Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032252.1 Gossypioides kirkii chromosome KI_10
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: 47257441
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3600 characters in sequence are not A, C, G, or T
File 24 of 163
Found at i:6461041 original size:14 final size:14
Alignment explanation
Indices: 6461022--6461048 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
6461012 TTTATTTTAA
6461022 ATTTAAATTTACTC
1 ATTTAAATTTACTC
6461036 ATTTAAATTTACT
1 ATTTAAATTTACT
6461049 TTAAATTTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (14 bp):
ATTTAAATTTACTC
Found at i:6461121 original size:14 final size:14
Alignment explanation
Indices: 6461102--6461146 Score: 72
Period size: 14 Copynumber: 3.2 Consensus size: 14
6461092 AATTAAAACT
6461102 AAAGTCCATTTACA
1 AAAGTCCATTTACA
*
6461116 AAAGTCCAATTACA
1 AAAGTCCATTTACA
*
6461130 AATGTCCATTTACA
1 AAAGTCCATTTACA
6461144 AAA
1 AAA
6461147 AAGAAAGCCC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.47, C:0.20, G:0.07, T:0.27
Consensus pattern (14 bp):
AAAGTCCATTTACA
Found at i:6462308 original size:17 final size:17
Alignment explanation
Indices: 6462282--6462316 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
6462272 AAGTTTCGAA
6462282 TCTTTGCCAGATCTGGG
1 TCTTTGCCAGATCTGGG
*
6462299 TCTTTTCCAGATCTGGG
1 TCTTTGCCAGATCTGGG
6462316 T
1 T
6462317 TTGGTTCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.11, C:0.23, G:0.26, T:0.40
Consensus pattern (17 bp):
TCTTTGCCAGATCTGGG
Found at i:6463384 original size:60 final size:59
Alignment explanation
Indices: 6463086--6463462 Score: 501
Period size: 59 Copynumber: 6.4 Consensus size: 59
6463076 CCTGGACTAT
* * **
6463086 CAAAAATTACTATTTTA-CCCTCGAA-TTTCCTAAAATTCCATTTTTAACCTCGGCTTCAC
1 CAAAAATTACCATTTTACCCCT-AAACTTTCC-AAAATTCCATTTTTAACCTCGATTTCAC
*
6463145 CAAAAATAACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCTC-AGTTTCAC
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCTCGA-TTTCAC
* * *
6463204 CAAAAATTACCATTTTACCCCTGAATTTTCTAAAATTCCATTTTTAACCTCGATTTCAC
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCAC
* * *
6463263 CAAAAATTACCATTTTATCCCTAAACTTTCCAAAATTCCATTTTTAACC-CTAATTTTAC
1 CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCTC-GATTTCAC
* * * *
6463322 CAAAAATTACCCTTTTATCCCTCGAACTTTCCAAAATTCCATTTTTGACCTCGATTTCAC
1 CAAAAATTACCATTTTACCCCT-AAACTTTCCAAAATTCCATTTTTAACCTCGATTTCAC
* *
6463382 CAAAAATTACCATCTTACCCCTAAACTTTCCCAAAATTCCATTTTTGACCTCGATTTCAC
1 CAAAAATTACCATTTTACCCCTAAACTTT-CCAAAATTCCATTTTTAACCTCGATTTCAC
* *
6463442 CAAAAATTATCATTTTGCCCC
1 CAAAAATTACCATTTTACCCC
6463463 CGGGTACCCA
Statistics
Matches: 283, Mismatches: 27, Indels: 15
0.87 0.08 0.05
Matches are distributed among these distances:
58 1 0.00
59 173 0.61
60 108 0.38
61 1 0.00
ACGTcount: A:0.32, C:0.28, G:0.03, T:0.36
Consensus pattern (59 bp):
CAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCTCGATTTCAC
Found at i:6463458 original size:30 final size:30
Alignment explanation
Indices: 6463176--6463458 Score: 113
Period size: 30 Copynumber: 9.5 Consensus size: 30
6463166 TAAACTTTCC
*
6463176 AAAATT-CCATTTTTAACCTC-AGTTTCACCA
1 AAAATTACCA-TTTTGACCTCGA-TTTCACCA
* * *
6463206 AAAATTACCATTTT-ACCCCTGAATTT--TCT
1 AAAATTACCATTTTGACCTC-G-ATTTCACCA
*
6463235 AAAATT-CCATTTTTAACCTCGATTTCACCA
1 AAAATTACCA-TTTTGACCTCGATTTCACCA
**
6463265 AAAATTACCATTTT-ATCCCTAAACTTT--CC-
1 AAAATTACCATTTTGA--CCTCGA-TTTCACCA
* * *
6463294 AAAATT-CCATTTTTAACC-CTAATTTTACCA
1 AAAATTACCA-TTTTGACCTC-GATTTCACCA
*
6463324 AAAATTACCCTTTT-ATCCCTCGAACTTT--CC-
1 AAAATTACCATTTTGA--CCTCG-A-TTTCACCA
6463354 AAAATT-CCATTTTTGACCTCGATTTCACCA
1 AAAATTACCA-TTTTGACCTCGATTTCACCA
* **
6463384 AAAATTACCATCTT-ACCCCTAAACTTTC-CC-
1 AAAATTACCATTTTGA--CCTCGA-TTTCACCA
6463414 AAAATT-CCATTTTTGACCTCGATTTCACCA
1 AAAATTACCA-TTTTGACCTCGATTTCACCA
*
6463444 AAAATTATCATTTTG
1 AAAATTACCATTTTG
6463459 CCCCCGGGTA
Statistics
Matches: 196, Mismatches: 19, Indels: 76
0.67 0.07 0.26
Matches are distributed among these distances:
27 6 0.03
28 19 0.10
29 49 0.25
30 77 0.39
31 32 0.16
32 10 0.05
33 3 0.02
ACGTcount: A:0.33, C:0.27, G:0.03, T:0.37
Consensus pattern (30 bp):
AAAATTACCATTTTGACCTCGATTTCACCA
Found at i:6470970 original size:30 final size:30
Alignment explanation
Indices: 6470930--6470991 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 30
6470920 ACGGAAAAAC
6470930 TGAATCAAAATTAAAGTTTTATGTATATAAT
1 TGAATCAAAATTAAAG-TTTATGTATATAAT
* *
6470961 TGAAT-AAAATTAAAGTTTGTGTATATGAT
1 TGAATCAAAATTAAAGTTTATGTATATAAT
6470990 TG
1 TG
6470992 CACATTGAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 14 0.48
30 10 0.34
31 5 0.17
ACGTcount: A:0.42, C:0.02, G:0.15, T:0.42
Consensus pattern (30 bp):
TGAATCAAAATTAAAGTTTATGTATATAAT
Found at i:6474085 original size:164 final size:169
Alignment explanation
Indices: 6473915--6474222 Score: 360
Period size: 171 Copynumber: 1.8 Consensus size: 169
6473905 ATATTCAAAA
* * * * *
6473915 CTACGATCTACA-AACA-CGT-A-ACTATAAACAATTGAGCTAGTAAACCAATTGTTTCATTCGT
1 CTACGATCTACATAACAGCATGAGACTACAAACAAGTAAGCTAGTAAACCAATTATTTCATTCGT
* * *
6473976 A-AAAACTACAATATATGAAGCTTTTCTCTATTGGTTAAATGATAATAAGTTACTT-GGCCTAAG
66 AGAAAA-TACAATATATGAAGCTTTTCTCCATTGGTTAAATGATAATAAATTA-TTCGCCCTAAG
6474039 -ATAAATAATAAAAATAATATAACTTATTCAACCCATAGCT
129 AATAAATAATAAAAATAATATAACTTATTCAACCCATAGCT
* * * * * *
6474079 CTACGATCTTCATGTTAATAGCATGAGGCTACAACCAAGTAAGTTAGTAAGCCAATTATTTCATT
1 CTACGATCTACA---TAACAGCATGAGACTACAAACAAGTAAGCTAGTAAACCAATTATTTCATT
* * *
6474144 TGTAGAAAATATAATATATGAAGTTTTTCTCCATTGGTTAAATGATAATAAATTATTCGCCCTAA
63 CGTAGAAAATACAATATATGAAGCTTTTCTCCATTGGTTAAATGATAATAAATTATTCGCCCTAA
6474209 GAAATAAATAATAA
128 G-AATAAATAATAA
6474223 TTTATTCAAC
Statistics
Matches: 116, Mismatches: 17, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
164 11 0.09
168 3 0.03
169 2 0.02
170 3 0.03
171 82 0.71
172 4 0.03
173 11 0.09
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.33
Consensus pattern (169 bp):
CTACGATCTACATAACAGCATGAGACTACAAACAAGTAAGCTAGTAAACCAATTATTTCATTCGT
AGAAAATACAATATATGAAGCTTTTCTCCATTGGTTAAATGATAATAAATTATTCGCCCTAAGAA
TAAATAATAAAAATAATATAACTTATTCAACCCATAGCT
Found at i:6481904 original size:15 final size:15
Alignment explanation
Indices: 6481881--6481922 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
6481871 CTCAGCACCC
6481881 TGAACCTGAACCTTT
1 TGAACCTGAACCTTT
* *
6481896 TGTACCTGAACATTT
1 TGAACCTGAACCTTT
6481911 TGAACCTGAACC
1 TGAACCTGAACC
6481923 GATTCCCTCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (15 bp):
TGAACCTGAACCTTT
Found at i:6486831 original size:30 final size:28
Alignment explanation
Indices: 6486761--6486831 Score: 79
Period size: 30 Copynumber: 2.4 Consensus size: 28
6486751 TTAGTTATTT
*
6486761 TTTAGGACTAAATTAGAATTTTGTCAAA
1 TTTAGGACTAAATTAGAAATTTGTCAAA
* * *
6486789 TTTAGTGTCTAAATTGGTAAATTTGTGAAA
1 TTTAG-GACTAAATTAG-AAATTTGTCAAA
6486819 TTTAAGGACTAAA
1 TTT-AGGACTAAA
6486832 GTGAACTCTG
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 5 0.14
29 9 0.26
30 19 0.54
31 2 0.06
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.39
Consensus pattern (28 bp):
TTTAGGACTAAATTAGAAATTTGTCAAA
Found at i:6487730 original size:80 final size:80
Alignment explanation
Indices: 6487590--6487740 Score: 225
Period size: 80 Copynumber: 1.9 Consensus size: 80
6487580 GACCCGCATG
* *
6487590 TGACCCGACCTGATCGTTGACCATGACTCATTGACCCGAGTTGACCGACCCAACCCATTGACCCT
1 TGACCCGACCCGATCGTTAACCATGACTCATTGACCCGAGTTGACCGACCCAACCCATTGA-CCT
6487655 -AGTTGATCAACCTGT
65 AAGTTGATCAACCTGT
* **
6487670 TGACCCGACCCGA-CTGTTAACCATGACTCATTGACCCGAGTTGACCGACCCGACTTATTGACCT
1 TGACCCGACCCGATC-GTTAACCATGACTCATTGACCCGAGTTGACCGACCCAACCCATTGACCT
6487734 AAGTTGA
65 AAGTTGA
6487741 CCGATGCATT
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
79 4 0.06
80 60 0.94
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (80 bp):
TGACCCGACCCGATCGTTAACCATGACTCATTGACCCGAGTTGACCGACCCAACCCATTGACCTA
AGTTGATCAACCTGT
Found at i:6487753 original size:80 final size:81
Alignment explanation
Indices: 6487585--6487753 Score: 204
Period size: 80 Copynumber: 2.1 Consensus size: 81
6487575 GATCCGACCC
* *
6487585 GCATGTGACCCGACCTGATCGTTGACCATGACTCATTGACCCGAGTTGACCGACCCAACCCATTG
1 GCAT-TGACCCGACCCGATCGTTAACCATGACTCATTGACCCGAGTTGACCGACCCAACCCATTG
*
6487650 ACCCTAGTTGATCAACCT
65 ACCCTAGTTGACCAA-CT
* **
6487668 G--TTGACCCGACCCGA-CTGTTAACCATGACTCATTGACCCGAGTTGACCGACCCGACTTATTG
1 GCATTGACCCGACCCGATC-GTTAACCATGACTCATTGACCCGAGTTGACCGACCCAACCCATTG
*
6487730 A-CCTAAGTTGACCGA-T
65 ACCCT-AGTTGACCAACT
6487746 GCATTGAC
1 GCATTGAC
6487754 TTTGACCCAT
Statistics
Matches: 75, Mismatches: 7, Indels: 11
0.81 0.08 0.12
Matches are distributed among these distances:
78 2 0.03
79 4 0.05
80 67 0.89
81 1 0.01
83 1 0.01
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (81 bp):
GCATTGACCCGACCCGATCGTTAACCATGACTCATTGACCCGAGTTGACCGACCCAACCCATTGA
CCCTAGTTGACCAACT
Found at i:6496673 original size:3 final size:3
Alignment explanation
Indices: 6496665--6496708 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
6496655 ACAAATTTAA
*
6496665 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AGT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
6496709 AATCAGGAGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:6501396 original size:22 final size:23
Alignment explanation
Indices: 6501351--6501407 Score: 80
Period size: 22 Copynumber: 2.5 Consensus size: 23
6501341 TCTCTCAACA
**
6501351 AAAATTACAAAAATAATTTAAAAT
1 AAAATT-CAAAAATAAAATAAAAT
6501375 AAAATTCAAAAATAAAAT-AAAT
1 AAAATTCAAAAATAAAATAAAAT
6501397 AAAATTCAAAA
1 AAAATTCAAAA
6501408 TATTTATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
22 15 0.48
23 10 0.32
24 6 0.19
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (23 bp):
AAAATTCAAAAATAAAATAAAAT
Found at i:6501421 original size:19 final size:19
Alignment explanation
Indices: 6501350--6501505 Score: 79
Period size: 22 Copynumber: 7.6 Consensus size: 19
6501340 CTCTCTCAAC
6501350 AAAAATTACAAAAATAATTTAAA
1 AAAAATT-C-AAAAT-ATTT-AA
**
6501373 ATAAAATTCAAAAATAAAATAA
1 A-AAAATTC-AAAAT-ATTTAA
*
6501395 ATAAAATTCAAAATATTTAT
1 A-AAAATTCAAAATATTTAA
6501415 AAAAATTCAAAATTTATATTAA
1 AAAAATTCAAAA--TAT-TTAA
*
6501437 AAAAATT-ATAAA-AATT-A
1 AAAAATTCA-AAATATTTAA
*
6501454 AAAAATTCTAAAAAATATATAA
1 AAAAATTC---AAAATATTTAA
*
6501476 AAAAGTT-AAAAT-TTTAA
1 AAAAATTCAAAATATTTAA
6501493 AAAAATTCTAAAA
1 AAAAATTC-AAAA
6501506 AAAATAATTT
Statistics
Matches: 108, Mismatches: 12, Indels: 30
0.72 0.08 0.20
Matches are distributed among these distances:
17 18 0.17
18 7 0.06
19 16 0.15
20 7 0.06
21 12 0.11
22 31 0.29
23 11 0.10
24 6 0.06
ACGTcount: A:0.65, C:0.04, G:0.01, T:0.30
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAA
Found at i:6501431 original size:17 final size:19
Alignment explanation
Indices: 6501397--6501505 Score: 66
Period size: 19 Copynumber: 5.6 Consensus size: 19
6501387 TAAAATAAAT
6501397 AAAATTCAAAATATTTATA
1 AAAATTCAAAATATTTATA
*
6501416 AAAATTCAAAATTTATATTAAA
1 AAAATTCAAAA--TAT-TTATA
*
6501438 AAAATT-ATAAA-AATTA-A
1 AAAATTCA-AAATATTTATA
* *
6501455 AAAATTCTAAAAAATATATAA
1 AAAATTC-AAAATATTTAT-A
*
6501476 AAAAGTT-AAAAT-TTTAAA
1 AAAA-TTCAAAATATTTATA
6501494 AAAATTCTAAAA
1 AAAATTC-AAAA
6501506 AAAATAATTT
Statistics
Matches: 71, Mismatches: 7, Indels: 24
0.70 0.07 0.24
Matches are distributed among these distances:
17 9 0.13
18 11 0.15
19 23 0.32
20 4 0.06
21 9 0.13
22 15 0.21
ACGTcount: A:0.63, C:0.04, G:0.01, T:0.32
Consensus pattern (19 bp):
AAAATTCAAAATATTTATA
Found at i:6501441 original size:23 final size:21
Alignment explanation
Indices: 6501350--6501441 Score: 62
Period size: 23 Copynumber: 4.2 Consensus size: 21
6501340 CTCTCTCAAC
*
6501350 AAAAATTACAAAAATAATTTAAA
1 AAAAATT-C-AAAATTATTTAAA
* **
6501373 ATAAAATTCAAAAATAAAATAAA
1 A-AAAATTC-AAAATTATTTAAA
* *
6501396 TAAAATTCAAAA-TATTT-AT
1 AAAAATTCAAAATTATTTAAA
6501415 AAAAATTCAAAATTTATATTAAA
1 AAAAATTCAAAA-TTAT-TTAAA
6501438 AAAA
1 AAAA
6501442 TTATAAAAAT
Statistics
Matches: 55, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
19 12 0.22
20 2 0.04
21 7 0.13
22 9 0.16
23 19 0.35
24 6 0.11
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.29
Consensus pattern (21 bp):
AAAAATTCAAAATTATTTAAA
Found at i:6501443 original size:22 final size:20
Alignment explanation
Indices: 6501375--6501505 Score: 89
Period size: 22 Copynumber: 6.5 Consensus size: 20
6501365 AATTTAAAAT
* *
6501375 AAAATTCAAAAATAAAATAAA
1 AAAATTC-AAAATATATTAAA
*
6501396 TAAAATTCAAAATAT-TTATA
1 -AAAATTCAAAATATATTAAA
6501416 AAAATTCAAAATTTATATTAAA
1 AAAATTCAAAA--TATATTAAA
6501438 AAAATT-ATAAA-A-ATT-AA
1 AAAATTCA-AAATATATTAAA
*
6501455 AAAATTCTAAAAAATATATAAA
1 AAAATTC-AAAATATAT-TAAA
*
6501477 AAAGTT-AAAAT-T-TTAAA
1 AAAATTCAAAATATATTAAA
6501494 AAAATTCTAAAA
1 AAAATTC-AAAA
6501506 AAAATAATTT
Statistics
Matches: 90, Mismatches: 7, Indels: 27
0.73 0.06 0.22
Matches are distributed among these distances:
17 17 0.19
18 7 0.08
19 19 0.21
20 9 0.10
21 11 0.12
22 27 0.30
ACGTcount: A:0.65, C:0.04, G:0.01, T:0.31
Consensus pattern (20 bp):
AAAATTCAAAATATATTAAA
Found at i:6501476 original size:11 final size:10
Alignment explanation
Indices: 6501432--6501507 Score: 56
Period size: 9 Copynumber: 8.1 Consensus size: 10
6501422 CAAAATTTAT
6501432 ATTA-AAAAA
1 ATTATAAAAA
6501441 ATTAT-AAAA
1 ATTATAAAAA
6501450 A-T-TAAAAA
1 ATTATAAAAA
*
6501458 ATTCTAAAAA
1 ATTATAAAAA
6501468 ATATATAAAAA
1 AT-TATAAAAA
* *
6501479 AGT-TAAAAT
1 ATTATAAAAA
*
6501488 TTTA-AAAAA
1 ATTATAAAAA
*
6501497 ATTCTAAAAA
1 ATTATAAAAA
6501507 A
1 A
6501508 AATAATTTTG
Statistics
Matches: 52, Mismatches: 8, Indels: 13
0.71 0.11 0.18
Matches are distributed among these distances:
7 1 0.02
8 6 0.12
9 22 0.42
10 15 0.29
11 8 0.15
ACGTcount: A:0.67, C:0.03, G:0.01, T:0.29
Consensus pattern (10 bp):
ATTATAAAAA
Found at i:6501477 original size:39 final size:40
Alignment explanation
Indices: 6501375--6501507 Score: 114
Period size: 39 Copynumber: 3.4 Consensus size: 40
6501365 AATTTAAAAT
* * * *
6501375 AAAATTC--AAAAATAAAATAAATAAAATTCAAAATATTTATA
1 AAAATTCTAAAAAATATATTAAA-AAAATT-AAAA-AATTAAA
**
6501416 AAAATTC-AAAATTTATATTAAAAAAATTATAAAAATT-AA
1 AAAATTCTAAAAAATATATTAAAAAAATTA-AAAAATTAAA
* **
6501455 AAAATTCTAAAAAATATA-TAAAAAAGTTAAAATTTTAAA
1 AAAATTCTAAAAAATATATTAAAAAAATTAAAAAATTAAA
6501494 AAAATTCTAAAAAA
1 AAAATTCTAAAAAA
6501508 AATAATTTTG
Statistics
Matches: 77, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
38 5 0.06
39 34 0.44
40 12 0.16
41 16 0.21
42 10 0.13
ACGTcount: A:0.65, C:0.04, G:0.01, T:0.30
Consensus pattern (40 bp):
AAAATTCTAAAAAATATATTAAAAAAATTAAAAAATTAAA
Found at i:6501485 original size:9 final size:9
Alignment explanation
Indices: 6501432--6501499 Score: 57
Period size: 9 Copynumber: 7.3 Consensus size: 9
6501422 CAAAATTTAT
6501432 ATTAAAAAA
1 ATTAAAAAA
*
6501441 ATTATAAAA
1 ATTAAAAAA
6501450 ATTAAAAAA
1 ATTAAAAAA
*
6501459 TTCTAAAAAA
1 AT-TAAAAAA
6501469 TATATAAAAAA
1 -AT-TAAAAAA
* *
6501480 GTT-AAAAT
1 ATTAAAAAA
*
6501488 TTTAAAAAA
1 ATTAAAAAA
6501497 ATT
1 ATT
6501500 CTAAAAAAAA
Statistics
Matches: 46, Mismatches: 10, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
8 6 0.13
9 24 0.52
10 8 0.17
11 8 0.17
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.31
Consensus pattern (9 bp):
ATTAAAAAA
Found at i:6503342 original size:10 final size:12
Alignment explanation
Indices: 6503314--6503338 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6503304 CATTTTATTT
6503314 AGAAATAAGGGG
1 AGAAATAAGGGG
6503326 AGAAATAAGGGG
1 AGAAATAAGGGG
6503338 A
1 A
6503339 AATATCTTAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.40, T:0.08
Consensus pattern (12 bp):
AGAAATAAGGGG
Found at i:6508626 original size:2 final size:2
Alignment explanation
Indices: 6508572--6508609 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
6508562 TGAATCTGTT
6508572 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
6508610 TTACGAGTAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6514516 original size:2 final size:2
Alignment explanation
Indices: 6514511--6514550 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
6514501 AGTTTACCCA
6514511 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6514551 ATAATGTACA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6515275 original size:32 final size:33
Alignment explanation
Indices: 6515231--6515311 Score: 94
Period size: 32 Copynumber: 2.5 Consensus size: 33
6515221 AAGCTTAGTC
* **
6515231 AAAATTGTTTATTTTATTAATTTTGTTTTGA-T
1 AAAATTATTTATTTTATTAATTTCATTTTGACT
* *
6515263 TAAATT-TGTTATTTTCTTAATTTCATTTTGACT
1 AAAATTAT-TTATTTTATTAATTTCATTTTGACT
6515296 AAAATTATTTATTTTA
1 AAAATTATTTATTTTA
6515312 AGTAAATAGA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
31 1 0.03
32 25 0.62
33 13 0.32
34 1 0.03
ACGTcount: A:0.30, C:0.04, G:0.06, T:0.60
Consensus pattern (33 bp):
AAAATTATTTATTTTATTAATTTCATTTTGACT
Found at i:6516265 original size:20 final size:22
Alignment explanation
Indices: 6516240--6516280 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
6516230 TTTATTTCAC
*
6516240 TTATTTA-TTTTAT-TTTTGTT
1 TTATTTAGTTTGATGTTTTGTT
6516260 TTATTTAGTTTGATGTTTTGT
1 TTATTTAGTTTGATGTTTTGT
6516281 CTCTAAACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 5 0.28
22 6 0.33
ACGTcount: A:0.15, C:0.00, G:0.12, T:0.73
Consensus pattern (22 bp):
TTATTTAGTTTGATGTTTTGTT
Found at i:6519011 original size:8 final size:7
Alignment explanation
Indices: 6518986--6519022 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
6518976 ACCCAAATTC
6518986 ATTTTT-
1 ATTTTTA
6518992 ATTTTTA
1 ATTTTTA
6518999 ATTTTTA
1 ATTTTTA
6519006 ATTTTTA
1 ATTTTTA
*
6519013 A-GTTTA
1 ATTTTTA
6519019 ATTT
1 ATTT
6519023 CAGTTGAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
6 11 0.41
7 16 0.59
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (7 bp):
ATTTTTA
Found at i:6522545 original size:26 final size:25
Alignment explanation
Indices: 6522516--6522570 Score: 74
Period size: 26 Copynumber: 2.2 Consensus size: 25
6522506 TGAAAATTCT
*
6522516 ATTTTGGTCAATATTAATTTTTTTTG
1 ATTTTGGTCAATATTAA-ATTTTTTG
**
6522542 ATTTTTTTCAATATTAAATTTTTTG
1 ATTTTGGTCAATATTAAATTTTTTG
6522567 ATTT
1 ATTT
6522571 AGTTACTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 11 0.42
26 15 0.58
ACGTcount: A:0.25, C:0.04, G:0.07, T:0.64
Consensus pattern (25 bp):
ATTTTGGTCAATATTAAATTTTTTG
Found at i:6523920 original size:23 final size:22
Alignment explanation
Indices: 6523895--6523938 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
6523885 AAAAATACTT
6523895 TTTTTTGTAAATCAACTCACCG
1 TTTTTTGTAAATCAACTCACCG
6523917 TTTTTTGTAAATCAACTCACCG
1 TTTTTTGTAAATCAACTCACCG
6523939 GTATAATTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.23, G:0.09, T:0.41
Consensus pattern (22 bp):
TTTTTTGTAAATCAACTCACCG
Found at i:6533826 original size:16 final size:17
Alignment explanation
Indices: 6533793--6533835 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
6533783 TATCATGATA
* *
6533793 ATAAAAATAAATATAAT
1 ATAAAAATTAACATAAT
6533810 ATAAAAATTAACA-AAT
1 ATAAAAATTAACATAAT
*
6533826 AAAAAAATTA
1 ATAAAAATTA
6533836 TAAAACACTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 12 0.52
17 11 0.48
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (17 bp):
ATAAAAATTAACATAAT
Found at i:6548213 original size:18 final size:18
Alignment explanation
Indices: 6548186--6548227 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
6548176 CCACTAGCAA
*
6548186 TGTTTCATACATGACACG
1 TGTTTAATACATGACACG
6548204 TGTTTAATACATGACACG
1 TGTTTAATACATGACACG
6548222 TGTTTA
1 TGTTTA
6548228 TTTTAATTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.38
Consensus pattern (18 bp):
TGTTTAATACATGACACG
Found at i:6548427 original size:25 final size:25
Alignment explanation
Indices: 6548393--6548446 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 25
6548383 ATTTAAAATT
*
6548393 TAAAATATTTAAGATAAATTCAAAA
1 TAAAAAATTTAAGATAAATTCAAAA
*** *
6548418 TAAAAAATTTATTTTAAATTCAAGA
1 TAAAAAATTTAAGATAAATTCAAAA
6548443 TAAA
1 TAAA
6548447 TATAAAATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.57, C:0.04, G:0.04, T:0.35
Consensus pattern (25 bp):
TAAAAAATTTAAGATAAATTCAAAA
Found at i:6550581 original size:25 final size:25
Alignment explanation
Indices: 6550552--6550599 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
6550542 TTTTTTTATA
6550552 ATTTTATA-ATTTTTACAAGTTTTTC
1 ATTTTATATATTTTTACAA-TTTTTC
*
6550577 ATTTTATATTTTTTTACAATTTT
1 ATTTTATATATTTTTACAATTTT
6550600 AAATGATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65
Consensus pattern (25 bp):
ATTTTATATATTTTTACAATTTTTC
Found at i:6558869 original size:218 final size:218
Alignment explanation
Indices: 6558490--6558915 Score: 613
Period size: 218 Copynumber: 2.0 Consensus size: 218
6558480 AAACAAGATT
* *
6558490 TGTGTGATCTTCCTATCTCCAGAAAAGTATGCTTGCAACTTGGTTAAAAAGTTTGACTTAAAAGG
1 TGTGTGATCTTCCTATCTCCAAAAAAGTATGCTCGCAACTTGGTTAAAAAGTTTGACTTAAAAGG
* * * *
6558555 ATCAATGATAATAAAGATACATATGAAAGCTTTAAAGGAATCAAGCTTAGATGTAGAGGGACTTG
66 ATCAATGATAATAAAGACACATATGAAAGCTTTAAAGGAACCAAGCTCAGATGTACAGGGACTTG
* *
6558620 CAACTAACCTTGACAATTATTGTAATATGATTGGTAGCCCTCTTTATCTCACTACAAATAAGCAA
131 CAACTAACCTTAACAATTATTGTAATATGATTGGAAGCCCTCTTTATCTCACTACAAATAAGCAA
6558685 GATTTGTGCTACATTATAGGGTG
196 GATTTGTGCTACATTATAGGGTG
* * *
6558708 TGTGTGATCTTCCTATCTCTAAAAAAGTATGCTCGCGACTTGGTTAAGAAGTTTGACTT-AAAGC
1 TGTGTGATCTTCCTATCTCCAAAAAAGTATGCTCGCAACTTGGTTAAAAAGTTTGACTTAAAAG-
* * * * * * * *
6558772 GATCAATTG-TAATTAAGACACCTATGAGAGTTTTAAAGGAACCAATCTCATATGTACATGGAGT
65 GATCAA-TGATAATAAAGACACATATGAAAGCTTTAAAGGAACCAAGCTCAGATGTACAGGGACT
* * * *
6558836 TGCAACTAATCTTAACAATTATTGTAGTATGATTGGAAGCGCTCTTTATCTCACTACAACTAAGC
129 TGCAACTAACCTTAACAATTATTGTAATATGATTGGAAGCCCTCTTTATCTCACTACAAATAAGC
6558901 AAGATTTGTGCTACA
194 AAGATTTGTGCTACA
6558916 ATATTTTTTG
Statistics
Matches: 183, Mismatches: 23, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
217 4 0.02
218 177 0.97
219 2 0.01
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (218 bp):
TGTGTGATCTTCCTATCTCCAAAAAAGTATGCTCGCAACTTGGTTAAAAAGTTTGACTTAAAAGG
ATCAATGATAATAAAGACACATATGAAAGCTTTAAAGGAACCAAGCTCAGATGTACAGGGACTTG
CAACTAACCTTAACAATTATTGTAATATGATTGGAAGCCCTCTTTATCTCACTACAAATAAGCAA
GATTTGTGCTACATTATAGGGTG
Found at i:6561376 original size:26 final size:26
Alignment explanation
Indices: 6561347--6561401 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
6561337 ACGGATAAAA
*
6561347 TTATCTATTT-TTATTTAATTAAATAT
1 TTAT-TATTTATTATCTAATTAAATAT
*
6561373 TTATTTTTTATTATCTAATTAAATAT
1 TTATTATTTATTATCTAATTAAATAT
6561399 TTA
1 TTA
6561402 AGATAATATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 4 0.15
26 22 0.85
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (26 bp):
TTATTATTTATTATCTAATTAAATAT
Found at i:6561478 original size:22 final size:23
Alignment explanation
Indices: 6561429--6561475 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
6561419 AATATTTATT
6561429 TTAAATTTTTTTGAAAATAATGA
1 TTAAATTTTTTTGAAAATAATGA
6561452 TTAAATTTTTTTGAAAATAATGA
1 TTAAATTTTTTTGAAAATAATGA
6561475 T
1 T
6561476 AAAACCTGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.49
Consensus pattern (23 bp):
TTAAATTTTTTTGAAAATAATGA
Found at i:6561620 original size:25 final size:25
Alignment explanation
Indices: 6561570--6561618 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
6561560 TAAAAAATAA
*
6561570 TAGATAATAAATATTTAAGTTAAAT
1 TAGATAATAAATATCTAAGTTAAAT
6561595 TAGATAAATAAATTATCTAA-TTAA
1 TAGAT-AATAAA-TATCTAAGTTAA
6561619 TTTTTAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 5 0.24
26 10 0.48
27 6 0.29
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.39
Consensus pattern (25 bp):
TAGATAATAAATATCTAAGTTAAAT
Found at i:6561881 original size:15 final size:15
Alignment explanation
Indices: 6561844--6561882 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
6561834 AAAAAGATAA
* *
6561844 TTTATTTAATTATTT
1 TTTATTTAATTAATG
6561859 TTTATTTAATTAATG
1 TTTATTTAATTAATG
*
6561874 TTTGTTTAA
1 TTTATTTAA
6561883 ATAAAAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (15 bp):
TTTATTTAATTAATG
Found at i:6578552 original size:15 final size:16
Alignment explanation
Indices: 6578534--6578563 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
6578524 TAAATTATTT
6578534 AAAAATA-TATAAAAC
1 AAAAATATTATAAAAC
6578549 AAAAATATTATAAAA
1 AAAAATATTATAAAA
6578564 TTATTAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAAATATTATAAAAC
Found at i:6581310 original size:18 final size:18
Alignment explanation
Indices: 6581283--6581332 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
6581273 TTCTTGAAAT
*
6581283 TTTTTATATATTTATTTTA
1 TTTTT-TATATTTATTTAA
6581302 TTTTTTATATTT-TTTAA
1 TTTTTTATATTTATTTAA
*
6581319 TTTATATATATTTA
1 TTT-TTTATATTTA
6581333 ATAAAAATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 7 0.26
18 15 0.56
19 5 0.19
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTTTATATTTATTTAA
Found at i:6581317 original size:21 final size:20
Alignment explanation
Indices: 6581281--6581323 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
6581271 ATTTCTTGAA
*
6581281 ATTTTTTATATATTTATTTT
1 ATTTTTTATATATTTAATTT
*
6581301 ATTTTTTATATTTTTTAATTT
1 ATTTTTTATA-TATTTAATTT
6581322 AT
1 AT
6581324 ATATATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (20 bp):
ATTTTTTATATATTTAATTT
Found at i:6581326 original size:16 final size:17
Alignment explanation
Indices: 6581285--6581331 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
6581275 CTTGAAATTT
*
6581285 TTTATATATTTATTTTAT
1 TTTATATA-TTATTTTAA
*
6581303 TTTTTATATT-TTTTAA
1 TTTATATATTATTTTAA
6581319 TTTATATA-TATTT
1 TTTATATATTATTT
6581332 AATAAAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
15 1 0.04
16 15 0.60
17 2 0.08
18 7 0.28
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTATATATTATTTTAA
Found at i:6581472 original size:23 final size:23
Alignment explanation
Indices: 6581445--6581491 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
6581435 AATGTATATT
*
6581445 TTAAATACCAAATTCAAAAAAAA
1 TTAAATACCAAAATCAAAAAAAA
* *
6581468 TTAAATATCAAAATGAAAAAAAA
1 TTAAATACCAAAATCAAAAAAAA
6581491 T
1 T
6581492 GAGCATACTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.66, C:0.09, G:0.02, T:0.23
Consensus pattern (23 bp):
TTAAATACCAAAATCAAAAAAAA
Found at i:6590088 original size:17 final size:18
Alignment explanation
Indices: 6590054--6590088 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
6590044 AATGTAAGTT
*
6590054 AAAAAAATGAGTTTAAGC
1 AAAAAAATGAGTTCAAGC
6590072 AAAAAAATGAG-TCAAGC
1 AAAAAAATGAGTTCAAGC
6590089 CTCAAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.57, C:0.09, G:0.17, T:0.17
Consensus pattern (18 bp):
AAAAAAATGAGTTCAAGC
Found at i:6591339 original size:38 final size:38
Alignment explanation
Indices: 6591297--6591380 Score: 159
Period size: 38 Copynumber: 2.2 Consensus size: 38
6591287 ATTTATTGAG
*
6591297 TTAATGTGCAATTTAATACCTCAATGATACCTTATTCA
1 TTAATATGCAATTTAATACCTCAATGATACCTTATTCA
6591335 TTAATATGCAATTTAATACCTCAATGATACCTTATTCA
1 TTAATATGCAATTTAATACCTCAATGATACCTTATTCA
6591373 TTAATATG
1 TTAATATG
6591381 GTACCTATGT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 45 1.00
ACGTcount: A:0.36, C:0.17, G:0.07, T:0.40
Consensus pattern (38 bp):
TTAATATGCAATTTAATACCTCAATGATACCTTATTCA
Found at i:6595465 original size:2 final size:2
Alignment explanation
Indices: 6595460--6595488 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6595450 ATATATATAA
6595460 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
6595489 TTAAACTGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6608399 original size:97 final size:97
Alignment explanation
Indices: 6608227--6608417 Score: 246
Period size: 97 Copynumber: 2.0 Consensus size: 97
6608217 TTTGGAAAAT
* * *
6608227 GATATTCGATTATCTCGATTTGAAGAAAAGTCGCACCTAGTAAGTTAAGGCACAAATTTTCATAA
1 GATATTCGATTATCTCGACTTGAAGAAAACTCGCACCTAGTAAGTTAAGGCACAAATTTTCAAAA
*
6608292 TCAGAGAT-AAAGAAACATTGCCTCGATTTAAG
66 TCAGAAATAAAAG-AACATTGCCTCGATTTAAG
* *
6608324 GATATTTGATTATTTCGACTTGAAGAAAAACT-G-AGCCTAGTAAGTTAAGGCACAAATTTTCAA
1 GATATTCGATTATCTCGACTTGAAG-AAAACTCGCA-CCTAGTAAGTTAAGGCACAAATTTTCAA
* *
6608387 AACTC-GAAATAAAAGAATATTGCCTTGATTT
64 AA-TCAGAAATAAAAGAACATTGCCTCGATTT
6608418 TAAAGTTTTC
Statistics
Matches: 82, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
96 1 0.01
97 70 0.85
98 11 0.13
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (97 bp):
GATATTCGATTATCTCGACTTGAAGAAAACTCGCACCTAGTAAGTTAAGGCACAAATTTTCAAAA
TCAGAAATAAAAGAACATTGCCTCGATTTAAG
Found at i:6608897 original size:3 final size:3
Alignment explanation
Indices: 6608889--6608914 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
6608879 ATTTGTTTAA
6608889 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
6608915 ATTCATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:6609543 original size:19 final size:19
Alignment explanation
Indices: 6609504--6609543 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
6609494 GTGTTTGTAA
*
6609504 TTGAATCTGGACTTTGGAT
1 TTGAATCTGGACTTTGAAT
* *
6609523 TTGAATTTGGACTTTTAAT
1 TTGAATCTGGACTTTGAAT
6609542 TT
1 TT
6609544 TATTTTAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.23, C:0.07, G:0.20, T:0.50
Consensus pattern (19 bp):
TTGAATCTGGACTTTGAAT
Found at i:6609570 original size:17 final size:17
Alignment explanation
Indices: 6609545--6609615 Score: 79
Period size: 17 Copynumber: 4.2 Consensus size: 17
6609535 TTTTAATTTT
*
6609545 ATTTTAATTTAAAATAA
1 ATTTAAATTTAAAATAA
*
6609562 ATTTAAATTTAAAGTAA
1 ATTTAAATTTAAAATAA
* * * *
6609579 ATTCAAACTCAAAATGA
1 ATTTAAATTTAAAATAA
*
6609596 ATTTGAATTTAAAATAA
1 ATTTAAATTTAAAATAA
6609613 ATT
1 ATT
6609616 CAAACTTTTT
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 42 1.00
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.39
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:6609593 original size:34 final size:34
Alignment explanation
Indices: 6609555--6609621 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
6609545 ATTTTAATTT
*
6609555 AAAATAAATTTAAATTTAAAGTAAATTCAAACTC
1 AAAATAAATTTAAATTTAAAATAAATTCAAACTC
* *
6609589 AAAATGAATTTGAATTTAAAATAAATTCAAACT
1 AAAATAAATTTAAATTTAAAATAAATTCAAACT
6609622 TTTTTAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.55, C:0.07, G:0.04, T:0.33
Consensus pattern (34 bp):
AAAATAAATTTAAATTTAAAATAAATTCAAACTC
Found at i:6610224 original size:39 final size:39
Alignment explanation
Indices: 6610181--6610304 Score: 124
Period size: 39 Copynumber: 3.2 Consensus size: 39
6610171 AATGACTACA
*
6610181 ATCTGCCCCAAGCTCGGGGTAAAAGATTGGCTAATGGTG
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGCTAATGGTG
* * ** * **
6610220 ATCTGCCCCAGGCTCGAGGTAAAAGATCGAATTACT-GCA
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCG-GCTAATGGTG
* * *
6610259 ATCTGCCCCAAGTTCGGGGTAAACGATCAGCTAATGGTG
1 ATCTGCCCCAAGCTCGGGGTAAAAGATCGGCTAATGGTG
*
6610298 ATTTGCC
1 ATCTGCC
6610305 TTATCTTTGT
Statistics
Matches: 64, Mismatches: 19, Indels: 4
0.74 0.22 0.05
Matches are distributed among these distances:
38 3 0.05
39 58 0.91
40 3 0.05
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (39 bp):
ATCTGCCCCAAGCTCGGGGTAAAAGATCGGCTAATGGTG
Found at i:6610233 original size:78 final size:78
Alignment explanation
Indices: 6610101--6610304 Score: 255
Period size: 78 Copynumber: 2.6 Consensus size: 78
6610091 CGGATAACTG
* * * * * * * *
6610101 CAATCTGCCCCATGATCGGGGTAAGATATTGGATAATGATGATCTGCCCTAGGCTTGGGGCAAAA
1 CAATCTGCCCCAAGATCGGGGTAAAAGATTGGCTAATGGTGATCTGCCCCAGGCTCGAGGCAAAA
6610166 GATCGAATGACTA
66 GATCGAATGACTA
* *
6610179 CAATCTGCCCCAAGCTCGGGGTAAAAGATTGGCTAATGGTGATCTGCCCCAGGCTCGAGGTAAAA
1 CAATCTGCCCCAAGATCGGGGTAAAAGATTGGCTAATGGTGATCTGCCCCAGGCTCGAGGCAAAA
* *
6610244 GATCGAATTACTG
66 GATCGAATGACTA
* * ** *
6610257 CAATCTGCCCCAAGTTCGGGGTAAACGATCAGCTAATGGTGATTTGCC
1 CAATCTGCCCCAAGATCGGGGTAAAAGATTGGCTAATGGTGATCTGCC
6610305 TTATCTTTGT
Statistics
Matches: 109, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
78 109 1.00
ACGTcount: A:0.28, C:0.22, G:0.26, T:0.24
Consensus pattern (78 bp):
CAATCTGCCCCAAGATCGGGGTAAAAGATTGGCTAATGGTGATCTGCCCCAGGCTCGAGGCAAAA
GATCGAATGACTA
Found at i:6611379 original size:9 final size:8
Alignment explanation
Indices: 6611362--6611413 Score: 50
Period size: 9 Copynumber: 5.8 Consensus size: 8
6611352 TCGACCTCTC
6611362 TTTTTTCT
1 TTTTTTCT
6611370 TTTTTCTCTTT
1 TTTTT-TC--T
6611381 GTTTTTTCTT
1 -TTTTTTC-T
6611391 TTTTTTCT
1 TTTTTTCT
6611399 TATTTTTCT
1 T-TTTTTCT
6611408 TTTTTT
1 TTTTTT
6611414 AGGTAAGATC
Statistics
Matches: 39, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
8 12 0.31
9 17 0.44
10 2 0.05
11 3 0.08
12 5 0.13
ACGTcount: A:0.02, C:0.12, G:0.02, T:0.85
Consensus pattern (8 bp):
TTTTTTCT
Found at i:6611385 original size:20 final size:18
Alignment explanation
Indices: 6611357--6611412 Score: 67
Period size: 18 Copynumber: 3.0 Consensus size: 18
6611347 TCACCTCGAC
*
6611357 CTCTCTTTTTTCTTTTTT
1 CTCTTTTTTTTCTTTTTT
6611375 CTCTTTGTTTTTTCTTTTTT
1 CTC-TT-TTTTTTCTTTTTT
* *
6611395 TTCTTATTTTTCTTTTTT
1 CTCTTTTTTTTCTTTTTT
6611413 TAGGTAAGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 15 0.45
19 3 0.09
20 15 0.45
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (18 bp):
CTCTTTTTTTTCTTTTTT
Found at i:6611413 original size:20 final size:19
Alignment explanation
Indices: 6611363--6611413 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
6611353 CGACCTCTCT
* *
6611363 TTTTTCTTTTTTCTCTTTGT
1 TTTTTCTTTTTTTTCTTT-A
6611383 TTTTTCTTTTTTTTC-TTA
1 TTTTTCTTTTTTTTCTTTA
6611401 TTTTTCTTTTTTT
1 TTTTTCTTTTTTT
6611414 AGGTAAGATC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 13 0.45
19 2 0.07
20 14 0.48
ACGTcount: A:0.02, C:0.12, G:0.02, T:0.84
Consensus pattern (19 bp):
TTTTTCTTTTTTTTCTTTA
Found at i:6616093 original size:97 final size:97
Alignment explanation
Indices: 6615898--6616072 Score: 264
Period size: 96 Copynumber: 1.8 Consensus size: 97
6615888 AACCTTAGAA
*
6615898 AAGGATATTCGATTATCTCGATTTGAAGAAAAGTAGCACCTAGTAAGTTAAGGCACAAATTTTCA
1 AAGGATATTCGATTATCTCGACTTGAAGAAAAGTAGCACCTAGTAAGTTAAGGCACAAATTTTCA
* *
6615963 GAATCAGAGATAAAGAAACATTGCCTCAATTT
66 AAATCAGAAATAAAGAAACATTGCCTCAATTT
* * **
6615995 AAGGATATTCGATTATTTCGACTTGAAGAAAA-TCGTGCCTAGTAAGTTAAGGCACAAATTTTCA
1 AAGGATATTCGATTATCTCGACTTGAAGAAAAGTAGCACCTAGTAAGTTAAGGCACAAATTTTCA
6616059 AAACTC-GAAATAAA
66 AAA-TCAGAAATAAA
6616073 AGAATATTGC
Statistics
Matches: 70, Mismatches: 7, Indels: 3
0.88 0.09 0.04
Matches are distributed among these distances:
96 38 0.54
97 32 0.46
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.28
Consensus pattern (97 bp):
AAGGATATTCGATTATCTCGACTTGAAGAAAAGTAGCACCTAGTAAGTTAAGGCACAAATTTTCA
AAATCAGAAATAAAGAAACATTGCCTCAATTT
Found at i:6616406 original size:30 final size:29
Alignment explanation
Indices: 6616361--6616616 Score: 159
Period size: 29 Copynumber: 8.6 Consensus size: 29
6616351 ACTTCGGGGT
*
6616361 AAAATGATAATTTTTGGAAATTTTGAGGTCA
1 AAAATGGT-ATTTTTGGAAATTTTGAGGT-A
* *
6616392 AAAATGGTGTTTTTGGACA-TTTGAGGGT-
1 AAAATGGTATTTTTGGAAATTTTGA-GGTA
* *
6616420 AAAATGGAAATTTTT-GAAAGTTTCGAGGTTA
1 AAAATGG-TATTTTTGGAAA-TTTTGAGG-TA
* *
6616451 AAAATGGAATTTTTGG-AAGTTTGAGGGTA
1 AAAATGGTATTTTTGGAAATTTTGA-GGTA
* * *
6616480 AAAAT-GTAATTTTTGAAAAGTTTGGGGGT-
1 AAAATGGT-ATTTTTGGAAA-TTTTGAGGTA
*
6616509 AAAATGGTAATTTTTGGAAGTTTTGAGGGTAA
1 AAAATGGT-ATTTTTGGAAATTTTGA-GGT-A
** * * * *
6616541 AAAATGAAATTTTTGGAAGTTTGGGGGCA
1 AAAATGGTATTTTTGGAAATTTTGAGGTA
*
6616570 AAAAT-GTAATTTTTGGAAAGTTTGAGGGT-
1 AAAATGGT-ATTTTTGGAAATTTTGA-GGTA
*
6616599 AAAATGGTAATTTTGGAA
1 AAAATGGTATTTTTGGAA
6616617 GTTTGGGGTT
Statistics
Matches: 176, Mismatches: 31, Indels: 38
0.72 0.13 0.16
Matches are distributed among these distances:
28 11 0.06
29 72 0.41
30 54 0.31
31 33 0.19
32 6 0.03
ACGTcount: A:0.35, C:0.02, G:0.27, T:0.36
Consensus pattern (29 bp):
AAAATGGTATTTTTGGAAATTTTGAGGTA
Found at i:6616423 original size:29 final size:30
Alignment explanation
Indices: 6616357--6616625 Score: 233
Period size: 30 Copynumber: 9.1 Consensus size: 30
6616347 AGACACTTCG
* *
6616357 GGGT-AAAATGATAATTTTTGGAAATTTTGA
1 GGGTAAAAATGGT-ATTTTTGGAAAGTTTGA
* *
6616387 -GGTCAAAAATGGTGTTTTTGGACA-TTTGA
1 GGGT-AAAAATGGTATTTTTGGAAAGTTTGA
*
6616416 GGGT-AAAATGGAAATTTTT-GAAAGTTTCGA
1 GGGTAAAAATGG-TATTTTTGGAAAGTTT-GA
* *
6616446 GGTTAAAAATGGAATTTTTGG-AAGTTTGA
1 GGGTAAAAATGGTATTTTTGGAAAGTTTGA
* *
6616475 GGGTAAAAAT-GTAATTTTTGAAAAGTTTGG
1 GGGTAAAAATGGT-ATTTTTGGAAAGTTTGA
6616505 GGGT-AAAATGGTAATTTTTGG-AAGTTTTGA
1 GGGTAAAAATGGT-ATTTTTGGAAAG-TTTGA
** *
6616535 GGGTAAAAAATGAAATTTTTGG-AAGTTTGG
1 GGGT-AAAAATGGTATTTTTGGAAAGTTTGA
*
6616565 GGGCAAAAAT-GTAATTTTTGGAAAGTTTGA
1 GGGTAAAAATGGT-ATTTTTGGAAAGTTTGA
*
6616595 GGGT-AAAATGGTAATTTTGG-AAGTTTG-
1 GGGTAAAAATGGTATTTTTGGAAAGTTTGA
6616622 GGGT
1 GGGT
6616626 TGAAAATATG
Statistics
Matches: 200, Mismatches: 22, Indels: 37
0.77 0.08 0.14
Matches are distributed among these distances:
27 4 0.02
28 18 0.09
29 68 0.34
30 78 0.39
31 26 0.13
32 6 0.03
ACGTcount: A:0.33, C:0.01, G:0.29, T:0.36
Consensus pattern (30 bp):
GGGTAAAAATGGTATTTTTGGAAAGTTTGA
Found at i:6616423 original size:59 final size:61
Alignment explanation
Indices: 6616357--6616620 Score: 279
Period size: 59 Copynumber: 4.5 Consensus size: 61
6616347 AGACACTTCG
*
6616357 GGGTAAAATGATAATTTTTGGAAA-TTTTGAGGTCAAAAATGGT-GTTTTTGGACA-TTTGA
1 GGGTAAAATGATAATTTTTGGAAAGTTTTGAGGTCAAAAATGGTAATTTTTGGA-AGTTTGA
* *
6616416 GGGTAAAATGGA-AATTTTT-GAAAGTTTCGAGGTTAAAAATGG-AATTTTTGGAAGTTTGA
1 GGGTAAAAT-GATAATTTTTGGAAAGTTTTGAGGTCAAAAATGGTAATTTTTGGAAGTTTGA
* * *
6616475 GGGTAAAAATG-TAATTTTTGAAAAGTTTGGGGGT--AAAATGGTAATTTTTGGAAGTTTTGA
1 GGGT-AAAATGATAATTTTTGGAAAGTTTTGAGGTCAAAAATGGTAATTTTTGGAAG-TTTGA
* *
6616535 GGGTAAAAAATGA-AATTTTTGG-AAG-TTTGGGGGCAAAAAT-GTAATTTTTGGAAAGTTTGA
1 GGGT--AAAATGATAATTTTTGGAAAGTTTTGAGGTCAAAAATGGTAATTTTTGG-AAGTTTGA
*
6616595 GGGTAAAATGGTAA-TTTTGG-AAGTTT
1 GGGTAAAATGATAATTTTTGGAAAGTTT
6616621 GGGGTTGAAA
Statistics
Matches: 179, Mismatches: 10, Indels: 32
0.81 0.05 0.14
Matches are distributed among these distances:
58 27 0.15
59 79 0.44
60 50 0.28
61 23 0.13
ACGTcount: A:0.34, C:0.02, G:0.28, T:0.37
Consensus pattern (61 bp):
GGGTAAAATGATAATTTTTGGAAAGTTTTGAGGTCAAAAATGGTAATTTTTGGAAGTTTGA
Found at i:6616641 original size:29 final size:27
Alignment explanation
Indices: 6616459--6616650 Score: 120
Period size: 30 Copynumber: 6.5 Consensus size: 27
6616449 TAAAAATGGA
6616459 ATTTTTGGAAGTTTGAGGGTAAAA-ATG
1 ATTTTTGGAAGTTTG-GGGTAAAATATG
* * *
6616486 TAATTTTTGAAAAGTTTGGGGGTAAAATGGTA
1 --ATTTTTG-GAAGTTT-GGGGTAAAAT-ATG
*
6616518 ATTTTTGGAAGTTTTGAGGGTAAAAAATG
1 ATTTTTGGAAG-TTTG-GGGTAAAATATG
*
6616547 AAATTTTTGGAAGTTTGGGGGCAAAA-ATG
1 --ATTTTTGGAAGTTT-GGGGTAAAATATG
*
6616576 TAATTTTTGGAAAGTTTGAGGGTAAAAT-GG
1 --ATTTTTGG-AAGTTTG-GGGTAAAATATG
*
6616606 TAATTTTGGAAGTTTGGGGTTGAAAATATG
1 -ATTTTTGGAAGTTTGGGG-T-AAAATATG
*
6616636 ATTTTTAGACAGTTT
1 ATTTTTGGA-AGTTT
6616651 AGGGACCTTT
Statistics
Matches: 131, Mismatches: 16, Indels: 31
0.74 0.09 0.17
Matches are distributed among these distances:
27 3 0.02
28 8 0.06
29 44 0.34
30 62 0.47
31 13 0.10
32 1 0.01
ACGTcount: A:0.33, C:0.01, G:0.28, T:0.38
Consensus pattern (27 bp):
ATTTTTGGAAGTTTGGGGTAAAATATG
Found at i:6618420 original size:17 final size:17
Alignment explanation
Indices: 6618395--6618465 Score: 70
Period size: 17 Copynumber: 4.2 Consensus size: 17
6618385 TTTTAATTTT
*
6618395 ATTTTAATTTAAAATAA
1 ATTTAAATTTAAAATAA
* *
6618412 ATTTAAATTGAAAGTAA
1 ATTTAAATTTAAAATAA
* * * *
6618429 ATTCAAACTCAAAATGA
1 ATTTAAATTTAAAATAA
*
6618446 ATTTGAATTTAAAATAA
1 ATTTAAATTTAAAATAA
6618463 ATT
1 ATT
6618466 CAAACTTATT
Statistics
Matches: 41, Mismatches: 13, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 41 1.00
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:6618449 original size:34 final size:34
Alignment explanation
Indices: 6618405--6618471 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
6618395 ATTTTAATTT
*
6618405 AAAATAAATTTAAATTGAAAGTAAATTCAAACTC
1 AAAATAAATTTAAATTGAAAATAAATTCAAACTC
* * *
6618439 AAAATGAATTTGAATTTAAAATAAATTCAAACT
1 AAAATAAATTTAAATTGAAAATAAATTCAAACT
6618472 TATTTAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.55, C:0.07, G:0.06, T:0.31
Consensus pattern (34 bp):
AAAATAAATTTAAATTGAAAATAAATTCAAACTC
Found at i:6618732 original size:19 final size:19
Alignment explanation
Indices: 6618691--6618758 Score: 73
Period size: 19 Copynumber: 3.6 Consensus size: 19
6618681 CAATATCAAC
*** *
6618691 TTGTGTGAGCAATACCAGC
1 TTGTGTGAGCAATGTTAGA
*
6618710 TTGTGTGAGTAATGTTAGA
1 TTGTGTGAGCAATGTTAGA
* *
6618729 TTGTGTAAGCAATGTTAGC
1 TTGTGTGAGCAATGTTAGA
6618748 TTGTGTGAGCA
1 TTGTGTGAGCA
6618759 TCCCTAATCT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.25, C:0.10, G:0.29, T:0.35
Consensus pattern (19 bp):
TTGTGTGAGCAATGTTAGA
Found at i:6622257 original size:15 final size:16
Alignment explanation
Indices: 6622237--6622273 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
6622227 AAATTTAAAG
*
6622237 AAAAATCAGTA-TTGT
1 AAAAATCAGAAGTTGT
6622252 AAAAAT-AGAAGTTGT
1 AAAAATCAGAAGTTGT
6622267 AAAAATC
1 AAAAATC
6622274 TTGGTTTAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 3 0.16
15 16 0.84
ACGTcount: A:0.54, C:0.05, G:0.14, T:0.27
Consensus pattern (16 bp):
AAAAATCAGAAGTTGT
Found at i:6622925 original size:24 final size:24
Alignment explanation
Indices: 6622894--6622943 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
6622884 CTTAAGGTAA
6622894 AAATTGAATCTTCGATCACTGGTT
1 AAATTGAATCTTCGATCACTGGTT
6622918 AAATTGAATCTTCGATCACTGGTT
1 AAATTGAATCTTCGATCACTGGTT
6622942 AA
1 AA
6622944 GGTAGGAGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (24 bp):
AAATTGAATCTTCGATCACTGGTT
Found at i:6623140 original size:13 final size:13
Alignment explanation
Indices: 6623122--6623147 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6623112 AATGCATTAA
6623122 AAACAACAAAAAC
1 AAACAACAAAAAC
6623135 AAACAACAAAAAC
1 AAACAACAAAAAC
6623148 CAAAGATATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.23, G:0.00, T:0.00
Consensus pattern (13 bp):
AAACAACAAAAAC
Found at i:6627769 original size:3 final size:3
Alignment explanation
Indices: 6627756--6627812 Score: 60
Period size: 3 Copynumber: 19.0 Consensus size: 3
6627746 GGATTCTCAC
* * * * *
6627756 ATG AAG ATG ATG ATG ATG ATG AAG ATG GTG ATG GTG ATA ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
*
6627804 ATG GTG ATG
1 ATG ATG ATG
6627813 GCAATGCAAA
Statistics
Matches: 42, Mismatches: 12, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.37, T:0.30
Consensus pattern (3 bp):
ATG
Found at i:6627779 original size:18 final size:18
Alignment explanation
Indices: 6627756--6627812 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
6627746 GGATTCTCAC
*
6627756 ATGAAGATGATGATGATG
1 ATGAAGATGATGATGGTG
*
6627774 ATGAAGATGGTGATGGTG
1 ATGAAGATGATGATGGTG
6627792 AT-AATGATGATGATGGTG
1 ATGAA-GATGATGATGGTG
6627810 ATG
1 ATG
6627813 GCAATGCAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
17 2 0.06
18 32 0.94
ACGTcount: A:0.33, C:0.00, G:0.37, T:0.30
Consensus pattern (18 bp):
ATGAAGATGATGATGGTG
Found at i:6627793 original size:24 final size:24
Alignment explanation
Indices: 6627761--6627813 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
6627751 CTCACATGAA
* *
6627761 GATGATGATGATGATGAAGATGGT
1 GATGGTGATAATGATGAAGATGGT
*
6627785 GATGGTGATAATGATGATGATGGT
1 GATGGTGATAATGATGAAGATGGT
6627809 GATGG
1 GATGG
6627814 CAATGCAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.30, C:0.00, G:0.40, T:0.30
Consensus pattern (24 bp):
GATGGTGATAATGATGAAGATGGT
Found at i:6630327 original size:22 final size:22
Alignment explanation
Indices: 6630302--6630344 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
6630292 TATCCAAATA
6630302 ATAATAACAAAATAGTAGCAAT
1 ATAATAACAAAATAGTAGCAAT
* *
6630324 ATAATAGCGAAATAGTAGCAA
1 ATAATAACAAAATAGTAGCAA
6630345 AACAACAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.56, C:0.09, G:0.14, T:0.21
Consensus pattern (22 bp):
ATAATAACAAAATAGTAGCAAT
Found at i:6631484 original size:33 final size:34
Alignment explanation
Indices: 6631413--6631485 Score: 89
Period size: 34 Copynumber: 2.2 Consensus size: 34
6631403 GGTTTAAGAT
* **
6631413 AAAAAAATTATTAAAATTATGTATAAATGGTATG
1 AAAAAAATTACTAAAATTATGTATAAATAATATG
6631447 AAAAAAATTACTAAAA-TAT-TATTAAATAAT-TG
1 AAAAAAATTACTAAAATTATGTA-TAAATAATATG
6631479 AAAAAAA
1 AAAAAAA
6631486 CCATAAATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
32 11 0.31
33 9 0.26
34 15 0.43
ACGTcount: A:0.60, C:0.01, G:0.07, T:0.32
Consensus pattern (34 bp):
AAAAAAATTACTAAAATTATGTATAAATAATATG
Found at i:6633374 original size:13 final size:13
Alignment explanation
Indices: 6633356--6633381 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
6633346 ATAAAAAGAA
6633356 TATTTTTATATTT
1 TATTTTTATATTT
6633369 TATTTTTATATTT
1 TATTTTTATATTT
6633382 AACAATAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TATTTTTATATTT
Found at i:6633928 original size:18 final size:19
Alignment explanation
Indices: 6633892--6633929 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
6633882 GTTAACACAT
**
6633892 AAAATCATAAAATTTATTA
1 AAAATCATAAAATAAATTA
6633911 AAAAT-ATAAAATAAATTA
1 AAAATCATAAAATAAATTA
6633929 A
1 A
6633930 TATATTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAATCATAAAATAAATTA
Found at i:6636017 original size:15 final size:14
Alignment explanation
Indices: 6635964--6636011 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
6635954 TCCATTAAGC
*
6635964 CCAAACCAAGGTGAA
1 CCAAACCAA-TTGAA
*
6635979 CCAAACCCATTTGAA
1 CCAAA-CCAATTGAA
6635994 CCAAACCAATTGAA
1 CCAAACCAATTGAA
6636008 CCAA
1 CCAA
6636012 GTCCAACCCA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
14 12 0.41
15 14 0.48
16 3 0.10
ACGTcount: A:0.46, C:0.31, G:0.10, T:0.12
Consensus pattern (14 bp):
CCAAACCAATTGAA
Found at i:6636072 original size:20 final size:20
Alignment explanation
Indices: 6636055--6636118 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
6636045 CGTTGACCAC
*
6636055 TGACTGTTGACTTTGACCGT
1 TGACCGTTGACTTTGACCGT
* *
6636075 TGACCGTTTACTTTGATCGT
1 TGACCGTTGACTTTGACCGT
6636095 TGACCGTTGACTTTGACCGT
1 TGACCGTTGACTTTGACCGT
6636115 TGAC
1 TGAC
6636119 TTTTTTTGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 39 1.00
ACGTcount: A:0.16, C:0.22, G:0.23, T:0.39
Consensus pattern (20 bp):
TGACCGTTGACTTTGACCGT
Found at i:6636076 original size:13 final size:13
Alignment explanation
Indices: 6636055--6636121 Score: 66
Period size: 13 Copynumber: 5.1 Consensus size: 13
6636045 CGTTGACCAC
*
6636055 TGACTGTTGACTT
1 TGACCGTTGACTT
6636068 TGACCGTTGACCGTT
1 TGACCGTTGA-C-TT
* *
6636083 T-A-CTTTGATCGT
1 TGACCGTTGA-CTT
6636095 TGACCGTTGACTT
1 TGACCGTTGACTT
6636108 TGACCGTTGACTT
1 TGACCGTTGACTT
6636121 T
1 T
6636122 TTTTGAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
12 2 0.05
13 32 0.73
14 7 0.16
15 3 0.07
ACGTcount: A:0.15, C:0.21, G:0.22, T:0.42
Consensus pattern (13 bp):
TGACCGTTGACTT
Found at i:6636078 original size:27 final size:27
Alignment explanation
Indices: 6636045--6636105 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
6636035 CGTTGACCGG
*
6636045 CGTTGACCACTGACTGTTGA-CTTTGAC
1 CGTTGACCACTGACT-TTGATCGTTGAC
** *
6636072 CGTTGACCGTTTACTTTGATCGTTGAC
1 CGTTGACCACTGACTTTGATCGTTGAC
6636099 CGTTGAC
1 CGTTGAC
6636106 TTTGACCGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 4 0.14
27 25 0.86
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (27 bp):
CGTTGACCACTGACTTTGATCGTTGAC
Found at i:6637164 original size:3 final size:3
Alignment explanation
Indices: 6637156--6637189 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
6637146 TTCTATTCTA
6637156 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
6637190 TTGGGATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:6639581 original size:23 final size:23
Alignment explanation
Indices: 6639554--6639598 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
6639544 ATTTTTGTAA
6639554 TTTAA-ATATTTAATTACTTTTAG
1 TTTAATATATTTAATTA-TTTTAG
* *
6639577 TTTAATTTATTTATTTATTTTA
1 TTTAATATATTTAATTATTTTA
6639599 TTAATTTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (23 bp):
TTTAATATATTTAATTATTTTAG
Found at i:6641513 original size:7 final size:7
Alignment explanation
Indices: 6641488--6641923 Score: 746
Period size: 7 Copynumber: 62.3 Consensus size: 7
6641478 TCTATGATCA
6641488 TCCCGTT
1 TCCCGTT
* *
6641495 ACCCATT
1 TCCCGTT
*
6641502 ACCCGTT
1 TCCCGTT
*
6641509 ACCCGTT
1 TCCCGTT
6641516 TCCCGTT
1 TCCCGTT
6641523 TCCCGTT
1 TCCCGTT
6641530 TCCCGTT
1 TCCCGTT
6641537 TCCCGTT
1 TCCCGTT
*
6641544 ACCCGTT
1 TCCCGTT
*
6641551 ACCCGTT
1 TCCCGTT
*
6641558 ACCCGTT
1 TCCCGTT
6641565 TCCCGTT
1 TCCCGTT
6641572 TCCCGTT
1 TCCCGTT
6641579 TCCCGTT
1 TCCCGTT
6641586 TCCCGTT
1 TCCCGTT
6641593 TCCCGTT
1 TCCCGTT
6641600 TCCCGTT
1 TCCCGTT
6641607 TCCCGTT
1 TCCCGTT
6641614 TCCCGTT
1 TCCCGTT
6641621 TCCCGTT
1 TCCCGTT
6641628 TCCCGTT
1 TCCCGTT
6641635 TCCCGTT
1 TCCCGTT
6641642 TCCCGTT
1 TCCCGTT
6641649 TCCCGTT
1 TCCCGTT
6641656 TCCCGTT
1 TCCCGTT
6641663 TCCCGTT
1 TCCCGTT
6641670 TCCCGTT
1 TCCCGTT
*
6641677 ACCCGTT
1 TCCCGTT
6641684 TCCCGTT
1 TCCCGTT
6641691 TCCCGTT
1 TCCCGTT
6641698 TCCCGTT
1 TCCCGTT
6641705 TCCCGTT
1 TCCCGTT
6641712 TCCCGTT
1 TCCCGTT
6641719 TCCCGTT
1 TCCCGTT
6641726 TCCCGTT
1 TCCCGTT
6641733 TCCCGTT
1 TCCCGTT
*
6641740 ACCCGTT
1 TCCCGTT
*
6641747 ACCCGTT
1 TCCCGTT
*
6641754 ACCCGTT
1 TCCCGTT
*
6641761 ACCCGTT
1 TCCCGTT
6641768 TCCCGTT
1 TCCCGTT
6641775 TCCCGTT
1 TCCCGTT
6641782 TCCCGTT
1 TCCCGTT
6641789 TCCCGTT
1 TCCCGTT
6641796 TCCCGTT
1 TCCCGTT
6641803 TCCCGTT
1 TCCCGTT
6641810 TCCCGTT
1 TCCCGTT
6641817 TCCCGTT
1 TCCCGTT
6641824 TCCCGTT
1 TCCCGTT
6641831 TCCCGTT
1 TCCCGTT
6641838 TCCCGTT
1 TCCCGTT
6641845 TCCCGTT
1 TCCCGTT
6641852 TCCCGTT
1 TCCCGTT
6641859 TCCCGTT
1 TCCCGTT
6641866 TCCCGTT
1 TCCCGTT
6641873 TCCCGTT
1 TCCCGTT
6641880 TCCCGTT
1 TCCCGTT
6641887 TCCCGTT
1 TCCCGTT
6641894 TCCCGTT
1 TCCCGTT
6641901 TCCCGTT
1 TCCCGTT
*
6641908 TCCAGTT
1 TCCCGTT
*
6641915 TCCAGTT
1 TCCCGTT
6641922 TC
1 TC
6641924 TAGTCCCTCA
Statistics
Matches: 418, Mismatches: 11, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 418 1.00
ACGTcount: A:0.03, C:0.42, G:0.14, T:0.40
Consensus pattern (7 bp):
TCCCGTT
Found at i:6647842 original size:24 final size:24
Alignment explanation
Indices: 6647815--6647866 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
6647805 ATAAGTATTT
*
6647815 AATAATAAAAATTTCATAATATGA
1 AATAATAAAAATTTAATAATATGA
* * * *
6647839 AATATTAATATTTTAATAGTATGA
1 AATAATAAAAATTTAATAATATGA
6647863 AATA
1 AATA
6647867 TTATTAAATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (24 bp):
AATAATAAAAATTTAATAATATGA
Found at i:6647855 original size:21 final size:21
Alignment explanation
Indices: 6647831--6647923 Score: 57
Period size: 21 Copynumber: 4.3 Consensus size: 21
6647821 AAAAATTTCA
6647831 TAATATGAAATATTAATATTT
1 TAATATGAAATATTAATATTT
*
6647852 TAATAGTATGAAATATTATTAAATTT
1 T-A-A-TATGAAATATTA--ATATTT
* * *
6647878 TATTAT--AATTTTAGTA-TT
1 TAATATGAAATATTAATATTT
**
6647896 TAGATATTTAATATTAATATTT
1 TA-ATATGAAATATTAATATTT
6647918 TAATAT
1 TAATAT
6647924 TTTTTACCGT
Statistics
Matches: 55, Mismatches: 8, Indels: 18
0.68 0.10 0.22
Matches are distributed among these distances:
18 4 0.07
19 4 0.07
21 19 0.35
22 5 0.09
23 4 0.07
24 12 0.22
25 1 0.02
26 6 0.11
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (21 bp):
TAATATGAAATATTAATATTT
Found at i:6649112 original size:14 final size:15
Alignment explanation
Indices: 6649052--6649123 Score: 62
Period size: 14 Copynumber: 4.9 Consensus size: 15
6649042 TAGCATGCGG
*
6649052 GAGCCTCCTTA-GTGT
1 GAGCCT-CTTATGTGC
*
6649067 GAGCC-CTTATCTGC
1 GAGCCTCTTATGTGC
*
6649081 GGGCC-CTTATGTGC
1 GAGCCTCTTATGTGC
*
6649095 GAGCCTCTTA-GTGT
1 GAGCCTCTTATGTGC
6649109 GAGCCTCTATATGTG
1 GAGCCTCT-TATGTG
6649124 AACCCTTAGG
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
13 4 0.09
14 29 0.62
15 11 0.23
16 3 0.06
ACGTcount: A:0.14, C:0.26, G:0.28, T:0.32
Consensus pattern (15 bp):
GAGCCTCTTATGTGC
Found at i:6649130 original size:42 final size:43
Alignment explanation
Indices: 6649052--6649138 Score: 106
Period size: 42 Copynumber: 2.0 Consensus size: 43
6649042 TAGCATGCGG
* ** *
6649052 GAGCCTCCTTAGTGTGAGCCCTTATCTGCGGGCCCTTATGTGC
1 GAGCCTCCTTAGTGTGAGCCCTTATATGCGAACCCTTAGGTGC
*
6649095 GAGCCT-CTTAGTGTGAG-CCTCTATATGTGAACCCTTAGGTGC
1 GAGCCTCCTTAGTGTGAGCCCT-TATATGCGAACCCTTAGGTGC
6649137 GA
1 GA
6649139 ACTTACCTGT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
41 3 0.08
42 29 0.76
43 6 0.16
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (43 bp):
GAGCCTCCTTAGTGTGAGCCCTTATATGCGAACCCTTAGGTGC
Found at i:6649645 original size:27 final size:27
Alignment explanation
Indices: 6649605--6649668 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
6649595 GTAGCAAAAG
* * *
6649605 TCATTGTCATAGATGACAAGTGAACAA
1 TCATCGTCACAGATGACAAGTAAACAA
*
6649632 TCATCGTCACAGATGACAAGTAAACGA
1 TCATCGTCACAGATGACAAGTAAACAA
*
6649659 CCATCGTCAC
1 TCATCGTCAC
6649669 CGAAAAACAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.22
Consensus pattern (27 bp):
TCATCGTCACAGATGACAAGTAAACAA
Found at i:6650321 original size:14 final size:15
Alignment explanation
Indices: 6650302--6650330 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
6650292 ATGAAAAGAC
6650302 AATAATATT-ATTAT
1 AATAATATTGATTAT
6650316 AATAATATTGATTAT
1 AATAATATTGATTAT
6650331 CTTTTAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (15 bp):
AATAATATTGATTAT
Found at i:6650514 original size:52 final size:51
Alignment explanation
Indices: 6650412--6650520 Score: 159
Period size: 52 Copynumber: 2.1 Consensus size: 51
6650402 ATCAACCGTT
*
6650412 TTTTATATAATTAATATATTATAAAAATAATTTTATAATACAATTTTTAAAA
1 TTTTATATAATTAATATATTATAAAAATAATTTTATAATACAA-TATTAAAA
6650464 TTTTATATAATTAATATATTATAAAAATAAATTTTAATAATTA-AA-ATTAAAA
1 TTTTATATAATTAATATATTATAAAAAT-AATTTT-ATAA-TACAATATTAAAA
6650516 TTTTA
1 TTTTA
6650521 AATTTAATGA
Statistics
Matches: 53, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
52 39 0.74
53 6 0.11
54 6 0.11
55 2 0.04
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (51 bp):
TTTTATATAATTAATATATTATAAAAATAATTTTATAATACAATATTAAAA
Found at i:6656034 original size:15 final size:16
Alignment explanation
Indices: 6655999--6656032 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
6655989 AATGTGCTCT
*
6655999 AAATTACATAATATAA
1 AAATAACATAATATAA
6656015 AAATAACATAATATAA
1 AAATAACATAATATAA
6656031 AA
1 AA
6656033 TATTATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (16 bp):
AAATAACATAATATAA
Found at i:6658577 original size:40 final size:40
Alignment explanation
Indices: 6658499--6658577 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 40
6658489 ATTTATATGC
* * * *
6658499 TTATGATTAATGACATGAATTTGTGAATTGTTTTATGATT
1 TTATGATTAATGACATAAACTTGTGAATTGTATCATGATT
*
6658539 TTATGATTAATGGCATAAACTTGTGAA-TGATATCATGAT
1 TTATGATTAATGACATAAACTTGTGAATTG-TATCATGAT
6658578 CATCGATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
39 2 0.06
40 31 0.94
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.44
Consensus pattern (40 bp):
TTATGATTAATGACATAAACTTGTGAATTGTATCATGATT
Found at i:6663267 original size:35 final size:35
Alignment explanation
Indices: 6663196--6663285 Score: 99
Period size: 35 Copynumber: 2.6 Consensus size: 35
6663186 ACAGTGGCAA
* ***
6663196 GCTTAACATGCGAATCATAATCAGATTTACAACAT
1 GCTTAACATGCGAATCATAAGCAGAACAACAACAT
* * *
6663231 GCTTAACATGCGAATCATACGCAGAACAATATCAT
1 GCTTAACATGCGAATCATAAGCAGAACAACAACAT
* *
6663266 GCTTAATATGCAAATCATAA
1 GCTTAACATGCGAATCATAA
6663286 TAAAAATATT
Statistics
Matches: 45, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 45 1.00
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.27
Consensus pattern (35 bp):
GCTTAACATGCGAATCATAAGCAGAACAACAACAT
Found at i:6664930 original size:221 final size:220
Alignment explanation
Indices: 6664483--6665022 Score: 1053
Period size: 221 Copynumber: 2.4 Consensus size: 220
6664473 TTCCCATGCA
6664483 TTACAACTTAGGAAAAGGATTGAATGAAACAGTGATACCACGTCATTTGTGTCCCTTTTCCAATA
1 TTACAAC-T-GGAAAAGGATTGAATGAAACAGTGATACCACGTCATTTGTGTCCCTTTTCCAATA
6664548 GTTTTATGCCACATCAGTATTTTCATTCTTAATTTCAATATTTCATCCTGAAAAAAATCAAATTA
64 GTTTTATGCCACATCAGTATTTTCATTCTTAATTTCAATATTTCATCCTGAAAAAAATCAAATTA
6664613 CAATTAAAATCCTGAAATTTAGGATGAAATTGTTGATGTGTCATAAAACTATTGGAAAGGGATAA
129 CAATTAAAATCCTGAAATTTAGGATGAAATTGTTGATGTGTCATAAAACTATTGGAAAGGGATAA
6664678 TATCCCTGTTTCATACAATCCTTTCTC
194 TATCCCTGTTTCATACAATCCTTTCTC
6664705 TTACAACTGGAAAAGGATTGAATGAAACAGTGATACCACGTCATTTGTGTCCCTTTTCCAATAGT
1 TTACAACTGGAAAAGGATTGAATGAAACAGTGATACCACGTCATTTGTGTCCCTTTTCCAATAGT
6664770 TTTATGCCACATCAGTATTTTCATTCTTAATTTCAATATTTCATCCTGAAAAAAAATCAAATTAC
66 TTTATGCCACATCAGTATTTTCATTCTTAATTTCAATATTTCATCCTG-AAAAAAATCAAATTAC
6664835 AATTAAAATCCTGAAATTTAGGATGAAATTGTTGATGTGTCATAAAACTATTGGAAAGGGATAAT
130 AATTAAAATCCTGAAATTTAGGATGAAATTGTTGATGTGTCATAAAACTATTGGAAAGGGATAAT
6664900 ATCCCTGTTTCATACAATCCTTTCTC
195 ATCCCTGTTTCATACAATCCTTTCTC
6664926 TTACAACTGGAAAAGGATTGAATGAAACAGTGATACCACGTCATTTGTGTCCCTTTTCCAATAGT
1 TTACAACTGGAAAAGGATTGAATGAAACAGTGATACCACGTCATTTGTGTCCCTTTTCCAATAGT
6664991 TTTATGCCACATCAGTATTTTCATTCTTAATT
66 TTTATGCCACATCAGTATTTTCATTCTTAATT
6665023 ACACATTTAA
Statistics
Matches: 317, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
220 105 0.33
221 205 0.65
222 7 0.02
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (220 bp):
TTACAACTGGAAAAGGATTGAATGAAACAGTGATACCACGTCATTTGTGTCCCTTTTCCAATAGT
TTTATGCCACATCAGTATTTTCATTCTTAATTTCAATATTTCATCCTGAAAAAAATCAAATTACA
ATTAAAATCCTGAAATTTAGGATGAAATTGTTGATGTGTCATAAAACTATTGGAAAGGGATAATA
TCCCTGTTTCATACAATCCTTTCTC
Found at i:6669742 original size:15 final size:17
Alignment explanation
Indices: 6669710--6669757 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 17
6669700 AATTGTATAA
6669710 TATTATATATAAACTTT
1 TATTATATATAAACTTT
*
6669727 TATTATATGT-AA-TTT
1 TATTATATATAAACTTT
6669742 TATT-TATA-AAA-TTT
1 TATTATATATAAACTTT
6669756 TA
1 TA
6669758 ATTTCATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
14 10 0.36
15 7 0.25
16 2 0.07
17 9 0.32
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (17 bp):
TATTATATATAAACTTT
Found at i:6669843 original size:6 final size:6
Alignment explanation
Indices: 6669834--6669861 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
6669824 TATATTTATC
6669834 AAATAT AAATAT AAATAT AAATAT AAAT
1 AAATAT AAATAT AAATAT AAATAT AAAT
6669862 TAATATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATAT
Found at i:6679329 original size:17 final size:17
Alignment explanation
Indices: 6679316--6679391 Score: 98
Period size: 17 Copynumber: 4.5 Consensus size: 17
6679306 AAAATTTTAT
6679316 TTTAAAATAAATTTAAA
1 TTTAAAATAAATTTAAA
* *
6679333 TTTCAAATAAACTTAAA
1 TTTAAAATAAATTTAAA
*
6679350 TTTATAATAAATTTAAA
1 TTTAAAATAAATTTAAA
* * *
6679367 CTTAAAATGAATTAAAA
1 TTTAAAATAAATTTAAA
6679384 TTTAAAAT
1 TTTAAAAT
6679392 CTAAAATTAG
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 49 1.00
ACGTcount: A:0.55, C:0.04, G:0.01, T:0.39
Consensus pattern (17 bp):
TTTAAAATAAATTTAAA
Found at i:6684587 original size:24 final size:23
Alignment explanation
Indices: 6684543--6684587 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
6684533 AGCCAGAAGC
* *
6684543 GTGCCACAAGGCAGAGGAAAAGT
1 GTGCCACAAGACAGAGAAAAAGT
*
6684566 GTGCCACAAAGACAGATAAAAA
1 GTGCCAC-AAGACAGAGAAAAA
6684588 CTAAAAAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 7 0.39
24 11 0.61
ACGTcount: A:0.47, C:0.18, G:0.27, T:0.09
Consensus pattern (23 bp):
GTGCCACAAGACAGAGAAAAAGT
Found at i:6693276 original size:31 final size:30
Alignment explanation
Indices: 6693228--6693300 Score: 96
Period size: 29 Copynumber: 2.4 Consensus size: 30
6693218 ATCTTAAAAC
6693228 TATACAT-AAATTATGATTTAATGTGCAATTG
1 TATACATGAAATTATGATTT--TGTGCAATTG
* *
6693259 TATACATGAACTT-TGATTTTGTGCAATTT
1 TATACATGAAATTATGATTTTGTGCAATTG
6693288 TATACATGAAATT
1 TATACATGAAATT
6693301 TTAATTTGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 21 0.55
31 13 0.34
32 4 0.11
ACGTcount: A:0.36, C:0.08, G:0.12, T:0.44
Consensus pattern (30 bp):
TATACATGAAATTATGATTTTGTGCAATTG
Found at i:6693308 original size:29 final size:29
Alignment explanation
Indices: 6693249--6693308 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
6693239 TATGATTTAA
* *
6693249 TGTGCAATTGTATACATGAACTTTGATTT
1 TGTGCAATTGTATACATGAAATTTGAATT
* *
6693278 TGTGCAATTTTATACATGAAATTTTAATT
1 TGTGCAATTGTATACATGAAATTTGAATT
6693307 TG
1 TG
6693309 ATCCAATTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.30, C:0.08, G:0.15, T:0.47
Consensus pattern (29 bp):
TGTGCAATTGTATACATGAAATTTGAATT
Found at i:6694300 original size:22 final size:22
Alignment explanation
Indices: 6694275--6694325 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
6694265 TATTAACTAG
*
6694275 AAAAATAATATAAAATAAAATT
1 AAAAATAATAAAAAATAAAATT
* *
6694297 AAAATTAATAAAAAATACAATT
1 AAAAATAATAAAAAATAAAATT
6694319 ATAAAAT
1 A-AAAAT
6694326 GAACCTTTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (22 bp):
AAAAATAATAAAAAATAAAATT
Found at i:6699803 original size:17 final size:17
Alignment explanation
Indices: 6699781--6699814 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
6699771 CATAAAAATC
*
6699781 ATAAAATAATTATAAAA
1 ATAAAAAAATTATAAAA
6699798 ATAAAAAAATTATAAAA
1 ATAAAAAAATTATAAAA
6699815 TAAGTCTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
ATAAAAAAATTATAAAA
Found at i:6699805 original size:28 final size:30
Alignment explanation
Indices: 6699774--6699830 Score: 91
Period size: 28 Copynumber: 2.0 Consensus size: 30
6699764 TTTTTCCCAT
6699774 AAAAATCATAAAATAA-T-TATAAAAATAA
1 AAAAATCATAAAATAAGTCTATAAAAATAA
*
6699802 AAAAATTATAAAATAAGTCTATAAAAATA
1 AAAAATCATAAAATAAGTCTATAAAAATA
6699831 TTAAATATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 15 0.58
29 1 0.04
30 10 0.38
ACGTcount: A:0.68, C:0.04, G:0.02, T:0.26
Consensus pattern (30 bp):
AAAAATCATAAAATAAGTCTATAAAAATAA
Found at i:6699885 original size:27 final size:26
Alignment explanation
Indices: 6699847--6699900 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 26
6699837 ATTAAAATTG
*
6699847 ATATAAACTTATTAAA-ATTATAAAAA
1 ATATAAAATTA-TAAAGATTATAAAAA
6699873 ATATAAAGATTATAAAGATTATAAAAA
1 ATATAAA-ATTATAAAGATTATAAAAA
6699900 A
1 A
6699901 AACTTGTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
26 11 0.44
27 14 0.56
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (26 bp):
ATATAAAATTATAAAGATTATAAAAA
Found at i:6699895 original size:18 final size:17
Alignment explanation
Indices: 6699788--6699898 Score: 55
Period size: 18 Copynumber: 6.1 Consensus size: 17
6699778 ATCATAAAAT
*
6699788 AATTAT-AAAAATAAAAA
1 AATTATAAAAAAT-ATAA
6699805 AATTATAAAATAAGTCTATAA
1 AATTATAAAA-AA---TATAA
* * *
6699826 AAATATTAAATAT-TAA
1 AATTATAAAAAATATAA
**
6699842 AATTGATATAAACTTATTAA
1 AATT-ATA-AAAAATA-TAA
6699862 AATTATAAAAAATATAA
1 AATTATAAAAAATATAA
* *
6699879 AGATTATAAAGATTATAA
1 A-ATTATAAAAAATATAA
6699897 AA
1 AA
6699899 AAAACTTGTA
Statistics
Matches: 72, Mismatches: 12, Indels: 20
0.69 0.12 0.19
Matches are distributed among these distances:
16 6 0.08
17 14 0.19
18 27 0.38
19 5 0.07
20 8 0.11
21 11 0.15
22 1 0.01
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (17 bp):
AATTATAAAAAATATAA
Found at i:6699941 original size:26 final size:26
Alignment explanation
Indices: 6699912--6699964 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
6699902 ACTTGTAAAT
* *
6699912 ATTATCAAAATATA-AAAATCTAATAA
1 ATTATAAAAAGATATAAAATC-AATAA
*
6699938 ATTATAAAAAGATATAGAATCAATAA
1 ATTATAAAAAGATATAAAATCAATAA
6699964 A
1 A
6699965 ACTTATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.62, C:0.06, G:0.04, T:0.28
Consensus pattern (26 bp):
ATTATAAAAAGATATAAAATCAATAA
Found at i:6700523 original size:41 final size:41
Alignment explanation
Indices: 6700421--6700563 Score: 200
Period size: 41 Copynumber: 3.5 Consensus size: 41
6700411 TTTACATAAA
* * * **
6700421 CGCCGCAAAAGGT-AAAGCAATCGCGGCGCTTATGGGTAAG
1 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGAAAAG
6700461 CGCCG-TAAAGGTCAGAGCAATAGCGGCGCTTATGGAAAAG
1 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGAAAAG
* * *
6700501 CGCTGCTAAAGGTCAGAGCAATAGCGGCACTTATGGTAAAG
1 CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGAAAAG
6700542 CGCCGCTAAAGGTCAGAGCAAT
1 CGCCGCTAAAGGTCAGAGCAAT
6700564 GGTAAAGCGC
Statistics
Matches: 92, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
39 6 0.07
40 32 0.35
41 54 0.59
ACGTcount: A:0.31, C:0.22, G:0.31, T:0.16
Consensus pattern (41 bp):
CGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGAAAAG
Found at i:6700566 original size:29 final size:29
Alignment explanation
Indices: 6700533--6700590 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
6700523 AGCGGCACTT
6700533 ATGGTAAAGCGCCGCTAAAGGTCAGAGCA
1 ATGGTAAAGCGCCGCTAAAGGTCAGAGCA
6700562 ATGGTAAAGCGCCGCTAAAGGTCAGAGCA
1 ATGGTAAAGCGCCGCTAAAGGTCAGAGCA
6700591 TTAGCGGCGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.21, G:0.31, T:0.14
Consensus pattern (29 bp):
ATGGTAAAGCGCCGCTAAAGGTCAGAGCA
Found at i:6700580 original size:70 final size:70
Alignment explanation
Indices: 6700492--6700633 Score: 196
Period size: 70 Copynumber: 2.0 Consensus size: 70
6700482 AGCGGCGCTT
* * *
6700492 ATGGAAAAGCGCTGCTAAAGGTCAGAGCAATAGCGGCACTT-ATGGTAAAGCGCCGCTAAAGGTC
1 ATGGAAAAGCGCCGCTAAAGGTCAGAGCAATAGCGGC-CTTGATGATAAAGCACCGCTAAAGGTC
6700556 AGAGCA
65 AGAGCA
* * * *
6700562 ATGGTAAAGCGCCGCTAAAGGTCAGAGCATTAGCGGCGTTGATGATAAAGCACCGTTAAAGGTCA
1 ATGGAAAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCCTTGATGATAAAGCACCGCTAAAGGTCA
*
6700627 GATCA
66 GAGCA
6700632 AT
1 AT
6700634 AGCGGAGCTT
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
69 2 0.03
70 61 0.97
ACGTcount: A:0.34, C:0.19, G:0.29, T:0.18
Consensus pattern (70 bp):
ATGGAAAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCCTTGATGATAAAGCACCGCTAAAGGTCA
GAGCA
Found at i:6700611 original size:41 final size:42
Alignment explanation
Indices: 6700562--6700675 Score: 121
Period size: 41 Copynumber: 2.8 Consensus size: 42
6700552 GGTCAGAGCA
* *
6700562 ATGG-TAAAGCGCCGCTAAAGGTCAGAGCATTAGCGGCG-TT
1 ATGGATAAAGCGCCGCTAAAGGTCAGAGCAATAGCGGAGCTT
* * *
6700602 GAT-GATAAAGCACCGTTAAAGGTCAGATCAATAGCGGAGCTT
1 -ATGGATAAAGCGCCGCTAAAGGTCAGAGCAATAGCGGAGCTT
* *
6700644 ATGGA-AAAGCGTCGCT-AAGGTTAGAGCAATAG
1 ATGGATAAAGCGCCGCTAAAGGTCAGAGCAATAG
6700676 ATAAGCGCCG
Statistics
Matches: 60, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
40 15 0.25
41 41 0.68
42 4 0.07
ACGTcount: A:0.33, C:0.17, G:0.30, T:0.20
Consensus pattern (42 bp):
ATGGATAAAGCGCCGCTAAAGGTCAGAGCAATAGCGGAGCTT
Found at i:6700682 original size:28 final size:29
Alignment explanation
Indices: 6700650--6700704 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
6700640 GCTTATGGAA
* *
6700650 AAGCGTCGCT-AAGGTTAGAGCAATAGAT
1 AAGCGCCGCTAAAGGTCAGAGCAATAGAT
*
6700678 AAGCGCCGCTAAAGGTCAGATCAATAG
1 AAGCGCCGCTAAAGGTCAGAGCAATAG
6700705 CGGCGCTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 9 0.39
29 14 0.61
ACGTcount: A:0.36, C:0.18, G:0.27, T:0.18
Consensus pattern (29 bp):
AAGCGCCGCTAAAGGTCAGAGCAATAGAT
Found at i:6700722 original size:69 final size:70
Alignment explanation
Indices: 6700609--6700741 Score: 207
Period size: 69 Copynumber: 1.9 Consensus size: 70
6700599 GTTGATGATA
* *
6700609 AAGCACCGTTAAAGGTCAGATCAATAGCGGAGCTTATGGAAAAGCGTCGCT-AAGGTTAGAGCAA
1 AAGCACCGCTAAAGGTCAGATCAATAGCGGAGCTTATGGAAAAGCGCCGCTAAAGGTTAGAGCAA
6700673 TAGAT
66 TAGAT
* *
6700678 AAGCGCCGCTAAAGGTCAGATCAATAGCGGCGCTTATAGG-AAAGCGCCGCTAAAGGTTAGAGCA
1 AAGCACCGCTAAAGGTCAGATCAATAGCGGAGCTTAT-GGAAAAGCGCCGCTAAAGGTTAGAGCA
6700742 TTAGCGGGGT
Statistics
Matches: 58, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
69 44 0.76
70 14 0.24
ACGTcount: A:0.35, C:0.19, G:0.29, T:0.18
Consensus pattern (70 bp):
AAGCACCGCTAAAGGTCAGATCAATAGCGGAGCTTATGGAAAAGCGCCGCTAAAGGTTAGAGCAA
TAGAT
Found at i:6700722 original size:110 final size:109
Alignment explanation
Indices: 6700457--6700748 Score: 376
Period size: 110 Copynumber: 2.7 Consensus size: 109
6700447 CGCTTATGGG
*
6700457 TAAGCGCCG-TAAAGGTCAGAGCAATAGCGGCGCTTATGGAAAAGCGCTGCTAAAGGTCAGAGCA
1 TAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGG-AAAGCGCCGCTAAAGGTCAGAGCA
* *
6700521 ATAGCGGCACTTATGGTAAAGCGCCGCTAAAGGTCAGAGCAATGG
65 ATAGCGGCACTTATGGAAAAGCGCCGCTAAAGGTCAGAGCAATGA
* * * * *
6700566 TAAAGCGCCGCTAAAGGTCAGAGCATTAGCGGCG-TTGATGATAAAGCACCGTTAAAGGTCAGAT
1 T-AAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTT-ATG-GAAAGCGCCGCTAAAGGTCAGAG
* *
6700630 CAATAGCGG-AGCTTATGGAAAAGCGTCGCT-AAGGTTAGAGCAATAGA
63 CAATAGCGGCA-CTTATGGAAAAGCGCCGCTAAAGGTCAGAGCAAT-GA
* *
6700677 TAAGCGCCGCTAAAGGTCAGATCAATAGCGGCGCTTATAGGAAAGCGCCGCTAAAGGTTAGAGCA
1 TAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTAT-GGAAAGCGCCGCTAAAGGTCAGAGCA
*
6700742 TTAGCGG
65 ATAGCGG
6700749 GGTTTTCCCA
Statistics
Matches: 157, Mismatches: 18, Indels: 15
0.83 0.09 0.08
Matches are distributed among these distances:
109 1 0.01
110 82 0.52
111 74 0.47
ACGTcount: A:0.33, C:0.19, G:0.30, T:0.18
Consensus pattern (109 bp):
TAAGCGCCGCTAAAGGTCAGAGCAATAGCGGCGCTTATGGAAAGCGCCGCTAAAGGTCAGAGCAA
TAGCGGCACTTATGGAAAAGCGCCGCTAAAGGTCAGAGCAATGA
Found at i:6701769 original size:2 final size:2
Alignment explanation
Indices: 6701762--6701805 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
6701752 TCTTATACTA
*
6701762 AT AT AT AT AT AT AC 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
6701804 AT
1 AT
6701806 TAATGTAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6702919 original size:41 final size:41
Alignment explanation
Indices: 6702871--6702990 Score: 168
Period size: 41 Copynumber: 2.9 Consensus size: 41
6702861 TGTTTATATG
* * *
6702871 AAAGCGCCGCTAAAGGTCGGAGTATTAGCGGCGTTTATGTC
1 AAAGCGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATGAC
* * * * *
6702912 CAAGCGCCGCTAATGGTCTGAGCAATAGCGGCGTTTATGAG
1 AAAGCGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATGAC
6702953 AAAGCGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTAT
1 AAAGCGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTAT
6702991 AAGGAAGCAT
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 68 1.00
ACGTcount: A:0.26, C:0.21, G:0.31, T:0.23
Consensus pattern (41 bp):
AAAGCGCCGCTAAAGGTCAGAGCATTAGCGGCGTTTATGAC
Found at i:6702948 original size:82 final size:81
Alignment explanation
Indices: 6702835--6702990 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
6702825 TCAAAAAAAA
* * * *
6702835 CGCCGCTAAAGGTTAAGTAATAGCAGTGTTTAT-ATGAAAGCGCCGCTAAAGGTCGGAGTATTAG
1 CGCCGCTAAAGGTTAAGCAATAGCAGCGTTTATGA-GAAAGCGCCGCTAAAGGTCAGAGCATTAG
6702899 CGGCGTTTATGTCCAAG
65 CGGCGTTTATGTCCAAG
* * *
6702916 CGCCGCTAATGGTCTGAGCAATAGCGGCGTTTATGAGAAAGCGCCGCTAAAGGTCAGAGCATTAG
1 CGCCGCTAAAGGT-TAAGCAATAGCAGCGTTTATGAGAAAGCGCCGCTAAAGGTCAGAGCATTAG
6702981 CGGCGTTTAT
65 CGGCGTTTAT
6702991 AAGGAAGCAT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 12 0.18
82 53 0.80
83 1 0.02
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.24
Consensus pattern (81 bp):
CGCCGCTAAAGGTTAAGCAATAGCAGCGTTTATGAGAAAGCGCCGCTAAAGGTCAGAGCATTAGC
GGCGTTTATGTCCAAG
Found at i:6703090 original size:15 final size:15
Alignment explanation
Indices: 6703066--6703109 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
6703056 CTAAAAACAG
* *
6703066 ATTTCGAAATTCCTA
1 ATTTCTAAATCCCTA
6703081 ATTTCTAAATCCCTA
1 ATTTCTAAATCCCTA
6703096 ATTTCTAAATCCCT
1 ATTTCTAAATCCCT
6703110 CTCCTCCTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.32, C:0.25, G:0.02, T:0.41
Consensus pattern (15 bp):
ATTTCTAAATCCCTA
Found at i:6712261 original size:26 final size:26
Alignment explanation
Indices: 6712220--6712274 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
6712210 TCATCATTCA
*
6712220 TCTAATCCAAACTATCAGACATGTTT
1 TCTAATCAAAACTATCAGACATGTTT
*
6712246 TCTAATCAAAAGTATCAGACATGTTT
1 TCTAATCAAAACTATCAGACATGTTT
6712272 TCT
1 TCT
6712275 GTTTTGTCGC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.35, C:0.20, G:0.09, T:0.36
Consensus pattern (26 bp):
TCTAATCAAAACTATCAGACATGTTT
Found at i:6713644 original size:16 final size:16
Alignment explanation
Indices: 6713605--6713644 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
6713595 ATAGAATAAA
*
6713605 TAAT-AAAGTTTGAAG
1 TAATAAAAGATTGAAG
6713620 TCAATAAAAGATTGAAG
1 T-AATAAAAGATTGAAG
6713637 TAATAAAA
1 TAATAAAA
6713645 ATAAATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 10 0.45
17 11 0.50
ACGTcount: A:0.55, C:0.03, G:0.15, T:0.28
Consensus pattern (16 bp):
TAATAAAAGATTGAAG
Found at i:6714790 original size:6 final size:6
Alignment explanation
Indices: 6714779--6714862 Score: 84
Period size: 6 Copynumber: 14.5 Consensus size: 6
6714769 TTGGACTCTT
** * *
6714779 TTTAAA TTTAAA -TTAAA TTTAAA AATAAA TTTAAA TTCAAA -ATAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
** *
6714825 TTTAAA TTTAAA -TTAAA TTTAAA AATAAA TTAAAA TTT
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTT
6714863 TAAAAAAATG
Statistics
Matches: 61, Mismatches: 14, Indels: 6
0.75 0.17 0.07
Matches are distributed among these distances:
5 13 0.21
6 48 0.79
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (6 bp):
TTTAAA
Found at i:6714799 original size:17 final size:17
Alignment explanation
Indices: 6714779--6714858 Score: 90
Period size: 17 Copynumber: 4.6 Consensus size: 17
6714769 TTGGACTCTT
6714779 TTTAAATTTAAA-TTAAA
1 TTTAAA-TTAAATTTAAA
*
6714796 TTTAAAAATAAATTTAAA
1 TTT-AAATTAAATTTAAA
* *
6714814 TTCAAAATAAATTTAAA
1 TTTAAATTAAATTTAAA
6714831 TTTAAATTAAATTTAAA
1 TTTAAATTAAATTTAAA
**
6714848 AATAAATTAAA
1 TTTAAATTAAA
6714859 ATTTTAAAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
17 45 0.82
18 10 0.18
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (17 bp):
TTTAAATTAAATTTAAA
Found at i:6714811 original size:23 final size:23
Alignment explanation
Indices: 6714781--6714861 Score: 110
Period size: 23 Copynumber: 3.5 Consensus size: 23
6714771 GGACTCTTTT
6714781 TAAATTTAAATTAAATTTAAAAA
1 TAAATTTAAATTAAATTTAAAAA
* **
6714804 TAAATTTAAATTCAAA-ATAAATT
1 TAAATTTAAATT-AAATTTAAAAA
6714827 TAAATTTAAATTAAATTTAAAAA
1 TAAATTTAAATTAAATTTAAAAA
*
6714850 TAAATTAAAATT
1 TAAATTTAAATT
6714862 TTAAAAAAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
22 3 0.06
23 43 0.88
24 3 0.06
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (23 bp):
TAAATTTAAATTAAATTTAAAAA
Found at i:6714849 original size:29 final size:29
Alignment explanation
Indices: 6714779--6714862 Score: 107
Period size: 29 Copynumber: 2.9 Consensus size: 29
6714769 TTGGACTCTT
* **
6714779 TTTAAATTTAAATTAAATTTAAAAATAAA
1 TTTAAATTTAAAATAAATTTAAATTTAAA
*
6714808 TTTAAATTCAAAATAAATTTAAATTTAAA
1 TTTAAATTTAAAATAAATTTAAATTTAAA
*
6714837 -TTAAATTTAAAAATAAATTAAAATTT
1 TTTAAATTT-AAAATAAATTTAAATTT
6714863 TAAAAAAATG
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
28 7 0.15
29 41 0.85
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (29 bp):
TTTAAATTTAAAATAAATTTAAATTTAAA
Done.