Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032249.1 Gossypioides kirkii chromosome KI_07
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: 37252039
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 2100 characters in sequence are not A, C, G, or T
File 102 of 120
Found at i:29491366 original size:27 final size:27
Alignment explanation
Indices: 29491328--29491390 Score: 117
Period size: 27 Copynumber: 2.3 Consensus size: 27
29491318 GTATAAATGG
29491328 GTGGTGCCTACCTGACAGGCGGCACCA
1 GTGGTGCCTACCTGACAGGCGGCACCA
*
29491355 GTGGTGCCTACCTGTCAGGCGGCACCA
1 GTGGTGCCTACCTGACAGGCGGCACCA
29491382 GTGGTGCCT
1 GTGGTGCCT
29491391 TTCTATCAGG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.14, C:0.32, G:0.35, T:0.19
Consensus pattern (27 bp):
GTGGTGCCTACCTGACAGGCGGCACCA
Found at i:29491399 original size:27 final size:27
Alignment explanation
Indices: 29491328--29491408 Score: 110
Period size: 27 Copynumber: 3.0 Consensus size: 27
29491318 GTATAAATGG
29491328 GTGGTGCCTACCTGA-CAGGCGGCACCA
1 GTGGTGCCTACCT-ATCAGGCGGCACCA
*
29491355 GTGGTGCCTACCTGTCAGGCGGCACCA
1 GTGGTGCCTACCTATCAGGCGGCACCA
** *
29491382 GTGGTGCCTTTCTATCAGGTGGCACCA
1 GTGGTGCCTACCTATCAGGCGGCACCA
29491409 ACTCGTATTT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.16, C:0.31, G:0.32, T:0.21
Consensus pattern (27 bp):
GTGGTGCCTACCTATCAGGCGGCACCA
Found at i:29491675 original size:57 final size:55
Alignment explanation
Indices: 29491561--29491691 Score: 142
Period size: 57 Copynumber: 2.4 Consensus size: 55
29491551 AAAAATTAAA
* * *
29491561 TTAAATATTAAATAAAAATAACTCAATATTTTTAAATAAATAATATAAAAAATAT
1 TTAAATATAAAATAATAATAACTCAAGATTTTTAAATAAATAATATAAAAAATAT
** * *
29491616 TTATTTATCAAAATAATAATAATCTCCAGATTTTTACAAT-AATAATATAAGAGAA-AT
1 TTAAATAT-AAAATAATAATAA-CTCAAGATTTTTA-AATAAATAATATAA-AAAATAT
29491673 TTAAATATAAAA-AATAATA
1 TTAAATATAAAATAATAATA
29491692 CACTTTTATA
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
55 13 0.21
56 15 0.24
57 29 0.46
58 6 0.10
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.36
Consensus pattern (55 bp):
TTAAATATAAAATAATAATAACTCAAGATTTTTAAATAAATAATATAAAAAATAT
Found at i:29491796 original size:27 final size:27
Alignment explanation
Indices: 29491755--29491815 Score: 104
Period size: 27 Copynumber: 2.3 Consensus size: 27
29491745 TTTTACAAGA
29491755 GGTGCCTACCAGGTAGGCGGCACTAGT
1 GGTGCCTACCAGGTAGGCGGCACTAGT
**
29491782 GGTGCCTACTGGGTAGGCGGCACTAGT
1 GGTGCCTACCAGGTAGGCGGCACTAGT
29491809 GGTGCCT
1 GGTGCCT
29491816 TTGTCAATGC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.15, C:0.25, G:0.39, T:0.21
Consensus pattern (27 bp):
GGTGCCTACCAGGTAGGCGGCACTAGT
Found at i:29491885 original size:25 final size:25
Alignment explanation
Indices: 29491850--29491899 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
29491840 CAGATCTGTT
29491850 TAACAGCAAATTTTTGAAGAAGGAA
1 TAACAGCAAATTTTTGAAGAAGGAA
*
29491875 TAACAGTAAATTTTTGAAGAAGGAA
1 TAACAGCAAATTTTTGAAGAAGGAA
29491900 AGGAAACAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.48, C:0.06, G:0.20, T:0.26
Consensus pattern (25 bp):
TAACAGCAAATTTTTGAAGAAGGAA
Found at i:29491947 original size:26 final size:26
Alignment explanation
Indices: 29491890--29491947 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
29491880 GTAAATTTTT
* * *
29491890 GAAGAAGGAAAGGAAACAAAAGTTTT
1 GAAGAAGAAAAGGAAACAAAAGGTTA
*
29491916 GAAGAAGAAAAGGAAACAGAAGGTTA
1 GAAGAAGAAAAGGAAACAAAAGGTTA
*
29491942 GCAGAA
1 GAAGAA
29491948 AATTTTAACT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.55, C:0.05, G:0.29, T:0.10
Consensus pattern (26 bp):
GAAGAAGAAAAGGAAACAAAAGGTTA
Found at i:29494747 original size:28 final size:28
Alignment explanation
Indices: 29494694--29494751 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
29494684 CATTTTTCTG
*
29494694 TTGGAATTAATTAAATTTATGATTGAAT
1 TTGGAATTAATTAAATTTATAATTGAAT
**
29494722 TTGGAATTAATTCTATTTA-AATTTGAAT
1 TTGGAATTAATTAAATTTATAA-TTGAAT
29494750 TT
1 TT
29494752 ATTTAATAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 1 0.04
28 25 0.96
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.50
Consensus pattern (28 bp):
TTGGAATTAATTAAATTTATAATTGAAT
Found at i:29494792 original size:26 final size:26
Alignment explanation
Indices: 29494737--29494792 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
29494727 ATTAATTCTA
* *
29494737 TTTAAATTTGAATTTATTTAATAGTT
1 TTTAAATTTGAATTAATTTAATAGTG
*
29494763 TTTATATTTGAATTAATTTAATTAG-G
1 TTTAAATTTGAATTAATTTAA-TAGTG
29494789 TTTA
1 TTTA
29494793 GCAAATGACA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 23 0.88
27 3 0.12
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (26 bp):
TTTAAATTTGAATTAATTTAATAGTG
Found at i:29494869 original size:6 final size:6
Alignment explanation
Indices: 29494858--29494915 Score: 109
Period size: 6 Copynumber: 9.8 Consensus size: 6
29494848 ATATTTGCAT
29494858 ACATAA ACAT-A ACATAA ACATAA ACATAA ACATAA ACATAA ACATAA
1 ACATAA ACATAA ACATAA ACATAA ACATAA ACATAA ACATAA ACATAA
29494905 ACATAA ACATA
1 ACATAA ACATA
29494916 TTTAATGGCC
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.10
6 46 0.90
ACGTcount: A:0.66, C:0.17, G:0.00, T:0.17
Consensus pattern (6 bp):
ACATAA
Found at i:29497278 original size:13 final size:12
Alignment explanation
Indices: 29497254--29497298 Score: 56
Period size: 13 Copynumber: 3.7 Consensus size: 12
29497244 ATTACTAATG
29497254 TTTTTT-ATTTT
1 TTTTTTAATTTT
29497265 TTTCTTTAATTTT
1 TTT-TTTAATTTT
*
29497278 TTGTTTTAAATTT
1 TT-TTTTAATTTT
29497291 TTTTTTAA
1 TTTTTTAA
29497299 AATATTTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
11 3 0.10
12 9 0.30
13 17 0.57
14 1 0.03
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (12 bp):
TTTTTTAATTTT
Found at i:29497329 original size:17 final size:16
Alignment explanation
Indices: 29497296--29497328 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
29497286 AATTTTTTTT
29497296 TAAAATATTTAATATA
1 TAAAATATTTAATATA
29497312 TAAAATATTTAA-ATA
1 TAAAATATTTAATATA
29497327 TA
1 TA
29497329 TCAATTGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAAATATTTAATATA
Found at i:29498307 original size:27 final size:27
Alignment explanation
Indices: 29498294--29498355 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
29498284 CTGGTAGGTT
29498294 GGCACCACTGGTGCCGCCTACCAGACA
1 GGCACCACTGGTGCCGCCTACCAGACA
29498321 GGCACCACTGGTGCCGCCTACCAGACA
1 GGCACCACTGGTGCCGCCTACCAGACA
29498348 GGCACCAC
1 GGCACCAC
29498356 CCAAAAATAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.23, C:0.42, G:0.26, T:0.10
Consensus pattern (27 bp):
GGCACCACTGGTGCCGCCTACCAGACA
Found at i:29509344 original size:2 final size:2
Alignment explanation
Indices: 29509337--29509364 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29509327 GTCAAATTTA
29509337 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
29509365 TGTAATTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29515671 original size:16 final size:16
Alignment explanation
Indices: 29515650--29515687 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
29515640 TGATGGTCAA
*
29515650 AGGTGTTTATCGTCCC
1 AGGTGTTTATCCTCCC
*
29515666 AGGTGTTTATCCTCTC
1 AGGTGTTTATCCTCCC
29515682 AGGTGT
1 AGGTGT
29515688 GGTTTGGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.13, C:0.21, G:0.26, T:0.39
Consensus pattern (16 bp):
AGGTGTTTATCCTCCC
Found at i:29518962 original size:17 final size:18
Alignment explanation
Indices: 29518935--29518969 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
29518925 TCACATCAAC
29518935 AAATAATTTAAAAATATA
1 AAATAATTTAAAAATATA
*
29518953 AAAT-ATTTAAATATATA
1 AAATAATTTAAAAATATA
29518970 TATTTCAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (18 bp):
AAATAATTTAAAAATATA
Found at i:29527964 original size:7 final size:7
Alignment explanation
Indices: 29527952--29527986 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
29527942 AATCTCTCGT
29527952 TATTTGG
1 TATTTGG
29527959 TATTTGG
1 TATTTGG
29527966 TATTTGG
1 TATTTGG
29527973 TATTTGG
1 TATTTGG
29527980 TATTTGG
1 TATTTGG
29527987 ATAATCCCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.14, C:0.00, G:0.29, T:0.57
Consensus pattern (7 bp):
TATTTGG
Found at i:29529737 original size:16 final size:15
Alignment explanation
Indices: 29529706--29529740 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
29529696 AATAAAATTA
*
29529706 TTTTCTTTTTCTTTT
1 TTTTCTTTTTCCTTT
29529721 TTTTCTTATTTCCTTT
1 TTTTCTT-TTTCCTTT
29529737 TTTT
1 TTTT
29529741 TTCATTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTCTTTTTCCTTT
Found at i:29529738 original size:17 final size:17
Alignment explanation
Indices: 29529713--29529768 Score: 69
Period size: 17 Copynumber: 3.2 Consensus size: 17
29529703 TTATTTTCTT
29529713 TTTCTTTTTTTTC-TTA
1 TTTCTTTTTTTTCATTA
29529729 TTTCCTTTTTTTTTCATTA
1 TTT-C-TTTTTTTTCATTA
* *
29529748 TTTCTTTGTTTTCATTC
1 TTTCTTTTTTTTCATTA
29529765 TTTC
1 TTTC
29529769 ACTTTTCACT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
16 3 0.09
17 16 0.46
18 10 0.29
19 6 0.17
ACGTcount: A:0.07, C:0.16, G:0.02, T:0.75
Consensus pattern (17 bp):
TTTCTTTTTTTTCATTA
Found at i:29529759 original size:19 final size:18
Alignment explanation
Indices: 29529706--29529751 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
29529696 AATAAAATTA
29529706 TTTTCTT-TTT-C-TTTT
1 TTTTCTTATTTCCTTTTT
29529721 TTTTCTTATTTCCTTTTT
1 TTTTCTTATTTCCTTTTT
29529739 TTTTCATTATTTC
1 TTTTC-TTATTTC
29529752 TTTGTTTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 7 0.26
16 3 0.11
17 1 0.04
18 9 0.33
19 7 0.26
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTCTTATTTCCTTTTT
Found at i:29530818 original size:18 final size:19
Alignment explanation
Indices: 29530797--29530833 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
29530787 AGGAAAAAGG
29530797 AAAAAT-GAAAAAT-GAAA
1 AAAAATAGAAAAATAGAAA
29530814 AAAAATAGAAAAATAGAAA
1 AAAAATAGAAAAATAGAAA
29530833 A
1 A
29530834 TGAGATTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
18 7 0.39
19 5 0.28
ACGTcount: A:0.78, C:0.00, G:0.11, T:0.11
Consensus pattern (19 bp):
AAAAATAGAAAAATAGAAA
Found at i:29531116 original size:15 final size:18
Alignment explanation
Indices: 29531096--29531132 Score: 53
Period size: 15 Copynumber: 2.2 Consensus size: 18
29531086 CATGATACAT
29531096 TTTATT-GTTTA-AATA-
1 TTTATTAGTTTATAATAC
29531111 TTTATTAGTTTATAATAC
1 TTTATTAGTTTATAATAC
29531129 TTTA
1 TTTA
29531133 ATATGTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.32
16 5 0.26
17 4 0.21
18 4 0.21
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.59
Consensus pattern (18 bp):
TTTATTAGTTTATAATAC
Found at i:29533831 original size:2 final size:2
Alignment explanation
Indices: 29533824--29533849 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
29533814 GAGGAACTGA
29533824 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
29533850 GATAAGAAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29541474 original size:29 final size:29
Alignment explanation
Indices: 29541434--29541528 Score: 172
Period size: 29 Copynumber: 3.3 Consensus size: 29
29541424 TAATAAGGGT
**
29541434 TACACACACGAACCCAGCTTTGAAATCGT
1 TACACACACGAACCCAGCTTTGAAATCAA
29541463 TACACACACGAACCCAGCTTTGAAATCAA
1 TACACACACGAACCCAGCTTTGAAATCAA
29541492 TACACACACGAACCCAGCTTTGAAATCAA
1 TACACACACGAACCCAGCTTTGAAATCAA
29541521 TACACACA
1 TACACACA
29541529 ACCCCTGGTC
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 64 1.00
ACGTcount: A:0.40, C:0.32, G:0.11, T:0.18
Consensus pattern (29 bp):
TACACACACGAACCCAGCTTTGAAATCAA
Found at i:29541552 original size:58 final size:57
Alignment explanation
Indices: 29541434--29541573 Score: 146
Period size: 58 Copynumber: 2.5 Consensus size: 57
29541424 TAATAAGGGT
** * *
29541434 TACACACACGAACCCAGCTTTGAAATCGTTACACACACGAACCCAGCTTTGAAATCAA
1 TACACACACGAACCCAGCTTTGAAATCAATACACACAC-AACCCAGCTCTGAAATAAA
* * *
29541492 TACACACACGAACCCAGCTTTGAAATCAATACACACA-ACCCCTGGTCTG-AA-AAA
1 TACACACACGAACCCAGCTTTGAAATCAATACACACACAACCCAGCTCTGAAATAAA
* *
29541546 TA-A-ATACGAACTCAGCTTTGAAAATCAA
1 TACACACACGAACCCAGCTTTG-AAATCAA
29541574 CACAGTCCCG
Statistics
Matches: 72, Mismatches: 9, Indels: 7
0.82 0.10 0.08
Matches are distributed among these distances:
52 15 0.21
53 8 0.11
54 4 0.06
55 2 0.03
56 8 0.11
58 35 0.49
ACGTcount: A:0.41, C:0.29, G:0.11, T:0.19
Consensus pattern (57 bp):
TACACACACGAACCCAGCTTTGAAATCAATACACACACAACCCAGCTCTGAAATAAA
Found at i:29543092 original size:59 final size:58
Alignment explanation
Indices: 29543023--29543345 Score: 364
Period size: 59 Copynumber: 5.5 Consensus size: 58
29543013 CAAAACTTTA
* *
29543023 AAAAATTACCATTTTACCCTCGAAATTTCTAAAATCTCATTTTTAACCTTGATTTCACC
1 AAAAATTACCATTTTACCC-CGAAATTTCTAAAATCCCATTTTTAACCTCGATTTCACC
* * *
29543082 AAAAATTACCATTTTACCCCAAAACTTTCCAAAATCCCATTTTTAACC-CAAATTTCACC
1 AAAAATTACCATTTTACCCCGAAA-TTTCTAAAATCCCATTTTTAACCTC-GATTTCACC
* * *
29543141 TAAAATTACCATTTTACCCCCAAACTTTCAAAAATCCCATTTTTAACCTCGATTTCACC
1 AAAAATTACCATTTTACCCCGAAA-TTTCTAAAATCCCATTTTTAACCTCGATTTCACC
* * * *
29543200 AAAAATTACCGTTTTACCCTCGAACTTTCTAAAATCCCATTTTTAACCTCGATTTAACT
1 AAAAATTACCATTTTACCC-CGAAATTTCTAAAATCCCATTTTTAACCTCGATTTCACC
* * * *
29543259 AAAAATTACCGTTTTACCCCTGAACTTTCTAAAAAATCCCA-TTTTAACC-CCAGTTTCACT
1 AAAAATTACCATTTTACCCC-GAAATTTCT--AAAATCCCATTTTTAACCTCGA-TTTCACC
* * * *
29543319 GAAAATTACCGTTTTACTCCTAAATTT
1 AAAAATTACCATTTTACCCCGAAATTT
29543346 TCCCAAAATT
Statistics
Matches: 234, Mismatches: 22, Indels: 16
0.86 0.08 0.06
Matches are distributed among these distances:
58 5 0.02
59 184 0.79
60 36 0.15
61 9 0.04
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.35
Consensus pattern (58 bp):
AAAAATTACCATTTTACCCCGAAATTTCTAAAATCCCATTTTTAACCTCGATTTCACC
Found at i:29543205 original size:30 final size:29
Alignment explanation
Indices: 29543169--29543264 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 29
29543159 CCCAAACTTT
29543169 CAAAAATCCCATTTTTAACCTCGATTTCAC
1 CAAAAATCCCATTTTTAACCTCGATTT-AC
* * *
29543199 CAAAAATTACC-GTTTTACCCTCGAACTTT--
1 CAAAAA-TCCCATTTTTAACCTCG-A-TTTAC
*
29543228 CTAAAATCCCATTTTTAACCTCGATTTAAC
1 CAAAAATCCCATTTTTAACCTCGATTT-AC
*
29543258 TAAAAAT
1 CAAAAAT
29543265 TACCGTTTTA
Statistics
Matches: 50, Mismatches: 9, Indels: 14
0.68 0.12 0.19
Matches are distributed among these distances:
27 3 0.06
28 4 0.08
29 15 0.30
30 21 0.42
31 4 0.08
32 3 0.06
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.34
Consensus pattern (29 bp):
CAAAAATCCCATTTTTAACCTCGATTTAC
Found at i:29543274 original size:30 final size:29
Alignment explanation
Indices: 29543181--29543334 Score: 86
Period size: 30 Copynumber: 5.2 Consensus size: 29
29543171 AAAATCCCAT
*
29543181 TTTTAACCTCGATTTCACCAAAAATTACCG
1 TTTTAACCTCGATTT-ACTAAAAATTACCG
* * *
29543211 TTTTACCCTCGAACTTT-CT-AAAA-TCCCAT
1 TTTTAACCTCG-A-TTTACTAAAAATTACC-G
29543240 TTTTAACCTCGATTTAACTAAAAATTACCG
1 TTTTAACCTCGATTT-ACTAAAAATTACCG
* * * *
29543270 TTTT-ACCCCTGAACTTT-CTAAAAAATCCCA
1 TTTTAACCTC-G-A-TTTACTAAAAATTACCG
* *
29543300 TTTTAACC-CCAGTTTCACTGAAAATTACCG
1 TTTTAACCTCGA-TTT-ACTAAAAATTACCG
29543330 TTTTA
1 TTTTA
29543335 CTCCTAAATT
Statistics
Matches: 94, Mismatches: 17, Indels: 26
0.69 0.12 0.19
Matches are distributed among these distances:
27 3 0.03
28 8 0.09
29 20 0.21
30 49 0.52
31 8 0.09
32 6 0.06
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.36
Consensus pattern (29 bp):
TTTTAACCTCGATTTACTAAAAATTACCG
Found at i:29543407 original size:28 final size:28
Alignment explanation
Indices: 29543348--29543408 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
29543338 CTAAATTTTC
*
29543348 CCAAAATTACATTTTTTCCCCCGAGAGT
1 CCAAAATTACATTTTTGCCCCCGAGAGT
29543376 -CAAAATTACCA-TTTTGCCCCCGAGTA-T
1 CCAAAATTA-CATTTTTGCCCCCGAG-AGT
29543403 CCAAAA
1 CCAAAA
29543409 GTCTCGTCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
27 21 0.72
28 8 0.28
ACGTcount: A:0.33, C:0.30, G:0.10, T:0.28
Consensus pattern (28 bp):
CCAAAATTACATTTTTGCCCCCGAGAGT
Found at i:29544958 original size:20 final size:20
Alignment explanation
Indices: 29544927--29544973 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
29544917 TAAATTTTAT
*
29544927 TTTATATAAGTTA-ATAATGTA
1 TTTAT-TAAGTTAGAGAAT-TA
29544948 TTTATTAAGTTAGAGAATTA
1 TTTATTAAGTTAGAGAATTA
29544968 TTTATT
1 TTTATT
29544974 CTATATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (20 bp):
TTTATTAAGTTAGAGAATTA
Found at i:29551681 original size:58 final size:58
Alignment explanation
Indices: 29551605--29551724 Score: 177
Period size: 58 Copynumber: 2.1 Consensus size: 58
29551595 AAAAAGAGTT
*
29551605 GTTTATGAGTGTTATTTAAGAATAAAATTATATTTGGATTTAAAAATATTTGGATTTA
1 GTTTATGAATGTTATTTAAGAATAAAATTATATTTGGATTTAAAAATATTTGGATTTA
* * ** * *
29551663 GTTTATGAATGTTTTTTAATAATGTAATTATATTTGGGTTTAAAAATATTTGGGTTTA
1 GTTTATGAATGTTATTTAAGAATAAAATTATATTTGGATTTAAAAATATTTGGATTTA
29551721 GTTT
1 GTTT
29551725 GTTGATGGGT
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (58 bp):
GTTTATGAATGTTATTTAAGAATAAAATTATATTTGGATTTAAAAATATTTGGATTTA
Found at i:29551738 original size:58 final size:58
Alignment explanation
Indices: 29551630--29551739 Score: 159
Period size: 58 Copynumber: 1.9 Consensus size: 58
29551620 TTAAGAATAA
**
29551630 AATTATATTTGGATTTAAAAATATTTGGATTTAGTTTATGAATGTTTTTTAATAATGT
1 AATTATATTTGGATTTAAAAATATTTGGATTTAGTTTATGAATGGGTTTTAATAATGT
* * *
29551688 AATTATATTTGGGTTTAAAAATATTTGGGTTTAGTTTGTTG-ATGGGTTTTAA
1 AATTATATTTGGATTTAAAAATATTTGGATTTAGTTT-ATGAATGGGTTTTAA
29551740 ATATTAGGAG
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
58 44 0.96
59 2 0.04
ACGTcount: A:0.31, C:0.00, G:0.18, T:0.51
Consensus pattern (58 bp):
AATTATATTTGGATTTAAAAATATTTGGATTTAGTTTATGAATGGGTTTTAATAATGT
Found at i:29555661 original size:64 final size:64
Alignment explanation
Indices: 29555555--29555682 Score: 229
Period size: 64 Copynumber: 2.0 Consensus size: 64
29555545 TCATAGTGGA
*
29555555 ATACTCCATTGGCAAAGCCTTGCAAACATAGGAAATGGTTTTGAACTCCTTAATCAATTCTCAT
1 ATACTCCATTGGCAAAGCCTTGCAAACATAGGAAATGCTTTTGAACTCCTTAATCAATTCTCAT
* *
29555619 ATACTCCATTGGCAAAGCCTTGCAAACATTGGAAATGCTTTTGAACTCCTTAATCAGTTCTCAT
1 ATACTCCATTGGCAAAGCCTTGCAAACATAGGAAATGCTTTTGAACTCCTTAATCAATTCTCAT
29555683 GTGCATTATT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.32
Consensus pattern (64 bp):
ATACTCCATTGGCAAAGCCTTGCAAACATAGGAAATGCTTTTGAACTCCTTAATCAATTCTCAT
Found at i:29556176 original size:3 final size:3
Alignment explanation
Indices: 29556163--29556245 Score: 157
Period size: 3 Copynumber: 27.3 Consensus size: 3
29556153 AATTTCACTC
29556163 AGA ATGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA A-GA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
29556209 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
29556246 AGTTACAATG
Statistics
Matches: 79, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
3 76 0.96
4 3 0.04
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.01
Consensus pattern (3 bp):
AGA
Found at i:29558499 original size:16 final size:16
Alignment explanation
Indices: 29558478--29558510 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
29558468 CAACACCAGT
29558478 TAATTTCTAGCATGCG
1 TAATTTCTAGCATGCG
*
29558494 TAATTTCTATCATGCG
1 TAATTTCTAGCATGCG
29558510 T
1 T
29558511 CAATGTGGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.24, C:0.18, G:0.15, T:0.42
Consensus pattern (16 bp):
TAATTTCTAGCATGCG
Found at i:29558974 original size:70 final size:67
Alignment explanation
Indices: 29558851--29558983 Score: 194
Period size: 70 Copynumber: 1.9 Consensus size: 67
29558841 ATAAACAATA
* * * *
29558851 TAATGGTTTTGTCTTTTAACTTAATGGGTAAACATTTATCAAAATGACATAATTTTACCTTTTAA
1 TAATGATTTTGACTTTTAACTTAAAGGGTAAACATTTATCAAAACGACATAATTTTACCTTTTAA
29558916 CT
66 CT
*
29558918 TAATGATTTTGACTTTTAACTTTAGAAAGGGTAAACATTTATCAAAACGACGTAATTTTACCTTT
1 TAATGATTTTGACTTTTAAC-TT--AAAGGGTAAACATTTATCAAAACGACATAATTTTACCTTT
29558983 T
63 T
29558984 TTTATTTGGA
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
67 18 0.31
68 2 0.03
70 38 0.66
ACGTcount: A:0.34, C:0.12, G:0.11, T:0.43
Consensus pattern (67 bp):
TAATGATTTTGACTTTTAACTTAAAGGGTAAACATTTATCAAAACGACATAATTTTACCTTTTAA
CT
Found at i:29559086 original size:9 final size:9
Alignment explanation
Indices: 29559068--29559098 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
29559058 CGAGTTGATC
29559068 CAAATAACT
1 CAAATAACT
*
29559077 CAATTAACT
1 CAAATAACT
29559086 CAAATAACT
1 CAAATAACT
29559095 CAAA
1 CAAA
29559099 CTATTTGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.55, C:0.23, G:0.00, T:0.23
Consensus pattern (9 bp):
CAAATAACT
Found at i:29589110 original size:26 final size:27
Alignment explanation
Indices: 29589070--29589124 Score: 85
Period size: 26 Copynumber: 2.1 Consensus size: 27
29589060 TTAGTTTTTT
*
29589070 TAATTATTTATATTTTATATAATGTTA
1 TAATTATTTATATTTTATATAATGATA
*
29589097 TAATT-TTTTTATTTTATATAATGATA
1 TAATTATTTATATTTTATATAATGATA
29589123 TA
1 TA
29589125 TTAAAAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 21 0.81
27 5 0.19
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (27 bp):
TAATTATTTATATTTTATATAATGATA
Found at i:29590044 original size:24 final size:25
Alignment explanation
Indices: 29589999--29590045 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
29589989 CATTTTGCAT
*
29589999 TTTTTTGTGTTGTTGTTGGTGTGAA
1 TTTTTTGTGTTGTTGTAGGTGTGAA
29590024 TTTTTTG-GTTGTTG-AGAGTGTG
1 TTTTTTGTGTTGTTGTAG-GTGTG
29590046 GTGAGGATGC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 1 0.05
24 12 0.60
25 7 0.35
ACGTcount: A:0.09, C:0.00, G:0.34, T:0.57
Consensus pattern (25 bp):
TTTTTTGTGTTGTTGTAGGTGTGAA
Found at i:29591090 original size:11 final size:11
Alignment explanation
Indices: 29591070--29591144 Score: 62
Period size: 11 Copynumber: 6.5 Consensus size: 11
29591060 AAGCCTCTCA
*
29591070 TCTTTCCTTTC
1 TCTTTTCTTTC
*
29591081 TCTTTTCTTTT
1 TCTTTTCTTTC
*
29591092 TCTCATTCATTTC
1 TCT-TTTC-TTTC
29591105 T-TATTTCTTTC
1 TCT-TTTCTTTC
29591116 TCTTTTCTTTTC
1 TCTTTTC-TTTC
* *
29591128 TATTTTCTTCC
1 TCTTTTCTTTC
29591139 TCTTTT
1 TCTTTT
29591145 AATCACACTT
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
11 29 0.57
12 18 0.35
13 4 0.08
ACGTcount: A:0.05, C:0.25, G:0.00, T:0.69
Consensus pattern (11 bp):
TCTTTTCTTTC
Found at i:29591131 original size:22 final size:22
Alignment explanation
Indices: 29591077--29591141 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
29591067 TCATCTTTCC
*
29591077 TTTCTCTTTTCTTTTTCTCATTCA
1 TTTCT-TTTTCTTTCTCTC-TTCA
* *
29591101 TTTCTTATTTCTTTCTCTTTTCT
1 TTTCTT-TTTCTTTCTCTCTTCA
*
29591124 TTTCTATTTTCTTCCTCT
1 TTTCT-TTTTCTTTCTCT
29591142 TTTAATCACA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
23 19 0.54
24 16 0.46
ACGTcount: A:0.06, C:0.25, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTCTTTTTCTTTCTCTCTTCA
Found at i:29591540 original size:22 final size:20
Alignment explanation
Indices: 29591515--29591579 Score: 51
Period size: 21 Copynumber: 3.0 Consensus size: 20
29591505 ACCCATTAAG
29591515 CCCAAATCCTATTTAAACAAAA
1 CCCAAAT-CTATTTAAAC-AAA
* *
29591537 CCCACATTTATTTAAATCAAA
1 CCCAAATCTATTTAAA-CAAA
*
29591558 TCCAAAT-TCATTTAAACCAAA
1 CCCAAATCT-ATTTAAA-CAAA
29591579 C
1 C
29591580 TCATTTGAAC
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
20 1 0.03
21 27 0.77
22 7 0.20
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28
Consensus pattern (20 bp):
CCCAAATCTATTTAAACAAA
Found at i:29591548 original size:21 final size:20
Alignment explanation
Indices: 29591524--29591579 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
29591514 GCCCAAATCC
*
29591524 TATTTAAACAAAACCCACATT
1 TATTTAAAC-AAACCCAAATT
*
29591545 TATTTAAATCAAATCCAAATT
1 TATTTAAA-CAAACCCAAATT
*
29591566 CATTTAAACCAAAC
1 TATTTAAA-CAAAC
29591580 TCATTTGAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
21 28 0.97
22 1 0.03
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.30
Consensus pattern (20 bp):
TATTTAAACAAACCCAAATT
Found at i:29591583 original size:15 final size:15
Alignment explanation
Indices: 29591559--29591594 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
29591549 TAAATCAAAT
*
29591559 CCAAATTCATTTAAA
1 CCAAACTCATTTAAA
*
29591574 CCAAACTCATTTGAA
1 CCAAACTCATTTAAA
29591589 CCAAAC
1 CCAAAC
29591595 CAAATGAACC
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:0.44, C:0.28, G:0.03, T:0.25
Consensus pattern (15 bp):
CCAAACTCATTTAAA
Found at i:29591645 original size:10 final size:10
Alignment explanation
Indices: 29591632--29591690 Score: 55
Period size: 10 Copynumber: 5.7 Consensus size: 10
29591622 AGTCAAACCA
29591632 TTGACCGACG
1 TTGACCGACG
* *
29591642 TTGATCGGCG
1 TTGACCGACG
29591652 TTGACCGACCG
1 TTGACCGA-CG
*
29591663 TTGACCGATG
1 TTGACCGACG
**
29591673 TTGATTGACCG
1 TTGACCGA-CG
29591684 TTGACCG
1 TTGACCG
29591691 TTGACCGTTG
Statistics
Matches: 37, Mismatches: 10, Indels: 3
0.74 0.20 0.06
Matches are distributed among these distances:
10 21 0.57
11 16 0.43
ACGTcount: A:0.17, C:0.25, G:0.31, T:0.27
Consensus pattern (10 bp):
TTGACCGACG
Found at i:29591675 original size:21 final size:21
Alignment explanation
Indices: 29591632--29591690 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 21
29591622 AGTCAAACCA
* *
29591632 TTGACCGA-CGTTGATCGGCG
1 TTGACCGACCGTTGACCGACG
*
29591652 TTGACCGACCGTTGACCGATG
1 TTGACCGACCGTTGACCGACG
**
29591673 TTGATTGACCGTTGACCG
1 TTGACCGACCGTTGACCG
29591691 TTGACCGTTG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
20 8 0.24
21 25 0.76
ACGTcount: A:0.17, C:0.25, G:0.31, T:0.27
Consensus pattern (21 bp):
TTGACCGACCGTTGACCGACG
Found at i:29591687 original size:7 final size:7
Alignment explanation
Indices: 29591677--29591735 Score: 68
Period size: 7 Copynumber: 8.7 Consensus size: 7
29591667 CCGATGTTGA
29591677 TTGACCG
1 TTGACCG
29591684 TTGACCG
1 TTGACCG
29591691 TTGACCG
1 TTGACCG
*
29591698 TTGA-CT
1 TTGACCG
29591704 TTGACCG
1 TTGACCG
*
29591711 TTGATCG
1 TTGACCG
* *
29591718 TT-AACT
1 TTGACCG
29591724 TTGACCG
1 TTGACCG
29591731 TTGAC
1 TTGAC
29591736 TTTTTCGAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
6 9 0.21
7 34 0.79
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.36
Consensus pattern (7 bp):
TTGACCG
Found at i:29591709 original size:20 final size:20
Alignment explanation
Indices: 29591684--29591735 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
29591674 TGATTGACCG
*
29591684 TTGACCGTTGACCGTTGACT
1 TTGACCGTTGACCGTTAACT
*
29591704 TTGACCGTTGATCGTTAACT
1 TTGACCGTTGACCGTTAACT
29591724 TTGACCGTTGAC
1 TTGACCGTTGAC
29591736 TTTTTCGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.37
Consensus pattern (20 bp):
TTGACCGTTGACCGTTAACT
Found at i:29591734 original size:27 final size:27
Alignment explanation
Indices: 29591677--29591735 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
29591667 CCGATGTTGA
* *
29591677 TTGACCGTTGACCGTTGACCGTTGACT
1 TTGACCGTTGACCGTTGAACGTTGACG
* *
29591704 TTGACCGTTGATCGTT-AACTTTGACCG
1 TTGACCGTTGACCGTTGAACGTTGA-CG
29591731 TTGAC
1 TTGAC
29591736 TTTTTCGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 6 0.22
27 21 0.78
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.36
Consensus pattern (27 bp):
TTGACCGTTGACCGTTGAACGTTGACG
Found at i:29592795 original size:3 final size:3
Alignment explanation
Indices: 29592787--29592836 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
29592777 TCTATTCTAT
29592787 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
29592835 TT
1 TT
29592837 TTGGGATGTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:29598869 original size:17 final size:19
Alignment explanation
Indices: 29598849--29598885 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
29598839 TATATATATA
29598849 TTTAAATAA-TATAA-AAT
1 TTTAAATAATTATAAGAAT
*
29598866 TTTAATTAATTATAAGAAT
1 TTTAAATAATTATAAGAAT
29598885 T
1 T
29598886 AATTATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 8 0.47
18 5 0.29
19 4 0.24
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (19 bp):
TTTAAATAATTATAAGAAT
Found at i:29608802 original size:36 final size:39
Alignment explanation
Indices: 29608733--29608807 Score: 111
Period size: 36 Copynumber: 2.0 Consensus size: 39
29608723 GTAAATGGTT
29608733 TTAAAATTATTAAAATTATTTTTTTGAAATATAAAATTA
1 TTAAAATTATTAAAATTATTTTTTTGAAATATAAAATTA
* *
29608772 TTAAAATTATT-ATATTA-TTTTTT-AAGTATAAAATTA
1 TTAAAATTATTAAAATTATTTTTTTGAAATATAAAATTA
29608808 CTATATGATT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
36 12 0.35
37 6 0.18
38 5 0.15
39 11 0.32
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.51
Consensus pattern (39 bp):
TTAAAATTATTAAAATTATTTTTTTGAAATATAAAATTA
Found at i:29609921 original size:36 final size:39
Alignment explanation
Indices: 29609881--29609958 Score: 126
Period size: 36 Copynumber: 2.1 Consensus size: 39
29609871 TAAAACCATA
29609881 TAATAATTTTATA-TTC-AAAAAATAA-TATAATAATTT
1 TAATAATTTTATATTTCAAAAAAATAATTATAATAATTT
*
29609917 TAATAATTTTATATTTCAAAAAAATAATTTTAATAATTT
1 TAATAATTTTATATTTCAAAAAAATAATTATAATAATTT
29609956 TAA
1 TAA
29609959 AATCATTTGC
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
36 13 0.34
37 3 0.08
38 9 0.24
39 13 0.34
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (39 bp):
TAATAATTTTATATTTCAAAAAAATAATTATAATAATTT
Found at i:29610314 original size:20 final size:21
Alignment explanation
Indices: 29610289--29610328 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
29610279 ACATCACTAT
29610289 ATATATAAAACT-TTAATTAA
1 ATATATAAAACTATTAATTAA
*
29610309 ATATATAAAATTATTAATTA
1 ATATATAAAACTATTAATTA
29610329 TTAACTTACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (21 bp):
ATATATAAAACTATTAATTAA
Found at i:29611948 original size:16 final size:16
Alignment explanation
Indices: 29611909--29611949 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
29611899 ATAATAAAAA
29611909 TATAATTTTATCATTT
1 TATAATTTTATCATTT
29611925 TA-ATATTTTAT-ATATT
1 TATA-ATTTTATCAT-TT
29611941 TATAATTTT
1 TATAATTTT
29611950 TAAAGAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 3 0.14
16 18 0.82
17 1 0.05
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.63
Consensus pattern (16 bp):
TATAATTTTATCATTT
Found at i:29612001 original size:29 final size:30
Alignment explanation
Indices: 29611933--29612011 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 30
29611923 TTTAATATTT
* * * *
29611933 TATATATTTATAATTTTTAAAGAATTAAAT
1 TATATTTTTATTATTTTTAAAGAATCAAAA
* *
29611963 TAAACTTTTATTATTTTTAAAG-ATCAAAA
1 TATATTTTTATTATTTTTAAAGAATCAAAA
*
29611992 TATATTTTTATTATTATTAA
1 TATATTTTTATTATTTTTAA
29612012 TTTAAAATTT
Statistics
Matches: 40, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
29 22 0.55
30 18 0.45
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.52
Consensus pattern (30 bp):
TATATTTTTATTATTTTTAAAGAATCAAAA
Found at i:29622091 original size:12 final size:12
Alignment explanation
Indices: 29622070--29622153 Score: 59
Period size: 12 Copynumber: 7.1 Consensus size: 12
29622060 TCATTAGCAT
*
29622070 TGTTCGTGAACA
1 TGTTCATGAACA
29622082 TGTTCATGAACA
1 TGTTCATGAACA
* *
29622094 TGTTCAAT-TATA
1 TGTTC-ATGAACA
*
29622106 TGTTCATTAACA
1 TGTTCATGAACA
*
29622118 TGTTCGAT-TA-A
1 TGTTC-ATGAACA
*
29622129 -GTTAAATGAACA
1 TGTT-CATGAACA
29622141 TGTTCATGAACA
1 TGTTCATGAACA
29622153 T
1 T
29622154 TAAACAAACG
Statistics
Matches: 56, Mismatches: 9, Indels: 14
0.71 0.11 0.18
Matches are distributed among these distances:
10 5 0.09
11 4 0.07
12 40 0.71
13 7 0.12
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.38
Consensus pattern (12 bp):
TGTTCATGAACA
Found at i:29622108 original size:24 final size:23
Alignment explanation
Indices: 29622081--29622146 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 23
29622071 GTTCGTGAAC
29622081 ATGTTCATGAACATGTTCAATTA
1 ATGTTCATGAACATGTTCAATTA
* *
29622104 TATGTTCATTAACATGTTCGATTA
1 -ATGTTCATGAACATGTTCAATTA
*
29622128 A-GTTAAATGAACATGTTCA
1 ATGTT-CATGAACATGTTCA
29622147 TGAACATTAA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
22 3 0.08
23 12 0.33
24 21 0.58
ACGTcount: A:0.35, C:0.12, G:0.14, T:0.39
Consensus pattern (23 bp):
ATGTTCATGAACATGTTCAATTA
Found at i:29628117 original size:319 final size:318
Alignment explanation
Indices: 29627539--29628176 Score: 1267
Period size: 319 Copynumber: 2.0 Consensus size: 318
29627529 CTCATGCAAA
29627539 TATAGACAATCAGGATTGCTGCAAGGCTGAAACCCCCAAAACAACTTCTCAATTATTTTTCAATT
1 TATAGACAATCAGGATTGCTGCAAGGCTGAAACCCCCAAAACAACTTCTCAATTATTTTTCAATT
29627604 ACAATAATAAATGTCATGTTTTACTTCTATATTTTCCATCATGTTTCTTTCCATTTGGCAATTTC
66 ACAATAATAAATGTCATGTTTTACTTCTATATTTTCCATCATGTTTCTTTCCATTTGGCAATTTC
29627669 AAATCTGGCATTTCACAACCTTTTCGTATTTAGCCCCTTCTATTCTAGATATTATTATTTTGTTT
131 AAATCTGGCATTTCACAACCTTTTCGTATTTAGCCCCTTCTATTCTAGATATTATTATTTTGTTT
29627734 GACAATGATGGTTATTGACTTCAATATTAATTTTATCATCGTTATGGTCTAAATTTATTTTCTAT
196 GACAATGATGGTTATTGACTTCAATATTAATTTTATCATCGTTATGGTCTAAATTTATTTTCTAT
29627799 AGTGTCCATGGATTGGGATCCCTTATCATGACACTATGTTTTCTTTCTAATTTTTAAT
261 AGTGTCCATGGATTGGGATCCCTTATCATGACACTATGTTTTCTTTCTAATTTTTAAT
29627857 TATAGACAATCAGGATTGCTGCAAGGCTGAAACCCCCCAAAACAACTTCTCAATTATTTTTCAAT
1 TATAGACAATCAGGATTGCTGCAAGGCTGAAA-CCCCCAAAACAACTTCTCAATTATTTTTCAAT
29627922 TACAATAATAAATGTCATGTTTTACTTCTATATTTTCCATCATGTTTCTTTCCATTTGGCAATTT
65 TACAATAATAAATGTCATGTTTTACTTCTATATTTTCCATCATGTTTCTTTCCATTTGGCAATTT
29627987 CAAATCTGGCATTTCACAACCTTTTCGTATTTAGCCCCTTCTATTCTAGATATTATTATTTTGTT
130 CAAATCTGGCATTTCACAACCTTTTCGTATTTAGCCCCTTCTATTCTAGATATTATTATTTTGTT
29628052 TGACAATGATGGTTATTGACTTCAATATTAATTTTATCATCGTTATGGTCTAAATTTATTTTCTA
195 TGACAATGATGGTTATTGACTTCAATATTAATTTTATCATCGTTATGGTCTAAATTTATTTTCTA
29628117 TAGTGTCCATGGATTGGGATCCCTTATCATGACACTATGTTTTCTTTCTAATTTTTAAT
260 TAGTGTCCATGGATTGGGATCCCTTATCATGACACTATGTTTTCTTTCTAATTTTTAAT
29628176 T
1 T
29628177 CCAATATGTT
Statistics
Matches: 319, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
318 32 0.10
319 287 0.90
ACGTcount: A:0.27, C:0.18, G:0.11, T:0.43
Consensus pattern (318 bp):
TATAGACAATCAGGATTGCTGCAAGGCTGAAACCCCCAAAACAACTTCTCAATTATTTTTCAATT
ACAATAATAAATGTCATGTTTTACTTCTATATTTTCCATCATGTTTCTTTCCATTTGGCAATTTC
AAATCTGGCATTTCACAACCTTTTCGTATTTAGCCCCTTCTATTCTAGATATTATTATTTTGTTT
GACAATGATGGTTATTGACTTCAATATTAATTTTATCATCGTTATGGTCTAAATTTATTTTCTAT
AGTGTCCATGGATTGGGATCCCTTATCATGACACTATGTTTTCTTTCTAATTTTTAAT
Found at i:29631480 original size:15 final size:15
Alignment explanation
Indices: 29631443--29631514 Score: 58
Period size: 15 Copynumber: 4.7 Consensus size: 15
29631433 CTGGTTTGAA
*
29631443 TATTAATATTAA-TT
1 TATTATTATTAATTT
*
29631457 TATTATATTTTAAATTT
1 TATTAT-TATT-AATTT
29631474 TATTATTATTAATTT
1 TATTATTATTAATTT
* *
29631489 TATAAATTATTTATTT
1 TAT-TATTATTAATTT
29631505 T-TTATATATT
1 TATTAT-TATT
29631515 GCTAAATTAA
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
14 7 0.15
15 16 0.34
16 16 0.34
17 8 0.17
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TATTATTATTAATTT
Found at i:29631653 original size:19 final size:19
Alignment explanation
Indices: 29631626--29631664 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
29631616 TTAATTTAAA
* * *
29631626 AAATTTTATTTTTATTTTT
1 AAATATTATATTTAGTTTT
29631645 AAATATTATATTTAGTTTT
1 AAATATTATATTTAGTTTT
29631664 A
1 A
29631665 CTTTAGTTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (19 bp):
AAATATTATATTTAGTTTT
Found at i:29634098 original size:17 final size:17
Alignment explanation
Indices: 29634070--29634102 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
29634060 ACAAAATCTT
29634070 GAACTAAAATTTCGAACC
1 GAACTAAAATTT-GAACC
29634088 GAACT-AAATTTGAAC
1 GAACTAAAATTTGAAC
29634103 AAACATAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 6 0.40
18 5 0.33
ACGTcount: A:0.45, C:0.18, G:0.12, T:0.24
Consensus pattern (17 bp):
GAACTAAAATTTGAACC
Found at i:29646801 original size:15 final size:15
Alignment explanation
Indices: 29646757--29646801 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
29646747 TTTAACAAGT
*
29646757 TGGTGGCGGTGGTGA
1 TGGTGGCGGTGGTGG
**
29646772 TGGTGGCGACGGTGG
1 TGGTGGCGGTGGTGG
29646787 TGGTGGCGGTGGTGG
1 TGGTGGCGGTGGTGG
29646802 CTCATGCATC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.04, C:0.09, G:0.62, T:0.24
Consensus pattern (15 bp):
TGGTGGCGGTGGTGG
Found at i:29647783 original size:30 final size:29
Alignment explanation
Indices: 29647747--29647804 Score: 89
Period size: 30 Copynumber: 2.0 Consensus size: 29
29647737 TTTTTCCTAT
* *
29647747 TTTTTTTCTATTTCATTTGTTTATTTTTAG
1 TTTTTTTCTATTTCACTTATTT-TTTTTAG
29647777 TTTTTTTCTATTTCACTTATTTTTTTTA
1 TTTTTTTCTATTTCACTTATTTTTTTTA
29647805 AATTTCCACC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 6 0.23
30 20 0.77
ACGTcount: A:0.14, C:0.09, G:0.03, T:0.74
Consensus pattern (29 bp):
TTTTTTTCTATTTCACTTATTTTTTTTAG
Found at i:29648187 original size:11 final size:11
Alignment explanation
Indices: 29648138--29648188 Score: 50
Period size: 11 Copynumber: 4.4 Consensus size: 11
29648128 TGAAATAGAA
*
29648138 TTTTATTTAAT
1 TTTTATATAAT
29648149 TTTTATATAAAT
1 TTTTATAT-AAT
29648161 TTTTACTA-AATGT
1 TTTTA-TATAA--T
29648174 TTTTATATAAT
1 TTTTATATAAT
29648185 TTTT
1 TTTT
29648189 TCACTCACAC
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
11 14 0.41
12 10 0.29
13 10 0.29
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (11 bp):
TTTTATATAAT
Found at i:29648189 original size:12 final size:12
Alignment explanation
Indices: 29648138--29648189 Score: 54
Period size: 12 Copynumber: 4.3 Consensus size: 12
29648128 TGAAATAGAA
*
29648138 TTTTATTTAA-T
1 TTTTATATAATT
*
29648149 TTTTATATAAAT
1 TTTTATATAATT
29648161 TTTTACTA-AATGT
1 TTTTA-TATAAT-T
29648174 TTTTATATAATT
1 TTTTATATAATT
29648186 TTTT
1 TTTT
29648190 CACTCACACG
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
11 9 0.26
12 15 0.43
13 11 0.31
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (12 bp):
TTTTATATAATT
Found at i:29652091 original size:14 final size:15
Alignment explanation
Indices: 29652065--29652101 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
29652055 TATAATTAAC
29652065 CACATA-ATATTTCA
1 CACATATATATTTCA
*
29652079 CACATATAT-TTTCT
1 CACATATATATTTCA
29652093 CACATATAT
1 CACATATAT
29652102 CATTATATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 19 0.90
15 2 0.10
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (15 bp):
CACATATATATTTCA
Found at i:29655007 original size:14 final size:14
Alignment explanation
Indices: 29654988--29655027 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
29654978 AGAGGTTCTT
*
29654988 TCTCTCTTTCTCCC
1 TCTCTCTTTATCCC
*
29655002 TCTCTCTTTATCGC
1 TCTCTCTTTATCCC
*
29655016 TCTCTCGTTATC
1 TCTCTCTTTATC
29655028 TTTCGATGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.05, C:0.40, G:0.05, T:0.50
Consensus pattern (14 bp):
TCTCTCTTTATCCC
Found at i:29658024 original size:16 final size:16
Alignment explanation
Indices: 29657985--29658024 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
29657975 AAAAAAAAAA
29657985 ACTTGAATTCAAAATT
1 ACTTGAATTCAAAATT
* *
29658001 AATCTGAATTCAAATTT
1 ACT-TGAATTCAAAATT
29658018 ACTTGAA
1 ACTTGAA
29658025 ATAATTAGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.38
Consensus pattern (16 bp):
ACTTGAATTCAAAATT
Found at i:29658247 original size:17 final size:15
Alignment explanation
Indices: 29658210--29658247 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
29658200 TAAAATAACA
29658210 TGAATTATTTAATTT
1 TGAATTATTTAATTT
29658225 TG-ATTATTTTAATATT
1 TGAATTA-TTTAAT-TT
29658241 TGAATTA
1 TGAATTA
29658248 ATCCTTGCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 4 0.20
15 8 0.40
16 4 0.20
17 4 0.20
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (15 bp):
TGAATTATTTAATTT
Found at i:29661613 original size:19 final size:19
Alignment explanation
Indices: 29661589--29661629 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
29661579 CATCAAACAA
29661589 AAGGAATTTCTTTTTTTCT
1 AAGGAATTTCTTTTTTTCT
29661608 AAGGAATTTCTTTTTTTCT
1 AAGGAATTTCTTTTTTTCT
29661627 AAG
1 AAG
29661630 TCACTAGAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.24, C:0.10, G:0.12, T:0.54
Consensus pattern (19 bp):
AAGGAATTTCTTTTTTTCT
Found at i:29664845 original size:72 final size:72
Alignment explanation
Indices: 29664689--29664829 Score: 176
Period size: 72 Copynumber: 2.0 Consensus size: 72
29664679 AAGAATCTTC
* * * * * *
29664689 TGGTAACCATTCAGTGTTCATCTCCATAGTCTTACCCATCTCTTTAGCACTTGTAGAATCTTCTA
1 TGGTAGCCATTCAGTGTTCACCTCCATAGTCATACCCATCTCTTTAGCAATTGTAGAACCATCTA
*
29664754 TAAGATA
66 AAAGATA
* * *
29664761 TGGTAGCAATTCAGTGTTCACCTCCATATTCATACCCATC-CTGTTGGCAATTGTAGAACCATCT
1 TGGTAGCCATTCAGTGTTCACCTCCATAGTCATACCCATCTCT-TTAGCAATTGTAGAACCATCT
29664825 AAAAG
65 AAAAG
29664830 CTTCGGTCGC
Statistics
Matches: 58, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
71 2 0.03
72 56 0.97
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (72 bp):
TGGTAGCCATTCAGTGTTCACCTCCATAGTCATACCCATCTCTTTAGCAATTGTAGAACCATCTA
AAAGATA
Found at i:29668045 original size:13 final size:13
Alignment explanation
Indices: 29668026--29668058 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
29668016 CTAATGTACA
29668026 AAATTAA-TAATT
1 AAATTAATTAATT
29668038 AAACTTAATTAATT
1 AAA-TTAATTAATT
29668052 AAATTAA
1 AAATTAA
29668059 GAGTAATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.16
13 8 0.42
14 8 0.42
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (13 bp):
AAATTAATTAATT
Found at i:29678158 original size:17 final size:17
Alignment explanation
Indices: 29678132--29678169 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
29678122 ATTTTTTTAT
*
29678132 AAATTTAAAA-TAAAAA
1 AAATTAAAAATTAAAAA
29678148 CAAATTAAAAATTAAAAA
1 -AAATTAAAAATTAAAAA
29678166 AAAT
1 AAAT
29678170 ATAATCACAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATTAAAAATTAAAAA
Found at i:29683471 original size:29 final size:24
Alignment explanation
Indices: 29683414--29683490 Score: 91
Period size: 24 Copynumber: 3.2 Consensus size: 24
29683404 GACTAATAAA
*
29683414 AATTTGACTCAAACAATTAAATAG
1 AATTTGACTCAAACAAATAAATAG
29683438 AATTTGACTCAAACAAATAAATAG
1 AATTTGACTCAAACAAATAAATAG
** * * * *
29683462 AGCTTAATTTAAACAAATAAACAG
1 AATTTGACTCAAACAAATAAATAG
29683486 AATTT
1 AATTT
29683491 AATTAAAAAT
Statistics
Matches: 44, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.52, C:0.12, G:0.08, T:0.29
Consensus pattern (24 bp):
AATTTGACTCAAACAAATAAATAG
Found at i:29684156 original size:15 final size:15
Alignment explanation
Indices: 29684136--29684193 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 15
29684126 ATTCAATATT
29684136 AATATTTTAATAATA
1 AATATTTTAATAATA
*
29684151 AATATTTATTACATTTATA
1 AATA-TT-TTA-A-TAATA
*
29684170 AATATATTAATAATA
1 AATATTTTAATAATA
*
29684185 AATGTTTTA
1 AATATTTTA
29684194 GTATAAAAGT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 15 0.44
16 3 0.09
17 6 0.18
18 2 0.06
19 8 0.24
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:29686900 original size:29 final size:29
Alignment explanation
Indices: 29686818--29686934 Score: 130
Period size: 29 Copynumber: 4.0 Consensus size: 29
29686808 GTAGGGGTTA
* *
29686818 AAAATGGAA-TTTTGGAAAGTTTGAGGGT-
1 AAAATGTAATTTTTGGAAATTTTG-GGGTC
*
29686846 AAAATAGGTAATTTTTGGAAGTTTTGGGGTC
1 AAAAT--GTAATTTTTGGAAATTTTGGGGTC
* *
29686877 AAAATGTAATTTTTTGAAAATTTGGGGTC
1 AAAATGTAATTTTTGGAAATTTTGGGGTC
* *
29686906 AAAATGTAGTTTTTTGAAATTTTGGGGTC
1 AAAATGTAATTTTTGGAAATTTTGGGGTC
29686935 TTATAGACAA
Statistics
Matches: 77, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
28 5 0.06
29 48 0.62
30 7 0.09
31 17 0.22
ACGTcount: A:0.32, C:0.03, G:0.26, T:0.39
Consensus pattern (29 bp):
AAAATGTAATTTTTGGAAATTTTGGGGTC
Found at i:29688796 original size:17 final size:17
Alignment explanation
Indices: 29688776--29688851 Score: 73
Period size: 17 Copynumber: 4.5 Consensus size: 17
29688766 AATTTATTTT
*
29688776 TAAATTTAAATTTATAA
1 TAAATTTAAATTTAAAA
* * **
29688793 TAAATTCAAATTTTATG
1 TAAATTTAAATTTAAAA
* *
29688810 CAAATTTAAATTCAAAA
1 TAAATTTAAATTTAAAA
29688827 TAAATTT-AATTTAAAA
1 TAAATTTAAATTTAAAA
29688843 CTAAATTTA
1 -TAAATTTA
29688852 TGTCTTTATT
Statistics
Matches: 44, Mismatches: 13, Indels: 3
0.73 0.22 0.05
Matches are distributed among these distances:
16 8 0.18
17 36 0.82
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.42
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:29688849 original size:34 final size:35
Alignment explanation
Indices: 29688776--29688851 Score: 84
Period size: 34 Copynumber: 2.2 Consensus size: 35
29688766 AATTTATTTT
* * * **
29688776 TAAATTTAAATTTATAATAAATTCAAATTTTATGC
1 TAAATTTAAATTCAAAATAAATTCAAATTTAAAAC
*
29688811 -AAATTTAAATTCAAAATAAATT-TAATTTAAAAC
1 TAAATTTAAATTCAAAATAAATTCAAATTTAAAAC
29688844 TAAATTTA
1 TAAATTTA
29688852 TGTCTTTATT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
33 7 0.21
34 27 0.79
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.42
Consensus pattern (35 bp):
TAAATTTAAATTCAAAATAAATTCAAATTTAAAAC
Found at i:29691901 original size:2 final size:2
Alignment explanation
Indices: 29691894--29691925 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
29691884 AGGTTAAATG
29691894 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29691926 CTATGAAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29692451 original size:19 final size:20
Alignment explanation
Indices: 29692427--29692464 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
29692417 CGATATTTTA
29692427 TGAAAA-ATATCGATACCTT
1 TGAAAATATATCGATACCTT
*
29692446 TGAAAATGTATCGATACCT
1 TGAAAATATATCGATACCT
29692465 GAGTTACAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.39, C:0.16, G:0.13, T:0.32
Consensus pattern (20 bp):
TGAAAATATATCGATACCTT
Found at i:29692994 original size:18 final size:18
Alignment explanation
Indices: 29692971--29693010 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
29692961 GAATAGGTTT
29692971 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
*
29692989 TTAATTAAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
29693007 TTAA
1 TTAA
29693011 CTACACCTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:29695731 original size:31 final size:32
Alignment explanation
Indices: 29695648--29695731 Score: 95
Period size: 31 Copynumber: 2.7 Consensus size: 32
29695638 ATAAATTCTA
*
29695648 GTGAAACTTTAA-TTTGGTGT-AATTATACAT
1 GTGAAACTTTAATTTTGGTTTAAATTATACAT
* *
29695678 GTGAAATTTTAATTGTGGTTTAAATATATAC-T
1 GTGAAACTTTAATTTTGGTTTAAAT-TATACAT
*
29695710 -TGAAACTTTAATTTTGATTTAA
1 GTGAAACTTTAATTTTGGTTTAA
29695732 TCATACACAT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
30 11 0.24
31 25 0.56
32 4 0.09
33 5 0.11
ACGTcount: A:0.35, C:0.05, G:0.14, T:0.46
Consensus pattern (32 bp):
GTGAAACTTTAATTTTGGTTTAAATTATACAT
Found at i:29695994 original size:31 final size:29
Alignment explanation
Indices: 29695950--29696014 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
29695940 AATTTACAAC
*
29695950 AATTAAATCAAATCAAAAATTTCATGTATAA
1 AATTAAATAAAATC-AAAATTT-ATGTATAA
* *
29695981 AATTACATAAAATCAAAATTTATGTATAT
1 AATTAAATAAAATCAAAATTTATGTATAA
29696010 AATTA
1 AATTA
29696015 TACATTAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 12 0.39
30 7 0.23
31 12 0.39
ACGTcount: A:0.54, C:0.08, G:0.03, T:0.35
Consensus pattern (29 bp):
AATTAAATAAAATCAAAATTTATGTATAA
Found at i:29696019 original size:31 final size:32
Alignment explanation
Indices: 29695959--29696025 Score: 86
Period size: 30 Copynumber: 2.1 Consensus size: 32
29695949 CAATTAAATC
29695959 AAATCAAAAATTTCATGTATAAAATTACA-TA
1 AAATCAAAAATTTCATGTATAAAATTACATTA
*
29695990 AAATC-AAAATTT-ATGTATATAATTATACATTA
1 AAATCAAAAATTTCATGTATA-AAAT-TACATTA
29696022 AAAT
1 AAAT
29696026 ATAATTCATA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
29 7 0.22
30 10 0.31
31 9 0.28
32 6 0.19
ACGTcount: A:0.54, C:0.07, G:0.03, T:0.36
Consensus pattern (32 bp):
AAATCAAAAATTTCATGTATAAAATTACATTA
Found at i:29696902 original size:118 final size:121
Alignment explanation
Indices: 29696763--29696986 Score: 303
Period size: 120 Copynumber: 1.9 Consensus size: 121
29696753 ATTTTATTTA
** *
29696763 TTTTTAATTTTTAATTAATAAACATGTT-TTTCAAGTAAT-TTTATTTTATTTTTATTTCATGTT
1 TTTTTAATTTTTAATTAATAAACACATTATTTCAAGTAATATTTA-TTTATTTTTAATTCATGTT
* * *
29696826 TTTAATTAATAACT-TTTTATTTA-TTAAAAAAAATAATAAATATGTGGTTGAAGCC
65 TTTAATGAATAACTCATTTACTTATTTAAAAAAAATAATAAATATGTGGTTGAAGCC
* **
29696881 TTTTTATTTTTTAATTAATAAACACATTGATTTCAAGTTTTATTTATTTATTTTTAATTCATGTT
1 TTTTTAATTTTTAATTAATAAACACATT-ATTTCAAGTAATATTTATTTATTTTTAATTCATGTT
* *
29696946 TTTAATGAATAGCTCATTTACTTATTTAAACAAAATAATAA
65 TTTAATGAATAACTCATTTACTTATTTAAAAAAAATAATAA
29696987 GCATGTACTT
Statistics
Matches: 90, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
118 25 0.28
120 39 0.43
121 11 0.12
122 15 0.17
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.52
Consensus pattern (121 bp):
TTTTTAATTTTTAATTAATAAACACATTATTTCAAGTAATATTTATTTATTTTTAATTCATGTTT
TTAATGAATAACTCATTTACTTATTTAAAAAAAATAATAAATATGTGGTTGAAGCC
Found at i:29699011 original size:28 final size:28
Alignment explanation
Indices: 29698980--29699033 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
29698970 TTTTCGTTTA
* *
29698980 ATTTAGAGTTAAATTGATTTTTAATTCT
1 ATTTAAAGTTAAATTGATTTTAAATTCT
* *
29699008 ATTTAAATTTAAATTTATTTTAAATT
1 ATTTAAAGTTAAATTGATTTTAAATT
29699034 TAAATTTAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.56
Consensus pattern (28 bp):
ATTTAAAGTTAAATTGATTTTAAATTCT
Found at i:29699019 original size:6 final size:6
Alignment explanation
Indices: 29699008--29699075 Score: 77
Period size: 6 Copynumber: 11.3 Consensus size: 6
29698998 TTTTAATTCT
*
29699008 ATTTAA ATTTAA ATTT-A TTTTAA ATTTAA ATTTAA TTATTTAA ATTT-A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA --ATTTAA ATTTAA
* *
29699056 CTTTGA ATTTAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA AT
29699076 AAAAATTAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
5 8 0.15
6 39 0.74
8 6 0.11
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (6 bp):
ATTTAA
Found at i:29699029 original size:17 final size:16
Alignment explanation
Indices: 29699002--29699072 Score: 83
Period size: 17 Copynumber: 4.4 Consensus size: 16
29698992 ATTGATTTTT
29699002 AATTCTATTTAAATTTA
1 AATT-TATTTAAATTTA
29699019 AATTTATTTTAAATTTA
1 AATTTA-TTTAAATTTA
*
29699036 AATTTAATT--ATTTA
1 AATTTATTTAAATTTA
*
29699050 AATTTACTTTGAATTTA
1 AATTTA-TTTAAATTTA
29699067 AATTTA
1 AATTTA
29699073 AATAAAAATT
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
14 11 0.23
15 2 0.04
16 4 0.08
17 31 0.65
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (16 bp):
AATTTATTTAAATTTA
Found at i:29699052 original size:31 final size:31
Alignment explanation
Indices: 29699014--29699073 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
29699004 TTCTATTTAA
*
29699014 ATTTAAATTTATTTTAAATTTAAATTTAATT
1 ATTTAAATTTACTTTAAATTTAAATTTAATT
*
29699045 ATTTAAATTTACTTTGAATTTAAATTTAA
1 ATTTAAATTTACTTTAAATTTAAATTTAA
29699074 ATAAAAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (31 bp):
ATTTAAATTTACTTTAAATTTAAATTTAATT
Found at i:29699096 original size:14 final size:15
Alignment explanation
Indices: 29699075--29699114 Score: 57
Period size: 14 Copynumber: 2.8 Consensus size: 15
29699065 TAAATTTAAA
29699075 TAAAAATTAAAACAT
1 TAAAAATTAAAACAT
*
29699090 T-AAAATT-TAACAT
1 TAAAAATTAAAACAT
29699103 TAAAAATTAAAA
1 TAAAAATTAAAA
29699115 GTTTAAAGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
13 6 0.29
14 12 0.57
15 3 0.14
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (15 bp):
TAAAAATTAAAACAT
Found at i:29699103 original size:13 final size:13
Alignment explanation
Indices: 29699066--29699112 Score: 51
Period size: 13 Copynumber: 3.6 Consensus size: 13
29699056 CTTTGAATTT
*
29699066 AAATTTAA-ATAA
1 AAATTTAACATTA
*
29699078 AAATTAAAACATTA
1 AAATT-TAACATTA
29699092 AAATTTAACATTA
1 AAATTTAACATTA
*
29699105 AAAATTAA
1 AAATTTAA
29699113 AAGTTTAAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
12 5 0.17
13 16 0.55
14 8 0.28
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
AAATTTAACATTA
Found at i:29699105 original size:21 final size:21
Alignment explanation
Indices: 29699080--29699120 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
29699070 TTAAATAAAA
29699080 ATTAAAACATTAAAA-TTTAAC
1 ATTAAAA-ATTAAAAGTTTAAC
29699101 ATTAAAAATTAAAAGTTTAA
1 ATTAAAAATTAAAAGTTTAA
29699121 AGTCCATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.34
Consensus pattern (21 bp):
ATTAAAAATTAAAAGTTTAAC
Found at i:29700401 original size:16 final size:18
Alignment explanation
Indices: 29700380--29700415 Score: 58
Period size: 16 Copynumber: 2.1 Consensus size: 18
29700370 CGCTTTGGAC
29700380 TGCCGGCC-TGGT-AGGT
1 TGCCGGCCATGGTGAGGT
29700396 TGCCGGCCATGGTGAGGT
1 TGCCGGCCATGGTGAGGT
29700414 TG
1 TG
29700416 AGAGAAAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
17 4 0.22
18 6 0.33
ACGTcount: A:0.08, C:0.22, G:0.44, T:0.25
Consensus pattern (18 bp):
TGCCGGCCATGGTGAGGT
Found at i:29700955 original size:161 final size:158
Alignment explanation
Indices: 29700689--29701005 Score: 428
Period size: 161 Copynumber: 2.0 Consensus size: 158
29700679 GCTTCCAATT
*
29700689 TAGTCCCTTGACTGTTTGACTGTACCAGAGGCACCACGTGTCCATTTTGGATCATTTCTGCATTT
1 TAGTCCCTTGACTGTTTGACTGTACCAGAGGCACCACGTGTCCATTTTGGATCATTTATGCATTT
*
29700754 AGTCCCTGATATTTTTAATTTGTTTAATTTAATCCCCAAATCAACTTATT-TT-AATTA-TAAAG
66 AGTCCCTGATATTTTTAATTTGTTTAATTTAATCCCCAAATCAACTT-TTATTCAATTACGAAA-
*
29700816 TTGGCCACAATAAATTTTCAAGGTTTATAAAC
129 TTGGCC-CAA-AAATTTTCAAGATTTATAAAC
* * * *
29700848 TAGTCCTTTGACTGTTTGACTGTACCAGAGGCTGCCACGTGTCACTTTTTGGATTATTTATGCAT
1 TAGTCCCTTGACTGTTTGACTGTACCAGAGGC-ACCACGTGTC-CATTTTGGATCATTTATGCAT
* **
29700913 TTAGTCCTTTTTTATTTTTAA-TTGTTTTAATTTAAT-CCCAAATCAACTTTTATTCAATTACGA
64 TTAGTCC-CTGATATTTTTAATTTG-TTTAATTTAATCCCCAAATCAACTTTTATTCAATTACGA
*
29700976 AATTGGCCCAAAAGTTTTCAAGATTTATAA
127 AATTGGCCCAAAAATTTTCAAGATTTATAA
29701006 TTGAATCCCT
Statistics
Matches: 140, Mismatches: 11, Indels: 13
0.85 0.07 0.08
Matches are distributed among these distances:
159 31 0.22
160 28 0.20
161 46 0.33
162 32 0.23
163 3 0.02
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42
Consensus pattern (158 bp):
TAGTCCCTTGACTGTTTGACTGTACCAGAGGCACCACGTGTCCATTTTGGATCATTTATGCATTT
AGTCCCTGATATTTTTAATTTGTTTAATTTAATCCCCAAATCAACTTTTATTCAATTACGAAATT
GGCCCAAAAATTTTCAAGATTTATAAAC
Found at i:29701185 original size:29 final size:29
Alignment explanation
Indices: 29701139--29701407 Score: 165
Period size: 29 Copynumber: 9.2 Consensus size: 29
29701129 TACATTCTGA
*
29701139 CCCCGAAACTTCCAAAAATTACCATTTTAC
1 CCCCGAATCTT-CAAAAATTACCATTTTAC
** *
29701169 CCCCGAATCTTTTAAAATT-CCATTTTTAA
1 CCCCGAATCTTCAAAAATTACCA-TTTTAC
* **
29701198 CCCCGATTTCACCAAAAATTACCATTTTA-
1 CCCCGA-ATCTTCAAAAATTACCATTTTAC
** *
29701227 CCCAAAAACTTCCAAAAATTACCATTTTAC
1 CCCCGAATCTT-CAAAAATTACCATTTTAC
* * *
29701257 CCCCAAATCTTCTAAAATT-CCATTTTTAA
1 CCCCGAATCTTCAAAAATTACCA-TTTTAC
* * ** *
29701286 CCCTGATTTCACCAAAAATTACCATTTT-G
1 CCCCGA-ATCTTCAAAAATTACCATTTTAC
* * *
29701315 CCCTGAAACTTCCAAAATTACCATTTTACC
1 CCCCGAATCTTCAAAAATTACCATTTTA-C
* *
29701345 CCCCGAATCTTC-TAAATT-CCATTTTTAA
1 CCCCGAATCTTCAAAAATTACCA-TTTTAC
* * * *
29701373 CCCTG-ATTTTACCAAAATTACCATTTTGC
1 CCCCGAATCTT-CAAAAATTACCATTTTAC
29701402 CCCCGA
1 CCCCGA
29701408 GTATCCAAAA
Statistics
Matches: 182, Mismatches: 42, Indels: 30
0.72 0.17 0.12
Matches are distributed among these distances:
27 4 0.02
28 31 0.17
29 83 0.46
30 58 0.32
31 6 0.03
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.33
Consensus pattern (29 bp):
CCCCGAATCTTCAAAAATTACCATTTTAC
Found at i:29701201 original size:59 final size:57
Alignment explanation
Indices: 29701138--29701407 Score: 178
Period size: 59 Copynumber: 4.6 Consensus size: 57
29701128 CTACATTCTG
**
29701138 ACCCCGAAACTTCCAAAAATTACCATTTTACCCCCGAATCTTTTAAAATT-CCATTTTT
1 ACCCCGAAACTTCC-AAAATTACCATTTTACCCCCGAATCTTCAAAAATTACCA-TTTT
* ** *
29701196 AACCCCG--ATTTCACCAAAAATTACCATTTTA-CCCAAAAACTTCCAAAAATTACCATTTT
1 -ACCCCGAAACTT--CC-AAAATTACCATTTTACCCCCGAATCTT-CAAAAATTACCATTTT
* * * * * **
29701255 ACCCCCAAATCTTCTAAAATT-CCATTTTTAACCCTGATTTCACCAAAAATTACCATTTT
1 ACCCCGAAA-CTTCCAAAATTACCA-TTTTACCCCCGA-ATCTTCAAAAATTACCATTTT
* * *
29701314 GCCCTGAAACTTCCAAAATTACCATTTTACCCCCCGAATCTTC-TAAATT-CCATTTTT
1 ACCCCGAAACTTCCAAAATTACCATTTTA-CCCCCGAATCTTCAAAAATTACCA-TTTT
* ** *
29701371 AACCCTG-ATTTTACCAAAATTACCATTTTGCCCCCGA
1 -ACCCCGAAACTT-CCAAAATTACCATTTTACCCCCGA
29701408 GTATCCAAAA
Statistics
Matches: 167, Mismatches: 29, Indels: 32
0.73 0.13 0.14
Matches are distributed among these distances:
56 3 0.02
57 25 0.15
58 63 0.38
59 69 0.41
60 5 0.03
61 2 0.01
ACGTcount: A:0.33, C:0.30, G:0.04, T:0.33
Consensus pattern (57 bp):
ACCCCGAAACTTCCAAAATTACCATTTTACCCCCGAATCTTCAAAAATTACCATTTT
Found at i:29701248 original size:88 final size:88
Alignment explanation
Indices: 29701144--29701399 Score: 419
Period size: 88 Copynumber: 2.9 Consensus size: 88
29701134 TCTGACCCCG
* *
29701144 AAACTTCCAAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGATTTCA
1 AAACTTCCAAAAATTACCATTTTACCCCCGAATCTTCTAAAATTCCATTTTTAACCCTGATTTCA
29701209 CCAAAAATTACCATTTTACCCAA
66 CCAAAAATTACCATTTTACCCAA
*
29701232 AAACTTCCAAAAATTACCATTTTACCCCCAAATCTTCTAAAATTCCATTTTTAACCCTGATTTCA
1 AAACTTCCAAAAATTACCATTTTACCCCCGAATCTTCTAAAATTCCATTTTTAACCCTGATTTCA
* **
29701297 CCAAAAATTACCATTTTGCCCTG
66 CCAAAAATTACCATTTTACCCAA
*
29701320 AAACTTCC-AAAATTACCATTTTACCCCCCGAATCTTCT-AAATTCCATTTTTAACCCTGATTTT
1 AAACTTCCAAAAATTACCATTTTA-CCCCCGAATCTTCTAAAATTCCATTTTTAACCCTGATTTC
29701383 ACC-AAAATTACCATTTT
65 ACCAAAAATTACCATTTT
29701400 GCCCCCGAGT
Statistics
Matches: 159, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
86 14 0.09
87 42 0.26
88 103 0.65
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.35
Consensus pattern (88 bp):
AAACTTCCAAAAATTACCATTTTACCCCCGAATCTTCTAAAATTCCATTTTTAACCCTGATTTCA
CCAAAAATTACCATTTTACCCAA
Found at i:29701425 original size:58 final size:58
Alignment explanation
Indices: 29701326--29701439 Score: 140
Period size: 58 Copynumber: 2.0 Consensus size: 58
29701316 CCTGAAACTT
* * * * *
29701326 CCAAAATTACCATTTTACCCCCCGAATCTTCTAAATTCCATTTTTAACCCTGATTTTA
1 CCAAAATTACCATTTTACCCCCCGAATATCCAAAATCCCATTTTTAACCCCGATTTTA
* * *
29701384 CCAAAATTACCATTTT-GCCCCCGAGTATCCAAAAATCCCATTTTTCACCCCGATTT
1 CCAAAATTACCATTTTACCCCCCGAATATCC-AAAATCCCATTTTTAACCCCGATTT
29701440 CATCGTTTAT
Statistics
Matches: 47, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
57 10 0.21
58 37 0.79
ACGTcount: A:0.29, C:0.32, G:0.05, T:0.34
Consensus pattern (58 bp):
CCAAAATTACCATTTTACCCCCCGAATATCCAAAATCCCATTTTTAACCCCGATTTTA
Found at i:29703103 original size:23 final size:25
Alignment explanation
Indices: 29703072--29703123 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 25
29703062 TGTGTACTTA
* *
29703072 ATATTTTATCAAATTT-ATAT-AAT
1 ATATCTTATAAAATTTAATATAAAT
29703095 ATATCTTATAAAATTTAATATAAAT
1 ATATCTTATAAAATTTAATATAAAT
29703120 ATAT
1 ATAT
29703124 AAAAATAACC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 14 0.56
24 4 0.16
25 7 0.28
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (25 bp):
ATATCTTATAAAATTTAATATAAAT
Found at i:29704780 original size:23 final size:23
Alignment explanation
Indices: 29704754--29704817 Score: 128
Period size: 23 Copynumber: 2.8 Consensus size: 23
29704744 CCACAATTTT
29704754 TATTATTATTACATCAATAATAC
1 TATTATTATTACATCAATAATAC
29704777 TATTATTATTACATCAATAATAC
1 TATTATTATTACATCAATAATAC
29704800 TATTATTATTACATCAAT
1 TATTATTATTACATCAAT
29704818 TATTACGTCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (23 bp):
TATTATTATTACATCAATAATAC
Found at i:29704821 original size:12 final size:12
Alignment explanation
Indices: 29704758--29704829 Score: 53
Period size: 12 Copynumber: 6.2 Consensus size: 12
29704748 AATTTTTATT
29704758 ATTATTACATCA
1 ATTATTACATCA
* *
29704770 A-TAATACTAT-T
1 ATTATTAC-ATCA
29704781 ATTATTACATCA
1 ATTATTACATCA
* *
29704793 A-TAATACTAT-T
1 ATTATTAC-ATCA
29704804 ATTATTACATCA
1 ATTATTACATCA
*
29704816 ATTATTACGTCA
1 ATTATTACATCA
29704828 AT
1 AT
29704830 AATACTATTA
Statistics
Matches: 45, Mismatches: 9, Indels: 12
0.68 0.14 0.18
Matches are distributed among these distances:
11 16 0.36
12 29 0.64
ACGTcount: A:0.42, C:0.14, G:0.01, T:0.43
Consensus pattern (12 bp):
ATTATTACATCA
Found at i:29707681 original size:60 final size:60
Alignment explanation
Indices: 29707598--29707729 Score: 176
Period size: 60 Copynumber: 2.2 Consensus size: 60
29707588 CAATTTGATC
* * *
29707598 CTAAATCTAAAAATTCAAAAAATTTAAC-CTTCAATGTTTACAAAATTTTTCATTTTAGTT
1 CTAAATCTAAAAATTCAAAAAATTTAACTC-TCAATATTTACAAAAATTTTCAATTTAGTT
* * * *
29707658 CTAATTCTAAAAATTTAATAAATTTAACTCTCTATATTTACAAAAATTTTCAATTTAGTT
1 CTAAATCTAAAAATTCAAAAAATTTAACTCTCAATATTTACAAAAATTTTCAATTTAGTT
*
29707718 CTAACTCTAAAA
1 CTAAATCTAAAA
29707730 GTTTTTAAGA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
60 62 0.98
61 1 0.02
ACGTcount: A:0.42, C:0.14, G:0.02, T:0.42
Consensus pattern (60 bp):
CTAAATCTAAAAATTCAAAAAATTTAACTCTCAATATTTACAAAAATTTTCAATTTAGTT
Found at i:29707790 original size:18 final size:19
Alignment explanation
Indices: 29707769--29707823 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 19
29707759 ACAGTTTTTG
29707769 GATTAAAAATT-TAAAAAT
1 GATTAAAAATTATAAAAAT
* *
29707787 GATTTAAAATTATAAAAAA
1 GATTAAAAATTATAAAAAT
*
29707806 GTATAAATAAATTATAAA
1 G-ATTAA-AAATTATAAA
29707824 TTAAAAGCCA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 10 0.33
19 7 0.23
20 3 0.10
21 10 0.33
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (19 bp):
GATTAAAAATTATAAAAAT
Found at i:29716183 original size:11 final size:11
Alignment explanation
Indices: 29716153--29716197 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
29716143 ACGTTAGCAC
*
29716153 CACCATGTCAG
1 CACCACGTCAG
*
29716164 CCTCCACGTCAG
1 -CACCACGTCAG
*
29716176 CACCACGTCAT
1 CACCACGTCAG
29716187 CACCACGTCAG
1 CACCACGTCAG
29716198 TCACGTGACC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
11 19 0.68
12 9 0.32
ACGTcount: A:0.24, C:0.44, G:0.16, T:0.16
Consensus pattern (11 bp):
CACCACGTCAG
Found at i:29723861 original size:19 final size:18
Alignment explanation
Indices: 29723803--29723861 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 18
29723793 TCATGTTATT
* *
29723803 TTTAGATTTTTTTGAAT-
1 TTTAAATTTTTTTAAATA
29723820 TTTAAA-TTTTTTAACATA
1 TTTAAATTTTTTTAA-ATA
29723838 TTTTAAATTTTTTTAAATTA
1 -TTTAAATTTTTTTAAA-TA
29723858 TTTA
1 TTTA
29723862 TTGATGTGAC
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
16 7 0.20
17 7 0.20
19 11 0.31
20 10 0.29
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (18 bp):
TTTAAATTTTTTTAAATA
Found at i:29725088 original size:23 final size:24
Alignment explanation
Indices: 29725043--29725093 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
29725033 ACCATTATTC
*
29725043 TAAATATTAAAAAAATTATAATTA
1 TAAATATTAAAAAAATTAAAATTA
* *
29725067 TAAATATT-AACAAATTAAAATTT
1 TAAATATTAAAAAAATTAAAATTA
29725090 TAAA
1 TAAA
29725094 AATAAAACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (24 bp):
TAAATATTAAAAAAATTAAAATTA
Found at i:29725155 original size:7 final size:8
Alignment explanation
Indices: 29725139--29725186 Score: 50
Period size: 8 Copynumber: 6.4 Consensus size: 8
29725129 TAAATTATGG
29725139 AAACTATA
1 AAACTATA
29725147 AAA-TATA
1 AAACTATA
*
29725154 AAATTATA
1 AAACTATA
29725162 AAACTA-A
1 AAACTATA
29725169 AATA-TATA
1 AA-ACTATA
29725177 AAACTA-A
1 AAACTATA
29725184 AAA
1 AAA
29725187 AAGTAAAGGT
Statistics
Matches: 35, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
7 17 0.49
8 18 0.51
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (8 bp):
AAACTATA
Found at i:29725155 original size:23 final size:21
Alignment explanation
Indices: 29725114--29725178 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 21
29725104 CTCAACCATT
*
29725114 TTATGAAA-TAAAAAT-TAAA
1 TTATAAAACTAAAAATATAAA
*
29725133 TTATGGAAACTATAAAATATAAAA
1 TTAT-AAAACTA-AAAATAT-AAA
29725157 TTATAAAACTAAAATATATAAA
1 TTATAAAACTAAAA-ATATAAA
29725179 ACTAAAAAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
19 4 0.10
20 4 0.10
21 2 0.05
22 11 0.28
23 11 0.28
24 7 0.18
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.31
Consensus pattern (21 bp):
TTATAAAACTAAAAATATAAA
Found at i:29725163 original size:15 final size:15
Alignment explanation
Indices: 29725143--29725185 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
29725133 TTATGGAAAC
29725143 TATAAAATATAAAAT-
1 TATAAAA-ATAAAATA
*
29725158 TATAAAACTAAAATA
1 TATAAAAATAAAATA
*
29725173 TATAAAACTAAAA
1 TATAAAAATAAAA
29725186 AAAGTAAAGG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 6 0.23
15 20 0.77
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (15 bp):
TATAAAAATAAAATA
Found at i:29725171 original size:14 final size:15
Alignment explanation
Indices: 29725152--29725185 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
29725142 CTATAAAATA
29725152 TAAAAT-TATAAAAC
1 TAAAATATATAAAAC
29725166 TAAAATATATAAAAC
1 TAAAATATATAAAAC
29725181 TAAAA
1 TAAAA
29725186 AAAGTAAAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAAATATATAAAAC
Found at i:29725187 original size:23 final size:23
Alignment explanation
Indices: 29725139--29725187 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
29725129 TAAATTATGG
* *
29725139 AAACTATAAAATATAAAATTATA
1 AAACTATAAAATATAAAACTAAA
29725162 AAACTA-AAATATATAAAACTAAA
1 AAACTATAAA-ATATAAAACTAAA
29725185 AAA
1 AAA
29725188 AGTAAAGGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 3 0.13
23 20 0.87
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.24
Consensus pattern (23 bp):
AAACTATAAAATATAAAACTAAA
Found at i:29725926 original size:28 final size:28
Alignment explanation
Indices: 29725873--29725926 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
29725863 ACGATTATAT
**
29725873 GTTTTATCTTTAGTTATATTTTTTTGAA
1 GTTTTATCTTTAGTTATATTGATTTGAA
*
29725901 GTTTTATCTTTGGATTAT-TTGATTTG
1 GTTTTATCTTTAG-TTATATTGATTTG
29725927 GATTTATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
28 18 0.82
29 4 0.18
ACGTcount: A:0.19, C:0.04, G:0.15, T:0.63
Consensus pattern (28 bp):
GTTTTATCTTTAGTTATATTGATTTGAA
Found at i:29725947 original size:21 final size:21
Alignment explanation
Indices: 29725922--29725972 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
29725912 GGATTATTTG
29725922 ATTTGGATTTATAAACTTTAT
1 ATTTGGATTTATAAACTTTAT
* *
29725943 GTTTGGATTTCTAAACTTTAT
1 ATTTGGATTTATAAACTTTAT
*
29725964 ATTAGGATT
1 ATTTGGATT
29725973 ATTCTATTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.29, C:0.06, G:0.14, T:0.51
Consensus pattern (21 bp):
ATTTGGATTTATAAACTTTAT
Found at i:29732722 original size:3 final size:3
Alignment explanation
Indices: 29732714--29732741 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
29732704 TTATTGTATA
29732714 GTG GTG GTG GTG GTG GTG GTG GTG GTG G
1 GTG GTG GTG GTG GTG GTG GTG GTG GTG G
29732742 AGAGGGCAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.68, T:0.32
Consensus pattern (3 bp):
GTG
Found at i:29732741 original size:48 final size:48
Alignment explanation
Indices: 29732671--29732777 Score: 171
Period size: 48 Copynumber: 2.2 Consensus size: 48
29732661 TGAATAATGA
*
29732671 GGTGGTGATGGTGGTGGTGGTGGAGAGGGCAGCTTATTGTAT-AGTGGT
1 GGTGGTGGTGGTGGTGGTGGTGGAGAGGGCAGCTTATTGTATGA-TGGT
29732719 GGTGGTGGTGGTGGTGGTGGTGGAGAGGGCAGCTTATTGTATGATGGT
1 GGTGGTGGTGGTGGTGGTGGTGGAGAGGGCAGCTTATTGTATGATGGT
* *
29732767 GATTGTGGTGG
1 GGTGGTGGTGG
29732778 GCTGGGCAGA
Statistics
Matches: 55, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
48 54 0.98
49 1 0.02
ACGTcount: A:0.13, C:0.04, G:0.51, T:0.32
Consensus pattern (48 bp):
GGTGGTGGTGGTGGTGGTGGTGGAGAGGGCAGCTTATTGTATGATGGT
Found at i:29736066 original size:14 final size:14
Alignment explanation
Indices: 29736044--29736082 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
29736034 TTTTCGAAAA
29736044 TTTAAAATTTAATT
1 TTTAAAATTTAATT
* *
29736058 TTTATAATTTTATT
1 TTTAAAATTTAATT
29736072 TTTAAAATTTA
1 TTTAAAATTTA
29736083 GTCCATTTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTAAAATTTAATT
Found at i:29736829 original size:19 final size:19
Alignment explanation
Indices: 29736785--29736830 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
29736775 ATTTATAACT
*
29736785 CATGAAAAAAATACTTAATA
1 CATG-AAAAAATACTTAAAA
*
29736805 CATGAAAAATTACTTAAAA
1 CATGAAAAAATACTTAAAA
*
29736824 CTTGAAA
1 CATGAAA
29736831 TGGTATTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 19 0.83
20 4 0.17
ACGTcount: A:0.57, C:0.11, G:0.07, T:0.26
Consensus pattern (19 bp):
CATGAAAAAATACTTAAAA
Found at i:29746217 original size:17 final size:18
Alignment explanation
Indices: 29746192--29746234 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
29746182 TATCTATTTC
*
29746192 TATATTTAAAT-GTTTAT
1 TATAATTAAATAGTTTAT
*
29746209 TATAATTAAATATTTTAT
1 TATAATTAAATAGTTTAT
29746227 TA-AATTAA
1 TATAATTAA
29746235 TATCACTCTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 16 0.70
18 7 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
TATAATTAAATAGTTTAT
Found at i:29756822 original size:5 final size:6
Alignment explanation
Indices: 29756780--29756821 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
29756770 AAATTATATG
* * *
29756780 AAGAAA AACAAT AATAAA AAGAAA AAGAAA AAG-AA AAGAAA A
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA A
29756822 GCAAAATAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
5 5 0.17
6 25 0.83
ACGTcount: A:0.81, C:0.02, G:0.12, T:0.05
Consensus pattern (6 bp):
AAGAAA
Found at i:29757708 original size:25 final size:25
Alignment explanation
Indices: 29757678--29757725 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
29757668 ATTTATATGT
* *
29757678 AGATATTTTTATATGAATGTAATTG
1 AGATATATTTACATGAATGTAATTG
*
29757703 AGATATATTTACATGTATGTAAT
1 AGATATATTTACATGAATGTAAT
29757726 AACAATTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.38, C:0.02, G:0.15, T:0.46
Consensus pattern (25 bp):
AGATATATTTACATGAATGTAATTG
Done.