 AGTAAT-ATATATA
1 AATAATAATA-ATA
1120156 ATATAAT-ATAAT-
1 A-ATAATAATAATA
*
1120168 AATAATACGTAATA
1 AATAATA-ATAATA
*
1120182 AATAATAATACT-
1 AATAATAATAATA
*
1120194 AATATATAATGATA
1 AATA-ATAATAATA
*
1120208 TATAATAATA
1 AATAATAATA
1120218 TAGCATAATA
Statistics
Matches: 98, Mismatches: 13, Indels: 27
0.71 0.09 0.20
Matches are distributed among these distances:
10 7 0.07
11 10 0.10
12 15 0.15
13 31 0.32
14 29 0.30
15 6 0.06
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (13 bp):
AATAATAATAATA
Found at i:1120114 original size:4 final size:3
Alignment explanation
Indices: 1120080--1120217 Score: 102
Period size: 3 Copynumber: 43.3 Consensus size: 3
1120070 ATGGGTCAGC
* *
1120080 AAT AAT AACT AAT AAAT AAT AGT AAT GAT AAAT AAT AAT AAT AAT AAT
1 AAT AAT AA-T AAT -AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT
*
1120128 AAAT AAAT AAAT AAT AGT AAT -AT ATAT AAT -AT AAT -AT AAT AAT AAT
1 -AAT -AAT -AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
* * *
1120174 ACGT AAT AAAT AAT AAT ACT AAT ATAT AAT GAT ATAT AAT AAT A
1 A-AT AAT -AAT AAT AAT AAT AAT A-AT AAT AAT A-AT AAT AAT A
1120218 TAGCATAATA
Statistics
Matches: 111, Mismatches: 12, Indels: 24
0.76 0.08 0.16
Matches are distributed among these distances:
2 6 0.05
3 72 0.65
4 33 0.30
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:1120189 original size:23 final size:21
Alignment explanation
Indices: 1120080--1120219 Score: 116
Period size: 19 Copynumber: 6.7 Consensus size: 21
1120070 ATGGGTCAGC
1120080 AATAATAACTAATA-AAT-AAT
1 AATAATAA-TAATATAATAAAT
* *
1120100 AGTAATGATAA-ATAAT-AAT
1 AATAATAATAATATAATAAAT
1120119 AATAATAATAA-ATAAATAAAT
1 AATAATAATAATAT-AATAAAT
*
1120140 AATAGTAATATATATAATATAAT
1 AATAATAATA-ATATAATA-AAT
1120163 -ATAATAATAATACGTAATAAAT
1 AATAATAATAATA--TAATAAAT
*
1120185 AATAATACTAATAT-AT-AAT
1 AATAATAATAATATAATAAAT
*
1120204 GATATATAATAATATA
1 AATA-ATAATAATATA
1120220 GCATAATATT
Statistics
Matches: 100, Mismatches: 9, Indels: 21
0.77 0.07 0.16
Matches are distributed among these distances:
18 1 0.01
19 26 0.26
20 20 0.20
21 16 0.16
22 16 0.16
23 21 0.21
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.34
Consensus pattern (21 bp):
AATAATAATAATATAATAAAT
Found at i:1120227 original size:46 final size:43
Alignment explanation
Indices: 1120080--1120227 Score: 153
Period size: 46 Copynumber: 3.4 Consensus size: 43
1120070 ATGGGTCAGC
*
1120080 AATAATA-AC-TAATAAATAATAGTAATGATAAATAATA-ATAAT
1 AATAATATACATAATAAATAATAGTAAT-ATATATAATATAT-AT
1120122 AATAATA-A-ATAAATAAATAATAGTAATATATATAATATAATAT
1 AATAATATACAT-AATAAATAATAGTAATATATATAATAT-ATAT
* * *
1120165 AATAATAATACGTAATAAATAATAATACTAATATATAATGATATAT
1 AATAAT-ATACATAATAAATAATAGTAAT-ATATATAAT-ATATAT
1120211 AATAATATAGCATAATA
1 AATAATATA-CATAATA
1120228 TTATATAGAC
Statistics
Matches: 91, Mismatches: 5, Indels: 16
0.81 0.04 0.14
Matches are distributed among these distances:
42 18 0.20
43 24 0.26
44 3 0.03
45 18 0.20
46 26 0.29
47 2 0.02
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.33
Consensus pattern (43 bp):
AATAATATACATAATAAATAATAGTAATATATATAATATATAT
Found at i:1120757 original size:16 final size:16
Alignment explanation
Indices: 1120736--1120775 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
1120726 TCATAAAAAA
*
1120736 AACACCTCTAGCATGT
1 AACACCCCTAGCATGT
1120752 AACACCCCTAGCATGT
1 AACACCCCTAGCATGT
1120768 AACACCCC
1 AACACCCC
1120776 AATTTATAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.33, C:0.40, G:0.10, T:0.17
Consensus pattern (16 bp):
AACACCCCTAGCATGT
Found at i:1127328 original size:12 final size:12
Alignment explanation
Indices: 1127311--1127345 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
1127301 AGATGTTTTC
1127311 TCTAATTTCTGT
1 TCTAATTTCTGT
1127323 TCTAATTTCTGT
1 TCTAATTTCTGT
*
1127335 TCTGATTTCTG
1 TCTAATTTCTG
1127346 ATATCTCTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.14, C:0.17, G:0.11, T:0.57
Consensus pattern (12 bp):
TCTAATTTCTGT
Found at i:1129657 original size:21 final size:21
Alignment explanation
Indices: 1129627--1129699 Score: 92
Period size: 21 Copynumber: 3.5 Consensus size: 21
1129617 ATATAATCAA
* *
1129627 ATTTAGGGTTTAAGGTTTATG
1 ATTTAGGGTTTAAAGTTTAGG
*
1129648 ATTTAAGGTTTAAAGTTTAGG
1 ATTTAGGGTTTAAAGTTTAGG
* *
1129669 ATTTAGGGTTTAGATTTTAGG
1 ATTTAGGGTTTAAAGTTTAGG
*
1129690 GTTTAGGGTT
1 ATTTAGGGTT
1129700 CATTACAGAT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 45 1.00
ACGTcount: A:0.25, C:0.00, G:0.29, T:0.47
Consensus pattern (21 bp):
ATTTAGGGTTTAAAGTTTAGG
Found at i:1129681 original size:7 final size:7
Alignment explanation
Indices: 1129628--1129699 Score: 63
Period size: 7 Copynumber: 10.3 Consensus size: 7
1129618 TATAATCAAA
1129628 TTTAGGG
1 TTTAGGG
*
1129635 TTTAAGG
1 TTTAGGG
* *
1129642 TTTATGA
1 TTTAGGG
*
1129649 TTTAAGG
1 TTTAGGG
**
1129656 TTTAAAG
1 TTTAGGG
*
1129663 TTTAGGA
1 TTTAGGG
1129670 TTTAGGG
1 TTTAGGG
**
1129677 TTTAGAT
1 TTTAGGG
1129684 TTTAGGG
1 TTTAGGG
1129691 TTTAGGG
1 TTTAGGG
1129698 TT
1 TT
1129700 CATTACAGAT
Statistics
Matches: 51, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 51 1.00
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.47
Consensus pattern (7 bp):
TTTAGGG
Found at i:1139511 original size:22 final size:22
Alignment explanation
Indices: 1139486--1139558 Score: 101
Period size: 22 Copynumber: 3.3 Consensus size: 22
1139476 GAATCGATAC
*
1139486 CCCCCTTGAAGGGGAACTGATT
1 CCCCCTTGAAGGGGAACCGATT
1139508 CCCCCTTTGAAGGGGAACCGATT
1 CCCCC-TTGAAGGGGAACCGATT
* * *
1139531 CCCCCTTGTAGGGGAATCGATA
1 CCCCCTTGAAGGGGAACCGATT
1139553 CCCCCT
1 CCCCCT
1139559 AGAGGTTCTG
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
22 25 0.54
23 21 0.46
ACGTcount: A:0.21, C:0.33, G:0.25, T:0.22
Consensus pattern (22 bp):
CCCCCTTGAAGGGGAACCGATT
Found at i:1139511 original size:23 final size:23
Alignment explanation
Indices: 1139474--1139557 Score: 98
Period size: 23 Copynumber: 3.7 Consensus size: 23
1139464 TTGGTGCAGA
* *
1139474 GGGAATCGATACCCCCCTTGAAG
1 GGGAACCGATTCCCCCCTTGAAG
* *
1139497 GGGAACTGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCCTTGAAG
*
1139520 GGGAACCGATT-CCCCCTTGTAG
1 GGGAACCGATTCCCCCCTTGAAG
* *
1139542 GGGAATCGATACCCCC
1 GGGAACCGATTCCCCC
1139558 TAGAGGTTCT
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
22 18 0.35
23 33 0.65
ACGTcount: A:0.23, C:0.31, G:0.26, T:0.20
Consensus pattern (23 bp):
GGGAACCGATTCCCCCCTTGAAG
Found at i:1144818 original size:64 final size:65
Alignment explanation
Indices: 1144725--1144933 Score: 223
Period size: 65 Copynumber: 3.2 Consensus size: 65
1144715 TTTCAAAGGG
* *
1144725 ATGCACCGATGCACCAATCCATGCATCGATGCAC-CATTGAATAAATTGAACATCGAATGCATTT
1 ATGCATCGATGCA-CAAACCATGCATCGATGCACTCATTGAATAAATTGAACATCGAATGCATTT
1144789 T
65 T
* * **
1144790 ATGCATCGATGCATATACCATGCATCGATGCACTCAGGGTTTTATAAA---AACATCGAATGCAT
1 ATGCATCGATGCACAAACCATGCATCGATGCACTCA---TTGAATAAATTGAACATCGAATGCAT
*
1144852 TTG
63 TTT
* ** **
1144855 ATGCATCGATGCACAAAACATGCATCGATGCACTCA--GGCTATTTTGAAACATCGAATGCATTT
1 ATGCATCGATGCACAAACCATGCATCGATGCACTCATTGAATAAATTG-AACATCGAATGCATTT
1144918 T
65 T
1144919 ATGCATCGATGCACA
1 ATGCATCGATGCACA
1144934 CTTAGTGCAC
Statistics
Matches: 120, Mismatches: 16, Indels: 17
0.78 0.10 0.11
Matches are distributed among these distances:
60 2 0.02
64 48 0.40
65 63 0.52
68 7 0.06
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.27
Consensus pattern (65 bp):
ATGCATCGATGCACAAACCATGCATCGATGCACTCATTGAATAAATTGAACATCGAATGCATTTT
Found at i:1144842 original size:65 final size:64
Alignment explanation
Indices: 1144773--1144933 Score: 243
Period size: 65 Copynumber: 2.5 Consensus size: 64
1144763 GAATAAATTG
* * * *
1144773 AACATCGAATGCATTTTATGCATCGATGCATATACCATGCATCGATGCACTCAGGGT-TTTATAA
1 AACATCGAATGCATTTTATGCATCGATGCACAAAACATGCATCGATGCACTCAGGCTATTT-T-A
1144837 A
64 A
* *
1144838 AACATCGAATGCATTTGATGCATCGATGCACAAAACATGCATCGATGCACTCAGGCTATTTTGA
1 AACATCGAATGCATTTTATGCATCGATGCACAAAACATGCATCGATGCACTCAGGCTATTTTAA
1144902 AACATCGAATGCATTTTATGCATCGATGCACA
1 AACATCGAATGCATTTTATGCATCGATGCACA
1144934 CTTAGTGCAC
Statistics
Matches: 88, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
64 32 0.36
65 53 0.60
66 3 0.03
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (64 bp):
AACATCGAATGCATTTTATGCATCGATGCACAAAACATGCATCGATGCACTCAGGCTATTTTAA
Found at i:1147343 original size:30 final size:30
Alignment explanation
Indices: 1147308--1147370 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
1147298 TTAGATTTAA
* * *
1147308 ATGCATATTATTGGTAATGCGTTATAAATG
1 ATGCATAGTATCGGTAATACGTTATAAATG
1147338 ATGCATAGTATCGGTAATACGTTATAAATG
1 ATGCATAGTATCGGTAATACGTTATAAATG
1147368 ATG
1 ATG
1147371 AATTTGTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.35, C:0.08, G:0.21, T:0.37
Consensus pattern (30 bp):
ATGCATAGTATCGGTAATACGTTATAAATG
Found at i:1153324 original size:16 final size:17
Alignment explanation
Indices: 1153305--1153349 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
1153295 AACATTATAA
1153305 AAATAG-AATAATACAT-
1 AAATAGAAATAATA-ATG
1153321 AAAT-GAAATAA-AATG
1 AAATAGAAATAATAATG
1153336 AAATAGAAATAATA
1 AAATAGAAATAATA
1153350 TGATTTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
14 2 0.08
15 6 0.24
16 16 0.64
17 1 0.04
ACGTcount: A:0.67, C:0.02, G:0.09, T:0.22
Consensus pattern (17 bp):
AAATAGAAATAATAATG
Found at i:1153594 original size:2 final size:2
Alignment explanation
Indices: 1153573--1153614 Score: 59
Period size: 2 Copynumber: 21.0 Consensus size: 2
1153563 ATTAGTTAAA
*
1153573 AT AT ACT AT AA AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1153615 CATAATATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 33 0.92
3 2 0.06
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:1154823 original size:24 final size:24
Alignment explanation
Indices: 1154791--1154847 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
1154781 GGATATATGT
1154791 TGATTTGTTTTCTACATTTTAGAG
1 TGATTTGTTTTCTACATTTTAGAG
1154815 TGATTTGTTTTCTACATTTTAGAG
1 TGATTTGTTTTCTACATTTTAGAG
1154839 TGATTTGTT
1 TGATTTGTT
1154848 CTCATTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.19, C:0.07, G:0.18, T:0.56
Consensus pattern (24 bp):
TGATTTGTTTTCTACATTTTAGAG
Found at i:1154856 original size:22 final size:23
Alignment explanation
Indices: 1154791--1154855 Score: 98
Period size: 24 Copynumber: 2.8 Consensus size: 23
1154781 GGATATATGT
1154791 TGATTTGTTTTCTACATTTTAGAG
1 TGATTTG-TTTCTACATTTTAGAG
1154815 TGATTTGTTTTCTACATTTTAGAG
1 TGATTTG-TTTCTACATTTTAGAG
1154839 TGATTTG-TTCT-CATTTT
1 TGATTTGTTTCTACATTTT
1154856 TTCACTGTAG
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
21 6 0.15
22 4 0.10
24 31 0.76
ACGTcount: A:0.18, C:0.09, G:0.15, T:0.57
Consensus pattern (23 bp):
TGATTTGTTTCTACATTTTAGAG
Found at i:1155270 original size:3 final size:3
Alignment explanation
Indices: 1155262--1155300 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
1155252 AAAAGTAAAT
*
1155262 TAA TAA TAA TTAA TAA TAA TAA TAA TAA -GA TAA TAA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1155301 AAAGACCCGG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 1 0.03
3 28 0.88
4 3 0.09
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:1155296 original size:14 final size:14
Alignment explanation
Indices: 1155262--1155305 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
1155252 AAAAGTAAAT
*
1155262 TAATAATAATTAATAA
1 TAATAATAA-TAA-GA
1155278 TAATAATAATAAGA
1 TAATAATAATAAGA
*
1155292 TAATAATAAAAAGA
1 TAATAATAATAAGA
1155306 CCCGGACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
14 14 0.54
15 3 0.12
16 9 0.35
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.30
Consensus pattern (14 bp):
TAATAATAATAAGA
Found at i:1157284 original size:49 final size:49
Alignment explanation
Indices: 1157212--1157378 Score: 237
Period size: 49 Copynumber: 3.4 Consensus size: 49
1157202 AGTTTATCAT
1157212 ATTCAAAACTTGTAAACTTCTGGTTTACCATAATATGTGATTTAATTTC
1 ATTCAAAACTTGTAAACTTCTGGTTTACCATAATATGTGATTTAATTTC
* * * *
1157261 ATTCATAACTTGTAAACTTCTGGTTTACCATAACAT-TTATTTAATCTC
1 ATTCAAAACTTGTAAACTTCTGGTTTACCATAATATGTGATTTAATTTC
* * ** * *
1157309 ATTTAAAACTTGTAAACTTTTAATTTACCTTAATATGTGATTTAAGTTC
1 ATTCAAAACTTGTAAACTTCTGGTTTACCATAATATGTGATTTAATTTC
1157358 ATTCAAAACTTGTAAACTTCT
1 ATTCAAAACTTGTAAACTTCT
1157379 ACTTTACTAT
Statistics
Matches: 101, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
48 39 0.39
49 62 0.61
ACGTcount: A:0.34, C:0.15, G:0.08, T:0.44
Consensus pattern (49 bp):
ATTCAAAACTTGTAAACTTCTGGTTTACCATAATATGTGATTTAATTTC
Found at i:1164530 original size:38 final size:38
Alignment explanation
Indices: 1164479--1164572 Score: 170
Period size: 38 Copynumber: 2.5 Consensus size: 38
1164469 GTCGAATGGT
*
1164479 GATGTTGCTTGGCGCCTTGGATGGTTGGCTTGGAAAGG
1 GATGTTGCTTGGCGCCTTGGACGGTTGGCTTGGAAAGG
1164517 GATGTTGCTTGGCGCCTTGGACGGTTGGCTTGGAAAGG
1 GATGTTGCTTGGCGCCTTGGACGGTTGGCTTGGAAAGG
*
1164555 GATGTTGCTTGGTGCCTT
1 GATGTTGCTTGGCGCCTT
1164573 AGACCAAATG
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 54 1.00
ACGTcount: A:0.12, C:0.15, G:0.40, T:0.33
Consensus pattern (38 bp):
GATGTTGCTTGGCGCCTTGGACGGTTGGCTTGGAAAGG
Found at i:1166402 original size:13 final size:13
Alignment explanation
Indices: 1166386--1166415 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1166376 AAAAAAAAAC
1166386 AAAAAAAGGCAAA
1 AAAAAAAGGCAAA
*
1166399 AAAAAAAGGTAAA
1 AAAAAAAGGCAAA
1166412 AAAA
1 AAAA
1166416 GGCACAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.80, C:0.03, G:0.13, T:0.03
Consensus pattern (13 bp):
AAAAAAAGGCAAA
Found at i:1166405 original size:23 final size:23
Alignment explanation
Indices: 1166375--1166446 Score: 83
Period size: 24 Copynumber: 3.1 Consensus size: 23
1166365 TATTTTTTTC
1166375 AAAAAAAAAA-CAAAAAAAGGCA
1 AAAAAAAAAAGCAAAAAAAGGCA
* *
1166397 AAAAAAAAAGGTAAAAAAAGGCA
1 AAAAAAAAAAGCAAAAAAAGGCA
* * *
1166420 CAAAAAAAGAAGCAACAAAAGCCA
1 -AAAAAAAAAAGCAAAAAAAGGCA
1166444 AAA
1 AAA
1166447 TTTCAAAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
22 9 0.22
23 14 0.34
24 18 0.44
ACGTcount: A:0.75, C:0.11, G:0.12, T:0.01
Consensus pattern (23 bp):
AAAAAAAAAAGCAAAAAAAGGCA
Found at i:1175251 original size:47 final size:46
Alignment explanation
Indices: 1175185--1175279 Score: 163
Period size: 47 Copynumber: 2.0 Consensus size: 46
1175175 ATATAAAATG
* *
1175185 ATCTGGACGAAATTGTTACTTTTAAAACTTTAAGAGGGAAAACGAAA
1 ATCTCGACGAAACTGTTACTTTTAAAACTTTAAG-GGGAAAACGAAA
1175232 ATCTCGACGAAACTGTTACTTTTAAAACTTTAAGGGGAAAACGAAA
1 ATCTCGACGAAACTGTTACTTTTAAAACTTTAAGGGGAAAACGAAA
1175278 AT
1 AT
1175280 TTACTCAAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
46 14 0.30
47 32 0.70
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (46 bp):
ATCTCGACGAAACTGTTACTTTTAAAACTTTAAGGGGAAAACGAAA
Found at i:1183730 original size:27 final size:28
Alignment explanation
Indices: 1183695--1183751 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 28
1183685 TTTATATTTG
1183695 AAAATAAAAAAAATC-CAAAATTAAAAA
1 AAAATAAAAAAAATCTCAAAATTAAAAA
* * *
1183722 AAAATAAAAAAATTCTGAAAATTACAAA
1 AAAATAAAAAAAATCTCAAAATTAAAAA
1183750 AA
1 AA
1183752 TAATGTTTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 14 0.54
28 12 0.46
ACGTcount: A:0.74, C:0.07, G:0.02, T:0.18
Consensus pattern (28 bp):
AAAATAAAAAAAATCTCAAAATTAAAAA
Found at i:1189947 original size:43 final size:43
Alignment explanation
Indices: 1189899--1190030 Score: 219
Period size: 43 Copynumber: 3.1 Consensus size: 43
1189889 TGGAGATTGG
* *
1189899 GTTTGGGTTCATTTCCGAAAGGAATGTTTTCAAGCCCAACGAT
1 GTTTGGGTTCATTTCCGAAAGGAATGTTTTCCAGCCCAACGAC
* *
1189942 GTTTGGGTTCATTTTCAAAAGGAATGTTTTCCAGCCCAACGAC
1 GTTTGGGTTCATTTCCGAAAGGAATGTTTTCCAGCCCAACGAC
*
1189985 GTTTGGGTTCATTTCTGAAAGGAATGTTTTCCAGCCCAACGAC
1 GTTTGGGTTCATTTCCGAAAGGAATGTTTTCCAGCCCAACGAC
1190028 GTT
1 GTT
1190031 CTAAGTTGTT
Statistics
Matches: 82, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 82 1.00
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (43 bp):
GTTTGGGTTCATTTCCGAAAGGAATGTTTTCCAGCCCAACGAC
Found at i:1191501 original size:12 final size:12
Alignment explanation
Indices: 1191484--1191508 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1191474 TTTGCTAAAA
1191484 TTACTATAGCAG
1 TTACTATAGCAG
1191496 TTACTATAGCAG
1 TTACTATAGCAG
1191508 T
1 T
1191509 GCAACGATAC
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (12 bp):
TTACTATAGCAG
Found at i:1194891 original size:10 final size:10
Alignment explanation
Indices: 1194878--1194928 Score: 52
Period size: 10 Copynumber: 5.3 Consensus size: 10
1194868 TTATATATAT
*
1194878 AAAAA-AAAG
1 AAAAAGAAAA
*
1194887 AAAAAG-AAT
1 AAAAAGAAAA
1194896 AAAAAGAAAA
1 AAAAAGAAAA
*
1194906 AAATAGAAAA
1 AAAAAGAAAA
*
1194916 GAAAAGAAAA
1 AAAAAGAAAA
1194926 AAA
1 AAA
1194929 GATGATTAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
9 13 0.38
10 21 0.62
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.04
Consensus pattern (10 bp):
AAAAAGAAAA
Found at i:1194901 original size:15 final size:15
Alignment explanation
Indices: 1194881--1194930 Score: 70
Period size: 15 Copynumber: 3.5 Consensus size: 15
1194871 TATATATAAA
1194881 AAAAAGAAAAAGAAT
1 AAAAAGAAAAAGAAT
1194896 AAAAAGAAAAA-AAT
1 AAAAAGAAAAAGAAT
1194910 AGAAAAG-AAAAGAA-
1 A-AAAAGAAAAAGAAT
1194924 AAAAAGA
1 AAAAAGA
1194931 TGATTAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
13 5 0.16
14 9 0.28
15 18 0.56
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.04
Consensus pattern (15 bp):
AAAAAGAAAAAGAAT
Found at i:1194940 original size:20 final size:19
Alignment explanation
Indices: 1194876--1194940 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 19
1194866 ATTTATATAT
1194876 ATAAAAA-AAAGAAAA-AGA
1 ATAAAAAGAAA-AAAAGAGA
*
1194894 ATAAAAAGAAAAAAATAGA
1 ATAAAAAGAAAAAAAGAGA
*
1194913 AAAGAAAAGAAAAAAAGATGA
1 ATA-AAAAGAAAAAAAGA-GA
*
1194934 TTAAAAA
1 ATAAAAA
1194941 ATATTTCACT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
18 11 0.28
19 8 0.21
20 17 0.44
21 3 0.08
ACGTcount: A:0.78, C:0.00, G:0.12, T:0.09
Consensus pattern (19 bp):
ATAAAAAGAAAAAAAGAGA
Found at i:1198597 original size:21 final size:20
Alignment explanation
Indices: 1198554--1198618 Score: 94
Period size: 20 Copynumber: 3.2 Consensus size: 20
1198544 ATCTTATATT
*
1198554 ACTATAAATAAACTAATAGC
1 ACTATAAATAAAATAATAGC
1198574 ACTATAAATAAAATAATAAGC
1 ACTATAAATAAAATAAT-AGC
**
1198595 ACTATAAATATTATAATAGC
1 ACTATAAATAAAATAATAGC
1198615 ACTA
1 ACTA
1198619 AGATTAAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 23 0.56
21 18 0.44
ACGTcount: A:0.55, C:0.12, G:0.05, T:0.28
Consensus pattern (20 bp):
ACTATAAATAAAATAATAGC
Found at i:1199216 original size:29 final size:29
Alignment explanation
Indices: 1199155--1199462 Score: 266
Period size: 29 Copynumber: 10.6 Consensus size: 29
1199145 GTAATGGTGT
* * *
1199155 TATTTTTGTAATTATTTTTAAAA-GGTGA
1 TATTTTGGTAATTATTGTTAAAACTGTGA
* * * *
1199183 TATTTTTGTAATTATTCTTAAAAGTGTGC
1 TATTTTGGTAATTATTGTTAAAACTGTGA
* * * *
1199212 TATTTTTGTAATTATTTTTAAAAATGGTGT
1 TATTTTGGTAATTATTGTTAAAACT-GTGA
* * ** *
1199242 TATTTTCGTAATTTATT-TTAGAACAATTA
1 TATTTTGGTAA-TTATTGTTAAAACTGTGA
*
1199271 TATTTTGGTAATTATTGTTAAAACGGTGA
1 TATTTTGGTAATTATTGTTAAAACTGTGA
1199300 TATTTTGGTAATTATTGTTAAAACTGTGA
1 TATTTTGGTAATTATTGTTAAAACTGTGA
* * **
1199329 TATTTTGGTAATTATTTTTCAAACAATGA
1 TATTTTGGTAATTATTGTTAAAACTGTGA
* *
1199358 TATTTAGGTAATTATTGTTAAAACAGTGA
1 TATTTTGGTAATTATTGTTAAAACTGTGA
* *
1199387 TATTTTGGTAATTGTTGTTAAAGA-GGTGA
1 TATTTTGGTAATTATTGTTAAA-ACTGTGA
* *
1199416 TATTTTTGG-AATTAATT-TTAAAAACAGTGC
1 TA-TTTTGGTAATT-ATTGTT-AAAACTGTGA
* *
1199446 TATTTTCGTAATAATTG
1 TATTTTGGTAATTATTG
1199463 ATGTGGAATA
Statistics
Matches: 234, Mismatches: 35, Indels: 20
0.81 0.12 0.07
Matches are distributed among these distances:
28 27 0.12
29 164 0.70
30 38 0.16
31 5 0.02
ACGTcount: A:0.32, C:0.04, G:0.15, T:0.49
Consensus pattern (29 bp):
TATTTTGGTAATTATTGTTAAAACTGTGA
Found at i:1199261 original size:87 final size:86
Alignment explanation
Indices: 1199147--1199437 Score: 329
Period size: 87 Copynumber: 3.3 Consensus size: 86
1199137 TAATTTCGGT
* * * *
1199147 AATGGTGTTATTTTTGTAATTATTTTTAAA-AGGTGATATTTTTGTAATTATTCTTAAAAGTGTG
1 AATGGTGATATTTTTGTAATTATTTTTAAACA-ATGATATTTTGGTAATTATTGTTAAAAG-GTG
* * *
1199211 CTATTTTTGTAATTATTTTTAAA
64 ATATTTTGGTAATTATTGTTAAA
* * *
1199234 AATGGTGTTATTTTCGTAATT-TATTTTAGAACAATTATATTTTGGTAATTATTGTTAAAACGGT
1 AATGGTGATATTTTTGTAATTAT-TTTTA-AACAATGATATTTTGGTAATTATTGTTAAAA-GGT
1199298 GATATTTTGGTAATTATTGTTAAA
63 GATATTTTGGTAATTATTGTTAAA
* * * *
1199322 ACT-GTGATATTTTGGTAATTATTTTTCAAACAATGATATTTAGGTAATTATTGTTAAAACAGTG
1 AATGGTGATATTTTTGTAATTATTTTT-AAACAATGATATTTTGGTAATTATTGTTAAAA-GGTG
*
1199386 ATATTTTGGTAATTGTTGTTAAA
64 ATATTTTGGTAATTATTGTTAAA
* * *
1199409 GA-GGTGATATTTTTGGAATTAATTTTAAA
1 AATGGTGATATTTTTGTAATTATTTTTAAA
1199438 AACAGTGCTA
Statistics
Matches: 177, Mismatches: 20, Indels: 15
0.83 0.09 0.07
Matches are distributed among these distances:
86 4 0.02
87 119 0.67
88 52 0.29
89 2 0.01
ACGTcount: A:0.32, C:0.03, G:0.16, T:0.49
Consensus pattern (86 bp):
AATGGTGATATTTTTGTAATTATTTTTAAACAATGATATTTTGGTAATTATTGTTAAAAGGTGAT
ATTTTGGTAATTATTGTTAAA
Found at i:1199332 original size:58 final size:56
Alignment explanation
Indices: 1199155--1199462 Score: 296
Period size: 58 Copynumber: 5.3 Consensus size: 56
1199145 GTAATGGTGT
* * * ** *
1199155 TATTTTTGTAATTATTTTTAAAAGGTGATATTTTTGTAATTATTCTTAAAAGTGTGC
1 TATTTTGGTAATTATTGTTAAAAGGTGATATTTTGGTAATTATT-TTAAAACAGTGA
* * * * * * *
1199212 TATTTTTGTAATTATTTTTAAAAATGGTGTTATTTTCGTAATTTATTTTAGAACAATTA
1 TATTTTGGTAATTATTGTT-AAAA-GGTGATATTTTGGTAA-TTATTTTAAAACAGTGA
*
1199271 TATTTTGGTAATTATTGTTAAAACGGTGATATTTTGGTAATTATTGTTAAAACTGTGA
1 TATTTTGGTAATTATTGTTAAAA-GGTGATATTTTGGTAATTATT-TTAAAACAGTGA
* * *
1199329 TATTTTGGTAATTATTTTTCAAACA-ATGATATTTAGGTAATTATTGTTAAAACAGTGA
1 TATTTTGGTAATTATTGTT-AAA-AGGTGATATTTTGGTAATTATT-TTAAAACAGTGA
* *
1199387 TATTTTGGTAATTGTTGTTAAAGAGGTGATATTTTTGG-AATTAATTTTAAAAACAGTGC
1 TATTTTGGTAATTATTGTTAAA-AGGTGATA-TTTTGGTAATT-ATTTT-AAAACAGTGA
* *
1199446 TATTTTCGTAATAATTG
1 TATTTTGGTAATTATTG
1199463 ATGTGGAATA
Statistics
Matches: 211, Mismatches: 30, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
57 28 0.13
58 106 0.50
59 71 0.34
60 6 0.03
ACGTcount: A:0.32, C:0.04, G:0.15, T:0.49
Consensus pattern (56 bp):
TATTTTGGTAATTATTGTTAAAAGGTGATATTTTGGTAATTATTTTAAAACAGTGA
Found at i:1206051 original size:21 final size:20
Alignment explanation
Indices: 1206008--1206073 Score: 87
Period size: 20 Copynumber: 3.2 Consensus size: 20
1205998 ATCTTATATT
*
1206008 ACTATAAATAAACTAATAGC
1 ACTATAAATAAAATAATAGC
1206028 ACTATAAATAAAATAATAAGC
1 ACTATAAATAAAATAAT-AGC
**
1206049 ACTATAAAATATTATAATAGC
1 ACTAT-AAATAAAATAATAGC
1206070 ACTA
1 ACTA
1206074 AGATTAAAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
20 16 0.39
21 15 0.37
22 10 0.24
ACGTcount: A:0.56, C:0.12, G:0.05, T:0.27
Consensus pattern (20 bp):
ACTATAAATAAAATAATAGC
Found at i:1206645 original size:29 final size:27
Alignment explanation
Indices: 1206611--1206894 Score: 246
Period size: 29 Copynumber: 9.9 Consensus size: 27
1206601 GTTATGGTGT
*
1206611 TATTTTTGTAATTATTTTTAAAAGGTA
1 TATTTTGGTAATTATTTTTAAAAGGTA
* * *
1206638 CTATTTTTGTAATTATTCTTAAAAGTGTGC
1 -TATTTTGGTAATTATTTTTAAAAG-GT-A
* *
1206668 TATTTTTGTAATTATTTTTAAAAATGGTGT
1 TATTTTGGTAATTATTTTT-AAAA-GGT-A
* **
1206698 TATTTTTGTAATT-TATTTTAGAACAATTA
1 TATTTTGGTAATTAT-TTTTA-AA-AGGTA
*
1206727 TATTTTGGTAATTATTGTTAAAACGGTGA
1 TATTTTGGTAATTATTTTTAAAA-GGT-A
* *
1206756 TATTTTGGTAATTATTGTTAAAACGATGA
1 TATTTTGGTAATTATTTTTAAAA-GGT-A
*
1206785 TATTTTGGTAATTATTTTTAAAATAGTGA
1 TATTTTGGTAATTATTTTTAAAA-GGT-A
* *
1206814 TATTTTGGTAATTATTGTTAAAATAGTAA
1 TATTTTGGTAATTATTTTTAAAA-GGT-A
1206843 TATTTTGGTAATTATTTTTAAAGAGGTGA
1 TATTTTGGTAATTATTTTTAAA-AGGT-A
*
1206872 TATTTTGGTAATTAATTTTAAAA
1 TATTTTGGTAATTATTTTTAAAA
1206895 ATAGTGCTAT
Statistics
Matches: 223, Mismatches: 22, Indels: 22
0.84 0.08 0.08
Matches are distributed among these distances:
27 1 0.00
28 27 0.12
29 164 0.74
30 29 0.13
31 2 0.01
ACGTcount: A:0.33, C:0.02, G:0.14, T:0.51
Consensus pattern (27 bp):
TATTTTGGTAATTATTTTTAAAAGGTA
Found at i:1206717 original size:87 final size:86
Alignment explanation
Indices: 1206604--1206895 Score: 333
Period size: 87 Copynumber: 3.4 Consensus size: 86
1206594 AATTTCAGTT
* * * * * *
1206604 ATGGTGTTATTTTTGTAATTATTTTTAAAAGGTACTATTTTTGTAATTATTCTTAAAAGTGTGCT
1 ATGGTGATATTTTGGTAATTATTTTTAAAAAGTA-TATTTTGGTAATTATTGTTAAAAGTGTGAT
*
1206669 ATTTTTGTAATTATTTTTAAAA
65 ATTTTGGTAATTATTTTTAAAA
* * *
1206691 ATGGTGTTATTTTTGTAATT-TATTTTAGAACAATTATATTTTGGTAATTATTGTTAAAACG-GT
1 ATGGTGATATTTTGGTAATTAT-TTTTA-AA-AAGTATATTTTGGTAATTATTGTTAAAA-GTGT
*
1206754 GATATTTTGGTAATTATTGTT-AAA
62 GATATTTTGGTAATTATTTTTAAAA
* * *
1206778 ACGATGATATTTTGGTAATTATTTTTAAAATAGTGATATTTTGGTAATTATTGTTAAAA-TAGTA
1 ATGGTGATATTTTGGTAATTATTTTTAAAA-AGT-ATATTTTGGTAATTATTGTTAAAAGT-GTG
*
1206842 ATATTTTGGTAATTATTTTTAAAG
63 ATATTTTGGTAATTATTTTTAAAA
*
1206866 A-GGTGATATTTTGGTAATTAATTTTAAAAA
1 ATGGTGATATTTTGGTAATTATTTTTAAAAA
1206896 TAGTGCTATT
Statistics
Matches: 178, Mismatches: 17, Indels: 21
0.82 0.08 0.10
Matches are distributed among these distances:
85 1 0.01
86 6 0.03
87 120 0.67
88 47 0.26
89 4 0.02
ACGTcount: A:0.33, C:0.02, G:0.15, T:0.50
Consensus pattern (86 bp):
ATGGTGATATTTTGGTAATTATTTTTAAAAAGTATATTTTGGTAATTATTGTTAAAAGTGTGATA
TTTTGGTAATTATTTTTAAAA
Found at i:1206788 original size:58 final size:55
Alignment explanation
Indices: 1206611--1206894 Score: 302
Period size: 58 Copynumber: 4.9 Consensus size: 55
1206601 GTTATGGTGT
* * * *
1206611 TATTTTTGTAATTATTTTTAAAAGGT-ACTATTTTTGTAATTATTCTTAAAAGTGTGC
1 TATTTTGGTAATTATTTTTAAAAGGTGA-TATTTTGGTAATTATT-TTAAAAG-ATGA
* * * *
1206668 TATTTTTGTAATTATTTTTAAAAATGGTGTTATTTTTGTAATTTATTTTAGAACA-ATTA
1 TATTTTGGTAATTATTTTT-AAAA-GGTGATATTTTGGTAA-TTATTTTA-AA-AGATGA
*
1206727 TATTTTGGTAATTATTGTTAAAACGGTGATATTTTGGTAATTATTGTTAAAACGATGA
1 TATTTTGGTAATTATTTTTAAAA-GGTGATATTTTGGTAATTATT-TTAAAA-GATGA
* * *
1206785 TATTTTGGTAATTATTTTTAAAATAGTGATATTTTGGTAATTATTGTTAAAATAGTAA
1 TATTTTGGTAATTATTTTTAAAA-GGTGATATTTTGGTAATTATT-TTAAAAGA-TGA
1206843 TATTTTGGTAATTATTTTTAAAGAGGTGATATTTTGGTAATTAATTTTAAAA
1 TATTTTGGTAATTATTTTTAAA-AGGTGATATTTTGGTAATT-ATTTTAAAA
1206895 ATAGTGCTAT
Statistics
Matches: 199, Mismatches: 16, Indels: 23
0.84 0.07 0.10
Matches are distributed among these distances:
56 1 0.01
57 27 0.14
58 124 0.62
59 39 0.20
60 7 0.04
61 1 0.01
ACGTcount: A:0.33, C:0.02, G:0.14, T:0.51
Consensus pattern (55 bp):
TATTTTGGTAATTATTTTTAAAAGGTGATATTTTGGTAATTATTTTAAAAGATGA
Found at i:1208773 original size:61 final size:61
Alignment explanation
Indices: 1208680--1208794 Score: 151
Period size: 61 Copynumber: 1.9 Consensus size: 61
1208670 AAAGGTGGAT
* * *
1208680 ACGACCTTATGTATCATGTCTAGATTAGCACTAGAGCGTAAGCTTAGTGTAGGTGGTGGGC
1 ACGACCTTATGTATCATGTCGAGATTAGCACTAGAACGTAAGCTTAGTGCAGGTGGTGGGC
* * * *
1208741 ACGACCTTATGTGT-ATTGTCGGGATTATCACTATAACGTAAGCTTAGTGCAGGT
1 ACGACCTTATGTATCA-TGTCGAGATTAGCACTAGAACGTAAGCTTAGTGCAGGT
1208795 TTAGCACTAC
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
60 1 0.02
61 45 0.98
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.31
Consensus pattern (61 bp):
ACGACCTTATGTATCATGTCGAGATTAGCACTAGAACGTAAGCTTAGTGCAGGTGGTGGGC
Found at i:1208954 original size:45 final size:45
Alignment explanation
Indices: 1208870--1209017 Score: 242
Period size: 45 Copynumber: 3.3 Consensus size: 45
1208860 TGTCTATGGT
1208870 TTACGAGCTTATGGAATTAAATGGTAAGTATATTGGTAAAATAAGC
1 TTACGAGCTTATGGAA-TAAATGGTAAGTATATTGGTAAAATAAGC
* * *
1208916 TTACGAGCTTATGGACTACATGGCAAGTATATTGGTAAAATAAGC
1 TTACGAGCTTATGGAATAAATGGTAAGTATATTGGTAAAATAAGC
*
1208961 TTACGAGCTTATGGAATAAATGATAAGTATATTGGTAAAATAAGC
1 TTACGAGCTTATGGAATAAATGGTAAGTATATTGGTAAAATAAGC
*
1209006 TTATGAGCTTAT
1 TTACGAGCTTAT
1209018 AAGATAAATG
Statistics
Matches: 94, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
45 79 0.84
46 15 0.16
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.32
Consensus pattern (45 bp):
TTACGAGCTTATGGAATAAATGGTAAGTATATTGGTAAAATAAGC
Found at i:1228455 original size:16 final size:16
Alignment explanation
Indices: 1228434--1228472 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
1228424 TCTTATGGCT
1228434 TCCCAAAGATCATGTC
1 TCCCAAAGATCATGTC
1228450 TCCCAAAGATCATGTC
1 TCCCAAAGATCATGTC
1228466 TCCCAAA
1 TCCCAAA
1228473 CCTTCATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.33, C:0.33, G:0.10, T:0.23
Consensus pattern (16 bp):
TCCCAAAGATCATGTC
Found at i:1235418 original size:22 final size:23
Alignment explanation
Indices: 1235369--1235412 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1235359 TTATAATAAT
1235369 AATT-AAAATCTATATTATAACG
1 AATTAAAAATCTATATTATAACG
1235391 AATTAAAAAT-TATTATTATAAC
1 AATTAAAAATCTA-TATTATAAC
1235413 CATTAATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (23 bp):
AATTAAAAATCTATATTATAACG
Found at i:1238881 original size:21 final size:19
Alignment explanation
Indices: 1238853--1238898 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
1238843 TCATTGAATC
1238853 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
1238873 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
1238892 ACTTAGT
1 A-TTAGT
1238899 AGGATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Found at i:1253403 original size:50 final size:50
Alignment explanation
Indices: 1253347--1253523 Score: 182
Period size: 50 Copynumber: 3.4 Consensus size: 50
1253337 GTGTCAACTC
1253347 TAATTCCTAATAAAATAATAAAAACTAAAAATATTGTTTTAACCCAACCT
1 TAATTCCTAATAAAATAATAAAAACTAAAAATATTGTTTTAACCCAACCT
* * * * * *
1253397 TAATTCCTAAATAACTAAAGAATAAAATAATAATAAACTA-AGCATGT--CTCAA-CT
1 TAATTCCT-AAT-A--AAATAATAAAA-ACTAA-AAA-TATTG-TTTTAACCCAACCT
*
1253451 CTAATTCCTAATAAAATAACAAAAACTAAAAATATTGTTTTAACCCAACCT
1 -TAATTCCTAATAAAATAATAAAAACTAAAAATATTGTTTTAACCCAACCT
1253502 TAATTCCTAATAAAATAATAAA
1 TAATTCCTAATAAAATAATAAA
1253524 TATGATCCTA
Statistics
Matches: 100, Mismatches: 14, Indels: 26
0.71 0.10 0.19
Matches are distributed among these distances:
48 4 0.04
49 4 0.04
50 37 0.37
51 14 0.14
52 1 0.01
53 1 0.01
54 15 0.15
55 16 0.16
56 4 0.04
57 4 0.04
ACGTcount: A:0.51, C:0.16, G:0.03, T:0.30
Consensus pattern (50 bp):
TAATTCCTAATAAAATAATAAAAACTAAAAATATTGTTTTAACCCAACCT
Found at i:1253478 original size:105 final size:105
Alignment explanation
Indices: 1253296--1253511 Score: 414
Period size: 105 Copynumber: 2.1 Consensus size: 105
1253286 GTTCTAAAGG
*
1253296 TCCTAAATAACTAAAGAATAAAATAATAATAAACTAAGCATGTGTCAACTCTAATTCCTAATAAA
1 TCCTAAATAACTAAAGAATAAAATAATAATAAACTAAGCATGTCTCAACTCTAATTCCTAATAAA
*
1253361 ATAATAAAAACTAAAAATATTGTTTTAACCCAACCTTAAT
66 ATAACAAAAACTAAAAATATTGTTTTAACCCAACCTTAAT
1253401 TCCTAAATAACTAAAGAATAAAATAATAATAAACTAAGCATGTCTCAACTCTAATTCCTAATAAA
1 TCCTAAATAACTAAAGAATAAAATAATAATAAACTAAGCATGTCTCAACTCTAATTCCTAATAAA
1253466 ATAACAAAAACTAAAAATATTGTTTTAACCCAACCTTAAT
66 ATAACAAAAACTAAAAATATTGTTTTAACCCAACCTTAAT
1253506 TCCTAA
1 TCCTAA
1253512 TAAAATAATA
Statistics
Matches: 109, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 109 1.00
ACGTcount: A:0.50, C:0.17, G:0.04, T:0.29
Consensus pattern (105 bp):
TCCTAAATAACTAAAGAATAAAATAATAATAAACTAAGCATGTCTCAACTCTAATTCCTAATAAA
ATAACAAAAACTAAAAATATTGTTTTAACCCAACCTTAAT
Found at i:1257644 original size:22 final size:22
Alignment explanation
Indices: 1257619--1257660 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1257609 CAATTCATTT
1257619 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
1257641 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
1257661 CCAGCACATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:1258036 original size:29 final size:29
Alignment explanation
Indices: 1257986--1258056 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
1257976 GCTATTTTTT
*
1257986 AACAAAAAAAAAAACAAAAAAGGCAAAAA
1 AACAAAAAAAAAAACAAAAAAGCCAAAAA
*
1258015 AACACAAAAAAAAAAC-AAAAAGCCAAAAT
1 AACA-AAAAAAAAAACAAAAAAGCCAAAAA
**
1258044 TTCAAAAAAAAAA
1 AACAAAAAAAAAA
1258057 TGCAAATGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 9 0.24
29 17 0.46
30 11 0.30
ACGTcount: A:0.79, C:0.13, G:0.04, T:0.04
Consensus pattern (29 bp):
AACAAAAAAAAAAACAAAAAAGCCAAAAA
Found at i:1262370 original size:22 final size:22
Alignment explanation
Indices: 1262345--1262386 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
1262335 CAATTCATTT
1262345 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
1262367 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
1262387 CCAGCACATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:1264389 original size:16 final size:16
Alignment explanation
Indices: 1264368--1264427 Score: 50
Period size: 16 Copynumber: 3.6 Consensus size: 16
1264358 GTACAAAACG
1264368 AAAGAAAAGACAAAAA
1 AAAGAAAAGACAAAAA
**
1264384 AAAGAAAATTTCATAAAA
1 AAAGAAAA-GACA-AAAA
*
1264402 GAAGAAAAGA-AAAAA
1 AAAGAAAAGACAAAAA
*
1264417 AGAAAAAAAGA
1 A-AAGAAAAGA
1264428 AATTCAAAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
15 4 0.12
16 17 0.50
17 2 0.06
18 11 0.32
ACGTcount: A:0.77, C:0.03, G:0.13, T:0.07
Consensus pattern (16 bp):
AAAGAAAAGACAAAAA
Found at i:1264409 original size:8 final size:8
Alignment explanation
Indices: 1264398--1264429 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
1264388 AAAATTTCAT
*
1264398 AAAAGAAG
1 AAAAGAAA
1264406 AAAAGAAA
1 AAAAGAAA
1264414 AAAAGAAA
1 AAAAGAAA
1264422 AAAAGAAA
1 AAAAGAAA
1264430 TTCAAAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (8 bp):
AAAAGAAA
Found at i:1269503 original size:24 final size:24
Alignment explanation
Indices: 1269476--1269522 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
1269466 CCTCAATGGT
*
1269476 CACAACTTGTGGCACTTCAAGTGA
1 CACAACTTGTGGAACTTCAAGTGA
* * *
1269500 CACATCTTTTTGAACTTCAAGTG
1 CACAACTTGTGGAACTTCAAGTG
1269523 GCATAACTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (24 bp):
CACAACTTGTGGAACTTCAAGTGA
Found at i:1276478 original size:22 final size:25
Alignment explanation
Indices: 1276430--1276482 Score: 85
Period size: 22 Copynumber: 2.2 Consensus size: 25
1276420 TTCTTTTCTT
1276430 TTTCTTCCTTTTTGAGTGCTTTCAA
1 TTTCTTCCTTTTTGAGTGCTTTCAA
1276455 TTTCTT-C-TTTTGAGTGC-TTCAA
1 TTTCTTCCTTTTTGAGTGCTTTCAA
1276477 TTTCTT
1 TTTCTT
1276483 TGCTGATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 11 0.39
23 10 0.36
24 1 0.04
25 6 0.21
ACGTcount: A:0.11, C:0.19, G:0.11, T:0.58
Consensus pattern (25 bp):
TTTCTTCCTTTTTGAGTGCTTTCAA
Found at i:1287094 original size:29 final size:30
Alignment explanation
Indices: 1287031--1287086 Score: 82
Period size: 27 Copynumber: 1.9 Consensus size: 30
1287021 TTTGAGTGTA
1287031 CTTTGCAATTTTTTCTTCAATTTTCTTTTTG
1 CTTTGCAATTTTTTCTTC-ATTTTCTTTTTG
1287062 CTTTG-AA-TTTTTCTTC-TTTTCTTTT
1 CTTTGCAATTTTTTCTTCATTTTCTTTT
1287087 CTTTCTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 9 0.36
29 9 0.36
30 2 0.08
31 5 0.20
ACGTcount: A:0.11, C:0.16, G:0.05, T:0.68
Consensus pattern (30 bp):
CTTTGCAATTTTTTCTTCATTTTCTTTTTG
Found at i:1289013 original size:25 final size:26
Alignment explanation
Indices: 1288979--1289039 Score: 97
Period size: 26 Copynumber: 2.3 Consensus size: 26
1288969 AACAAGGAAT
1288979 AACCTATACT-AAAAGTATAAACCCA
1 AACCTATACTAAAAAGTATAAACCCA
*
1289004 AACCTATACTAAAAAGTATAAACCCG
1 AACCTATACTAAAAAGTATAAACCCA
1289030 AACCTTATAC
1 AACC-TATAC
1289040 GTTCATTGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
25 10 0.30
26 18 0.55
27 5 0.15
ACGTcount: A:0.49, C:0.25, G:0.05, T:0.21
Consensus pattern (26 bp):
AACCTATACTAAAAAGTATAAACCCA
Found at i:1300460 original size:18 final size:18
Alignment explanation
Indices: 1300437--1300473 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1300427 ATAGGTTGAA
*
1300437 TTTCTTGAGTCATTTTCC
1 TTTCTTGAGTAATTTTCC
1300455 TTTCTTGAGTAATTTTCC
1 TTTCTTGAGTAATTTTCC
1300473 T
1 T
1300474 ACGTCATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.14, C:0.19, G:0.11, T:0.57
Consensus pattern (18 bp):
TTTCTTGAGTAATTTTCC
Found at i:1309247 original size:24 final size:25
Alignment explanation
Indices: 1309203--1309252 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 25
1309193 TTAATATTTC
*
1309203 ATTTCATTTTCTTTCATCTTTTCTT
1 ATTTCATTTACTTTCATCTTTTCTT
1309228 ATTTCA-TTACTTT-ATCCTTTTCTT
1 ATTTCATTTACTTTCAT-CTTTTCTT
1309252 A
1 A
1309253 ACCTTTTCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 2 0.09
24 15 0.65
25 6 0.26
ACGTcount: A:0.16, C:0.20, G:0.00, T:0.64
Consensus pattern (25 bp):
ATTTCATTTACTTTCATCTTTTCTT
Found at i:1317579 original size:21 final size:19
Alignment explanation
Indices: 1317550--1317588 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
1317540 ACTCCCCCAT
1317550 AGAAAAAAAGTGTGAATAAAG
1 AGAAAAAAAGT-TG-ATAAAG
*
1317571 AGAATAAAAGTTGATAAA
1 AGAAAAAAAGTTGATAAA
1317589 TAACTAGGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 2 0.12
21 10 0.59
ACGTcount: A:0.62, C:0.00, G:0.21, T:0.18
Consensus pattern (19 bp):
AGAAAAAAAGTTGATAAAG
Found at i:1319354 original size:21 final size:19
Alignment explanation
Indices: 1319326--1319371 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
1319316 TCATTGAATC
1319326 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
1319346 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
1319365 ACTTAGT
1 A-TTAGT
1319372 AGGATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Found at i:1319755 original size:81 final size:81
Alignment explanation
Indices: 1319604--1319839 Score: 197
Period size: 81 Copynumber: 2.9 Consensus size: 81
1319594 TATAATTCAT
* * * * * * * * * * * **
1319604 TTATTCTTTTACCCAAAGGTATTTAGCCTTTCATATAACTTGCATATTTGACACTATTTTATCAA
1 TTATTATTTTACTCAACGTTATTTAACCATTCATCTAACTAGCATAATTGACACTGTTATGCCAA
* * **
1319669 TTGCACAGTGAGTCCA
66 ATGCACAATGAGGACA
* * *
1319685 TTATTATTTTACTCAACAG-TGTTTAACCGTTCATCTAACTGGCATAATTGACACCT-TTATGCC
1 TTATTATTTTACTCAAC-GTTATTTAACCATTCATCTAACTAGCATAATTGACA-CTGTTATGCC
* *
1319748 AAATGCACAATTAGGATA
64 AAATGCACAATGAGGACA
* * * *
1319766 TTATTCTTTTACTTAACGTTATTTATCCATTCATCTAACTAGCATAATTGACATTGTTATGCCAA
1 TTATTATTTTACTCAACGTTATTTAACCATTCATCTAACTAGCATAATTGACACTGTTATGCCAA
*
1319831 ATACACAAT
66 ATGCACAAT
1319840 TAGGCCTCAA
Statistics
Matches: 125, Mismatches: 26, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
80 2 0.02
81 120 0.96
82 3 0.02
ACGTcount: A:0.31, C:0.19, G:0.10, T:0.39
Consensus pattern (81 bp):
TTATTATTTTACTCAACGTTATTTAACCATTCATCTAACTAGCATAATTGACACTGTTATGCCAA
ATGCACAATGAGGACA
Found at i:1319914 original size:68 final size:68
Alignment explanation
Indices: 1319828--1320117 Score: 413
Period size: 68 Copynumber: 4.3 Consensus size: 68
1319818 ATTGTTATGC
* * * * * *
1319828 CAAATACACAATTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACAGGAATAGATGACTCCTTTC
1 CAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTC
1319893 AGT
66 AGT
*
1319896 CAAATGTACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTC
1 CAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTC
1319961 TA-T
66 -AGT
*
1319964 CAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACATTTC
1 CAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTC
*
1320029 TGT
66 AGT
* * * * * *
1320032 CAAATGCACATTTATGCCTCAAAGGCACTTACCCTTTAATCTAATTTGCATAAATGACACCTTTC
1 CAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTC
1320097 -GT
66 AGT
*
1320099 CAAATACACAGTTAGGCCT
1 CAAATGCACAGTTAGGCCT
1320118 ATTAATCTTT
Statistics
Matches: 200, Mismatches: 20, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
67 18 0.09
68 181 0.90
69 1 0.00
ACGTcount: A:0.32, C:0.25, G:0.14, T:0.29
Consensus pattern (68 bp):
CAAATGCACAGTTAGGCCTCAAAGGCACTTAGCCTTTCATCTAACTGGCATAAATGACACCTTTC
AGT
Found at i:1320051 original size:136 final size:136
Alignment explanation
Indices: 1319795--1320117 Score: 429
Period size: 136 Copynumber: 2.4 Consensus size: 136
1319785 TATTTATCCA
* *
1319795 TTCATCTAACTAGCATAATTGACA--TTGT-TATGCCAAATACACAATTAGGCCTCAAAGGCACT
1 TTCATCTAACTAGCATAAATGACACCTT-TCTAT--CAAATACACAGTTAGGCCTCAAAGGCACT
* * * *
1319857 TAGCCTTTCATCTAACAGGAATAGATGACTCCTTTCAGTCAAATGTACAGTTAGGCCTCAAAGGC
63 TAGCCTTTCATCTAACAGGAATAAATGACACATTTCAGTCAAATGCACAGTTAGGCCTCAAAGGC
*
1319922 ACTTAGCCT
128 ACTTACCCT
* *
1319931 TTCATCTAACTGGCATAAATGACACCTTTCTATCAAATGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTAGCATAAATGACACCTTTCTATCAAATACACAGTTAGGCCTCAAAGGCACTTAG
* * * * *
1319996 CCTTTCATCTAACTGGCATAAATGACACATTTCTGTCAAATGCACATTTATGCCTCAAAGGCACT
66 CCTTTCATCTAACAGGAATAAATGACACATTTCAGTCAAATGCACAGTTAGGCCTCAAAGGCACT
1320061 TACCCT
131 TACCCT
* * * *
1320067 TTAATCTAATTTGCATAAATGACACCTTTC-GTCAAATACACAGTTAGGCCT
1 TTCATCTAACTAGCATAAATGACACCTTTCTATCAAATACACAGTTAGGCCT
1320118 ATTAATCTTT
Statistics
Matches: 165, Mismatches: 19, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
135 19 0.12
136 140 0.85
137 1 0.01
138 5 0.03
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.30
Consensus pattern (136 bp):
TTCATCTAACTAGCATAAATGACACCTTTCTATCAAATACACAGTTAGGCCTCAAAGGCACTTAG
CCTTTCATCTAACAGGAATAAATGACACATTTCAGTCAAATGCACAGTTAGGCCTCAAAGGCACT
TACCCT
Found at i:1320410 original size:55 final size:55
Alignment explanation
Indices: 1320300--1320443 Score: 209
Period size: 55 Copynumber: 2.6 Consensus size: 55
1320290 TCCCATTCAA
* * *
1320300 AAATTCATACACTTGGTATGAATTTCTTA-TTTCGCACACATAGTGCCTATACAG
1 AAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAGAGTGCCTATACAG
* * *
1320354 AAATTCGTACACTTATTATAAATTTCTTAGTTTTGCACACAGAGTGCCTATACAG
1 AAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAGAGTGCCTATACAG
*
1320409 AAATTCATACAATTAGTATGAATTTCTTAAGTTTT
1 AAATTCATACACTTAGTATGAATTTCTT-AGTTTT
1320444 TACACACTTA
Statistics
Matches: 78, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
54 25 0.32
55 47 0.60
56 6 0.08
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (55 bp):
AAATTCATACACTTAGTATGAATTTCTTAGTTTTGCACACAGAGTGCCTATACAG
Found at i:1324789 original size:101 final size:101
Alignment explanation
Indices: 1324614--1324816 Score: 352
Period size: 101 Copynumber: 2.0 Consensus size: 101
1324604 AAGTCTCTAT
** * *
1324614 AAGTGATCAAATGGGAAGTTGAAGGTAACTCGGGGAGGTGCTAAGGAAACAAGGAGGTCTCGTCT
1 AAGTGATCAAATGGGAAGCAGAAGGTAACTCGGAGAGGTGCTAAGGAAACAAAGAGGTCTCGTCT
1324679 AGGAAGCTCATTCATATCCAACCTTTGCATTGCTAG
66 AGGAAGCTCATTCATATCCAACCTTTGCATTGCTAG
* *
1324715 AAGTGATCAAATGGGCAGCAGAAGGTAACTTGGAGAGGTGCTAAGGAAACAAAGAGGTCTCGTCT
1 AAGTGATCAAATGGGAAGCAGAAGGTAACTCGGAGAGGTGCTAAGGAAACAAAGAGGTCTCGTCT
1324780 AGGAAGCTCATTCATATCCAACCTTTGCATTGCTAG
66 AGGAAGCTCATTCATATCCAACCTTTGCATTGCTAG
1324816 A
1 A
1324817 TGGCTACACA
Statistics
Matches: 96, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
101 96 1.00
ACGTcount: A:0.32, C:0.17, G:0.28, T:0.23
Consensus pattern (101 bp):
AAGTGATCAAATGGGAAGCAGAAGGTAACTCGGAGAGGTGCTAAGGAAACAAAGAGGTCTCGTCT
AGGAAGCTCATTCATATCCAACCTTTGCATTGCTAG
Found at i:1328278 original size:13 final size:14
Alignment explanation
Indices: 1328255--1328283 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
1328245 ATAAGATACT
1328255 ATCTGTCCATCACC
1 ATCTGTCCATCACC
1328269 ATCT-TCCATCACC
1 ATCTGTCCATCACC
1328282 AT
1 AT
1328284 ATCACGCCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.24, C:0.41, G:0.03, T:0.31
Consensus pattern (14 bp):
ATCTGTCCATCACC
Found at i:1328965 original size:16 final size:16
Alignment explanation
Indices: 1328928--1328997 Score: 54
Period size: 16 Copynumber: 4.4 Consensus size: 16
1328918 GAGTTGTAAG
1328928 TTATCTTCACTTT-CTTA
1 TTAT-TTCA-TTTCCTTA
* *
1328945 CTATTTTATTTCCTTA
1 TTATTTCATTTCCTTA
* *
1328961 TTATTTCATCT-ATTA
1 TTATTTCATTTCCTTA
*
1328976 TTATTTCATTACCTTA
1 TTATTTCATTTCCTTA
*
1328992 TCATTT
1 TTATTT
1328998 TCATAACCTT
Statistics
Matches: 41, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
15 15 0.37
16 23 0.56
17 3 0.07
ACGTcount: A:0.21, C:0.19, G:0.00, T:0.60
Consensus pattern (16 bp):
TTATTTCATTTCCTTA
Found at i:1332771 original size:13 final size:13
Alignment explanation
Indices: 1332753--1332789 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
1332743 ATACTATTTG
1332753 TCCATCACCATCT
1 TCCATCACCATCT
1332766 TCCATCACCATCT
1 TCCATCACCATCT
1332779 TCCATCACCAT
1 TCCATCACCAT
1332790 ATCACTCCTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.24, C:0.46, G:0.00, T:0.30
Consensus pattern (13 bp):
TCCATCACCATCT
Found at i:1332807 original size:35 final size:35
Alignment explanation
Indices: 1332768--1332847 Score: 133
Period size: 35 Copynumber: 2.3 Consensus size: 35
1332758 CACCATCTTC
*
1332768 CATCACCATCTTCCATCACCATATCACTCCTATAT
1 CATCACCATCTTCCATCACCATATCACGCCTATAT
* *
1332803 CATCACCATTTTCCATCACCATTTCACGCCTATAT
1 CATCACCATCTTCCATCACCATATCACGCCTATAT
1332838 CATCACCATC
1 CATCACCATC
1332848 CCTTAACCAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.28, C:0.40, G:0.01, T:0.31
Consensus pattern (35 bp):
CATCACCATCTTCCATCACCATATCACGCCTATAT
Found at i:1341706 original size:13 final size:13
Alignment explanation
Indices: 1341688--1341714 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1341678 CTCACAAAGG
1341688 TTATATCAGCTCA
1 TTATATCAGCTCA
1341701 TTATATCAGCTCA
1 TTATATCAGCTCA
1341714 T
1 T
1341715 GGAGACTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.41
Consensus pattern (13 bp):
TTATATCAGCTCA
Found at i:1365112 original size:15 final size:14
Alignment explanation
Indices: 1365082--1365119 Score: 67
Period size: 15 Copynumber: 2.6 Consensus size: 14
1365072 TGTTATAACA
1365082 TATATATATTCATC
1 TATATATATTCATC
1365096 TATATATATTACATC
1 TATATATATT-CATC
1365111 TATATATAT
1 TATATATAT
1365120 ATGATAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 10 0.43
15 13 0.57
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (14 bp):
TATATATATTCATC
Found at i:1377299 original size:22 final size:22
Alignment explanation
Indices: 1377274--1377319 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
1377264 ACTTTGCAAC
1377274 TTGCTTCACTTTTCTTTTGCTT
1 TTGCTTCACTTTTCTTTTGCTT
** * *
1377296 TTGCTTTTCTTTTTTTTTTCTT
1 TTGCTTCACTTTTCTTTTGCTT
1377318 TT
1 TT
1377320 TTTTTTCTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.02, C:0.17, G:0.07, T:0.74
Consensus pattern (22 bp):
TTGCTTCACTTTTCTTTTGCTT
Found at i:1377307 original size:11 final size:11
Alignment explanation
Indices: 1377282--1377332 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
1377272 ACTTGCTTCA
1377282 CTTTT-CTTTT
1 CTTTTGCTTTT
1377292 GCTTTTGCTTTT
1 -CTTTTGCTTTT
**
1377304 CTTTTTTTTTT
1 CTTTTGCTTTT
**
1377315 CTTTTTTTTTT
1 CTTTTGCTTTT
1377326 CTTTTGC
1 CTTTTGC
1377333 ACTCCAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
11 30 0.86
12 5 0.14
ACGTcount: A:0.00, C:0.16, G:0.06, T:0.78
Consensus pattern (11 bp):
CTTTTGCTTTT
Found at i:1377325 original size:22 final size:22
Alignment explanation
Indices: 1377282--1377330 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1377272 ACTTGCTTCA
1377282 CTTTTCTTTTGCTTTTGCTTTT
1 CTTTTCTTTTGCTTTTGCTTTT
* * **
1377304 CTTTTTTTTTTCTTTTTTTTTT
1 CTTTTCTTTTGCTTTTGCTTTT
1377326 CTTTT
1 CTTTT
1377331 GCACTCCAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.00, C:0.14, G:0.04, T:0.82
Consensus pattern (22 bp):
CTTTTCTTTTGCTTTTGCTTTT
Found at i:1377386 original size:24 final size:24
Alignment explanation
Indices: 1377354--1377400 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
1377344 GATGTAGGAG
1377354 TCTTTTTCTT-TT-CTCTTTTGTTT
1 TCTTTTTCTTGTTGCT-TTTTGTTT
1377377 TCTTCTTTCTTGTTGCTTTTTGTT
1 TCTT-TTTCTTGTTGCTTTTTGTT
1377401 GTAGCACTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 6 0.29
25 9 0.43
26 2 0.10
ACGTcount: A:0.00, C:0.17, G:0.09, T:0.74
Consensus pattern (24 bp):
TCTTTTTCTTGTTGCTTTTTGTTT
Found at i:1381754 original size:16 final size:16
Alignment explanation
Indices: 1381725--1381773 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
1381715 TTGCTTCACT
**
1381725 TTTCTTTTGCTTTTGC
1 TTTCTTTTTTTTTTGC
*
1381741 TTTCTTTTTTTTTTTC
1 TTTCTTTTTTTTTTGC
*
1381757 TTTTTTTTTTCTTTTGC
1 TTTCTTTTTT-TTTTGC
1381774 ACTCCAAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
16 22 0.81
17 5 0.19
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (16 bp):
TTTCTTTTTTTTTTGC
Found at i:1381760 original size:11 final size:11
Alignment explanation
Indices: 1381741--1381771 Score: 53
Period size: 11 Copynumber: 2.7 Consensus size: 11
1381731 TTGCTTTTGC
1381741 TTTCTTTTTTTT
1 TTTC-TTTTTTT
1381753 TTTCTTTTTTT
1 TTTCTTTTTTT
1381764 TTTCTTTT
1 TTTCTTTT
1381772 GCACTCCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 15 0.79
12 4 0.21
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (11 bp):
TTTCTTTTTTT
Found at i:1381827 original size:24 final size:24
Alignment explanation
Indices: 1381795--1381841 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
1381785 GATGTAGGAG
1381795 TCTTTTTCTT-TT-CTCTTTTGTTT
1 TCTTTTTCTTGTTGCT-TTTTGTTT
1381818 TCTTCTTTCTTGTTGCTTTTTGTT
1 TCTT-TTTCTTGTTGCTTTTTGTT
1381842 GTAGCACTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 6 0.29
25 9 0.43
26 2 0.10
ACGTcount: A:0.00, C:0.17, G:0.09, T:0.74
Consensus pattern (24 bp):
TCTTTTTCTTGTTGCTTTTTGTTT
Found at i:1389854 original size:36 final size:36
Alignment explanation
Indices: 1389803--1389906 Score: 165
Period size: 36 Copynumber: 2.9 Consensus size: 36
1389793 GATACAATCT
*
1389803 GTCCATCACCATTATCACGCCTATATCTTCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
1389839 GTCTATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
1389875 TTCCATCACCA-TATCACGCCTATATTATCACC
1 GTCCATCACCATTATCACGCCTATATCATCACC
1389907 CACTTATAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
35 20 0.32
36 43 0.68
ACGTcount: A:0.29, C:0.36, G:0.05, T:0.31
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:1390323 original size:17 final size:18
Alignment explanation
Indices: 1390295--1390328 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
1390285 CAACAAAAAA
1390295 AAAGCAACAAGAAAGAAG
1 AAAGCAACAAGAAAGAAG
1390313 AAAGCAA-AAGAAAGAA
1 AAAGCAACAAGAAAGAA
1390329 AAGAAAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.71, C:0.09, G:0.21, T:0.00
Consensus pattern (18 bp):
AAAGCAACAAGAAAGAAG
Found at i:1390350 original size:14 final size:14
Alignment explanation
Indices: 1390306--1390351 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
1390296 AAGCAACAAG
1390306 AAAGAAG-AAAGCA
1 AAAGAAGAAAAGCA
*
1390319 AAAGAAAGAAAAGAA
1 AAAG-AAGAAAAGCA
*
1390334 AAAGAAGAAAATCA
1 AAAGAAGAAAAGCA
1390348 AAAG
1 AAAG
1390352 CAAAAGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 4 0.14
14 15 0.54
15 9 0.32
ACGTcount: A:0.74, C:0.04, G:0.20, T:0.02
Consensus pattern (14 bp):
AAAGAAGAAAAGCA
Found at i:1393532 original size:19 final size:20
Alignment explanation
Indices: 1393508--1393550 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1393498 AGCATTTATC
*
1393508 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
1393527 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
1393547 TTCA
1 TTCA
1393551 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:1393943 original size:36 final size:36
Alignment explanation
Indices: 1393892--1393995 Score: 174
Period size: 36 Copynumber: 2.9 Consensus size: 36
1393882 GATACAATCT
1393892 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
1393928 GTCTATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
1393964 TTCCATCACCA-TATCACGCCTATATTATCACC
1 GTCCATCACCATTATCACGCCTATATCATCACC
1393996 CACTTATAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 20 0.31
36 44 0.69
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:1394418 original size:28 final size:28
Alignment explanation
Indices: 1394379--1394451 Score: 76
Period size: 28 Copynumber: 2.5 Consensus size: 28
1394369 TGCTACAACA
*
1394379 AAAAAAAAGAAACA-AGAAAGAAGAAAGC
1 AAAAAAAAGAAA-AGAAAAAGAAGAAAGC
* *
1394407 AAAAGAAAGAAAAGAAAAAGAAGAAAATC
1 AAAAAAAAGAAAAGAAAAAGAAG-AAAGC
1394436 AAAAGCAAAAGAAAAG
1 AAAA--AAAAGAAAAG
1394452 TGAAGCAAGT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
27 1 0.03
28 19 0.51
29 8 0.22
31 9 0.24
ACGTcount: A:0.75, C:0.05, G:0.18, T:0.01
Consensus pattern (28 bp):
AAAAAAAAGAAAAGAAAAAGAAGAAAGC
Found at i:1394439 original size:14 final size:14
Alignment explanation
Indices: 1394395--1394440 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
1394385 AAGAAACAAG
1394395 AAAGAAG-AAAGCA
1 AAAGAAGAAAAGCA
*
1394408 AAAGAAAGAAAAGAA
1 AAAG-AAGAAAAGCA
*
1394423 AAAGAAGAAAATCA
1 AAAGAAGAAAAGCA
1394437 AAAG
1 AAAG
1394441 CAAAAGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 4 0.14
14 15 0.54
15 9 0.32
ACGTcount: A:0.74, C:0.04, G:0.20, T:0.02
Consensus pattern (14 bp):
AAAGAAGAAAAGCA
Found at i:1397621 original size:19 final size:20
Alignment explanation
Indices: 1397597--1397639 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
1397587 AGCATTTATC
*
1397597 TTCATT-AAAATTATGTATT
1 TTCATTAAAAATCATGTATT
*
1397616 TTCATTAAAAATCATGTGTT
1 TTCATTAAAAATCATGTATT
1397636 TTCA
1 TTCA
1397640 AAGGGGTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.49
Consensus pattern (20 bp):
TTCATTAAAAATCATGTATT
Found at i:1398032 original size:36 final size:36
Alignment explanation
Indices: 1397981--1398084 Score: 165
Period size: 36 Copynumber: 2.9 Consensus size: 36
1397971 GATACAATCT
1397981 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
1398017 GTCTATCACCATTATCAAGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
1398053 TTCCATCACCA-TATCACGCCTATATTATCACC
1 GTCCATCACCATTATCACGCCTATATCATCACC
1398085 CACTTATAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 19 0.31
36 43 0.69
ACGTcount: A:0.31, C:0.35, G:0.05, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:1410898 original size:13 final size:12
Alignment explanation
Indices: 1410864--1410905 Score: 52
Period size: 11 Copynumber: 3.7 Consensus size: 12
1410854 TTGCAATTCC
*
1410864 TTTATCTT-TTC
1 TTTATCTTATTT
1410875 TTTATCTT-TTT
1 TTTATCTTATTT
*
1410886 TTAATCTTATTT
1 TTTATCTTATTT
1410898 TTTATCTT
1 TTTATCTT
1410906 GTTTCCAGCA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
11 17 0.63
12 10 0.37
ACGTcount: A:0.14, C:0.12, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTATCTTATTT
Found at i:1417241 original size:790 final size:790
Alignment explanation
Indices: 1415634--1417913 Score: 4172
Period size: 790 Copynumber: 2.9 Consensus size: 790
1415624 AAGCTTGAAA
*
1415634 TGAAGACAATACACGCCCAAATTACTGCTGCACATCCTACACGAAATTGCACTACAAAACAGCCC
1 TGAAGACAATACACGCCCAAATTGCTGCTGCACATCCTACACGAAATTGCACTACAAAACAGCCC
*
1415699 ATGTGCATGCCAACAAAG-AATATGCTTGTCTCCACTTAGCAACAACTTGAAGAATTCGG-CAAA
66 ATGTGCATGCCAACAAAGCAAGATGCTTGTCTCCACTTAGCAACAACTTGAAGAATTCGGCCAAA
*
1415762 ACACTTCTAAGTCCTATAAATAGGCTTTCATATTGCATTATAACGGAGCTCATTATGATGAATTA
131 A-ACTTCTAAGCCCTATAAATAGGCTTTCATATTGCATTATAACGGAGCTCATTATGATGAATTA
1415827 AGTGAGATTATTCTCTTGTTTAAGTCCTTGTGACTTTTTATCGACCAAACAAGTAACTTGTTACT
195 AGTGAGATTATTCTCTTGTTTAAGTCCTTGTGACTTTTTATCGACCAAACAAGTAACTTGTTACT
* * * *
1415892 TGTGGCGTCAATTCCTTTCATTATGGTAATTCTGGTTCCTATCTCTATATAGATAGTGGGTCAAA
260 TGTGGCGTCATTTCCTTTCATTATGATAATTCTAGTTCCTATCTCTATATATATAGTGGGTCAAA
* * * *
1415957 TTCCTTGTTACCGCCCCTTAGAACGATTTGTGAGGATGGGTCTTTGCTCGTTATAGCACTGGTTC
325 TTCCTTGTTACCACCCCTTAGAATGATTTGTAAGGCTGGGTCTTTGCTCGTTATAGCACTGGTTC
*
1416022 TTCCTTGGTTATTCTAAGATACTGTCCATTCCATATTTACCATCCATTATTGGAGCAATATAAAA
390 TTCCTTGGTTATTCTAAGATACTATCCATTCCATATTTACCATCCATTATTGGAGCAATATAAAA
*
1416087 TTTGGGTCTTTCTTCTTTAACATTGGTTCTTCTTTGAGTATTCCTTAAGATACTATCATATTTAC
455 TCTGGGTCTTTCTTCTTTAACATTGGTTCTTCTTTGAGTATTCCTTAAGATACTATCATATTTAC
*
1416152 CATTATGTTATTTCGTTTCTTTATCATAACCACAACCAAGTCTTACGCTGCCATCTCTTATCCGA
520 CATTATGTTATTTCGTTTCTTTATCATAACCAAAACCAAGTCTTACGCTGCCATCTCTTATCCGA
1416217 CCATTTACCATCACGTTTACCACTTAAACTATCCATTTCTTACCCTTTTCTTATGTAGGTTGTTT
585 CCATTTACCATCACGTTTACCACTTAAACTATCCATTTCTTACCCTTTTCTTATGTAGGTTGTTT
1416282 TGCTTCCTTCCTGGATCCACAATCATTCGATAAGGCAGATCAGATCATATCATATGGTAACCAGA
650 TGCTTCCTTCCTGGATCCACAATCATTCGATAAGGCAGATCAGATCATATCATATGGTAACCAGA
1416347 GCCTTGGTGGAAGAAGCAACGTGCAACAGAAACAAAACCAAAAAAAAATACACTAAAGAGAAGTC
715 GCCTTGGTGGAAGAAGCAACGTGCAACAGAAACAAAACCAAAAAAAAATACACTAAAGAGAAGTC
1416412 ACCCTTCGATT
780 ACCCTTCGATT
*
1416423 TGAAGACAATACACGCCCAAATTGCTGCTGCACATCCTACATGAAATTGCACTACAAAACAGCCC
1 TGAAGACAATACACGCCCAAATTGCTGCTGCACATCCTACACGAAATTGCACTACAAAACAGCCC
1416488 ATGTGCATGCCAACAAAGCAAGATGCTTGTCTCCACTTAGCAACAACTTGAAGAATTCGGCCAAA
66 ATGTGCATGCCAACAAAGCAAGATGCTTGTCTCCACTTAGCAACAACTTGAAGAATTCGGCCAAA
1416553 AACTTCTAAGCCCTATAAATAGGCTTTCATATTGCATTATAACGGAGCTCATTATGATGAATTAA
131 AACTTCTAAGCCCTATAAATAGGCTTTCATATTGCATTATAACGGAGCTCATTATGATGAATTAA
1416618 GTGAGATTATTCTCTTGTTTAAGTCCTTGTGACTTTTTATCGACCAAACAAGTAACTTGTTACTT
196 GTGAGATTATTCTCTTGTTTAAGTCCTTGTGACTTTTTATCGACCAAACAAGTAACTTGTTACTT
1416683 GTGGCGTCATTTCCTTTCATTATGATAATTCTAGTTCCTATCTCTATATATATAGTGGGTCAAAT
261 GTGGCGTCATTTCCTTTCATTATGATAATTCTAGTTCCTATCTCTATATATATAGTGGGTCAAAT
1416748 TCCTTGTTACCACCCCTTAGAATGATTTGTAAGGCTGGGTCTTTGCTCGTTATAGCACTGGTTCT
326 TCCTTGTTACCACCCCTTAGAATGATTTGTAAGGCTGGGTCTTTGCTCGTTATAGCACTGGTTCT
*
1416813 TCCTTGGTTATTCTAAGATACTATCCATTCCATATTTACCATCCCTTATTGGAGCAATATAAAAT
391 TCCTTGGTTATTCTAAGATACTATCCATTCCATATTTACCATCCATTATTGGAGCAATATAAAAT
1416878 CTGGGTCTTTCTTCTTTAACATTGGTTCTTCTTTGAGTATTCCTTAAGATACTATCATATTTACC
456 CTGGGTCTTTCTTCTTTAACATTGGTTCTTCTTTGAGTATTCCTTAAGATACTATCATATTTACC
* *
1416943 ATTATGTTATTTCATTTCTTTATCATAACCATAACCAAGTCTTACGCTGCCATCTCTTATCCGAC
521 ATTATGTTATTTCGTTTCTTTATCATAACCAAAACCAAGTCTTACGCTGCCATCTCTTATCCGAC
1417008 CATTTACCATCACGTTTACCACTTAAACTATCCATTTCTTACCCTTTTCTTATGTAGGTTGTTTT
586 CATTTACCATCACGTTTACCACTTAAACTATCCATTTCTTACCCTTTTCTTATGTAGGTTGTTTT
1417073 GCTTCCTTCCTGGATCCACAATCATTCGATAAGGCAGATCAGATCATATCATATGGTAACCAGAG
651 GCTTCCTTCCTGGATCCACAATCATTCGATAAGGCAGATCAGATCATATCATATGGTAACCAGAG
*
1417138 CCTTGGTGGAAGAAGCAACGTGCAACAGAAACAAAACTAAAAAAAAATACACTAAAGAGAAGTCA
716 CCTTGGTGGAAGAAGCAACGTGCAACAGAAACAAAACCAAAAAAAAATACACTAAAGAGAAGTCA
1417203 CCCTTCGATT
781 CCCTTCGATT
1417213 TGAAGACAATACACGCCCAAATTGCTGCTGCACATCCTACACGAAATTGCACTACAAAACAGCCC
1 TGAAGACAATACACGCCCAAATTGCTGCTGCACATCCTACACGAAATTGCACTACAAAACAGCCC
1417278 ATGTGCATGCCAACAAAGCAAGATGCTTGTCTCCACTTAGCAACAACTTGAAGAATTCGGCCAAA
66 ATGTGCATGCCAACAAAGCAAGATGCTTGTCTCCACTTAGCAACAACTTGAAGAATTCGGCCAAA
1417343 AACTTCTAAGCCCTATAAATAGGCTTTCATATTGCATTATAACGGAGCTCATTATGATGAATTAA
131 AACTTCTAAGCCCTATAAATAGGCTTTCATATTGCATTATAACGGAGCTCATTATGATGAATTAA
1417408 GTGAGATTATTCTCTTGTTTAAGTCCTTGTGACTTTTTATCGACCAAACAAGTAACTTGTTACTT
196 GTGAGATTATTCTCTTGTTTAAGTCCTTGTGACTTTTTATCGACCAAACAAGTAACTTGTTACTT
1417473 GTGGCGTCATTTCCTTTCATTATGATAATTCTAGTTCCTATCTCTATATATATAGTGGGTCAAAT
261 GTGGCGTCATTTCCTTTCATTATGATAATTCTAGTTCCTATCTCTATATATATAGTGGGTCAAAT
*
1417538 TCCTTGTTACCACCCCTTAGAATGATTTGTAAGGCTGGGTCTCTGCTC-TTCATAGCACTGGTTC
326 TCCTTGTTACCACCCCTTAGAATGATTTGTAAGGCTGGGTCTTTGCTCGTT-ATAGCACTGGTTC
* *
1417602 TTCCTTGGTTATTCTAAGATACTATCCATTCCTTATTTACCATCCTTTATTGGAGCAATATAAAG
390 TTCCTTGGTTATTCTAAGATACTATCCATTCCATATTTACCATCCATTATTGGAGCAATATAAA-
*
1417667 A-CTGGGTCTTTGTTCTTTAACATTGGTTCTTCTTTGAGTATTCCTTAAGATACTATCATATTTA
454 ATCTGGGTCTTTCTTCTTTAACATTGGTTCTTCTTTGAGTATTCCTTAAGATACTATCATATTTA
* * * * * *
1417731 CCATTCTGTCATTTCGTTTCTATATCATAACCAAAACCAAGTCTTCCGCTACCATCTCTTATCCA
519 CCATTATGTTATTTCGTTTCTTTATCATAACCAAAACCAAGTCTTACGCTGCCATCTCTTATCCG
* * *
1417796 ACCATTTACCATCATGTTTACCACTTATACTATCTATTTCTTACCCTTTTCTTATGTAGGTTGTT
584 ACCATTTACCATCACGTTTACCACTTAAACTATCCATTTCTTACCCTTTTCTTATGTAGGTTGTT
* * * * *
1417861 TTGCTTCCTTCCTAGATCCATAATCATTCGATAAGGTAGATCGGATCGTATCA
649 TTGCTTCCTTCCTGGATCCACAATCATTCGATAAGGCAGATCAGATCATATCA
1417914 GTACATAATG
Statistics
Matches: 1448, Mismatches: 39, Indels: 7
0.97 0.03 0.00
Matches are distributed among these distances:
789 83 0.06
790 1359 0.94
791 6 0.00
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (790 bp):
TGAAGACAATACACGCCCAAATTGCTGCTGCACATCCTACACGAAATTGCACTACAAAACAGCCC
ATGTGCATGCCAACAAAGCAAGATGCTTGTCTCCACTTAGCAACAACTTGAAGAATTCGGCCAAA
AACTTCTAAGCCCTATAAATAGGCTTTCATATTGCATTATAACGGAGCTCATTATGATGAATTAA
GTGAGATTATTCTCTTGTTTAAGTCCTTGTGACTTTTTATCGACCAAACAAGTAACTTGTTACTT
GTGGCGTCATTTCCTTTCATTATGATAATTCTAGTTCCTATCTCTATATATATAGTGGGTCAAAT
TCCTTGTTACCACCCCTTAGAATGATTTGTAAGGCTGGGTCTTTGCTCGTTATAGCACTGGTTCT
TCCTTGGTTATTCTAAGATACTATCCATTCCATATTTACCATCCATTATTGGAGCAATATAAAAT
CTGGGTCTTTCTTCTTTAACATTGGTTCTTCTTTGAGTATTCCTTAAGATACTATCATATTTACC
ATTATGTTATTTCGTTTCTTTATCATAACCAAAACCAAGTCTTACGCTGCCATCTCTTATCCGAC
CATTTACCATCACGTTTACCACTTAAACTATCCATTTCTTACCCTTTTCTTATGTAGGTTGTTTT
GCTTCCTTCCTGGATCCACAATCATTCGATAAGGCAGATCAGATCATATCATATGGTAACCAGAG
CCTTGGTGGAAGAAGCAACGTGCAACAGAAACAAAACCAAAAAAAAATACACTAAAGAGAAGTCA
CCCTTCGATT
Found at i:1421117 original size:17 final size:18
Alignment explanation
Indices: 1421080--1421121 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
1421070 ATTTCTTTTC
1421080 TTTTCTTCTTTTCTGATT
1 TTTTCTTCTTTTCTGATT
1421098 TTTTCTTCTTTT-TG-TCT
1 TTTTCTTCTTTTCTGAT-T
1421115 TTTTCTT
1 TTTTCTT
1421122 TTCTTTGTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.04
17 10 0.43
18 12 0.52
ACGTcount: A:0.02, C:0.17, G:0.05, T:0.76
Consensus pattern (18 bp):
TTTTCTTCTTTTCTGATT
Found at i:1421386 original size:27 final size:26
Alignment explanation
Indices: 1421356--1421412 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
1421346 TAAGAAAGAA
* *
1421356 AAATGATTAATA-AAGGAAGATTAAATG
1 AAATGATAAATATAA-GAA-ATGAAATG
1421383 AAATGATAAATATAAGAAATGAAATG
1 AAATGATAAATATAAGAAATGAAATG
1421409 AAAT
1 AAAT
1421413 AAAGATGGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 11 0.41
27 14 0.52
28 2 0.07
ACGTcount: A:0.60, C:0.00, G:0.16, T:0.25
Consensus pattern (26 bp):
AAATGATAAATATAAGAAATGAAATG
Found at i:1425174 original size:20 final size:20
Alignment explanation
Indices: 1425128--1425175 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
1425118 AAAAAAAAAC
1425128 AAAAAAAAGGCAAAAATACA
1 AAAAAAAAGGCAAAAATACA
* * *
1425148 AACAAAAAAGTCAAAATTTCA
1 AA-AAAAAAGGCAAAAATACA
1425169 AAAAAAA
1 AAAAAAA
1425176 TTGAAAACGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.73, C:0.10, G:0.06, T:0.10
Consensus pattern (20 bp):
AAAAAAAAGGCAAAAATACA
Found at i:1427178 original size:34 final size:35
Alignment explanation
Indices: 1427113--1427191 Score: 115
Period size: 34 Copynumber: 2.3 Consensus size: 35
1427103 ACTATTTGTC
*
1427113 CATCACCATCTTCCGTCACCATATCACGCCTATAT
1 CATCACCATCTTCCATCACCATATCACGCCTATAT
* * *
1427148 CATCACCAT-TTCCATTACCATTTCATGCCTATAT
1 CATCACCATCTTCCATCACCATATCACGCCTATAT
1427182 CATCACCATC
1 CATCACCATC
1427192 CCTTAACCAT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
34 30 0.77
35 9 0.23
ACGTcount: A:0.27, C:0.38, G:0.04, T:0.32
Consensus pattern (35 bp):
CATCACCATCTTCCATCACCATATCACGCCTATAT
Found at i:1427904 original size:17 final size:17
Alignment explanation
Indices: 1427879--1427911 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1427869 ATTCTACCTC
1427879 TACCATAACCATTTCTA
1 TACCATAACCATTTCTA
*
1427896 TACCCTAACCATTTCT
1 TACCATAACCATTTCT
1427912 TTTAAGCCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.36
Consensus pattern (17 bp):
TACCATAACCATTTCTA
Found at i:1430014 original size:20 final size:20
Alignment explanation
Indices: 1429991--1430028 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1429981 CATTTCCATT
*
1429991 TCATCATCATCCATCATCCA
1 TCATCAACATCCATCATCCA
*
1430011 TCATCAACATCCTTCATC
1 TCATCAACATCCATCATC
1430029 AAGACCATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.39, G:0.00, T:0.32
Consensus pattern (20 bp):
TCATCAACATCCATCATCCA
Found at i:1430096 original size:17 final size:19
Alignment explanation
Indices: 1430064--1430108 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 19
1430054 CGCAGCCATC
1430064 TCTA-TCATTTCTTTAT-T
1 TCTATTCATTTCTTTATCT
1430081 TCTATTCATTTC-TTATCT
1 TCTATTCATTTCTTTATCT
1430099 T-TATT-ATTTC
1 TCTATTCATTTC
1430109 ACTTATTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 5 0.19
17 12 0.46
18 9 0.35
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (19 bp):
TCTATTCATTTCTTTATCT
Found at i:1430392 original size:17 final size:18
Alignment explanation
Indices: 1430370--1430411 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
1430360 GCAAAAAGAA
1430370 AAGAAAAAGA-CA-AAAAG
1 AAGAAAAA-ATCAGAAAAG
1430387 AAGAAAAAATCAGAAAAG
1 AAGAAAAAATCAGAAAAG
1430405 AAGAAAA
1 AAGAAAA
1430412 GAAAAGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.04
17 10 0.43
18 12 0.52
ACGTcount: A:0.76, C:0.05, G:0.17, T:0.02
Consensus pattern (18 bp):
AAGAAAAAATCAGAAAAG
Found at i:1430419 original size:18 final size:18
Alignment explanation
Indices: 1430363--1430420 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
1430353 TTGGAGTGCA
1430363 AAAAGAAAAG-A-AAAAG
1 AAAAGAAAAGAAGAAAAG
*
1430379 -ACA-AAAAGAAGAAAA-
1 AAAAGAAAAGAAGAAAAG
*
1430394 AATCAGAAAAGAAGAAAAG
1 AA-AAGAAAAGAAGAAAAG
1430413 AAAAGAAA
1 AAAAGAAA
1430421 TTCAAAAGAG
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 5 0.15
15 3 0.09
16 5 0.15
17 2 0.06
18 17 0.50
19 2 0.06
ACGTcount: A:0.78, C:0.03, G:0.17, T:0.02
Consensus pattern (18 bp):
AAAAGAAAAGAAGAAAAG
Found at i:1433713 original size:17 final size:18
Alignment explanation
Indices: 1433682--1433720 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
1433672 CATCTCTATC
*
1433682 ATTTCTTTATTTTTATTA
1 ATTTCTTTATCTTTATTA
1433700 ATTT-TTTATCTTTATT-
1 ATTTCTTTATCTTTATTA
1433716 ATTTC
1 ATTTC
1433721 ACTTATTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
16 4 0.21
17 11 0.58
18 4 0.21
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.72
Consensus pattern (18 bp):
ATTTCTTTATCTTTATTA
Found at i:1439091 original size:15 final size:15
Alignment explanation
Indices: 1439071--1439105 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
1439061 AAAGTAAATG
1439071 GAAATGGAAAGAATT
1 GAAATGGAAAGAATT
1439086 GAAATGGAAAGAATT
1 GAAATGGAAAGAATT
1439101 GAAAT
1 GAAAT
1439106 ATAAAGGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.26, T:0.20
Consensus pattern (15 bp):
GAAATGGAAAGAATT
Found at i:1439111 original size:15 final size:15
Alignment explanation
Indices: 1439071--1439111 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1439061 AAAGTAAATG
*
1439071 GAAATGGAAAGAATT
1 GAAATAGAAAGAATT
*
1439086 GAAATGGAAAGAATT
1 GAAATAGAAAGAATT
*
1439101 GAAATATAAAG
1 GAAATAGAAAG
1439112 GAATGTTATC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.56, C:0.00, G:0.24, T:0.20
Consensus pattern (15 bp):
GAAATAGAAAGAATT
Found at i:1442899 original size:15 final size:16
Alignment explanation
Indices: 1442879--1442908 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1442869 AAAGTAAATG
1442879 GAAATGGAAA-GAATT
1 GAAATGGAAATGAATT
1442894 GAAATGGAAATGAAT
1 GAAATGGAAATGAAT
1442909 GTTATCAAAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.00, G:0.27, T:0.20
Consensus pattern (16 bp):
GAAATGGAAATGAATT
Found at i:1443838 original size:35 final size:37
Alignment explanation
Indices: 1443792--1443871 Score: 119
Period size: 35 Copynumber: 2.2 Consensus size: 37
1443782 TTTGAGAATT
*
1443792 TGGTGATGATATAGGCGTGAT-ATGGTA-ATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
1443827 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
1443864 TGGGGATG
1 TGGTGATG
1443872 GAAATAGTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
35 21 0.52
36 5 0.12
37 14 0.35
ACGTcount: A:0.29, C:0.04, G:0.38, T:0.30
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:1446635 original size:20 final size:21
Alignment explanation
Indices: 1446598--1446636 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
1446588 TTTGGTCTTG
*
1446598 ATGAAGGATGTTGATGATGAA
1 ATGAAGGATGGTGATGATGAA
*
1446619 ATGAA-GATGGTGGTGATG
1 ATGAAGGATGGTGATGATG
1446637 TTGTATCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.33, C:0.00, G:0.38, T:0.28
Consensus pattern (21 bp):
ATGAAGGATGGTGATGATGAA
Found at i:1448960 original size:24 final size:25
Alignment explanation
Indices: 1448906--1448960 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
1448896 TTGTGAATCA
*
1448906 CCAAAAGTCATGGCTATTGGTTCTT
1 CCAAAAGTCATAGCTATTGGTTCTT
* * *
1448931 -CGAAAGTCATATCTTTTGGTT-TT
1 CCAAAAGTCATAGCTATTGGTTCTT
1448954 CCAAAAG
1 CCAAAAG
1448961 CCATGATTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
23 2 0.08
24 22 0.92
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.36
Consensus pattern (25 bp):
CCAAAAGTCATAGCTATTGGTTCTT
Found at i:1450289 original size:28 final size:30
Alignment explanation
Indices: 1450228--1450301 Score: 93
Period size: 29 Copynumber: 2.5 Consensus size: 30
1450218 CTTTCCATGG
*
1450228 CTTTGCTTTCTTTTTGAAATTCTTCTTTTT
1 CTTTTCTTTCTTTTTGAAATTCTTCTTTTT
1450258 CTTTTC-TTCTTTTCTG-AATT-TT-TTTTGT
1 CTTTTCTTTCTTTT-TGAAATTCTTCTTTT-T
1450286 CTTTTCTTTCTTTTTG
1 CTTTTCTTTCTTTTTG
1450302 TACGCCAATT
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
27 4 0.10
28 11 0.28
29 18 0.45
30 7 0.17
ACGTcount: A:0.07, C:0.16, G:0.07, T:0.70
Consensus pattern (30 bp):
CTTTTCTTTCTTTTTGAAATTCTTCTTTTT
Found at i:1461068 original size:23 final size:23
Alignment explanation
Indices: 1461025--1461069 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1461015 TGTCCTTGGA
1461025 AGGACCAATGAACATGACCTATG
1 AGGACCAATGAACATGACCTATG
*
1461048 AGGACTCAATGATCATG-CCTAT
1 AGGAC-CAATGAACATGACCTAT
1461070 TGGAGTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (23 bp):
AGGACCAATGAACATGACCTATG
Found at i:1462615 original size:35 final size:35
Alignment explanation
Indices: 1462576--1462655 Score: 124
Period size: 35 Copynumber: 2.3 Consensus size: 35
1462566 ACTATTTGTC
* *
1462576 CATCACCATCTTCTATCACCATATCACACCTATAT
1 CATCACCATCTTCCATCACAATATCACACCTATAT
* *
1462611 CATCACCATCTTCCATCACAATTTCACGCCTATAT
1 CATCACCATCTTCCATCACAATATCACACCTATAT
1462646 CATCACCATC
1 CATCACCATC
1462656 AGTTAACCAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.30, C:0.39, G:0.01, T:0.30
Consensus pattern (35 bp):
CATCACCATCTTCCATCACAATATCACACCTATAT
Found at i:1480240 original size:16 final size:16
Alignment explanation
Indices: 1480219--1480252 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
1480209 AAGACCAGAA
*
1480219 TTCTTTTTCTTTTCTT
1 TTCTTTTTCTTTTATT
*
1480235 TTCTTTTTTTTTTATT
1 TTCTTTTTCTTTTATT
1480251 TT
1 TT
1480253 TTTAATTTTC
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:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (16 bp):
TTCTTTTTCTTTTATT
Found at i:1488197 original size:29 final size:30
Alignment explanation
Indices: 1488144--1488210 Score: 79
Period size: 29 Copynumber: 2.3 Consensus size: 30
1488134 ATTGGCTTGC
*
1488144 TTTCTTTTTTTGAATTCTTTTTC-TTTTCT
1 TTTCTTTTTTTGAATTCTTTCTCTTTTTCT
1488173 TTTCTTCTTTTCTG-ATT-TTTCTCTTTTTC-
1 TTTCTT-TTTT-TGAATTCTTTCTCTTTTTCT
1488202 TTTCTTTTT
1 TTTCTTTTT
1488211 GCACTCCAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
28 3 0.09
29 17 0.50
30 12 0.35
31 2 0.06
ACGTcount: A:0.04, C:0.16, G:0.03, T:0.76
Consensus pattern (30 bp):
TTTCTTTTTTTGAATTCTTTCTCTTTTTCT
Found at i:1488506 original size:19 final size:20
Alignment explanation
Indices: 1488478--1488517 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
1488468 GGATAATAAT
1488478 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
*
1488498 ATAAG-AATGAAATGAAATA
1 ATAAGTAATGAAAAGAAATA
1488517 A
1 A
1488518 AGAAAGGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.20
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:1493137 original size:50 final size:50
Alignment explanation
Indices: 1493062--1493188 Score: 236
Period size: 50 Copynumber: 2.5 Consensus size: 50
1493052 CACACTCCAA
*
1493062 TTTGCCTTTTCATTGCGACTAGTAGGGATGGTCAGAGCCATATTATCGTG
1 TTTGCCATTTCATTGCGACTAGTAGGGATGGTCAGAGCCATATTATCGTG
1493112 TTTGCCATTTCATTGCGACTAGTAGGGATGGTCAGAGCCATATTATCGTG
1 TTTGCCATTTCATTGCGACTAGTAGGGATGGTCAGAGCCATATTATCGTG
*
1493162 TTTGCCATTTCATTGCGACTAGGAGGG
1 TTTGCCATTTCATTGCGACTAGTAGGG
1493189 CTCGATAAGA
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
50 75 1.00
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.35
Consensus pattern (50 bp):
TTTGCCATTTCATTGCGACTAGTAGGGATGGTCAGAGCCATATTATCGTG
Found at i:1495729 original size:17 final size:17
Alignment explanation
Indices: 1495705--1495750 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 17
1495695 ATTATCATAT
*
1495705 CCATTTCTATTCCCTAA
1 CCATTTCTATACCCTAA
*
1495722 CTATTTCTATACCCTAA
1 CCATTTCTATACCCTAA
1495739 CCATTTCCTATA
1 CCATTT-CTATA
1495751 GCCGACGCAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 20 0.80
18 5 0.20
ACGTcount: A:0.26, C:0.33, G:0.00, T:0.41
Consensus pattern (17 bp):
CCATTTCTATACCCTAA
Found at i:1500577 original size:457 final size:457
Alignment explanation
Indices: 1499723--1501085 Score: 2649
Period size: 457 Copynumber: 3.0 Consensus size: 457
1499713 ATTGAAGTCC
1499723 AAGTTCTATGGAAACTTGACTAGGACAACTCCAGGACAGCTCAAGAACATTTTGGGATGAAGTTT
1 AAGTTCTATGGAAACTTGACTAGGACAACTCCAGGACAGCTCAAGAACATTTTGGGATGAAGTTT
*
1499788 CTAGCTGACCCCTGAGCTTATAGTTGACTTGAGCTGGTCTTTTCAGCTAGCTAAAGACCTCATTT
66 CTAGCTGACCCCTGAGCTCATAGTTGACTTGAGCTGGTCTTTTCAGCTAGCTAAAGACCTCATTT
1499853 TAGCTAGAGAGTTATACCATCATCACCACCACACAGAGTACTTCAAATATGGTCTAGGTTAATTT
131 TAGCTAGAGAGTTATACCATCATCACCACCACACAGAGTACTTCAAATATGGTCTAGGTTAATTT
1499918 TTGTGGATTCGTACCTTTTCGCGAAGAGTTGTCATTCCAAGAGGTGTCATTTCACAATGAGCTTA
196 TTGTGGATTCGTACCTTTTCGCGAAGAGTTGTCATTCCAAGAGGTGTCATTTCACAATGAGCTTA
1499983 CCAAAGACTCACCTACATGTCCTTCATCTATGGCTAGCTCATATTCATCTCAAACACATGGAAAA
261 CCAAAGACTCACCTACATGTCCTTCATCTATGGCTAGCTCATATTCATCTCAAACACATGGAAAA
1500048 TAACTCAAATGATGAAAGGTTACCTTCCAAAAATGTGACCTTTCATAACAAGTTGCTTCCCAATT
326 TAACTCAAATGATGAAAGGTTACCTTCCAAAAATGTGACCTTTCATAACAAGTTGCTTCCCAATT
1500113 GATGACATGTCATTTAGACACATGTTGGATGCCAAGTCACGCCTAACTTGCTGCTTATCTTGGGA
391 GATGACATGTCATTTAGACACATGTTGGATGCCAAGTCACGCCTAACTTGCTGCTTATCTTGGGA
1500178 TG
456 TG
1500180 AAGTTCTATGGAAACTTGACTAGGACAACTCCAGGACAGCTCAAGAACATTTTGGGATGAAGTTT
1 AAGTTCTATGGAAACTTGACTAGGACAACTCCAGGACAGCTCAAGAACATTTTGGGATGAAGTTT
*
1500245 CTAGCTGACCCCTGAGCTCATAGTTGGCTTGAGCTGGTCTTTTCAGCTAGCTAAAGACCTCATTT
66 CTAGCTGACCCCTGAGCTCATAGTTGACTTGAGCTGGTCTTTTCAGCTAGCTAAAGACCTCATTT
1500310 TAGCTAGAGAGTTATACCATCATCACCACCACACAGAGTACTTCAAATATGGTCTAGGTTAATTT
131 TAGCTAGAGAGTTATACCATCATCACCACCACACAGAGTACTTCAAATATGGTCTAGGTTAATTT
*
1500375 TTGTGGATTCGTACATTTTCGCGAAGAGTTGTCATTCCAAGAGGTGTCATTTCACAATGAGCTTA
196 TTGTGGATTCGTACCTTTTCGCGAAGAGTTGTCATTCCAAGAGGTGTCATTTCACAATGAGCTTA
*
1500440 CCAAAGACTCACCTATATGTCCTTCATCTATGGCTAGCTCATATTCATCTCAAACACATGGAAAA
261 CCAAAGACTCACCTACATGTCCTTCATCTATGGCTAGCTCATATTCATCTCAAACACATGGAAAA
1500505 TAACTCAAATGATGAAAGGTTACCTTCCAAAAATGTGACCTTTCATAACAAGTTGCTTCCCAATT
326 TAACTCAAATGATGAAAGGTTACCTTCCAAAAATGTGACCTTTCATAACAAGTTGCTTCCCAATT
1500570 GATGACATGTCATTTAGACACATGTTGGATGCCAAGTCACGCCTAACTTGCTGCTTATCTTGGGA
391 GATGACATGTCATTTAGACACATGTTGGATGCCAAGTCACGCCTAACTTGCTGCTTATCTTGGGA
1500635 TG
456 TG
*
1500637 AAGTTCTATGGAAACTTGACTAGGACAACTCCAGGACAGCTCAAGAACATTTTAGGATGAAGTTT
1 AAGTTCTATGGAAACTTGACTAGGACAACTCCAGGACAGCTCAAGAACATTTTGGGATGAAGTTT
1500702 CTAGCTGACCCCTGAGCTCATAGTTGACTTGAGCTGGTCTTTTCAGCTAGCTAAAGACCTCATTT
66 CTAGCTGACCCCTGAGCTCATAGTTGACTTGAGCTGGTCTTTTCAGCTAGCTAAAGACCTCATTT
1500767 TAGCTAGAGAGTTATACCATCATCACCACCACACAGAGTACTTCAAATATGGTCTAGGTTAATTT
131 TAGCTAGAGAGTTATACCATCATCACCACCACACAGAGTACTTCAAATATGGTCTAGGTTAATTT
1500832 TTGTGGATTCGTACCTTTTCGCGAAGAGTTGTCATTCCAAGAGGTGTCATTTCACAATGAGCTTA
196 TTGTGGATTCGTACCTTTTCGCGAAGAGTTGTCATTCCAAGAGGTGTCATTTCACAATGAGCTTA
*
1500897 CCAAAGACTCACCTACATGTCCTTCATCTATGGCTAGCTCATATTCATCTCAAACACGTGGAAAA
261 CCAAAGACTCACCTACATGTCCTTCATCTATGGCTAGCTCATATTCATCTCAAACACATGGAAAA
1500962 TAACTCAAATGATGAAAGG-T-CCTTCCAAAAATGTGACCTTTCATAACAAGTTGCTTCCCAATT
326 TAACTCAAATGATGAAAGGTTACCTTCCAAAAATGTGACCTTTCATAACAAGTTGCTTCCCAATT
*
1501025 GTTGACATGTCATTTAGACACATGTTGGATGCCAAGTCACGCCTAACTTGCTGCTTATCTT
391 GATGACATGTCATTTAGACACATGTTGGATGCCAAGTCACGCCTAACTTGCTGCTTATCTT
1501086 CACTCCATGG
Statistics
Matches: 896, Mismatches: 10, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
455 103 0.11
456 1 0.00
457 792 0.88
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.30
Consensus pattern (457 bp):
AAGTTCTATGGAAACTTGACTAGGACAACTCCAGGACAGCTCAAGAACATTTTGGGATGAAGTTT
CTAGCTGACCCCTGAGCTCATAGTTGACTTGAGCTGGTCTTTTCAGCTAGCTAAAGACCTCATTT
TAGCTAGAGAGTTATACCATCATCACCACCACACAGAGTACTTCAAATATGGTCTAGGTTAATTT
TTGTGGATTCGTACCTTTTCGCGAAGAGTTGTCATTCCAAGAGGTGTCATTTCACAATGAGCTTA
CCAAAGACTCACCTACATGTCCTTCATCTATGGCTAGCTCATATTCATCTCAAACACATGGAAAA
TAACTCAAATGATGAAAGGTTACCTTCCAAAAATGTGACCTTTCATAACAAGTTGCTTCCCAATT
GATGACATGTCATTTAGACACATGTTGGATGCCAAGTCACGCCTAACTTGCTGCTTATCTTGGGA
TG
Found at i:1503324 original size:24 final size:23
Alignment explanation
Indices: 1503266--1503325 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 23
1503256 AAAATCAGCA
*
1503266 AAGAAAATA-AAAACACTCAAAAG
1 AAGAAAA-AGAAAGCACTCAAAAG
**
1503289 AAGAAATTGAAAGCACTCAAAAAG
1 AAGAAAAAGAAAGCACTC-AAAAG
1503313 AAGAAAAAGAAAG
1 AAGAAAAAGAAAG
1503326 AAAGAAAAGT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
23 14 0.47
24 16 0.53
ACGTcount: A:0.67, C:0.10, G:0.15, T:0.08
Consensus pattern (23 bp):
AAGAAAAAGAAAGCACTCAAAAG
Found at i:1526405 original size:36 final size:35
Alignment explanation
Indices: 1526354--1526463 Score: 132
Period size: 35 Copynumber: 3.1 Consensus size: 35
1526344 TAAGATACTA
* *
1526354 CCTA-AACATCACCATCTTCCATCACTATTTTCATG
1 CCTATAACATCACCATCTTCCATCACCA-TTTCACG
* *
1526389 CCTATAACATCACCATCTTCCATTACCATTGCACG
1 CCTATAACATCACCATCTTCCATCACCATTTCACG
* * * *
1526424 TCTATATCATTACCATCTTCTATCACCATTTCACG
1 CCTATAACATCACCATCTTCCATCACCATTTCACG
1526459 CCTAT
1 CCTAT
1526464 TATAACCACC
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
35 42 0.67
36 21 0.33
ACGTcount: A:0.27, C:0.35, G:0.04, T:0.35
Consensus pattern (35 bp):
CCTATAACATCACCATCTTCCATCACCATTTCACG
Done.