Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 36 of 193
Found at i:11036357 original size:31 final size:32
Alignment explanation
Indices: 11036319--11036686 Score: 160
Period size: 31 Copynumber: 10.6 Consensus size: 32
11036309 TATCCAACCC
11036319 TACTTCAATTTCAAGAGGATGACGTTGT-TCT
1 TACTTCAATTTCAAGAGGATGACGTTGTATCT
** *
11036350 TACTTCAATTTCAGAGATAAAGAC-TTGATATCCAATTT
1 TACTTCAATTTCA-AGAGGATGACGTTG-TAT-C----T
* *
11036388 TACTTCAATTTCAAGAGGATAGGAAATGATGTTACTCT
1 TACTTCAATTTCAAGAGGAT--G--ACGTTG-TA-TCT
* *
11036426 TACTTCAATTTCAGAGATGAAGACGTAT-TATCCACT
1 TACTTCAATTTCA-AGAGGATGACGT-TGTAT---CT
* *
11036462 CTACTTCAATTTCAAGGGGATGACGTTG-CTCT
1 -TACTTCAATTTCAAGAGGATGACGTTGTATCT
* *
11036494 TACTTCAATTTCAGAGACGAAGACG-TGTTATCCACT
1 TACTTCAATTTCA-AGAGGATGACGTTG-TAT---CT
* *
11036530 CTACTTCAATTTCAAGGGGATGACGTTG-CTCT
1 -TACTTCAATTTCAAGAGGATGACGTTGTATCT
* *
11036562 TACTTCAATTTCAGAGACGAAGACG-TGTTATCCACT
1 TACTTCAATTTCA-AGAGGATGACGTTG-TAT---CT
* *
11036598 CTACTTCAATTTCAAGGGGATGACGTTG-CTCT
1 -TACTTCAATTTCAAGAGGATGACGTTGTATCT
* *
11036630 TACTTCAATTTCAGAGACGAAGACG-TGTTATCCACT
1 TACTTCAATTTCA-AGAGGATGACGTTG-TAT---CT
*
11036666 CTACTTCAATTTCAAGGGGAT
1 -TACTTCAATTTCAAGAGGAT
11036687 AGGAAAAGGT
Statistics
Matches: 253, Mismatches: 40, Indels: 83
0.67 0.11 0.22
Matches are distributed among these distances:
31 61 0.24
32 38 0.15
33 5 0.02
34 3 0.01
35 6 0.02
36 38 0.15
37 61 0.24
38 28 0.11
39 6 0.02
41 1 0.00
42 5 0.02
43 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.34
Consensus pattern (32 bp):
TACTTCAATTTCAAGAGGATGACGTTGTATCT
Found at i:11036531 original size:68 final size:69
Alignment explanation
Indices: 11036123--11036686 Score: 708
Period size: 68 Copynumber: 8.0 Consensus size: 69
11036113 AGGATAGGAA
* * * *
11036123 ATGATGTTACTCTTACTTCAATTTCAGAGATGAAGACTTGTTATCCAACTTTACTTCAATTTCAA
1 ATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCAACTCTACTTCAATTTCAA
*
11036188 GAGG
66 GGGG
* *
11036192 ATGATGTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCAACTCTACTTCAATTTCCA
1 ATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCAACTCTACTTCAATTT---
*
11036257 GCAAATAGGGA
63 -C--A-AGGGG
* * * * *
11036268 AAGATC-TTGCTCTTACTTCAATTTCAGAGAT-AATGGCTTGATATCCAACCCTACTTCAATTTC
1 ATGA-CGTTGCTCTTACTTCAATTTCAGAGATGAA-GACGTGTTATCCAACTCTACTTCAATTTC
*
11036331 AAGAGG
64 AAGGGG
* * * * * *
11036337 ATGACGTTGTTCTTACTTCAATTTCAGAGATAAAGACTTGATATCCAATTTTACTTCAATTTCAA
1 ATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCAACTCTACTTCAATTTC-A
11036402 GAGGATAGG
65 -AGG---GG
* * *
11036411 AAATGATGTTACTCTTACTTCAATTTCAGAGATGAAGACGTATTATCC-ACTCTACTTCAATTTC
1 --ATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCAACTCTACTTCAATTTC
11036475 AAGGGG
64 AAGGGG
*
11036481 ATGACGTTGCTCTTACTTCAATTTCAGAGACGAAGACGTGTTATCC-ACTCTACTTCAATTTCAA
1 ATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCAACTCTACTTCAATTTCAA
11036545 GGGG
66 GGGG
*
11036549 ATGACGTTGCTCTTACTTCAATTTCAGAGACGAAGACGTGTTATCC-ACTCTACTTCAATTTCAA
1 ATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCAACTCTACTTCAATTTCAA
11036613 GGGG
66 GGGG
*
11036617 ATGACGTTGCTCTTACTTCAATTTCAGAGACGAAGACGTGTTATCC-ACTCTACTTCAATTTCAA
1 ATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCAACTCTACTTCAATTTCAA
11036681 GGGG
66 GGGG
11036685 AT
1 AT
11036687 AGGAAAAGGT
Statistics
Matches: 443, Mismatches: 34, Indels: 37
0.86 0.07 0.07
Matches are distributed among these distances:
68 203 0.46
69 113 0.26
70 6 0.01
71 2 0.00
72 1 0.00
73 4 0.01
74 3 0.01
75 17 0.04
76 94 0.21
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.34
Consensus pattern (69 bp):
ATGACGTTGCTCTTACTTCAATTTCAGAGATGAAGACGTGTTATCCAACTCTACTTCAATTTCAA
GGGG
Found at i:11048908 original size:30 final size:30
Alignment explanation
Indices: 11048874--11049072 Score: 141
Period size: 29 Copynumber: 6.7 Consensus size: 30
11048864 TTTAGAAACT
11048874 TCGGGGGTAAAATGGTAATTTTCAGTGAAA
1 TCGGGGGTAAAATGGTAATTTTCAGTGAAA
*
11048904 TCGGGGTTAAAAATGG-AATTTT-A--GAAGA
1 TCGGGGGT-AAAATGGTAATTTTCAGTGAA-A
*
11048932 TTCAGGGGTAAAATGGTAATTTTC-GATGAAA
1 -TCGGGGGTAAAATGGTAATTTTCAG-TGAAA
* * * * ** *
11048963 TCGAGGTTAAAAATGG-GATTTTAAAAG-AT
1 TCGGGGGT-AAAATGGTAATTTTCAGTGAAA
*
11048992 TCGGGGGTAAAATGGTAATTTTCGGTGAAA
1 TCGGGGGTAAAATGGTAATTTTCAGTGAAA
*
11049022 TCGGGGTTAAAAATGG-AATTTT-A--GAAGA
1 TCGGGGGT-AAAATGGTAATTTTCAGTGAA-A
*
11049050 TTCAGGGGTAAAATGGTAATTTT
1 -TCGGGGGTAAAATGGTAATTTT
11049073 TAGAAGTTTC
Statistics
Matches: 130, Mismatches: 23, Indels: 33
0.70 0.12 0.18
Matches are distributed among these distances:
27 6 0.05
28 23 0.18
29 38 0.29
30 38 0.29
31 22 0.17
32 3 0.02
ACGTcount: A:0.36, C:0.05, G:0.28, T:0.31
Consensus pattern (30 bp):
TCGGGGGTAAAATGGTAATTTTCAGTGAAA
Found at i:11048915 original size:59 final size:59
Alignment explanation
Indices: 11048817--11049072 Score: 381
Period size: 59 Copynumber: 4.4 Consensus size: 59
11048807 TATGGATACC
* * ***
11048817 CAGGGGCAAAATGGTAATTTT-GGTAAAATCGGGGTTAAAAACAAAATTTTAGAA-ACTT
1 CAGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGA-TT
* *
11048875 CGGGGGTAAAATGGTAATTTTCAGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATT
1 CAGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATT
* * * *
11048934 CAGGGGTAAAATGGTAATTTTCGATGAAATCGAGGTTAAAAATGGGATTTTAAAAGATT
1 CAGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATT
*
11048993 CGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATT
1 CAGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATT
11049052 CAGGGGTAAAATGGTAATTTT
1 CAGGGGTAAAATGGTAATTTT
11049073 TAGAAGTTTC
Statistics
Matches: 177, Mismatches: 19, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
58 19 0.11
59 157 0.89
60 1 0.01
ACGTcount: A:0.37, C:0.06, G:0.27, T:0.30
Consensus pattern (59 bp):
CAGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATT
Found at i:11049078 original size:30 final size:28
Alignment explanation
Indices: 11048863--11049077 Score: 126
Period size: 30 Copynumber: 7.3 Consensus size: 28
11048853 AAAAACAAAA
11048863 TTTTAGAAACTTCGGGGGTAAAATGGTAAT
1 TTTTAGAAA-TTC-GGGGTAAAATGGTAAT
*
11048893 TTTCAGTGAAA-TCGGGGTTAAAAATGG-AA-
1 TTTTA--GAAATTCGGGG-T-AAAATGGTAAT
11048922 TTTTAGAAGATTCAGGGGTAAAATGGTAAT
1 TTTTAGAA-ATTC-GGGGTAAAATGGTAAT
* * *
11048952 TTTCGATGAAA-TCGAGGTTAAAAATGG-GA-
1 TTT-TA-GAAATTCG-GGGT-AAAATGGTAAT
*
11048981 TTTTAAAAGATTCGGGGGTAAAATGGTAAT
1 TTTTAGAA-ATTC-GGGGTAAAATGGTAAT
11049011 TTTCGGT-GAAA-TCGGGGTTAAAAATGG-AA-
1 TTT---TAGAAATTCGGGG-T-AAAATGGTAAT
11049040 TTTTAGAAGATTCAGGGGTAAAATGGTAAT
1 TTTTAGAA-ATTC-GGGGTAAAATGGTAAT
11049070 TTTTAGAA
1 TTTTAGAA
11049078 GTTTCGAGAT
Statistics
Matches: 146, Mismatches: 10, Indels: 58
0.68 0.05 0.27
Matches are distributed among these distances:
26 1 0.01
27 8 0.05
28 25 0.17
29 35 0.24
30 43 0.29
31 24 0.16
32 9 0.06
33 1 0.01
ACGTcount: A:0.36, C:0.05, G:0.27, T:0.32
Consensus pattern (28 bp):
TTTTAGAAATTCGGGGTAAAATGGTAAT
Found at i:11049110 original size:30 final size:30
Alignment explanation
Indices: 11049087--11049161 Score: 141
Period size: 30 Copynumber: 2.5 Consensus size: 30
11049077 AGTTTCGAGA
11049087 TCAAAATATAATTTTGGAAAAGTTTTGGGG
1 TCAAAATATAATTTTGGAAAAGTTTTGGGG
*
11049117 TTAAAATATAATTTTGGAAAAGTTTTGGGG
1 TCAAAATATAATTTTGGAAAAGTTTTGGGG
11049147 TCAAAATATAATTTT
1 TCAAAATATAATTTT
11049162 TGAACAATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.39, C:0.03, G:0.19, T:0.40
Consensus pattern (30 bp):
TCAAAATATAATTTTGGAAAAGTTTTGGGG
Found at i:11049129 original size:118 final size:117
Alignment explanation
Indices: 11048873--11049131 Score: 337
Period size: 118 Copynumber: 2.2 Consensus size: 117
11048863 TTTTAGAAAC
*
11048873 TTCGGGGGTAAAATGGTAATTTTCAGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTCAGG
1 TTCGGGGGTAAAATGATAATTTTCAGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTCAGG
* * *
11048938 GGTAAAATGGTAATTTTCGATGAAATCGAGGTTAAAAATGGGATTTTAAAAGA
66 GGTAAAATGGTAATTTTCGATGAAATCGAGATCAAAAAT-GAATTTTAAAAGA
* *
11048991 TTCGGGGGTAAAATGGTAATTTTCGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTCAGG
1 TTCGGGGGTAAAATGATAATTTTCAGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTCAGG
* * *
11049056 GGTAAAATGGTAATTTT-TA-GAAGTTTCGAGATCAAAATAT-AATTTTGGAAAAGT
66 GGTAAAATGGTAATTTTCGATGAA--ATCGAGATCAAAA-ATGAATTTT--AAAAGA
* *
11049110 TTTGGGGTTAAAAT-ATAATTTT
1 TTCGGGGGTAAAATGATAATTTT
11049132 GGAAAAGTTT
Statistics
Matches: 126, Mismatches: 10, Indels: 10
0.86 0.07 0.07
Matches are distributed among these distances:
116 3 0.02
117 6 0.05
118 98 0.78
119 19 0.15
ACGTcount: A:0.36, C:0.05, G:0.26, T:0.33
Consensus pattern (117 bp):
TTCGGGGGTAAAATGATAATTTTCAGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGATTCAGG
GGTAAAATGGTAATTTTCGATGAAATCGAGATCAAAAATGAATTTTAAAAGA
Found at i:11050425 original size:19 final size:19
Alignment explanation
Indices: 11050383--11050444 Score: 56
Period size: 19 Copynumber: 3.3 Consensus size: 19
11050373 TATTACTAAC
11050383 ATTATTATTACTAATTATT
1 ATTATTATTACTAATTATT
* *
11050402 GTTATTATTATTAA-TATTT
1 ATTATTATTACTAATTA-TT
* *
11050421 ATTA-TATTAATAGTTATT
1 ATTATTATTACTAATTATT
*
11050439 AATATT
1 ATTATT
11050445 TTAGCTACTA
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
18 14 0.41
19 20 0.59
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (19 bp):
ATTATTATTACTAATTATT
Found at i:11050995 original size:20 final size:20
Alignment explanation
Indices: 11050957--11050995 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
11050947 CAGGGCATGG
*
11050957 TGGAGCTTGGTGGTGGCAGA
1 TGGAGCTTGGTGGTAGCAGA
11050977 TGGAGC-TGGTGGTCAGCAG
1 TGGAGCTTGGTGGT-AGCAG
11050996 CAGCAGAGGC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.15, C:0.13, G:0.49, T:0.23
Consensus pattern (20 bp):
TGGAGCTTGGTGGTAGCAGA
Found at i:11051206 original size:17 final size:16
Alignment explanation
Indices: 11051186--11051254 Score: 77
Period size: 17 Copynumber: 4.1 Consensus size: 16
11051176 GACTTTCTTT
11051186 TTAAATTTATAA-TAACA
1 TTAAATTTA-AATTAA-A
11051203 TTAAATTTAAATTAAA
1 TTAAATTTAAATTAAA
11051219 TTCAAATTTAAATTTAAA
1 TT-AAATTTAAA-TTAAA
* *
11051237 TTGAATTTAAAATAAA
1 TTAAATTTAAATTAAA
11051253 TT
1 TT
11051255 TAAGATTAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
16 11 0.23
17 29 0.62
18 7 0.15
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.43
Consensus pattern (16 bp):
TTAAATTTAAATTAAA
Found at i:11051212 original size:6 final size:6
Alignment explanation
Indices: 11051203--11051257 Score: 62
Period size: 6 Copynumber: 9.7 Consensus size: 6
11051193 TATAATAACA
* *
11051203 TTAAAT TTAAA- TTAAAT TCAAAT TTAAAT TTAAA- TTGAAT TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
11051248 ATAAAT TTAA
1 TTAAAT TTAA
11051258 GATTAAAATA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
5 13 0.32
6 27 0.68
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (6 bp):
TTAAAT
Found at i:11051218 original size:11 final size:11
Alignment explanation
Indices: 11051202--11051264 Score: 81
Period size: 11 Copynumber: 5.5 Consensus size: 11
11051192 TTATAATAAC
11051202 ATTAAATTTAA
1 ATTAAATTTAA
*
11051213 ATTAAATTCAA
1 ATTAAATTTAA
11051224 ATTTAAATTTAA
1 A-TTAAATTTAA
*
11051236 ATTGAATTTAA
1 ATTAAATTTAA
*
11051247 AATAAATTTAA
1 ATTAAATTTAA
11051258 GATTAAA
1 -ATTAAA
11051265 ATAAATTTGA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
11 29 0.66
12 15 0.34
ACGTcount: A:0.54, C:0.02, G:0.03, T:0.41
Consensus pattern (11 bp):
ATTAAATTTAA
Found at i:11051462 original size:19 final size:18
Alignment explanation
Indices: 11051425--11051469 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
11051415 ATACGTTCTC
*
11051425 TCTTTTTCTTTCCTATTT
1 TCTTTTTCTTTACTATTT
*
11051443 TCTTTGTTCTTTACTCTTT
1 TCTTT-TTCTTTACTATTT
11051462 TACTTTTT
1 T-CTTTTT
11051470 ATTTTATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 14 0.61
20 4 0.17
ACGTcount: A:0.07, C:0.20, G:0.02, T:0.71
Consensus pattern (18 bp):
TCTTTTTCTTTACTATTT
Found at i:11052587 original size:20 final size:20
Alignment explanation
Indices: 11052566--11052602 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
11052556 ATTTTTTAAT
11052566 TTTTTA-TATTTTAAAATAA
1 TTTTTATTATTTTAAAATAA
*
11052585 TTTTTATTTTTTTAAAAT
1 TTTTTATTATTTTAAAAT
11052603 TTAAAGAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTTTATTATTTTAAAATAA
Found at i:11052614 original size:26 final size:27
Alignment explanation
Indices: 11052558--11052623 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 27
11052548 AACATTAAAT
* * * *
11052558 TTTTTAATTTTTTATATTTTAAAATAA
1 TTTTTATTTTTTTAAAATTTAAAAGAA
*
11052585 TTTTTATTTTTTTAAAATTT-AAAGAG
1 TTTTTATTTTTTTAAAATTTAAAAGAA
*
11052611 TTTTTATGTTTTT
1 TTTTTATTTTTTT
11052624 CATAAATATT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 16 0.48
27 17 0.52
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.65
Consensus pattern (27 bp):
TTTTTATTTTTTTAAAATTTAAAAGAA
Found at i:11058590 original size:11 final size:11
Alignment explanation
Indices: 11058574--11058599 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
11058564 GTGATTGTCA
11058574 GAAATCTTATT
1 GAAATCTTATT
11058585 GAAATCTTATT
1 GAAATCTTATT
11058596 GAAA
1 GAAA
11058600 ACAGGGGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (11 bp):
GAAATCTTATT
Found at i:11059135 original size:7 final size:7
Alignment explanation
Indices: 11059123--11059147 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
11059113 ATTGGATTTC
11059123 TTTTCTT
1 TTTTCTT
11059130 TTTTCTT
1 TTTTCTT
11059137 TTTTCTT
1 TTTTCTT
11059144 TTTT
1 TTTT
11059148 AATTTTGCCC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTCTT
Found at i:11060535 original size:16 final size:17
Alignment explanation
Indices: 11060506--11060581 Score: 73
Period size: 17 Copynumber: 4.5 Consensus size: 17
11060496 CCCAATGAGA
11060506 TAAATTTGATTTTAAA-T
1 TAAATTT-ATTTTAAATT
11060523 TAAATTTATTTTAAATT
1 TAAATTTATTTTAAATT
****
11060540 TAAATTTACACAAAATT
1 TAAATTTATTTTAAATT
* * *
11060557 TAAGTTTATTATAAATA
1 TAAATTTATTTTAAATT
11060574 TAAATTTA
1 TAAATTTA
11060582 AAATTAAATT
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
16 8 0.17
17 39 0.83
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (17 bp):
TAAATTTATTTTAAATT
Found at i:11060783 original size:30 final size:29
Alignment explanation
Indices: 11060732--11060921 Score: 147
Period size: 29 Copynumber: 6.4 Consensus size: 29
11060722 ATAGGTCCCT
11060732 AAACTGTCCAAAAATTA-CATTTTGACCCCA
1 AAACT-TCCAAAAATTACCATTTT-ACCCCA
*
11060762 AAACTTCCAAAAATTACCATTTTACCCTCG
1 AAACTTCCAAAAATTACCATTTTACCC-CA
** *
11060792 ATCCTTCCAAAAATT-CCATTTTAACCC-
1 AAACTTCCAAAAATTACCATTTTACCCCA
** * * **
11060819 TGATTTCACCAAAAATTACTATTTTACCCTTG
1 AAACTT--CCAAAAATTACCATTTTACCC-CA
* *
11060851 AACCTT-CTAAAATT-CCATTTTTGACCCCA
1 AAACTTCCAAAAATTACCA-TTTT-ACCCCA
*
11060880 AAACTTCCAAAAATTACCATTTTACCCCC
1 AAACTTCCAAAAATTACCATTTTACCCCA
11060909 AAACTTTCCAAAA
1 AAAC-TTCCAAAA
11060922 TCCCATTTTT
Statistics
Matches: 126, Mismatches: 22, Indels: 24
0.73 0.13 0.14
Matches are distributed among these distances:
27 2 0.02
28 3 0.02
29 59 0.47
30 57 0.45
31 3 0.02
32 2 0.02
ACGTcount: A:0.36, C:0.29, G:0.03, T:0.32
Consensus pattern (29 bp):
AAACTTCCAAAAATTACCATTTTACCCCA
Found at i:11060812 original size:59 final size:59
Alignment explanation
Indices: 11060742--11060999 Score: 256
Period size: 59 Copynumber: 4.4 Consensus size: 59
11060732 AAACTGTCCA
* * *
11060742 AAAATTACA-TTTTGACCCCAAAACTTCCAAAAATTACCATTTTACCCTCGATCCTTCC
1 AAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTACCATTTTACCCTCGAACCTTCC
** * * * *
11060800 AAAAATTCCA-TTTTAA-CCC-TGATTTCACCAAAAATTACTATTTTACCCTTGAACCTTCT
1 -AAAATTCCATTTTTAACCCCAAAACTT--CCAAAAATTACCATTTTACCCTCGAACCTTCC
* * * *
11060859 AAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTACCATTTTACCCCCAAACTTTCC
1 AAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTACCATTTTACCCTCGAACCTTCC
* * * ** **
11060918 AAAATCCCATTTTTAACCTCGATTCCACCAAAAATTACCATTTTACCCAT-GAACCTTCC
1 AAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTACCATTTTACCC-TCGAACCTTCC
*
11060977 AAAATCCCATTTTTAACCCCAAA
1 AAAATTCCATTTTTAACCCCAAA
11061000 TTTTCTCGAA
Statistics
Matches: 160, Mismatches: 33, Indels: 12
0.78 0.16 0.06
Matches are distributed among these distances:
57 3 0.02
58 12 0.08
59 139 0.87
60 3 0.02
61 3 0.02
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.32
Consensus pattern (59 bp):
AAAATTCCATTTTTAACCCCAAAACTTCCAAAAATTACCATTTTACCCTCGAACCTTCC
Found at i:11060949 original size:118 final size:118
Alignment explanation
Indices: 11060742--11060999 Score: 369
Period size: 118 Copynumber: 2.2 Consensus size: 118
11060732 AAACTGTCCA
* * * *
11060742 AAAATTACA-TTTTGACCCCAAAACTTCCAAAAATTACCATTTTACCCTCGATCCTTCCAAAAAT
1 AAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTACCATTTTACCCCCAAACCTTCCAAAAAT
* * * * *
11060806 TCCATTTTAACCCTGATTTCACCAAAAATTACTATTTTACCCTTGAACCTTCT
66 CCCATTTTAACCCTGATTCCACCAAAAATTACCATTTTACCCATGAACCTTCC
*
11060859 AAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTACCATTTTACCCCCAAACTTTCC-AAAAT
1 AAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTACCATTTTACCCCCAAACCTTCCAAAAAT
11060923 CCCATTTTTAA-CCTCGATTCCACCAAAAATTACCATTTTACCCATGAACCTTCC
66 CCCA-TTTTAACCCT-GATTCCACCAAAAATTACCATTTTACCCATGAACCTTCC
* *
11060977 AAAATCCCATTTTTAACCCCAAA
1 AAAATTCCATTTTTGACCCCAAA
11061000 TTTTCTCGAA
Statistics
Matches: 126, Mismatches: 12, Indels: 5
0.88 0.08 0.03
Matches are distributed among these distances:
117 19 0.15
118 107 0.85
ACGTcount: A:0.35, C:0.30, G:0.03, T:0.32
Consensus pattern (118 bp):
AAAATTCCATTTTTGACCCCAAAACTTCCAAAAATTACCATTTTACCCCCAAACCTTCCAAAAAT
CCCATTTTAACCCTGATTCCACCAAAAATTACCATTTTACCCATGAACCTTCC
Found at i:11060990 original size:29 final size:29
Alignment explanation
Indices: 11060840--11060991 Score: 73
Period size: 29 Copynumber: 5.2 Consensus size: 29
11060830 AAAATTACTA
* * *
11060840 TTTTACCCTTGAACCTTCTAAAATTCCAT
1 TTTTACCCATGAACCTTCCAAAATACCAT
*
11060869 TTTTGACCCCA--AAACTTCCAAAAATTACCA-
1 TTTT-A-CCCATGAACCTTCC-AAAA-TACCAT
*** * *
11060899 TTTTACCCCCAAACTTTCCAAAATCCCAT
1 TTTTACCCATGAACCTTCCAAAATACCAT
* * *
11060928 TTTTAACC-TCGATTCC-ACCAAAAATTACCA-
1 TTTTACCCAT-GA-ACCTTCC-AAAA-TACCAT
*
11060958 TTTTACCCATGAACCTTCCAAAATCCCAT
1 TTTTACCCATGAACCTTCCAAAATACCAT
11060987 TTTTA
1 TTTTA
11060992 ACCCCAAATT
Statistics
Matches: 90, Mismatches: 19, Indels: 28
0.66 0.14 0.20
Matches are distributed among these distances:
28 11 0.12
29 36 0.40
30 31 0.34
31 12 0.13
ACGTcount: A:0.33, C:0.31, G:0.03, T:0.34
Consensus pattern (29 bp):
TTTTACCCATGAACCTTCCAAAATACCAT
Found at i:11065170 original size:21 final size:22
Alignment explanation
Indices: 11065146--11065195 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
11065136 AGGACCTCCC
*
11065146 TAGGCAAATGGAGGA-AAAGTA
1 TAGGCAAATGGAGGAGAAAATA
* * *
11065167 TAGGCTATTGGAGGAGAAAATT
1 TAGGCAAATGGAGGAGAAAATA
11065189 TAGGCAA
1 TAGGCAA
11065196 TACAAGGAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.42, C:0.06, G:0.32, T:0.20
Consensus pattern (22 bp):
TAGGCAAATGGAGGAGAAAATA
Found at i:11073083 original size:200 final size:199
Alignment explanation
Indices: 11072740--11073674 Score: 1309
Period size: 200 Copynumber: 4.8 Consensus size: 199
11072730 AGGCGGTCAT
* *
11072740 CTTCCTGATGAGACACTGAGAAACAGGTCGAAGCAATAAAATGGTTAACTTCCTGATGAGATACA
1 CTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACA
* * *
11072805 GAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATCAAAACAAGTGATACGA
66 GAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATCAAAACAAGCGA-GCGG
*
11072870 TCATCTTCCTGATGAAATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCCAATCTTCGAA
130 TCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCCAATCTTCGAA
11072935 CCCAG
195 CCCAG
* *
11072940 CTTCCTGATGAGACATTGAGAAGCAGGTTGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACA
1 CTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACA
*
11073005 GAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATCAAAATAAGCGAGGCGG
66 GAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATCAAAACAAGCGA-GCGG
11073070 TCATCTTCCTGATGAGATACAGAGAAGAAT----AC-CAA--CTC-A-AC--G-----C-TC-AA
130 TCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCCAATCTTCGAA
11073117 CCCAG
195 CCCAG
*
11073122 CTTCCTAATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACA
1 CTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACA
*
11073187 GAGAAGTGGACCAGATTCGTCTTACTGAGGAGATCCAGAGAAGCGAATCAAAACAAGCGACGCGG
66 GAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATCAAAACAAGCGA-GCGG
*
11073252 TCATCTTCCTGATGAGATACAGAGAAGAATACCAACACAACGCTCAACACGAGCCAATCTTCGAA
130 TCATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCCAATCTTCGAA
11073317 CCCAG
195 CCCAG
*
11073322 CTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATAGTTAGCTTCCTGATGAGATACA
1 CTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACA
*
11073387 GAGAAGTGGACCAAATTCGTCTTCCTG-GGAGATCCAGAGAAGCGAATCAAAACAAGCGA---G-
66 GAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATCAAAACAAGCGAGCGGT
* * * * *
11073447 ------CCTGATGAGATACAGAGAAGAATACCAGCTCAACGTTTAACGCGAGCAAATCTTCGAAC
131 CATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCCAATCTTCGAAC
11073506 CCAG
196 CCAG
* * ** *
11073510 CTTCCTGATGAGATACTGAGAAGCAGGTCAAAGCAATAAAAAAGTTAGCTTCCTGATGAGACACA
1 CTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACA
* * * * *
11073575 GAGAAGTGGCCCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCGATTTAAAAC-AGATGATCGC
66 GAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATCAAAACAAG-CGA--GC
* * * *
11073639 TGTCATCTTTCTGATGAGACACAGAGAAGAAGACCA
128 GGTCATCTTCCTGATGAGATACAGAGAAGAATACCA
11073675 GGTCAATGAA
Statistics
Matches: 666, Mismatches: 37, Indels: 63
0.87 0.05 0.08
Matches are distributed among these distances:
182 161 0.24
183 2 0.00
184 1 0.00
186 2 0.00
187 3 0.00
188 146 0.22
189 30 0.05
190 1 0.00
191 4 0.01
192 1 0.00
193 4 0.01
194 1 0.00
195 4 0.01
196 2 0.00
198 1 0.00
199 34 0.05
200 245 0.37
201 24 0.04
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.19
Consensus pattern (199 bp):
CTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCCTGATGAGATACA
GAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATCAAAACAAGCGAGCGGT
CATCTTCCTGATGAGATACAGAGAAGAATACCAACTCAACGCTCAACACGAGCCAATCTTCGAAC
CCAG
Found at i:11073088 original size:86 final size:85
Alignment explanation
Indices: 11072988--11073278 Score: 243
Period size: 86 Copynumber: 3.3 Consensus size: 85
11072978 AAATGGTTAG
11072988 CTTCCTGATGAGATACAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAAT
1 CTTCCTGATGAGATACAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAAT
11073053 CAAAATAAGCGAGGCGGTCAT
66 CAAAATAAGCGA-GCGGTCAT
*** * * *
11073074 CTTCCTGATGAGATACAGAGAAGAATACCA-ACTCAACGCTCAACCCAGCTTCCTAATGAGA-CA
1 CTTCCTGATGAGATACAGAGAAGTGGACCAGA-T--TCG-T--------CTTCCTGAGGAGATC-
* * ** * *
11073137 CTGAGAAGC-AGGTCGAAGCAATAA---AATGGTTAG
53 CAGAGAAGCGA-ATC-AA--AATAAGCGAGCGGTCAT
*
11073170 CTTCCTGATGAGATACAGAGAAGTGGACCAGATTCGTCTTACTGAGGAGATCCAGAGAAGCGAAT
1 CTTCCTGATGAGATACAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAAT
*
11073235 CAAAACAAGCGACGCGGTCAT
66 CAAAATAAGCGA-GCGGTCAT
11073256 CTTCCTGATGAGATACAGAGAAG
1 CTTCCTGATGAGATACAGAGAAG
11073279 AATACCAACA
Statistics
Matches: 155, Mismatches: 26, Indels: 48
0.68 0.11 0.21
Matches are distributed among these distances:
82 4 0.03
84 2 0.01
85 22 0.14
86 57 0.37
88 2 0.01
89 1 0.01
93 1 0.01
94 2 0.01
96 34 0.22
97 23 0.15
98 2 0.01
100 5 0.03
ACGTcount: A:0.35, C:0.21, G:0.25, T:0.19
Consensus pattern (85 bp):
CTTCCTGATGAGATACAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAAT
CAAAATAAGCGAGCGGTCAT
Found at i:11073254 original size:182 final size:188
Alignment explanation
Indices: 11072928--11073669 Score: 910
Period size: 182 Copynumber: 3.9 Consensus size: 188
11072918 ACGAGCCAAT
* * *
11072928 CTTCGAACCCAGCTTCCTGATGAGACATTGAGAAGCAGGTTGAAGCAATAAAATGGTTAGCTTCC
1 CTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATAGTTAGCTTCC
*
11072993 TGATGAGATACAGAGAAGTGGACCAGATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATCAAAA
66 TGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATCAAAA
* *
11073058 TAAGCGAGGCGGTCATCTTCCTGATGAGATACAGAGAAGAAT-AC-CAACTCAAC-G-
131 CAAGCGACGCGGTCATCTTCCTGATGAGATACAGAGAAGAATCACACAACTCAACAGA
* *
11073112 C-TC-AACCCAGCTTCCTAATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATGGTTAGCTTCC
1 CTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATAGTTAGCTTCC
* *
11073175 TGATGAGATACAGAGAAGTGGACCAGATTCGTCTTACTGAGGAGATCCAGAGAAGCGAATCAAAA
66 TGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATCAAAA
11073240 CAAGCGACGCGGTCATCTTCCTGATGAGATACAGAGAAGAATACCAACACAACGCTCAACACGAG
131 CAAGCGACGCGGTCATCTTCCTGATGAGATACAGAGAAGAAT--C-ACACAA--CTC-A-AC-AG
11073305 CCAA
188 ---A
11073309 TCTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATAGTTAGCTTC
1 -CTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATAGTTAGCTTC
11073374 CTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTG-GGAGATCCAGAGAAGCGAATCAAA
65 CTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATCAAA
* *
11073438 ACAAGCGA----G-------CCTGATGAGATACAGAGAAGAATACCAGCTCAACGTTTAACGCGA
130 ACAAGCGACGCGGTCATCTTCCTGATGAGATACAGAGAAGAAT--CA-CACAAC--TCAA--C-A
11073492 GCAAA
187 G---A
* * *
11073497 TCTTCGAACCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCAAAGCAATAAAAAAGTTAGCTTC
1 -CTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATAGTTAGCTTC
* * * *
11073562 CTGATGAGACACAGAGAAGTGGCCCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCGATTTAAA
65 CTGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATCAAA
* * * *
11073627 AC-AGATGATCGCTGTCATCTTTCTGATGAGACACAGAGAAGAA
130 ACAAG-CGA-CGCGGTCATCTTCCTGATGAGATACAGAGAAGAA
11073670 GACCAGGTCA
Statistics
Matches: 498, Mismatches: 23, Indels: 57
0.86 0.04 0.10
Matches are distributed among these distances:
182 161 0.32
183 2 0.00
184 1 0.00
186 4 0.01
187 5 0.01
188 140 0.28
189 29 0.06
190 1 0.00
191 2 0.00
193 1 0.00
194 1 0.00
195 1 0.00
198 1 0.00
199 34 0.07
200 95 0.19
201 20 0.04
ACGTcount: A:0.35, C:0.21, G:0.24, T:0.20
Consensus pattern (188 bp):
CTTCGAACCCAGCTTCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATAGTTAGCTTCC
TGATGAGATACAGAGAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATCAAAA
CAAGCGACGCGGTCATCTTCCTGATGAGATACAGAGAAGAATCACACAACTCAACAGA
Found at i:11073578 original size:188 final size:189
Alignment explanation
Indices: 11073259--11073629 Score: 618
Period size: 188 Copynumber: 2.0 Consensus size: 189
11073249 CGGTCATCTT
*
11073259 CCTGATGAGATACAGAGAAGAATACCAACACAACGCTCAACACGAGCCAATCTTCGAACCCAGCT
1 CCTGATGAGATACAGAGAAGAATACCAACACAACGCTCAACACGAGCAAATCTTCGAACCCAGCT
* * *
11073324 TCCTGATGAGACACTGAGAAGCAGGTCGAAGCAATAAAATAGTTAGCTTCCTGATGAGATACAGA
66 TCCTGATGAGACACTGAGAAGCAGGTCAAAGCAATAAAAAAGTTAGCTTCCTGATGAGACACAGA
11073389 GAAGTGGACCAAATTCGTCTTCCTG-GGAGATCCAGAGAAGCGAATCAAAACAAGCGAG
131 GAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATCAAAACAAGCGAG
* * * * *
11073447 CCTGATGAGATACAGAGAAGAATACCAGCTCAACGTTTAACGCGAGCAAATCTTCGAACCCAGCT
1 CCTGATGAGATACAGAGAAGAATACCAACACAACGCTCAACACGAGCAAATCTTCGAACCCAGCT
*
11073512 TCCTGATGAGATACTGAGAAGCAGGTCAAAGCAATAAAAAAGTTAGCTTCCTGATGAGACACAGA
66 TCCTGATGAGACACTGAGAAGCAGGTCAAAGCAATAAAAAAGTTAGCTTCCTGATGAGACACAGA
* * *
11073577 GAAGTGGCCCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCGATTTAAAACA
131 GAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATCAAAACA
11073630 GATGATCGCT
Statistics
Matches: 169, Mismatches: 13, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
188 144 0.85
189 25 0.15
ACGTcount: A:0.37, C:0.22, G:0.23, T:0.18
Consensus pattern (189 bp):
CCTGATGAGATACAGAGAAGAATACCAACACAACGCTCAACACGAGCAAATCTTCGAACCCAGCT
TCCTGATGAGACACTGAGAAGCAGGTCAAAGCAATAAAAAAGTTAGCTTCCTGATGAGACACAGA
GAAGTGGACCAAATTCGTCTTCCTGAGGAGATCCAGAGAAGCGAATCAAAACAAGCGAG
Found at i:11074082 original size:17 final size:17
Alignment explanation
Indices: 11074019--11074082 Score: 53
Period size: 17 Copynumber: 3.8 Consensus size: 17
11074009 AATTTGGTTT
*
11074019 TAAA-TTAAATTTATTT
1 TAAATTTAAATTTATTA
*
11074035 TAAATTTATATTTGCA-TA
1 TAAATTTAAATTT--ATTA
*
11074053 -AAATTTAAGTTTATTA
1 TAAATTTAAATTTATTA
*
11074069 TAAATATAAATTTA
1 TAAATTTAAATTTA
11074083 AAATTAAATT
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
15 1 0.03
16 6 0.16
17 28 0.76
18 1 0.03
19 1 0.03
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (17 bp):
TAAATTTAAATTTATTA
Found at i:11074276 original size:29 final size:30
Alignment explanation
Indices: 11074233--11074289 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
11074223 ATAGGTCCCT
*
11074233 AAACTGTCCAGAAATTA-CATTTTGACCCCA
1 AAACTGTCCAAAAATTACCATTTT-ACCCCA
11074263 AAACT-TCCAAAAATTACCATTTTACCC
1 AAACTGTCCAAAAATTACCATTTTACCC
11074290 TCGATCATTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.39, C:0.28, G:0.05, T:0.28
Consensus pattern (30 bp):
AAACTGTCCAAAAATTACCATTTTACCCCA
Found at i:11074341 original size:58 final size:59
Alignment explanation
Indices: 11074269--11074434 Score: 185
Period size: 59 Copynumber: 2.8 Consensus size: 59
11074259 CCCAAAACTT
* * * * **
11074269 CCAAAAATTACCATTTTACCCTCGATCATTCGAAAATC-C-TATTTTAATCTCGATTTTA
1 CCAAAAATTACCATTTTACCCCCGAACATTCCAAAATCTCAT-TTTTAACCTCGATTCCA
* *
11074327 CCCAAAATTACCATTTTACCCCCGAACTTTCCAAAATCTCATTTTTAACCTCGATTCCA
1 CCAAAAATTACCATTTTACCCCCGAACATTCCAAAATCTCATTTTTAACCTCGATTCCA
** * * *
11074386 CCAAAAATTACCATTTTACCCCTAAACCTTTCAAAATCCCA-TTTTAACC
1 CCAAAAATTACCATTTTACCCCCGAACATTCCAAAATCTCATTTTTAACC
11074435 CCAAATTTCC
Statistics
Matches: 92, Mismatches: 14, Indels: 4
0.84 0.13 0.04
Matches are distributed among these distances:
58 41 0.45
59 50 0.54
60 1 0.01
ACGTcount: A:0.33, C:0.30, G:0.03, T:0.34
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCCCGAACATTCCAAAATCTCATTTTTAACCTCGATTCCA
Found at i:11074360 original size:29 final size:29
Alignment explanation
Indices: 11074234--11074363 Score: 72
Period size: 29 Copynumber: 4.4 Consensus size: 29
11074224 TAGGTCCCTA
* **
11074234 AACTGTCCAGAAATTA-CATTTTGACCCCAA
1 AACTTTCCA-AAATTACCATTTT-ACCCCCG
*
11074264 AAC-TTCCAAAAATTACCATTTTACCCTCG
1 AACTTTCC-AAAATTACCATTTTACCCCCG
* * * ** *
11074293 ATCATTCGAAAA-T-CCTATTTTAATCTCG
1 AACTTTCCAAAATTACC-ATTTTACCCCCG
*
11074321 -ATTTTACCCAAAATTACCATTTTACCCCCG
1 AACTTT--CCAAAATTACCATTTTACCCCCG
11074351 AACTTTCCAAAAT
1 AACTTTCCAAAAT
11074364 CTCATTTTTA
Statistics
Matches: 75, Mismatches: 16, Indels: 19
0.68 0.15 0.17
Matches are distributed among these distances:
27 4 0.05
28 11 0.15
29 31 0.41
30 23 0.31
31 6 0.08
ACGTcount: A:0.35, C:0.28, G:0.05, T:0.32
Consensus pattern (29 bp):
AACTTTCCAAAATTACCATTTTACCCCCG
Found at i:11074382 original size:59 final size:58
Alignment explanation
Indices: 11074272--11074452 Score: 179
Period size: 58 Copynumber: 3.1 Consensus size: 58
11074262 AAAACTTCCA
* * * * *
11074272 AAAATTACCATTTTACCCTCGATCATTCGAAAATCC-TATTTTAATCTCGATTTTACCC
1 AAAATTACCATTTTACCCCCGAACTTTCCAAAATCCAT-TTTTAACCTCGATTTTACCC
** *
11074330 AAAATTACCATTTTACCCCCGAACTTTCCAAAATCTCATTTTTAACCTCGATTCCACCA
1 AAAATTACCATTTTACCCCCGAACTTTCCAAAATC-CATTTTTAACCTCGATTTTACCC
** * * * *
11074389 AAAATTACCATTTTACCCCTAAACCTTT-CAAAATCCCA-TTTTAACCCCAAATTTCCCC
1 AAAATTACCATTTTACCCCCGAA-CTTTCCAAAAT-CCATTTTTAACCTCGATTTTACCC
11074447 AAAATT
1 AAAATT
11074453 TCATTTTTGC
Statistics
Matches: 102, Mismatches: 17, Indels: 8
0.80 0.13 0.06
Matches are distributed among these distances:
58 50 0.49
59 46 0.45
60 6 0.06
ACGTcount: A:0.34, C:0.30, G:0.03, T:0.34
Consensus pattern (58 bp):
AAAATTACCATTTTACCCCCGAACTTTCCAAAATCCATTTTTAACCTCGATTTTACCC
Found at i:11084671 original size:16 final size:17
Alignment explanation
Indices: 11084627--11084661 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
11084617 ATATAAGAAT
11084627 AAAGAAAGAAA-AAAAG
1 AAAGAAAGAAACAAAAG
11084643 AAAGAAAGAAACAAAAG
1 AAAGAAAGAAACAAAAG
11084660 AA
1 AA
11084662 GAACAAAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (17 bp):
AAAGAAAGAAACAAAAG
Found at i:11085723 original size:17 final size:18
Alignment explanation
Indices: 11085683--11085727 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
11085673 ATGTGAAAAA
11085683 GAAAAATTGAATAGAAAT
1 GAAAAATTGAATAGAAAT
11085701 GAAAAATTGAATAGAAAT
1 GAAAAATTGAATAGAAAT
11085719 G-AAAATTGA
1 GAAAAATTGA
11085728 GGCATATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 8 0.30
18 19 0.70
ACGTcount: A:0.60, C:0.00, G:0.18, T:0.22
Consensus pattern (18 bp):
GAAAAATTGAATAGAAAT
Found at i:11087979 original size:19 final size:20
Alignment explanation
Indices: 11087939--11087979 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
11087929 GATAGCAAAT
*
11087939 AAAATAAAATAAAGGAAGAA
1 AAAATAAAATAAAGGAAAAA
11087959 AAAATAACAA-AAA-GAAAAA
1 AAAATAA-AATAAAGGAAAAA
11087978 AA
1 AA
11087980 CAAGAAAGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 7 0.37
20 10 0.53
21 2 0.11
ACGTcount: A:0.80, C:0.02, G:0.10, T:0.07
Consensus pattern (20 bp):
AAAATAAAATAAAGGAAAAA
Found at i:11098738 original size:23 final size:23
Alignment explanation
Indices: 11098698--11098771 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 23
11098688 AACACTCTAG
* * * *
11098698 AATAACAATTACATCGAAGTGAC
1 AATAACGATCACACCGAAGTGCC
*
11098721 AATAATGATCACACCGAAGTGCC
1 AATAACGATCACACCGAAGTGCC
** *
11098744 AATAACGATTGCACTGAAGTGCC
1 AATAACGATCACACCGAAGTGCC
11098767 AATAA
1 AATAA
11098772 GCTCCCACCA
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.43, C:0.20, G:0.16, T:0.20
Consensus pattern (23 bp):
AATAACGATCACACCGAAGTGCC
Found at i:11100613 original size:252 final size:252
Alignment explanation
Indices: 11100165--11100671 Score: 777
Period size: 252 Copynumber: 2.0 Consensus size: 252
11100155 TTATTTTTCT
11100165 TCACCATTGGAAGAATCCTCACCGATCCAAGTAGAAACATTGGCCTTATGTTTTTCTTTGCTTGA
1 TCACCATTGGAAGAATCCTCACCGATCCAAGTAGAAACATTGGCCTTATGTTTTTCTTTGCTTGA
* * * *
11100230 CCCTTTTTTCTTTCATTGGGGATAATCGAACTTGATATGTCTTGGCTTTTTGCATTCATAACAAA
66 CCCTTTTTTCTTCCATTGGGGACAATCAAACTTGAGATGTCTTGGCTTTTTGCATTCATAACAAA
* *
11100295 TTACGGGATAATTCTCCTTGTTAGATTCAAGCTTCAATCCTTCTTTTCTTTGAAATCTTCTTCCC
131 TAACGGGATAATTCTCCTTGTTAGATTCAAGCTTCAATCCTTCTTTTCTTTGAAATCTTATTCCC
* ** * *
11100360 TTGTTTGACTTCATGAATTTATTGAATTTCTTAGCAAACATAGTCATTTCTTTATCC
196 TTGCTCAACTTCATGAATCTATTGAATCTCTTAGCAAACATAGTCATTTCTTTATCC
* *
11100417 TCACCATTGGAA-AAGTCCTCACTGCTCCAAGTAGAAACATTGGCCTTATGTTTTTCTTTGCTTG
1 TCACCATTGGAAGAA-TCCTCACCGATCCAAGTAGAAACATTGGCCTTATGTTTTTCTTTGCTTG
*
11100481 ACCCTTTTTTCTTCCATTGGAGG-CAATCAAACTT-AGGATGTCTTGGCTTTTTGCGTTCATAAC
65 ACCCTTTTTTCTTCCATTGG-GGACAATCAAACTTGA-GATGTCTTGGCTTTTTGCATTCATAAC
* ** * *
11100544 AAATAATGGGATCTTTTTCCTTGTTGGATTCAAGCTTCAATCCTTCTTTTCTTTGAAATCTTATT
128 AAATAACGGGATAATTCTCCTTGTTAGATTCAAGCTTCAATCCTTCTTTTCTTTGAAATCTTATT
* *
11100609 CCCTTGCTCAACTTCATGAATCTCTTGAATCTCTTAGCAAACATGGTCATTTCTTTATCC
193 CCCTTGCTCAACTTCATGAATCTATTGAATCTCTTAGCAAACATAGTCATTTCTTTATCC
11100669 TCA
1 TCA
11100672 TCCACTTCAT
Statistics
Matches: 231, Mismatches: 21, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
251 3 0.01
252 226 0.98
253 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.14, T:0.41
Consensus pattern (252 bp):
TCACCATTGGAAGAATCCTCACCGATCCAAGTAGAAACATTGGCCTTATGTTTTTCTTTGCTTGA
CCCTTTTTTCTTCCATTGGGGACAATCAAACTTGAGATGTCTTGGCTTTTTGCATTCATAACAAA
TAACGGGATAATTCTCCTTGTTAGATTCAAGCTTCAATCCTTCTTTTCTTTGAAATCTTATTCCC
TTGCTCAACTTCATGAATCTATTGAATCTCTTAGCAAACATAGTCATTTCTTTATCC
Found at i:11112018 original size:79 final size:79
Alignment explanation
Indices: 11111882--11112446 Score: 685
Period size: 79 Copynumber: 7.2 Consensus size: 79
11111872 CTAGTTTTAG
* * * * *
11111882 GGGTAAAAGATTGGATTGTTTCAATCTACCTCATGGTCGAGGTAAGAGATCGAATGGTCTTCAAT
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTTCAAT
* *
11111947 CTGCCCTTTGGTTA
66 CTGCCCTCTAGTTA
** *
11111961 GGGTAAAAGATTATATTGCTTCAATCTGTCCCATGGTCGGGGTAAGAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTTCAAT
*
11112026 CTGCCCTCTAG-TC
66 CTGCCCTCTAGTTA
*** * * ** *
11112039 GAGGTAAAAGATCAAATGGCCTTCAATCTACCTTATGGTC-GGGTAAGAGATCGGATGCTCTTCA
1 G-GGTAAAAGATTGGATTG-CTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTTCA
*
11112103 ATCTGCCTTCTAGTTA
64 ATCTGCCCTCTAGTTA
* *
11112119 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGATCAGGGTAAGAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTTCAAT
*
11112184 CTACCCTCTAGTTA
66 CTGCCCTCTAGTTA
* * * *
11112198 GGGTAAAAGATTGGATTGCTTCAATTTGCCCTATGATCGGGGTAAGAGATCAGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTTCAAT
11112263 -TCGCCCTCTAGTTA
66 CT-GCCCTCTAGTTA
* *
11112277 GGGTTAAATATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTTCAAT
1 GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTTCAAT
* **
11112342 CTGCCCTCTGGTCG
66 CTGCCCTCTAGTTA
* * *
11112356 GGGTAAAAGATTGGATGGTCTTTAATCTGCCCCA-GGCTCGGGGTAAGAGATCAGAT--TACTTC
1 GGGTAAAAGATTGGATTG-CTTCAATCTGCCCCATGG-TCGGGGTAAGAGATCGGATGGT-CTTC
* *
11112418 AATCTGCCC-CATGGTTG
63 AATCTGCCCTC-TAGTTA
11112435 GGGTAAAAGATT
1 GGGTAAAAGATT
11112447 CGAGGTTGTA
Statistics
Matches: 424, Mismatches: 52, Indels: 20
0.85 0.10 0.04
Matches are distributed among these distances:
78 21 0.05
79 352 0.83
80 51 0.12
ACGTcount: A:0.25, C:0.19, G:0.26, T:0.30
Consensus pattern (79 bp):
GGGTAAAAGATTGGATTGCTTCAATCTGCCCCATGGTCGGGGTAAGAGATCGGATGGTCTTCAAT
CTGCCCTCTAGTTA
Found at i:11112541 original size:50 final size:50
Alignment explanation
Indices: 11112487--11112630 Score: 135
Period size: 50 Copynumber: 2.9 Consensus size: 50
11112477 CAGGAGTATA
* *
11112487 AGATTCGTCCTTGTGACTTCAATCTGCCCCTCTACAGCTTTAGGCGAATG
1 AGATTCGTCATTGCGACTTCAATCTGCCCCTCTACAGCTTTAGGCGAATG
* * * * * * *
11112537 AGATTCGTCATTGCGGCTTCATTTTTCCCCTCTATAGCTTTAGGTGTATG
1 AGATTCGTCATTGCGACTTCAATCTGCCCCTCTACAGCTTTAGGCGAATG
*** * * ** *
11112587 AGATTTACCATTACGGCTTCAATCTGCATCTCCACAGCTTTAGG
1 AGATTCGTCATTGCGACTTCAATCTGCCCCTCTACAGCTTTAGG
11112631 GGTAAAAGAT
Statistics
Matches: 74, Mismatches: 20, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
50 74 1.00
ACGTcount: A:0.20, C:0.26, G:0.19, T:0.35
Consensus pattern (50 bp):
AGATTCGTCATTGCGACTTCAATCTGCCCCTCTACAGCTTTAGGCGAATG
Found at i:11129161 original size:3 final size:3
Alignment explanation
Indices: 11129153--11129184 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
11129143 CATTATATGT
11129153 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
11129185 GATATTAAGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:11141742 original size:20 final size:19
Alignment explanation
Indices: 11141717--11141759 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
11141707 AATTTTTATT
**
11141717 AAAATTAAACTAAATTATAA
1 AAAATT-AACTAAAACATAA
11141737 AAAATTAACTAAAACATAA
1 AAAATTAACTAAAACATAA
11141756 AAAA
1 AAAA
11141760 GTGCTTGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (19 bp):
AAAATTAACTAAAACATAA
Found at i:11145996 original size:18 final size:18
Alignment explanation
Indices: 11145970--11146006 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
11145960 CCTGTACTTG
* *
11145970 AGCCGTTACTACAGATTA
1 AGCCATTACTACAAATTA
11145988 AGCCATTACTACAAATTA
1 AGCCATTACTACAAATTA
11146006 A
1 A
11146007 TCTTGTAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.41, C:0.22, G:0.11, T:0.27
Consensus pattern (18 bp):
AGCCATTACTACAAATTA
Found at i:11146401 original size:86 final size:86
Alignment explanation
Indices: 11146256--11146501 Score: 402
Period size: 86 Copynumber: 2.9 Consensus size: 86
11146246 TACTAACTGA
* *
11146256 TATGGACCCTCCGATGGCTGAGATCTTGCATATGTTGCGGATTCTTGATAGCTTGTGTGAGCAGC
1 TATGGACCCTCCGATGGCTGAGATCCTGCATATGTTGCGGATTCTTGACAGCTTGTGTGAGCAGC
11146321 ATCGAGAGTGGGTGTTGCATT
66 ATCGAGAGTGGGTGTTGCATT
* * *
11146342 TATGGACCCTCTGATGGCTGAGATCCTGCATAAGTTGCGGATTCTTGACAGCTTGTGTGAGTAGC
1 TATGGACCCTCCGATGGCTGAGATCCTGCATATGTTGCGGATTCTTGACAGCTTGTGTGAGCAGC
11146407 ATCGAGAGTGGGTGTTGCATT
66 ATCGAGAGTGGGTGTTGCATT
* * * *
11146428 TATAGACCCTCCGATGGCTGAGATCCTGCATATGTTGCGAAATCTTGACAGTTTGTGTGAGCAGC
1 TATGGACCCTCCGATGGCTGAGATCCTGCATATGTTGCGGATTCTTGACAGCTTGTGTGAGCAGC
*
11146493 ATCGTGAGT
66 ATCGAGAGT
11146502 AGTAATATGA
Statistics
Matches: 147, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
86 147 1.00
ACGTcount: A:0.20, C:0.18, G:0.30, T:0.31
Consensus pattern (86 bp):
TATGGACCCTCCGATGGCTGAGATCCTGCATATGTTGCGGATTCTTGACAGCTTGTGTGAGCAGC
ATCGAGAGTGGGTGTTGCATT
Found at i:11151667 original size:51 final size:51
Alignment explanation
Indices: 11151583--11151860 Score: 162
Period size: 51 Copynumber: 5.5 Consensus size: 51
11151573 AAATCATTAC
* * * * ** *
11151583 TTTACTTAAAAATCTGAATTTTTATTTCGAAATAGTTAAAAAAATCAAAAT
1 TTTATTTAAAAATCTAAACTTTTCTTTTAAAATAGCTAAAAAAATCAAAAT
* * * * *
11151634 TTTGTTTAAAAATTTAAACTTTTCTTTTAAAATAACTAAAAAAA-CATATT
1 TTTATTTAAAAATCTAAACTTTTCTTTTAAAATAGCTAAAAAAATCAAAAT
* * **
11151684 TTTATTTTTAAAAATCTAAACTTTCTCTTTTTAAA-AG-----AAAATTACTAT
1 TTTA--TTTAAAAATCTAAACTTT-TCTTTTAAAATAGCTAAAAAAATCAAAAT
* * * * ** *
11151732 TTTACTAAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAAT
1 TTTATTTAAAAATCTAAACTTTTCTTTTAAAATAGCTAAAAAAATCAAAAT
* * * * * * * *
11151783 TTTGTTTAAAATTTTAAAATTTT-TCTTTAAAATAACT-AAAAAGT-AGATT
1 TTTATTTAAAAATCTAAACTTTTCT-TTTAAAATAGCTAAAAAAATCAAAAT
11151832 TTTATTTAAAAATCTAAACTTTCTCTTTT
1 TTTATTTAAAAATCTAAACTTT-TCTTTT
11151861 TTAAAGAAAA
Statistics
Matches: 167, Mismatches: 47, Indels: 27
0.69 0.20 0.11
Matches are distributed among these distances:
45 7 0.04
46 17 0.10
47 4 0.02
48 6 0.04
49 21 0.13
50 18 0.11
51 67 0.40
52 18 0.11
53 9 0.05
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.44
Consensus pattern (51 bp):
TTTATTTAAAAATCTAAACTTTTCTTTTAAAATAGCTAAAAAAATCAAAAT
Found at i:11151675 original size:149 final size:147
Alignment explanation
Indices: 11151422--11151933 Score: 633
Period size: 149 Copynumber: 3.4 Consensus size: 147
11151412 TAATTAAAAC
* * * * * *
11151422 AAAAACACTACTTTATTTCAAAATTAAAATTTTTATTTCGAAATAGTTAAAAAAGATCAAAACTT
1 AAAATCACTATTTTACTTAAAAATCAAAACTTTTATTTCGAAATAGTTAAAAAA-ATCAAAACTT
* * *
11151487 TT-TTAAAAAATTTAAACTTTTTCTTTAAAATCATTAAAAAAACATTTTTTTATTTTTTTAAAAA
65 TTGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAAACA-TTTTTTA--TTTTTAAAAA
*
11151551 TCTAAACTTTCTTTTTTAATG
127 TCTAAACTTTCTTTTTTAAAG
* * ** *
11151572 AAAATCATTACTTTACTTAAAAATCTGAATTTTTATTTCGAAATAGTTAAAAAAATCAAAA-TTT
1 AAAATCACTATTTTACTTAAAAATCAAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
11151636 TGTTTAAAAATTTAAAC-TTTTCTTTTAAAATAACTAAAAAAACATATTTTTATTTTTAAAAATC
66 TGTTTAAAAATTTAAACTTTTTC-TTTAAAATAACTAAAAAAACAT-TTTTTATTTTTAAAAATC
11151700 TAAACTTTCTCTTTTTAAAAG
129 TAAACTTTCT-TTTTT-AAAG
* * *
11151721 AAAATTACTATTTTACTAAAAAATCCAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAA-TTT
1 AAAATCACTATTTTACTTAAAAATCAAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
* * * *
11151785 TGTTTAAAATTTTAAAATTTTTCTTTAAAATAACTAAAAAGTAGA-TTTTTA--TTTAAAAATCT
66 TGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAA-AACATTTTTTATTTTTAAAAATCT
11151847 AAACTTTCTCTTTTTTAAAG
130 AAAC-TT-TCTTTTTTAAAG
* * * *
11151867 AAAATCACTATTTTTCTTAAAAATCAAAACTTTTATTTTGAAATTGTTTTAAAAAATCAAAACTT
1 AAAATCACTATTTTACTTAAAAATCAAAACTTTTATTTCGAAATAG-TTAAAAAAATCAAAACTT
11151932 TT
65 TT
11151934 CCCAAAATCA
Statistics
Matches: 322, Mismatches: 29, Indels: 24
0.86 0.08 0.06
Matches are distributed among these distances:
146 59 0.18
147 43 0.13
148 28 0.09
149 138 0.43
150 54 0.17
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.43
Consensus pattern (147 bp):
AAAATCACTATTTTACTTAAAAATCAAAACTTTTATTTCGAAATAGTTAAAAAAATCAAAACTTT
TGTTTAAAAATTTAAACTTTTTCTTTAAAATAACTAAAAAAACATTTTTTATTTTTAAAAATCTA
AACTTTCTTTTTTAAAG
Found at i:11152393 original size:3 final size:3
Alignment explanation
Indices: 11152387--11152426 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
11152377 CTACTACTAC
* * *
11152387 TAA TAA TAA TAA TAA TAA CAA TAG TAA TGA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
11152427 TTGGGCCCTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.60, C:0.03, G:0.05, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:11152771 original size:21 final size:21
Alignment explanation
Indices: 11152745--11152798 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
11152735 TGGTGCAGGT
*
11152745 TTCTACCGATACAAGT-GTGAC
1 TTCTACCGATACAAGTCATG-C
*
11152766 TTCTACCGAAACAAGTCATGC
1 TTCTACCGATACAAGTCATGC
*
11152787 TTTTACCGATAC
1 TTCTACCGATAC
11152799 TAAAAACACT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 26 0.93
22 2 0.07
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.30
Consensus pattern (21 bp):
TTCTACCGATACAAGTCATGC
Found at i:11156129 original size:17 final size:17
Alignment explanation
Indices: 11156107--11156140 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
11156097 GGCAAGAACA
11156107 TTATGTTTTAATAAATC
1 TTATGTTTTAATAAATC
*
11156124 TTATGTTTTATTAAATC
1 TTATGTTTTAATAAATC
11156141 ATAATAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.56
Consensus pattern (17 bp):
TTATGTTTTAATAAATC
Found at i:11167412 original size:16 final size:16
Alignment explanation
Indices: 11167382--11167411 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
11167372 AAAAATGAGA
11167382 AAAAAGAAAGAAAAAG
1 AAAAAGAAAGAAAAAG
11167398 AAAAAG-AAGAAAAA
1 AAAAAGAAAGAAAAA
11167412 ACTTTATGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAGAAAAAG
Found at i:11168475 original size:32 final size:32
Alignment explanation
Indices: 11168429--11168495 Score: 125
Period size: 32 Copynumber: 2.1 Consensus size: 32
11168419 ATTGTATTTG
11168429 TTGACCCCTCTTTTTATGTTGATGAATTAATC
1 TTGACCCCTCTTTTTATGTTGATGAATTAATC
*
11168461 TTGACCCCTTTTTTTATGTTGATGAATTAATC
1 TTGACCCCTCTTTTTATGTTGATGAATTAATC
11168493 TTG
1 TTG
11168496 CATAATCTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.21, C:0.16, G:0.13, T:0.49
Consensus pattern (32 bp):
TTGACCCCTCTTTTTATGTTGATGAATTAATC
Found at i:11180320 original size:30 final size:29
Alignment explanation
Indices: 11180265--11180322 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 29
11180255 ACTAAATTAG
11180265 GGGATTAAATTATGATTTTAGTAAAATTTT
1 GGGATTAAATTA-GATTTTAGTAAAATTTT
*
11180295 GGGATTAAATT-GAATTTTATTTAAAATT
1 GGGATTAAATTAG-ATTTTA-GTAAAATT
11180323 CTGTGGCCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 1 0.04
29 6 0.24
30 18 0.72
ACGTcount: A:0.38, C:0.00, G:0.16, T:0.47
Consensus pattern (29 bp):
GGGATTAAATTAGATTTTAGTAAAATTTT
Found at i:11189440 original size:20 final size:21
Alignment explanation
Indices: 11189415--11189475 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
11189405 AATTTGAGTT
*
11189415 TTGTCTCAAGACAACAA-GAC
1 TTGTCTCAAGACAAAAACGAC
*
11189435 TTGTCTCAAGACAAAAATCTAC
1 TTGTCTCAAGACAAAAA-CGAC
11189457 TTGTCTCAAGACAGAAAAC
1 TTGTCTCAAGACA-AAAAC
11189476 ATCGAAGCTA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
20 16 0.44
22 16 0.44
23 4 0.11
ACGTcount: A:0.41, C:0.23, G:0.13, T:0.23
Consensus pattern (21 bp):
TTGTCTCAAGACAAAAACGAC
Found at i:11192842 original size:18 final size:18
Alignment explanation
Indices: 11192812--11192861 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
11192802 AAAACCCTCC
11192812 TAAATAATT-AAATTTTTT
1 TAAA-AATTAAAATTTTTT
*
11192830 TAAAAATTAAAATATTTT
1 TAAAAATTAAAATTTTTT
*
11192848 TAAGAATTAAAATT
1 TAAAAATTAAAATT
11192862 AATTGAAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 4 0.14
18 24 0.86
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
TAAAAATTAAAATTTTTT
Found at i:11201799 original size:21 final size:19
Alignment explanation
Indices: 11201754--11201799 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
11201744 TGAAAATAAA
11201754 CTAAAACTACATAAAAATC
1 CTAAAACTACATAAAAATC
11201773 CT-AAACTACCAACTAAAAA-C
1 CTAAAACTA-C-A-TAAAAATC
11201793 CTAAAAC
1 CTAAAAC
11201800 GGCTTGGCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
18 6 0.26
19 3 0.13
20 4 0.17
21 10 0.43
ACGTcount: A:0.57, C:0.26, G:0.00, T:0.17
Consensus pattern (19 bp):
CTAAAACTACATAAAAATC
Found at i:11202377 original size:12 final size:12
Alignment explanation
Indices: 11202356--11202385 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
11202346 AAAATATAGA
*
11202356 AAAACCAAAAAG
1 AAAACAAAAAAG
11202368 AAAACAAAAAAG
1 AAAACAAAAAAG
11202380 AAAACA
1 AAAACA
11202386 CACGACTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.80, C:0.13, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAACAAAAAAG
Found at i:11206894 original size:13 final size:13
Alignment explanation
Indices: 11206876--11206906 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
11206866 AAACCACTTC
11206876 AATTTGAACTCCA
1 AATTTGAACTCCA
11206889 AATTTGAACTCCA
1 AATTTGAACTCCA
11206902 AATTT
1 AATTT
11206907 TAAACTCACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.35
Consensus pattern (13 bp):
AATTTGAACTCCA
Found at i:11207371 original size:16 final size:18
Alignment explanation
Indices: 11207346--11207383 Score: 53
Period size: 16 Copynumber: 2.2 Consensus size: 18
11207336 CATTTTTTAT
11207346 TATTAATATAA-TTAA-A
1 TATTAATATAACTTAATA
*
11207362 TATTATTATAACTTAATA
1 TATTAATATAACTTAATA
11207380 TATT
1 TATT
11207384 TGTCACGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 10 0.53
17 4 0.21
18 5 0.26
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
TATTAATATAACTTAATA
Found at i:11211045 original size:21 final size:22
Alignment explanation
Indices: 11211007--11211048 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
11210997 AATCTTACCC
11211007 TTTAAAAGTAAATAAAAATTATT
1 TTTAAAAG-AAATAAAAATTATT
*
11211030 TTTAAAA-AAATTAAAATTA
1 TTTAAAAGAAATAAAAATTA
11211049 ACCTTTTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
23 7 0.39
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (22 bp):
TTTAAAAGAAATAAAAATTATT
Found at i:11211141 original size:17 final size:17
Alignment explanation
Indices: 11211085--11211141 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 17
11211075 TTCAAATTTT
* *
11211085 AAAAATATATATCTTTA
1 AAAAATAAAAATCTTTA
*
11211102 AAAAATACAAAAT-TATGA
1 AAAAATA-AAAATCT-TTA
11211120 TAAAAATAAAAATCTTTA
1 -AAAAATAAAAATCTTTA
11211138 AAAA
1 AAAA
11211142 TGATTTTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
17 12 0.38
18 12 0.38
19 8 0.25
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (17 bp):
AAAAATAAAAATCTTTA
Found at i:11212785 original size:149 final size:146
Alignment explanation
Indices: 11212578--11212860 Score: 377
Period size: 149 Copynumber: 1.9 Consensus size: 146
11212568 GTTACGCATT
* * * * * *
11212578 ATTAATATAAAAATGTATATTATAATATCATAATTGTGCATACGGTTACATATTATTAATAATCT
1 ATTAATATAAAAATGTAAATTACAATAACATAATTGTACATACGGATACATATCATTAATAATCT
* *
11212643 ATCTTAATTAAATAATGCTAATTGTATATATATTATAATCTACCATAAAGTTAGTTTCACGTTTA
66 A-CATAATTAAATAATGCTAATTGTATA-A-ATTATAATCTACCATAAAATTAGTTTCACGTTTA
*
11212708 GGGTTTAAGTTTGTGTATC
128 AGGTTTAAGTTTGTGTATC
* * ** *
11212727 ATTAATATTAAAATGTAAATTACAATAACATAGTTGTATTTAGGGATACATATCATTAATAATCT
1 ATTAATATAAAAATGTAAATTACAATAACATAATTGTACATACGGATACATATCATTAATAATCT
* * * *
11212792 ACATAATTATATAATGTTAATTGTATAAATTATAATTTACCATAAAATTAGTTTCATGTTTAAGG
66 ACATAATTAAATAATGCTAATTGTATAAATTATAATCTACCATAAAATTAGTTTCACGTTTAAGG
11212857 TTTA
131 TTTA
11212861 GGTTGCATAT
Statistics
Matches: 116, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
146 37 0.32
147 1 0.01
148 23 0.20
149 55 0.47
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.42
Consensus pattern (146 bp):
ATTAATATAAAAATGTAAATTACAATAACATAATTGTACATACGGATACATATCATTAATAATCT
ACATAATTAAATAATGCTAATTGTATAAATTATAATCTACCATAAAATTAGTTTCACGTTTAAGG
TTTAAGTTTGTGTATC
Found at i:11215774 original size:17 final size:17
Alignment explanation
Indices: 11215731--11215887 Score: 115
Period size: 17 Copynumber: 9.4 Consensus size: 17
11215721 CTACACATTG
*
11215731 ACACAGTTTGCATAT-A
1 ACACAGCTTGCATATAA
*
11215747 ACATA-CTTGCATATAA
1 ACACAGCTTGCATATAA
11215763 ACACAGCTTGCATATAA
1 ACACAGCTTGCATATAA
* * *
11215780 ACATAGGTAGCATATAA
1 ACACAGCTTGCATATAA
* * *
11215797 ATATAGCTCAG-ATATAA
1 ACACAGCT-TGCATATAA
* * *
11215814 ACACATCTCGCATACAA
1 ACACAGCTTGCATATAA
* *
11215831 ACACAACTAGCATATAA
1 ACACAGCTTGCATATAA
*
11215848 ACATAG-TTCGCATATAA
1 ACACAGCTT-GCATATAA
* * *
11215865 GCACAACTCGCATATAA
1 ACACAGCTTGCATATAA
11215882 ACACAG
1 ACACAG
11215888 TTTGTCTCAT
Statistics
Matches: 110, Mismatches: 25, Indels: 11
0.75 0.17 0.08
Matches are distributed among these distances:
15 8 0.07
16 11 0.10
17 88 0.80
18 3 0.03
ACGTcount: A:0.44, C:0.22, G:0.11, T:0.24
Consensus pattern (17 bp):
ACACAGCTTGCATATAA
Found at i:11215815 original size:51 final size:51
Alignment explanation
Indices: 11215740--11215886 Score: 165
Period size: 51 Copynumber: 2.9 Consensus size: 51
11215730 GACACAGTTT
* * * * **
11215740 GCATAT-AACATA-CTTGCATATAAACACAGCTTGCATATAAACATAGGTA
1 GCATATAAACATAGCTCGCATATAAACACAACTCGCATATAAACACAACTA
* * *
11215789 GCATATAAATATAGCTCAG-ATATAAACACATCTCGCATACAAACACAACTA
1 GCATATAAACATAGCTC-GCATATAAACACAACTCGCATATAAACACAACTA
* *
11215840 GCATATAAACATAGTTCGCATATAAGCACAACTCGCATATAAACACA
1 GCATATAAACATAGCTCGCATATAAACACAACTCGCATATAAACACA
11215887 GTTTGTCTCA
Statistics
Matches: 81, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
49 6 0.07
50 6 0.07
51 68 0.84
52 1 0.01
ACGTcount: A:0.45, C:0.22, G:0.10, T:0.23
Consensus pattern (51 bp):
GCATATAAACATAGCTCGCATATAAACACAACTCGCATATAAACACAACTA
Found at i:11220603 original size:18 final size:18
Alignment explanation
Indices: 11220555--11220603 Score: 73
Period size: 18 Copynumber: 2.7 Consensus size: 18
11220545 TTTCGGGTCA
11220555 AATCGAATTAATTCGGTT
1 AATCGAATTAATTCGGTT
*
11220573 AACCG-ATTGAATTCGGTT
1 AATCGAATT-AATTCGGTT
11220591 AATCGAATTAATT
1 AATCGAATTAATT
11220604 TGGTCGGGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 3 0.11
18 21 0.78
19 3 0.11
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.37
Consensus pattern (18 bp):
AATCGAATTAATTCGGTT
Found at i:11225987 original size:126 final size:126
Alignment explanation
Indices: 11225762--11226141 Score: 751
Period size: 126 Copynumber: 3.0 Consensus size: 126
11225752 TGGCTAGCTC
*
11225762 TTGAAAGATTCAAATTGAAGCAACAATATTAATACTTTAAGGATTTAGGTAAAACATTTTAAAGT
1 TTGAAAGATTTAAATTGAAGCAACAATATTAATACTTTAAGGATTTAGGTAAAACATTTTAAAGT
11225827 TTGAGGGCAAATTTAAGATATGAACGTTTGAGGTATAATAAATTTATTTATTTTTAGTGAA
66 TTGAGGGCAAATTTAAGATATGAACGTTTGAGGTATAATAAATTTATTTATTTTTAGTGAA
11225888 TTGAAAGATTTAAATTGAAGCAACAATATTAATACTTTAAGGATTTAGGTAAAACATTTTAAAGT
1 TTGAAAGATTTAAATTGAAGCAACAATATTAATACTTTAAGGATTTAGGTAAAACATTTTAAAGT
11225953 TTGAGGGCAAATTTAAGATATGAACGTTTGAGGTATAATAAATTTATTTATTTTTAGTGAA
66 TTGAGGGCAAATTTAAGATATGAACGTTTGAGGTATAATAAATTTATTTATTTTTAGTGAA
11226014 TTGAAAGATTTAAATTGAAGCAACAATATTAATACTTTAAGGATTTAGGTAAAACATTTTAAAGT
1 TTGAAAGATTTAAATTGAAGCAACAATATTAATACTTTAAGGATTTAGGTAAAACATTTTAAAGT
11226079 TTGAGGGCAAATTTAAGATATGAACGTTTGAGGTATAATAAATTTATTTATTTTTAGTGAA
66 TTGAGGGCAAATTTAAGATATGAACGTTTGAGGTATAATAAATTTATTTATTTTTAGTGAA
11226140 TT
1 TT
11226142 ACAAGAGAAG
Statistics
Matches: 253, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
126 253 1.00
ACGTcount: A:0.40, C:0.05, G:0.17, T:0.38
Consensus pattern (126 bp):
TTGAAAGATTTAAATTGAAGCAACAATATTAATACTTTAAGGATTTAGGTAAAACATTTTAAAGT
TTGAGGGCAAATTTAAGATATGAACGTTTGAGGTATAATAAATTTATTTATTTTTAGTGAA
Found at i:11226736 original size:113 final size:113
Alignment explanation
Indices: 11226598--11226846 Score: 471
Period size: 113 Copynumber: 2.2 Consensus size: 113
11226588 TTTTGATTTT
* *
11226598 AGTTTAAATATATTTTGGTTATTTTTTTGGTGAATTACAAACAAATTAATACGACTCGAACTCAG
1 AGTTCAAATATATTTTGGTTATTTTTTTGGTGAATTACAAACAAATTAATACGACTCGAACTCAA
*
11226663 GTCACATTTGAGACGATGAACACCCTTAATCATCAGATAAATACATGG
66 ATCACATTTGAGACGATGAACACCCTTAATCATCAGATAAATACATGG
11226711 AGTTCAAATATATTTTGGTTATTTTTTTGGTGAATTACAAACAAATTAATACGACTCGAACTCAA
1 AGTTCAAATATATTTTGGTTATTTTTTTGGTGAATTACAAACAAATTAATACGACTCGAACTCAA
11226776 ATCACATTTGAGACGATGAACACCCTTAATCATCAGATAAATACATGG
66 ATCACATTTGAGACGATGAACACCCTTAATCATCAGATAAATACATGG
11226824 AGTTCAAATATATTTTGGTTATT
1 AGTTCAAATATATTTTGGTTATT
11226847 AATTTGATGT
Statistics
Matches: 133, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
113 133 1.00
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (113 bp):
AGTTCAAATATATTTTGGTTATTTTTTTGGTGAATTACAAACAAATTAATACGACTCGAACTCAA
ATCACATTTGAGACGATGAACACCCTTAATCATCAGATAAATACATGG
Found at i:11227730 original size:31 final size:30
Alignment explanation
Indices: 11227679--11227737 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
11227669 ATGATATGTG
*
11227679 AACTTTAATTTGTTTCAATTATAGATATAA
1 AACTTTAATTTGTTTCAATTATAAATATAA
*
11227709 AACTTTGATTTTGATTT-AATTATAAATAT
1 AACTTT-AATTTG-TTTCAATTATAAATAT
11227738 TTTTAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 6 0.24
31 16 0.64
32 3 0.12
ACGTcount: A:0.39, C:0.05, G:0.07, T:0.49
Consensus pattern (30 bp):
AACTTTAATTTGTTTCAATTATAAATATAA
Found at i:11237652 original size:20 final size:20
Alignment explanation
Indices: 11237615--11237653 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
11237605 ATTTTTTATA
* *
11237615 CATATTTTCATATTTTTAAG
1 CATATTTTCACATATTTAAG
*
11237635 CATATTTTTACATATTTAA
1 CATATTTTCACATATTTAA
11237654 AAAAATTTTA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.10, G:0.03, T:0.54
Consensus pattern (20 bp):
CATATTTTCACATATTTAAG
Found at i:11238014 original size:103 final size:103
Alignment explanation
Indices: 11237893--11238083 Score: 310
Period size: 103 Copynumber: 1.9 Consensus size: 103
11237883 AACCATAACA
** * *
11237893 AAACAAAAACAGTCATGAACCATAACAAATATAACTCCAACACTCAATTCCATGTCCATCCAAAC
1 AAACAAAAACAAACATGAACAATAACAAATATAACTCCAACACTCAACTCCATGTCCATCCAAAC
* *
11237958 AGTCATGAAGCATATCATATCAAACGAACTAATCACTT
66 AGTCATCAAGCATATAATATCAAACGAACTAATCACTT
*
11237996 AAACAAAAACAAACATGAACAATAACAAATATAACTCCAACAGTCAACTCCATGTCCATCCAAAC
1 AAACAAAAACAAACATGAACAATAACAAATATAACTCCAACACTCAACTCCATGTCCATCCAAAC
*
11238061 AGTCATCAATCATATAATATCAA
66 AGTCATCAAGCATATAATATCAA
11238084 CATATTCAAG
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
103 80 1.00
ACGTcount: A:0.48, C:0.26, G:0.06, T:0.20
Consensus pattern (103 bp):
AAACAAAAACAAACATGAACAATAACAAATATAACTCCAACACTCAACTCCATGTCCATCCAAAC
AGTCATCAAGCATATAATATCAAACGAACTAATCACTT
Found at i:11239166 original size:21 final size:21
Alignment explanation
Indices: 11239120--11239166 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
11239110 CCCTTATTTG
* *
11239120 ATATGTTTGATTTTTGTTATT
1 ATATTTTTGATTTTTATTATT
*
11239141 TTATTTTTGATTTATTATTA-T
1 ATATTTTTGATTT-TTATTATT
11239162 ATATT
1 ATATT
11239167 AGCATTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.68
Consensus pattern (21 bp):
ATATTTTTGATTTTTATTATT
Found at i:11241058 original size:18 final size:18
Alignment explanation
Indices: 11241021--11241067 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
11241011 TGGTTTGAAT
11241021 ATGAAATG-AAA-TTGAG
1 ATGAAATGAAAATTTGAG
11241037 ATGAGAATGAAAATTTGA-
1 ATGA-AATGAAAATTTGAG
*
11241055 ATGATATGAAAAT
1 ATGAAATGAAAAT
11241068 GGAAATGGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
16 4 0.15
17 12 0.44
18 7 0.26
19 4 0.15
ACGTcount: A:0.51, C:0.00, G:0.21, T:0.28
Consensus pattern (18 bp):
ATGAAATGAAAATTTGAG
Found at i:11242421 original size:29 final size:29
Alignment explanation
Indices: 11242374--11242467 Score: 134
Period size: 29 Copynumber: 3.2 Consensus size: 29
11242364 ATACAACCTA
* *
11242374 ACACACGACCATGTATTGGCCCGTGTGTG
1 ACACACGACCGTGTGTTGGCCCGTGTGTG
* *
11242403 ACACACGGCCGTGTGTTGGCCTGTGTGTG
1 ACACACGACCGTGTGTTGGCCCGTGTGTG
* *
11242432 ACACACGATCGTGTGTTGGCCCATGTGTG
1 ACACACGACCGTGTGTTGGCCCGTGTGTG
11242461 ACACACG
1 ACACACG
11242468 GTCTGGACAC
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 57 1.00
ACGTcount: A:0.18, C:0.27, G:0.31, T:0.24
Consensus pattern (29 bp):
ACACACGACCGTGTGTTGGCCCGTGTGTG
Found at i:11242580 original size:56 final size:56
Alignment explanation
Indices: 11242520--11242729 Score: 167
Period size: 56 Copynumber: 3.7 Consensus size: 56
11242510 ACCTTAACAT
* *
11242520 ACAAAATAGTATACACACATGGTCTGGCACACGCTCGTGTGCGTAGCCCATGTGTC
1 ACAAAATAGTATACACACACGGTCTAGCACACGCTCGTGTGCGTAGCCCATGTGTC
* * * * *
11242576 ACAAAACAGTATACACACACGGACTAGCACAAG-TCCGTATGTCTCCTGTA-CCTTAT-T-TC
1 ACAAAATAGTATACACACACGGTCTAGCACACGCT-CG--TG--TGC-GTAGCC-CATGTGTC
* * * * * * * *
11242635 TCAAAATAGTATACGCACATGGTCTAGCATACGCACGTTTGTGCAGCCCATGTGTC
1 ACAAAATAGTATACACACACGGTCTAGCACACGCTCGTGTGCGTAGCCCATGTGTC
* * *
11242691 ACAAAATAGTATACACACACAGTCTGGCACACGCCCGTG
1 ACAAAATAGTATACACACACGGTCTAGCACACGCTCGTG
11242730 GGTTTAGCTC
Statistics
Matches: 115, Mismatches: 28, Indels: 22
0.70 0.17 0.13
Matches are distributed among these distances:
54 4 0.03
55 5 0.04
56 63 0.55
57 1 0.01
58 2 0.02
59 30 0.26
60 5 0.04
61 5 0.04
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.23
Consensus pattern (56 bp):
ACAAAATAGTATACACACACGGTCTAGCACACGCTCGTGTGCGTAGCCCATGTGTC
Found at i:11243853 original size:21 final size:21
Alignment explanation
Indices: 11243829--11243881 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
11243819 TTATGCTAGC
11243829 TCTACCGATACAAGT-ATG-A
1 TCTACCGATACAAGTCATGCA
*
11243848 TTTCTAACGATACAAGTCATGCA
1 --TCTACCGATACAAGTCATGCA
11243871 TCTACCGATAC
1 TCTACCGATAC
11243882 CAAAAACTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 24 0.86
22 3 0.11
23 1 0.04
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.28
Consensus pattern (21 bp):
TCTACCGATACAAGTCATGCA
Found at i:11243959 original size:21 final size:22
Alignment explanation
Indices: 11243935--11243997 Score: 58
Period size: 21 Copynumber: 2.8 Consensus size: 22
11243925 TGATATAAGC
11243935 ATACAAACTACCGATACAT-CA
1 ATACAAACTACCGATACATGCA
* *
11243956 ATACTATTAACTACCGATACTTGTA
1 ATAC-A--AACTACCGATACATGCA
*
11243981 ATTC-AACTACCGATACA
1 ATACAAACTACCGATACA
11243998 ACTCAAGTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
21 16 0.47
22 1 0.03
24 13 0.38
25 4 0.12
ACGTcount: A:0.41, C:0.25, G:0.06, T:0.27
Consensus pattern (22 bp):
ATACAAACTACCGATACATGCA
Found at i:11245225 original size:21 final size:22
Alignment explanation
Indices: 11245201--11245243 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
11245191 ACTTTCATCA
11245201 TTAAGCTTAATT-AACCCATTT
1 TTAAGCTTAATTAAACCCATTT
* *
11245222 TTAATCTTGATTAAACCCATTT
1 TTAAGCTTAATTAAACCCATTT
11245244 ATACTTAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.33, C:0.19, G:0.05, T:0.44
Consensus pattern (22 bp):
TTAAGCTTAATTAAACCCATTT
Found at i:11254491 original size:26 final size:26
Alignment explanation
Indices: 11254448--11254505 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
11254438 CATTACCCCT
* *
11254448 AGAATTGTCGCTGCAAGAACTTGTTC
1 AGAATTGTCACTGCAAGAACTTATTC
*
11254474 AGAATTGTCACTGGAAGAACTTATTC
1 AGAATTGTCACTGCAAGAACTTATTC
11254500 AGAATT
1 AGAATT
11254506 ATCGTTATGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.31
Consensus pattern (26 bp):
AGAATTGTCACTGCAAGAACTTATTC
Found at i:11256671 original size:16 final size:16
Alignment explanation
Indices: 11256650--11256681 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
11256640 TAAGTCATTA
*
11256650 CAGTTATTCAGTTATC
1 CAGTTATTAAGTTATC
11256666 CAGTTATTAAGTTATC
1 CAGTTATTAAGTTATC
11256682 GATACACTGT
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:0.28, C:0.16, G:0.12, T:0.44
Consensus pattern (16 bp):
CAGTTATTAAGTTATC
Found at i:11257863 original size:56 final size:56
Alignment explanation
Indices: 11257795--11257994 Score: 161
Period size: 56 Copynumber: 3.5 Consensus size: 56
11257785 CTTAACCTGT
* * *
11257795 AAAACAGTATACACACACAGTTTGACGCACGCCCATGTGCGCAGCCTATGTGTCAC
1 AAAATAGTATACACAAACAGTTTGACACACGCCCATGTGCGCAGCCTATGTGTCAC
* ** ** * * *
11257851 AAAATAATATACACAAATGGACTGACACACGCCCATGTGTCTCTTGTACCTTAT-T-TCTC
1 AAAATAGTATACACAAACAGTTTGACACACGCCCATGTG-CGC-AG--CC-TATGTGTCAC
* * * * *
11257910 AAAATAGTATACACAAACAGTTTGGCACACACCCGTGTACGCAGCCCATGTGTCAC
1 AAAATAGTATACACAAACAGTTTGACACACGCCCATGTGCGCAGCCTATGTGTCAC
* * * *
11257966 AAAATAGCATACACACACGGTCTGACACA
1 AAAATAGTATACACAAACAGTTTGACACA
11257995 TACTCATGGG
Statistics
Matches: 108, Mismatches: 29, Indels: 14
0.72 0.19 0.09
Matches are distributed among these distances:
54 2 0.02
55 3 0.03
56 58 0.54
57 3 0.03
58 3 0.03
59 33 0.31
60 3 0.03
61 3 0.03
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.22
Consensus pattern (56 bp):
AAAATAGTATACACAAACAGTTTGACACACGCCCATGTGCGCAGCCTATGTGTCAC
Found at i:11263477 original size:20 final size:20
Alignment explanation
Indices: 11263441--11263490 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
11263431 TCATTAAGCT
* *
11263441 TTAATTAACCACTTTTAATC
1 TTAATTAAACACTTTTAAAC
11263461 TTAATTAAAC-CTATTTAAAC
1 TTAATTAAACACT-TTTAAAC
11263481 TTAATATAAA
1 TTAAT-TAAA
11263491 TCATGCTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 2 0.08
20 20 0.77
21 4 0.15
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.42
Consensus pattern (20 bp):
TTAATTAAACACTTTTAAAC
Found at i:11266598 original size:20 final size:21
Alignment explanation
Indices: 11266562--11266603 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
11266552 AAATAACATT
11266562 ATTATTTAATGTATTTATAAC
1 ATTATTTAATGTATTTATAAC
*
11266583 ATTATTT-ATTTATTTATAAC
1 ATTATTTAATGTATTTATAAC
11266603 A
1 A
11266604 ATTCTTTAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.55
Consensus pattern (21 bp):
ATTATTTAATGTATTTATAAC
Found at i:11272783 original size:24 final size:24
Alignment explanation
Indices: 11272751--11272797 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
11272741 ATGGATGTTC
11272751 AACCTTTCATC-TCTCTTAACCTTT
1 AACCTTTCATCTTCT-TTAACCTTT
11272775 AACCTTTCATCTTCTTTAACCTT
1 AACCTTTCATCTTCTTTAACCTT
11272798 GCATATTCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 19 0.86
25 3 0.14
ACGTcount: A:0.21, C:0.32, G:0.00, T:0.47
Consensus pattern (24 bp):
AACCTTTCATCTTCTTTAACCTTT
Found at i:11272791 original size:17 final size:17
Alignment explanation
Indices: 11272771--11272812 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
11272761 CTCTCTTAAC
* *
11272771 CTTTAACCTTTCATCTT
1 CTTTAACCTTGCATATT
11272788 CTTTAACCTTGCATATT
1 CTTTAACCTTGCATATT
11272805 CTTGTAAC
1 CTT-TAAC
11272813 TATTTTTTCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 18 0.82
18 4 0.18
ACGTcount: A:0.21, C:0.26, G:0.05, T:0.48
Consensus pattern (17 bp):
CTTTAACCTTGCATATT
Found at i:11276391 original size:19 final size:20
Alignment explanation
Indices: 11276362--11276400 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
11276352 ACTTGAATTT
11276362 TTTACAAAAATTATA-TAAAA
1 TTTACAAAAA-TATACTAAAA
11276382 TTTA-AAAAATATACTAAAA
1 TTTACAAAAATATACTAAAA
11276401 AACTTAGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
19 10 0.56
20 4 0.22
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (20 bp):
TTTACAAAAATATACTAAAA
Found at i:11281696 original size:32 final size:32
Alignment explanation
Indices: 11281643--11281704 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
11281633 AAAAATACTT
** * *
11281643 AAAACTCAAAATAGTTTAAACTTGAAATGATC
1 AAAACTCAAAATAACTAAAACTTAAAATGATC
11281675 AAAACTCAAAATAACTAAAACTTAAAATGA
1 AAAACTCAAAATAACTAAAACTTAAAATGA
11281705 CCCGAACAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.56, C:0.13, G:0.06, T:0.24
Consensus pattern (32 bp):
AAAACTCAAAATAACTAAAACTTAAAATGATC
Found at i:11284941 original size:21 final size:21
Alignment explanation
Indices: 11284899--11284942 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
11284889 GAAGTATAGG
* *
11284899 TTGTATCGGTAGTACCCATAC
1 TTGTATCGATAGAACCCATAC
11284920 TTGTATCGATAGAACTCC-TAC
1 TTGTATCGATAGAAC-CCATAC
11284941 TT
1 TT
11284943 CTACTGGTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 18 0.90
22 2 0.10
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (21 bp):
TTGTATCGATAGAACCCATAC
Found at i:11286808 original size:13 final size:14
Alignment explanation
Indices: 11286782--11286814 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
11286772 AATAAAAGAA
11286782 ATTTTATGTAAATT
1 ATTTTATGTAAATT
*
11286796 TTTTTATGT-AATT
1 ATTTTATGTAAATT
11286809 ATTTTA
1 ATTTTA
11286815 ATTTTAGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (14 bp):
ATTTTATGTAAATT
Found at i:11288373 original size:22 final size:22
Alignment explanation
Indices: 11288346--11288395 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
11288336 GAAATTTAAA
*
11288346 ACAAAACATTATGAGGAGAGTT
1 ACAAAACATTATAAGGAGAGTT
*
11288368 ATAAAACATTATAAGGAGAGTT
1 ACAAAACATTATAAGGAGAGTT
11288390 ACAAAA
1 ACAAAA
11288396 TAATGTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.52, C:0.08, G:0.18, T:0.22
Consensus pattern (22 bp):
ACAAAACATTATAAGGAGAGTT
Found at i:11303241 original size:19 final size:19
Alignment explanation
Indices: 11303219--11303263 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
11303209 TTATATTAGG
11303219 ATTTAATATTTAAGATCT-T
1 ATTTAATATTTAA-ATCTGT
* *
11303238 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATCTGT
11303257 ATTTAAT
1 ATTTAAT
11303264 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATCTGT
Found at i:11304111 original size:21 final size:22
Alignment explanation
Indices: 11304071--11304116 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
11304061 TTCTATTTCC
11304071 TTTAATTCTATCTACTTTTATT
1 TTTAATTCTATCTACTTTTATT
* *
11304093 TTTAATTCTGT-TTCTTTTATT
1 TTTAATTCTATCTACTTTTATT
11304114 TTT
1 TTT
11304117 CCTTAGATAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.55
22 10 0.45
ACGTcount: A:0.17, C:0.11, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTAATTCTATCTACTTTTATT
Found at i:11308038 original size:13 final size:11
Alignment explanation
Indices: 11308010--11308052 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
11308000 AGTTAAATAT
11308010 TATTTTATTAA
1 TATTTTATTAA
11308021 TATTTTACTTAGA
1 TATTTTA-TTA-A
*
11308034 TA-TTTATTAT
1 TATTTTATTAA
11308044 TATTTTATT
1 TATTTTATT
11308053 TAGAAAATAG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 2 0.07
11 16 0.57
12 7 0.25
13 3 0.11
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:11308039 original size:23 final size:23
Alignment explanation
Indices: 11308013--11308056 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
11308003 TAAATATTAT
11308013 TTTATTAATATTTTACTTAGATA
1 TTTATTAATATTTTACTTAGATA
* *
11308036 TTTATTATTATTTTATTTAGA
1 TTTATTAATATTTTACTTAGA
11308057 AAATAGTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (23 bp):
TTTATTAATATTTTACTTAGATA
Found at i:11315127 original size:22 final size:24
Alignment explanation
Indices: 11315084--11315127 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
11315074 TTCATATACT
*
11315084 TTATATTTAAATATAATTTAAAAA
1 TTATATATAAATATAATTTAAAAA
11315108 TTATATATAAAT-T-ATTTAAA
1 TTATATATAAATATAATTTAAA
11315128 TTAAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 1 0.05
24 11 0.58
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
TTATATATAAATATAATTTAAAAA
Found at i:11315823 original size:23 final size:23
Alignment explanation
Indices: 11315797--11315841 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
11315787 ATTTTCGAAT
**
11315797 TTCGAATTATTCGAATCGAGTTA
1 TTCGAATTAAACGAATCGAGTTA
*
11315820 TTCGAGTTAAACGAATCGAGTT
1 TTCGAATTAAACGAATCGAGTT
11315842 GAATTTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.31, C:0.13, G:0.20, T:0.36
Consensus pattern (23 bp):
TTCGAATTAAACGAATCGAGTTA
Found at i:11327044 original size:58 final size:59
Alignment explanation
Indices: 11326920--11327094 Score: 232
Period size: 58 Copynumber: 3.0 Consensus size: 59
11326910 GAAAAAAAAA
* *
11326920 TTTGGTGTT-AGCCAATGCTTGGTTGACACCACCTTTTTTATCTGATAAAAAATAAATTT
1 TTTGGTGTTGA-CCAATGCTTGGTCGACACCACCTTTTTTATCAGATAAAAAATAAATTT
* **
11326979 TTTGGTGTTGACC-ATGCATTGGTCGATACCACC-TTTTTATCAGATAAAAAATAGTTTT
1 TTTGGTGTTGACCAATGC-TTGGTCGACACCACCTTTTTTATCAGATAAAAAATAAATTT
***
11327037 TTTGGTGTTGACCAATGCTTAACCGACACCACCTTTTTTATCAGATAAAAAA-AAATTT
1 TTTGGTGTTGACCAATGCTTGGTCGACACCACCTTTTTTATCAGATAAAAAATAAATTT
11327095 GGCCGACACT
Statistics
Matches: 101, Mismatches: 11, Indels: 9
0.83 0.09 0.07
Matches are distributed among these distances:
58 54 0.53
59 46 0.46
60 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (59 bp):
TTTGGTGTTGACCAATGCTTGGTCGACACCACCTTTTTTATCAGATAAAAAATAAATTT
Found at i:11327160 original size:57 final size:59
Alignment explanation
Indices: 11327107--11327225 Score: 143
Period size: 60 Copynumber: 2.0 Consensus size: 59
11327097 CCGACACTAC
* *
11327107 ATTTCTTTCAGATAAAAAT-ATTTTTTTTACTGTTGGTCAATGCTTGGCAGACACCACCTT
1 ATTTATTTCAGAAAAAAATAATTTTTTTTA-TGTTGGTCAATGCTTGGCAGACACCACC-T
* * * *
11327167 ATTTATTTGATAAAAAAATAATTTTTTTTATGTTGGTC-ATGCATTGACGGACACCACCT
1 ATTTATTTCAGAAAAAAATAATTTTTTTTATGTTGGTCAATGC-TTGGCAGACACCACCT
11327226 TTCTATCCTT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
59 5 0.10
60 36 0.71
61 10 0.20
ACGTcount: A:0.29, C:0.16, G:0.13, T:0.41
Consensus pattern (59 bp):
ATTTATTTCAGAAAAAAATAATTTTTTTTATGTTGGTCAATGCTTGGCAGACACCACCT
Found at i:11328044 original size:22 final size:20
Alignment explanation
Indices: 11328018--11328066 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
11328008 AAATGTTAAG
11328018 AAATAATTATTATTGA-AAAA
1 AAATAATTA-TATTGACAAAA
11328038 TTAAAT-A-TATATTGACAAAA
1 --AAATAATTATATTGACAAAA
11328058 AAATAATTA
1 AAATAATTA
11328067 AAATTCATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
18 4 0.17
19 7 0.29
20 8 0.33
21 1 0.04
22 4 0.17
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (20 bp):
AAATAATTATATTGACAAAA
Found at i:11331114 original size:17 final size:16
Alignment explanation
Indices: 11331092--11331126 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
11331082 ATTTGTGTAA
*
11331092 AAATTAATTTGAAAATT
1 AAATTAAGTTG-AAATT
11331109 AAATTAAGTTGAAATT
1 AAATTAAGTTGAAATT
11331125 AA
1 AA
11331127 TTTCAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (16 bp):
AAATTAAGTTGAAATT
Found at i:11331400 original size:37 final size:37
Alignment explanation
Indices: 11331359--11331433 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
11331349 AAATAATATG
11331359 TTGATTTGACAATACATTATTTACCAAATTCAAAATT
1 TTGATTTGACAATACATTATTTACCAAATTCAAAATT
*
11331396 TTGATTTGACAATACATTATTTACTAAATTCAAAATT
1 TTGATTTGACAATACATTATTTACCAAATTCAAAATT
11331433 T
1 T
11331434 AAAATTATTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.40, C:0.12, G:0.05, T:0.43
Consensus pattern (37 bp):
TTGATTTGACAATACATTATTTACCAAATTCAAAATT
Found at i:11331577 original size:94 final size:94
Alignment explanation
Indices: 11331396--11331706 Score: 489
Period size: 94 Copynumber: 3.3 Consensus size: 94
11331386 ATTCAAAATT
*
11331396 TTGATTTGACAATACATTATTTACTAAATTCAAAATTTAAAATTATTTAAATTAAAAAGATTATT
1 TTGATTTGACAATACATTATTTACCAAATTCAAAATTTAAAATTATTTAAA-TAAAAAGATTATT
*
11331461 ATAATATTTCAA-TTTATATCAAATAACGTG
65 ATAATATTTCAATTTTA-ATCAAATAATGTG
* * * *
11331491 TTGATTTGACAATACATTATTTACCATATTCAAATTTTAAATTTATTTATATAAAAAGATTATTA
1 TTGATTTGACAATACATTATTTACCAAATTCAAAATTTAAAATTATTTAAATAAAAAGATTATTA
*
11331556 TAATATTTTAATTTTAATCAAATAATGTG
66 TAATATTTCAATTTTAATCAAATAATGTG
* * *
11331585 TTGATTTTACAATACACTATTTACCAAATTCAAAATTTAAAATTATTTACATAAAAAGATTATTA
1 TTGATTTGACAATACATTATTTACCAAATTCAAAATTTAAAATTATTTAAATAAAAAGATTATTA
*
11331650 TAATATTTCAATTTTTATCAAATAATGTG
66 TAATATTTCAATTTTAATCAAATAATGTG
*
11331679 TTGATTTGATAATACATTATTTACCAAA
1 TTGATTTGACAATACATTATTTACCAAA
11331707 ATAACCTTAA
Statistics
Matches: 197, Mismatches: 18, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
94 147 0.75
95 50 0.25
ACGTcount: A:0.43, C:0.08, G:0.05, T:0.44
Consensus pattern (94 bp):
TTGATTTGACAATACATTATTTACCAAATTCAAAATTTAAAATTATTTAAATAAAAAGATTATTA
TAATATTTCAATTTTAATCAAATAATGTG
Found at i:11331804 original size:22 final size:22
Alignment explanation
Indices: 11331778--11331822 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
11331768 ATTGGGCCAA
11331778 CCAAATTACAGCTCACCAACAC
1 CCAAATTACAGCTCACCAACAC
* *
11331800 CCAAATTCCAGCTCACCACCAC
1 CCAAATTACAGCTCACCAACAC
11331822 C
1 C
11331823 TTCTCACTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.47, G:0.04, T:0.13
Consensus pattern (22 bp):
CCAAATTACAGCTCACCAACAC
Found at i:11332372 original size:7 final size:7
Alignment explanation
Indices: 11332360--11332385 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
11332350 TCATCCCATT
11332360 TTCTTTC
1 TTCTTTC
11332367 TTCTTTC
1 TTCTTTC
11332374 TTCTTTC
1 TTCTTTC
11332381 TTCTT
1 TTCTT
11332386 CACATGGCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (7 bp):
TTCTTTC
Found at i:11335556 original size:19 final size:18
Alignment explanation
Indices: 11335532--11335575 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
11335522 TTTACATATA
*
11335532 TTTTTTATATTTTCGAAAT
1 TTTTTTAGATTTTC-AAAT
* *
11335551 TTTTTTAGCTTTTCAATT
1 TTTTTTAGATTTTCAAAT
11335569 TTTTTTA
1 TTTTTTA
11335576 AAATTATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 10 0.45
19 12 0.55
ACGTcount: A:0.20, C:0.07, G:0.05, T:0.68
Consensus pattern (18 bp):
TTTTTTAGATTTTCAAAT
Found at i:11335556 original size:77 final size:77
Alignment explanation
Indices: 11335441--11335587 Score: 183
Period size: 77 Copynumber: 1.9 Consensus size: 77
11335431 TATTTTCGAA
*
11335441 TTTTTTAAAATATTTTTTTAGCATTTTCGAAATGTTTTTTATATTTTCAA-ATTTTTTAAAATAA
1 TTTTTTAAAATATTTTTTTAGCATTTTCGAAA-GTTTTTTAGATTTTCAATATTTTTTAAAATAA
11335505 TATTTTTGAATTAC
65 T-TTTTTGAATTAC
* * * * * *
11335519 TTTTTT-ACATATATTTTTTA-TATTTTCGAAATTTTTTTAGCTTTTCAATTTTTTTTAAAATTA
1 TTTTTTAAAATAT-TTTTTTAGCATTTTCGAAAGTTTTTTAGATTTTCAATATTTTTTAAAATAA
11335582 TTTTTT
65 TTTTTT
11335588 ATATCTTCGA
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
76 19 0.32
77 28 0.47
78 13 0.22
ACGTcount: A:0.29, C:0.05, G:0.04, T:0.62
Consensus pattern (77 bp):
TTTTTTAAAATATTTTTTTAGCATTTTCGAAAGTTTTTTAGATTTTCAATATTTTTTAAAATAAT
TTTTTGAATTAC
Found at i:11336812 original size:17 final size:17
Alignment explanation
Indices: 11336783--11336843 Score: 55
Period size: 17 Copynumber: 3.9 Consensus size: 17
11336773 ATTTTTTAAA
11336783 TTTAATTTGTAATTTCG
1 TTTAATTTGTAATTTCG
11336800 TTTATATTT-TAA-----
1 TTTA-ATTTGTAATTTCG
11336812 TTTAATTTGTAATTTCG
1 TTTAATTTGTAATTTCG
11336829 TTTATATTT-TAATTT
1 TTTA-ATTTGTAATTT
11336844 AATTTCTAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 16
0.69 0.00 0.31
Matches are distributed among these distances:
11 4 0.11
12 7 0.19
17 17 0.47
18 8 0.22
ACGTcount: A:0.26, C:0.03, G:0.07, T:0.64
Consensus pattern (17 bp):
TTTAATTTGTAATTTCG
Found at i:11336823 original size:29 final size:30
Alignment explanation
Indices: 11336765--11336909 Score: 213
Period size: 29 Copynumber: 4.9 Consensus size: 30
11336755 ATTCTGATTT
* *
11336765 TTTCGTTTATTTTTTAAATTTAATTTGTAA
1 TTTCGTTTATATTTTAAATTTAATTTCTAA
*
11336795 TTTCGTTTATATTTT-AATTTAATTTGTAA
1 TTTCGTTTATATTTTAAATTTAATTTCTAA
11336824 TTTCGTTTATATTTT-AATTTAATTTCTAA
1 TTTCGTTTATATTTTAAATTTAATTTCTAA
* *
11336853 TTTCATTTATATTTTTAAATTTCATTTCTAA
1 TTTCGTTTATA-TTTTAAATTTAATTTCTAA
*
11336884 TTTCGTTTATATTTTAAATTTCATTT
1 TTTCGTTTATATTTTAAATTTAATTT
11336910 TAAATTATTA
Statistics
Matches: 108, Mismatches: 5, Indels: 4
0.92 0.04 0.03
Matches are distributed among these distances:
29 52 0.48
30 33 0.31
31 23 0.21
ACGTcount: A:0.27, C:0.06, G:0.04, T:0.63
Consensus pattern (30 bp):
TTTCGTTTATATTTTAAATTTAATTTCTAA
Found at i:11336860 original size:17 final size:17
Alignment explanation
Indices: 11336782--11336879 Score: 54
Period size: 17 Copynumber: 5.2 Consensus size: 17
11336772 TATTTTTTAA
*
11336782 ATTTAATTTGTAATTTC
1 ATTTAATTTCTAATTTC
* *
11336799 GTTTATATTT-TAATTTA
1 ATTTA-ATTTCTAATTTC
*
11336816 ATTTGTAATTTCGTTTATATTTTA
1 A-TT-TAATTTC---TA-A-TTTC
11336840 ATTTAATTTCTAATTTC
1 ATTTAATTTCTAATTTC
*
11336857 ATTTATATTTTTAAATTTC
1 ATTTA-ATTTCT-AATTTC
11336876 ATTT
1 ATTT
11336880 CTAATTTCGT
Statistics
Matches: 65, Mismatches: 5, Indels: 20
0.72 0.06 0.22
Matches are distributed among these distances:
17 18 0.28
18 16 0.25
19 14 0.22
22 9 0.14
23 3 0.05
24 5 0.08
ACGTcount: A:0.29, C:0.05, G:0.04, T:0.62
Consensus pattern (17 bp):
ATTTAATTTCTAATTTC
Found at i:11337912 original size:116 final size:115
Alignment explanation
Indices: 11337773--11338170 Score: 352
Period size: 116 Copynumber: 3.5 Consensus size: 115
11337763 AACACCAAAA
* * *
11337773 AAATTTATTTTTTTATTTGAT-AAAAAGGTGGTGTCGACCAATGCATGGCCAACACCAAAAAAAT
1 AAATTT-TTTTTTTATCTAATAAAAAAGGTGGTGTCGGCCAATGCATGGCCAACACCAAAAAAA-
* * * *
11337837 TTGTTTCTTTTATCAGATAAATAAGATGGTGTCGGCCAAGCATTGGCCAACGCC
64 TT-ATT-TTTTATCAGATAAAAAAGATGGTGTCGGCCAAGCATTAGCCAACACC
** * * *
11337891 -AATTTTTTTTTTATCTAATAAAAAAACACTAGTGTCGGCCAATGCATGGTCGACACCAAAAAAA
1 AAATTTTTTTTTTATCTAAT-AAAAAA-GGTGGTGTCGGCCAATGCATGGCCAACACCAAAAAAA
*
11337955 TTATTTTTTATCAGATAAAAAAGGTGGTGTCGGCCAAGCATTAGCCAACACC
64 TTATTTTTTATCAGATAAAAAAGATGGTGTCGGCCAAGCATTAGCCAACACC
** * * * * * *
11338007 AAAAAAATATTTCTTATCAAATAAAAAAGGTGGTATCGGGCAATGCATGACCAACACC----AAA
1 --AAATTTTTTTTTTATCTAATAAAAAAGGTGGTGTCGGCCAATGCATGGCCAACACCAAAAAAA
* * * * **
11338068 -T-TTTTTTATCTGATAAAAATA-CTGGTGTTGGCCAATGCA-TGGCCAACATT
64 TTATTTTTTATCAGATAAAAA-AGATGGTGTCGGCCAA-GCATTAGCCAACACC
* *
11338118 AAA-ATTTTTTTTATCTAACAAAAAAGGTGGTGTCGGCCAA-GCATAGGCCAACA
1 AAATTTTTTTTTTATCTAATAAAAAAGGTGGTGTCGGCCAATGCAT-GGCCAACA
11338171 ACAATTTTTT
Statistics
Matches: 232, Mismatches: 39, Indels: 28
0.78 0.13 0.09
Matches are distributed among these distances:
107 4 0.02
108 38 0.16
109 3 0.01
111 37 0.16
112 5 0.02
113 3 0.01
116 55 0.24
117 29 0.12
118 13 0.06
119 45 0.19
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.29
Consensus pattern (115 bp):
AAATTTTTTTTTTATCTAATAAAAAAGGTGGTGTCGGCCAATGCATGGCCAACACCAAAAAAATT
ATTTTTTATCAGATAAAAAAGATGGTGTCGGCCAAGCATTAGCCAACACC
Found at i:11338006 original size:59 final size:59
Alignment explanation
Indices: 11337744--11338170 Score: 290
Period size: 58 Copynumber: 7.4 Consensus size: 59
11337734 GGAAAGTTGA
* **
11337744 TGTCGGTCAATGCAT-GACCAACACCAAAAAAATTTATTTTTTTATTTGAT-AAAAAGGTGG
1 TGTCGGCCAATGCATAG-CCAACACCAAAAAAA-TTA-TTTTTTATCAGATAAAAAAGGTGG
* * * * *
11337804 TGTCGACCAATGCATGGCCAACACCAAAAAAATTTGTTTCTTTTATCAGATAAATAAGATGG
1 TGTCGGCCAATGCATAGCCAACACCAAAAAAA-TT-ATT-TTTTATCAGATAAAAAAGGTGG
* * * * ** *
11337866 TGTCGGCCAA-GCATTGGCCAACGCC----AATTTTTTTTTTATCTA-ATAAAAAAACACTAG
1 TGTCGGCCAATGCA-TAGCCAACACCAAAAAAATTATTTTTTATC-AGAT-AAAAAA-GGTGG
* * *
11337923 TGTCGGCCAATGCATGGTCGACACCAAAAAAATTATTTTTTATCAGATAAAAAAGGTGG
1 TGTCGGCCAATGCATAGCCAACACCAAAAAAATTATTTTTTATCAGATAAAAAAGGTGG
* *
11337982 TGTCGGCCAA-GCATTAGCCAACACCAAAAAAA-TATTTCTTATCAAATAAAAAAGGTGG
1 TGTCGGCCAATGCA-TAGCCAACACCAAAAAAATTATTTTTTATCAGATAAAAAAGGTGG
* * * *
11338040 TATCGGGCAATGCAT-GACCAACACC----AAA-T-TTTTTTATCTGATAAAAATA-CTGG
1 TGTCGGCCAATGCATAG-CCAACACCAAAAAAATTATTTTTTATCAGATAAAAA-AGGTGG
* * ** *
11338093 TGTTGGCCAATGCATGGCC-A-A-CATTAAAATT-TTTTTTATCTA-ACAAAAAAGGTGG
1 TGTCGGCCAATGCATAGCCAACACCAAAAAAATTATTTTTTATC-AGATAAAAAAGGTGG
11338148 TGTCGGCCAA-GCATAGGCCAACA
1 TGTCGGCCAATGCATA-GCCAACA
11338171 ACAATTTTTT
Statistics
Matches: 297, Mismatches: 41, Indels: 61
0.74 0.10 0.15
Matches are distributed among these distances:
50 1 0.00
51 1 0.00
52 1 0.00
53 32 0.11
54 14 0.05
55 40 0.13
56 10 0.03
57 24 0.08
58 49 0.16
59 30 0.10
60 40 0.13
61 28 0.09
62 27 0.09
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.29
Consensus pattern (59 bp):
TGTCGGCCAATGCATAGCCAACACCAAAAAAATTATTTTTTATCAGATAAAAAAGGTGG
Found at i:11338030 original size:119 final size:119
Alignment explanation
Indices: 11337803--11338034 Score: 299
Period size: 119 Copynumber: 1.9 Consensus size: 119
11337793 TAAAAAGGTG
* *
11337803 GTGTCGACCAATGCATGGCCAACACCAAAAAAATTTGTTTCTTTTATCAGATAAATAAGATGGTG
1 GTGTCGACCAATGCATGGCCAACACCAAAAAAATTTGATTCTTTTATCAGATAAAAAAGATGGTG
* * ** * * *
11337868 TCGGCCAAGCATTGGCCAACGCCAATTTTTTTTTTATCTAATAAAAAAACACTA
66 TCGGCCAAGCATTAGCCAACACCAAAATATTTCTTATCAAATAAAAAAACACTA
* * * *
11337922 GTGTCGGCCAATGCATGGTCGACACCAAAAAAA-TT-ATT-TTTTATCAGATAAAAAAGGTGGTG
1 GTGTCGACCAATGCATGGCCAACACCAAAAAAATTTGATTCTTTTATCAGATAAAAAAGATGGTG
11337984 TCGGCCAAGCATTAGCCAACACCAAAAAAATATTTCTTATCAAATAAAAAA
66 TCGGCCAAGCATTAGCCAACACC---AAAATATTTCTTATCAAATAAAAAA
11338035 GGTGGTATCG
Statistics
Matches: 97, Mismatches: 13, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
116 43 0.44
117 2 0.02
118 2 0.02
119 50 0.52
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.28
Consensus pattern (119 bp):
GTGTCGACCAATGCATGGCCAACACCAAAAAAATTTGATTCTTTTATCAGATAAAAAAGATGGTG
TCGGCCAAGCATTAGCCAACACCAAAATATTTCTTATCAAATAAAAAAACACTA
Found at i:11338104 original size:53 final size:53
Alignment explanation
Indices: 11337863--11338182 Score: 166
Period size: 53 Copynumber: 5.7 Consensus size: 53
11337853 ATAAATAAGA
** * * *
11337863 TGGTGTCGGCCAA-GCATTGGCCAACGCCAATTTTTTTTTTATCTAATAAAAAAACAC
1 TGGTGTCGGCCAATGCA-TGGCCAACAACAA--ATTTTTTTATCTAA-CAAAAAA-GC
* * * * *
11337920 TAGTGTCGGCCAATGCATGGTCGACACCAAAAAAATTATTTTTTATC-AGATAAAAAAGG
1 TGGTGTCGGCCAATGCATGG-C--CAAC-AACAAA-T-TTTTTTATCTA-ACAAAAAAGC
* * * * * *
11337979 TGGTGTCGGCCAA-GCATTAGCCAACACCAAAAAAATATTTCTTATCAAATAAAAAAGG
1 TGGTGTCGGCCAATGCA-TGGCC-A-A-C-AACAAAT-TTTTTTATCTAACAAAAAAGC
* * * * * *
11338037 TGGTATCGGGCAATGCATGACCAACACCAAATTTTTTTATCTGATAAAAATA-C
1 TGGTGTCGGCCAATGCATGGCCAACAACAAATTTTTTTATCTAACAAAAA-AGC
* *
11338090 TGGTGTTGGCCAATGCATGGCCAACATTA-AAATTTTTTTTATCTAACAAAAAAGG
1 TGGTGTCGGCCAATGCATGGCCAACA--ACAAA-TTTTTTTATCTAACAAAAAAGC
*
11338145 TGGTGTCGGCCAA-GCATAGGCCAACAACAATTTTTTTT
1 TGGTGTCGGCCAATGCAT-GGCCAACAACAAATTTTTTT
11338183 TCAAAATCTC
Statistics
Matches: 209, Mismatches: 33, Indels: 46
0.73 0.11 0.16
Matches are distributed among these distances:
53 45 0.22
54 16 0.08
55 38 0.18
56 2 0.01
57 17 0.08
58 42 0.20
59 26 0.12
60 11 0.05
61 12 0.06
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (53 bp):
TGGTGTCGGCCAATGCATGGCCAACAACAAATTTTTTTATCTAACAAAAAAGC
Found at i:11344029 original size:19 final size:19
Alignment explanation
Indices: 11343983--11344021 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
11343973 GGTAACTGCA
*
11343983 GATTAGTTAGTTGGTCGTT
1 GATTAGTTAGTTGGTAGTT
11344002 GATTAGTTAGTTGAGTAGTT
1 GATTAGTTAGTTG-GTAGTT
11344022 ATTGGTTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.21, C:0.03, G:0.31, T:0.46
Consensus pattern (19 bp):
GATTAGTTAGTTGGTAGTT
Found at i:11347796 original size:16 final size:17
Alignment explanation
Indices: 11347775--11347807 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
11347765 TTTTTTTTTT
11347775 AAAATTT-TAACTCTTG
1 AAAATTTATAACTCTTG
*
11347791 AAAATTTATAATTCTTG
1 AAAATTTATAACTCTTG
11347808 TATAATATGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.45
Consensus pattern (17 bp):
AAAATTTATAACTCTTG
Found at i:11348913 original size:44 final size:43
Alignment explanation
Indices: 11348835--11348935 Score: 123
Period size: 44 Copynumber: 2.3 Consensus size: 43
11348825 ATTATTGTAA
* * *
11348835 TTTAAATTCTAATTATTTTTAAATATGTAGTTATC-AAAACTTT
1 TTTAAATTATAATTATTTTTAAATATATAATTATCTAAAA-TTT
* *
11348878 TATTAAATTATAATTATTTTTAAATGTATAATTATCTCAAATTT
1 T-TTAAATTATAATTATTTTTAAATATATAATTATCTAAAATTT
*
11348922 TTTAAATAATAATT
1 TTTAAATTATAATT
11348936 CTAAATTAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
43 13 0.26
44 34 0.68
45 3 0.06
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.51
Consensus pattern (43 bp):
TTTAAATTATAATTATTTTTAAATATATAATTATCTAAAATTT
Found at i:11353357 original size:27 final size:27
Alignment explanation
Indices: 11353327--11353383 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
11353317 TTCTTGGCGT
**
11353327 ACTTCCCCGTTTTTAGTGTCCTGATAG
1 ACTTCCCCGCATTTAGTGTCCTGATAG
*
11353354 ACTTCCCCGCATTTAGTGTCCTGATGG
1 ACTTCCCCGCATTTAGTGTCCTGATAG
11353381 ACT
1 ACT
11353384 AACTATGATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.16, C:0.28, G:0.19, T:0.37
Consensus pattern (27 bp):
ACTTCCCCGCATTTAGTGTCCTGATAG
Found at i:11353643 original size:44 final size:44
Alignment explanation
Indices: 11353520--11353650 Score: 147
Period size: 44 Copynumber: 3.0 Consensus size: 44
11353510 GTGCTTTCAT
* *
11353520 ATGATGTCATAACGTCTTTCAACCATGGTCTTACTC-TTTCCTATC
1 ATGATGTCATAGCGTCTTTCAACTATGGTCTTACTCATTT--TATC
* * *
11353565 ATGATGTCATAGCGTCTTTTAATTATGGTTTTACTCATTTTATC
1 ATGATGTCATAGCGTCTTTCAACTATGGTCTTACTCATTTTATC
* * * * *
11353609 CTTATGTCATAGCATCTTTCAGCTATGATCTTACTCATTTTA
1 ATGATGTCATAGCGTCTTTCAACTATGGTCTTACTCATTTTA
11353651 GGCGTATAGC
Statistics
Matches: 72, Mismatches: 13, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
44 38 0.53
45 31 0.43
46 3 0.04
ACGTcount: A:0.23, C:0.21, G:0.11, T:0.45
Consensus pattern (44 bp):
ATGATGTCATAGCGTCTTTCAACTATGGTCTTACTCATTTTATC
Found at i:11354896 original size:45 final size:45
Alignment explanation
Indices: 11354847--11355288 Score: 496
Period size: 45 Copynumber: 9.9 Consensus size: 45
11354837 TTATATTCGA
* * * *
11354847 ACTCATACATGCGAACTCGTAGAAGAATATTCATAGATATGACAA
1 ACTCATACATGCGAATTCATAGAAGAAGATTCATAGATATGACAG
* * * * *
11354892 ACTCATACATGCGGATTCATAAAAGAGGATTCGTAGATATGATAG
1 ACTCATACATGCGAATTCATAGAAGAAGATTCATAGATATGACAG
* * * *
11354937 ACTCATACATGCGAATTCGTAGAAGAAGATTTAT-GATATGGCAA
1 ACTCATACATGCGAATTCATAGAAGAAGATTCATAGATATGACAG
* * * * *
11354981 ACTCATACATGCGGATTCATAAAAGAGGATTCGTAGATATGATAG
1 ACTCATACATGCGAATTCATAGAAGAAGATTCATAGATATGACAG
* *
11355026 ACTCATACATGCGAATTCATAGAAGAGGATTCGTAGATATGACAG
1 ACTCATACATGCGAATTCATAGAAGAAGATTCATAGATATGACAG
* * *
11355071 ACTCATACATGCGAATTCGTAGAAGAAGATTTAT-GATATGGCAG
1 ACTCATACATGCGAATTCATAGAAGAAGATTCATAGATATGACAG
* * * * *
11355115 ACTCATACATGCGGATTCATAAAAGAGGATTCGTAGATATGACGG
1 ACTCATACATGCGAATTCATAGAAGAAGATTCATAGATATGACAG
* * *
11355160 AGTCATACATGCGAGTTCATAGAAGAAGATTCAT-GATATGGCAG
1 ACTCATACATGCGAATTCATAGAAGAAGATTCATAGATATGACAG
* * * * * **
11355204 ACTCATACATGCGGATTTATAAAAGAGGATTCGTAGATATGATGG
1 ACTCATACATGCGAATTCATAGAAGAAGATTCATAGATATGACAG
* *
11355249 ACTCATATATGTGAATTCATAGAAGAAGATTCAT-GATATG
1 ACTCATACATGCGAATTCATAGAAGAAGATTCATAGATATG
11355289 TCTGAATCAA
Statistics
Matches: 326, Mismatches: 68, Indels: 7
0.81 0.17 0.02
Matches are distributed among these distances:
44 113 0.35
45 213 0.65
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.27
Consensus pattern (45 bp):
ACTCATACATGCGAATTCATAGAAGAAGATTCATAGATATGACAG
Found at i:11354999 original size:89 final size:89
Alignment explanation
Indices: 11354847--11355288 Score: 455
Period size: 89 Copynumber: 5.0 Consensus size: 89
11354837 TTATATTCGA
* * *
11354847 ACTCATACATGCGAACTCGTAGAAGAATATTCATAGATATGACAAACTCATACATGCGGATTCAT
1 ACTCATACATGCGAATTCATAGAAGAAGATTC-TAGATATGACAAACTCATACATGCGGATTCAT
* *
11354912 AAAAGAGGATTCGTAGATATGATAG
65 AAAAGAAGATTCGTAGATATGACAG
* *
11354937 ACTCATACATGCGAATTCGTAGAAGAAGATT-TATGATATGGCAAACTCATACATGCGGATTCAT
1 ACTCATACATGCGAATTCATAGAAGAAGATTCTA-GATATGACAAACTCATACATGCGGATTCAT
* *
11355001 AAAAGAGGATTCGTAGATATGATAG
65 AAAAGAAGATTCGTAGATATGACAG
* * * *
11355026 ACTCATACATGCGAATTCATAGAAGAGGATTCGTAGATATGACAGACTCATACATGCGAATTCGT
1 ACTCATACATGCGAATTCATAGAAGAAGATTC-TAGATATGACAAACTCATACATGCGGATTCAT
* *
11355091 AGAAGAAGATT--TATGATATGGCAG
65 AAAAGAAGATTCGTA-GATATGACAG
* * * ** *
11355115 ACTCATACATGCGGATTCATAAAAGAGGATTCGTAGATATGACGGAGTCATACATGC-GAGTTCA
1 ACTCATACATGCGAATTCATAGAAGAAGATTC-TAGATATGACAAACTCATACATGCGGA-TTCA
* * *
11355179 TAGAAGAAGATTCAT-GATATGGCAG
64 TAAAAGAAGATTCGTAGATATGACAG
* * * * *** * * *
11355204 ACTCATACATGCGGATTTATAAAAGAGGATTCGTAGATATGATGGACTCATATATGTGAATTCAT
1 ACTCATACATGCGAATTCATAGAAGAAGATTC-TAGATATGACAAACTCATACATGCGGATTCAT
* *
11355269 AGAAGAAGATTCAT-GATATG
65 AAAAGAAGATTCGTAGATATG
11355289 TCTGAATCAA
Statistics
Matches: 319, Mismatches: 25, Indels: 17
0.88 0.07 0.05
Matches are distributed among these distances:
88 5 0.02
89 246 0.77
90 65 0.20
91 3 0.01
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.27
Consensus pattern (89 bp):
ACTCATACATGCGAATTCATAGAAGAAGATTCTAGATATGACAAACTCATACATGCGGATTCATA
AAAGAAGATTCGTAGATATGACAG
Found at i:11355086 original size:134 final size:134
Alignment explanation
Indices: 11354846--11355216 Score: 564
Period size: 134 Copynumber: 2.8 Consensus size: 134
11354836 CTTATATTCG
* * * * ** * * *
11354846 AACTCATACATGCGAACTCGTAGAAGAATATTCATAGATATGACAAACTCATACATGCGGATTCA
1 AACTCATACATGCGGATTCATAAAAGAGGATTCGTAGATATGACAGACTCATACATGCGAATTCA
* *
11354911 TAAAAGAGGATTCGTAGATATGATAGACTCATACATGCGAATTCGTAGAAGAAGATTTATGATAT
66 TAGAAGAGGATTCGTAGATATGACAGACTCATACATGCGAATTCGTAGAAGAAGATTTATGATAT
11354976 GGCA
131 GGCA
*
11354980 AACTCATACATGCGGATTCATAAAAGAGGATTCGTAGATATGATAGACTCATACATGCGAATTCA
1 AACTCATACATGCGGATTCATAAAAGAGGATTCGTAGATATGACAGACTCATACATGCGAATTCA
11355045 TAGAAGAGGATTCGTAGATATGACAGACTCATACATGCGAATTCGTAGAAGAAGATTTATGATAT
66 TAGAAGAGGATTCGTAGATATGACAGACTCATACATGCGAATTCGTAGAAGAAGATTTATGATAT
11355110 GGCA
131 GGCA
* * * *
11355114 GACTCATACATGCGGATTCATAAAAGAGGATTCGTAGATATGACGGAGTCATACATGCGAGTTCA
1 AACTCATACATGCGGATTCATAAAAGAGGATTCGTAGATATGACAGACTCATACATGCGAATTCA
* * *
11355179 TAGAAGAAGATTCAT-GATATGGCAGACTCATACATGCG
66 TAGAAGAGGATTCGTAGATATGACAGACTCATACATGCG
11355217 GATTTATAAA
Statistics
Matches: 217, Mismatches: 20, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
133 22 0.10
134 195 0.90
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.26
Consensus pattern (134 bp):
AACTCATACATGCGGATTCATAAAAGAGGATTCGTAGATATGACAGACTCATACATGCGAATTCA
TAGAAGAGGATTCGTAGATATGACAGACTCATACATGCGAATTCGTAGAAGAAGATTTATGATAT
GGCA
Found at i:11355243 original size:134 final size:134
Alignment explanation
Indices: 11354847--11355288 Score: 541
Period size: 134 Copynumber: 3.3 Consensus size: 134
11354837 TTATATTCGA
* * * * *
11354847 ACTCATACATGCGAACTCGTAGAAGAATATTCATAGATATGACAAACTCATACATGCG-GATTCA
1 ACTCATACATGCGAATTCATAAAAGAAGATTCATAGATATGACAGACTCATACATGCGAG-TTCA
* *
11354911 TAAAAGAGGATTCGTAGATATGATAGACTCATACATGCGAATTCGTAGAAGAAGATTTATGATAT
65 TAGAAGAGGATTCGTAGATATGACAGACTCATACATGCGAATTCGTAGAAGAAGATTTATGATAT
*
11354976 GGCAA
130 GGCAG
* * * * *
11354981 ACTCATACATGCGGATTCATAAAAGAGGATTCGTAGATATGATAGACTCATACATGCGAATTCAT
1 ACTCATACATGCGAATTCATAAAAGAAGATTCATAGATATGACAGACTCATACATGCGAGTTCAT
11355046 AGAAGAGGATTCGTAGATATGACAGACTCATACATGCGAATTCGTAGAAGAAGATTTATGATATG
66 AGAAGAGGATTCGTAGATATGACAGACTCATACATGCGAATTCGTAGAAGAAGATTTATGATATG
11355111 GCAG
131 GCAG
* * * * *
11355115 ACTCATACATGCGGATTCATAAAAGAGGATTCGTAGATATGACGGAGTCATACATGCGAGTTCAT
1 ACTCATACATGCGAATTCATAAAAGAAGATTCATAGATATGACAGACTCATACATGCGAGTTCAT
* * * * ** * *
11355180 AGAAGAAGATTCAT-GATATGGCAGACTCATACATGCGGATTTATAAAAGAGGATTCGTA-GATA
66 AGAAGAGGATTCGTAGATATGACAGACTCATACATGCGAATTCGTAGAAGAAGATT--TATGATA
***
11355243 TGATGG
129 TGGCAG
* * *
11355249 ACTCATATATGTGAATTCATAGAAGAAGATTCAT-GATATG
1 ACTCATACATGCGAATTCATAAAAGAAGATTCATAGATATG
11355289 TCTGAATCAA
Statistics
Matches: 271, Mismatches: 34, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
133 41 0.15
134 228 0.84
135 2 0.01
ACGTcount: A:0.38, C:0.14, G:0.22, T:0.27
Consensus pattern (134 bp):
ACTCATACATGCGAATTCATAAAAGAAGATTCATAGATATGACAGACTCATACATGCGAGTTCAT
AGAAGAGGATTCGTAGATATGACAGACTCATACATGCGAATTCGTAGAAGAAGATTTATGATATG
GCAG
Found at i:11357684 original size:90 final size:90
Alignment explanation
Indices: 11357541--11357800 Score: 265
Period size: 90 Copynumber: 2.9 Consensus size: 90
11357531 TACAACTTTG
* * **
11357541 ATGGTTCATCCA-CAGA-TTTTCTAGCAGCTTTTATCTGCAAATATGGTAAGCATTCACAACCAT
1 ATGGTTCATCCACCA-ATTTTTC-AGCAGCTATTATCTGCAAATATGTTGTGCATTCACAACCAT
* * * * *
11357604 CTGGTAGCGTATTAACTTGCAACACTG
64 CTGGCAACGTATTAACCTACAACACTA
* * * * *
11357631 GTGGTTCATCCACCCATTTTTCAGCAACTATTATCTGCAAATACGTTGTGCATTCAAAACCATCT
1 ATGGTTCATCCACCAATTTTTCAGCAGCTATTATCTGCAAATATGTTGTGCATTCACAACCATCT
** *
11357696 AACAATGTATTAACCTACAACACTA
66 GGCAACGTATTAACCTACAACACTA
* * * * *
11357721 ATGGTTCATCCACCAAATTTTT-GGTAGCTCTTATATGCAAATATGTTGTGCATTCACAACCTTC
1 ATGGTTCATCCACC-AATTTTTCAGCAGCTATTATCTGCAAATATGTTGTGCATTCACAACCATC
*
11357785 TGGCAATGTATTAACC
65 TGGCAACGTATTAACC
11357801 AGCAAATTTT
Statistics
Matches: 138, Mismatches: 29, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
90 126 0.91
91 12 0.09
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (90 bp):
ATGGTTCATCCACCAATTTTTCAGCAGCTATTATCTGCAAATATGTTGTGCATTCACAACCATCT
GGCAACGTATTAACCTACAACACTA
Done.