Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 129432109
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: 129432109
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 102 of 425
Found at i:29591675 original size:40 final size:39
Alignment explanation
Indices: 29591620--29591788 Score: 189
Period size: 40 Copynumber: 4.2 Consensus size: 39
29591610 CAATTGAATG
* * *
29591620 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTG-TT
29591660 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCAAG-TGTT
* * *
29591700 ATATCCGGGCTAATACCCGAAGGCATTTGTGCGAGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGT-GTT
**
29591740 ATTATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGTGTGGTT
1 A-TATCCGGGCTAAGACCCGAAGGCAATT-GTGCAAGT-GTT
29591781 ATATCCGG
1 ATATCCGG
29591789 TTGTATTTCC
Statistics
Matches: 113, Mismatches: 10, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
39 4 0.04
40 72 0.64
41 37 0.33
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTGTT
Found at i:29591802 original size:81 final size:80
Alignment explanation
Indices: 29591620--29591788 Score: 241
Period size: 81 Copynumber: 2.1 Consensus size: 80
29591610 CAATTGAATG
* * *
29591620 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCA
1 ATATCCGGGCTAATACCCGAAGGCAATTGTGCGAGTGACTATATCCGGGCTAAGACCCGAAGGCA
*
29591685 TTCGTGCAAGTTGTT
66 TTCGTGCAAGTGGTT
* *
29591700 ATATCCGGGCTAATACCCGAAGGCATTTGTGCGAGTCG-TTATTATCCGGGCTAAGACCCGAAGG
1 ATATCCGGGCTAATACCCGAAGGCAATTGTGCGAGT-GACTA-TATCCGGGCTAAGACCCGAAGG
**
29591764 CATTCGTGCGTGTGGTT
64 CATTCGTGCAAGTGGTT
29591781 ATATCCGG
1 ATATCCGG
29591789 TTGTATTTCC
Statistics
Matches: 79, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
80 34 0.43
81 45 0.57
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (80 bp):
ATATCCGGGCTAATACCCGAAGGCAATTGTGCGAGTGACTATATCCGGGCTAAGACCCGAAGGCA
TTCGTGCAAGTGGTT
Found at i:29593951 original size:16 final size:16
Alignment explanation
Indices: 29593926--29593957 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
29593916 CAATATTTAT
*
29593926 AAAATTTTTGTTTTCG
1 AAAATCTTTGTTTTCG
29593942 AAAATCTTTGTTTTCG
1 AAAATCTTTGTTTTCG
29593958 TAAACCCATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.09, G:0.12, T:0.53
Consensus pattern (16 bp):
AAAATCTTTGTTTTCG
Found at i:29594950 original size:27 final size:27
Alignment explanation
Indices: 29594920--29595026 Score: 137
Period size: 27 Copynumber: 3.9 Consensus size: 27
29594910 GGCTGCCATA
* * *
29594920 ACAGATAATGTGACAGAGTCACCAAAT
1 ACAGATAATGTGGCAGAGCCACCAGAT
29594947 ACAGATAATCGTGGCAGAGCCACCAGA-
1 ACAGATAAT-GTGGCAGAGCCACCAGAT
29594974 ACAGATATATGTGGCAGAGCCACCAGAT
1 ACAGATA-ATGTGGCAGAGCCACCAGAT
*
29595002 -CAGATAATTGTGGCATAGCCACCAG
1 ACAGATAA-TGTGGCAGAGCCACCAG
29595027 GACGCTTCCT
Statistics
Matches: 72, Mismatches: 4, Indels: 8
0.86 0.05 0.10
Matches are distributed among these distances:
26 1 0.01
27 55 0.76
28 16 0.22
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.17
Consensus pattern (27 bp):
ACAGATAATGTGGCAGAGCCACCAGAT
Found at i:29595008 original size:54 final size:54
Alignment explanation
Indices: 29594919--29595026 Score: 155
Period size: 54 Copynumber: 2.0 Consensus size: 54
29594909 TGGCTGCCAT
*
29594919 AACAGATAATGTGACAGAGTCACCAAATACAGATAATCGTGGCAGAGCCACCAG
1 AACAGATAATGTGACAGAGCCACCAAATACAGATAATCGTGGCAGAGCCACCAG
* * * *
29594973 AACAGATATATGTGGCAGAGCCACCAGAT-CAGATAATTGTGGCATAGCCACCAG
1 AACAGATA-ATGTGACAGAGCCACCAAATACAGATAATCGTGGCAGAGCCACCAG
29595027 GACGCTTCCT
Statistics
Matches: 48, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
54 31 0.65
55 17 0.35
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.17
Consensus pattern (54 bp):
AACAGATAATGTGACAGAGCCACCAAATACAGATAATCGTGGCAGAGCCACCAG
Found at i:29598043 original size:13 final size:13
Alignment explanation
Indices: 29598025--29598050 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29598015 TGGCATCATT
29598025 ACTTGTAACACCC
1 ACTTGTAACACCC
29598038 ACTTGTAACACCC
1 ACTTGTAACACCC
29598051 CTTACATGAG
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:0.31, C:0.38, G:0.08, T:0.23
Consensus pattern (13 bp):
ACTTGTAACACCC
Found at i:29599529 original size:55 final size:53
Alignment explanation
Indices: 29599420--29599608 Score: 202
Period size: 55 Copynumber: 3.5 Consensus size: 53
29599410 GAATTACCAT
* * *
29599420 TGCCATGTCTTGAG-ATGGTCTTACGTGGTATCCTTGCCTTAT-GAACTCACCAA
1 TGCCATGCCTTG-GCATGGTCTTACATGGTA-CCTTGCCTTATAGAACTCATCAA
* * *
29599473 TGCGATGCCTTGGCATGGTCTTACATGGGACCTTTGCATTATAGTAACTCATCAA
1 TGCCATGCCTTGGCATGGTCTTACATGGTACC-TTGCCTTATAG-AACTCATCAA
* * * * * * *
29599528 TGCCATGTCTTGACATGGTTTTACATGATTTCCTTACCTTATAGAACTTATCAA
1 TGCCATGCCTTGGCATGGTCTTACATG-GTACCTTGCCTTATAGAACTCATCAA
29599582 TGCCATGCCTTGGCATGGTCTTACATG
1 TGCCATGCCTTGGCATGGTCTTACATG
29599609 ATATCCTTAT
Statistics
Matches: 112, Mismatches: 19, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
52 3 0.03
53 32 0.29
54 34 0.30
55 41 0.37
56 2 0.02
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (53 bp):
TGCCATGCCTTGGCATGGTCTTACATGGTACCTTGCCTTATAGAACTCATCAA
Found at i:29599606 original size:54 final size:54
Alignment explanation
Indices: 29599420--29599622 Score: 214
Period size: 54 Copynumber: 3.8 Consensus size: 54
29599410 GAATTACCAT
* * * * *
29599420 TGCCATGTCTTGAG-ATGGTCTTACGTGGTATCCTTGCCTTAT-GAACTCACCAA
1 TGCCATGCCTTG-GCATGGTCTTACATGATATCCTTACCTTATAGAACTCATCAA
* ** * *
29599473 TGCGATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCATTATAGTAACTCATCAA
1 TGCCATGCCTTGGCATGGTCTTACATGATATCC-TTACCTTATAG-AACTCATCAA
* * * * *
29599528 TGCCATGTCTTGACATGGTTTTACATGATTTCCTTACCTTATAGAACTTATCAA
1 TGCCATGCCTTGGCATGGTCTTACATGATATCCTTACCTTATAGAACTCATCAA
*
29599582 TGCCATGCCTTGGCATGGTCTTACATGATATCCTTATCTTA
1 TGCCATGCCTTGGCATGGTCTTACATGATATCCTTACCTTA
29599623 CCAAATGCCA
Statistics
Matches: 124, Mismatches: 21, Indels: 9
0.81 0.14 0.06
Matches are distributed among these distances:
52 3 0.02
53 32 0.26
54 46 0.37
55 41 0.33
56 2 0.02
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (54 bp):
TGCCATGCCTTGGCATGGTCTTACATGATATCCTTACCTTATAGAACTCATCAA
Found at i:29599651 original size:47 final size:47
Alignment explanation
Indices: 29599595--29599716 Score: 217
Period size: 47 Copynumber: 2.6 Consensus size: 47
29599585 CATGCCTTGG
* *
29599595 CATGGTCTTACATGATATCCTTATCTTACCAAATGCCATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
*
29599642 TATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
29599689 CATGGTCTTACATGGTATCCTTGTCTTA
1 CATGGTCTTACATGGTATCCTTGTCTTA
29599717 TGCCAATGCC
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 71 1.00
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.37
Consensus pattern (47 bp):
CATGGTCTTACATGGTATCCTTGTCTTACCAAATGCCATGTTCCAAA
Found at i:29600455 original size:30 final size:31
Alignment explanation
Indices: 29600412--29600469 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 31
29600402 CTAACTCAAA
*
29600412 CTTTGGCAAAATTACAATTTTGTCCCTAAAC
1 CTTTGGCAAAATTACAATTTTGCCCCTAAAC
*
29600443 CTTT-GCAGAATTACAATTTTGCCCCTA
1 CTTTGGCAAAATTACAATTTTGCCCCTA
29600470 GGCTCAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.36
Consensus pattern (31 bp):
CTTTGGCAAAATTACAATTTTGCCCCTAAAC
Found at i:29606657 original size:20 final size:20
Alignment explanation
Indices: 29606632--29606674 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
29606622 CAAGGACGTA
29606632 CATACTCATCAAATAAATTC
1 CATACTCATCAAATAAATTC
29606652 CATACTCATCAAATAAATTC
1 CATACTCATCAAATAAATTC
29606672 CAT
1 CAT
29606675 GTACAATATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.44, C:0.26, G:0.00, T:0.30
Consensus pattern (20 bp):
CATACTCATCAAATAAATTC
Found at i:29612949 original size:43 final size:44
Alignment explanation
Indices: 29612901--29613004 Score: 113
Period size: 43 Copynumber: 2.4 Consensus size: 44
29612891 TTTAGATATC
* * * *
29612901 GTCTTACATGTTATCACA-TATCGATGCCACTGTCCCAGACAGG
1 GTCTTACATGTAATCACATTAACAATGCCAATGTCCCAGACAGG
*** * *
29612944 GTCTTACACAAAATCA-ATTAACAATGCCAATGTCCCAGCCATG
1 GTCTTACATGTAATCACATTAACAATGCCAATGTCCCAGACAGG
29612987 GTCTTACATGTAATCACA
1 GTCTTACATGTAATCACA
29613005 ATACAATAAC
Statistics
Matches: 47, Mismatches: 12, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
42 1 0.02
43 45 0.96
44 1 0.02
ACGTcount: A:0.32, C:0.27, G:0.14, T:0.27
Consensus pattern (44 bp):
GTCTTACATGTAATCACATTAACAATGCCAATGTCCCAGACAGG
Found at i:29625067 original size:42 final size:43
Alignment explanation
Indices: 29624959--29625072 Score: 142
Period size: 43 Copynumber: 2.7 Consensus size: 43
29624949 AGCTCGTACA
* * * *
29624959 ATGCCAATGTCCTAAACGTGGTCTTACATGTAATCAAATATCG
1 ATGCCAATGTCCTAGACGTGGTCTTACACGAAATAAAATATCG
* *
29625002 ATGCCACTATCCTAGACAG-GGTCTTACACGAAATAAAATA-CG
1 ATGCCAATGTCCTAGAC-GTGGTCTTACACGAAATAAAATATCG
*
29625044 ATGCCAATGTCCCAGACGTGGTCTTACAC
1 ATGCCAATGTCCTAGACGTGGTCTTACAC
29625073 AATAACACAT
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
41 1 0.02
42 26 0.43
43 32 0.53
44 1 0.02
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (43 bp):
ATGCCAATGTCCTAGACGTGGTCTTACACGAAATAAAATATCG
Found at i:29625773 original size:30 final size:31
Alignment explanation
Indices: 29625716--29625773 Score: 75
Period size: 30 Copynumber: 1.9 Consensus size: 31
29625706 GGCTTGATAG
*
29625716 ATTACTAAGAAATGATCACAAAAACATAAAA
1 ATTACTAAAAAATGATCACAAAAACATAAAA
*
29625747 ATTA-TAAAAAATGGATCA-AAACACATA
1 ATTACTAAAAAAT-GATCACAAAAACATA
29625774 CCTTAATCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 15 0.62
31 9 0.38
ACGTcount: A:0.60, C:0.12, G:0.07, T:0.21
Consensus pattern (31 bp):
ATTACTAAAAAATGATCACAAAAACATAAAA
Found at i:29633428 original size:25 final size:25
Alignment explanation
Indices: 29633400--29633447 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
29633390 TTACACCATG
* * *
29633400 AAAATGACCGTTTTTCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
29633425 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
29633448 GTTTATGTAT
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:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:29633550 original size:20 final size:20
Alignment explanation
Indices: 29633490--29633550 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
29633480 ATAAATATGG
*
29633490 TATGTATGAGATGCACATGA
1 TATGTATGATATGCACATGA
*
29633510 CATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
29633530 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
29633550 T
1 T
29633551 GTAATCATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.33
Consensus pattern (20 bp):
TATGTATGATATGCACATGA
Found at i:29633627 original size:24 final size:24
Alignment explanation
Indices: 29633600--29633718 Score: 170
Period size: 24 Copynumber: 5.0 Consensus size: 24
29633590 GAGGAAGTGA
*
29633600 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
29633624 AAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATT
29633647 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
29633671 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
29633695 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
29633719 ATGATAAAGC
Statistics
Matches: 86, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
23 22 0.26
24 53 0.62
25 11 0.13
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:29633669 original size:47 final size:48
Alignment explanation
Indices: 29633600--29633718 Score: 170
Period size: 47 Copynumber: 2.5 Consensus size: 48
29633590 GAGGAAGTGA
29633600 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
** *
29633647 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
*
29633695 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
29633719 ATGATAAAGC
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
47 43 0.66
48 11 0.17
49 11 0.17
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (48 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
Found at i:29633944 original size:30 final size:31
Alignment explanation
Indices: 29633910--29633972 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 31
29633900 CGTTTACAGT
29633910 AAAGGCTTCGGCCCAGTAATATGAAAT-TGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
29633940 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
29633971 AA
1 AA
29633973 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 25 0.83
31 5 0.17
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.24
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:29638572 original size:20 final size:20
Alignment explanation
Indices: 29638512--29638572 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
29638502 ATAAATATGG
*
29638512 TATGTATGAGATGCACATGA
1 TATGTATGATATGCACATGA
*
29638532 CATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
29638552 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
29638572 T
1 T
29638573 GTAATCATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.33
Consensus pattern (20 bp):
TATGTATGATATGCACATGA
Found at i:29638649 original size:24 final size:24
Alignment explanation
Indices: 29638622--29638740 Score: 170
Period size: 24 Copynumber: 5.0 Consensus size: 24
29638612 GAGGAAGTGA
*
29638622 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
29638646 AAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATT
29638669 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
29638693 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
29638717 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
29638741 ATGATAAAGC
Statistics
Matches: 86, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
23 22 0.26
24 53 0.62
25 11 0.13
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:29638691 original size:47 final size:48
Alignment explanation
Indices: 29638622--29638740 Score: 170
Period size: 47 Copynumber: 2.5 Consensus size: 48
29638612 GAGGAAGTGA
29638622 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
** *
29638669 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
*
29638717 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
29638741 ATGATAAAGC
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
47 43 0.66
48 11 0.17
49 11 0.17
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (48 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
Found at i:29638992 original size:30 final size:31
Alignment explanation
Indices: 29638932--29638994 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
29638922 CGTTTACAGT
29638932 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
29638963 AAAGGCTTCGGCCCAGTGTTATG-AATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
29638993 AA
1 AA
29638995 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 9 0.30
31 21 0.70
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.24
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:29643477 original size:25 final size:25
Alignment explanation
Indices: 29643448--29643495 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
29643438 CCTTATAATG
* * *
29643448 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
29643473 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
29643496 GTTTATGTAT
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:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:29643598 original size:20 final size:20
Alignment explanation
Indices: 29643538--29643598 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
29643528 ATAAATATGG
*
29643538 TATGTATGAGATGCACATGA
1 TATGTATGATATGCACATGA
*
29643558 CATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
29643578 TATGTATGATATGCACATGA
1 TATGTATGATATGCACATGA
29643598 T
1 T
29643599 GTAATCATAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.34, C:0.11, G:0.21, T:0.33
Consensus pattern (20 bp):
TATGTATGATATGCACATGA
Found at i:29643675 original size:24 final size:24
Alignment explanation
Indices: 29643648--29643766 Score: 170
Period size: 24 Copynumber: 5.0 Consensus size: 24
29643638 GAGGAAGTGA
*
29643648 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATT
29643672 AAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATT
29643695 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
29643719 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
29643743 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
29643767 ATGATAAAGC
Statistics
Matches: 86, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
23 22 0.26
24 53 0.62
25 11 0.13
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:29643717 original size:47 final size:48
Alignment explanation
Indices: 29643648--29643766 Score: 170
Period size: 47 Copynumber: 2.5 Consensus size: 48
29643638 GAGGAAGTGA
29643648 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTA-T
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
** *
29643695 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
*
29643743 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
29643767 ATGATAAAGC
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
47 43 0.66
48 11 0.17
49 11 0.17
ACGTcount: A:0.29, C:0.22, G:0.23, T:0.27
Consensus pattern (48 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATT
Found at i:29643993 original size:31 final size:31
Alignment explanation
Indices: 29643958--29644021 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
29643948 CGTTTACAGT
29643958 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
29643989 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
29644020 AA
1 AA
29644022 TATGAAAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.38, C:0.16, G:0.23, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:29651048 original size:27 final size:28
Alignment explanation
Indices: 29651018--29651087 Score: 97
Period size: 27 Copynumber: 2.5 Consensus size: 28
29651008 ATAGTGAATC
*
29651018 CGCACACTTAGTGCTATAAAATC-AGCT
1 CGCACACTTAGTGCTATAAAATCAAACT
* * *
29651045 CGCACACATAGTGCTATATAATCAAATT
1 CGCACACTTAGTGCTATAAAATCAAACT
29651073 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
29651088 GTACAAATTT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 21 0.57
28 16 0.43
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.27
Consensus pattern (28 bp):
CGCACACTTAGTGCTATAAAATCAAACT
Found at i:29652864 original size:40 final size:40
Alignment explanation
Indices: 29652820--29653040 Score: 237
Period size: 40 Copynumber: 5.7 Consensus size: 40
29652810 GCTACTCGTT
* * *
29652820 CAAATACCTTCGGGACATAGCCCGG-TTATAGTAGCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
29652860 CAAATGCCTTCGGGACTTATCCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
29652900 CAAATGCCTTC-GGATCTTAGTCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCA
*
29652940 C-AAT--CTTC-GGATCTTAG-TCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAACTCGCA
* * * *
29652976 CAAATGCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
29653017 CAAA-GCCTTC-GGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
29653041 CATCATTCGA
Statistics
Matches: 162, Mismatches: 12, Indels: 15
0.86 0.06 0.08
Matches are distributed among these distances:
36 19 0.12
37 16 0.10
39 29 0.18
40 88 0.54
41 10 0.06
ACGTcount: A:0.26, C:0.26, G:0.21, T:0.27
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:29661008 original size:40 final size:40
Alignment explanation
Indices: 29660964--29661105 Score: 139
Period size: 40 Copynumber: 3.6 Consensus size: 40
29660954 GCTACTCGTT
* *
29660964 CAAATACCTTCGGGACATAGCCCGG-TTATAGTAGCTCGCA
1 CAAATGCCTTCGGGACATAGCCCGGATT-TAGTAACTCGCA
* *
29661004 CAAATGCCTTCGGGACTTATCCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACATAGCCCGGATTTAGTAACTCGCA
* * * * *
29661044 CAAATGCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCA
1 CAAATGCCTTCGGGA-CATAGCCCGGATTTAGTAAC-TCGCA
*
29661085 CAAA-GCCTTC-GGACTTAGCCC
1 CAAATGCCTTCGGGACATAGCCC
29661106 ACATCATTCG
Statistics
Matches: 89, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
39 10 0.11
40 69 0.78
41 10 0.11
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAGCCCGGATTTAGTAACTCGCA
Found at i:29665757 original size:54 final size:55
Alignment explanation
Indices: 29665669--29665799 Score: 151
Period size: 54 Copynumber: 2.4 Consensus size: 55
29665659 ATACCCCCAG
* * * *
29665669 TTGTAAAATTACCAAAGTA-CCTCCGGTTTATAAAATTACCCAAATATCCTCAAT
1 TTGTAAAATTATCAAAGTACCCTCCAGTTTATAAAATTACCCAAATACCCTCAAC
* ** *
29665723 TTGTAAAATTATCGAAA-TACCCT-CAGTTTGTAAAATTACTGAAATACCCTCGAC
1 TTGTAAAATTATC-AAAGTACCCTCCAGTTTATAAAATTACCCAAATACCCTCAAC
*
29665777 ATGTAAAATTATCAAAGTACCCT
1 TTGTAAAATTATCAAAGTACCCT
29665800 TGAATTACAA
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
53 3 0.05
54 56 0.86
55 6 0.09
ACGTcount: A:0.39, C:0.21, G:0.09, T:0.31
Consensus pattern (55 bp):
TTGTAAAATTATCAAAGTACCCTCCAGTTTATAAAATTACCCAAATACCCTCAAC
Found at i:29665771 original size:27 final size:27
Alignment explanation
Indices: 29665648--29665773 Score: 125
Period size: 27 Copynumber: 4.7 Consensus size: 27
29665638 TTAGTTTACC
*
29665648 AAATTACTGAAATACCCCCAG-TTGTA
1 AAATTACTGAAATACCCTCAGTTTGTA
* * *
29665674 AAATTAC-CAAAGTA-CCTCCGGTTTATA
1 AAATTACTGAAA-TACCCT-CAGTTTGTA
** * *
29665701 AAATTACCCAAATATCCTCAATTTGTA
1 AAATTACTGAAATACCCTCAGTTTGTA
29665728 AAATTA-TCGAAATACCCTCAGTTTGTA
1 AAATTACT-GAAATACCCTCAGTTTGTA
29665755 AAATTACTGAAATACCCTC
1 AAATTACTGAAATACCCTC
29665774 GACATGTAAA
Statistics
Matches: 82, Mismatches: 11, Indels: 13
0.77 0.10 0.12
Matches are distributed among these distances:
25 5 0.06
26 11 0.13
27 58 0.71
28 8 0.10
ACGTcount: A:0.39, C:0.22, G:0.09, T:0.30
Consensus pattern (27 bp):
AAATTACTGAAATACCCTCAGTTTGTA
Found at i:29665781 original size:27 final size:27
Alignment explanation
Indices: 29665724--29665799 Score: 86
Period size: 27 Copynumber: 2.8 Consensus size: 27
29665714 ATCCTCAATT
**
29665724 TGTAAAATTATCGAAATACCCTCAGTT
1 TGTAAAATTATCGAAATACCCTCAGCA
29665751 TGTAAAATTA-CTGAAATACCCTC-GACA
1 TGTAAAATTATC-GAAATACCCTCAG-CA
29665778 TGTAAAATTATC-AAAGTACCCT
1 TGTAAAATTATCGAAA-TACCCT
29665800 TGAATTACAA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
26 5 0.12
27 37 0.86
28 1 0.02
ACGTcount: A:0.39, C:0.20, G:0.11, T:0.30
Consensus pattern (27 bp):
TGTAAAATTATCGAAATACCCTCAGCA
Found at i:29665824 original size:27 final size:27
Alignment explanation
Indices: 29665794--29666283 Score: 651
Period size: 27 Copynumber: 18.2 Consensus size: 27
29665784 ATTATCAAAG
* *
29665794 TACCCTTGAATTACAAAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
29665821 TACCCTCGATTTACAAAATTA-TCGTTT
1 TACCCTCGATTTACAAAATTACT-GTTT
*
29665848 TACCCTCGATTTACAAAATTACCGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
29665875 TACCCTCGATTTACAAAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
* * *
29665902 TACCCTTGATTTATAAAATTACTATTT
1 TACCCTCGATTTACAAAATTACTGTTT
*
29665929 TACCCTCGATTTACAAAATTACTATTT
1 TACCCTCGATTTACAAAATTACTGTTT
*
29665956 TACCCTCGATTTACTAAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
* * * *
29665983 TACCCTTGATTTACAGAATTACTATCT
1 TACCCTCGATTTACAAAATTACTGTTT
*
29666010 TACCCTCGATTTACAAAATTACTATTT
1 TACCCTCGATTTACAAAATTACTGTTT
* * *
29666037 TACCCTCAATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
29666064 TACCCTCGATTTACAAAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
* * **
29666091 TACCCTTGTTTTACTGAATTACT-TTT
1 TACCCTCGATTTACAAAATTACTGTTT
* *
29666117 TGCCCTCGATTTACAAAATTACTATTT
1 TACCCTCGATTTACAAAATTACTGTTT
* *
29666144 TACCCTTGATTTACAAAATTACCGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
* * * *
29666171 TACCCTCGATTGATAGAATTACTATTT
1 TACCCTCGATTTACAAAATTACTGTTT
29666198 TACCCTCGATTTACAAAATTACTGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
* * *
29666225 TACCCTCAATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAAAATTACTGTTT
* **
29666252 TACCCTCGATTTATAAAATTACCATTT
1 TACCCTCGATTTACAAAATTACTGTTT
29666279 TACCC
1 TACCC
29666284 CTAGGGTGTT
Statistics
Matches: 404, Mismatches: 56, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
26 22 0.05
27 382 0.95
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.41
Consensus pattern (27 bp):
TACCCTCGATTTACAAAATTACTGTTT
Found at i:29666564 original size:27 final size:26
Alignment explanation
Indices: 29666520--29666570 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
29666510 CTCGTTGCAA
*
29666520 TCTGGTGGCCTCGCCACATATATCTGT
1 TCTGGTGACCTCGCCACA-ATATCTGT
* *
29666547 TCTGGTGACTTCGTCACAATATCT
1 TCTGGTGACCTCGCCACAATATCT
29666571 AGCAGCCTCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 6 0.29
27 15 0.71
ACGTcount: A:0.18, C:0.27, G:0.20, T:0.35
Consensus pattern (26 bp):
TCTGGTGACCTCGCCACAATATCTGT
Found at i:29666623 original size:2 final size:2
Alignment explanation
Indices: 29666618--29666651 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
29666608 ACACACACAC
29666618 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29666652 CTGTTTTGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29666861 original size:31 final size:31
Alignment explanation
Indices: 29666826--29666902 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
29666816 TTGCATTCAC
* * *
29666826 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTCTGATTCTGTCACCTAATACTG
* *
29666857 ATTCTGATTCTAATTCTGTCACCTAATTCTG
1 ATTCTGATTCTGATTCTGTCACCTAATACTG
29666888 ATTCTGATTCTGATT
1 ATTCTGATTCTGATT
29666903 TTGATTCTGT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.21, C:0.18, G:0.13, T:0.48
Consensus pattern (31 bp):
ATTCTGATTCTGATTCTGTCACCTAATACTG
Found at i:29666865 original size:6 final size:6
Alignment explanation
Indices: 29666826--29666956 Score: 72
Period size: 6 Copynumber: 21.3 Consensus size: 6
29666816 TTGCATTCAC
* * *
29666826 ATTCTG ATTTTG ATTCTG -TTACCTG ATACTG ATTCTG ATTCTA ATTCTG
1 ATTCTG ATTCTG ATTCTG ATT--CTG ATTCTG ATTCTG ATTCTG ATTCTG
* * * * * * *
29666875 -TCACCTA ATTCTG ATTCTG ATTCTG ATTTTG ATTCTG -TCACCCG ATCCTA
1 AT--TCTG ATTCTG ATTCTG ATTCTG ATTCTG ATTCTG AT--TCTG ATTCTG
*
29666925 ATTCTG ATTCTC ATTCTG ATTCT- AGTTCTG AT
1 ATTCTG ATTCTG ATTCTG ATTCTG A-TTCTG AT
29666957 AATGTTTCTT
Statistics
Matches: 94, Mismatches: 20, Indels: 22
0.69 0.15 0.16
Matches are distributed among these distances:
5 5 0.05
6 78 0.83
7 8 0.09
8 3 0.03
ACGTcount: A:0.20, C:0.21, G:0.13, T:0.47
Consensus pattern (6 bp):
ATTCTG
Found at i:29666929 original size:37 final size:37
Alignment explanation
Indices: 29666854--29666947 Score: 125
Period size: 37 Copynumber: 2.5 Consensus size: 37
29666844 TTACCTGATA
* * * *
29666854 CTGATTCTGATTCTAATTCTGTCACCTAATTCTGATT
1 CTGATTCTGATTCTGATTCTGTCACCCAATCCTAATT
* *
29666891 CTGATTCTGATTTTGATTCTGTCACCCGATCCTAATT
1 CTGATTCTGATTCTGATTCTGTCACCCAATCCTAATT
*
29666928 CTGATTCTCATTCTGATTCT
1 CTGATTCTGATTCTGATTCT
29666948 AGTTCTGATA
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 49 1.00
ACGTcount: A:0.19, C:0.23, G:0.12, T:0.46
Consensus pattern (37 bp):
CTGATTCTGATTCTGATTCTGTCACCCAATCCTAATT
Found at i:29666932 original size:31 final size:31
Alignment explanation
Indices: 29666826--29666942 Score: 99
Period size: 31 Copynumber: 3.6 Consensus size: 31
29666816 TTGCATTCAC
* * *
29666826 ATTCTGATTTTGATTCTGTTACCTGATACTG
1 ATTCTGATTCTGATTCTGTCACCCGATACTG
* *
29666857 ATTCTGATTCTAATTCTGTCACCTAATTCTGATTCTG
1 ATTCTGATTCTGATTCTGTCACC-----C-GATACTG
* * *
29666894 ATTCTGATTTTGATTCTGTCACCCGATCCTA
1 ATTCTGATTCTGATTCTGTCACCCGATACTG
*
29666925 ATTCTGATTCTCATTCTG
1 ATTCTGATTCTGATTCTG
29666943 ATTCTAGTTC
Statistics
Matches: 69, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
31 41 0.59
32 1 0.01
37 27 0.39
ACGTcount: A:0.20, C:0.21, G:0.13, T:0.46
Consensus pattern (31 bp):
ATTCTGATTCTGATTCTGTCACCCGATACTG
Found at i:29667771 original size:18 final size:17
Alignment explanation
Indices: 29667731--29667764 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
29667721 TATATGTGGC
29667731 TAATATGAATGGTTATA
1 TAATATGAATGGTTATA
*
29667748 TGATATGGAATGGTTAT
1 TAATAT-GAATGGTTAT
29667765 GAAATATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.35, C:0.00, G:0.24, T:0.41
Consensus pattern (17 bp):
TAATATGAATGGTTATA
Found at i:29670144 original size:25 final size:25
Alignment explanation
Indices: 29670115--29670162 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
29670105 TTATAACTTG
* * *
29670115 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
29670140 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
29670163 GTTTATGTAT
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:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:29670229 original size:20 final size:20
Alignment explanation
Indices: 29670206--29670263 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
29670196 TAAACATGGT
29670206 ATGTATGATATGCACATGAC
1 ATGTATGATATGCACATGAC
*
29670226 ATGTATGATATGCACATGAT
1 ATGTATGATATGCACATGAC
29670246 ATGTATGATATGCACATG
1 ATGTATGATATGCACATG
29670264 CTGTATTCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (20 bp):
ATGTATGATATGCACATGAC
Found at i:29670246 original size:11 final size:11
Alignment explanation
Indices: 29670210--29670263 Score: 53
Period size: 11 Copynumber: 5.3 Consensus size: 11
29670200 CATGGTATGT
29670210 ATGATATGCAC
1 ATGATATGCAC
* *
29670221 ATGACATG--T
1 ATGATATGCAC
29670230 ATGATATGCAC
1 ATGATATGCAC
*
29670241 ATGATATG--T
1 ATGATATGCAC
29670250 ATGATATGCAC
1 ATGATATGCAC
29670261 ATG
1 ATG
29670264 CTGTATTCAT
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
9 15 0.45
11 18 0.55
ACGTcount: A:0.35, C:0.13, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:29670346 original size:23 final size:23
Alignment explanation
Indices: 29670316--29670435 Score: 204
Period size: 23 Copynumber: 5.1 Consensus size: 23
29670306 AGGAAGTGAA
29670316 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
29670339 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
29670362 AAAAGGGCTTATGCCCCAGTTATT
1 -AAAGGGCTTATGCCCCAGTTATT
29670386 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
* *
29670409 AAAAAGGCTTTTGCCCCAGTTATT
1 -AAAGGGCTTATGCCCCAGTTATT
29670433 AAA
1 AAA
29670436 AGAGGCTAGG
Statistics
Matches: 93, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
23 49 0.53
24 44 0.47
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:29670371 original size:24 final size:24
Alignment explanation
Indices: 29670315--29670442 Score: 215
Period size: 24 Copynumber: 5.4 Consensus size: 24
29670305 GAGGAAGTGA
29670315 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
29670339 -AAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
29670362 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
29670386 -AAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
* *
29670409 AAAAAGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
29670433 AAAAGAGGCT
1 AAAAG-GGCT
29670443 AGGCCTCTAG
Statistics
Matches: 98, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
23 46 0.47
24 48 0.49
25 4 0.04
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.29
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:29670384 original size:47 final size:47
Alignment explanation
Indices: 29670315--29670435 Score: 224
Period size: 47 Copynumber: 2.6 Consensus size: 47
29670305 GAGGAAGTGA
29670315 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATT
29670362 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATT
* *
29670409 AAAAAGGCTTTTGCCCCAGTTATTAAA
1 AAAAGGGCTTATGCCCCAGTTATTAAA
29670436 AGAGGCTAGG
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 72 1.00
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.30
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATT
Found at i:29670685 original size:31 final size:31
Alignment explanation
Indices: 29670650--29670713 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
29670640 CGTTTATAGT
29670650 AAAGGCTTCGACCCAATAATATGAAATATGA
1 AAAGGCTTCGACCCAATAATATGAAATATGA
* * **
29670681 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGACCCAATAATATGAAATATGA
29670712 AA
1 AA
29670714 TATGAAAAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGACCCAATAATATGAAATATGA
Found at i:29672514 original size:28 final size:27
Alignment explanation
Indices: 29672448--29672517 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
29672438 ATAGTGAGTC
*
29672448 CGCACACTTAGTGCTATATAATCAGCT
1 CGCACACTTAGTGCTATATAATCAACT
*
29672475 CGCACACTTAGTGCTATATAATCAAATT
1 CGCACACTTAGTGCTATATAATC-AACT
29672503 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
29672518 GTACAAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 23 0.57
28 17 0.43
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:29675518 original size:29 final size:29
Alignment explanation
Indices: 29675483--29675673 Score: 267
Period size: 29 Copynumber: 6.6 Consensus size: 29
29675473 ATAAACGATC
* * *
29675483 TCGCACACTTAGTGCCATGCGATTTAAGC
1 TCGCACACTTAGTGCCATACAATTTAAGT
* *
29675512 TCGCACACATAGTGCCATATAATTTAAGT
1 TCGCACACTTAGTGCCATACAATTTAAGT
* *
29675541 TTGCACACTTAGTGCCATATAATTTAAGT
1 TCGCACACTTAGTGCCATACAATTTAAGT
29675570 TCGCACACTTAGTGCCATACAATTTAAGT
1 TCGCACACTTAGTGCCATACAATTTAAGT
29675599 TCGCACACTTAGTGCCATACAATTTAAGT
1 TCGCACACTTAGTGCCATACAATTTAAGT
* * *
29675628 TCGCACACTTAGTGCCATAC-CTTCCAAGC
1 TCGCACACTTAGTGCCATACAATT-TAAGT
*
29675657 CCGCACACTTAGTGCCA
1 TCGCACACTTAGTGCCA
29675674 ATCTTGTCAC
Statistics
Matches: 148, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
28 2 0.01
29 146 0.99
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (29 bp):
TCGCACACTTAGTGCCATACAATTTAAGT
Found at i:29683304 original size:29 final size:29
Alignment explanation
Indices: 29683269--29683459 Score: 267
Period size: 29 Copynumber: 6.6 Consensus size: 29
29683259 ATAAACGATC
* * *
29683269 TCGCACACTTAGTGCCATGCGATTTAAGC
1 TCGCACACTTAGTGCCATACAATTTAAGT
* *
29683298 TCGCACACATAGTGCCATATAATTTAAGT
1 TCGCACACTTAGTGCCATACAATTTAAGT
* *
29683327 TTGCACACTTAGTGCCATATAATTTAAGT
1 TCGCACACTTAGTGCCATACAATTTAAGT
29683356 TCGCACACTTAGTGCCATACAATTTAAGT
1 TCGCACACTTAGTGCCATACAATTTAAGT
29683385 TCGCACACTTAGTGCCATACAATTTAAGT
1 TCGCACACTTAGTGCCATACAATTTAAGT
* * *
29683414 TCGCACACTTAGTGCCATAC-CTTCCAAGC
1 TCGCACACTTAGTGCCATACAATT-TAAGT
*
29683443 CCGCACACTTAGTGCCA
1 TCGCACACTTAGTGCCA
29683460 ATCTTGTCAC
Statistics
Matches: 148, Mismatches: 13, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
28 2 0.01
29 146 0.99
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (29 bp):
TCGCACACTTAGTGCCATACAATTTAAGT
Found at i:29689463 original size:28 final size:27
Alignment explanation
Indices: 29689397--29689466 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
29689387 ATAGTGAGTC
*
29689397 CGCACACTTAGTGCTATATAATCAGCT
1 CGCACACTTAGTGCTATATAATCAACT
*
29689424 CGCACACTTAGTGCTATATAATCAAATT
1 CGCACACTTAGTGCTATATAATC-AACT
29689452 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
29689467 GTACAAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
27 23 0.57
28 17 0.43
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:29692350 original size:39 final size:39
Alignment explanation
Indices: 29692307--29692440 Score: 207
Period size: 39 Copynumber: 3.4 Consensus size: 39
29692297 TACAATTGAG
29692307 TATTGTGATATATGCTTGAATGTTATGTGATTATATGAT
1 TATTGTGATATATGCTTGAATGTTATGTGATTATATGAT
*
29692346 TATTGTGATATATGCTTGAATGTTATGTGATTATATGAG
1 TATTGTGATATATGCTTGAATGTTATGTGATTATATGAT
* *
29692385 TATTGTGATATATGCTTAAACGTTATGTGATTATATG-T
1 TATTGTGATATATGCTTGAATGTTATGTGATTATATGAT
* *
29692423 GTAATGTGATACATGCTT
1 -TATTGTGATATATGCTT
29692441 AAAAGTGAAT
Statistics
Matches: 88, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
39 88 1.00
ACGTcount: A:0.28, C:0.04, G:0.21, T:0.46
Consensus pattern (39 bp):
TATTGTGATATATGCTTGAATGTTATGTGATTATATGAT
Found at i:29694215 original size:40 final size:41
Alignment explanation
Indices: 29694160--29694256 Score: 137
Period size: 40 Copynumber: 2.4 Consensus size: 41
29694150 CGACTACGAC
*
29694160 TGGCACTAAGTGTGCG-GTTTAATATAGCTTCAGCTATA-AA
1 TGGCACTAAGTGTGCGAG-TTAACATAGCTTCAGCTATATAA
**
29694200 TGGCACTAAGTGTGCGAGTTGGCATAGCTTCAGCTATATAA
1 TGGCACTAAGTGTGCGAGTTAACATAGCTTCAGCTATATAA
29694241 -GGCACTAAGTGTGCGA
1 TGGCACTAAGTGTGCGA
29694257 TACTGACTTA
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
40 49 0.94
41 3 0.06
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (41 bp):
TGGCACTAAGTGTGCGAGTTAACATAGCTTCAGCTATATAA
Found at i:29697081 original size:22 final size:22
Alignment explanation
Indices: 29697053--29697097 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
29697043 AGATATGTTA
29697053 CACATAGGATGTCTAATGCTTG
1 CACATAGGATGTCTAATGCTTG
29697075 CACATAGGATGTCTAATGCTTG
1 CACATAGGATGTCTAATGCTTG
29697097 C
1 C
29697098 CACCATGACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (22 bp):
CACATAGGATGTCTAATGCTTG
Found at i:29701634 original size:27 final size:27
Alignment explanation
Indices: 29701523--29701628 Score: 176
Period size: 27 Copynumber: 3.9 Consensus size: 27
29701513 ACGCCCTATT
29701523 TGATAAAATGACTGTTTTGCCCCTACA
1 TGATAAAATGACTGTTTTGCCCCTACA
* *
29701550 TGATAAAATGATTGTTTTGCCCTTACA
1 TGATAAAATGACTGTTTTGCCCCTACA
*
29701577 TGATAAAATGACTGTTTTGCCCTTACA
1 TGATAAAATGACTGTTTTGCCCCTACA
*
29701604 TGATAAAATGACTATTTTGCCCCTA
1 TGATAAAATGACTGTTTTGCCCCTA
29701629 TGTGATGTAT
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 74 1.00
ACGTcount: A:0.30, C:0.19, G:0.14, T:0.37
Consensus pattern (27 bp):
TGATAAAATGACTGTTTTGCCCCTACA
Found at i:29703589 original size:40 final size:40
Alignment explanation
Indices: 29703530--29703737 Score: 218
Period size: 40 Copynumber: 5.2 Consensus size: 40
29703520 CAATTGAATG
* * * *
29703530 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * * *
29703570 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
29703610 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
29703650 AAATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * **
29703690 CTATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
29703730 ATATCCGG
1 ATATCCGG
29703738 TTGTATTCCG
Statistics
Matches: 142, Mismatches: 26, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 142 1.00
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
Found at i:29703668 original size:80 final size:80
Alignment explanation
Indices: 29703531--29703737 Score: 247
Period size: 80 Copynumber: 2.6 Consensus size: 80
29703521 AATTGAATGA
* * ** * * *
29703531 TATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATTATATCCGGGTTAAGACCCGAAGGCAA
1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAA
*
29703596 TTGTGCTAGT-G-AC
66 TTGTGCAAGTCGTAC
* * *
29703609 TACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAAATCCGGGCTAATACCCGAAGGC
1 T--ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGC
* *
29703674 ATTTGTGCAAGTCGTTC
64 AATTGTGCAAGTCGTAC
* *
29703691 TATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTTATATCCGG
1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGG
29703738 TTGTATTCCG
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
78 1 0.01
80 105 0.96
81 1 0.01
82 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (80 bp):
TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAA
TTGTGCAAGTCGTAC
Found at i:29711597 original size:40 final size:40
Alignment explanation
Indices: 29711538--29711745 Score: 218
Period size: 40 Copynumber: 5.2 Consensus size: 40
29711528 CAATTGAATG
* * * *
29711538 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * * *
29711578 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
29711618 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
29711658 AAATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * **
29711698 CTATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
29711738 ATATCCGG
1 ATATCCGG
29711746 TTGTATTCCG
Statistics
Matches: 142, Mismatches: 26, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 142 1.00
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
Found at i:29711676 original size:80 final size:80
Alignment explanation
Indices: 29711539--29711745 Score: 247
Period size: 80 Copynumber: 2.6 Consensus size: 80
29711529 AATTGAATGA
* * ** * * *
29711539 TATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATTATATCCGGGTTAAGACCCGAAGGCAA
1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAA
*
29711604 TTGTGCTAGT-G-AC
66 TTGTGCAAGTCGTAC
* * *
29711617 TACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAAATCCGGGCTAATACCCGAAGGC
1 T--ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGC
* *
29711682 ATTTGTGCAAGTCGTTC
64 AATTGTGCAAGTCGTAC
* *
29711699 TATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTTATATCCGG
1 TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGG
29711746 TTGTATTCCG
Statistics
Matches: 109, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
78 1 0.01
80 105 0.96
81 1 0.01
82 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.26
Consensus pattern (80 bp):
TATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCAA
TTGTGCAAGTCGTAC
Found at i:29715945 original size:2 final size:2
Alignment explanation
Indices: 29715938--29715962 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29715928 AAAGCTTAAC
29715938 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
29715963 AGTCGACACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29720439 original size:40 final size:40
Alignment explanation
Indices: 29720384--29720551 Score: 239
Period size: 40 Copynumber: 4.2 Consensus size: 40
29720374 CAATTGAATG
*
29720384 ATATCCGGGTTAAGACCCGAAGGCAATT-GTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTTGTT
*
29720424 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAATTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
* * * *
29720464 ATATCCGGGCTAATACCCGAAGGCATTTGTGCGAGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
** *
29720504 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCGTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
29720544 ATATCCGG
1 ATATCCGG
29720552 TTGTATCCGA
Statistics
Matches: 116, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
39 3 0.03
40 113 0.97
ACGTcount: A:0.24, C:0.21, G:0.28, T:0.26
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
Found at i:29722044 original size:29 final size:29
Alignment explanation
Indices: 29721943--29722036 Score: 179
Period size: 29 Copynumber: 3.2 Consensus size: 29
29721933 GTGACGAGAT
29721943 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
29721972 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
29722001 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
*
29722030 CGGCACT
1 TGGCACT
29722037 GGGTGTGCGA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 64 1.00
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.27
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:29722061 original size:58 final size:58
Alignment explanation
Indices: 29721939--29722074 Score: 177
Period size: 58 Copynumber: 2.4 Consensus size: 58
29721929 TACGGTGACG
* *
29721939 AGAT-TGGCACTAAGTGTGCATGCTGGAAATATATGGCACTAAGTGTGCATGCTGGAA
1 AGATATGGCACTAAGTGTGCATGCTGGAAATATACGGCACTAAGTGTGCATGCTCGAA
* **
29721996 ATATATGGCACTAAGTGTGCATGCTGGAAATATACGGCACTGGGTGTGCGA-GCTCGAA
1 AGATATGGCACTAAGTGTGCATGCTGGAAATATACGGCACTAAGTGTGC-ATGCTCGAA
* * *
29722054 GGGTATGGCACTATGTGTGCA
1 AGATATGGCACTAAGTGTGCA
29722075 GGCTTAAATC
Statistics
Matches: 68, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
57 3 0.04
58 64 0.94
59 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.32, T:0.26
Consensus pattern (58 bp):
AGATATGGCACTAAGTGTGCATGCTGGAAATATACGGCACTAAGTGTGCATGCTCGAA
Found at i:29729806 original size:29 final size:29
Alignment explanation
Indices: 29729773--29729837 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
29729763 GTGACGAGAT
29729773 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
29729802 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
*
29729831 CGGCACT
1 TGGCACT
29729838 GGGTGTGCGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:29735036 original size:28 final size:28
Alignment explanation
Indices: 29734971--29735071 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
29734961 ATAGTGAATC
*
29734971 CGCACACTTAGTGCTATATGTATTC-AACT
1 CGCACACTTAGTGCTATA--TAATCAAACT
29735000 CGCACACTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
29735028 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
29735058 CGCACACTTAGTGC
1 CGCACACTTAGTGC
29735072 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 4 0.06
28 23 0.36
29 18 0.28
30 19 0.30
ACGTcount: A:0.30, C:0.27, G:0.14, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:29735552 original size:2 final size:2
Alignment explanation
Indices: 29735545--29735569 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
29735535 TAATGGCCGA
29735545 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
29735570 CAATGTCAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29736865 original size:49 final size:49
Alignment explanation
Indices: 29736812--29736908 Score: 194
Period size: 49 Copynumber: 2.0 Consensus size: 49
29736802 TACTGATGGA
29736812 ACAACCAAGTCAGTCTTAATCATCAATAAATGAGTTTTCAAGAAATCTT
1 ACAACCAAGTCAGTCTTAATCATCAATAAATGAGTTTTCAAGAAATCTT
29736861 ACAACCAAGTCAGTCTTAATCATCAATAAATGAGTTTTCAAGAAATCT
1 ACAACCAAGTCAGTCTTAATCATCAATAAATGAGTTTTCAAGAAATCT
29736909 CTTCCAGTCG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.41, C:0.19, G:0.10, T:0.30
Consensus pattern (49 bp):
ACAACCAAGTCAGTCTTAATCATCAATAAATGAGTTTTCAAGAAATCTT
Found at i:29737250 original size:17 final size:15
Alignment explanation
Indices: 29737185--29737260 Score: 73
Period size: 15 Copynumber: 5.0 Consensus size: 15
29737175 TAAAAATGAC
*
29737185 AAGAAAACCAA-ATA
1 AAGAAATCCAAGATA
* *
29737199 AAGAAGTCCAAGACA
1 AAGAAATCCAAGATA
*
29737214 GAGAAATCCAAGATA
1 AAGAAATCCAAGATA
*
29737229 AAGAAACTTCCAAGATT
1 AAGAAA--TCCAAGATA
*
29737246 TAGAAATCCAAGATA
1 AAGAAATCCAAGATA
29737261 CAATACCATA
Statistics
Matches: 49, Mismatches: 10, Indels: 5
0.77 0.16 0.08
Matches are distributed among these distances:
14 9 0.18
15 27 0.55
17 13 0.27
ACGTcount: A:0.55, C:0.16, G:0.14, T:0.14
Consensus pattern (15 bp):
AAGAAATCCAAGATA
Found at i:29747306 original size:49 final size:49
Alignment explanation
Indices: 29747252--29747372 Score: 197
Period size: 49 Copynumber: 2.5 Consensus size: 49
29747242 TCTGGTACGC
* *
29747252 ATAGTAGCCTGCACATAGTACTACACATGCGACCAATTATCCGGTACAT
1 ATAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCCGGTACAT
*
29747301 ATAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACAT
1 ATAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCCGGTACAT
* *
29747350 GTAGTAGCATGCACTTAGTACTA
1 ATAGTAGCCTGCACTTAGTACTA
29747373 TCTCTAATAC
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 67 1.00
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.26
Consensus pattern (49 bp):
ATAGTAGCCTGCACTTAGTACTACACACGCGACCAATTATCCGGTACAT
Found at i:29750542 original size:20 final size:20
Alignment explanation
Indices: 29750519--29750556 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
29750509 CACATCCAAA
*
29750519 TACAAAATTTTAAAAATCTT
1 TACAAAATATTAAAAATCTT
*
29750539 TACAAAATATTGAAAATC
1 TACAAAATATTAAAAATC
29750557 GCGAATAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.34
Consensus pattern (20 bp):
TACAAAATATTAAAAATCTT
Found at i:29756840 original size:28 final size:28
Alignment explanation
Indices: 29756794--29756890 Score: 178
Period size: 28 Copynumber: 3.5 Consensus size: 28
29756784 TTTAAAACCC
*
29756794 TAGGGGT-ATATCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
29756821 TAGGGGTAATTTCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
29756849 TAGGGGTAATTTCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
29756877 TAGGGGTAATTTCG
1 TAGGGGTAATTTCG
29756891 TGATCTACGC
Statistics
Matches: 68, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
27 7 0.10
28 61 0.90
ACGTcount: A:0.19, C:0.10, G:0.27, T:0.44
Consensus pattern (28 bp):
TAGGGGTAATTTCGGTAATTTTGCTCTT
Found at i:29758530 original size:20 final size:20
Alignment explanation
Indices: 29758507--29758544 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
29758497 CACCTCCAAA
*
29758507 TACAAAATTTTAAAAATCTT
1 TACAAAATATTAAAAATCTT
*
29758527 TACAAAATATTGAAAATC
1 TACAAAATATTAAAAATC
29758545 GCGAATAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.11, G:0.03, T:0.34
Consensus pattern (20 bp):
TACAAAATATTAAAAATCTT
Found at i:29759658 original size:24 final size:24
Alignment explanation
Indices: 29759629--29759682 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
29759619 TTTGTGGTCC
29759629 CAAAACCACTAGTTCGACTAGGGT
1 CAAAACCACTAGTTCGACTAGGGT
*
29759653 CAAAACCACTATTTCGACTAGGGT
1 CAAAACCACTAGTTCGACTAGGGT
*
29759677 CTAAAC
1 CAAAAC
29759683 TAGACTGTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (24 bp):
CAAAACCACTAGTTCGACTAGGGT
Found at i:29763369 original size:39 final size:39
Alignment explanation
Indices: 29763291--29763414 Score: 212
Period size: 39 Copynumber: 3.2 Consensus size: 39
29763281 TATGATAACC
* *
29763291 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
29763331 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
29763370 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
29763409 CGCACA
1 CGCACA
29763415 TTCATACACA
Statistics
Matches: 81, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
39 64 0.79
40 17 0.21
ACGTcount: A:0.26, C:0.33, G:0.19, T:0.22
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:29773232 original size:28 final size:28
Alignment explanation
Indices: 29773192--29773246 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
29773182 ATATATACGA
* *
29773192 ATGTGTTGATCCAGGATCTATCAAAGCT
1 ATGTGTCGATCCAAGATCTATCAAAGCT
29773220 ATGTGTCGATCCAAGATCTATCAAAGC
1 ATGTGTCGATCCAAGATCTATCAAAGC
29773247 AATCACATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (28 bp):
ATGTGTCGATCCAAGATCTATCAAAGCT
Found at i:29775792 original size:10 final size:10
Alignment explanation
Indices: 29775779--29775817 Score: 69
Period size: 10 Copynumber: 3.8 Consensus size: 10
29775769 ATATGTGAAT
29775779 ATATCATGGC
1 ATATCATGGC
29775789 ATATCATGTGC
1 ATATCATG-GC
29775800 ATATCATGGC
1 ATATCATGGC
29775810 ATATCATG
1 ATATCATG
29775818 TACAAAAGTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 18 0.64
11 10 0.36
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (10 bp):
ATATCATGGC
Found at i:29775805 original size:21 final size:21
Alignment explanation
Indices: 29775779--29775818 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
29775769 ATATGTGAAT
29775779 ATATCATGGCATATCATGTGC
1 ATATCATGGCATATCATGTGC
29775800 ATATCATGGCATATCATGT
1 ATATCATGGCATATCATGT
29775819 ACAAAAGTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (21 bp):
ATATCATGGCATATCATGTGC
Found at i:29775886 original size:25 final size:25
Alignment explanation
Indices: 29775858--29775906 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
29775848 ATAACATAAC
* * *
29775858 CCTAGGGGTATAATGGTCATTTTCT
1 CCTAGGGGCAAAAAGGTCATTTTCT
29775883 CCTAGGGGCAAAAAGGTCATTTTC
1 CCTAGGGGCAAAAAGGTCATTTTC
29775907 ACATTATAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAAAGGTCATTTTCT
Found at i:29783589 original size:25 final size:25
Alignment explanation
Indices: 29783560--29783624 Score: 96
Period size: 25 Copynumber: 2.6 Consensus size: 25
29783550 TTAATAACAG
29783560 GGGCAAAGCCCTTTTCAGTAAACTA
1 GGGCAAAGCCCTTTTCAGTAAACTA
* *
29783585 GGGCAAAG-CCTTTCTCGGTAAACTG
1 GGGCAAAGCCCTTT-TCAGTAAACTA
29783610 GGGCAAAGCCCTTTT
1 GGGCAAAGCCCTTTT
29783625 AGCACTTCCT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
24 5 0.14
25 26 0.72
26 5 0.14
ACGTcount: A:0.26, C:0.25, G:0.25, T:0.25
Consensus pattern (25 bp):
GGGCAAAGCCCTTTTCAGTAAACTA
Found at i:29783684 original size:10 final size:10
Alignment explanation
Indices: 29783671--29783709 Score: 69
Period size: 10 Copynumber: 3.8 Consensus size: 10
29783661 ATATTTGAAT
29783671 ATATCATGGC
1 ATATCATGGC
29783681 ATATCATGTGC
1 ATATCATG-GC
29783692 ATATCATGGC
1 ATATCATGGC
29783702 ATATCATG
1 ATATCATG
29783710 TACAAAAGCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 18 0.64
11 10 0.36
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (10 bp):
ATATCATGGC
Found at i:29783697 original size:21 final size:21
Alignment explanation
Indices: 29783671--29783710 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
29783661 ATATTTGAAT
29783671 ATATCATGGCATATCATGTGC
1 ATATCATGGCATATCATGTGC
29783692 ATATCATGGCATATCATGT
1 ATATCATGGCATATCATGT
29783711 ACAAAAGCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (21 bp):
ATATCATGGCATATCATGTGC
Found at i:29783778 original size:25 final size:25
Alignment explanation
Indices: 29783750--29783800 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
29783740 ATAACATAAC
* * *
29783750 CCTAGGGGTATAATGGTCATTTTCA
1 CCTAGGGGCAAAAAGGTCATTTTCA
29783775 CCTAGGGGCAAAAAGGTCATTTTCA
1 CCTAGGGGCAAAAAGGTCATTTTCA
29783800 C
1 C
29783801 ATTATAAGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (25 bp):
CCTAGGGGCAAAAAGGTCATTTTCA
Found at i:29789904 original size:40 final size:40
Alignment explanation
Indices: 29789859--29790002 Score: 200
Period size: 40 Copynumber: 3.6 Consensus size: 40
29789849 CTCGCACAAG
* *
29789859 GCCTTCAGGTCTTAGCCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCATAAAT
* *
29789899 GCCTTCGGGTCTTAGCCCGGATATAG-CAACTCGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAGTC-ACTAGCATAAAT
* * *
29789939 GCCTTCGGATCTTAGTCCGGATATAGTCACTAGCATAAAA
1 GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCATAAAT
*
29789979 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGTCTTAGCCCGGATAT
29790003 TATTCGAATA
Statistics
Matches: 90, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
39 1 0.01
40 88 0.98
41 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAGTCACTAGCATAAAT
Found at i:29789959 original size:80 final size:79
Alignment explanation
Indices: 29789823--29790002 Score: 240
Period size: 80 Copynumber: 2.3 Consensus size: 79
29789813 ACCCAAGTAT
* * *
29789823 CTTCGGGAT-TTAG-CCAGATATAACCACTCGCACAAGGCCTTCAGGTCTTAGCCCGGATATGGT
1 CTTCGGG-TCTTAGCCCGGATATAACAACTCGCACAAGGCCTTCAGGTCTTAGCCCGGATATAGT
*
29789886 CACTAGCATAAATGC
65 CACTAGCATAAAAGC
* * *
29789901 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATAG
1 CTTCGGGTCTTAGCCCGGATATAACAACTCGCAC-AAGGCCTTCAGG-TCTTAGCCCGGATATAG
29789965 TCACTAGCATAAAAGC
64 TCACTAGCATAAAAGC
*
29789981 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGTCTTAGCCCGGATAT
29790003 TATTCGAATA
Statistics
Matches: 90, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
77 1 0.01
78 11 0.12
79 19 0.21
80 59 0.66
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (79 bp):
CTTCGGGTCTTAGCCCGGATATAACAACTCGCACAAGGCCTTCAGGTCTTAGCCCGGATATAGTC
ACTAGCATAAAAGC
Found at i:29792791 original size:40 final size:40
Alignment explanation
Indices: 29792732--29792858 Score: 152
Period size: 40 Copynumber: 3.2 Consensus size: 40
29792722 CAGAATACAA
* * *
29792732 CCGGATATAACCACGTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATAGAAGCACTTGCACGAATGCCTTCGGGTCTTAGC
29792772 CCGGATAGAATG-ACTTGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATAGAA-GCACTTGCACGAATGCCTTCGGGTCTTAGC
* * *
29792812 CCGGAT-GTAGCCACTAGCAC-AATTGCCTTCGGGTCTTAAC
1 CCGGATAGAAG-CACTTGCACGAA-TGCCTTCGGGTCTTAGC
29792852 CCGGATA
1 CCGGATA
29792859 TAATTTCCAG
Statistics
Matches: 76, Mismatches: 6, Indels: 9
0.84 0.07 0.10
Matches are distributed among these distances:
38 1 0.01
39 4 0.05
40 71 0.93
ACGTcount: A:0.23, C:0.28, G:0.25, T:0.24
Consensus pattern (40 bp):
CCGGATAGAAGCACTTGCACGAATGCCTTCGGGTCTTAGC
Found at i:29794712 original size:25 final size:25
Alignment explanation
Indices: 29794684--29794735 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
29794674 TTCTTATGTA
29794684 TTATGACATGTTGATCATTTTTTTC
1 TTATGACATGTTGATCATTTTTTTC
29794709 TTATGACATGTTGATCATTTTTTTC
1 TTATGACATGTTGATCATTTTTTTC
29794734 TT
1 TT
29794736 CTATGGCAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.19, C:0.12, G:0.12, T:0.58
Consensus pattern (25 bp):
TTATGACATGTTGATCATTTTTTTC
Found at i:29798511 original size:27 final size:27
Alignment explanation
Indices: 29798459--29798511 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
29798449 TTGAAATTAA
* **
29798459 AAGGTTAATTAAGTAAATTAACAAATT
1 AAGGTTAATTAAATAAAGCAACAAATT
29798486 AAGGTTAATTCAAATAAAGCAA-AAAT
1 AAGGTTAATT-AAATAAAGCAACAAAT
29798512 GATCATCATC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 14 0.64
28 8 0.36
ACGTcount: A:0.55, C:0.06, G:0.11, T:0.28
Consensus pattern (27 bp):
AAGGTTAATTAAATAAAGCAACAAATT
Found at i:29799707 original size:24 final size:24
Alignment explanation
Indices: 29799680--29799733 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
29799670 TAAATTGGTG
29799680 GAATTCATGT-TTAA-TCTTTGGATT
1 GAATT-ATGTGTTAAGT-TTTGGATT
29799704 GAATATATGTGTTAAGTTTTGGATT
1 GAAT-TATGTGTTAAGTTTTGGATT
*
29799729 AAATT
1 GAATT
29799734 TGAATTGCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
24 9 0.35
25 16 0.62
26 1 0.04
ACGTcount: A:0.30, C:0.04, G:0.19, T:0.48
Consensus pattern (24 bp):
GAATTATGTGTTAAGTTTTGGATT
Found at i:29800485 original size:13 final size:13
Alignment explanation
Indices: 29800467--29800505 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
29800457 TGGGTAGAGA
29800467 CACAGGCATGTGT
1 CACAGGCATGTGT
29800480 CACAGGCATGTGT
1 CACAGGCATGTGT
*
29800493 CACAGCCATGTGT
1 CACAGGCATGTGT
29800506 GACACACGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.23, C:0.26, G:0.28, T:0.23
Consensus pattern (13 bp):
CACAGGCATGTGT
Found at i:29804255 original size:15 final size:15
Alignment explanation
Indices: 29804224--29804272 Score: 64
Period size: 14 Copynumber: 3.3 Consensus size: 15
29804214 ATAACTTAAA
*
29804224 TTTAGCATTTAAATTT
1 TTTAACATTT-AATTT
*
29804240 TTTAATATTTAA-TT
1 TTTAACATTTAATTT
29804254 TTTAACATTTAATTT
1 TTTAACATTTAATTT
29804269 TTTA
1 TTTA
29804273 TTTTTCAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
14 13 0.45
15 8 0.28
16 8 0.28
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (15 bp):
TTTAACATTTAATTT
Found at i:29819410 original size:40 final size:40
Alignment explanation
Indices: 29819213--29819396 Score: 307
Period size: 40 Copynumber: 4.6 Consensus size: 40
29819203 GGATTGATAC
29819213 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAT-A
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
* * * *
29819252 TCGAGCTATGTCCTGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
29819292 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATCA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
29819332 CCGGGCTAAGTCCCGAAGGCATTTGTGAGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
29819372 CCGGGCTAAGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
29819397 AGCTAGTAGC
Statistics
Matches: 133, Mismatches: 11, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
39 34 0.26
40 99 0.74
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:29826047 original size:28 final size:28
Alignment explanation
Indices: 29826007--29826061 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
29825997 CCCATTGCCG
29826007 TGACTAGACAAAGAAAAGAAAAAAAAAA
1 TGACTAGACAAAGAAAAGAAAAAAAAAA
29826035 TGACTAGACAAAGAAAAGAAAAAAAAA
1 TGACTAGACAAAGAAAAGAAAAAAAAA
29826062 TCATCCTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.71, C:0.07, G:0.15, T:0.07
Consensus pattern (28 bp):
TGACTAGACAAAGAAAAGAAAAAAAAAA
Found at i:29827624 original size:40 final size:40
Alignment explanation
Indices: 29827388--29827610 Score: 376
Period size: 40 Copynumber: 5.6 Consensus size: 40
29827378 ATTGATACCG
* * *
29827388 GGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTA-AATCT
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA-CC
* *
29827428 GGGCTAAGTCTCGAAGGCATTTGTGCGAGTTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACC
29827468 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACC
*
29827508 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATCACC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACC
29827548 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACC
29827588 GGGCTAAGTCCCGAAGGCATTTG
1 GGGCTAAGTCCCGAAGGCATTTG
29827611 AGCTAGTAGC
Statistics
Matches: 173, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
40 172 0.99
41 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAACC
Found at i:29830124 original size:28 final size:28
Alignment explanation
Indices: 29830091--29830144 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
29830081 AAATTTTATA
*
29830091 ACTTAA-ATTTAGCATTTAAATTTTTAAT
1 ACTTAATATTTAACATTT-AATTTTTAAT
*
29830119 ACTTAATTTTTAACATTTAATTTTTA
1 ACTTAATATTTAACATTTAATTTTTA
29830145 TTTTTCAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 14 0.61
29 9 0.39
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.54
Consensus pattern (28 bp):
ACTTAATATTTAACATTTAATTTTTAAT
Found at i:29830128 original size:14 final size:14
Alignment explanation
Indices: 29830109--29830144 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
29830099 TTAGCATTTA
*
29830109 AATTTTTAATACTT
1 AATTTTTAACACTT
*
29830123 AATTTTTAACATTT
1 AATTTTTAACACTT
29830137 AATTTTTA
1 AATTTTTA
29830145 TTTTTCAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (14 bp):
AATTTTTAACACTT
Found at i:29841833 original size:44 final size:44
Alignment explanation
Indices: 29841768--29841851 Score: 107
Period size: 44 Copynumber: 1.9 Consensus size: 44
29841758 TTGATATCTC
* * *
29841768 AAAGTCCATGGTTGTACCATGGTAATTAAGGAAGAATTGACGGA
1 AAAGTCCATGGTTATAACATGGCAATTAAGGAAGAATTGACGGA
* *
29841812 AAAGTCCAT-GTTCATAACATGGCATTTAAGGAGGAATTGA
1 AAAGTCCATGGTT-ATAACATGGCAATTAAGGAAGAATTGA
29841852 TGGTTAAGGA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 3 0.09
44 31 0.91
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.26
Consensus pattern (44 bp):
AAAGTCCATGGTTATAACATGGCAATTAAGGAAGAATTGACGGA
Found at i:29842053 original size:47 final size:47
Alignment explanation
Indices: 29841991--29842112 Score: 217
Period size: 47 Copynumber: 2.6 Consensus size: 47
29841981 GCATTGGCAC
*
29841991 TAAGACAAGGGTACCATGTAAGACCATGTTTGGAACATGGCATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
29842038 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
1 TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
* *
29842085 TAAGATAAGGATATCATGTAAGACCATG
1 TAAGACAAGGATACCATGTAAGACCATG
29842113 CCAAGGCATG
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 72 1.00
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.25
Consensus pattern (47 bp):
TAAGACAAGGATACCATGTAAGACCATGTTTGGAACATGGCATTTGG
Found at i:29842219 original size:55 final size:54
Alignment explanation
Indices: 29842091--29842287 Score: 245
Period size: 55 Copynumber: 3.6 Consensus size: 54
29842081 TTGGTAAGAT
* * *
29842091 AAGGATATCATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGC
* * * *
29842145 AAGGAAATCATGTAAGACCATGTCAAGACATGTCATTGATGAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTT-CTATAAGGC
* * *
29842200 AAAGG-TCCCATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGC
* * *
29842253 AAGGTTACCACGTAAGACCATGTCAAGACATGGCA
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCA
29842288 ATGGTAAGTT
Statistics
Matches: 124, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
52 4 0.03
53 33 0.27
54 41 0.33
55 42 0.34
56 4 0.03
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.22
Consensus pattern (54 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGATGAGTTCTATAAGGC
Found at i:29842299 original size:53 final size:53
Alignment explanation
Indices: 29842099--29842298 Score: 231
Period size: 53 Copynumber: 3.7 Consensus size: 53
29842089 ATAAGGATAT
* * *
29842099 CATGTAAGACCATGCCAAGGCATGGCATTGATAAGTTCTATAAGGCAAGGAAAT
1 CATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCTATAAGGCAAGG-TAC
* * * *
29842153 CATGTAAGACCATGTCAAGACATGTCATTGATGAGTTACTATAAGGCAAAGGTCC
1 CATGTAAGACCATGCCAAGACATGGCATTGATAAGTT-CTATAAGGC-AAGGTAC
* * *
29842208 CATGTAAGACCATGCCAAGGCATGGCATTGGTGAGTTC-ATAAGGCAAGGTTAC
1 CATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCTATAAGGCAAGG-TAC
* * * *
29842261 CACGTAAGACCATGTCAAGACATGGCAATGGTAAGTTC
1 CATGTAAGACCATGCCAAGACATGGCATTGATAAGTTC
29842299 AAAAAGGAAA
Statistics
Matches: 126, Mismatches: 17, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
52 4 0.03
53 42 0.33
54 34 0.27
55 42 0.33
56 4 0.03
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.23
Consensus pattern (53 bp):
CATGTAAGACCATGCCAAGACATGGCATTGATAAGTTCTATAAGGCAAGGTAC
Found at i:29844269 original size:20 final size:20
Alignment explanation
Indices: 29844244--29844307 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
29844234 CACAAACGTG
29844244 CCCCTGTTTGTACTTCGGTA
1 CCCCTGTTTGTACTTCGGTA
* * ** *
29844264 CCCCTGAATTGCACTTATGTG
1 CCCCTG-TTTGTACTTCGGTA
*
29844285 CCCCTATTTGTACTTCGGTA
1 CCCCTGTTTGTACTTCGGTA
29844305 CCC
1 CCC
29844308 TTGAATTGCA
Statistics
Matches: 32, Mismatches: 11, Indels: 2
0.71 0.24 0.04
Matches are distributed among these distances:
20 18 0.56
21 14 0.44
ACGTcount: A:0.14, C:0.33, G:0.17, T:0.36
Consensus pattern (20 bp):
CCCCTGTTTGTACTTCGGTA
Found at i:29844288 original size:21 final size:21
Alignment explanation
Indices: 29844264--29844331 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 21
29844254 TACTTCGGTA
29844264 CCCCTGAATTGCACTTATGTG
1 CCCCTGAATTGCACTTATGTG
* * ** *
29844285 CCCCT-ATTTGTACTTCGGTA
1 CCCCTGAATTGCACTTATGTG
* *
29844305 CCCTTGAATTGCACATATGTG
1 CCCCTGAATTGCACTTATGTG
29844326 CCCCTG
1 CCCCTG
29844332 TTTATACTTC
Statistics
Matches: 33, Mismatches: 13, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
20 14 0.42
21 19 0.58
ACGTcount: A:0.18, C:0.31, G:0.18, T:0.34
Consensus pattern (21 bp):
CCCCTGAATTGCACTTATGTG
Found at i:29844368 original size:82 final size:82
Alignment explanation
Indices: 29844226--29844396 Score: 252
Period size: 82 Copynumber: 2.1 Consensus size: 82
29844216 AAGATTATTA
* * *
29844226 TTGAATTGCACAAACGTGCCCCTGTTTGTACTTCGGTACCCCTGAATTGCACTTATGTGCCCCTA
1 TTGAATTGCACAAACGTGCCCCTGTTTATACTTCGGTACCCCCGAATTGCACTTACGTGCCCCTA
*
29844291 TTTGTACTTCGGTACCC
66 TTTGTACTTCGATACCC
* * * * *
29844308 TTGAATTGCACATATGTGCCCCTGTTTATACTTCGGTTCCCCCGAATTGCACTTACGTGCCCTTG
1 TTGAATTGCACAAACGTGCCCCTGTTTATACTTCGGTACCCCCGAATTGCACTTACGTGCCCCTA
*
29844373 TTTGTACTTCGATGCCC
66 TTTGTACTTCGATACCC
29844390 TTGAATT
1 TTGAATT
29844397 TTTCTTGTGC
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
82 79 1.00
ACGTcount: A:0.18, C:0.28, G:0.18, T:0.36
Consensus pattern (82 bp):
TTGAATTGCACAAACGTGCCCCTGTTTATACTTCGGTACCCCCGAATTGCACTTACGTGCCCCTA
TTTGTACTTCGATACCC
Found at i:29844396 original size:41 final size:41
Alignment explanation
Indices: 29844226--29844396 Score: 216
Period size: 41 Copynumber: 4.2 Consensus size: 41
29844216 AAGATTATTA
*
29844226 TTGAATTGCACAAACGTGCCCCTGTTTGTACTTCGGTACCC
1 TTGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCC
* * * *
29844267 CTGAATTGCACTTATGTGCCCCTATTTGTACTTCGGTACCC
1 TTGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCC
* * *
29844308 TTGAATTGCACATATGTGCCCCTGTTTATACTTCGGTTCCC
1 TTGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCC
** * * * *
29844349 CCGAATTGCACTTACGTGCCCTTGTTTGTACTTCGATGCCC
1 TTGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCC
29844390 TTGAATT
1 TTGAATT
29844397 TTTCTTGTGC
Statistics
Matches: 110, Mismatches: 20, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 110 1.00
ACGTcount: A:0.18, C:0.28, G:0.18, T:0.36
Consensus pattern (41 bp):
TTGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCC
Found at i:29847869 original size:40 final size:40
Alignment explanation
Indices: 29847775--29847999 Score: 249
Period size: 40 Copynumber: 5.6 Consensus size: 40
29847765 TATTCGAATG
*
29847775 ATATCCGGGCTAAG-TCCCGAAGGCTTTTGTGCTAGGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCTA-GTGACT
* * * *
29847816 ATAACCGGACTAAGATCCGAAGGCATTCGTGCGAGTTG-CT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAG-TGACT
* * *
29847856 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT
* * *
29847896 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT
* * *
29847936 ATATCTGGGCTAAG-TCCCGAAGGCATTTATGCTAGTGACC
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCTAGTGACT
* *
29847976 ACATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGATCCGAAGGC
29848000 CTTGTGCAAG
Statistics
Matches: 156, Mismatches: 23, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
39 1 0.01
40 125 0.80
41 29 0.19
42 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT
Found at i:29847955 original size:80 final size:80
Alignment explanation
Indices: 29847775--29848035 Score: 303
Period size: 80 Copynumber: 3.3 Consensus size: 80
29847765 TATTCGAATG
* * * *
29847775 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACTATAACCGGACTAAGATCCGAAGGC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTA-GTGACTATATCCGGGCTAAGACCCGAAGGC
*
29847840 ATTCGTGCGAGTTGCT
65 ATTCGTGCGAGTCGCT
* * * *
29847856 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATTATATCCGGGCTAAAACCCGAAGGCA
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCA
* *
29847921 TTTGTGCTAG-CGACT
66 TTCGTGCGAGTCG-CT
* * * * *
29847936 ATATCTGGGCTAAGTCCCGAAGGCATTTATGCTAGTGACCACATCCGGGCTAAGACCCGAAGGCC
1 ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCA
* * *
29848001 TT-GTGCAAGTAGTT
66 TTCGTGCGAGTCGCT
*
29848015 ATATCC-GGCTAAGTCCTGAAG
1 ATATCCGGGCTAAGTCCCGAAG
29848036 ATTACTTGAG
Statistics
Matches: 153, Mismatches: 25, Indels: 7
0.83 0.14 0.04
Matches are distributed among these distances:
78 14 0.09
79 13 0.08
80 94 0.61
81 32 0.21
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (80 bp):
ATATCCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTATATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCGCT
Found at i:29847989 original size:120 final size:121
Alignment explanation
Indices: 29847775--29847999 Score: 303
Period size: 120 Copynumber: 1.9 Consensus size: 121
29847765 TATTCGAATG
** * *
29847775 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACTATAACCGGACTAAGATCCGAAGGC
1 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGGCGACTATAACCGGACTAAGATCCGAAGGC
* * *
29847840 ATTCGTGCGAGTTGCTATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATT
66 ATTCATGCGAGTTGCCACATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATT
* * *
29847896 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTA-GCGACTATATCTGGGCTAAG-TCCCGAAGG
1 ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGGCGACTATAACCGGACTAAGAT-CCGAAGG
* *
29847959 CATTTATGCTAG-TGACCACATCCGGGCTAAGACCCGAAGGC
65 CATTCATGCGAGTTG-CCACATCCGGGCTAAGACCCGAAGGC
29848000 CTTGTGCAAG
Statistics
Matches: 90, Mismatches: 12, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
119 3 0.03
120 56 0.62
121 31 0.34
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (121 bp):
ATATCCGGGCTAAAACCCGAAGGCATTTGTGCTAGGCGACTATAACCGGACTAAGATCCGAAGGC
ATTCATGCGAGTTGCCACATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGATT
Found at i:29849668 original size:13 final size:13
Alignment explanation
Indices: 29849650--29849674 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29849640 GCACACAAGT
29849650 GTGTGACTTGGCC
1 GTGTGACTTGGCC
29849663 GTGTGACTTGGC
1 GTGTGACTTGGC
29849675 TATGTAACCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.08, C:0.20, G:0.40, T:0.32
Consensus pattern (13 bp):
GTGTGACTTGGCC
Found at i:29853720 original size:17 final size:19
Alignment explanation
Indices: 29853698--29853732 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
29853688 CTAATTTCAC
29853698 CATTCTC-CAT-TTTCTCT
1 CATTCTCTCATCTTTCTCT
29853715 CATTCTCTCATCTTTCTC
1 CATTCTCTCATCTTTCTC
29853733 AAATTGTTGC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 3 0.19
19 6 0.38
ACGTcount: A:0.11, C:0.37, G:0.00, T:0.51
Consensus pattern (19 bp):
CATTCTCTCATCTTTCTCT
Found at i:29855776 original size:96 final size:96
Alignment explanation
Indices: 29855609--29855812 Score: 245
Period size: 96 Copynumber: 2.1 Consensus size: 96
29855599 GTTTGTTGAT
* * *
29855609 CTAAGATCACAACCCATATAGCTCGTCGACCTAAGATCGCGATTGAAATTATTCAAGTCCACTAA
1 CTAAGATCACAACACATACAGCTCGCCGACCTAAGATCGCGATTGAAATTATTCAAGTCCACTAA
*
29855674 CATAAGATCACGACCT-TAGTGGCTCGTCAACC
66 CATAAGATCACGACCTAT-GTGGCTCATCAA-C
* * * *
29855706 CT-AGATCACAACACATGCAGCTCGCCGACCTAAGATTGCGATTGAAATTA-TCACCGTTCGA-T
1 CTAAGATCACAACACATACAGCTCGCCGACCTAAGATCGCGATTGAAATTATTCA-AG-TCCACT
* * *
29855768 GACGTAAGATCACGACCTATGTGGCTCATCGAC
64 AACATAAGATCACGACCTATGTGGCTCATCAAC
29855801 CTAAGATCACAA
1 CTAAGATCACAA
29855813 TCAAAATTAT
Statistics
Matches: 92, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
95 6 0.07
96 80 0.87
97 6 0.07
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.23
Consensus pattern (96 bp):
CTAAGATCACAACACATACAGCTCGCCGACCTAAGATCGCGATTGAAATTATTCAAGTCCACTAA
CATAAGATCACGACCTATGTGGCTCATCAAC
Found at i:29856001 original size:132 final size:126
Alignment explanation
Indices: 29855767--29856077 Score: 302
Period size: 132 Copynumber: 2.4 Consensus size: 126
29855757 CACCGTTCGA
* *** * ** **
29855767 TGACGTAAGATCACGACCTATGTGGCTCATCGACCTAAGATCACAATCAAAATTATTCTCGTCCG
1 TGACATAAGATCACGACCTATGTGGCTTGCCAACCTAAGATCGTAGCCAAAATTATTCTCGTCCG
* ** *
29855832 CTGACCTAAGATCACAACCGATACAACTTGACGACCTAAGATTGCGATTGAAATTATTTGAGTCC
66 CTGACCTAAGATCACAACCGATACAACTTCACGACCTAAGATCACGACT-AAA--A-TT-A-TCC
29855897 GC
125 GC
* * * * * **
29855899 TGACATAAGATCATGGCCTATGTGGCTTGCTAACTTAAGATCGTAGCCAAAATTATTCTGGTTTG
1 TGACATAAGATCACGACCTATGTGGCTTGCCAACCTAAGATCGTAGCCAAAATTATTCTCGTCCG
* * * * *
29855964 CTGACCTAAGATCACAACTC-ATATAGC-TCACTTACCTAAGATCACGACTAAAATTATTCGT
66 CTGACCTAAGATCACAAC-CGATACAACTTCAC-GACCTAAGATCACGACTAAAATTATCCGC
*
29856025 TGACATAAGATCACGACCTATGTGGCTTGCCGACCTAAGATCGTAGCCAAAAT
1 TGACATAAGATCACGACCTATGTGGCTTGCCAACCTAAGATCGTAGCCAAAAT
29856078 CCCATGGCTA
Statistics
Matches: 147, Mismatches: 30, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
126 51 0.35
127 1 0.01
128 2 0.01
129 1 0.01
131 6 0.04
132 85 0.58
133 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.27
Consensus pattern (126 bp):
TGACATAAGATCACGACCTATGTGGCTTGCCAACCTAAGATCGTAGCCAAAATTATTCTCGTCCG
CTGACCTAAGATCACAACCGATACAACTTCACGACCTAAGATCACGACTAAAATTATCCGC
Found at i:29859314 original size:28 final size:28
Alignment explanation
Indices: 29859247--29859347 Score: 96
Period size: 28 Copynumber: 3.5 Consensus size: 28
29859237 ATAGTGAATC
* *
29859247 CGCACACTTAGTGCTATATACGTTC-AGCT
1 CGCACACTTAGTGCTATATA--ATCAAACT
*
29859276 CGCACATTTAGTGCTATATAATCAAACT
1 CGCACACTTAGTGCTATATAATCAAACT
* * * *
29859304 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA--TCAAACT
29859334 CGCACACTTAGTGC
1 CGCACACTTAGTGC
29859348 CAATCTTGTC
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
27 2 0.03
28 21 0.34
29 19 0.31
30 19 0.31
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCTATATAATCAAACT
Found at i:29874771 original size:48 final size:48
Alignment explanation
Indices: 29874680--29874900 Score: 288
Period size: 48 Copynumber: 4.7 Consensus size: 48
29874670 TCTCATATCG
**
29874680 ATGCCATGTCCCAGACATGG---T-CATGAAATCACATATCGATGCCA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATCGATGCCA
** * * *
29874724 ACACCATATCCCAGATATGGTCTTACATGGGATCGCATATCGATGCCA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATCGATGCCA
*
29874772 ATGCCATGTCCCAGACATGGTCTTATATGGGATCACATATCGATGCCA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATCGATGCCA
** * *
29874820 ATGCCATGTCTTAGACATGGTCTTACTTGGGATCACATATCAATGCCA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATCGATGCCA
* *
29874868 GTGCCATGTCCCATACATGGTCTTACATGGGAT
1 ATGCCATGTCCCAGACATGGTCTTACATGGGAT
29874901 TTCAATGCCA
Statistics
Matches: 150, Mismatches: 23, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
44 16 0.11
47 1 0.01
48 133 0.89
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (48 bp):
ATGCCATGTCCCAGACATGGTCTTACATGGGATCACATATCGATGCCA
Found at i:29874925 original size:37 final size:37
Alignment explanation
Indices: 29874884--29874968 Score: 125
Period size: 37 Copynumber: 2.3 Consensus size: 37
29874874 TGTCCCATAC
* *
29874884 ATGGTCTTACATGGGATTTCAATGCCATAGCCCAGCT
1 ATGGTCTTACATGGCATTACAATGCCATAGCCCAGCT
* * *
29874921 ATGGTCTTACATGTCATTACGATGCCATAGCCTAGCT
1 ATGGTCTTACATGGCATTACAATGCCATAGCCCAGCT
29874958 ATGGTCTTACA
1 ATGGTCTTACA
29874969 CTTACTCAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 43 1.00
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.32
Consensus pattern (37 bp):
ATGGTCTTACATGGCATTACAATGCCATAGCCCAGCT
Found at i:29877395 original size:40 final size:40
Alignment explanation
Indices: 29877287--29877396 Score: 148
Period size: 40 Copynumber: 2.8 Consensus size: 40
29877277 ATTGAATGAT
* * * * *
29877287 ATCCGGGCTAAGTCCCGAAGACATTTATGCTGGTAATTAC
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTAACTAC
* * *
29877327 ATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTAC
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTAACTAC
29877367 ATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGC
29877397 AAATTGTGAA
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 60 1.00
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (40 bp):
ATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTAACTAC
Found at i:29877411 original size:40 final size:39
Alignment explanation
Indices: 29877287--29877436 Score: 133
Period size: 40 Copynumber: 3.8 Consensus size: 39
29877277 ATTGAATGAT
* * * * * * *
29877287 ATCCGGGCTAAGTCCCGAAGACATTTATGCTGGTAATTAC
1 ATCCGGGTTAAGACCCGAAGGCATTTGTGCTAGTGA-CAC
*
29877327 ATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGACTAC
1 ATCCGGGTTAAGACCCGAAGGCATTTGTGCTAGTGAC-AC
* *
29877367 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATTGTGA-A-
1 ATCCGGGTTAAGACCCGAAGGCATTTGTGC---TAGTGACAC
* *
29877407 ATCCGGGTTAAGTCCCGAAGGCCTTTGTGC
1 ATCCGGGTTAAGACCCGAAGGCATTTGTGC
29877437 GGGTTACCAT
Statistics
Matches: 92, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
40 86 0.93
41 1 0.01
43 5 0.05
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.25
Consensus pattern (39 bp):
ATCCGGGTTAAGACCCGAAGGCATTTGTGCTAGTGACAC
Found at i:29880367 original size:48 final size:48
Alignment explanation
Indices: 29880292--29880513 Score: 206
Period size: 48 Copynumber: 4.8 Consensus size: 48
29880282 CAGTTAATGA
*
29880292 GAGCCAATGTAAGACCATGTCTAGGACATGGCATCGGCGTTGATATGT
1 GAGCCAATGTAAGACCATGTCTGGGACATGGCATCGGCGTTGATATGT
* * **
29880340 GAGCCAGTGTAAGACCATGTTTGGGACATGGCATCGGCGTTGATACAT
1 GAGCCAATGTAAGACCATGTCTGGGACATGGCATCGGCGTTGATATGT
* * * * * *
29880388 GTGCCAATGTAAGACCATATCTGGGATATGGCATCGGCATCGGTATGT
1 GAGCCAATGTAAGACCATGTCTGGGACATGGCATCGGCGTTGATATGT
** * *
29880436 GATTTC-ATGTAAGACCATATCTGGG--AT---AT-GGCGTTGATATGA
1 GA-GCCAATGTAAGACCATGTCTGGGACATGGCATCGGCGTTGATATGT
*****
29880478 GATTTTGTGTAAGACCATGTCTGGGACATGGCATCG
1 GAGCCAATGTAAGACCATGTCTGGGACATGGCATCG
29880514 ATGTGAGGCC
Statistics
Matches: 141, Mismatches: 25, Indels: 16
0.77 0.14 0.09
Matches are distributed among these distances:
41 2 0.01
42 28 0.20
43 2 0.01
44 2 0.01
46 2 0.01
47 2 0.01
48 102 0.72
49 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (48 bp):
GAGCCAATGTAAGACCATGTCTGGGACATGGCATCGGCGTTGATATGT
Found at i:29880461 original size:96 final size:96
Alignment explanation
Indices: 29880294--29880467 Score: 233
Period size: 96 Copynumber: 1.8 Consensus size: 96
29880284 GTTAATGAGA
* * * *
29880294 GCCAATGTAAGACCATGTCTAGGACATGGCATCGGCGTTGATATGTGAGCCAGTGTAAGACCATG
1 GCCAATGTAAGACCATATCTAGGACATGGCATCGGCATCGATATGTGAGCCAGTGTAAGACCATA
*
29880359 TTTGGGACATGGCATCGGCGTTGATACATGT
66 TCTGGGACATGGCATCGGCGTTGATACATGT
* * * **
29880390 GCCAATGTAAGACCATATCTGGGATATGGCATCGGCATCGGTATGTGATTTCA-TGTAAGACCAT
1 GCCAATGTAAGACCATATCTAGGACATGGCATCGGCATCGATATGTGA-GCCAGTGTAAGACCAT
*
29880454 ATCTGGGATATGGC
65 ATCTGGGACATGGC
29880468 GTTGATATGA
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
96 64 0.97
97 2 0.03
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.27
Consensus pattern (96 bp):
GCCAATGTAAGACCATATCTAGGACATGGCATCGGCATCGATATGTGAGCCAGTGTAAGACCATA
TCTGGGACATGGCATCGGCGTTGATACATGT
Found at i:29891052 original size:40 final size:40
Alignment explanation
Indices: 29890855--29891058 Score: 230
Period size: 40 Copynumber: 5.1 Consensus size: 40
29890845 TGAATGATAC
* * ** * **
29890855 CCGGGCTAAGTCCCGAAGACATTTATGCTAGTATTTATAT
1 CCGGGCTAAGACCCGAAGGCATTCGTGCAAGTGGTTATAT
* * ** *
29890895 CCGGGTTAAGACCCGAAGGCAATT-GTGCTAGTGACTACAT
1 CCGGGCTAAGACCCGAAGGC-ATTCGTGCAAGTGGTTATAT
*
29890935 CCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTCGTGCAAGTGGTTATAT
* * *
29890975 CCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTCGTGCAAGTGGTTATAT
**
29891015 CCGGGCTAAGACCCGAAGGCATTCGTGCGTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTCGTGCAAGTGGTTATAT
29891055 CCGG
1 CCGG
29891059 TTGTATTCCA
Statistics
Matches: 140, Mismatches: 22, Indels: 4
0.84 0.13 0.02
Matches are distributed among these distances:
39 3 0.02
40 134 0.96
41 3 0.02
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.26
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTCGTGCAAGTGGTTATAT
Done.