Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014738.1 Corchorus capsularis cultivar CVL-1 contig14759, 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: 113093
ACGTcount: A:0.30, C:0.18, G:0.19, T:0.33
Found at i:16840 original size:60 final size:60
Alignment explanation
Indices: 16721--16840 Score: 154
Period size: 60 Copynumber: 2.0 Consensus size: 60
16711 GGGATTCGAT
* * *
16721 CCCTACTTACCCTAACTACTTAGTAAGGATTTTTGGGGATTATTTTTATGGTTTGCTGAC
1 CCCTACTTACCCTAACTACTTAGTAAGGATTTGTGGGGATTATTTTTATGATTTACTGAC
* * *
16781 CCCTACTTACCCTAGCTATTTAGTTAA-GATTTGTGGGGATT-TATTTTGTGATTTACTGAC
1 CCCTACTTACCCTAACTACTTAG-TAAGGATTTGTGGGGATTAT-TTTTATGATTTACTGAC
16841 GGCGATTTTC
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
59 1 0.02
60 48 0.92
61 3 0.06
ACGTcount: A:0.22, C:0.17, G:0.18, T:0.42
Consensus pattern (60 bp):
CCCTACTTACCCTAACTACTTAGTAAGGATTTGTGGGGATTATTTTTATGATTTACTGAC
Found at i:18051 original size:22 final size:23
Alignment explanation
Indices: 18008--18053 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
17998 CGAGCTAAAA
***
18008 TTAACCCTATTTTTATGTGTATT
1 TTAACCCTATTTTTACAAGTATT
18031 TTAACCCTA-TTTTACAAGTATT
1 TTAACCCTATTTTTACAAGTATT
18053 T
1 T
18054 GTGTTTTTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.26, C:0.15, G:0.07, T:0.52
Consensus pattern (23 bp):
TTAACCCTATTTTTACAAGTATT
Found at i:21138 original size:39 final size:40
Alignment explanation
Indices: 21084--21189 Score: 126
Period size: 42 Copynumber: 2.6 Consensus size: 40
21074 AAATTGTTCT
* * *
21084 TGTGTTATATGTGTTTAGGGACTTTAGTA-TAG-GTGCCTC
1 TGTGTTATATGTGTTT-GGGACTTTAGAAGGAGAGTGCCCC
*
21123 TGTGTTATATGTGTTTGAGGACTTTAGAAGGAGAATTGCCCC
1 TGTGTTATATGTGTTTG-GGACTTTAGAAGGAG-AGTGCCCC
21165 TGTGTTATATGTGTTTGGGGACTTT
1 TGTGTTATATGTGTTT-GGGACTTT
21190 GGGGAGAATT
Statistics
Matches: 58, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
38 1 0.02
39 26 0.45
40 2 0.03
42 28 0.48
43 1 0.02
ACGTcount: A:0.19, C:0.09, G:0.29, T:0.42
Consensus pattern (40 bp):
TGTGTTATATGTGTTTGGGACTTTAGAAGGAGAGTGCCCC
Found at i:23102 original size:31 final size:31
Alignment explanation
Indices: 23067--23130 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
23057 TCTTATCTAA
*
23067 ACGCCATTAAATAGCGACGTCTGAAT-TTAAG
1 ACGCCACTAAATAGCGACGTCT-AATATTAAG
* *
23098 ACGCCACTAAGTAGCGGCGTCTAATATTAAG
1 ACGCCACTAAATAGCGACGTCTAATATTAAG
23129 AC
1 AC
23131 TCCGCTATCT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 3 0.10
31 26 0.90
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.23
Consensus pattern (31 bp):
ACGCCACTAAATAGCGACGTCTAATATTAAG
Found at i:24578 original size:72 final size:72
Alignment explanation
Indices: 24463--24952 Score: 621
Period size: 72 Copynumber: 6.8 Consensus size: 72
24453 GAAGAACAAA
* * * * *
24463 GATTGTGCGAAGGACTGGC--ATGCGGGAACTACCTCGGCTACAATCACAATGAGGAAGATAATT
1 GATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAGGAAGATAATC
*
24526 ACATAAG
66 ACGTAAG
* *
24533 GATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGATGAATATAATC
1 GATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAGGAAGATAATC
* *
24598 GCATAAG
66 ACGTAAG
* * * * *
24605 GGTTGTGTGAAGGACTGCCAAATGTTGGAACTGCCTCGGCTACAATCGCAATGATGAATATAATC
1 GATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAGGAAGATAATC
* *
24670 GCCTAAG
66 ACGTAAG
* * *
24677 GGTTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAACCGCAAT-ATGGAAGATTAT
1 GATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGA-GGAAGATAAT
*
24741 CATGTAAG
65 CACGTAAG
* * *
24749 GATTGTGCGAAGGACTGTCAAATGTGGGAACTGCCTCGGCTACAACCGCAAT-ATGGAAGATTAT
1 GATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGA-GGAAGATAAT
*
24813 CATGTAAG
65 CACGTAAG
* * **
24821 GATTCTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAACCGCAAT-ATGGAAGATTGT
1 GATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGA-GGAAGATAAT
*
24885 CATGTAAG
65 CACGTAAG
* * *
24893 GATTGTGCGAAGGACTGCCACATATGGGAACTGCCTCGGCTACAATCGCAATGAAGAAGA
1 GATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAGGAAGA
24953 AGACCATGGG
Statistics
Matches: 385, Mismatches: 31, Indels: 6
0.91 0.07 0.01
Matches are distributed among these distances:
70 18 0.05
71 1 0.00
72 365 0.95
73 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.28, T:0.22
Consensus pattern (72 bp):
GATTGTGCGAAGGACTGCCAAATGTGGGAACTGCCTCGGCTACAATCGCAATGAGGAAGATAATC
ACGTAAG
Found at i:26289 original size:58 final size:58
Alignment explanation
Indices: 26220--26506 Score: 470
Period size: 58 Copynumber: 4.9 Consensus size: 58
26210 GGGACTTTGA
26220 TATAGATGCCTCTGTGTTTAGGGACTTATGAATGCCCTTGTGTTTGAGGACTTTTTAG
1 TATAGATGCCTCTGTGTTTAGGGACTTATGAATGCCCTTGTGTTTGAGGACTTTTTAG
*
26278 TATAGATGCCTCTGTGTTTAGGGACTTATGAATGCCCTTGTGTTTAAGGACTTTTTAG
1 TATAGATGCCTCTGTGTTTAGGGACTTATGAATGCCCTTGTGTTTGAGGACTTTTTAG
* * *
26336 TAGAGATGCCTCTGTGTTTAGAGACTTATGAATGCCCTTGTGTTTGAGGACTTTTTAA
1 TATAGATGCCTCTGTGTTTAGGGACTTATGAATGCCCTTGTGTTTGAGGACTTTTTAG
* * *
26394 TAGAGATGCCTCTGTGTTTAGGGGCTTATGAATGCCCATGTGTTTGAGGACTTTTT-G
1 TATAGATGCCTCTGTGTTTAGGGACTTATGAATGCCCTTGTGTTTGAGGACTTTTTAG
*
26451 -ATAGAAATGCCTCTGTGTTTAGGGACTTATGAATGCCCTGGTGTTTGAGGACTTTT
1 TATAG--ATGCCTCTGTGTTTAGGGACTTATGAATGCCCTTGTGTTTGAGGACTTTT
26507 GATAGAGAAT
Statistics
Matches: 214, Mismatches: 13, Indels: 4
0.93 0.06 0.02
Matches are distributed among these distances:
56 3 0.01
58 211 0.99
ACGTcount: A:0.20, C:0.14, G:0.26, T:0.40
Consensus pattern (58 bp):
TATAGATGCCTCTGTGTTTAGGGACTTATGAATGCCCTTGTGTTTGAGGACTTTTTAG
Found at i:26294 original size:32 final size:30
Alignment explanation
Indices: 26223--26514 Score: 167
Period size: 26 Copynumber: 10.1 Consensus size: 30
26213 ACTTTGATAT
26223 AGATGCCTCTGTGTTTAGGGAC---TTAT-G
1 AGATGCCTCTGTGTTTA-GGACTTTTTATAG
*
26250 A-ATGCC-CTTGTGTTTGAGGACTTTTTAGTAT
1 AGATGCCTC-TGTGTTT-AGGACTTTTTA-TAG
26281 AGATGCCTCTGTGTTTAGGGAC---TTAT-G
1 AGATGCCTCTGTGTTTA-GGACTTTTTATAG
26308 A-ATGCC-CTTGTGTTTAAGGACTTTTTAGTAG
1 AGATGCCTC-TGTGTTT-AGGACTTTTTA-TAG
26339 AGATGCCTCTGTGTTTAGAGAC---TTAT-G
1 AGATGCCTCTGTGTTTAG-GACTTTTTATAG
26366 A-ATGCC-CTTGTGTTTGAGGACTTTTTAATAG
1 AGATGCCTC-TGTGTTT-AGGACTTTTT-ATAG
*
26397 AGATGCCTCTGTGTTTAGGGGC---TTAT-G
1 AGATGCCTCTGTGTTTA-GGACTTTTTATAG
26424 A-ATGCC-CATGTGTTTGAGGACTTTTTGATAG
1 AGATGCCTC-TGTGTTT-AGGACTTTTT-ATAG
*
26455 AAATGCCTCTGTGTTTAGGGAC---TTAT-G
1 AGATGCCTCTGTGTTTA-GGACTTTTTATAG
*
26482 A-ATGCC-CTGGTGTTTGAGGACTTTTGATAG
1 AGATGCCTCT-GTGTTT-AGGACTTTTTATAG
26512 AGA
1 AGA
26515 ATATTAGATT
Statistics
Matches: 213, Mismatches: 5, Indels: 90
0.69 0.02 0.29
Matches are distributed among these distances:
25 6 0.03
26 77 0.36
27 14 0.07
28 6 0.03
29 23 0.11
30 8 0.04
31 13 0.06
32 62 0.29
33 4 0.02
ACGTcount: A:0.21, C:0.14, G:0.27, T:0.39
Consensus pattern (30 bp):
AGATGCCTCTGTGTTTAGGACTTTTTATAG
Found at i:26401 original size:116 final size:116
Alignment explanation
Indices: 26196--26514 Score: 493
Period size: 116 Copynumber: 2.8 Consensus size: 116
26186 TTTGAGAGAT
* * *
26196 TGCCCATGTGCTTAGGGAC--TTTGATATAGATGCCTCTGTGTTTAGGGACTTATGAATGCCCTT
1 TGCCCATGTGTTTAAGGACTTTTTGATAGAGATGCCTCTGTGTTTAGGGACTTATGAATGCCCTT
* *
26259 GTGTTTGAGGACTTTTTAGTATAGATGCCTCTGTGTTTAGGGACTTATGAA
66 GTGTTTGAGGACTTTTTAATAGAGATGCCTCTGTGTTTAGGGACTTATGAA
* *
26310 TGCCCTTGTGTTTAAGGACTTTTT-AGTAGAGATGCCTCTGTGTTTAGAGACTTATGAATGCCCT
1 TGCCCATGTGTTTAAGGACTTTTTGA-TAGAGATGCCTCTGTGTTTAGGGACTTATGAATGCCCT
*
26374 TGTGTTTGAGGACTTTTTAATAGAGATGCCTCTGTGTTTAGGGGCTTATGAA
65 TGTGTTTGAGGACTTTTTAATAGAGATGCCTCTGTGTTTAGGGACTTATGAA
* * *
26426 TGCCCATGTGTTTGAGGACTTTTTGATAGAAATGCCTCTGTGTTTAGGGACTTATGAATGCCCTG
1 TGCCCATGTGTTTAAGGACTTTTTGATAGAGATGCCTCTGTGTTTAGGGACTTATGAATGCCCTT
*
26491 GTGTTTGAGGAC-TTTTGATAGAGA
66 GTGTTTGAGGACTTTTTAATAGAGA
26515 ATATTAGATT
Statistics
Matches: 187, Mismatches: 14, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
114 16 0.09
115 12 0.06
116 158 0.84
117 1 0.01
ACGTcount: A:0.21, C:0.14, G:0.27, T:0.39
Consensus pattern (116 bp):
TGCCCATGTGTTTAAGGACTTTTTGATAGAGATGCCTCTGTGTTTAGGGACTTATGAATGCCCTT
GTGTTTGAGGACTTTTTAATAGAGATGCCTCTGTGTTTAGGGACTTATGAA
Found at i:28406 original size:22 final size:21
Alignment explanation
Indices: 28375--28687 Score: 265
Period size: 22 Copynumber: 15.1 Consensus size: 21
28365 TATACTTTTC
28375 TTACTGATTACCATTTTTACTT
1 TTACTGATTACCA-TTTTACTT
*
28397 TTGCTGATTACC-TTTTACTCT
1 TTACTGATTACCATTTTACT-T
* *
28418 TTACTGATTACCATTTTGCTC
1 TTACTGATTACCATTTTACTT
28439 TTACTGATTACCATTTTACCTT
1 TTACTGATTACCATTTTA-CTT
* *
28461 TTACTGATTATCA--TCACTT
1 TTACTGATTACCATTTTACTT
** * * *
28480 TT--TTTTTACTATTTTGCTC
1 TTACTGATTACCATTTTACTT
**
28499 TTACTGATTACTTTTTTACTCT
1 TTACTGATTACCATTTTACT-T
* *
28521 TTACTGATTACCATTTTGCTC
1 TTACTGATTACCATTTTACTT
28542 TTACTGATTACCATTTTACCTT
1 TTACTGATTACCATTTTA-CTT
* *
28564 TTACTGATTATCA--TCAC-T
1 TTACTGATTACCATTTTACTT
*
28582 TT--T--TTACTATTTTACTCT
1 TTACTGATTACCATTTTACT-T
28600 TTACTGATTACC-TTCTTACTTT
1 TTACTGATTACCATT-TTAC-TT
*
28622 TTACTGATTACTATTTTACTCT
1 TTACTGATTACCATTTTACT-T
* *
28644 TTACTGATTACCATTTTGCTC
1 TTACTGATTACCATTTTACTT
*
28665 TTACTGATTACCCTTTTACTT
1 TTACTGATTACCATTTTACTT
28686 TT
1 TT
28688 TACCATTTTT
Statistics
Matches: 231, Mismatches: 39, Indels: 43
0.74 0.12 0.14
Matches are distributed among these distances:
14 4 0.02
16 4 0.02
17 5 0.02
18 6 0.03
19 11 0.05
20 12 0.05
21 81 0.35
22 105 0.45
23 3 0.01
ACGTcount: A:0.20, C:0.21, G:0.06, T:0.53
Consensus pattern (21 bp):
TTACTGATTACCATTTTACTT
Found at i:28426 original size:43 final size:42
Alignment explanation
Indices: 28375--28687 Score: 242
Period size: 43 Copynumber: 7.5 Consensus size: 42
28365 TATACTTTTC
*
28375 TTACTGATTACCATTTTTACTTTTGCTGATTACCTTTTACTCT
1 TTACTGATTACCA-TTTTACTTTTACTGATTACCTTTTACTCT
* *
28418 TTACTGATTACCATTTTGCTCTTACTGATTACCATTTTAC-CTT
1 TTACTGATTACCATTTTACTTTTACTGATTACC-TTTTACTC-T
* * ** * *
28461 TTACTGATTATCA--TCACTTTT--TTTTTACTATTTTGCTC-
1 TTACTGATTACCATTTTACTTTTACTGATTAC-CTTTTACTCT
** *
28499 TTACTGATTACTTTTTTACTCTTTACTGATTACCATTTTGCTC-
1 TTACTGATTACCATTTTACT-TTTACTGATTACC-TTTTACTCT
** *
28542 TTACTGATTACCATTTTACCTTTTACTGATTA--TCAT-CACT
1 TTACTGATTACCATTTTA-CTTTTACTGATTACCTTTTACTCT
* *
28582 TT--T--TTACTATTTTACTCTTTACTGATTACCTTCTTACTTT
1 TTACTGATTACCATTTTACT-TTTACTGATTACCTT-TTACTCT
* *
28622 TTACTGATTACTATTTTACTCTTTACTGATTACCATTTTGCTC-
1 TTACTGATTACCATTTTACT-TTTACTGATTACC-TTTTACTCT
*
28665 TTACTGATTACCCTTTTACTTTT
1 TTACTGATTACCATTTTACTTTT
28688 TACCATTTTT
Statistics
Matches: 216, Mismatches: 32, Indels: 45
0.74 0.11 0.15
Matches are distributed among these distances:
35 2 0.01
36 21 0.10
38 12 0.06
39 13 0.06
40 13 0.06
41 8 0.04
42 22 0.10
43 90 0.42
44 33 0.15
45 2 0.01
ACGTcount: A:0.20, C:0.21, G:0.06, T:0.53
Consensus pattern (42 bp):
TTACTGATTACCATTTTACTTTTACTGATTACCTTTTACTCT
Found at i:28519 original size:103 final size:100
Alignment explanation
Indices: 28389--28711 Score: 420
Period size: 103 Copynumber: 3.2 Consensus size: 100
28379 TGATTACCAT
* *
28389 TTTTACT-TTTGCTGATTACCTTTTACTCTTTACTGATTACCATTTTGCTCTTACTGATTACCAT
1 TTTTACTCTTTACTGATTACTTTTTACTCTTTACTGATTACCATTTTGCTCTTACTGATTACCAT
28453 TTTACCTTTTACTGATTATCATCACTTTTTTTTTACTA
66 TTTACCTTTTACTGATTATCATCAC---TTTTTTACTA
*
28491 TTTTGCTC-TTACTGATTACTTTTTTACTCTTTACTGATTACCATTTTGCTCTTACTGATTACCA
1 TTTTACTCTTTACTGATTAC-TTTTTACTCTTTACTGATTACCATTTTGCTCTTACTGATTACCA
28555 TTTTACCTTTTACTGATTATCATCACTTTTTTACTA
65 TTTTACCTTTTACTGATTATCATCACTTTTTTACTA
* * * *
28591 TTTTACTCTTTACTGATTACCTTCTTACTTTTTACTGATTACTATTTTACTCTTTACTGATTACC
1 TTTTACTCTTTACTGATTA-CTTTTTACTCTTTACTGATTACCATTTTGCTC-TTACTGATTACC
* * * * * *
28656 ATTTT-GCTCTTACTGATTACCCTTTTAC-TTTTTACCA
64 ATTTTACCTTTTACTGATTA-TC-ATCACTTTTTTACTA
28693 TTTTTACTCTTTACTGATT
1 -TTTTACTCTTTACTGATT
28712 TACTGATTAC
Statistics
Matches: 199, Mismatches: 14, Indels: 15
0.87 0.06 0.07
Matches are distributed among these distances:
100 17 0.09
101 49 0.25
102 43 0.22
103 90 0.45
ACGTcount: A:0.20, C:0.21, G:0.06, T:0.54
Consensus pattern (100 bp):
TTTTACTCTTTACTGATTACTTTTTACTCTTTACTGATTACCATTTTGCTCTTACTGATTACCAT
TTTACCTTTTACTGATTATCATCACTTTTTTACTA
Found at i:28546 original size:36 final size:38
Alignment explanation
Indices: 28506--28669 Score: 92
Period size: 36 Copynumber: 4.1 Consensus size: 38
28496 CTCTTACTGA
*
28506 TTACTTTTTTACTCTTTACTGATTA-C-CATTTTGCTC
1 TTACTATTTTACTCTTTACTGATTACCTCATTTTGCTC
* *
28542 TTACTGATTACCATTTTAC-CTTTTACTGATTATCATCACTTT--T-
1 TTAC----T---ATTTTACTC-TTTACTGATTA-CCTCATTTTGCTC
* *
28585 TTACTATTTTACTCTTTACTGATTACCTTCTTACTTTTTACTGA
1 TTACTATTTTACTCTTTACTGATTACC-TC--A--TTTTGCT-C
28629 TTACTATTTTACTCTTTACTGATTA-C-CATTTTGCTC
1 TTACTATTTTACTCTTTACTGATTACCTCATTTTGCTC
28665 TTACT
1 TTACT
28670 GATTACCCTT
Statistics
Matches: 100, Mismatches: 7, Indels: 42
0.67 0.05 0.28
Matches are distributed among these distances:
35 1 0.01
36 29 0.29
37 7 0.07
38 1 0.01
39 2 0.02
40 4 0.04
41 1 0.01
42 2 0.02
43 22 0.22
44 26 0.26
46 5 0.05
ACGTcount: A:0.20, C:0.21, G:0.05, T:0.54
Consensus pattern (38 bp):
TTACTATTTTACTCTTTACTGATTACCTCATTTTGCTC
Found at i:28604 original size:15 final size:15
Alignment explanation
Indices: 28584--28648 Score: 57
Period size: 15 Copynumber: 4.4 Consensus size: 15
28574 TCATCACTTT
28584 TTTACTATTTTACTC
1 TTTACTATTTTACTC
28599 TTTACTGA--TTAC-C
1 TTTACT-ATTTTACTC
*
28612 TTCTTACT-TTTTACTG
1 -T-TTACTATTTTACTC
*
28628 ATTACTATTTTACTC
1 TTTACTATTTTACTC
28643 TTTACT
1 TTTACT
28649 GATTACCATT
Statistics
Matches: 39, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
13 1 0.03
14 10 0.26
15 27 0.69
16 1 0.03
ACGTcount: A:0.20, C:0.20, G:0.03, T:0.57
Consensus pattern (15 bp):
TTTACTATTTTACTC
Found at i:28754 original size:40 final size:41
Alignment explanation
Indices: 28710--28841 Score: 137
Period size: 40 Copynumber: 3.3 Consensus size: 41
28700 TCTTTACTGA
28710 TTTACTGATTACTTCTTTTACTCTT-ACTCTTAATTACCAT
1 TTTACTGATTACTTCTTTTACTCTTGACTCTTAATTACCAT
* *
28750 TTTACTGATTACTTCTTTTACT-TTGACTTTTTAATTACTGAT
1 TTTACTGATTACTTCTTTTACTCTTGAC-TCTTAATTAC-CAT
* * * * * *
28792 TTCACTGATTA-ATCTCTTAC-CTTGACTCTTGATTATCAA
1 TTTACTGATTACTTCTTTTACTCTTGACTCTTAATTACCAT
*
28831 ATTACTGATTA
1 TTTACTGATTA
28842 ATCCCTTTTT
Statistics
Matches: 76, Mismatches: 12, Indels: 9
0.78 0.12 0.09
Matches are distributed among these distances:
39 12 0.16
40 31 0.41
41 21 0.28
42 12 0.16
ACGTcount: A:0.24, C:0.19, G:0.06, T:0.51
Consensus pattern (41 bp):
TTTACTGATTACTTCTTTTACTCTTGACTCTTAATTACCAT
Found at i:31854 original size:13 final size:13
Alignment explanation
Indices: 31836--31861 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31826 AATTGCTGTA
31836 TATACATTTAAAT
1 TATACATTTAAAT
31849 TATACATTTAAAT
1 TATACATTTAAAT
31862 AGAGTGCCTG
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:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (13 bp):
TATACATTTAAAT
Found at i:43596 original size:16 final size:17
Alignment explanation
Indices: 43569--43601 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
43559 TGCAGAATGC
43569 AAAGCGAAACAACAAAA
1 AAAGCGAAACAACAAAA
43586 AAAGC-AAACAACAAAA
1 AAAGCGAAACAACAAAA
43602 GAAATTAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.73, C:0.18, G:0.09, T:0.00
Consensus pattern (17 bp):
AAAGCGAAACAACAAAA
Found at i:44812 original size:16 final size:16
Alignment explanation
Indices: 44788--44834 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
44778 ATTTATTAAC
44788 TACCATTTTTACTAAT
1 TACCATTTTTACTAAT
* *
44804 TATCCTTTTCTTACTGAT
1 TA-CCATTT-TTACTAAT
44822 TACCATTTTTACT
1 TACCATTTTTACT
44835 TTTGCTGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 7 0.27
17 10 0.38
18 9 0.35
ACGTcount: A:0.23, C:0.21, G:0.02, T:0.53
Consensus pattern (16 bp):
TACCATTTTTACTAAT
Found at i:44845 original size:22 final size:21
Alignment explanation
Indices: 44814--45191 Score: 300
Period size: 22 Copynumber: 18.1 Consensus size: 21
44804 TATCCTTTTC
44814 TTACTGATTACCATTTTTACTT
1 TTACTGATTACCA-TTTTACTT
* *
44836 TTGCTGATTACC-TTTTATTCT
1 TTACTGATTACCATTTTACT-T
* * *
44857 TTATTGATTACCATTTTGCTC
1 TTACTGATTACCATTTTACTT
44878 TTACTGATTACCATTTTACCTT
1 TTACTGATTACCATTTTA-CTT
* *
44900 TTACTGATTATCA--TCACTT
1 TTACTGATTACCATTTTACTT
* *
44919 TT--T-TTTACTATTTTACTCT
1 TTACTGATTACCATTTTACT-T
*
44938 TTATTGATTACC-TTCTTACTTT
1 TTACTGATTACCATT-TTAC-TT
*
44960 TTACTGATTACTATTTTACTCT
1 TTACTGATTACCATTTTACT-T
* *
44982 TTACTGATTACCATTTTGCTC
1 TTACTGATTACCATTTTACTT
**
45003 TTACTGATTACTTTTTTACTCT
1 TTACTGATTACCATTTTACT-T
* * *
45025 TTACTGATTACAATTTTGCTC
1 TTACTGATTACCATTTTACTT
45046 TTACTGATTACCATTTTACCTT
1 TTACTGATTACCATTTTA-CTT
* *
45068 TTACTGATTATCA--TCAC-T
1 TTACTGATTACCATTTTACTT
*
45086 TT--T--TTACTATTTTACTCT
1 TTACTGATTACCATTTTACT-T
45104 TTACTGATTACC-TTCTTACTTT
1 TTACTGATTACCATT-TTAC-TT
* *
45126 TTACTGATTACTATTTTGCTCT
1 TTACTGATTACCATTTTACT-T
* *
45148 TTACTGATTACCATTTTGCTC
1 TTACTGATTACCATTTTACTT
*
45169 TTACTGATTACCCTTTTACTT
1 TTACTGATTACCATTTTACTT
45190 TT
1 TT
45192 TACCATTTTT
Statistics
Matches: 282, Mismatches: 47, Indels: 55
0.73 0.12 0.14
Matches are distributed among these distances:
14 4 0.01
16 8 0.03
17 1 0.00
18 10 0.04
19 9 0.03
20 11 0.04
21 87 0.31
22 146 0.52
23 6 0.02
ACGTcount: A:0.20, C:0.20, G:0.06, T:0.54
Consensus pattern (21 bp):
TTACTGATTACCATTTTACTT
Found at i:44866 original size:43 final size:43
Alignment explanation
Indices: 44814--45194 Score: 314
Period size: 43 Copynumber: 9.1 Consensus size: 43
44804 TATCCTTTTC
* * *
44814 TTACTGATTACCATTTTTACTTTTGCTGATTAC-CTTTTATTCT
1 TTACTGATTACCA-TTTTACTCTTACTGATTACTCTTTTACTCT
* *
44857 TTATTGATTACCATTTTGCTCTTACTGATTAC-CATTTTAC-CTT
1 TTACTGATTACCATTTTACTCTTACTGATTACTC-TTTTACTC-T
* * ** *
44900 TTACTGATTATCA--TCACT-TT--TTTTTACTATTTTACTCT
1 TTACTGATTACCATTTTACTCTTACTGATTACTCTTTTACTCT
* * *
44938 TTATTGATTACC-TTCTTACTTTTTACTGATTACTATTTTACTCT
1 TTACTGATTACCATT-TTAC-TCTTACTGATTACTCTTTTACTCT
* *
44982 TTACTGATTACCATTTTGCTCTTACTGATTACTTTTTTACTCT
1 TTACTGATTACCATTTTACTCTTACTGATTACTCTTTTACTCT
* *
45025 TTACTGATTACAATTTTGCTCTTACTGATTAC-CATTTTAC-CTT
1 TTACTGATTACCATTTTACTCTTACTGATTACTC-TTTTACTC-T
* * *
45068 TTACTGATTATCA--TCACT-TT--T--TTACTATTTTACTCT
1 TTACTGATTACCATTTTACTCTTACTGATTACTCTTTTACTCT
* * *
45104 TTACTGATTACC-TTCTTACTTTTTACTGATTACTATTTTGCTCT
1 TTACTGATTACCATT-TTAC-TCTTACTGATTACTCTTTTACTCT
* * *
45148 TTACTGATTACCATTTTGCTCTTACTGATTACCCTTTTACTTT
1 TTACTGATTACCATTTTACTCTTACTGATTACTCTTTTACTCT
45191 TTAC
1 TTAC
45195 CATTTTTACT
Statistics
Matches: 275, Mismatches: 37, Indels: 52
0.76 0.10 0.14
Matches are distributed among these distances:
36 22 0.08
37 1 0.00
38 26 0.09
39 2 0.01
40 9 0.03
41 7 0.03
42 22 0.08
43 123 0.45
44 59 0.21
45 4 0.01
ACGTcount: A:0.20, C:0.20, G:0.06, T:0.54
Consensus pattern (43 bp):
TTACTGATTACCATTTTACTCTTACTGATTACTCTTTTACTCT
Found at i:45164 original size:166 final size:166
Alignment explanation
Indices: 44814--45194 Score: 629
Period size: 166 Copynumber: 2.3 Consensus size: 166
44804 TATCCTTTTC
* * * * * *
44814 TTACTGATTACCATTTTTACTTTTGCTGATTACCTTTTATTCTTTATTGATTACCATTTTGCTCT
1 TTACTGATTACCA-TTTTGCTCTTACTGATTACCTTTTACTCTTTACTGATTACAATTTTGCTCT
*
44879 TACTGATTACCATTTTACCTTTTACTGATTATCATCACTTTTTTTTACTATTTTACTCTTTATTG
65 TACTGATTACCATTTTACCTTTTACTGATTATCATCAC-TTTTTTTACTATTTTACTCTTTACTG
44944 ATTACCTTCTTACTTTTTACTGATTACTATTTTACTCT
129 ATTACCTTCTTACTTTTTACTGATTACTATTTTACTCT
*
44982 TTACTGATTACCATTTTGCTCTTACTGATTACTTTTTTACTCTTTACTGATTACAATTTTGCTCT
1 TTACTGATTACCATTTTGCTCTTACTGATTAC-CTTTTACTCTTTACTGATTACAATTTTGCTCT
45047 TACTGATTACCATTTTACCTTTTACTGATTATCATCAC-TTTTTTACTATTTTACTCTTTACTGA
65 TACTGATTACCATTTTACCTTTTACTGATTATCATCACTTTTTTTACTATTTTACTCTTTACTGA
*
45111 TTACCTTCTTACTTTTTACTGATTACTATTTTGCTCT
130 TTACCTTCTTACTTTTTACTGATTACTATTTTACTCT
*
45148 TTACTGATTACCATTTTGCTCTTACTGATTACCCTTTTACTTTTTAC
1 TTACTGATTACCATTTTGCTCTTACTGATTA-CCTTTTACTCTTTAC
45195 CATTTTTACT
Statistics
Matches: 200, Mismatches: 11, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
166 104 0.52
167 17 0.09
168 79 0.40
ACGTcount: A:0.20, C:0.20, G:0.06, T:0.54
Consensus pattern (166 bp):
TTACTGATTACCATTTTGCTCTTACTGATTACCTTTTACTCTTTACTGATTACAATTTTGCTCTT
ACTGATTACCATTTTACCTTTTACTGATTATCATCACTTTTTTTACTATTTTACTCTTTACTGAT
TACCTTCTTACTTTTTACTGATTACTATTTTACTCT
Found at i:45203 original size:16 final size:17
Alignment explanation
Indices: 45182--45216 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
45172 CTGATTACCC
*
45182 TTTTACTTTTTACC-AT
1 TTTTACTCTTTACCGAT
45198 TTTTACTCTTTACCGAT
1 TTTTACTCTTTACCGAT
45215 TT
1 TT
45217 ACTGATTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.17, C:0.20, G:0.03, T:0.60
Consensus pattern (17 bp):
TTTTACTCTTTACCGAT
Found at i:45240 original size:22 final size:21
Alignment explanation
Indices: 45089--45241 Score: 89
Period size: 22 Copynumber: 6.9 Consensus size: 21
45079 CATCACTTTT
*
45089 TTACTATTTTACTCTTTACTGA
1 TTACTCTTTTACTC-TTACTGA
*
45111 TTAC-CTTCTTACTTTTTACTGA
1 TTACTCTT-TTAC-TCTTACTGA
* *
45133 TTACTATTTTGCTCTTTACTGA
1 TTACTCTTTTACTC-TTACTGA
*
45155 TTAC-CATTTTGCTCTTACTGA
1 TTACTC-TTTTACTCTTACTGA
* * **
45176 TTACCCTTTTACTTTTTACCATTT
1 TTACTCTTTTAC-TCTTA-C-TGA
45200 TTACTC-TTTAC-CGATTTACTGA
1 TTACTCTTTTACTC---TTACTGA
45222 TTACTTCTTTTACTCTTACT
1 TTAC-TCTTTTACTCTTACT
45242 CTTAATTACC
Statistics
Matches: 102, Mismatches: 14, Indels: 30
0.70 0.10 0.21
Matches are distributed among these distances:
21 19 0.19
22 56 0.55
23 12 0.12
24 14 0.14
25 1 0.01
ACGTcount: A:0.19, C:0.22, G:0.05, T:0.54
Consensus pattern (21 bp):
TTACTCTTTTACTCTTACTGA
Found at i:45251 original size:40 final size:41
Alignment explanation
Indices: 45207--45345 Score: 144
Period size: 40 Copynumber: 3.4 Consensus size: 41
45197 TTTTTACTCT
45207 TTACCGATTTACTGATTACTTCTTTTACTCTT-ACTCTTAA
1 TTACCGATTTACTGATTACTTCTTTTACTCTTGACTCTTAA
*
45247 TTACC-ATTTTACTGATTACTTCTTTTACT-TTGACTCTTTCA
1 TTACCGA-TTTACTGATTACTTCTTTTACTCTTGACTC-TTAA
* * * *
45288 TTACTGATTTCACTGATTA-ATCTCTTAC-CTTGACTCTTGA
1 TTACCGATTT-ACTGATTACTTCTTTTACTCTTGACTCTTAA
* * *
45328 TTATCAAATTACTGATTA
1 TTACCGATTTACTGATTA
45346 ATCCATTTTT
Statistics
Matches: 84, Mismatches: 9, Indels: 13
0.79 0.08 0.12
Matches are distributed among these distances:
39 11 0.13
40 40 0.48
41 24 0.29
42 9 0.11
ACGTcount: A:0.24, C:0.21, G:0.06, T:0.49
Consensus pattern (41 bp):
TTACCGATTTACTGATTACTTCTTTTACTCTTGACTCTTAA
Found at i:46194 original size:2 final size:2
Alignment explanation
Indices: 46187--46215 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
46177 ACTTACTTAG
46187 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
46216 CCTAAAATCT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:50912 original size:39 final size:41
Alignment explanation
Indices: 50852--50965 Score: 126
Period size: 39 Copynumber: 2.8 Consensus size: 41
50842 AGAAGAAAAT
* * *
50852 TGCCCTTGTGTTATATGTGTTTAGGGACTTTAGTA-TAG-G
1 TGCCCCTGTGTTATATGTGTTTAGGGACTTTAGAAGGAGAG
* * * *
50891 TGCCTCTGTGTTATATGTGTTTAAGGACATTAGAAGGAGAAT
1 TGCCCCTGTGTTATATGTGTTTAGGGACTTTAGAAGGAG-AG
50933 TGCCCCTGTGTTATATGTGTTT-GGGAACTTTAG
1 TGCCCCTGTGTTATATGTGTTTAGGG-ACTTTAG
50966 GGAGAATTTA
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
39 30 0.49
40 2 0.03
41 2 0.03
42 27 0.44
ACGTcount: A:0.21, C:0.11, G:0.27, T:0.40
Consensus pattern (41 bp):
TGCCCCTGTGTTATATGTGTTTAGGGACTTTAGAAGGAGAG
Found at i:60320 original size:54 final size:54
Alignment explanation
Indices: 60239--61062 Score: 1066
Period size: 54 Copynumber: 15.2 Consensus size: 54
60229 TTAGCCAAGT
* * *
60239 TTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTACAGTGGTTTAAGTTCATC
1 TTCAAGTGATCCAGTGCAGTCAATCAAGAAAGTTTCCAGTGGTTTAAGTTTATC
* *
60293 TTCAAGTGATCCAGTGCAGTCAGTCAAGAAAGTTTACAGTGGTTTAAGTTTATC
1 TTCAAGTGATCCAGTGCAGTCAATCAAGAAAGTTTCCAGTGGTTTAAGTTTATC
*
60347 TTCAAGTGATCCAGTGCAGTCAATCAAGAAAG--TCCAGTGGTATTAAGTTCATC
1 TTCAAGTGATCCAGTGCAGTCAATCAAGAAAGTTTCCAGTGGT-TTAAGTTTATC
* **
60400 TTCAAGTGATCCAGTGCAGTCAGTCAA-AAAGTTTAAAGTGGTTTAAGTTTATC
1 TTCAAGTGATCCAGTGCAGTCAATCAAGAAAGTTTCCAGTGGTTTAAGTTTATC
*
60453 TTCAAGTGATCCAGTGCAGTCAATCAAGAAAGTTTCCAGTGGTATTAAGTTCATC
1 TTCAAGTGATCCAGTGCAGTCAATCAAGAAAGTTTCCAGTGGT-TTAAGTTTATC
* *
60508 TTCAAGTGATCCAGTACAGTCAGTCAAGAAAGTTTCCAGTGGTTTAAGTTTATC
1 TTCAAGTGATCCAGTGCAGTCAATCAAGAAAGTTTCCAGTGGTTTAAGTTTATC
*
60562 TTCAAGTGATCCAGTGCAGTCAATCAAGAAAGTTTCCAGTGGTATTAAGTTCATC
1 TTCAAGTGATCCAGTGCAGTCAATCAAGAAAGTTTCCAGTGGT-TTAAGTTTATC
* *
60617 TTCAAGTGATCCAGTGCAGTCAGTCAAGAAAGTTTCCAGTGGTTTAAGTTCATC
1 TTCAAGTGATCCAGTGCAGTCAATCAAGAAAGTTTCCAGTGGTTTAAGTTTATC
*
60671 TTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAGTGGTATTAAGTTTATC
1 TTCAAGTGATCCAGTGCAGTCAATCAAGAAAGTTTCCAGTGGT-TTAAGTTTATC
* * * *
60726 TTCAAATGAT-CATGTGCGGT-AAGTCAAGAAAGTTTACAGTTGTTTAAGTTTATC
1 TTCAAGTGATCCA-GTGCAGTCAA-TCAAGAAAGTTTCCAGTGGTTTAAGTTTATC
* * * *
60780 TTCAAGTGATCCATTGCAGTCAATCATGAAACTATT-TAGTGGTATTAAGTTTATC
1 TTCAAGTGATCCAGTGCAGTCAATCAAGAAAGT-TTCCAGTGGT-TTAAGTTTATC
* * * *
60835 TTCAAGTGATCCAGTGCGGTCAATAAAGAAAGTTTCCTGTGGTTTAAGTTTGTC
1 TTCAAGTGATCCAGTGCAGTCAATCAAGAAAGTTTCCAGTGGTTTAAGTTTATC
* * *
60889 TTCAAGTGATCCAGTGCGGTCAATAAAGAAAGTTTCCAGTGGTTTAGGTTTATC
1 TTCAAGTGATCCAGTGCAGTCAATCAAGAAAGTTTCCAGTGGTTTAAGTTTATC
* * * * * * * * *
60943 ATCGAGTGATCCAATACGGTCAATCAAGAAAGTCTCAAGTGGTAATAATTTTATC
1 TTCAAGTGATCCAGTGCAGTCAATCAAGAAAGTTTCCAGTGGT-TTAAGTTTATC
* * ** * * * **
60998 TTTAAGTGAACCAGTGTGGTCAATCAAGGAAGTTTTCAGTGATTTGGGGTTTATC
1 TTCAAGTGATCCAGTGCAGTCAATCAAGAAAGTTTCCAGTGGTTT-AAGTTTATC
*
61053 TTTAAGTGAT
1 TTCAAGTGAT
61063 TCGGTAAATT
Statistics
Matches: 682, Mismatches: 72, Indels: 31
0.87 0.09 0.04
Matches are distributed among these distances:
52 12 0.02
53 72 0.11
54 347 0.51
55 251 0.37
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.33
Consensus pattern (54 bp):
TTCAAGTGATCCAGTGCAGTCAATCAAGAAAGTTTCCAGTGGTTTAAGTTTATC
Found at i:60587 original size:109 final size:109
Alignment explanation
Indices: 60239--61038 Score: 1128
Period size: 109 Copynumber: 7.4 Consensus size: 109
60229 TTAGCCAAGT
* *
60239 TTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTACAGTGGT-TTAAGTTCATCTTCAAGTGAT
1 TTCAAGTGATCCAGTGCAGTCAATCAAGAAAGTTTCCAGTGGTATTAAGTTCATCTTCAAGTGAT
*
60303 CCAGTGCAGTCAGTCAAGAAAGTTTACAGTGGTTTAAGTTTATC
66 CCAGTGCAGTCAGTCAAGAAAGTTTCCAGTGGTTTAAGTTTATC
60347 TTCAAGTGATCCAGTGCAGTCAATCAAGAAAG--TCCAGTGGTATTAAGTTCATCTTCAAGTGAT
1 TTCAAGTGATCCAGTGCAGTCAATCAAGAAAGTTTCCAGTGGTATTAAGTTCATCTTCAAGTGAT
**
60410 CCAGTGCAGTCAGTCAA-AAAGTTTAAAGTGGTTTAAGTTTATC
66 CCAGTGCAGTCAGTCAAGAAAGTTTCCAGTGGTTTAAGTTTATC
60453 TTCAAGTGATCCAGTGCAGTCAATCAAGAAAGTTTCCAGTGGTATTAAGTTCATCTTCAAGTGAT
1 TTCAAGTGATCCAGTGCAGTCAATCAAGAAAGTTTCCAGTGGTATTAAGTTCATCTTCAAGTGAT
*
60518 CCAGTACAGTCAGTCAAGAAAGTTTCCAGTGGTTTAAGTTTATC
66 CCAGTGCAGTCAGTCAAGAAAGTTTCCAGTGGTTTAAGTTTATC
60562 TTCAAGTGATCCAGTGCAGTCAATCAAGAAAGTTTCCAGTGGTATTAAGTTCATCTTCAAGTGAT
1 TTCAAGTGATCCAGTGCAGTCAATCAAGAAAGTTTCCAGTGGTATTAAGTTCATCTTCAAGTGAT
*
60627 CCAGTGCAGTCAGTCAAGAAAGTTTCCAGTGGTTTAAGTTCATC
66 CCAGTGCAGTCAGTCAAGAAAGTTTCCAGTGGTTTAAGTTTATC
* * *
60671 TTCAAGTGATCCAGTGCGGTCAATCAAGAAAGTTTCCAGTGGTATTAAGTTTATCTTCAAATGAT
1 TTCAAGTGATCCAGTGCAGTCAATCAAGAAAGTTTCCAGTGGTATTAAGTTCATCTTCAAGTGAT
* * * *
60736 -CATGTGCGGTAAGTCAAGAAAGTTTACAGTTGTTTAAGTTTATC
66 CCA-GTGCAGTCAGTCAAGAAAGTTTCCAGTGGTTTAAGTTTATC
* * * * *
60780 TTCAAGTGATCCATTGCAGTCAATCATGAAACTATT-TAGTGGTATTAAGTTTATCTTCAAGTGA
1 TTCAAGTGATCCAGTGCAGTCAATCAAGAAAGT-TTCCAGTGGTATTAAGTTCATCTTCAAGTGA
* * * * *
60844 TCCAGTGCGGTCAATAAAGAAAGTTTCCTGTGGTTTAAGTTTGTC
65 TCCAGTGCAGTCAGTCAAGAAAGTTTCCAGTGGTTTAAGTTTATC
* * * * * *
60889 TTCAAGTGATCCAGTGCGGTCAATAAAGAAAGTTTCCAGTGGT-TTAGGTTTATCATCGAGTGAT
1 TTCAAGTGATCCAGTGCAGTCAATCAAGAAAGTTTCCAGTGGTATTAAGTTCATCTTCAAGTGAT
* * * * * * * *
60953 CCAATACGGTCAATCAAGAAAGTCTCAAGTGGTAATAATTTTATC
66 CCAGTGCAGTCAGTCAAGAAAGTTTCCAGTGGT-TTAAGTTTATC
* * ** * *
60998 TTTAAGTGAACCAGTGTGGTCAATCAAGGAAGTTTTCAGTG
1 TTCAAGTGATCCAGTGCAGTCAATCAAGAAAGTTTCCAGTG
61039 ATTTGGGGTT
Statistics
Matches: 630, Mismatches: 53, Indels: 17
0.90 0.08 0.02
Matches are distributed among these distances:
106 65 0.10
107 38 0.06
108 127 0.20
109 396 0.63
110 4 0.01
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (109 bp):
TTCAAGTGATCCAGTGCAGTCAATCAAGAAAGTTTCCAGTGGTATTAAGTTCATCTTCAAGTGAT
CCAGTGCAGTCAGTCAAGAAAGTTTCCAGTGGTTTAAGTTTATC
Found at i:60685 original size:29 final size:29
Alignment explanation
Indices: 60596--60686 Score: 73
Period size: 25 Copynumber: 3.2 Consensus size: 29
60586 CAAGAAAGTT
60596 TCCAGTGGTATTAAGTTCATCTTCAAGTGA
1 TCCAGTGGT-TTAAGTTCATCTTCAAGTGA
*** * *** *
60626 TCCAGTGCAGTCAG-TCA--AGAAAGT-T
1 TCCAGTGGTTTAAGTTCATCTTCAAGTGA
60651 TCCAGTGGTTTAAGTTCATCTTCAAGTGA
1 TCCAGTGGTTTAAGTTCATCTTCAAGTGA
60680 TCCAGTG
1 TCCAGTG
60687 CGGTCAATCA
Statistics
Matches: 41, Mismatches: 16, Indels: 9
0.62 0.24 0.14
Matches are distributed among these distances:
25 10 0.24
26 7 0.17
28 7 0.17
29 10 0.24
30 7 0.17
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (29 bp):
TCCAGTGGTTTAAGTTCATCTTCAAGTGA
Found at i:61162 original size:39 final size:40
Alignment explanation
Indices: 61073--61219 Score: 133
Period size: 39 Copynumber: 3.7 Consensus size: 40
61063 TCGGTAAATT
* *
61073 AGATGACTCGGTGAAGCATC-TTCAAAGTTGGATTCGGTGAATC
1 AGATGACTCGGTGCAGCATCTTTCAAA----GATTCGGTGAACC
* *
61116 AGATGACTCGGTGCATCATC-TTCATAGATTCGGTGAACC
1 AGATGACTCGGTGCAGCATCTTTCAAAGATTCGGTGAACC
* * **
61155 AGGTGACTCGGTGTAGCATCTTTCAAAGATT-GGT--TTC
1 AGATGACTCGGTGCAGCATCTTTCAAAGATTCGGTGAACC
* *
61192 AGATGACTCGGCGTAGCATCTTTCAAAG
1 AGATGACTCGGTGCAGCATCTTTCAAAG
61220 TTGCTTTCAG
Statistics
Matches: 91, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
37 27 0.30
39 32 0.35
40 9 0.10
43 23 0.25
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.29
Consensus pattern (40 bp):
AGATGACTCGGTGCAGCATCTTTCAAAGATTCGGTGAACC
Found at i:61235 original size:36 final size:35
Alignment explanation
Indices: 61158--61563 Score: 478
Period size: 35 Copynumber: 11.4 Consensus size: 35
61148 GTGAACCAGG
*
61158 TGACTCGGTGTAGCATCTTTCAAAGATTGGTTTCAGA
1 TGACTCGGTGTAGCATC-TTCAAAG-TTGGATTCAGA
* **
61195 TGACTCGGCGTAGCATCTTTCAAAGTTGCTTTCAGA
1 TGACTCGGTGTAGCATC-TTCAAAGTTGGATTCAGA
* *
61231 TGACTCGGTATAGCATCTTTCAAAATTGGATTCAGA
1 TGACTCGGTGTAGCATC-TTCAAAGTTGGATTCAGA
*
61267 TGATTCGGTGTAGCATCTTCAAAAGTTGGATTCAGA
1 TGACTCGGTGTAGCATCTTC-AAAGTTGGATTCAGA
**
61303 TGACTCGGTGTAATATCTTTCAAAGTTGGATTCAGA
1 TGACTCGGTGTAGCATC-TTCAAAGTTGGATTCAGA
* *
61339 TGACTCGGTGTAGCATCTTCAAAATTGGATTCGGA
1 TGACTCGGTGTAGCATCTTCAAAGTTGGATTCAGA
* *
61374 TGACTCGGTGTAGCATCTTCAAAATTGGATTCGGA
1 TGACTCGGTGTAGCATCTTCAAAGTTGGATTCAGA
* *
61409 TGACTCGGTGTAGCGTCTTCAAAGTTGGATTTAGA
1 TGACTCGGTGTAGCATCTTCAAAGTTGGATTCAGA
** *
61444 TGACTCGGTGTATAATCTTCAAAGTTGGGA-TAAGA
1 TGACTCGGTGTAGCATCTTCAAAGTT-GGATTCAGA
* * *
61479 TGACTCGGTGAAGCATCTTCAGAA--TGGAATAAGA
1 TGACTCGGTGTAGCATCTTCA-AAGTTGGATTCAGA
* * *
61513 TGACTCGGTGTAGTATCTTTAAAGTTGGAATTC-GG
1 TGACTCGGTGTAGCATCTTCAAAGTTGG-ATTCAGA
61548 TGAGCTCGGTGTAGCA
1 TGA-CTCGGTGTAGCA
61564 CATTTTCAAA
Statistics
Matches: 325, Mismatches: 35, Indels: 19
0.86 0.09 0.05
Matches are distributed among these distances:
33 5 0.02
34 24 0.07
35 137 0.42
36 132 0.41
37 27 0.08
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.33
Consensus pattern (35 bp):
TGACTCGGTGTAGCATCTTCAAAGTTGGATTCAGA
Found at i:61669 original size:89 final size:90
Alignment explanation
Indices: 61528--62445 Score: 892
Period size: 89 Copynumber: 10.2 Consensus size: 90
61518 CGGTGTAGTA
* * * * *
61528 TCTTTAAAG-TTGGAATTCGGTGAGCTCGGTGTAGCACATTTTCAAATAGATCATGGTGATTCAG
1 TCTTCAAAGATTGGAATTCAGTGAGCTCGGTGCAGCACATTTTCAAACAGATCATGGTGATTCGG
61592 TGAATCAAGTTAATGCGGTGC-ATT
66 TGAATCAAGTTAATGCGGTGCTATT
* * * * *
61616 TCTTCAAAGATTGGAAATCTGTGAGGTCGGTGCAGCACATTTTCAAATAGATCATGGTGATTCAG
1 TCTTCAAAGATTGGAATTCAGTGAGCTCGGTGCAGCACATTTTCAAACAGATCATGGTGATTCGG
*
61681 TGAATCAAGTTAATGCAGTGC-ATT
66 TGAATCAAGTTAATGCGGTGCTATT
* * *
61705 TCTTTAAAGATTGGAAATCAGTGAGCTCGGTGCAGCACATTTTCAAATAGATCATGGTGATTCGG
1 TCTTCAAAGATTGGAATTCAGTGAGCTCGGTGCAGCACATTTTCAAACAGATCATGGTGATTCGG
61770 TGAATCAAGTTAATGCGGTGC-ATT
66 TGAATCAAGTTAATGCGGTGCTATT
* *
61794 TCTTCAAAGATTGGAATTCAGTGAGCTCGGTGCAGCATATTTTCAAACA-ATTCA-GGATTATTC
1 TCTTCAAAGATTGGAATTCAGTGAGCTCGGTGCAGCACATTTTCAAACAGA-TCATGG-TGATTC
* *
61857 GGTGAATCAATTTAAAGCGGTGCATTATT
64 GGTGAATCAAGTTAATGCGGTGC--TATT
* * * *
61886 TCTTCAAAGA-TGGAATTCGGTGAGCTCGGTGCAGCATATTCTCAAACAGTTCA-GGATGATTCG
1 TCTTCAAAGATTGGAATTCAGTGAGCTCGGTGCAGCACATTTTCAAACAGATCATGG-TGATTCG
61949 GTGAATCAAGTTAATGCGGTGCATTATT
65 GTGAATCAAGTTAATGCGGTGC--TATT
* * * * * *
61977 TCTTCAAA-ATTGG-ATTCAGTGAGCTGGGTGCAGTAGATTTTCAAACAG-TGCAAGATCATTCG
1 TCTTCAAAGATTGGAATTCAGTGAGCTCGGTGCAGCACATTTTCAAACAGAT-CATGGTGATTCG
* ***
62039 GTGAATCCAGTTGGGGCGGTGCCTTATT
65 GTGAATCAAGTTAATGCGGTG-C-TATT
* ** * *
62067 TCTTCAAAGATTGG-ATTCGGTGAGCTCGGTGCAGCACATTTTCAAATTGTTC-GGGATGATTCG
1 TCTTCAAAGATTGGAATTCAGTGAGCTCGGTGCAGCACATTTTCAAACAGATCATGG-TGATTCG
** *
62130 GTGAATCAAGTT-GGGCGGTGCCTTACT
65 GTGAATCAAGTTAATGCGGTG-C-TATT
* ** * * * * *
62157 TATTCAAAG-TCAG-ATTCAGTGAGCTCGGTGCAGCAGATTTTCAAACAGTTCAAGTTCATTCGG
1 TCTTCAAAGATTGGAATTCAGTGAGCTCGGTGCAGCACATTTTCAAACAGATCATGGTGATTCGG
***
62220 TGAATCAAG-TGGGGCGGTGCCTTATT
66 TGAATCAAGTTAATGCGGTG-C-TATT
* * * * *
62246 TCTTCAAAGATT-GTATTCGGTGAGCTCGGTACAGCATATTTTCAAACAGTTCA-GGATGATTCG
1 TCTTCAAAGATTGGAATTCAGTGAGCTCGGTGCAGCACATTTTCAAACAGATCATGG-TGATTCG
* *
62309 GTGAATCAAGTTGAGGCGGTGCCTTATT
65 GTGAATCAAGTTAATGCGGTG-C-TATT
* * * * * *
62337 TCTTC-GAGATCGAAATTCAGTGAGCTCGGTGCAGCACATTTTCAAATAGATTATGAG-GATTCA
1 TCTTCAAAGATTGGAATTCAGTGAGCTCGGTGCAGCACATTTTCAAACAGATCATG-GTGATTCG
**
62400 GTGAATCAAGTGGATGCGGTGCATTATT
65 GTGAATCAAGTTAATGCGGTGC--TATT
62428 TCTTCAAAG-TTGG-ATTCA
1 TCTTCAAAGATTGGAATTCA
62446 TTTTTGATTC
Statistics
Matches: 724, Mismatches: 81, Indels: 48
0.85 0.09 0.06
Matches are distributed among these distances:
88 12 0.02
89 309 0.43
90 156 0.22
91 229 0.32
92 17 0.02
93 1 0.00
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (90 bp):
TCTTCAAAGATTGGAATTCAGTGAGCTCGGTGCAGCACATTTTCAAACAGATCATGGTGATTCGG
TGAATCAAGTTAATGCGGTGCTATT
Found at i:62042 original size:270 final size:271
Alignment explanation
Indices: 61528--62445 Score: 1014
Period size: 270 Copynumber: 3.4 Consensus size: 271
61518 CGGTGTAGTA
* * *
61528 TCTTTAAAG-TTGGAATTCGGTGAGCTCGGTGTAGCACATTTTCAAATAGA-TCATGG-TGATTC
1 TCTTCAAAGATTGGAATTCAGTGAGCTCGGTGCAGCACATTTTCAAATAGATTCA-GGATGATTC
* * *
61590 AGTGAATCAAGTTAATGCGGTGC---ATTTCTTCAAAGATTGGAAATCTGTGAGGTCGGTGCAGC
65 AGTGAATCAAGTTAATGCGGTGCATTATTTCTTCAAAGA-TGGAATTCAGTGAGCTCGGTGCAGC
* * * * *
61652 ACATTTTCAAATAGATCATGGTGATTCAGTGAATCAAGTTAATGCAGTGC--ATTTCTTTAAAGA
129 ACATTTTCAAACAGTTCA-GGTGATTCGGTGAATCAAGTTAATGCGGTGCTTATTTCTTCAAAGA
* * * *
61715 TTGGAAATCAGTGAGCTCGGTGCAGCACATTTTCAAATAGATCATGGTGATTCGGTGAATCAAGT
193 TTGG-ATTCAGTGAGCTCGGTGCAGCACATTTTCAAACAG-TCAAGATGATTCGGTGAATCAAGT
* *
61780 TAATGCGGTG-C-ATT
256 TGAGGCGGTGCCTATT
* * * *
61794 TCTTCAAAGATTGGAATTCAGTGAGCTCGGTGCAGCATATTTTCAAACA-ATTCAGGATTATTCG
1 TCTTCAAAGATTGGAATTCAGTGAGCTCGGTGCAGCACATTTTCAAATAGATTCAGGATGATTCA
* * * *
61858 GTGAATCAATTTAAAGCGGTGCATTATTTCTTCAAAGATGGAATTCGGTGAGCTCGGTGCAGCAT
66 GTGAATCAAGTTAATGCGGTGCATTATTTCTTCAAAGATGGAATTCAGTGAGCTCGGTGCAGCAC
*
61923 ATTCTCAAACAGTTCAGGATGATTCGGTGAATCAAGTTAATGCGGTGCATTATTTCTTCAAA-AT
131 ATTTTCAAACAGTTCAGG-TGATTCGGTGAATCAAGTTAATGCGGTGC-TTATTTCTTCAAAGAT
* * * * *
61987 TGGATTCAGTGAGCTGGGTGCAGTAGATTTTCAAACAGTGCAAGATCATTCGGTGAATCCAGTTG
194 TGGATTCAGTGAGCTCGGTGCAGCACATTTTCAAACAGT-CAAGATGATTCGGTGAATCAAGTTG
*
62052 GGGCGGTGCCTTATT
258 AGGCGGTGCC-TATT
* * * *
62067 TCTTCAAAGATTGG-ATTCGGTGAGCTCGGTGCAGCACATTTTCAAATTG-TTCGGGATGATTCG
1 TCTTCAAAGATTGGAATTCAGTGAGCTCGGTGCAGCACATTTTCAAATAGATTCAGGATGATTCA
** * * * *
62130 GTGAATCAAGTT-GGGCGGTGCCTTACTTATTCAAAG-T-CAGATTCAGTGAGCTCGGTGCAGCA
66 GTGAATCAAGTTAATGCGGTGCATTATTTCTTCAAAGATGGA-ATTCAGTGAGCTCGGTGCAGCA
* * * ***
62192 GATTTTCAAACAGTTCAAGTTCATTCGGTGAATCAAG-TGGGGCGGTGCCTTATTTCTTCAAAGA
130 CATTTTCAAACAGTTC-AGGTGATTCGGTGAATCAAGTTAATGCGGTG-CTTATTTCTTCAAAGA
* * * * *
62256 TTGTATTCGGTGAGCTCGGTACAGCATATTTTCAAACAGTTCAGGATGATTCGGTGAATCAAGTT
193 TTGGATTCAGTGAGCTCGGTGCAGCACATTTTCAAACAG-TCAAGATGATTCGGTGAATCAAGTT
62321 GAGGCGGTGCCTTATT
257 GAGGCGGTGCC-TATT
* * * * *
62337 TCTTC-GAGATCGAAATTCAGTGAGCTCGGTGCAGCACATTTTCAAATAGATT-ATGAGGATTCA
1 TCTTCAAAGATTGGAATTCAGTGAGCTCGGTGCAGCACATTTTCAAATAGATTCAGGATGATTCA
** *
62400 GTGAATCAAGTGGATGCGGTGCATTATTTCTTCAAAGTTGG-ATTCA
66 GTGAATCAAGTTAATGCGGTGCATTATTTCTTCAAAGATGGAATTCA
62446 TTTTTGATTC
Statistics
Matches: 549, Mismatches: 78, Indels: 45
0.82 0.12 0.07
Matches are distributed among these distances:
266 11 0.02
267 63 0.11
268 2 0.00
269 90 0.16
270 248 0.45
271 54 0.10
272 64 0.12
273 17 0.03
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (271 bp):
TCTTCAAAGATTGGAATTCAGTGAGCTCGGTGCAGCACATTTTCAAATAGATTCAGGATGATTCA
GTGAATCAAGTTAATGCGGTGCATTATTTCTTCAAAGATGGAATTCAGTGAGCTCGGTGCAGCAC
ATTTTCAAACAGTTCAGGTGATTCGGTGAATCAAGTTAATGCGGTGCTTATTTCTTCAAAGATTG
GATTCAGTGAGCTCGGTGCAGCACATTTTCAAACAGTCAAGATGATTCGGTGAATCAAGTTGAGG
CGGTGCCTATT
Found at i:63044 original size:5 final size:5
Alignment explanation
Indices: 63034--63062 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
63024 GGATTTGCAT
63034 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
63063 TTTGCGCTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:64970 original size:17 final size:18
Alignment explanation
Indices: 64939--64979 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
64929 ATAAAAAAAG
64939 ATTTTA-TTTACTTTTTA
1 ATTTTAGTTTACTTTTTA
*
64956 TTTTTAGTTTA-TTTTTA
1 ATTTTAGTTTACTTTTTA
64973 ATTTTAG
1 ATTTTAG
64980 AAATTAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71
Consensus pattern (18 bp):
ATTTTAGTTTACTTTTTA
Found at i:67640 original size:67 final size:67
Alignment explanation
Indices: 67528--68245 Score: 1022
Period size: 67 Copynumber: 10.8 Consensus size: 67
67518 TTAATTTACG
*
67528 AAAA-TACCCTTTCGGTGGAAGGGTCATTTTCGTCTTTTGCATTTAAGTTTAGTATTTTCTTTTC
1 AAAAGTACCCTTTCGGTGGAAGGGTCATTTTCGTCTTTCGCATTTAAGTTTAGTATTTTCTTTTC
67592 CC
66 CC
67594 AAAAGTACCCTTTCGGTGGAAGGGTCATTTTCGTCTTTCGCATTTAAGTTTAGTATTTTCTTTTC
1 AAAAGTACCCTTTCGGTGGAAGGGTCATTTTCGTCTTTCGCATTTAAGTTTAGTATTTTCTTTTC
67659 CC
66 CC
* * *
67661 AAAAGTACCCTTTCGGTGGAAGGGTCGTTTTCGTCTTTCGCATTTAATTTTAGTATTATCTTTTC
1 AAAAGTACCCTTTCGGTGGAAGGGTCATTTTCGTCTTTCGCATTTAAGTTTAGTATTTTCTTTTC
*
67726 CA
66 CC
*
67728 AAAAGTACCCTTTCGGTGGAAGGGTCATTTTTGTCTTTCGCATTTAAGTTTAGTATTTTCTTTTC
1 AAAAGTACCCTTTCGGTGGAAGGGTCATTTTCGTCTTTCGCATTTAAGTTTAGTATTTTCTTTTC
67793 CC
66 CC
*
67795 AAAAGTACCCTTTCGGTGGAAGGGTCATTTTCGTCTTTCGCATTTAAGTTTAGTATTATCTTTTC
1 AAAAGTACCCTTTCGGTGGAAGGGTCATTTTCGTCTTTCGCATTTAAGTTTAGTATTTTCTTTTC
67860 CC
66 CC
* * *
67862 AAAATTACCCTTTCAGTGGAAGGGTCATTTTCATCTTTCGCATTTAAGTTTAGTATTTTCTTTTC
1 AAAAGTACCCTTTCGGTGGAAGGGTCATTTTCGTCTTTCGCATTTAAGTTTAGTATTTTCTTTTC
67927 CC
66 CC
67929 AAAAGTACCCTTTCGGTGGAAGGGTCATTTTCGTCTTTCGCATTTAAGTTTAGTATTTTCTTTTC
1 AAAAGTACCCTTTCGGTGGAAGGGTCATTTTCGTCTTTCGCATTTAAGTTTAGTATTTTCTTTTC
67994 CC
66 CC
* * *
67996 AAAAGTACCCTTTTGGTGGAAGGGTCATTTTCGTCTTTCACATTTAAGTTTAGTATCTTC-TTT-
1 AAAAGTACCCTTTCGGTGGAAGGGTCATTTTCGTCTTTCGCATTTAAGTTTAGTATTTTCTTTTC
68059 CC
66 CC
* ** * * * * ** *
68061 AAAAATACCCTTTCGGTTAAAGGGTCAATATT-GTCTTTTGCATTCAAGTTTAGCATTCCCATTT
1 AAAAGTACCCTTTCGGTGGAAGGGTC-ATTTTCGTCTTTCGCATTTAAGTTTAGTATTTTCTTTT
68125 -CC
65 CCC
** ** * * *
68127 AGGAGTACCCTTTCGGTCAAAGGGTCAGTGTT-GTCTTTTGC-TTTCAAGTTTAGTATTTTCATT
1 AAAAGTACCCTTTCGGTGGAAGGGTCA-TTTTCGTCTTTCGCATTT-AAGTTTAGTATTTTCTTT
*
68190 T-CA
64 TCCC
* * * *
68193 AAAAATACCCTTCCGGTCGAAGGGTCATTTTCGTCTTGT-GCATATAAGTTTAG
1 AAAAGTACCCTTTCGGTGGAAGGGTCATTTTCGTCTT-TCGCATTTAAGTTTAG
68246 CTTTTATTTC
Statistics
Matches: 593, Mismatches: 51, Indels: 16
0.90 0.08 0.02
Matches are distributed among these distances:
65 51 0.09
66 104 0.18
67 438 0.74
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.42
Consensus pattern (67 bp):
AAAAGTACCCTTTCGGTGGAAGGGTCATTTTCGTCTTTCGCATTTAAGTTTAGTATTTTCTTTTC
CC
Found at i:77314 original size:15 final size:15
Alignment explanation
Indices: 77294--77329 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
77284 AGATGTTACG
77294 AGCTTATCAAGTTCA
1 AGCTTATCAAGTTCA
*
77309 AGCTTATCGAGTTCA
1 AGCTTATCAAGTTCA
*
77324 AACTTA
1 AGCTTA
77330 GAACAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.33
Consensus pattern (15 bp):
AGCTTATCAAGTTCA
Found at i:82364 original size:49 final size:49
Alignment explanation
Indices: 82299--82423 Score: 150
Period size: 49 Copynumber: 2.6 Consensus size: 49
82289 ATTTCCTGCG
* *
82299 CTTTTTCTCAAATTTTACAACAAAATTGAAAC-TTTA-ATTTTCCTTGCA
1 CTTTTTCTCAATTTTTACAACAAAATTGAAACATTTACATTTT-ATTGCA
**
82347 CATTTTTCTCAATTTTTATGACAAAATTG-AACATTTACATTTTATTGCA
1 C-TTTTTCTCAATTTTTACAACAAAATTGAAACATTTACATTTTATTGCA
* *
82396 CTTTTTATCAATTTTT-GAACAAAATTGA
1 CTTTTTCTCAATTTTTACAACAAAATTGA
82424 TTGGCACGCT
Statistics
Matches: 66, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
47 9 0.14
48 18 0.27
49 34 0.52
50 5 0.08
ACGTcount: A:0.34, C:0.15, G:0.06, T:0.46
Consensus pattern (49 bp):
CTTTTTCTCAATTTTTACAACAAAATTGAAACATTTACATTTTATTGCA
Found at i:82986 original size:18 final size:18
Alignment explanation
Indices: 82963--83009 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
82953 GCACCAGGTG
*
82963 CCACACCCAGTGGCCGCA
1 CCACACCAAGTGGCCGCA
*
82981 CCACACCAAGTGGCTGCA
1 CCACACCAAGTGGCCGCA
*
82999 CCGCACCAAGT
1 CCACACCAAGT
83010 TGCCACGCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.26, C:0.45, G:0.21, T:0.09
Consensus pattern (18 bp):
CCACACCAAGTGGCCGCA
Found at i:84137 original size:18 final size:15
Alignment explanation
Indices: 84114--84205 Score: 96
Period size: 15 Copynumber: 6.1 Consensus size: 15
84104 GCCATGGAAG
*
84114 AAGATGACGGCACCA
1 AAGATGATGGCACCA
84129 AAGATGATGGCACCA
1 AAGATGATGGCACCA
* * *
84144 AAGATGGTCGCACCG
1 AAGATGATGGCACCA
* * * *
84159 AA-ATCAACGACACCG
1 AAGAT-GATGGCACCA
84174 AAGATGATGGCACCA
1 AAGATGATGGCACCA
84189 AAGATGATGGCACCA
1 AAGATGATGGCACCA
84204 AA
1 AA
84206 AGTGTTAACT
Statistics
Matches: 62, Mismatches: 13, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
14 2 0.03
15 58 0.94
16 2 0.03
ACGTcount: A:0.40, C:0.24, G:0.25, T:0.11
Consensus pattern (15 bp):
AAGATGATGGCACCA
Found at i:86912 original size:49 final size:49
Alignment explanation
Indices: 86818--86913 Score: 129
Period size: 49 Copynumber: 2.0 Consensus size: 49
86808 TTCTTGCACT
* * *
86818 TTTTCTCAATTTTTACAACAAAATTGAACCTTTAATTTTCCTTGCACCC
1 TTTTCTCAACTTTTACAACAAAATTGAACATTTAATTTTCATTGCACCC
** * *
86867 TTTTCTCAACTTTTATGACAAAATTGAACATTTACTTTTTATTGCAC
1 TTTTCTCAACTTTTACAACAAAATTGAACATTTAATTTTCATTGCAC
86914 TTTATATCAA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
49 40 1.00
ACGTcount: A:0.29, C:0.21, G:0.05, T:0.45
Consensus pattern (49 bp):
TTTTCTCAACTTTTACAACAAAATTGAACATTTAATTTTCATTGCACCC
Found at i:93085 original size:18 final size:18
Alignment explanation
Indices: 93045--93189 Score: 157
Period size: 18 Copynumber: 8.1 Consensus size: 18
93035 TGTTGAACAA
* * *
93045 GTGCGGCCAATTGGTGCG
1 GTGCGACCACTTGGTGTG
* * *
93063 ATGCGGCCAGTTGGTGTG
1 GTGCGACCACTTGGTGTG
* **
93081 GTGCGACCACTTGATAAG
1 GTGCGACCACTTGGTGTG
93099 GTGC-AGCCACTTGGTGTG
1 GTGCGA-CCACTTGGTGTG
93117 GTGCGACCACTTGGTGTG
1 GTGCGACCACTTGGTGTG
* * *
93135 GTGCGATCAATTGGGGTG
1 GTGCGACCACTTGGTGTG
*
93153 GTGCGACCACTTGGGGTG
1 GTGCGACCACTTGGTGTG
93171 GTGCGACCACTTGGTGTG
1 GTGCGACCACTTGGTGTG
93189 G
1 G
93190 CGCCATTTGC
Statistics
Matches: 107, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
17 1 0.01
18 105 0.98
19 1 0.01
ACGTcount: A:0.14, C:0.20, G:0.41, T:0.26
Consensus pattern (18 bp):
GTGCGACCACTTGGTGTG
Found at i:98412 original size:11 final size:10
Alignment explanation
Indices: 98396--98443 Score: 55
Period size: 11 Copynumber: 4.8 Consensus size: 10
98386 GAAGTTAGTG
98396 TTTGAAGATTA
1 TTTGAAGA-TA
98407 TTTGAAGATA
1 TTTGAAGATA
98417 TTTTGAAGA-A
1 -TTTGAAGATA
98427 -TTGAAGATA
1 TTTGAAGATA
*
98436 ATTGAAGA
1 TTTGAAGA
98444 ATTATTTCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
8 7 0.21
9 1 0.03
10 10 0.29
11 16 0.47
ACGTcount: A:0.42, C:0.00, G:0.21, T:0.38
Consensus pattern (10 bp):
TTTGAAGATA
Found at i:98442 original size:18 final size:19
Alignment explanation
Indices: 98408--98446 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
98398 TGAAGATTAT
*
98408 TTGAAGATATTTTGAAGAA
1 TTGAAGATATATTGAAGAA
98427 TTGAAGATA-ATTGAAGAA
1 TTGAAGATATATTGAAGAA
98445 TT
1 TT
98447 ATTTCAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.44, C:0.00, G:0.21, T:0.36
Consensus pattern (19 bp):
TTGAAGATATATTGAAGAA
Found at i:98456 original size:30 final size:30
Alignment explanation
Indices: 98397--98456 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
98387 AAGTTAGTGT
* *
98397 TTGAAGATTATTTGAAGATATTTTGAAGAA
1 TTGAAGATTAATTGAAGATATTTTCAAGAA
98427 TTGAAGA-TAATTGAAGA-ATTATTTCAAGAA
1 TTGAAGATTAATTGAAGATA-T-TTTCAAGAA
98457 GCAAAATTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
28 1 0.04
29 10 0.38
30 15 0.58
ACGTcount: A:0.43, C:0.02, G:0.18, T:0.37
Consensus pattern (30 bp):
TTGAAGATTAATTGAAGATATTTTCAAGAA
Found at i:99776 original size:6 final size:6
Alignment explanation
Indices: 99765--99795 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
99755 ATAATTGCTA
99765 TAGATT TAGATT TAGATT TAGATT TA-ATT TA
1 TAGATT TAGATT TAGATT TAGATT TAGATT TA
99796 CTTTGCTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (6 bp):
TAGATT
Found at i:100138 original size:16 final size:16
Alignment explanation
Indices: 100103--100162 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
100093 ATAAAAAAAT
*
100103 AAAAAATTTGCGTCGGAA
1 AAAAAATTTGCGT--AAA
100121 AAAAAATTTGCGTAAA
1 AAAAAATTTGCGTAAA
* *
100137 AAAAAAATTGTGTAGAA
1 AAAAAATTTGCGTA-AA
*
100154 AATAAATTT
1 AAAAAATTT
100163 AGGGTTTGCG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
16 14 0.39
17 9 0.25
18 13 0.36
ACGTcount: A:0.53, C:0.05, G:0.15, T:0.27
Consensus pattern (16 bp):
AAAAAATTTGCGTAAA
Found at i:100139 original size:17 final size:18
Alignment explanation
Indices: 100098--100145 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
100088 TAAAAATAAA
100098 AAAATAAAAAATTTGCGTC
1 AAAA-AAAAAATTTGCGTC
**
100117 GGAAAAAAAATTTGCGT-
1 AAAAAAAAAATTTGCGTC
100134 AAAAAAAAAATT
1 AAAAAAAAAATT
100146 GTGTAGAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 10 0.40
18 13 0.52
19 2 0.08
ACGTcount: A:0.58, C:0.06, G:0.12, T:0.23
Consensus pattern (18 bp):
AAAAAAAAAATTTGCGTC
Found at i:100212 original size:17 final size:17
Alignment explanation
Indices: 100180--100213 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
100170 GCGTTAATTT
* *
100180 TAAAAAAAATTGTTTTC
1 TAAAAAAAAATATTTTC
100197 TAAAAAAAAATATTTTC
1 TAAAAAAAAATATTTTC
100214 CTTTATTTTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (17 bp):
TAAAAAAAAATATTTTC
Found at i:101147 original size:15 final size:15
Alignment explanation
Indices: 101127--101167 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
101117 CCTTGCTAAG
101127 CCAGAAGATGAGCCA
1 CCAGAAGATGAGCCA
101142 CCAGAAGATGAGCCA
1 CCAGAAGATGAGCCA
*
101157 CAAGAAGATGA
1 CCAGAAGATGA
101168 ACAACTTGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.44, C:0.22, G:0.27, T:0.07
Consensus pattern (15 bp):
CCAGAAGATGAGCCA
Found at i:105357 original size:6 final size:6
Alignment explanation
Indices: 105346--105376 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
105336 ATAATTGCTA
105346 TAGATT TAGATT TAGATT TAGATT TA-ATT TA
1 TAGATT TAGATT TAGATT TAGATT TAGATT TA
105377 TTTTGCTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (6 bp):
TAGATT
Found at i:106309 original size:15 final size:15
Alignment explanation
Indices: 106289--106344 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
106279 GGTTCAAATG
106289 GGGGAGGGGTGGGGT
1 GGGGAGGGGTGGGGT
106304 GGGGAGGGGTGGGGT
1 GGGGAGGGGTGGGGT
*
106319 AGGGA-GGGTGAGGAGT
1 GGGGAGGGGTG-GG-GT
*
106335 TGGGAGGGGT
1 GGGGAGGGGT
106345 TTTAGAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
14 5 0.14
15 21 0.58
16 6 0.17
17 4 0.11
ACGTcount: A:0.12, C:0.00, G:0.73, T:0.14
Consensus pattern (15 bp):
GGGGAGGGGTGGGGT
Found at i:106960 original size:17 final size:17
Alignment explanation
Indices: 106929--106962 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
106919 GGGTGATGAC
*
106929 CACCCCTTCCTACCCCT
1 CACCCCTTCCAACCCCT
*
106946 CACCCCTTGCAACCCCT
1 CACCCCTTCCAACCCCT
106963 TCAACCAAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.62, G:0.03, T:0.21
Consensus pattern (17 bp):
CACCCCTTCCAACCCCT
Found at i:111789 original size:21 final size:21
Alignment explanation
Indices: 111764--111804 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
111754 CAATCAAGCA
111764 AATCA-AGCAATTCAAAGCATC
1 AATCATAGCAA-TCAAAGCATC
*
111785 AATCATAGTAATCAAAGCAT
1 AATCATAGCAATCAAAGCAT
111805 ATGAGTCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.49, C:0.20, G:0.10, T:0.22
Consensus pattern (21 bp):
AATCATAGCAATCAAAGCATC
Done.