Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001444.1 Hibiscus syriacus cultivar Beakdansim tig00002793_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: 2564052
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 12
Found at i:1100420 original size:31 final size:30
Alignment explanation
Indices: 1100382--1100532 Score: 179
Period size: 29 Copynumber: 5.1 Consensus size: 30
1100372 TTAATTTAAG
* *
1100382 ATATATTTTTAAAAGTTAATATAATAATAA
1 ATATATTTTTAAAAGTTAAAATAAGAATAA
*
1100412 TATATATTTTT--AAGTTAAAATAAGATTAAA
1 -ATATATTTTTAAAAGTTAAAATAAGAAT-AA
*
1100442 ATATATTTTTAAAAGTTAATATAAGAATAA
1 ATATATTTTTAAAAGTTAAAATAAGAATAA
*
1100472 GATATATTTTT-AAA-TTAAAATAAGATTAA
1 -ATATATTTTTAAAAGTTAAAATAAGAATAA
*
1100501 ATATATTTTT-AAAGTCAAAATAA-AATAA
1 ATATATTTTTAAAAGTTAAAATAAGAATAA
1100529 ATAT
1 ATAT
1100533 TTAATAATTA
Statistics
Matches: 106, Mismatches: 9, Indels: 13
0.83 0.07 0.10
Matches are distributed among these distances:
28 21 0.20
29 44 0.42
30 7 0.07
31 34 0.32
ACGTcount: A:0.53, C:0.01, G:0.05, T:0.41
Consensus pattern (30 bp):
ATATATTTTTAAAAGTTAAAATAAGAATAA
Found at i:1100446 original size:60 final size:60
Alignment explanation
Indices: 1100377--1100513 Score: 231
Period size: 60 Copynumber: 2.3 Consensus size: 60
1100367 TTATTTTAAT
* * * *
1100377 TTAAGATATATTTTTAAAAGTTAATATAATAATAATATATATTTTTAAGTTAAAATAAGA
1 TTAAAATATATTTTTAAAAGTTAATATAAGAATAAGATATATTTTTAAATTAAAATAAGA
1100437 TTAAAATATATTTTTAAAAGTTAATATAAGAATAAGATATATTTTTAAATTAAAATAAGA
1 TTAAAATATATTTTTAAAAGTTAATATAAGAATAAGATATATTTTTAAATTAAAATAAGA
1100497 TT-AAATATATTTTTAAA
1 TTAAAATATATTTTTAAA
1100514 GTCAAAATAA
Statistics
Matches: 73, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
59 15 0.21
60 58 0.79
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (60 bp):
TTAAAATATATTTTTAAAAGTTAATATAAGAATAAGATATATTTTTAAATTAAAATAAGA
Found at i:1101017 original size:21 final size:21
Alignment explanation
Indices: 1100987--1101111 Score: 96
Period size: 21 Copynumber: 6.0 Consensus size: 21
1100977 GATTTACATA
1100987 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* * *
1101008 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCATTGCGA--TAGTCCAAG
*
1101031 TT--TATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* * *
1101050 TTCGCATTGCGATTTATTACAAA
1 TTCGCATTGCGA--TAGTCCAAG
*
1101073 TTCG--TTACGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
1101092 TTCACGTTGCGATAGTCCAA
1 TTCGCATTGCGATAGTCCAA
1101112 AATCGTAACG
Statistics
Matches: 79, Mismatches: 17, Indels: 16
0.71 0.15 0.14
Matches are distributed among these distances:
19 18 0.23
21 42 0.53
23 19 0.24
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:1101043 original size:42 final size:42
Alignment explanation
Indices: 1100991--1101104 Score: 174
Period size: 42 Copynumber: 2.7 Consensus size: 42
1100981 TACATATTCG
*
1100991 CATTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
1 CATTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATT
* *
1101033 TATTGCGATAGTCCAAGTTCGCATTGCGATTTATTACAAATT
1 CATTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATT
* * *
1101075 CGTTACGATAGTCCAAGTTCACGTTGCGAT
1 CATTGCGATAGTCCAAGTTCGCGTTGCGAT
1101105 AGTCCAAAAT
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 64 1.00
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.35
Consensus pattern (42 bp):
CATTGCGATAGTCCAAGTTCGCGTTGCGATTTATTACAAATT
Found at i:1101212 original size:6 final size:6
Alignment explanation
Indices: 1101201--1101252 Score: 83
Period size: 6 Copynumber: 9.2 Consensus size: 6
1101191 GACACGTATT
1101201 ACCACG ACCACG ACCACG ACCACG ACCACG ---ACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1101246 ACCACG A
1 ACCACG A
1101253 GACGAGACGG
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
3 3 0.07
6 40 0.93
ACGTcount: A:0.35, C:0.48, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1101236 original size:15 final size:15
Alignment explanation
Indices: 1101201--1101247 Score: 67
Period size: 15 Copynumber: 2.9 Consensus size: 15
1101191 GACACGTATT
1101201 ACCACGACCACGACCACG
1 ACCACGACCACG---ACG
1101219 ACCACGACCACGACG
1 ACCACGACCACGACG
1101234 ACCACGACCACGAC
1 ACCACGACCACGAC
1101248 CACGAGACGA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
15 17 0.59
18 12 0.41
ACGTcount: A:0.34, C:0.49, G:0.17, T:0.00
Consensus pattern (15 bp):
ACCACGACCACGACG
Found at i:1101236 original size:21 final size:21
Alignment explanation
Indices: 1101210--1101252 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
1101200 TACCACGACC
1101210 ACGACCACGACCACGACCACG
1 ACGACCACGACCACGACCACG
1101231 ACGACCACGACCACGACCACG
1 ACGACCACGACCACGACCACG
1101252 A
1 A
1101253 GACGAGACGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.47, G:0.19, T:0.00
Consensus pattern (21 bp):
ACGACCACGACCACGACCACG
Found at i:1102024 original size:21 final size:19
Alignment explanation
Indices: 1101991--1102181 Score: 148
Period size: 19 Copynumber: 9.3 Consensus size: 19
1101981 CGTTGCGATT
*
1101991 TTGGACTATCGCAACGAAT
1 TTGGACTATCGCAACGAAC
*
1102010 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA--CGAAC
* *
1102033 TTCGACTATCGTAACGAAC
1 TTGGACTATCGCAACGAAC
*
1102052 TTGGAATAAATCGCAACACGAAC
1 TTGGACT--ATCGC-A-ACGAAC
*
1102075 TTCGACTATCGCAACGCGAAC
1 TTGGACTATCGCAA--CGAAC
1102096 TTGGACTATCGCAACGAAC
1 TTGGACTATCGCAACGAAC
* *
1102115 TTGGACTATCACAACGAAT
1 TTGGACTATCGCAACGAAC
*
1102134 TTGGAATAAATCGCAACGTGGAAC
1 TTGGACT--ATCGCAAC---GAAC
* *
1102158 TTAGACTATCGCAACGAAT
1 TTGGACTATCGCAACGAAC
1102177 TTGGA
1 TTGGA
1102182 AAATAGCATT
Statistics
Matches: 137, Mismatches: 20, Indels: 30
0.73 0.11 0.16
Matches are distributed among these distances:
19 52 0.38
20 1 0.01
21 47 0.34
22 9 0.07
23 20 0.15
24 8 0.06
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.23
Consensus pattern (19 bp):
TTGGACTATCGCAACGAAC
Found at i:1102056 original size:42 final size:42
Alignment explanation
Indices: 1101994--1102182 Score: 242
Period size: 42 Copynumber: 4.5 Consensus size: 42
1101984 TGCGATTTTG
1101994 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* * *
1102036 GACTATCGTAACGAACTTGGAATAAATCGCAACACGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* * *
1102078 GACTATCGCAACGCGAACTTGGACT--ATCGCAA--CGAACTTG
1 GACTATCGCAA--CGAATTTGGAATAAATCGCAACGCGAACTTC
* * *
1102118 GACTATCACAACGAATTTGGAATAAATCGCAACGTGGAACTTA
1 GACTATCGCAACGAATTTGGAATAAATCGCAACG-CGAACTTC
1102161 GACTATCGCAACGAATTTGGAA
1 GACTATCGCAACGAATTTGGAA
1102183 AATAGCATTG
Statistics
Matches: 128, Mismatches: 12, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
38 10 0.08
40 24 0.19
42 56 0.44
43 27 0.21
44 11 0.09
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.22
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:1102216 original size:21 final size:21
Alignment explanation
Indices: 1102187--1102237 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
1102177 TTGGAAAATA
*
1102187 GCATTGCGATAGTTGAAGTTC
1 GCATTGCGATAGTCGAAGTTC
* *
1102208 GCGTTGCGATAGTCGATGTTC
1 GCATTGCGATAGTCGAAGTTC
1102229 GCATTGCGA
1 GCATTGCGA
1102238 ATCTGGAAAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.20, C:0.18, G:0.31, T:0.31
Consensus pattern (21 bp):
GCATTGCGATAGTCGAAGTTC
Found at i:1111118 original size:27 final size:27
Alignment explanation
Indices: 1111088--1111140 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
1111078 CCGTTGAGAT
1111088 CACGTCTGCTTGAATGTGACTATGTAA
1 CACGTCTGCTTGAATGTGACTATGTAA
1111115 CACGTCTGCTTGAATGTGACTATGTA
1 CACGTCTGCTTGAATGTGACTATGTA
1111141 GTGCCTCCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.34
Consensus pattern (27 bp):
CACGTCTGCTTGAATGTGACTATGTAA
Found at i:1112359 original size:2 final size:2
Alignment explanation
Indices: 1112352--1112404 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
1112342 ATGTAGTACG
1112352 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1112394 AT AT AT A- AT AT
1 AT AT AT AT AT AT
1112405 TCATTCCGTC
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1114145 original size:27 final size:28
Alignment explanation
Indices: 1114115--1114180 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 28
1114105 TATTATAGTT
1114115 TAAAATGATAAAAAAAATATTATTA-AG-
1 TAAAATGATAAAAAAAATATT-TTATAGA
* * *
1114142 TAAATTGAT-ATAAAAATGTTTTATAGA
1 TAAAATGATAAAAAAAATATTTTATAGA
1114169 TAAAATGATAAA
1 TAAAATGATAAA
1114181 TTCAATCTGC
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
25 3 0.10
26 11 0.35
27 16 0.52
28 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.09, T:0.33
Consensus pattern (28 bp):
TAAAATGATAAAAAAAATATTTTATAGA
Found at i:1114653 original size:4 final size:4
Alignment explanation
Indices: 1114644--1114698 Score: 67
Period size: 4 Copynumber: 13.8 Consensus size: 4
1114634 CGTGTACGCA
* * *
1114644 CACG CACG CACG CACG CACG CAC- AAGCG CGCG CACA CACG CACG CACG
1 CACG CACG CACG CACG CACG CACG CA-CG CACG CACG CACG CACG CACG
1114692 CACG CAC
1 CACG CAC
1114699 AGTTTAAATT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
3 1 0.02
4 42 0.98
ACGTcount: A:0.27, C:0.49, G:0.24, T:0.00
Consensus pattern (4 bp):
CACG
Found at i:1116484 original size:124 final size:124
Alignment explanation
Indices: 1116264--1116514 Score: 502
Period size: 124 Copynumber: 2.0 Consensus size: 124
1116254 GAGGGGGTGA
1116264 ATTGACAATTAAAATTTCGGTGGAAGCTTTTGCAGAAAATTAAAAATATTTGCACAGCGATTTAG
1 ATTGACAATTAAAATTTCGGTGGAAGCTTTTGCAGAAAATTAAAAATATTTGCACAGCGATTTAG
1116329 AGTGGTTCGACTTTCTCAACCAAAGTCTACGTCCACTACCTTAGTTATCCACACTAAGG
66 AGTGGTTCGACTTTCTCAACCAAAGTCTACGTCCACTACCTTAGTTATCCACACTAAGG
1116388 ATTGACAATTAAAATTTCGGTGGAAGCTTTTGCAGAAAATTAAAAATATTTGCACAGCGATTTAG
1 ATTGACAATTAAAATTTCGGTGGAAGCTTTTGCAGAAAATTAAAAATATTTGCACAGCGATTTAG
1116453 AGTGGTTCGACTTTCTCAACCAAAGTCTACGTCCACTACCTTAGTTATCCACACTAAGG
66 AGTGGTTCGACTTTCTCAACCAAAGTCTACGTCCACTACCTTAGTTATCCACACTAAGG
1116512 ATT
1 ATT
1116515 TTCCACAAAT
Statistics
Matches: 127, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
124 127 1.00
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (124 bp):
ATTGACAATTAAAATTTCGGTGGAAGCTTTTGCAGAAAATTAAAAATATTTGCACAGCGATTTAG
AGTGGTTCGACTTTCTCAACCAAAGTCTACGTCCACTACCTTAGTTATCCACACTAAGG
Found at i:1118278 original size:21 final size:21
Alignment explanation
Indices: 1118252--1118298 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
1118242 CCGGAAGAGG
*
1118252 AGGAGGAGCACGAGAATAGCT
1 AGGAGGAGCACGAGAAGAGCT
1118273 AGGAGGAGCACGAGAAGAGCT
1 AGGAGGAGCACGAGAAGAGCT
1118294 AGGAG
1 AGGAG
1118299 CAGCTCGTGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.38, C:0.13, G:0.43, T:0.06
Consensus pattern (21 bp):
AGGAGGAGCACGAGAAGAGCT
Found at i:1118310 original size:21 final size:21
Alignment explanation
Indices: 1118252--1118311 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
1118242 CCGGAAGAGG
* *
1118252 AGGAGGAGCACGAGAATAGCT
1 AGGAGCAGCACGAGAAGAGCT
*
1118273 AGGAGGAGCACGAGAAGAGCT
1 AGGAGCAGCACGAGAAGAGCT
* *
1118294 AGGAGCAGCTCGTGAAGA
1 AGGAGCAGCACGAGAAGA
1118312 ACTGGCTCCC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.15, G:0.40, T:0.08
Consensus pattern (21 bp):
AGGAGCAGCACGAGAAGAGCT
Found at i:1119377 original size:21 final size:23
Alignment explanation
Indices: 1119327--1119390 Score: 89
Period size: 21 Copynumber: 2.9 Consensus size: 23
1119317 GCATGGCCTT
*
1119327 GTGCATCGATACACATTCAATGA
1 GTGCATCGATGCACATTCAATGA
1119350 GTGCATCGATGCATC-TTC-ATGA
1 GTGCATCGATGCA-CATTCAATGA
1119372 -TGCATCGATGCACATTCAA
1 GTGCATCGATGCACATTCAA
1119391 AGGGATACAT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
20 1 0.03
21 15 0.41
22 5 0.14
23 15 0.41
24 1 0.03
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (23 bp):
GTGCATCGATGCACATTCAATGA
Found at i:1119386 original size:44 final size:45
Alignment explanation
Indices: 1119327--1119428 Score: 127
Period size: 45 Copynumber: 2.3 Consensus size: 45
1119317 GCATGGCCTT
* * *
1119327 GTGCATCGATACACATTCAATGAG-TGCATCGATGCATCTTCAT-
1 GTGCATCGATGCACATTCAAAGAGATACATCGATGCATCTTCATA
* *
1119370 GATGCATCGATGCACATTCAAAGGGATACATCGATGCATTTTCATA
1 G-TGCATCGATGCACATTCAAAGAGATACATCGATGCATCTTCATA
*
1119416 GTGTATCGATGCA
1 GTGCATCGATGCA
1119429 TTATGCACAA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
43 1 0.02
44 20 0.40
45 28 0.56
46 1 0.02
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (45 bp):
GTGCATCGATGCACATTCAAAGAGATACATCGATGCATCTTCATA
Found at i:1125277 original size:64 final size:64
Alignment explanation
Indices: 1125209--1125367 Score: 150
Period size: 64 Copynumber: 2.5 Consensus size: 64
1125199 TACACTGATA
* * *
1125209 GTGCATCGA-TGCATAAATATGC-TTCGATGTTTTGAAAATGCCT-GAGTGCATCGATGCATGGC
1 GTGCATCGAGTGCATAAA-AT-CATTCGATGTTTT-AAAATACATGGAGTCCATCGATGCATGG-
1125271 T-T
62 TAT
* *
1125273 GTGCATC-AGTGCATAAAATCAATTCGATGTTTTAATATATATGGAGTCCATCGATGCATGGTAT
1 GTGCATCGAGTGCATAAAATC-ATTCGATGTTTTAAAATACATGGAGTCCATCGATGCATGGTAT
* * *
1125337 GTGCATCG-GTACACAAAAGCCATTCGATGTT
1 GTGCATCGAGTGCATAAAA-TCATTCGATGTT
1125368 CAATTAAAAC
Statistics
Matches: 80, Mismatches: 8, Indels: 14
0.78 0.08 0.14
Matches are distributed among these distances:
62 1 0.01
63 9 0.11
64 69 0.86
65 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (64 bp):
GTGCATCGAGTGCATAAAATCATTCGATGTTTTAAAATACATGGAGTCCATCGATGCATGGTAT
Found at i:1125987 original size:241 final size:241
Alignment explanation
Indices: 1125564--1126019 Score: 885
Period size: 241 Copynumber: 1.9 Consensus size: 241
1125554 ATTTTGATAT
1125564 TCGAATATACTTTAAAAAGATTATTTGTAAAATCTTAAAATTCATTTAAACTTAGTTTGTTATAT
1 TCGAATATACTTTAAAAAGATTATTTGTAAAATCTTAAAATTCATTTAAACTTAGTTTGTTATAT
*
1125629 CGAAAAATCAAAATGTTTTCAACAGTTTGTGTTTTTAAAGTAGGGTAGAGTTAAAGTTCAATGTA
66 CGAAAAATCAAAATGTTTTCAACAGTTTGTGTTTTTAAAGTAGGGTAGAGTTAAAGTTCAATATA
1125694 TGTTAGATTGTAAGAAATAAACGTTAAACATTTAATTAGAAAATTATATAGATAGACGAAAGGGT
131 TGTTAGATTGTAAGAAATAAACGTTAAACATTTAATTAGAAAATTATATAGATAGACGAAAGGGT
1125759 CATCTTGTAAAATAAACAAGATTATTTTGATAGTCGAATAATTATA
196 CATCTTGTAAAATAAACAAGATTATTTTGATAGTCGAATAATTATA
1125805 TCGAATATACTTTAAAAAGATTATTTGTAAAATCTTAAAATTCATTTAAACTTAGTTTGTTATAT
1 TCGAATATACTTTAAAAAGATTATTTGTAAAATCTTAAAATTCATTTAAACTTAGTTTGTTATAT
*
1125870 CGAAACATCAAAATGTTTTCAACAGTTTGTGTTTTTAAAGTAGGGTAGAGTTAAAGTTCAATATA
66 CGAAAAATCAAAATGTTTTCAACAGTTTGTGTTTTTAAAGTAGGGTAGAGTTAAAGTTCAATATA
1125935 TGTTAGATTGTAAGAAATAAACGTTAAACATTTAATTAGAAAATTATATAGATAGACGAAAGGGT
131 TGTTAGATTGTAAGAAATAAACGTTAAACATTTAATTAGAAAATTATATAGATAGACGAAAGGGT
*
1126000 TATCTTGTAAAATAAACAAG
196 CATCTTGTAAAATAAACAAG
1126020 CTAAAATCAC
Statistics
Matches: 212, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
241 212 1.00
ACGTcount: A:0.42, C:0.07, G:0.14, T:0.37
Consensus pattern (241 bp):
TCGAATATACTTTAAAAAGATTATTTGTAAAATCTTAAAATTCATTTAAACTTAGTTTGTTATAT
CGAAAAATCAAAATGTTTTCAACAGTTTGTGTTTTTAAAGTAGGGTAGAGTTAAAGTTCAATATA
TGTTAGATTGTAAGAAATAAACGTTAAACATTTAATTAGAAAATTATATAGATAGACGAAAGGGT
CATCTTGTAAAATAAACAAGATTATTTTGATAGTCGAATAATTATA
Found at i:1128537 original size:31 final size:31
Alignment explanation
Indices: 1128411--1128537 Score: 121
Period size: 31 Copynumber: 4.1 Consensus size: 31
1128401 GAGTCGAGGG
* *
1128411 TTTACCTATGTTCTACGGAACATATGGACAAA
1 TTTACCTATGTTCTTCGGGACATATGGAC-AA
* *
1128443 ATTATCTATG-TCTTTCGGGACATATGGACAA
1 TTTACCTATGTTC-TTCGGGACATATGGACAA
* ** * * *
1128474 TATACCTATGTTCTAAGGAATATATGTACAA
1 TTTACCTATGTTCTTCGGGACATATGGACAA
* *
1128505 TTTACCTAGGTTCTTCGGGACTTATGGACAA
1 TTTACCTATGTTCTTCGGGACATATGGACAA
1128536 TT
1 TT
1128538 GTCGAGGTTC
Statistics
Matches: 73, Mismatches: 20, Indels: 5
0.74 0.20 0.05
Matches are distributed among these distances:
31 49 0.67
32 24 0.33
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (31 bp):
TTTACCTATGTTCTTCGGGACATATGGACAA
Found at i:1129434 original size:30 final size:25
Alignment explanation
Indices: 1129371--1129418 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
1129361 TAGTACTGTT
*
1129371 ATTTTGTAAGAATATCGTTTGTAAA
1 ATTTTATAAGAATATCGTTTGTAAA
1129396 ATTTTATAAGAATATCGTTTGTA
1 ATTTTATAAGAATATCGTTTGTA
1129419 CCTCAAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.35, C:0.04, G:0.15, T:0.46
Consensus pattern (25 bp):
ATTTTATAAGAATATCGTTTGTAAA
Found at i:1132258 original size:16 final size:17
Alignment explanation
Indices: 1132237--1132281 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
1132227 CCATTTTCTT
1132237 AGTTTGAGAGTTTTA-A
1 AGTTTGAGAGTTTTACA
*
1132253 AGTTTGAAAG-TTTACA
1 AGTTTGAGAGTTTTACA
*
1132269 CGTTTGAGAGTTT
1 AGTTTGAGAGTTT
1132282 GAGATTTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 4 0.17
16 18 0.75
17 2 0.08
ACGTcount: A:0.29, C:0.04, G:0.24, T:0.42
Consensus pattern (17 bp):
AGTTTGAGAGTTTTACA
Found at i:1134676 original size:28 final size:28
Alignment explanation
Indices: 1134644--1134724 Score: 68
Period size: 28 Copynumber: 3.1 Consensus size: 28
1134634 TCGATTTTAT
1134644 GAGAGTCTAGTTCAATATGTTAAAAGGG
1 GAGAGTCTAGTTCAATATGTTAAAAGGG
* * * * *
1134672 GAGAGTTTTGATCGAT-T-TT---A--T
1 GAGAGTCTAGTTCAATATGTTAAAAGGG
1134693 GAGAGTCTAGTTCAATATGTTAAAAGGG
1 GAGAGTCTAGTTCAATATGTTAAAAGGG
1134721 GAGA
1 GAGA
1134725 TGCCTTGATC
Statistics
Matches: 36, Mismatches: 10, Indels: 14
0.60 0.17 0.23
Matches are distributed among these distances:
21 12 0.33
22 1 0.03
23 3 0.08
26 3 0.08
27 1 0.03
28 16 0.44
ACGTcount: A:0.33, C:0.06, G:0.28, T:0.32
Consensus pattern (28 bp):
GAGAGTCTAGTTCAATATGTTAAAAGGG
Found at i:1134683 original size:49 final size:49
Alignment explanation
Indices: 1134628--1134724 Score: 194
Period size: 49 Copynumber: 2.0 Consensus size: 49
1134618 TGCTTTTAGT
1134628 TTTTGATCGATTTTATGAGAGTCTAGTTCAATATGTTAAAAGGGGAGAG
1 TTTTGATCGATTTTATGAGAGTCTAGTTCAATATGTTAAAAGGGGAGAG
1134677 TTTTGATCGATTTTATGAGAGTCTAGTTCAATATGTTAAAAGGGGAGA
1 TTTTGATCGATTTTATGAGAGTCTAGTTCAATATGTTAAAAGGGGAGA
1134725 TGCCTTGATC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.31, C:0.06, G:0.26, T:0.37
Consensus pattern (49 bp):
TTTTGATCGATTTTATGAGAGTCTAGTTCAATATGTTAAAAGGGGAGAG
Found at i:1138457 original size:2 final size:2
Alignment explanation
Indices: 1138450--1138510 Score: 54
Period size: 2 Copynumber: 29.5 Consensus size: 2
1138440 TATGTTGCTA
* *
1138450 AT AT AT AT AT AT AT AT AT -T ACT TT AA AGT GAGT AT A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT A-T AT AT A-T -A-T AT AT AT AT AT
1138492 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
1138511 CTTTAAAAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
1 2 0.04
2 43 0.86
3 2 0.04
4 3 0.06
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.46
Consensus pattern (2 bp):
AT
Found at i:1141058 original size:20 final size:22
Alignment explanation
Indices: 1141013--1141070 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
1141003 GCATGGATGG
1141013 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
1141037 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
*
1141057 TGTATCGATGCACT
1 TGCATCGATGCACT
1141071 TCAAGGGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:1142000 original size:32 final size:31
Alignment explanation
Indices: 1141958--1142085 Score: 125
Period size: 31 Copynumber: 4.1 Consensus size: 31
1141948 AGAGTCGAGG
1141958 GTTTACCTATGTTCTACGGAACATATGGACAA
1 GTTTACCTATGTTCTACGGAACATATGGAC-A
* *
1141990 TTTTACCTATG-TCTTTC-GAGACATATGGACA
1 GTTTACCTATGTTC-TACGGA-ACATATGGACA
* * *
1142021 GTATACCTATGTTCTAAGGAACATATAGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
* * * * *
1142052 GTTTACCTAGGTTATTCGGGACCTATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
1142083 GTT
1 GTT
1142086 GTCGAGGTTC
Statistics
Matches: 77, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
31 51 0.66
32 26 0.34
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTACGGAACATATGGACA
Found at i:1147274 original size:20 final size:20
Alignment explanation
Indices: 1147245--1147295 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1147235 TGCTTGATGT
* *
1147245 TGTTTTATATTGTTTGCTTC
1 TGTTTGATATTGCTTGCTTC
1147265 TGTTTGATATTGCTTGCTTC
1 TGTTTGATATTGCTTGCTTC
**
1147285 TACTTGATATT
1 TGTTTGATATT
1147296 TGTAAGGGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.14, C:0.12, G:0.16, T:0.59
Consensus pattern (20 bp):
TGTTTGATATTGCTTGCTTC
Found at i:1148125 original size:18 final size:18
Alignment explanation
Indices: 1148066--1148125 Score: 52
Period size: 18 Copynumber: 3.2 Consensus size: 18
1148056 TGAATTGGAA
* *
1148066 TTAACATAAATATCAAATT
1 TTAATATAAA-ATTAAATT
1148085 TATAATATACAAATTATAA--
1 T-TAATATA-AAATTA-AATT
1148104 TTAATATAAAATTAAATT
1 TTAATATAAAATTAAATT
1148122 TTAA
1 TTAA
1148126 AAAGTAATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
16 2 0.06
17 6 0.18
18 11 0.32
19 2 0.06
20 9 0.26
21 4 0.12
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (18 bp):
TTAATATAAAATTAAATT
Found at i:1148154 original size:17 final size:17
Alignment explanation
Indices: 1148132--1148222 Score: 71
Period size: 17 Copynumber: 5.4 Consensus size: 17
1148122 TTAAAAAGTA
1148132 ATCATATTAATTTAATT
1 ATCATATTAATTTAATT
* *
1148149 ATCATAATAATTT-ATG
1 ATCATATTAATTTAATT
* * * *
1148165 ATAAAATTTCAA--AAAGT
1 ATCATA-TT-AATTTAATT
1148182 AATCATATTAATTTAATT
1 A-TCATATTAATTTAATT
*
1148200 ATCATAATAATTTAATT
1 ATCATATTAATTTAATT
1148217 ATCATA
1 ATCATA
1148223 AGTTTATTAT
Statistics
Matches: 55, Mismatches: 13, Indels: 12
0.69 0.16 0.15
Matches are distributed among these distances:
16 8 0.15
17 38 0.69
18 9 0.16
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (17 bp):
ATCATATTAATTTAATT
Found at i:1148179 original size:51 final size:51
Alignment explanation
Indices: 1148117--1148213 Score: 185
Period size: 51 Copynumber: 1.9 Consensus size: 51
1148107 ATATAAAATT
*
1148117 AAATTTTAAAAAGTAATCATATTAATTTAATTATCATAATAATTTATGATA
1 AAATTTCAAAAAGTAATCATATTAATTTAATTATCATAATAATTTATGATA
1148168 AAATTTCAAAAAGTAATCATATTAATTTAATTATCATAATAATTTA
1 AAATTTCAAAAAGTAATCATATTAATTTAATTATCATAATAATTTA
1148214 ATTATCATAA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.42
Consensus pattern (51 bp):
AAATTTCAAAAAGTAATCATATTAATTTAATTATCATAATAATTTATGATA
Found at i:1148223 original size:17 final size:17
Alignment explanation
Indices: 1148183--1148223 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
1148173 TCAAAAAGTA
*
1148183 ATCATATTAATTTAATT
1 ATCATAATAATTTAATT
1148200 ATCATAATAATTTAATT
1 ATCATAATAATTTAATT
1148217 ATCATAA
1 ATCATAA
1148224 GTTTATTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (17 bp):
ATCATAATAATTTAATT
Found at i:1154227 original size:18 final size:19
Alignment explanation
Indices: 1154204--1154287 Score: 77
Period size: 18 Copynumber: 4.5 Consensus size: 19
1154194 TTTCATTTTA
1154204 AATTATTATAATAATA-AT
1 AATTATTATAATAATATAT
*
1154222 AATTATTATCAT-AT-TAT
1 AATTATTATAATAATATAT
* *
1154239 TATTATTATTATAA-ATAT
1 AATTATTATAATAATATAT
*
1154257 TATTATTATTAATAATATTAT
1 AATTATTA-TAATAATA-TAT
1154278 ATATTATTAT
1 A-ATTATTAT
1154288 TAAATAAAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
17 14 0.26
18 23 0.43
19 5 0.09
20 1 0.02
21 4 0.07
22 7 0.13
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (19 bp):
AATTATTATAATAATATAT
Found at i:1154229 original size:3 final size:3
Alignment explanation
Indices: 1154223--1154289 Score: 73
Period size: 3 Copynumber: 22.3 Consensus size: 3
1154213 AATAATAATA
* * * *
1154223 ATT ATT ATC A-T ATT ATT ATT ATT ATT ATA AAT ATT ATT ATT ATT AAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
1154270 AAT ATT ATAT ATT ATT ATT A
1 ATT ATT AT-T ATT ATT ATT A
1154290 AATAAAAATA
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
2 1 0.02
3 50 0.93
4 3 0.06
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:1154259 original size:15 final size:14
Alignment explanation
Indices: 1154205--1154284 Score: 60
Period size: 15 Copynumber: 5.8 Consensus size: 14
1154195 TTCATTTTAA
*
1154205 ATTATTATAATAAT
1 ATTATTATTATAAT
* *
1154219 AATAATTATTATCAT
1 -ATTATTATTATAAT
1154234 ATTATTATTAT--T
1 ATTATTATTATAAT
* *
1154246 ATTA-TA-AATATT
1 ATTATTATTATAAT
1154258 ATTATTATTAATAAT
1 ATTATTATT-ATAAT
1154273 ATTATATATTAT
1 ATTAT-TATTAT
1154285 TATTAAATAA
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
10 2 0.04
11 2 0.04
12 10 0.19
13 2 0.04
14 10 0.19
15 22 0.42
16 4 0.08
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (14 bp):
ATTATTATTATAAT
Found at i:1160274 original size:21 final size:21
Alignment explanation
Indices: 1160248--1160292 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1160238 CAATTAAAAA
* *
1160248 TCAAGGAGCTTTACTTCATAG
1 TCAAGGAGCCTTACTTCAAAG
*
1160269 TCAAGGCGCCTTACTTCAAAG
1 TCAAGGAGCCTTACTTCAAAG
1160290 TCA
1 TCA
1160293 TAGCTCGTCT
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:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (21 bp):
TCAAGGAGCCTTACTTCAAAG
Found at i:1164840 original size:19 final size:21
Alignment explanation
Indices: 1164803--1164845 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
1164793 TAACTTTTTC
1164803 TTTTATCTTTCATTATTAA-T
1 TTTTATCTTTCATTATTAACT
*
1164823 TTTTCTCTTTCATT-TTAACT
1 TTTTATCTTTCATTATTAACT
1164843 TTT
1 TTT
1164846 ACCTTTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATCTTTCATTATTAACT
Found at i:1164851 original size:19 final size:20
Alignment explanation
Indices: 1164802--1164851 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1164792 TTAACTTTTT
*
1164802 CTTTTATCTTTCATTATTAA
1 CTTTTACCTTTCATTATTAA
*
1164822 -TTTTTCTCTTTCATT-TTAA
1 CTTTTAC-CTTTCATTATTAA
1164841 CTTTTACCTTT
1 CTTTTACCTTT
1164852 TTTCTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTTACCTTTCATTATTAA
Found at i:1169376 original size:76 final size:75
Alignment explanation
Indices: 1169200--1169449 Score: 356
Period size: 76 Copynumber: 3.3 Consensus size: 75
1169190 CTTAGCAAGA
** *
1169200 AGCAAATGTTAGGGCATGCTGAAAGCCCATTTCAATCAGAAATTGGAATATTGACGCATTTTGAG
1 AGCAAATACTAGGGCATGCTGAAAGCCCATTTCAATCAGAAATTGGAATATTGACGCATTTTGAA
1169265 CGTTTGTATC
66 CGTTTGTATC
* * * **
1169275 AGCAAATGCTGGGGCATGCTGAAAGCCTATTTCAATCAGAAATTGGAATATTGAAACAATTTTGA
1 AGCAAATACTAGGGCATGCTGAAAGCCCATTTCAATCAGAAATTGGAATATTGACGC-ATTTTGA
*
1169340 AAGTTTGTATC
65 ACGTTTGTATC
* *
1169351 AGCAAATACTAGGGCATGCTGAAAGCCCATTTCAATCAGAAATAGGAATGGTTGACGCATTTTGA
1 AGCAAATACTAGGGCATGCTGAAAGCCCATTTCAATCAGAAATTGGAAT-ATTGACGCATTTTGA
**
1169416 ACGTTCATATC
65 ACGTTTGTATC
*
1169427 AGAAAATACTAGGGCATGCTGAA
1 AGCAAATACTAGGGCATGCTGAA
1169450 GGCCTATATC
Statistics
Matches: 155, Mismatches: 18, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
75 52 0.34
76 98 0.63
77 5 0.03
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (75 bp):
AGCAAATACTAGGGCATGCTGAAAGCCCATTTCAATCAGAAATTGGAATATTGACGCATTTTGAA
CGTTTGTATC
Found at i:1169717 original size:54 final size:54
Alignment explanation
Indices: 1169642--1169775 Score: 160
Period size: 54 Copynumber: 2.5 Consensus size: 54
1169632 GAAATCTGTG
* * * * * *
1169642 CAGAAGTCACATGAAATGATGAATGTGTTATCAAATGCTTTACGAACATTTGGC
1 CAGAAGCCACAAGAAAGGATGAATGTGTTATCAAAAGCTTTACAAAAATTTGGC
* *
1169696 CAGAAGCCACAAGAAAGGATGAATGTGTTATTAAAAGCTTTACAAAAATTTGGG
1 CAGAAGCCACAAGAAAGGATGAATGTGTTATCAAAAGCTTTACAAAAATTTGGC
* ***
1169750 CATAAGCCTTGAGAAAGGATGAATGT
1 CAGAAGCCACAAGAAAGGATGAATGT
1169776 ATTGTCACAT
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
54 68 1.00
ACGTcount: A:0.39, C:0.13, G:0.22, T:0.26
Consensus pattern (54 bp):
CAGAAGCCACAAGAAAGGATGAATGTGTTATCAAAAGCTTTACAAAAATTTGGC
Found at i:1170167 original size:22 final size:22
Alignment explanation
Indices: 1170142--1170196 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
1170132 ATATCTATAT
*
1170142 TCTTCAAAGATGATAGATTTTC
1 TCTTCAAAGATGATAGATTCTC
*
1170164 TCTTCAAAGATGATATATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
1170186 TTTTCAAAGAT
1 TCTTCAAAGAT
1170197 AAGCTTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.42
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:1170967 original size:45 final size:45
Alignment explanation
Indices: 1170918--1171021 Score: 145
Period size: 45 Copynumber: 2.3 Consensus size: 45
1170908 GGGAGCTTTT
* *
1170918 TGATGTTTTCAAAACCTTTGGAAAATTTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTTGGAAAATCTGTAAGCCCTACAGTGCA
***
1170963 TGATGTTTTCAAAACCTTTGGGTCATCTGTAAGCCCTACAGTGCA
1 TGATGTTTTCAAAACCTTTGGAAAATCTGTAAGCCCTACAGTGCA
* *
1171008 GGATGTTGTCAAAA
1 TGATGTTTTCAAAA
1171022 AACCTTCGGG
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTTGGAAAATCTGTAAGCCCTACAGTGCA
Found at i:1171089 original size:43 final size:45
Alignment explanation
Indices: 1171039--1171140 Score: 136
Period size: 45 Copynumber: 2.3 Consensus size: 45
1171029 GGGAGCTTTT
* * *
1171039 TGATGTTTTCAAAACCTT-TGG-CATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCAGGTCATCTGTAAGCCCTACAATGCA
*
1171082 TGATGTTTTCAAAACCTTCAGGTCATTTGTAAGCCCTACAATGCA
1 TGATGTTTTCAAAACCTTCAGGTCATCTGTAAGCCCTACAATGCA
* *
1171127 GGATGTTGTCAAAA
1 TGATGTTTTCAAAA
1171141 AGCCTTCGGG
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
43 18 0.35
44 2 0.04
45 31 0.61
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCAGGTCATCTGTAAGCCCTACAATGCA
Found at i:1171136 original size:119 final size:120
Alignment explanation
Indices: 1170865--1171216 Score: 553
Period size: 119 Copynumber: 2.9 Consensus size: 120
1170855 CTATTTCCCA
*
1170865 CATCTGTAAGCCCTACAGTGCAGGATGTTGTCATAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTACAGTGCAGGATGTTGTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* * **
1170930 AACCTTTGGAAAATTTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTTGGGT
66 AACCTTTGG-ACATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCAGGT
*
1170986 CATCTGTAAGCCCTACAGTGCAGGATGTTGTCAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTACAGTGCAGGATGTTGTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1171051 AACCTTTGG-CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCAGGT
66 AACCTTTGGACATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCAGGT
* *
1171105 CATTTGTAAGCCCTACAATGCAGGATGTTGTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTACAGTGCAGGATGTTGTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* * * * * *
1171170 AGCCTTCGAGTCATCTGTAAGCCCTACAGTGCAGGATGTTGTCAAAA
66 AACCTTTG-GACATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAA
1171217 AGCCTTCGGG
Statistics
Matches: 215, Mismatches: 14, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
119 109 0.51
120 1 0.00
121 105 0.49
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (120 bp):
CATCTGTAAGCCCTACAGTGCAGGATGTTGTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AACCTTTGGACATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCAGGT
Found at i:1171208 original size:76 final size:76
Alignment explanation
Indices: 1171082--1171300 Score: 336
Period size: 76 Copynumber: 2.9 Consensus size: 76
1171072 CTTCAGTGCA
* *
1171082 TGATGTTTTCAAAACCTTC-AGGTCATTTGTAAGCCCTACAATGCAGGATGTTGTCAAAAAGCCT
1 TGATGTTTTCAAAACCTTCGA-GTCATCTGTAAGCCCTACAGTGCAGGATGTTGTCAAAAAGCCT
1171146 TCGGGAGCTTTT
65 TCGGGAGCTTTT
*
1171158 TGATGTTTTCAAAGCCTTCGAGTCATCTGTAAGCCCTACAGTGCAGGATGTTGTCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGAGTCATCTGTAAGCCCTACAGTGCAGGATGTTGTCAAAAAGCCTT
*
1171223 CGGGAGTTTTT
66 CGGGAGCTTTT
* * * *
1171234 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAA-CCTT
1 TGATGTTTTCAAAACCTTCGAGTCATCTGTAAGCCCTACAGTGCAGGATGTTGTCAAAAAGCCTT
1171297 CGGG
66 CGGG
1171301 TCATCTGTAA
Statistics
Matches: 133, Mismatches: 9, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
74 8 0.06
75 4 0.03
76 120 0.90
77 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.22, T:0.33
Consensus pattern (76 bp):
TGATGTTTTCAAAACCTTCGAGTCATCTGTAAGCCCTACAGTGCAGGATGTTGTCAAAAAGCCTT
CGGGAGCTTTT
Found at i:1171283 original size:121 final size:121
Alignment explanation
Indices: 1171158--1171587 Score: 686
Period size: 121 Copynumber: 3.6 Consensus size: 121
1171148 GGGAGCTTTT
* *
1171158 TGATGTTTTCAAAGCCTTCGAGTCATCTGTAAGCCCTACAGTGCAGGATGTTGTCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCAGGATGTTGTCAAAAAGCCTT
1171223 CGGGAGTTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
66 CGGGAGTTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
1171279 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGTAGAATGTTGTCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCAGGATGTTGTCAAAAAGCCTT
* * * * *
1171344 CGAGAGCTTTTTGATGTTTTCAAAGCCTTTGGGTCATCTGTTAA-CCTTTCAGTGCA
66 CGGGAGTTTTTTGATGTTTTCAAAACCTTCGGGTCATCTG-TAAGCCCTTCAGTGCA
* * *
1171400 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTACATGATATTGTCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCAGGATGTTGTCAAAAAGCCTT
*
1171465 CGGGAGTTTTTTGATGTTTTCAAAACATTCGGGTCATCTGTAAGCCCTTCAGTGCA
66 CGGGAGTTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * *
1171521 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTACAGTGCATGATGTTTTC--AAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCAGGATGTTGTCAAAAAGCCTT
1171584 CGGG
66 CGGG
1171588 TCATCCGTAA
Statistics
Matches: 283, Mismatches: 24, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
119 12 0.04
120 3 0.01
121 265 0.94
122 3 0.01
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (121 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCAGGATGTTGTCAAAAAGCCTT
CGGGAGTTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:1171337 original size:45 final size:45
Alignment explanation
Indices: 1171234--1171321 Score: 167
Period size: 45 Copynumber: 2.0 Consensus size: 45
1171224 GGGAGTTTTT
*
1171234 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCA
1171279 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTG
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTG
1171322 TAGAATGTTG
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.33
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCA
Found at i:1171356 original size:197 final size:194
Alignment explanation
Indices: 1170963--1171421 Score: 724
Period size: 197 Copynumber: 2.4 Consensus size: 194
1170953 CTTCAGTGCA
*
1170963 TGATGTTTTCAAAACCTTTGGGTCATCTGTAAGCCCTACAGTGCAGGATGTTGTCAAAAAACCTT
1 TGATGTTTTCAAAGCCTTTGGGTCATCTGTAAGCCCTACAGTGCAGGATGTTGTC-AAAAACCTT
*
1171028 CGGGAGCTTTTTGATGTTTTCAAAACCTTTGGCATCTGTAAGCCCTTCAGTGCATGATGTTTTCA
65 CGGGAGCTTTTTGATGTTTTCAAAACCTTGGGCATCTGTAAGCCCTTCAGTGCATGATGTTTTCA
* * *
1171093 AAACCTTCAGGTCATTTGTAAGCCCTACAATGCAGGATGTTGTCAAAAAGCCTTCGGGAGCTTTT
130 AAACCTTCAGGTCATCTGTAAGCCCTACAATGCAGAATGTTGTCAAAAAGCCTTCGAGAGCTTTT
* *
1171158 TGATGTTTTCAAAGCCTTCGAGTCATCTGTAAGCCCTACAGTGCAGGATGTTGTCAAAAAGCCTT
1 TGATGTTTTCAAAGCCTTTGGGTCATCTGTAAGCCCTACAGTGCAGGATGTTGTCAAAAA-CCTT
*
1171223 CGGGAGTTTTTTGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTT
65 CGGGAGCTTTTTGATGTTTTCAAAACCTT-GGG-CATCTGTAAGCCCTTCAGTGCATGATGTTTT
* * *
1171288 CAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGTAGAATGTTGTCAAAAAGCCTTCGAGAGCTT
128 CAAAACCTTCAGGTCATCTGTAAGCCCTACAATGCAGAATGTTGTCAAAAAGCCTTCGAGAGCTT
1171353 TT
193 TT
* * * *
1171355 TGATGTTTTCAAAGCCTTTGGGTCATCTGTTAA-CCTTTCAGTGCATGATGTTTTC-AAAACCTT
1 TGATGTTTTCAAAGCCTTTGGGTCATCTG-TAAGCCCTACAGTGCAGGATGTTGTCAAAAACCTT
1171418 CGGG
65 CGGG
1171422 TCATCTGTAA
Statistics
Matches: 243, Mismatches: 17, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
194 5 0.02
195 92 0.38
196 6 0.02
197 137 0.56
198 3 0.01
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.34
Consensus pattern (194 bp):
TGATGTTTTCAAAGCCTTTGGGTCATCTGTAAGCCCTACAGTGCAGGATGTTGTCAAAAACCTTC
GGGAGCTTTTTGATGTTTTCAAAACCTTGGGCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAA
AACCTTCAGGTCATCTGTAAGCCCTACAATGCAGAATGTTGTCAAAAAGCCTTCGAGAGCTTTT
Found at i:1171447 original size:45 final size:45
Alignment explanation
Indices: 1171355--1171468 Score: 131
Period size: 45 Copynumber: 2.5 Consensus size: 45
1171345 GAGAGCTTTT
* * * * *
1171355 TGATGTTTTCAAAGCCTTTGGGTCATCTGTTAACCTTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTTAACCCTACAGTACA
1171400 TGATGTTTTCAAAACCTTCGGGTCATCTG-TAAGCCCTACAGTACA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTTAA-CCCTACAGTACA
* *
1171445 TGATATTGTCAAAAAGCCTTCGGG
1 TGATGTTTTC-AAAA-CCTTCGGG
1171469 AGTTTTTTGA
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
44 3 0.05
45 44 0.75
46 4 0.07
47 8 0.14
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTTAACCCTACAGTACA
Found at i:1171525 original size:45 final size:45
Alignment explanation
Indices: 1171476--1171634 Score: 246
Period size: 45 Copynumber: 3.5 Consensus size: 45
1171466 GGGAGTTTTT
* *
1171476 TGATGTTTTCAAAACATTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCA
*
1171521 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTACAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCA
* *
1171566 TGATGTTTTCAAAGCCTTCGGGTCATCCGTAAGCCCTACAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCA
*
1171611 GGATGTTTTCAAAAAGCCTTCGGG
1 TGATGTTTTC-AAAA-CCTTCGGG
1171635 AACTTTTTGA
Statistics
Matches: 106, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
45 95 0.90
46 3 0.03
47 8 0.08
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.31
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTGCA
Found at i:1171527 original size:166 final size:166
Alignment explanation
Indices: 1171355--1171667 Score: 502
Period size: 166 Copynumber: 1.9 Consensus size: 166
1171345 GAGAGCTTTT
* * *
1171355 TGATGTTTTCAAAGCCTTTGGGTCATCTGTTAA-CCTTTCAGTGCATGATGTTTTCAAAACCTTC
1 TGATGTTTTCAAAGCCTTCGGGTCATCTG-TAAGCCCTACAGTGCATGATGTTTTCAAAACCTTC
* * **
1171419 GGGTCATCTGTAAGCCCTACAGTACATGATATTGTCAAAAAGCCTTCGGGAGTTTTTTGATGTTT
65 GGGTCATCCGTAAGCCCTACAGTACAGGATATTGTCAAAAAGCCTTCGGGAACTTTTTGATGTTT
1171484 TCAAAACATTCGGGTCATCTGTAAGCCCTTCAGTGCA
130 TCAAAACATTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
1171521 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTACAGTGCATGATGTTTTCAAAGCCTTCG
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTACAGTGCATGATGTTTTCAAAACCTTCG
* * *
1171586 GGTCATCCGTAAGCCCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAACTTTTTGATGTTTT
66 GGTCATCCGTAAGCCCTACAGTACAGGATATTGTCAAAAAGCCTTCGGGAACTTTTTGATGTTTT
*
1171651 CAAAACCTTCGGGTCAT
131 CAAAACATTCGGGTCAT
1171668 TTATAAGACC
Statistics
Matches: 134, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
165 3 0.02
166 131 0.98
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (166 bp):
TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTACAGTGCATGATGTTTTCAAAACCTTCG
GGTCATCCGTAAGCCCTACAGTACAGGATATTGTCAAAAAGCCTTCGGGAACTTTTTGATGTTTT
CAAAACATTCGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:1171533 original size:76 final size:74
Alignment explanation
Indices: 1171400--1171542 Score: 223
Period size: 76 Copynumber: 1.9 Consensus size: 74
1171390 TTTCAGTGCA
*
1171400 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACAGTACATGATATTGTCAAAAAGCCTT
1 TGATGTTTTCAAAACATTCGGGTCATCTGTAAGCCCTACAGTACATGATATTGTC--AAAGCCTT
1171465 CGGGAGTTTTT
64 CGGGAGTTTTT
* * * *
1171476 TGATGTTTTCAAAACATTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAGCCTTCG
1 TGATGTTTTCAAAACATTCGGGTCATCTGTAAGCCCTACAGTACATGATATTGTCAAAGCCTTCG
1171541 GG
66 GG
1171543 TCATCTGTAA
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
74 12 0.19
76 50 0.81
ACGTcount: A:0.24, C:0.20, G:0.21, T:0.34
Consensus pattern (74 bp):
TGATGTTTTCAAAACATTCGGGTCATCTGTAAGCCCTACAGTACATGATATTGTCAAAGCCTTCG
GGAGTTTTT
Found at i:1171537 original size:316 final size:315
Alignment explanation
Indices: 1170865--1171542 Score: 1063
Period size: 316 Copynumber: 2.1 Consensus size: 315
1170855 CTATTTCCCA
1170865 CATCTGTAAGCCCTACAGTGCAGGATGTTGTCATAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTACAGTGCAGGATGTTGTCA-AAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
* * *
1170930 AACCTTTGGAAAATTTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTTGGGTCATCTGTAA
65 AACCTTCGGAAAATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAA
* *
1170995 GCCCTACAGTGCAGGATGTTGTCAAAAAACCTTCGGGAGCTTTTTGATGTTTTCAAAACCTTTGG
130 GCCCTACAGTGCAGAATGTTGTCAAAAAACCTTCGAGAGCTTTTTGATGTTTTCAAAACCTTTGG
* *
1171060 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCAGGTCATTTGTAAGCCCTACAATG
195 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCAGGTCATCTGTAAGCCCTACAATA
* * *
1171125 CAGGATGTTGTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTCGAGT
260 CAGGATATTGTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACATTCGAGT
*
1171181 CATCTGTAAGCCCTACAGTGCAGGATGTTGTCAAAAAGCCTTCGGGAGTTTTTTGATGTTTTCAA
1 CATCTGTAAGCCCTACAGTGCAGGATGTTGTC-AAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
***
1171246 AACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAA
65 AACCTTCGGAAAATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAA
* * *
1171311 GCCCTACAGTGTAGAATGTTGTCAAAAAGCCTTCGAGAGCTTTTTGATGTTTTCAAAGCCTTTGG
130 GCCCTACAGTGCAGAATGTTGTCAAAAAACCTTCGAGAGCTTTTTGATGTTTTCAAAACCTTT-G
* *
1171376 GTCATCTGTTAA-CCTTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTACA
194 G-CATCTG-TAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCAGGTCATCTGTAAGCCCTACA
* * * *
1171440 GTACATGATATTGTCAAAAAGCCTTCGGGAGTTTTTTGATGTTTTCAAAACATTCGGGT
257 ATACAGGATATTGTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACATTCGAGT
* * *
1171499 CATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAGCCTTCGGG
1 CATCTGTAAGCCCTACAGTGCAGGATGTTGTCAAAAGCCTTCGGG
1171543 TCATCTGTAA
Statistics
Matches: 332, Mismatches: 26, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
316 191 0.58
317 3 0.01
318 135 0.41
319 3 0.01
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (315 bp):
CATCTGTAAGCCCTACAGTGCAGGATGTTGTCAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAA
ACCTTCGGAAAATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTGTAAG
CCCTACAGTGCAGAATGTTGTCAAAAAACCTTCGAGAGCTTTTTGATGTTTTCAAAACCTTTGGC
ATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCAGGTCATCTGTAAGCCCTACAATAC
AGGATATTGTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAACATTCGAGT
Found at i:1171839 original size:3 final size:3
Alignment explanation
Indices: 1171824--1171882 Score: 82
Period size: 3 Copynumber: 19.7 Consensus size: 3
1171814 TCCTTTTTAA
* * *
1171824 ATT ATT ATA ATT ATT ATT ATT ATT ATA AAT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
1171872 ATT AAT ATT AT
1 ATT ATT ATT AT
1171883 ATATATATAT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
ATT
Found at i:1174507 original size:111 final size:111
Alignment explanation
Indices: 1174313--1174534 Score: 426
Period size: 111 Copynumber: 2.0 Consensus size: 111
1174303 TGTAACTTTG
*
1174313 CATTTTAGTCATTGAAATCAAATTTTGAATCTTTTAATTTGATTTTCAAAGTTTGGTTTATTATA
1 CATTTTAGTCATTGAAATCAAATTCTGAATCTTTTAATTTGATTTTCAAAGTTTGGTTTATTATA
1174378 ATTTAGTCCCTGACATAATTATATATATTTATGGTAAAATATGTAT
66 ATTTAGTCCCTGACATAATTATATATATTTATGGTAAAATATGTAT
1174424 CATTTTAGTCATTGAAATCAAATTCTGAATCTTTTAATTTGATTTTCAAAGTTTGGTTTATTATA
1 CATTTTAGTCATTGAAATCAAATTCTGAATCTTTTAATTTGATTTTCAAAGTTTGGTTTATTATA
*
1174489 ATTTAGTCTCTGACATAATTATATATATTTATGGTAAAATATGTAT
66 ATTTAGTCCCTGACATAATTATATATATTTATGGTAAAATATGTAT
1174535 TTAGTCCTTA
Statistics
Matches: 109, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
111 109 1.00
ACGTcount: A:0.33, C:0.08, G:0.11, T:0.48
Consensus pattern (111 bp):
CATTTTAGTCATTGAAATCAAATTCTGAATCTTTTAATTTGATTTTCAAAGTTTGGTTTATTATA
ATTTAGTCCCTGACATAATTATATATATTTATGGTAAAATATGTAT
Found at i:1175315 original size:22 final size:22
Alignment explanation
Indices: 1175288--1175332 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
1175278 AATCGACAAA
*
1175288 GACCAATTTTGGGCGTTGTGAG
1 GACCAATTTTGGGCATTGTGAG
1175310 GACCAATTTTGGGCATTGTGAG
1 GACCAATTTTGGGCATTGTGAG
1175332 G
1 G
1175333 GTGATAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.20, C:0.13, G:0.36, T:0.31
Consensus pattern (22 bp):
GACCAATTTTGGGCATTGTGAG
Found at i:1197052 original size:82 final size:82
Alignment explanation
Indices: 1196913--1197355 Score: 515
Period size: 82 Copynumber: 5.4 Consensus size: 82
1196903 GATACATCAA
* * * *
1196913 TGAAAAGTTACTGAAGATGATAA-GACACCACTATTTTACCCT-TTGTCTGAAAAGTTGTTTAAA
1 TGAAAAGTTGCAGAAGATGATAATG-CACCACTATTTCA-CCTGTTTTCTGAAAAGTTGTTTAAA
*
1196976 TTATGCATTGAATGGTCTC
64 TTATGCATTGAATGGACTC
* ** * * *
1196995 TAAAAAGTTATAAAAGATGATAATGCACCACTATTTCACGTATTTTCTGAAAAGTTGTTTAAATT
1 TGAAAAGTTGCAGAAGATGATAATGCACCACTATTTCACCTGTTTTCTGAAAAGTTGTTTAAATT
* * *
1197060 ATGCGTAGAA-CGACCTC
66 ATGCATTGAATGGA-CTC
* * * *
1197077 TGAAAAGTTGCAGAAGATGATAATGTACCACTATTTTACCCGTTTTCTG-AAAGTTGTTTAACTT
1 TGAAAAGTTGCAGAAGATGATAATGCACCACTATTTCACCTGTTTTCTGAAAAGTTGTTTAAATT
* *
1197141 ATACATTGAAT-GACCTA
66 ATGCATTGAATGGA-CTC
* * *
1197158 TG-AAAGTTGCAGAAGATGATAATGCACCACTATTTCACCTGTTTTCTGAAAAGCTATTTGAATT
1 TGAAAAGTTGCAGAAGATGATAATGCACCACTATTTCACCTGTTTTCTGAAAAGTTGTTTAAATT
*
1197222 ATGTATTGAAT-GACCTC
66 ATGCATTGAATGGA-CTC
* * * *
1197239 TGAAAAGTTGCAGAAGATGATAATGCACCATTATTTCACCTGTTTTCTAAAAAGCTATTTAAATT
1 TGAAAAGTTGCAGAAGATGATAATGCACCACTATTTCACCTGTTTTCTGAAAAGTTGTTTAAATT
1197304 ATGCATTGAAT-GACATC
66 ATGCATTGAATGGAC-TC
*
1197321 TGAAAAGTTGGAGAAGATGATAATGCACCACTATT
1 TGAAAAGTTGCAGAAGATGATAATGCACCACTATT
1197356 ATTTGACCTA
Statistics
Matches: 313, Mismatches: 41, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
80 43 0.14
81 59 0.19
82 210 0.67
83 1 0.00
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (82 bp):
TGAAAAGTTGCAGAAGATGATAATGCACCACTATTTCACCTGTTTTCTGAAAAGTTGTTTAAATT
ATGCATTGAATGGACTC
Found at i:1197224 original size:162 final size:162
Alignment explanation
Indices: 1196913--1197355 Score: 550
Period size: 162 Copynumber: 2.7 Consensus size: 162
1196903 GATACATCAA
* *
1196913 TGAAAAGTTACTGAAGATGATAA-GACACCACTATTTTACCC-TTTGTCTGAAAAGTTGTTTAAA
1 TGAAAAGTTGCAGAAGATGATAATG-CACCACTATTTTACCCGTTT-TCTG-AAAGTTGTTTAAA
* * ** * *
1196976 TTATGCATTGAATGGTCTCTA-AAAAGTTATAAAAGATGATAATGCACCACTATTTCACGTATTT
63 TTATGCATTGAAT-GAC-CTATGAAAGTTGCAGAAGATGATAATGCACCACTATTTCACCTATTT
* * *
1197040 TCTGAAAAGTTGTTTAAATTATGCGTAGAACGACCTC
126 TCTGAAAAGCTATTTAAATTATGCATAGAACGACCTC
* *
1197077 TGAAAAGTTGCAGAAGATGATAATGTACCACTATTTTACCCGTTTTCTGAAAGTTGTTTAACTTA
1 TGAAAAGTTGCAGAAGATGATAATGCACCACTATTTTACCCGTTTTCTGAAAGTTGTTTAAATTA
* *
1197142 TACATTGAATGACCTATGAAAGTTGCAGAAGATGATAATGCACCACTATTTCACCTGTTTTCTGA
66 TGCATTGAATGACCTATGAAAGTTGCAGAAGATGATAATGCACCACTATTTCACCTATTTTCTGA
* * * *
1197207 AAAGCTATTTGAATTATGTATTGAATGACCTC
131 AAAGCTATTTAAATTATGCATAGAACGACCTC
* * * * * *
1197239 TGAAAAGTTGCAGAAGATGATAATGCACCATTATTTCACCTGTTTTCTAAAAAGCTATTTAAATT
1 TGAAAAGTTGCAGAAGATGATAATGCACCACTATTTTACCCGTTTTCT-GAAAGTTGTTTAAATT
* * *
1197304 ATGCATTGAATGACATCTGAAAAGTTGGAGAAGATGATAATGCACCACTATT
65 ATGCATTGAATGACCTATG-AAAGTTGCAGAAGATGATAATGCACCACTATT
1197356 ATTTGACCTA
Statistics
Matches: 243, Mismatches: 31, Indels: 10
0.86 0.11 0.04
Matches are distributed among these distances:
161 3 0.01
162 113 0.47
163 52 0.21
164 71 0.29
165 4 0.02
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (162 bp):
TGAAAAGTTGCAGAAGATGATAATGCACCACTATTTTACCCGTTTTCTGAAAGTTGTTTAAATTA
TGCATTGAATGACCTATGAAAGTTGCAGAAGATGATAATGCACCACTATTTCACCTATTTTCTGA
AAAGCTATTTAAATTATGCATAGAACGACCTC
Found at i:1197354 original size:244 final size:244
Alignment explanation
Indices: 1196916--1197355 Score: 614
Period size: 244 Copynumber: 1.8 Consensus size: 244
1196906 ACATCAATGA
* * * *
1196916 AAAGTTACTGAAGATGATAAGACACCACTATTTTACCCTTTGTCTGAAAAGTTGTTTAAATTATG
1 AAAGTTACAGAAGATGATAAGACACCACTATTTCACCCTTTGTCTGAAAAGCTATTTAAATTATG
** * * *
1196981 CATTGAATGGTCTCTAAAAAGTTATAAAAGATGATAATGCACCACTATTTCACGTATTTTCTGAA
66 CATTGAATGACCTCTAAAAAGTTACAAAAGATGATAATGCACCACTATTTCACCTATTTTCTAAA
* * * * *
1197046 AAGTTGTTTAAATTATGCGTAGAACGACCTCTGAAAAGTTGCAGAAGATGATAATGTACCACTAT
131 AAGCTATTTAAATTATGCATAGAACGACATCTGAAAAGTTGCAGAAGATGATAATGCACCACTAT
1197111 TTTACCCGTTTTCTGAAAGTTGTTTAACTTATACATTGAATGACCTATG
196 TTTACCCGTTTTCTGAAAGTTGTTTAACTTATACATTGAATGACCTATG
* * *
1197160 AAAGTTGCAGAAGATGATAATG-CACCACTATTTCA-CCTGTTTTCTGAAAAGCTATTTGAATTA
1 AAAGTTACAGAAGATGATAA-GACACCACTATTTCACCCT-TTGTCTGAAAAGCTATTTAAATTA
* * * * * *
1197223 TGTATTGAATGACCTCTGAAAAGTTGCAGAAGATGATAATGCACCATTATTTCACCTGTTTTCTA
64 TGCATTGAATGACCTCTAAAAAGTTACAAAAGATGATAATGCACCACTATTTCACCTATTTTCTA
* * *
1197288 AAAAGCTATTTAAATTATGCATTGAATGACATCTGAAAAGTTGGAGAAGATGATAATGCACCACT
129 AAAAGCTATTTAAATTATGCATAGAACGACATCTGAAAAGTTGCAGAAGATGATAATGCACCACT
1197353 ATT
194 ATT
1197356 ATTTGACCTA
Statistics
Matches: 168, Mismatches: 26, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
243 3 0.02
244 164 0.98
245 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (244 bp):
AAAGTTACAGAAGATGATAAGACACCACTATTTCACCCTTTGTCTGAAAAGCTATTTAAATTATG
CATTGAATGACCTCTAAAAAGTTACAAAAGATGATAATGCACCACTATTTCACCTATTTTCTAAA
AAGCTATTTAAATTATGCATAGAACGACATCTGAAAAGTTGCAGAAGATGATAATGCACCACTAT
TTTACCCGTTTTCTGAAAGTTGTTTAACTTATACATTGAATGACCTATG
Found at i:1199171 original size:20 final size:20
Alignment explanation
Indices: 1199139--1199176 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1199129 TAATGGATGG
*
1199139 TTGTTTTTGTATGTTGTTAT
1 TTGTTTTTGTATGATGTTAT
1199159 TTGTTTTCT-TATGATGTT
1 TTGTTTT-TGTATGATGTT
1199177 TAATGCCTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 15 0.94
21 1 0.06
ACGTcount: A:0.11, C:0.03, G:0.18, T:0.68
Consensus pattern (20 bp):
TTGTTTTTGTATGATGTTAT
Found at i:1199273 original size:18 final size:18
Alignment explanation
Indices: 1199250--1199304 Score: 110
Period size: 18 Copynumber: 3.1 Consensus size: 18
1199240 AGAGAATGAC
1199250 TAAGTAGCATATCTTTAG
1 TAAGTAGCATATCTTTAG
1199268 TAAGTAGCATATCTTTAG
1 TAAGTAGCATATCTTTAG
1199286 TAAGTAGCATATCTTTAG
1 TAAGTAGCATATCTTTAG
1199304 T
1 T
1199305 GTTCGAGAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 37 1.00
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (18 bp):
TAAGTAGCATATCTTTAG
Found at i:1200166 original size:12 final size:12
Alignment explanation
Indices: 1200123--1200172 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
1200113 CATAACATTT
1200123 TTATTTTACTTG
1 TTATTTTACTTG
1200135 TTCATTTT--TTG
1 TT-ATTTTACTTG
1200146 TATAGTTTTACTTG
1 T-TA-TTTTACTTG
*
1200160 TTATTTTCCTTG
1 TTATTTTACTTG
1200172 T
1 T
1200173 CTTTTTAGGG
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
11 5 0.16
12 16 0.50
13 7 0.22
14 4 0.12
ACGTcount: A:0.14, C:0.10, G:0.10, T:0.66
Consensus pattern (12 bp):
TTATTTTACTTG
Found at i:1202005 original size:807 final size:805
Alignment explanation
Indices: 1200454--1202066 Score: 3093
Period size: 807 Copynumber: 2.0 Consensus size: 805
1200444 ACTCATGAGG
*
1200454 ATGCAAGGTAACATGTTTGGGCATTTTTGGAGGTTTGTAACTCATTTCGACAACAAGGTGTGCAT
1 ATGCAAGGTAACATGTTTGGGCATTTTTGGAGGTTTGTAACTAATTTCGACAACAAGGTGTGCAT
1200519 AAAGATATGCTGAAATTGAAATTATTTCCATATTCTTTGAAAGATCATGCCAGGGCATGCTTAAT
66 AAAGATATGCTGAAATTGAAATTATTTCCATATTCTTTGAAAGATCATGCCAGGGCATGCTTAAT
*
1200584 GGAGTACCTTCTGGCTTGATAAGGTCCTGGGTAGACTTGTGCAAATATTTTTTGTTATGACATAA
131 GGAGGACCTTCTGGCTTGATAAGGTCCTGGGTAGACTTGTGCAAATATTTTTTGTTATGACATAA
1200649 TCCACCGAATATGAAAAACCATCTTAGGAATGTCATAGCATCTTTTCGACAACGCAATGAAAAGT
196 TCCACCGAATATGAAAAACCATCTTAGGAATGTCATAGCATCTTTTCGACAACGCAATGAAAAGT
* *
1200714 CTATGTATTAGTGTTGAAACTGAAATAAAAGTTTGATTCGCAAGTGCACCAATCATGGATTCCAC
261 CTATGTATGAGTGCTGAAACTGAAATAAAAGTTTGATTCGCAAGTGCACCAATCATGGATTCCAC
1200779 AGCTGGACTCAAGCTATGATGTTTTACAATAGAGTCAATGCACCCACGAATATGATGCTAGATGC
326 AGCTGGACTCAAGCTATGATGTTTTACAATAGAGTCAATGCACCCACGAATATGATGCTAGATGC
1200844 CTAGACAAATGGGACATTGCTCGATGAATCACATACAGAGGCATTCAACATTCTGGATAGGATTG
391 CTAGACAAATGGGACATTGCTCGATGAATCACATACAGAGGCATTCAACATTCTGGATAGGATTG
1200909 CCAACAATGATTATCAATTCCCATCTACAAAGTTTGAAATTGGGCAAAAATCACATAGGGCATTC
456 CCAACAATGATTATCAATTCCCATCTACAAAGTTTGAAATTGGGCAAAAATCACATAGGGCATTC
1200974 GAGTTAGATACTAAGGATTATGTGTCTGCCCAACTTGCTACTATCACCAATATATTGAAGAATTT
521 GAGTTAGATACTAAGGATTATGTGTCTGCCCAACTTGCTACTATCACCAATATATTGAAGAATTT
*
1201039 GCAAAGACCAGGTGAGGGGAAATAAGTGAAGGCAACTAATTCAGCATGTTTATTATGCCATGACA
586 GCAAAGACCAGGTGAGGGGAAATAAGTGAAGGCAACTAATTCAGCATGTTTAGTATGCCATGACA
1201104 ATCACCATGAGAGTGAGTGACCTACCAATCAGGAATCCATCAACTATGTAGGAAACTAAAATTAA
651 ATCACCATGAGAGTGAGTGACCTACCAATCAGGAATCCATCAACTATGTAGGAAACTAAAATTAA
* * *
1201169 GGTAACAACAACCCCTATTTTAATACATATAATCCTGGATAGTGTCAGCATCCAAACTTCTCTTG
716 GGTAACAACAACCCCTACTCTAATACATATAATCATGGATAGTGTCAGCATCCAAACTTCTCTTG
1201234 GGGAAATCAATGAACCATCAATGAT
781 GGGAAATCAATGAACCATCAATGAT
1201259 ATGCAAGGTAACATGTTTGGGCATTTTTGGAGGTTTGTAACTAATTTCGACAACAAGGTGTGCAT
1 ATGCAAGGTAACATGTTTGGGCATTTTTGGAGGTTTGTAACTAATTTCGACAACAAGGTGTGCAT
1201324 AAAGATATGCTGAAATTGAAATTATTTCCATATTCTTTGAAAGATCATGCCAGGGCATGGCTTAA
66 AAAGATATGCTGAAATTGAAATTATTTCCATATTCTTTGAAAGATCATGCCAGGGCAT-GCTTAA
1201389 TGGAGGACCTTCTGGCTTGATAAGGTCCTGGGTAGACTTGTGCAAATATTTTTTGTTATGACATA
130 TGGAGGACCTTCTGGCTTGATAAGGTCCTGGGTAGACTTGTGCAAATATTTTTTGTTATGACAT-
1201454 AATCCACCGAATATGAAAAACCATCTTAGGAATGTCATAGCATCTTTTCGACAACGCAATGAAAA
194 AATCCACCGAATATGAAAAACCATCTTAGGAATGTCATAGCATCTTTTCGACAACGCAATGAAAA
1201519 GTCTATGTATGAGTGCTGAAACTGAAATAAAAGTTTGATTCGCAAGTGCACCAATCATGGATTCC
259 GTCTATGTATGAGTGCTGAAACTGAAATAAAAGTTTGATTCGCAAGTGCACCAATCATGGATTCC
*
1201584 ACAGCTGGACTCAAGCTGTGATGTTTTACAATAGAGTCAATGCACCCACG-ATGATGATGCTAGA
324 ACAGCTGGACTCAAGCTATGATGTTTTACAATAGAGTCAATGCACCCACGAAT-ATGATGCTAGA
*
1201648 TGCCTAGACAAATGGGATATTGCTCGATGAATCACATACAGAGGCATTCAACATTCTGGATAGGA
388 TGCCTAGACAAATGGGACATTGCTCGATGAATCACATACAGAGGCATTCAACATTCTGGATAGGA
1201713 TTGCCAACAATGATTATCAATTCCCATCTACAAAGTTTGAAATTGGGCAAAAATCACATAGGGCA
453 TTGCCAACAATGATTATCAATTCCCATCTACAAAGTTTGAAATTGGGCAAAAATCACATAGGGCA
1201778 TTCGAGTTAGATACTAAGGATTATGTGTCTGCCCAACTTGCTACTATCACCAATATATTGAAGAA
518 TTCGAGTTAGATACTAAGGATTATGTGTCTGCCCAACTTGCTACTATCACCAATATATTGAAGAA
1201843 TTTGCAAAGACCAGGTGAGGGGAAATAAGTGAAGGCAACTAATTCAGCATGTTTAGTATGCCATG
583 TTTGCAAAGACCAGGTGAGGGGAAATAAGTGAAGGCAACTAATTCAGCATGTTTAGTATGCCATG
1201908 ACAATCACCATGAGAGTGAGTGACCTACCAATCAGGAATCCATCAACTATGTAGGAAACTAAAAT
648 ACAATCACCATGAGAGTGAGTGACCTACCAATCAGGAATCCATCAACTATGTAGGAAACTAAAAT
*
1201973 TGAGGTAACAACAACCCCTACTCTAATACATATAATCATGGATAGTGTCAGCATCCAAACTTCTC
713 TAAGGTAACAACAACCCCTACTCTAATACATATAATCATGGATAGTGTCAGCATCCAAACTTCTC
1202038 TTGGGGAAATCAATGAACCATCAATGAT
778 TTGGGGAAATCAATGAACCATCAATGAT
1202066 A
1 A
1202067 GGCAGTAGAA
Statistics
Matches: 794, Mismatches: 11, Indels: 4
0.98 0.01 0.00
Matches are distributed among these distances:
805 122 0.15
806 71 0.09
807 601 0.76
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (805 bp):
ATGCAAGGTAACATGTTTGGGCATTTTTGGAGGTTTGTAACTAATTTCGACAACAAGGTGTGCAT
AAAGATATGCTGAAATTGAAATTATTTCCATATTCTTTGAAAGATCATGCCAGGGCATGCTTAAT
GGAGGACCTTCTGGCTTGATAAGGTCCTGGGTAGACTTGTGCAAATATTTTTTGTTATGACATAA
TCCACCGAATATGAAAAACCATCTTAGGAATGTCATAGCATCTTTTCGACAACGCAATGAAAAGT
CTATGTATGAGTGCTGAAACTGAAATAAAAGTTTGATTCGCAAGTGCACCAATCATGGATTCCAC
AGCTGGACTCAAGCTATGATGTTTTACAATAGAGTCAATGCACCCACGAATATGATGCTAGATGC
CTAGACAAATGGGACATTGCTCGATGAATCACATACAGAGGCATTCAACATTCTGGATAGGATTG
CCAACAATGATTATCAATTCCCATCTACAAAGTTTGAAATTGGGCAAAAATCACATAGGGCATTC
GAGTTAGATACTAAGGATTATGTGTCTGCCCAACTTGCTACTATCACCAATATATTGAAGAATTT
GCAAAGACCAGGTGAGGGGAAATAAGTGAAGGCAACTAATTCAGCATGTTTAGTATGCCATGACA
ATCACCATGAGAGTGAGTGACCTACCAATCAGGAATCCATCAACTATGTAGGAAACTAAAATTAA
GGTAACAACAACCCCTACTCTAATACATATAATCATGGATAGTGTCAGCATCCAAACTTCTCTTG
GGGAAATCAATGAACCATCAATGAT
Found at i:1205717 original size:21 final size:20
Alignment explanation
Indices: 1205684--1205722 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1205674 TCATGGATGG
*
1205684 TTGTTTTTGTATGTTGTTAT
1 TTGTTTTTGTATGATGTTAT
*
1205704 TTGTTTTTCTTATGATGTT
1 TTGTTTTT-GTATGATGTT
1205723 TAATGCCTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.10, C:0.03, G:0.18, T:0.69
Consensus pattern (20 bp):
TTGTTTTTGTATGATGTTAT
Found at i:1208957 original size:23 final size:22
Alignment explanation
Indices: 1208931--1208976 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
1208921 TTCATAAAAC
*
1208931 TTAAATCAACAAATTTTATAATT
1 TTAAAT-AACAAATTTTAGAATT
* *
1208954 TTAAATATCTAATTTTAGAATT
1 TTAAATAACAAATTTTAGAATT
1208976 T
1 T
1208977 ATTATCATCG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (22 bp):
TTAAATAACAAATTTTAGAATT
Found at i:1212118 original size:21 final size:21
Alignment explanation
Indices: 1212094--1212192 Score: 67
Period size: 21 Copynumber: 4.7 Consensus size: 21
1212084 GCGTTGCATT
1212094 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* * ** **
1212115 TCGCGTTGTGAT-CTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
* *
1212135 TCGCGTTGCGATAGTCT-ACAG
1 TCGCGTTGCGATAGT-TGAAAA
* *
1212156 TTGTCGTTGTGATAGTTGAAAA
1 TCG-CGTTGCGATAGTTGAAAA
*
1212178 CCGCGTTGCGATAGT
1 TCGCGTTGCGATAGT
1212193 CTCGGGTCGT
Statistics
Matches: 55, Mismatches: 19, Indels: 8
0.67 0.23 0.10
Matches are distributed among these distances:
20 14 0.25
21 26 0.47
22 15 0.27
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.34
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:1212239 original size:29 final size:31
Alignment explanation
Indices: 1212206--1212269 Score: 96
Period size: 33 Copynumber: 2.1 Consensus size: 31
1212196 GGGTCGTGGT
1212206 CGTGGT-C-GCGATTTTCAACTATCGCAACG
1 CGTGGTCCGGCGATTTTCAACTATCGCAACG
1212235 CGTGGTCGCGTGCGATTTTCAACTATCGCAACG
1 CGTGGTC-CG-GCGATTTTCAACTATCGCAACG
1212268 CG
1 CG
1212270 ATTTTCAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
29 6 0.19
31 1 0.03
33 24 0.77
ACGTcount: A:0.19, C:0.28, G:0.27, T:0.27
Consensus pattern (31 bp):
CGTGGTCCGGCGATTTTCAACTATCGCAACG
Found at i:1212309 original size:20 final size:20
Alignment explanation
Indices: 1212284--1212331 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
1212274 TCAACTATCG
1212284 CAACGCGAAATGGAAAATCA
1 CAACGCGAAATGGAAAATCA
*
1212304 CAACGCGAAATGGAAAATCG
1 CAACGCGAAATGGAAAATCA
1212324 CAACGCGA
1 CAACGCGA
1212332 TTTTCAACTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.46, C:0.23, G:0.23, T:0.08
Consensus pattern (20 bp):
CAACGCGAAATGGAAAATCA
Found at i:1212360 original size:21 final size:21
Alignment explanation
Indices: 1212254--1212360 Score: 101
Period size: 21 Copynumber: 5.2 Consensus size: 21
1212244 GTGCGATTTT
** *
1212254 CAACTATCGCAACGCGATTTT
1 CAACTATCGCAACGCGAAATG
1212275 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
* * *
1212296 GAA-AATCACAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
* * ** *
1212316 GAA-AATCGCAACGCGATTTT
1 CAACTATCGCAACGCGAAATG
1212336 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
1212357 CAAC
1 CAAC
1212361 GCGAATTTGC
Statistics
Matches: 70, Mismatches: 15, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
20 33 0.47
21 37 0.53
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (21 bp):
CAACTATCGCAACGCGAAATG
Found at i:1214845 original size:11 final size:11
Alignment explanation
Indices: 1214829--1214853 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1214819 ATCCCCCCCC
1214829 ATACCCACCTA
1 ATACCCACCTA
1214840 ATACCCACCTA
1 ATACCCACCTA
1214851 ATA
1 ATA
1214854 TTTTTATCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.40, G:0.00, T:0.20
Consensus pattern (11 bp):
ATACCCACCTA
Found at i:1223854 original size:27 final size:28
Alignment explanation
Indices: 1223817--1223875 Score: 111
Period size: 27 Copynumber: 2.1 Consensus size: 28
1223807 AAAATTTACA
1223817 AACATTCAAGTGAAATGTAATGTAGTTC
1 AACATTCAAGTGAAATGTAATGTAGTTC
1223845 AACATT-AAGTGAAATGTAATGTAGTTC
1 AACATTCAAGTGAAATGTAATGTAGTTC
1223872 AACA
1 AACA
1223876 ACTAGAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 25 0.81
28 6 0.19
ACGTcount: A:0.42, C:0.10, G:0.17, T:0.31
Consensus pattern (28 bp):
AACATTCAAGTGAAATGTAATGTAGTTC
Found at i:1224438 original size:13 final size:13
Alignment explanation
Indices: 1224420--1224444 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1224410 AATGAATTTT
1224420 AAGATTTTCTAAA
1 AAGATTTTCTAAA
1224433 AAGATTTTCTAA
1 AAGATTTTCTAA
1224445 GTATATTCGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (13 bp):
AAGATTTTCTAAA
Found at i:1230530 original size:20 final size:20
Alignment explanation
Indices: 1230505--1230568 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
1230495 CCCCCTTTGA
**
1230505 AGGGGAACCGATTGCCCCCT
1 AGGGGAACCGATACCCCCCT
* *
1230525 AGGGGAATCTATACCCCCCT
1 AGGGGAACCGATACCCCCCT
* *
1230545 AGGGGAATCTATACCCCCCT
1 AGGGGAACCGATACCCCCCT
1230565 -GGGG
1 AGGGG
1230569 TTCTGGAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
19 4 0.10
20 36 0.90
ACGTcount: A:0.22, C:0.33, G:0.28, T:0.17
Consensus pattern (20 bp):
AGGGGAACCGATACCCCCCT
Found at i:1230561 original size:19 final size:20
Alignment explanation
Indices: 1230519--1230568 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
1230509 GAACCGATTG
1230519 CCCCCTAGGGGAATCTATAC
1 CCCCCTAGGGGAATCTATAC
1230539 CCCCCTAGGGGAATCTATAC
1 CCCCCTAGGGGAATCTATAC
1230559 CCCCCT-GGGG
1 CCCCCTAGGGG
1230569 TTCTGGAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 4 0.13
20 26 0.87
ACGTcount: A:0.20, C:0.38, G:0.24, T:0.18
Consensus pattern (20 bp):
CCCCCTAGGGGAATCTATAC
Found at i:1232817 original size:16 final size:16
Alignment explanation
Indices: 1232796--1232854 Score: 72
Period size: 16 Copynumber: 3.9 Consensus size: 16
1232786 ACAAAAAGGG
1232796 GGGAGAAGTGTTAAAT
1 GGGAGAAGTGTTAAAT
1232812 GGGAGAAGTGTTAAA-
1 GGGAGAAGTGTTAAAT
* *
1232827 --G-TAAGGGTTAAAT
1 GGGAGAAGTGTTAAAT
1232840 GGGAGAAGTGTTAAA
1 GGGAGAAGTGTTAAA
1232855 GTAAGGGGTA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
12 9 0.26
13 1 0.03
15 1 0.03
16 24 0.69
ACGTcount: A:0.39, C:0.00, G:0.37, T:0.24
Consensus pattern (16 bp):
GGGAGAAGTGTTAAAT
Found at i:1232845 original size:28 final size:28
Alignment explanation
Indices: 1232805--1232861 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
1232795 GGGGAGAAGT
1232805 GTTAAATGGGAGAAGTGTTAAAGTAAGG
1 GTTAAATGGGAGAAGTGTTAAAGTAAGG
1232833 GTTAAATGGGAGAAGTGTTAAAGTAAGG
1 GTTAAATGGGAGAAGTGTTAAAGTAAGG
1232861 G
1 G
1232862 GTAGTAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.39, C:0.00, G:0.37, T:0.25
Consensus pattern (28 bp):
GTTAAATGGGAGAAGTGTTAAAGTAAGG
Found at i:1235060 original size:20 final size:19
Alignment explanation
Indices: 1235031--1235071 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
1235021 CAAAAACAAA
*
1235031 TTTAAAAGTGTTTATGAAT
1 TTTAAAAGTGTTTATAAAT
1235050 TTTATAAAGTGTTTATAAAT
1 TTTA-AAAGTGTTTATAAAT
1235070 TT
1 TT
1235072 GGCTTACCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (19 bp):
TTTAAAAGTGTTTATAAAT
Found at i:1236100 original size:23 final size:23
Alignment explanation
Indices: 1236072--1236125 Score: 108
Period size: 23 Copynumber: 2.3 Consensus size: 23
1236062 GCATGCATGT
1236072 AGCCTTGTTTTTCAGCATGCGTC
1 AGCCTTGTTTTTCAGCATGCGTC
1236095 AGCCTTGTTTTTCAGCATGCGTC
1 AGCCTTGTTTTTCAGCATGCGTC
1236118 AGCCTTGT
1 AGCCTTGT
1236126 GGAGAAGCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.13, C:0.26, G:0.22, T:0.39
Consensus pattern (23 bp):
AGCCTTGTTTTTCAGCATGCGTC
Found at i:1236134 original size:23 final size:23
Alignment explanation
Indices: 1236085--1236136 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
1236075 CTTGTTTTTC
*****
1236085 AGCATGCGTCAGCCTTGTTTTTC
1 AGCATGCGTCAGCCTTGTGGAGA
1236108 AGCATGCGTCAGCCTTGTGGAGA
1 AGCATGCGTCAGCCTTGTGGAGA
1236131 AGCATG
1 AGCATG
1236137 TAGCAGCTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.19, C:0.23, G:0.29, T:0.29
Consensus pattern (23 bp):
AGCATGCGTCAGCCTTGTGGAGA
Found at i:1236197 original size:14 final size:14
Alignment explanation
Indices: 1236178--1236273 Score: 77
Period size: 14 Copynumber: 7.4 Consensus size: 14
1236168 CTTAATTTTT
1236178 TTATTAAATCATCA
1 TTATTAAATCATCA
1236192 TTATT--A--A-CA
1 TTATTAAATCATCA
1236201 TTATTAAATCATCA
1 TTATTAAATCATCA
1236215 TTA-T---TCA-CA
1 TTATTAAATCATCA
* *
1236224 TTATCAAATCATATTA
1 TTATTAAATC--ATCA
1236240 TTATTAAATCATCA
1 TTATTAAATCATCA
*
1236254 TTATTAAGTCATCA
1 TTATTAAATCATCA
1236268 TTATTA
1 TTATTA
1236274 TTAGACATTA
Statistics
Matches: 65, Mismatches: 5, Indels: 24
0.69 0.05 0.26
Matches are distributed among these distances:
9 12 0.18
10 4 0.06
11 1 0.02
12 1 0.02
13 4 0.06
14 32 0.49
15 1 0.02
16 10 0.15
ACGTcount: A:0.41, C:0.14, G:0.01, T:0.45
Consensus pattern (14 bp):
TTATTAAATCATCA
Found at i:1236206 original size:23 final size:23
Alignment explanation
Indices: 1236178--1236242 Score: 105
Period size: 23 Copynumber: 2.9 Consensus size: 23
1236168 CTTAATTTTT
1236178 TTATTAAATCATCATTATTAACA
1 TTATTAAATCATCATTATTAACA
*
1236201 TTATTAAATCATCATTATTCACA
1 TTATTAAATCATCATTATTAACA
*
1236224 TTATCAAATCAT-ATTATTA
1 TTATTAAATCATCATTATTA
1236243 TTAAATCATC
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 6 0.15
23 33 0.85
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.45
Consensus pattern (23 bp):
TTATTAAATCATCATTATTAACA
Found at i:1245361 original size:65 final size:64
Alignment explanation
Indices: 1245253--1245385 Score: 230
Period size: 65 Copynumber: 2.1 Consensus size: 64
1245243 CATGTATGCA
* *
1245253 TTTTTTAAGCTTGTATAGTTGTATTTTGTTTGTTTGGATAGAATTTATTGCCTTATCACCTTGT
1 TTTTTTAAGCTTGTATAGCTGTATTTTGTTTGTTCGGATAGAATTTATTGCCTTATCACCTTGT
*
1245317 TTTTCTTAAGCTTGTATAGCTGTATTTTGTTTGTTCGGCTAGAATTTATTGCCTTATCACCTTGT
1 TTTT-TTAAGCTTGTATAGCTGTATTTTGTTTGTTCGGATAGAATTTATTGCCTTATCACCTTGT
1245382 TTTT
1 TTTT
1245386 GTACATCTTA
Statistics
Matches: 65, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
64 4 0.06
65 61 0.94
ACGTcount: A:0.17, C:0.12, G:0.17, T:0.54
Consensus pattern (64 bp):
TTTTTTAAGCTTGTATAGCTGTATTTTGTTTGTTCGGATAGAATTTATTGCCTTATCACCTTGT
Found at i:1245468 original size:15 final size:16
Alignment explanation
Indices: 1245435--1245469 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1245425 AATTTACGTA
1245435 TTTGTTTCTGGAATTT
1 TTTGTTTCTGGAATTT
*
1245451 TTTGTTTCT-GATTTT
1 TTTGTTTCTGGAATTT
1245466 TTTG
1 TTTG
1245470 GGACTTCCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.09, C:0.06, G:0.17, T:0.69
Consensus pattern (16 bp):
TTTGTTTCTGGAATTT
Found at i:1248684 original size:59 final size:59
Alignment explanation
Indices: 1248581--1248694 Score: 140
Period size: 59 Copynumber: 1.9 Consensus size: 59
1248571 AATGTTATTC
* * * *
1248581 ATAGTTTAGGATTGGTATAAAATATTTTAAAGTTTAAAGATTAATTTGA-AATGTGGGTA
1 ATAGTTAAAGATTGATATAAAATAGTTTAAAGTTTAAAGATTAATTT-ATAATGTGGGTA
* ** *
1248640 ATAGTTAAAGATTGATATAAAATAGTTTAACGTTTAGGGGTTAATTTATAATGTG
1 ATAGTTAAAGATTGATATAAAATAGTTTAAAGTTTAAAGATTAATTTATAATGTG
1248695 TCATAGTGTG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
58 1 0.02
59 45 0.98
ACGTcount: A:0.39, C:0.01, G:0.20, T:0.40
Consensus pattern (59 bp):
ATAGTTAAAGATTGATATAAAATAGTTTAAAGTTTAAAGATTAATTTATAATGTGGGTA
Found at i:1251420 original size:44 final size:44
Alignment explanation
Indices: 1251357--1251447 Score: 182
Period size: 44 Copynumber: 2.1 Consensus size: 44
1251347 ATATTATTTA
1251357 TAAGGCATTCTTTCTTTAAATATTACTAATTTAACACATTTTTT
1 TAAGGCATTCTTTCTTTAAATATTACTAATTTAACACATTTTTT
1251401 TAAGGCATTCTTTCTTTAAATATTACTAATTTAACACATTTTTT
1 TAAGGCATTCTTTCTTTAAATATTACTAATTTAACACATTTTTT
1251445 TAA
1 TAA
1251448 TAAAGTGTGG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.33, C:0.13, G:0.04, T:0.49
Consensus pattern (44 bp):
TAAGGCATTCTTTCTTTAAATATTACTAATTTAACACATTTTTT
Found at i:1252042 original size:18 final size:19
Alignment explanation
Indices: 1252021--1252058 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
1252011 AATGTTTTAT
*
1252021 TTAA-TTATTTTTTTAGTA
1 TTAATTTATATTTTTAGTA
*
1252039 TTAATTTATATTTTTCGTA
1 TTAATTTATATTTTTAGTA
1252058 T
1 T
1252059 ACTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.66
Consensus pattern (19 bp):
TTAATTTATATTTTTAGTA
Found at i:1253741 original size:25 final size:25
Alignment explanation
Indices: 1253709--1253791 Score: 83
Period size: 25 Copynumber: 3.6 Consensus size: 25
1253699 CATGTGGTGT
1253709 TGTTTTTATTTATTTTGTTTCTTAA
1 TGTTTTTATTTATTTTGTTTCTTAA
* *
1253734 TGTTTTTATTTAATTATG------GA
1 TGTTTTTATTT-ATTTTGTTTCTTAA
1253754 T-TTTTTATTTATTTTGTTTCTTAA
1 TGTTTTTATTTATTTTGTTTCTTAA
1253778 TGTTTTTA-TTATTT
1 TGTTTTTATTTATTT
1253792 AATTATTTGA
Statistics
Matches: 46, Mismatches: 4, Indels: 17
0.69 0.06 0.25
Matches are distributed among these distances:
18 5 0.11
19 9 0.20
20 2 0.04
24 8 0.17
25 17 0.37
26 5 0.11
ACGTcount: A:0.18, C:0.02, G:0.08, T:0.71
Consensus pattern (25 bp):
TGTTTTTATTTATTTTGTTTCTTAA
Found at i:1256765 original size:13 final size:13
Alignment explanation
Indices: 1256747--1256784 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
1256737 TCAATTGATA
1256747 ATTAATAAATAAT
1 ATTAATAAATAAT
**
1256760 ATTAATAAATTTT
1 ATTAATAAATAAT
1256773 A-TAATAAATAAT
1 ATTAATAAATAAT
1256785 CGATAAAAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
ATTAATAAATAAT
Found at i:1263246 original size:156 final size:156
Alignment explanation
Indices: 1263048--1263356 Score: 537
Period size: 156 Copynumber: 2.0 Consensus size: 156
1263038 AGGAGGGGCA
*
1263048 CTTTCAGAAGCTAATCATGAAAAAAATTCTTTGCAGAAGAAGATTGATAATCTTGAAAATTATTG
1 CTTTCAGAAGCTAAGCATGAAAAAAATTCTTTGCAGAAGAAGATTGATAATCTTGAAAATTATTG
* * * *
1263113 TGGGTCACTAGCTGCTGATTTGGAAGAGTCAGAAAAGAGAGTATCTAGTCTTGAGGCTGACCTTC
66 TGGGTCACTAGCTACTGATTTGGAAGAATCAGAAAAGAGAGCATCTAGTCTTGAGGCAGACCTTC
1263178 AATCAGTTATGCTGGAGAGGGATGCT
131 AATCAGTTATGCTGGAGAGGGATGCT
* * *
1263204 CTTTCAGATGCTAAGCATGAAAGAAATTCTTTGCAGAAGAAGATTGATAGTCTTGAAAATTATTG
1 CTTTCAGAAGCTAAGCATGAAAAAAATTCTTTGCAGAAGAAGATTGATAATCTTGAAAATTATTG
1263269 TGGGTCACTAGCTACTGATTTGGAAGAATCAGAAAAGAGAGCATCTAGTCTTGAGGCAGACCTTC
66 TGGGTCACTAGCTACTGATTTGGAAGAATCAGAAAAGAGAGCATCTAGTCTTGAGGCAGACCTTC
*
1263334 AATCAGTTATGCTTGAGAGGGAT
131 AATCAGTTATGCTGGAGAGGGAT
1263357 CAGTTTTCTG
Statistics
Matches: 144, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
156 144 1.00
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (156 bp):
CTTTCAGAAGCTAAGCATGAAAAAAATTCTTTGCAGAAGAAGATTGATAATCTTGAAAATTATTG
TGGGTCACTAGCTACTGATTTGGAAGAATCAGAAAAGAGAGCATCTAGTCTTGAGGCAGACCTTC
AATCAGTTATGCTGGAGAGGGATGCT
Found at i:1264801 original size:13 final size:13
Alignment explanation
Indices: 1264783--1264812 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
1264773 CTGTCTTTCC
1264783 TTTGTGCATTCAG
1 TTTGTGCATTCAG
1264796 TTTGTGCATTCAG
1 TTTGTGCATTCAG
1264809 TTTG
1 TTTG
1264813 GGGTAATTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.13, C:0.13, G:0.23, T:0.50
Consensus pattern (13 bp):
TTTGTGCATTCAG
Found at i:1268647 original size:2 final size:2
Alignment explanation
Indices: 1268635--1268668 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
1268625 TTATACGATC
*
1268635 AT AT AT A- AT AT AT AT AT AT AT AT AT AT AA AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1268669 AAGTGTTAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1269271 original size:50 final size:50
Alignment explanation
Indices: 1269170--1269271 Score: 111
Period size: 50 Copynumber: 2.0 Consensus size: 50
1269160 ACATAACGAG
* * * * *
1269170 TTTTAATAAAATATATTTTTTATTCAAAATTTTCATTCCGATGTGATAAA
1 TTTTAATAAAATATATATTTTATTCAAAATTGTAATTCCGACGTGACAAA
1269220 TTTTAATAAATATATATATTTTATT-AAAATTCGTAATAT-C-ACGTGACAAA
1 TTTTAATAAA-ATATATATTTTATTCAAAATT-GTAAT-TCCGACGTGACAAA
1269270 TT
1 TT
1269272 CAAATAATAA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
50 26 0.59
51 17 0.39
52 1 0.02
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (50 bp):
TTTTAATAAAATATATATTTTATTCAAAATTGTAATTCCGACGTGACAAA
Found at i:1271787 original size:109 final size:109
Alignment explanation
Indices: 1271589--1271787 Score: 274
Period size: 109 Copynumber: 1.8 Consensus size: 109
1271579 TTTTGAGGTG
* * *
1271589 TCTTCTGGTTCTGCCTCTTTACTTTTCTGCTTCTACACCTAAAGGATTAACTTCTTTGCTGCCCG
1 TCTTCTGGGTCTGCCTCATTACTTTTCTGCTTCTACACCTAAAGGATTAACTTCTCTGCTGCCCG
* *
1271654 GATATGAGATCTTCAATACTTGATCACTGTGGGTCAATTTGATA
66 GATATGAGATATTCAATACATGATCACTGTGGGTCAATTTGATA
* * * *
1271698 TCTTCTGGGTCTGCCTCATTACTTTTCTGCTTCCT-CACCTAAGGGATTTACTTCTCTGTTGCCT
1 TCTTCTGGGTCTGCCTCATTACTTTTCTGCTT-CTACACCTAAAGGATTAACTTCTCTGCTGCCC
* * *
1271762 GGCTATGGGATATTCAGTACATGATC
65 GGATATGAGATATTCAATACATGATC
1271788 TTTGTTGCCT
Statistics
Matches: 77, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
109 75 0.97
110 2 0.03
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (109 bp):
TCTTCTGGGTCTGCCTCATTACTTTTCTGCTTCTACACCTAAAGGATTAACTTCTCTGCTGCCCG
GATATGAGATATTCAATACATGATCACTGTGGGTCAATTTGATA
Found at i:1278500 original size:31 final size:31
Alignment explanation
Indices: 1278462--1278525 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
1278452 AAAAAAAACA
1278462 TAAGATAT-GACAACTTTCATTTTTATTCAAT
1 TAAGATATGGAC-ACTTTCATTTTTATTCAAT
* * *
1278493 TAAGATATGGTCACTTTCGTTTTTATTTAAT
1 TAAGATATGGACACTTTCATTTTTATTCAAT
1278524 TA
1 TA
1278526 CGATGTGGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 27 0.93
32 2 0.07
ACGTcount: A:0.31, C:0.11, G:0.09, T:0.48
Consensus pattern (31 bp):
TAAGATATGGACACTTTCATTTTTATTCAAT
Found at i:1278535 original size:31 final size:31
Alignment explanation
Indices: 1278474--1278536 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
1278464 AGATATGACA
1278474 ACTTTCATTTTTATTCAATTAAGATATGGTC
1 ACTTTCATTTTTATTCAATTAAGATATGGTC
* * * *
1278505 ACTTTCGTTTTTATTTAATTACGATGTGGTC
1 ACTTTCATTTTTATTCAATTAAGATATGGTC
1278536 A
1 A
1278537 TCACGGGTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.25, C:0.13, G:0.13, T:0.49
Consensus pattern (31 bp):
ACTTTCATTTTTATTCAATTAAGATATGGTC
Found at i:1278744 original size:25 final size:27
Alignment explanation
Indices: 1278693--1278753 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 27
1278683 TGAAAATAAA
*
1278693 AATAAAATAT-TTTAAATTAAGTTAAT
1 AATAAAATATATGTAAATTAAGTTAAT
1278719 AATAAAATATATGT-AA-TAAGTTAAT
1 AATAAAATATATGTAAATTAAGTTAAT
1278744 -ATAAAA-ATAT
1 AATAAAATATAT
1278754 TTTTTAAGTC
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
23 4 0.12
24 6 0.18
25 9 0.27
26 12 0.36
27 2 0.06
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (27 bp):
AATAAAATATATGTAAATTAAGTTAAT
Found at i:1278761 original size:23 final size:23
Alignment explanation
Indices: 1278708--1278777 Score: 68
Period size: 25 Copynumber: 2.8 Consensus size: 23
1278698 AATATTTTAA
1278708 ATTAAGTTAATAATAAAATATATGT
1 ATTAAGTTAAT-ATAAAA-ATATGT
* *
1278733 AATAAGTTAATATAAAAATATTT
1 ATTAAGTTAATATAAAAATATGT
*
1278756 TTTAAGTCTATATATATAAAAT
1 ATTAAGT-TA-ATATA-AAAAT
1278778 GTTATGAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
23 10 0.26
24 8 0.21
25 15 0.39
26 5 0.13
ACGTcount: A:0.51, C:0.01, G:0.06, T:0.41
Consensus pattern (23 bp):
ATTAAGTTAATATAAAAATATGT
Found at i:1283636 original size:189 final size:188
Alignment explanation
Indices: 1283409--1283992 Score: 677
Period size: 189 Copynumber: 3.1 Consensus size: 188
1283399 TAAAGCATCA
* * * * * **
1283409 TTTTGGTAACAAACGTCGTAAATAATTCGTAATTTAGTGTCATTTTGTCAAAAAACGCATTAAAT
1 TTTTGGTAACAAACGCCGCAAATAATTCGTACTTTAGTGTCGTTTTGTCAAAAAATGC-GCAAAT
* *
1283474 GTTTTTTATTTAAACGCCATTAACTTTAGACATATAGCGGCGTGTTTTAATAAACGCCGCAATAT
65 GTTTTTTATTTAAACGCCATTAACTTTAGACATATAGCGGCGTTTTTTAATAAACGCCGCAATAA
* * *
1283539 ATTAGTACTACAACGGCGTTTTGACAAAAATGGCGCAAGAGGGTTAACATATAGCGATG
130 ATTAGTACTACAGCGGCGTTTTGACAAAAATGCCGCAAGAGGGTTAACATATAGCGACG
* * * *
1283598 TTTTGGTAACAAATGGCACAAATAATTCGTACTTTAGTGGCGTTTTGTCAAAAAATGCCGCAAAT
1 TTTTGGTAACAAACGCCGCAAATAATTCGTACTTTAGTGTCGTTTTGTCAAAAAATG-CGCAAAT
* * * * *
1283663 GTTTTGTATTTGAACGCCATTAACTTTAGACATATAACGGCGTTTTTTAATAAACGCCGCAACAG
65 GTTTTTTATTTAAACGCCATTAACTTTAGACATATAGCGGCGTTTTTTAATAAACGCCGCAATAA
* * * *
1283728 ATTAGTACTACAGTGGCGTTTTGACAAAAACGCCACAAGAGGGTTAACATATAGCGACA
130 ATTAGTACTACAGCGGCGTTTTGACAAAAATGCCGCAAGAGGGTTAACATATAGCGACG
* * *** * *
1283787 TATTGGTAACAAACGCCGCAAATTATTAAAATCATTAGTGGT-GTTTTGACAAAAAAATGTCGCA
1 TTTTGGTAACAAACGCCGCAAATAATTCGTA-CTTTAGT-GTCGTTTTGTC-AAAAAATG-CGCA
* ** * *
1283851 GATGTTTTTTTATTTAAACATCA-TAAATTTAGACATATAGGGGCGTTTTTTAATAAACGCCGCA
62 AATG-TTTTTTATTTAAACGCCATTAACTTTAGACATATAGCGGCGTTTTTTAATAAACGCCGCA
** * * * * * *
1283915 ATAAATTAGTACTTTAGCAGCGTTTTGACAAAAATGCCGCAATATGGTTCACGTATAGCGGCG
126 ATAAATTAGTACTACAGCGGCGTTTTGACAAAAATGCCGCAAGAGGGTTAACATATAGCGACG
*
1283978 TTTTAGTAACAAACG
1 TTTTGGTAACAAACG
1283993 ACGTAATATG
Statistics
Matches: 331, Mismatches: 59, Indels: 8
0.83 0.15 0.02
Matches are distributed among these distances:
189 187 0.56
190 14 0.04
191 116 0.35
192 14 0.04
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (188 bp):
TTTTGGTAACAAACGCCGCAAATAATTCGTACTTTAGTGTCGTTTTGTCAAAAAATGCGCAAATG
TTTTTTATTTAAACGCCATTAACTTTAGACATATAGCGGCGTTTTTTAATAAACGCCGCAATAAA
TTAGTACTACAGCGGCGTTTTGACAAAAATGCCGCAAGAGGGTTAACATATAGCGACG
Found at i:1284003 original size:42 final size:42
Alignment explanation
Indices: 1283955--1284040 Score: 136
Period size: 42 Copynumber: 2.0 Consensus size: 42
1283945 AAAATGCCGC
*
1283955 AATATGGTTCACGTATAGCGGCGTTTTAGTAACAAACGACGT
1 AATATGGTTCACATATAGCGGCGTTTTAGTAACAAACGACGT
* * *
1283997 AATATGGTTCACATATAGCTGTGTTTTAGTAACAAACGTCGT
1 AATATGGTTCACATATAGCGGCGTTTTAGTAACAAACGACGT
1284039 AA
1 AA
1284041 ATTATTCGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (42 bp):
AATATGGTTCACATATAGCGGCGTTTTAGTAACAAACGACGT
Found at i:1289421 original size:43 final size:43
Alignment explanation
Indices: 1289374--1289487 Score: 124
Period size: 43 Copynumber: 2.6 Consensus size: 43
1289364 TATCGGTGTC
*
1289374 TGTATACTAAAACACTGCTATATACCAGACCATCATCGGCATT
1 TGTATCCTAAAACACTGCTATATACCAGACCATCATCGGCATT
* * * * *
1289417 TGTATCCTAAAA-ACGTCGCTATATACCAGATCTTTATCTGCGTT
1 TGTATCCTAAAACAC-T-GCTATATACCAGACCATCATCGGCATT
*
1289461 T-TATCCTAAAATCGCTGCTATATACCA
1 TGTATCCTAAAA-CACTGCTATATACCA
1289488 AATTTTTAGC
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
42 2 0.03
43 33 0.55
44 24 0.40
45 1 0.02
ACGTcount: A:0.32, C:0.25, G:0.11, T:0.32
Consensus pattern (43 bp):
TGTATCCTAAAACACTGCTATATACCAGACCATCATCGGCATT
Found at i:1291732 original size:31 final size:31
Alignment explanation
Indices: 1291697--1291759 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
1291687 GGACAAGGCT
*
1291697 TGTGAGCTTCTCTAACATCTCCTTAGCGCCA
1 TGTGAGCTTCTCTAACATCTCCTCAGCGCCA
1291728 TGTGAGCTTCTCTAACATCTCCTCAGCGCCA
1 TGTGAGCTTCTCTAACATCTCCTCAGCGCCA
1291759 T
1 T
1291760 CGCCTCAACT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.19, C:0.33, G:0.16, T:0.32
Consensus pattern (31 bp):
TGTGAGCTTCTCTAACATCTCCTCAGCGCCA
Found at i:1294001 original size:2 final size:2
Alignment explanation
Indices: 1293994--1294018 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1293984 TAAATTAACA
1293994 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1294019 ACGTGCAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1296598 original size:15 final size:16
Alignment explanation
Indices: 1296573--1296602 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1296563 TATATATTAA
1296573 AAAACAATAAATAAAT
1 AAAACAATAAATAAAT
1296589 AAAA-AATAAATAAA
1 AAAACAATAAATAAA
1296603 AATCATTTTT
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:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (16 bp):
AAAACAATAAATAAAT
Found at i:1296834 original size:25 final size:25
Alignment explanation
Indices: 1296805--1296876 Score: 98
Period size: 25 Copynumber: 3.0 Consensus size: 25
1296795 TGTTTTCAAA
1296805 ATGTTTTCAAAACTATATAATATAT
1 ATGTTTTCAAAACTATATAATATAT
1296830 ATGTTTTCAAAAC--TAT-ATA-AT
1 ATGTTTTCAAAACTATATAATATAT
*
1296851 ATGTTTTCAAAAACTATATATTATAT
1 ATGTTTTC-AAAACTATATAATATAT
1296877 TTTCAAAATG
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
21 10 0.24
22 8 0.20
23 3 0.07
24 3 0.07
25 15 0.37
26 2 0.05
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.44
Consensus pattern (25 bp):
ATGTTTTCAAAACTATATAATATAT
Found at i:1296835 original size:36 final size:36
Alignment explanation
Indices: 1296775--1296948 Score: 117
Period size: 36 Copynumber: 4.5 Consensus size: 36
1296765 GTTATTTTAA
1296775 AAAACTATATAGTATATATATGTTTTCAAAATGTTTTC
1 AAAACTATATA--ATATATATGTTTTCAAAATGTTTTC
1296813 AAAACTATATAATATATATGTTTTCAAAACTATATAATATGTTTTC
1 AAAACTATATAATATATATGTTTT-----C---A-AA-ATGTTTTC
*
1296859 AAAAACTATAT-AT-TATA--TTTTCAAAATGTTTTTT
1 -AAAACTATATAATATATATGTTTTCAAAATG-TTTTC
** *
1296893 AAAAAAATCAT-ATATTATATAGTTTTCAAAATGATTTC
1 AAAACTAT-ATAATA-TATAT-GTTTTCAAAATGTTTTC
1296931 -AAACTATATAATATATAT
1 AAAACTATATAATATATAT
1296949 AAATAAAATT
Statistics
Matches: 110, Mismatches: 7, Indels: 40
0.70 0.04 0.25
Matches are distributed among these distances:
33 9 0.08
34 10 0.09
35 1 0.01
36 24 0.22
37 8 0.07
38 15 0.14
39 11 0.10
41 1 0.01
43 4 0.04
44 1 0.01
45 6 0.05
46 10 0.09
47 10 0.09
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (36 bp):
AAAACTATATAATATATATGTTTTCAAAATGTTTTC
Found at i:1296866 original size:22 final size:21
Alignment explanation
Indices: 1296805--1296884 Score: 97
Period size: 22 Copynumber: 3.6 Consensus size: 21
1296795 TGTTTTCAAA
1296805 ATGTTTTCAAAACTATATAATATAT
1 ATGTTTTCAAAAC--TAT-ATA-AT
1296830 ATGTTTTCAAAACTATATAAT
1 ATGTTTTCAAAACTATATAAT
*
1296851 ATGTTTTCAAAAACTATATATT
1 ATGTTTTC-AAAACTATATAAT
*
1296873 ATATTTTCAAAA
1 ATGTTTTCAAAA
1296885 TGTTTTTTAA
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
21 14 0.27
22 22 0.42
23 3 0.06
25 13 0.25
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.44
Consensus pattern (21 bp):
ATGTTTTCAAAACTATATAAT
Found at i:1304182 original size:21 final size:21
Alignment explanation
Indices: 1304158--1304216 Score: 118
Period size: 21 Copynumber: 2.8 Consensus size: 21
1304148 ATTAAGACAC
1304158 AAACTTGAAATCCATAACAAG
1 AAACTTGAAATCCATAACAAG
1304179 AAACTTGAAATCCATAACAAG
1 AAACTTGAAATCCATAACAAG
1304200 AAACTTGAAATCCATAA
1 AAACTTGAAATCCATAA
1304217 TAATAAATCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.53, C:0.19, G:0.08, T:0.20
Consensus pattern (21 bp):
AAACTTGAAATCCATAACAAG
Found at i:1306240 original size:21 final size:21
Alignment explanation
Indices: 1306202--1306241 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1306192 TTGCGAAAGT
*
1306202 AATCAAAAGAAAAAGAAAAAA
1 AATCAAAACAAAAAGAAAAAA
* *
1306223 AATCAAAACATAAGGAAAA
1 AATCAAAACAAAAAGAAAA
1306242 TTCAACAGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.75, C:0.07, G:0.10, T:0.07
Consensus pattern (21 bp):
AATCAAAACAAAAAGAAAAAA
Found at i:1306925 original size:40 final size:40
Alignment explanation
Indices: 1306855--1306983 Score: 136
Period size: 40 Copynumber: 3.1 Consensus size: 40
1306845 ATGTAAACTT
1306855 GCGGCATTTGTAAATAAAAACGCCACTAAAGTATGAGTATTTA
1 GCGGCATTTGTAAA-AAAAA--CCACTAAAGTATGAGTATTTA
1306898 GCGGCATTTGTAAAAAAAACCACTAAAGTACT-AGGT-TTTA
1 GCGGCATTTGTAAAAAAAACCACTAAAGTA-TGA-GTATTTA
* ** * **
1306938 GCGACATTTGTCTGAGAACGCCACTAAAGTATGAGTATTTA
1 GCGGCATTTGT-AAAAAAAACCACTAAAGTATGAGTATTTA
1306979 GCGGC
1 GCGGC
1306984 GTTTTTGCTT
Statistics
Matches: 74, Mismatches: 7, Indels: 12
0.80 0.08 0.13
Matches are distributed among these distances:
40 29 0.39
41 26 0.35
42 5 0.07
43 14 0.19
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (40 bp):
GCGGCATTTGTAAAAAAAACCACTAAAGTATGAGTATTTA
Found at i:1307021 original size:42 final size:41
Alignment explanation
Indices: 1306871--1307044 Score: 131
Period size: 41 Copynumber: 4.2 Consensus size: 41
1306861 TTTGTAAATA
* * **
1306871 AAAACGCCACTAAAGTATGA-GTATTTAGCGGCATTTGT-AA
1 AAAACGCCACTAAAGTATTAGGT-TTTAGCGACATTTGTCTG
** *
1306911 AAAAAACCACTAAAGTACTAGGTTTTAGCGACATTTGTCTG
1 AAAACGCCACTAAAGTATTAGGTTTTAGCGACATTTGTCTG
* * * * * *
1306952 AGAACGCCACTAAAGTATGA-GTATTTAGCGGCGTTTTTGCTT
1 AAAACGCCACTAAAGTATTAGGT-TTTAGCGACATTTGT-CTG
* * *
1306994 AAAACGCCACAAAAGTATTAGGTTTTAGCTG-CATTTATCTA
1 AAAACGCCACTAAAGTATTAGGTTTTAGC-GACATTTGTCTG
*
1307035 AAAATGCCAC
1 AAAACGCCAC
1307045 GATATATTTA
Statistics
Matches: 105, Mismatches: 23, Indels: 11
0.76 0.17 0.08
Matches are distributed among these distances:
40 32 0.30
41 40 0.38
42 30 0.29
43 3 0.03
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.29
Consensus pattern (41 bp):
AAAACGCCACTAAAGTATTAGGTTTTAGCGACATTTGTCTG
Found at i:1313493 original size:17 final size:18
Alignment explanation
Indices: 1313462--1313497 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
1313452 AAAATTTCGG
*
1313462 TATATATAAATTTAAAAT
1 TATATATAAAATTAAAAT
1313480 TATA-ATAAAATTAAAAT
1 TATATATAAAATTAAAAT
1313497 T
1 T
1313498 TTATTCATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
TATATATAAAATTAAAAT
Found at i:1314813 original size:2 final size:2
Alignment explanation
Indices: 1314806--1314835 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1314796 AAATTGTATT
1314806 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1314836 CATTGAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1314896 original size:19 final size:19
Alignment explanation
Indices: 1314856--1314902 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
1314846 TAGAATTTAT
*
1314856 TTTTTAAATTATAAATATA
1 TTTTTAAATTATAAATAAA
**
1314875 TTTTTAAATTATATTTAAA
1 TTTTTAAATTATAAATAAA
1314894 TTTATTAAA
1 TTT-TTAAA
1314903 CAAAATTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 19 0.79
20 5 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTTTAAATTATAAATAAA
Found at i:1316230 original size:32 final size:31
Alignment explanation
Indices: 1316176--1316238 Score: 90
Period size: 32 Copynumber: 2.0 Consensus size: 31
1316166 GTTCTATCAA
* *
1316176 GTCATTTACCATTAATGCTTAACTGAGAAACT
1 GTCATTTACCATTAATACTTAAC-GAAAAACT
*
1316208 GTCATTTACCATTAATATTTAACGAAAAACT
1 GTCATTTACCATTAATACTTAACGAAAAACT
1316239 ATCGTGATAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 7 0.25
32 21 0.75
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (31 bp):
GTCATTTACCATTAATACTTAACGAAAAACT
Found at i:1324310 original size:21 final size:21
Alignment explanation
Indices: 1324251--1324390 Score: 90
Period size: 20 Copynumber: 6.8 Consensus size: 21
1324241 TTTTTGACTT
* *
1324251 AAAGGATTGATCCCTTAG-CAC
1 AAAGGATCGATCCCTTTGAC-C
* *
1324272 AAA-GATTGATCCATTTGACC
1 AAAGGATCGATCCCTTTGACC
* * *
1324292 AAAGAATCGATCCCCTTGA-A
1 AAAGGATCGATCCCTTTGACC
* * *
1324312 AAATGATCTATCACTTTGACC
1 AAAGGATCGATCCCTTTGACC
* * *
1324333 AAAGGATCGATTCCATTGA-A
1 AAAGGATCGATCCCTTTGACC
*
1324353 AAAGGATCGATCCCTTTGGCC
1 AAAGGATCGATCCCTTTGACC
* *
1324374 AAATGATTGATTCCCTT
1 AAAGGATCGA-TCCCTT
1324391 GAAAAATGAT
Statistics
Matches: 89, Mismatches: 25, Indels: 9
0.72 0.20 0.07
Matches are distributed among these distances:
20 46 0.52
21 37 0.42
22 6 0.07
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (21 bp):
AAAGGATCGATCCCTTTGACC
Found at i:1324330 original size:41 final size:40
Alignment explanation
Indices: 1324285--1324404 Score: 150
Period size: 41 Copynumber: 2.9 Consensus size: 40
1324275 GATTGATCCA
* *
1324285 TTTGACCAAAGAATCGATCCCCTTGAAAAATGATCTATCAC
1 TTTGACCAAAG-ATCGATTCCCTTGAAAAATGATCGATCAC
* * *
1324326 TTTGACCAAAGGATCGATTCCATTGAAAAAGGATCGATCCC
1 TTTGACCAAA-GATCGATTCCCTTGAAAAATGATCGATCAC
* *
1324367 TTTGGCCAAATGATTGATTCCCTTGAAAAATGATCGAT
1 TTTGACCAAA-GATCGATTCCCTTGAAAAATGATCGAT
1324405 TCATTGGATA
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
41 67 0.99
42 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (40 bp):
TTTGACCAAAGATCGATTCCCTTGAAAAATGATCGATCAC
Found at i:1324358 original size:20 final size:20
Alignment explanation
Indices: 1324333--1324410 Score: 68
Period size: 20 Copynumber: 3.9 Consensus size: 20
1324323 CACTTTGACC
1324333 AAAGGATCGATTCCATTGAA
1 AAAGGATCGATTCCATTGAA
* * **
1324353 AAAGGATCGATCCCTTTGGCC
1 AAAGGATCGATTCCATT-GAA
* * *
1324374 AAATGATTGATTCCCTTGAA
1 AAAGGATCGATTCCATTGAA
*
1324394 AAATGATCGATT-CATTG
1 AAAGGATCGATTCCATTG
1324411 GATAACAGTG
Statistics
Matches: 45, Mismatches: 12, Indels: 3
0.75 0.20 0.05
Matches are distributed among these distances:
19 4 0.09
20 27 0.60
21 14 0.31
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.29
Consensus pattern (20 bp):
AAAGGATCGATTCCATTGAA
Found at i:1327261 original size:21 final size:20
Alignment explanation
Indices: 1327218--1327292 Score: 89
Period size: 21 Copynumber: 3.6 Consensus size: 20
1327208 AGTGAGTTTG
1327218 GGATCGATCCCTTGACAAAA
1 GGATCGATCCCTTGACAAAA
*
1327238 GGATCGATCCCTCGTGA-GAAA
1 GGATCGATCCCT--TGACAAAA
**
1327259 GGATCGATCCCTTCCCAAAAA
1 GGATCGATCCCTTGAC-AAAA
1327280 GGATCGATCCCTT
1 GGATCGATCCCTT
1327293 TGGTATAATG
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
19 1 0.02
20 12 0.26
21 31 0.66
22 3 0.06
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.21
Consensus pattern (20 bp):
GGATCGATCCCTTGACAAAA
Done.