Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 12 of 135
Found at i:5433186 original size:15 final size:16
Alignment explanation
Indices: 5433149--5433186 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
5433139 CACAACATTC
5433149 AGATCTTAGTAATTTT
1 AGATCTTAGTAATTTT
*
5433165 -GAGCTTAG-AATTTT
1 AGATCTTAGTAATTTT
5433179 AGATCTTA
1 AGATCTTA
5433187 AACCCTGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
14 6 0.32
15 13 0.68
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.45
Consensus pattern (16 bp):
AGATCTTAGTAATTTT
Found at i:5440130 original size:15 final size:15
Alignment explanation
Indices: 5440102--5440148 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
5440092 CCATTTTATA
* *
5440102 TTATTTATATAATTT
1 TTATTTTTAAAATTT
5440117 TTATTTTTAAAA-TT
1 TTATTTTTAAAATTT
* *
5440131 ATATTTTTTAAATTT
1 TTATTTTTAAAATTT
5440146 TTA
1 TTA
5440149 GAATTAATAC
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 12 0.46
15 14 0.54
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (15 bp):
TTATTTTTAAAATTT
Found at i:5442118 original size:59 final size:60
Alignment explanation
Indices: 5441981--5442118 Score: 187
Period size: 59 Copynumber: 2.3 Consensus size: 60
5441971 ACTCCCTATT
*
5441981 TAAAAAAATTGC--ATTTTTGGGTGTTGGCTATTGCATGGTCGACACCCCCTTTTCTCGA
1 TAAAAAAATTGCAAATTTTTGGGTATTGGCTATTGCATGGTCGACACCCCCTTTTCTCGA
* *
5442039 GAAAAAAATT-CAAATTTTTTTGGTATT-GCTATTGCATGG-CTGACACCCCCTTTTCTCGGA
1 TAAAAAAATTGCAAA-TTTTTGGGTATTGGCTATTGCATGGTC-GACACCCCCTTTTCTC-GA
5442099 TAAAAAAATTGCAAATTTTT
1 TAAAAAAATTGCAAATTTTT
5442119 TTGATGTTGG
Statistics
Matches: 70, Mismatches: 4, Indels: 10
0.83 0.05 0.12
Matches are distributed among these distances:
57 1 0.01
58 10 0.14
59 29 0.41
60 26 0.37
61 4 0.06
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (60 bp):
TAAAAAAATTGCAAATTTTTGGGTATTGGCTATTGCATGGTCGACACCCCCTTTTCTCGA
Found at i:5442997 original size:30 final size:30
Alignment explanation
Indices: 5442963--5443032 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
5442953 AAAAAATAAT
*
5442963 AATTAAAATATACAGGAAATTAGAAAGAAA
1 AATTAAAATATACAAGAAATTAGAAAGAAA
**
5442993 AATTAAAATATACAAGAAATTAGAAATTAA
1 AATTAAAATATACAAGAAATTAGAAAGAAA
*
5443023 ATTTAAAATA
1 AATTAAAATA
5443033 AAAACGAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.63, C:0.03, G:0.09, T:0.26
Consensus pattern (30 bp):
AATTAAAATATACAAGAAATTAGAAAGAAA
Found at i:5443042 original size:30 final size:29
Alignment explanation
Indices: 5442978--5443065 Score: 104
Period size: 30 Copynumber: 2.9 Consensus size: 29
5442968 AAATATACAG
** * *
5442978 GAAATTAGAAAGAAAAATTAAAATATACAA
1 GAAATTAGAAATTAAATTTAAAATA-AAAA
5443008 GAAATTAGAAATTAAATTTAAAATAAAAA
1 GAAATTAGAAATTAAATTTAAAATAAAAA
*
5443037 CGAAATTACAAATTAAATTTAAAAGTAAA
1 -GAAATTAGAAATTAAATTTAAAA-TAAA
5443066 CGGAAAAAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
29 3 0.06
30 44 0.86
31 4 0.08
ACGTcount: A:0.64, C:0.03, G:0.08, T:0.25
Consensus pattern (29 bp):
GAAATTAGAAATTAAATTTAAAATAAAAA
Found at i:5443538 original size:24 final size:24
Alignment explanation
Indices: 5443495--5443553 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 24
5443485 GATACTGGGG
* *
5443495 ATCGGGTTGGTGCTCCGGCTAGTA
1 ATCGGGTTGGTCCTCAGGCTAGTA
* * *
5443519 CTCGGGTTGGTCCTGAGGCTCGTA
1 ATCGGGTTGGTCCTCAGGCTAGTA
*
5443543 ATCGGGCTGGT
1 ATCGGGTTGGT
5443554 TATCGGCCTC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.10, C:0.22, G:0.39, T:0.29
Consensus pattern (24 bp):
ATCGGGTTGGTCCTCAGGCTAGTA
Found at i:5444189 original size:21 final size:21
Alignment explanation
Indices: 5444135--5444191 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
5444125 GATTTTTTTT
*
5444135 TGTAAAACAATATTTCGAAAA
1 TGTAAAAAAATATTTCGAAAA
*****
5444156 TGTATTTTTATATTTCGAAAA
1 TGTAAAAAAATATTTCGAAAA
5444177 TGTAAAAAAATATTT
1 TGTAAAAAAATATTT
5444192 GTAAAAAATA
Statistics
Matches: 26, Mismatches: 10, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.46, C:0.05, G:0.09, T:0.40
Consensus pattern (21 bp):
TGTAAAAAAATATTTCGAAAA
Found at i:5445693 original size:92 final size:89
Alignment explanation
Indices: 5445443--5445703 Score: 461
Period size: 89 Copynumber: 2.9 Consensus size: 89
5445433 TAAATTTAAA
5445443 ATATGATAAAAATTGTAATATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAAT
1 ATATGATAAAAATTGTAATATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAAT
5445508 AATGTATTATCAAATCAACACATT
66 AATGTATTATCAAATCAACACATT
5445532 ATATGATAAAAATTGTAATATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAAT
1 ATATGATAAAAATTGTAATATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAAT
* *
5445597 AATGTATTGTTAAATCAACACATT
66 AATGTATTATCAAATCAACACATT
5445621 ATATGATAAAAATTGTAATATAATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATA
1 ATATGATAAAAATTGT-A-AT-ATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATA
5445686 AATAATGTA-TAGTCAAAT
63 AATAATGTATTA-TCAAAT
5445704 TAAAACATGT
Statistics
Matches: 164, Mismatches: 4, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
89 103 0.63
90 1 0.01
91 3 0.02
92 57 0.35
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (89 bp):
ATATGATAAAAATTGTAATATAATAATAATAATAATTTTTATTTAAAGATATAAAATTAATAAAT
AATGTATTATCAAATCAACACATT
Found at i:5449529 original size:62 final size:59
Alignment explanation
Indices: 5449449--5449581 Score: 169
Period size: 62 Copynumber: 2.2 Consensus size: 59
5449439 GGGGAAGTTA
*
5449449 GTGTCAGCCATTACATGGCCAACA-CAAAAAAAATTTGTAATTTTTTTATCCGAGAAAAGAGG
1 GTGTCGGCCATTACATGGCCAACATC-AAAAAAA-TT-TAATTTTTTTAT-CGAGAAAAGAGG
** * *
5449511 GTGTCGGCCATTTGATGGCCAACATCAAAAAAATTTAATTTTTTTCTCGAGAAAAGGGG
1 GTGTCGGCCATTACATGGCCAACATCAAAAAAATTTAATTTTTTTATCGAGAAAAGAGG
*
5449570 GTGTCGACCATT
1 GTGTCGGCCATT
5449582 GTTAACACCC
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
59 22 0.34
60 11 0.17
61 2 0.03
62 28 0.44
63 1 0.02
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (59 bp):
GTGTCGGCCATTACATGGCCAACATCAAAAAAATTTAATTTTTTTATCGAGAAAAGAGG
Found at i:5449846 original size:114 final size:113
Alignment explanation
Indices: 5449509--5450097 Score: 698
Period size: 114 Copynumber: 5.2 Consensus size: 113
5449499 CGAGAAAAGA
* * * *
5449509 GGGTGTCGGCCATTTGATGGCCAACATCAAAAAAATTT-AATTTTTTTCTCGAGAAAAGGGGGTG
1 GGGTGTCGGCCATTTGATGGCCAACACCAAAAAATTTTAAATTTTTTTCTCGAAAAAAAGGGGTG
* * *
5449573 TCGACCAT----TG-TTAACACCCAAAAATGCATTTTTTTTAAATAGG
66 TCGGCCATGCAATGATCAACACCCAAAAATGCAATTTTTTTAAATAGG
* * *
5449616 GGGTGTCGACCATTTGATGGCCAACACCAAAAAATTTTGAATTTTTTTCTCG-AGAAAAGGGGTG
1 GGGTGTCGGCCATTTGATGGCCAACACCAAAAAATTTTAAATTTTTTTCTCGAAAAAAAGGGGTG
* ** *
5449680 TTGG-C-TGC-ATGGCCAACACCCAAAAATTCAATTTTTTTAAATAGG
66 TCGGCCATGCAATGATCAACACCCAAAAATGCAATTTTTTTAAATAGG
* *
5449725 GGTTGTCGGCCATTTGATGACCAACACCAAAAAATTTTAAATTTTTTTTCTCGAAAAAAAGGGGT
1 GGGTGTCGGCCATTTGATGGCCAACACCAAAAAATTTTAAA-TTTTTTTCTCGAAAAAAAGGGGT
5449790 GTCGGCCATGCAATGATCAACACCCAAAAATGCAATTTTTTTAAATAGG
65 GTCGGCCATGCAATGATCAACACCCAAAAATGCAATTTTTTTAAATAGG
* * *
5449839 GGGTGTCGGTCATTTGATGGCCAACATCAAAAAATTTTAAATTTTTTTCTCGAGAAAAAGGGGTG
1 GGGTGTCGGCCATTTGATGGCCAACACCAAAAAATTTTAAATTTTTTTCTCGAAAAAAAGGGGTG
* * * *
5449904 TCGGCTATGCAATGACCAACACCTAAAAATGCAATTTTTTTTAAAATAAG
66 TCGGCCATGCAATGATCAACACCCAAAAATGCAA-TTTTTTT-AAATAGG
* * * * * * *
5449954 AGGTGTCGACCATTTGATGACCAACACAAAAAAATTTTGAATTTTTTTTCTC-AAACAAGGGGGT
1 GGGTGTCGGCCATTTGATGGCCAACACCAAAAAATTTT-AAATTTTTTTCTCGAAAAAAAGGGGT
* * * * *
5450018 GTCGGTCATGCAAT-AGTCAACACCCAAGAATGTAATTTTTTTTCTAGAAAAAG
65 GTCGGCCATGCAATGA-TCAACACCCAAAAATGCAA--TTTTTT-TA-AATAGG
5450071 GGGTGTCGGCCATTTGATGGCCAACAC
1 GGGTGTCGGCCATTTGATGGCCAACAC
5450098 ACCCAAATTT
Statistics
Matches: 415, Mismatches: 50, Indels: 24
0.85 0.10 0.05
Matches are distributed among these distances:
105 1 0.00
106 1 0.00
107 46 0.11
108 15 0.04
109 66 0.16
110 11 0.03
111 14 0.03
112 1 0.00
113 57 0.14
114 79 0.19
115 74 0.18
116 20 0.05
117 30 0.07
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (113 bp):
GGGTGTCGGCCATTTGATGGCCAACACCAAAAAATTTTAAATTTTTTTCTCGAAAAAAAGGGGTG
TCGGCCATGCAATGATCAACACCCAAAAATGCAATTTTTTTAAATAGG
Found at i:5449978 original size:115 final size:113
Alignment explanation
Indices: 5449509--5450097 Score: 704
Period size: 115 Copynumber: 5.2 Consensus size: 113
5449499 CGAGAAAAGA
* * *
5449509 GGGTGTCGGCCATTTGATGGCCAACATCAAAAAAATTT-AATTTTTTTCTCGAGAAAAGGGGGTG
1 GGGTGTCGGCCATTTGATGGCCAACACCAAAAAATTTTAAATTTTTTTCTCGAGAAAAAGGGGTG
* * * *
5449573 TC-G-A-CCATTG-TTAACACCCAAAAATGC-ATTTTTTTTAAATAGG
66 TCGGCATGCAATGATCAACACCCAAAAATGCAATTTTTTTTAAATAAG
* *
5449616 GGGTGTCGACCATTTGATGGCCAACACCAAAAAATTTTGAATTTTTTTCTCGAG-AAAAGGGGTG
1 GGGTGTCGGCCATTTGATGGCCAACACCAAAAAATTTTAAATTTTTTTCTCGAGAAAAAGGGGTG
* ** *
5449680 TTGGC-TGC-ATGGCCAACACCCAAAAATTCAA-TTTTTTTAAAT-AG
66 TCGGCATGCAATGATCAACACCCAAAAATGCAATTTTTTTTAAATAAG
* *
5449724 GGGTTGTCGGCCATTTGATGACCAACACCAAAAAATTTTAAATTTTTTTTCTCGAAAAAAAGGGG
1 GGG-TGTCGGCCATTTGATGGCCAACACCAAAAAATTTTAAA-TTTTTTTCTCGAGAAAAAGGGG
*
5449789 TGTCGGCCATGCAATGATCAACACCCAAAAATGCAA-TTTTTTTAAATAGG
64 TGTCGG-CATGCAATGATCAACACCCAAAAATGCAATTTTTTTTAAATAAG
* *
5449839 GGGTGTCGGTCATTTGATGGCCAACATCAAAAAATTTTAAATTTTTTTCTCGAGAAAAAGGGGTG
1 GGGTGTCGGCCATTTGATGGCCAACACCAAAAAATTTTAAATTTTTTTCTCGAGAAAAAGGGGTG
* *
5449904 TCGGCTATGCAATGACCAACACCTAAAAATGCAATTTTTTTTAAAATAAG
66 TCGGC-ATGCAATGATCAACACCCAAAAATGCAATTTTTTTT-AAATAAG
* * * * * *
5449954 AGGTGTCGACCATTTGATGACCAACACAAAAAAATTTTGAATTTTTTTTCTC-A-AACAAGGGGG
1 GGGTGTCGGCCATTTGATGGCCAACACCAAAAAATTTT-AAATTTTTTTCTCGAGAA-AAAGGGG
* * *
5450017 TGTCGGTCATGCAAT-AGTCAACACCCAAGAATGTAATTTTTTTTCTAGAAAAAG
64 TGTCGG-CATGCAATGA-TCAACACCCAAAAATGCAA-TTTTTTT-TA-AATAAG
5450071 GGGTGTCGGCCATTTGATGGCCAACAC
1 GGGTGTCGGCCATTTGATGGCCAACAC
5450098 ACCCAAATTT
Statistics
Matches: 416, Mismatches: 43, Indels: 36
0.84 0.09 0.07
Matches are distributed among these distances:
107 45 0.11
108 22 0.05
109 61 0.15
110 13 0.03
111 13 0.03
112 2 0.00
113 56 0.13
114 76 0.18
115 77 0.19
116 21 0.05
117 30 0.07
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (113 bp):
GGGTGTCGGCCATTTGATGGCCAACACCAAAAAATTTTAAATTTTTTTCTCGAGAAAAAGGGGTG
TCGGCATGCAATGATCAACACCCAAAAATGCAATTTTTTTTAAATAAG
Found at i:5450550 original size:19 final size:19
Alignment explanation
Indices: 5450526--5450567 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
5450516 GCTTCTGTTA
5450526 TTAAACAAATAGTAATAGT
1 TTAAACAAATAGTAATAGT
5450545 TTAAACAAATAGTAATAGT
1 TTAAACAAATAGTAATAGT
5450564 TTAA
1 TTAA
5450568 GAAGAAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.52, C:0.05, G:0.10, T:0.33
Consensus pattern (19 bp):
TTAAACAAATAGTAATAGT
Found at i:5466965 original size:2 final size:2
Alignment explanation
Indices: 5466960--5467002 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
5466950 TTAAAAAAAG
5466960 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5467002 T
1 T
5467003 TAAAATTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5479777 original size:13 final size:13
Alignment explanation
Indices: 5479759--5479783 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5479749 TAAGCTCTCT
5479759 CCCCCCCCCCCCA
1 CCCCCCCCCCCCA
5479772 CCCCCCCCCCCC
1 CCCCCCCCCCCC
5479784 CCATAGTGGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.04, C:0.96, G:0.00, T:0.00
Consensus pattern (13 bp):
CCCCCCCCCCCCA
Found at i:5482734 original size:32 final size:32
Alignment explanation
Indices: 5482693--5482756 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
5482683 CACCTAAAAC
5482693 TCAATGTTTTGTCCTTACATAACATTCATTAG
1 TCAATGTTTTGTCCTTACATAACATTCATTAG
*
5482725 TCAATGTTTTGTCCTTATATAACATTCATTAG
1 TCAATGTTTTGTCCTTACATAACATTCATTAG
5482757 GTTGACCATA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.28, C:0.17, G:0.09, T:0.45
Consensus pattern (32 bp):
TCAATGTTTTGTCCTTACATAACATTCATTAG
Found at i:5486212 original size:28 final size:28
Alignment explanation
Indices: 5486172--5486231 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
5486162 CAATGACTAA
5486172 GATTCAGATCACGAAGGGATTCCATCTT
1 GATTCAGATCACGAAGGGATTCCATCTT
5486200 GATTCAGATCACGAAGGGATTCCATCTT
1 GATTCAGATCACGAAGGGATTCCATCTT
5486228 GATT
1 GATT
5486232 GATACAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (28 bp):
GATTCAGATCACGAAGGGATTCCATCTT
Found at i:5486358 original size:217 final size:217
Alignment explanation
Indices: 5485983--5486412 Score: 630
Period size: 217 Copynumber: 2.0 Consensus size: 217
5485973 CAATGACTAA
* *
5485983 GATTCAGATCACGAAGGGATTCCATCTTGATGGATAAATTTTTTACCCTTGAGCCACTCATATCT
1 GATTCAGATCACGAAGGGATTCCATCTTGATGGATAAATTTTTGACCATTGAGCCACTCATATCT
* *
5486048 AACATCTGCAGATTACCTAGAGAGTCGAGAGACAAGTACACCTCTTCAATTTGAGTTCCAGATAA
66 AACATCTGAAGATTACCTAGAGAGTCGAGAGACAAGCACACCTCTTCAATTTGAGTTCCAGATAA
* * * * * *
5486113 GTTTAATTTTGTTAAGCTTCGTGGGATTTC-GGGAAATTTGACTATTGGACAATGACTAAGATTC
131 GTTTAATTTTGTCAAACTTCGTGGGATTTCTGGG-AATTCGACCATCGGACAATGACTAAGATCC
*
5486177 AGATCACGAAGGGATTCCATCTT
195 AGATAACGAAGGGATTCCATCTT
*
5486200 GATTCAGATCACGAAGGGATTCCATCTTGATTGATACAA-TTTTGACCATTGAGCCACTCATATC
1 GATTCAGATCACGAAGGGATTCCATCTTGATGGATA-AATTTTTGACCATTGAGCCACTCATATC
** * * * *
5486264 TAAGGTCTGAAGATTACTTGGAGTGTCGAGAGACAAGCACACCTCTTCAATTTGAGTTTCAGATA
65 TAACATCTGAAGATTACCTAGAGAGTCGAGAGACAAGCACACCTCTTCAATTTGAGTTCCAGATA
**
5486329 AGTTTAATTTTGTCAAACTTTTTGGGATTTCTGGGAATTCGACCATCGGACAATGACTAAGATCC
130 AGTTTAATTTTGTCAAACTTCGTGGGATTTCTGGGAATTCGACCATCGGACAATGACTAAGATCC
* *
5486394 AGATAATGAAGTGATTCCA
195 AGATAACGAAGGGATTCCA
5486413 GCTTTGAAAT
Statistics
Matches: 189, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
217 184 0.97
218 5 0.03
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (217 bp):
GATTCAGATCACGAAGGGATTCCATCTTGATGGATAAATTTTTGACCATTGAGCCACTCATATCT
AACATCTGAAGATTACCTAGAGAGTCGAGAGACAAGCACACCTCTTCAATTTGAGTTCCAGATAA
GTTTAATTTTGTCAAACTTCGTGGGATTTCTGGGAATTCGACCATCGGACAATGACTAAGATCCA
GATAACGAAGGGATTCCATCTT
Found at i:5492093 original size:1 final size:1
Alignment explanation
Indices: 5492082--5492118 Score: 56
Period size: 1 Copynumber: 37.0 Consensus size: 1
5492072 ACAGTAACAA
* *
5492082 CCCCCCGCCCCCCCCCCCCCCCCCCCCCCCCACCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
5492119 ACAAAAACCT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.03, C:0.95, G:0.03, T:0.00
Consensus pattern (1 bp):
C
Found at i:5499666 original size:4 final size:4
Alignment explanation
Indices: 5499657--5499718 Score: 79
Period size: 4 Copynumber: 15.2 Consensus size: 4
5499647 CGTAGTGGTA
* * * *
5499657 ATGT ATGT ATGC ATGT ATGT ATGT ATGC ATGT ATGT ATGC ATGC ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
5499705 ATGT ATGT AATGT A
1 ATGT ATGT -ATGT A
5499719 CCTGAATGGA
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
4 47 0.92
5 4 0.08
ACGTcount: A:0.27, C:0.06, G:0.24, T:0.42
Consensus pattern (4 bp):
ATGT
Found at i:5499678 original size:16 final size:16
Alignment explanation
Indices: 5499657--5499713 Score: 105
Period size: 16 Copynumber: 3.6 Consensus size: 16
5499647 CGTAGTGGTA
5499657 ATGTATGTATGCATGT
1 ATGTATGTATGCATGT
5499673 ATGTATGTATGCATGT
1 ATGTATGTATGCATGT
*
5499689 ATGTATGCATGCATGT
1 ATGTATGTATGCATGT
5499705 ATGTATGTA
1 ATGTATGTA
5499714 ATGTACCTGA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.26, C:0.07, G:0.25, T:0.42
Consensus pattern (16 bp):
ATGTATGTATGCATGT
Found at i:5510934 original size:330 final size:330
Alignment explanation
Indices: 5510333--5510992 Score: 1257
Period size: 330 Copynumber: 2.0 Consensus size: 330
5510323 ACAATGCTAT
* *
5510333 TGTCACGGACCGCGCATCGAGGCCCGAGATCAGCTCGTGTCAAGTTGCCCAAGAAGCACTCCGGA
1 TGTCACGGACCGCGCATCGAGGCCCGAGACCAGCTCGTGTCAAGCTGCCCAAGAAGCACTCCGGA
* *
5510398 GCATTTTGGGCCTATCACTAGTTAGCCCAACACTTGGGTTTAAAGAGCCTTTCAAAAGAAGATAA
66 GCATTTTGGGCCTATCACCAGTTAGCCAAACACTTGGGTTTAAAGAGCCTTTCAAAAGAAGATAA
*
5510463 GGGAAGTGGCATATACTTAGGAATATTCCTTTTTGATACCTTTCCATATCTTTGTAAAACTCTTA
131 GGGAAGTGGCATATACTTAAGAATATTCCTTTTTGATACCTTTCCATATCTTTGTAAAACTCTTA
5510528 TAGCTGTATCTCAACCGTCGATGTACTTTAATCCCAACCGTTGGATGTAGGGGGCTTCAACTATA
196 TAGCTGTATCTCAACCGTCGATGTACTTTAATCCCAACCGTTGGATGTAGGGGGCTTCAACTATA
5510593 AATAGAGGCTTACCCCCACCTCATTTGAAACTTAACTTGACTTGTCTTCACTTTTGAGGAATATA
261 AATAGAGGCTTACCCCCACCTCATTTGAAACTTAACTTGACTTGTCTTCACTTTTGAGGAATATA
5510658 CAGAG
326 CAGAG
5510663 TGTCACGGACCGCGCATCGAGGCCCGAGACCAGCTCGTGTCAAGCTGCCCAAGAAGCACTCCGGA
1 TGTCACGGACCGCGCATCGAGGCCCGAGACCAGCTCGTGTCAAGCTGCCCAAGAAGCACTCCGGA
*
5510728 GCATTTTGGGCCTATCACCAGTTAGCCAAACACTTGGGTTTGAAGAGCCTTTCAAAAGAAGATAA
66 GCATTTTGGGCCTATCACCAGTTAGCCAAACACTTGGGTTTAAAGAGCCTTTCAAAAGAAGATAA
5510793 GGGAAGTGGCATATACTTAAGAATATTCCTTTTTGATACCTTTCCATATCTTTGTAAAACTCTTA
131 GGGAAGTGGCATATACTTAAGAATATTCCTTTTTGATACCTTTCCATATCTTTGTAAAACTCTTA
5510858 TAGCTGTATCTCAACCGTCGATGTACTTTAATCCCAACCGTTGGATGTAGGGGGCTTCAACTATA
196 TAGCTGTATCTCAACCGTCGATGTACTTTAATCCCAACCGTTGGATGTAGGGGGCTTCAACTATA
*
5510923 AATAGAGGCTTACCCCCACCTCATTTGGAACTTAACTTGACTTGTCTTCACTTTTGAGGAATATA
261 AATAGAGGCTTACCCCCACCTCATTTGAAACTTAACTTGACTTGTCTTCACTTTTGAGGAATATA
5510988 CAGAG
326 CAGAG
5510993 CATTCACTCA
Statistics
Matches: 323, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
330 323 1.00
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (330 bp):
TGTCACGGACCGCGCATCGAGGCCCGAGACCAGCTCGTGTCAAGCTGCCCAAGAAGCACTCCGGA
GCATTTTGGGCCTATCACCAGTTAGCCAAACACTTGGGTTTAAAGAGCCTTTCAAAAGAAGATAA
GGGAAGTGGCATATACTTAAGAATATTCCTTTTTGATACCTTTCCATATCTTTGTAAAACTCTTA
TAGCTGTATCTCAACCGTCGATGTACTTTAATCCCAACCGTTGGATGTAGGGGGCTTCAACTATA
AATAGAGGCTTACCCCCACCTCATTTGAAACTTAACTTGACTTGTCTTCACTTTTGAGGAATATA
CAGAG
Found at i:5511294 original size:182 final size:182
Alignment explanation
Indices: 5510987--5511352 Score: 732
Period size: 182 Copynumber: 2.0 Consensus size: 182
5510977 TGAGGAATAT
5510987 ACAGAGCATTCACTCAAATTTCTTCCTTGTCTTTTTGCTTTGCCTTTTCTTTCAGAGTTCTTTTG
1 ACAGAGCATTCACTCAAATTTCTTCCTTGTCTTTTTGCTTTGCCTTTTCTTTCAGAGTTCTTTTG
5511052 CTTCCGCTAGGATCTAAGCACTTTAGCTTCGATCGAGTTTCAGGCTTACTTAGGCGTTGCGTGAT
66 CTTCCGCTAGGATCTAAGCACTTTAGCTTCGATCGAGTTTCAGGCTTACTTAGGCGTTGCGTGAT
5511117 CGAGAAGCGTCTAAGGCCGCACGCTCCAAGATTCAAGTTTTAGGGACGTGAC
131 CGAGAAGCGTCTAAGGCCGCACGCTCCAAGATTCAAGTTTTAGGGACGTGAC
5511169 ACAGAGCATTCACTCAAATTTCTTCCTTGTCTTTTTGCTTTGCCTTTTCTTTCAGAGTTCTTTTG
1 ACAGAGCATTCACTCAAATTTCTTCCTTGTCTTTTTGCTTTGCCTTTTCTTTCAGAGTTCTTTTG
5511234 CTTCCGCTAGGATCTAAGCACTTTAGCTTCGATCGAGTTTCAGGCTTACTTAGGCGTTGCGTGAT
66 CTTCCGCTAGGATCTAAGCACTTTAGCTTCGATCGAGTTTCAGGCTTACTTAGGCGTTGCGTGAT
5511299 CGAGAAGCGTCTAAGGCCGCACGCTCCAAGATTCAAGTTTTAGGGACGTGAC
131 CGAGAAGCGTCTAAGGCCGCACGCTCCAAGATTCAAGTTTTAGGGACGTGAC
5511351 AC
1 AC
5511353 TATGCATCAC
Statistics
Matches: 184, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
182 184 1.00
ACGTcount: A:0.20, C:0.24, G:0.21, T:0.35
Consensus pattern (182 bp):
ACAGAGCATTCACTCAAATTTCTTCCTTGTCTTTTTGCTTTGCCTTTTCTTTCAGAGTTCTTTTG
CTTCCGCTAGGATCTAAGCACTTTAGCTTCGATCGAGTTTCAGGCTTACTTAGGCGTTGCGTGAT
CGAGAAGCGTCTAAGGCCGCACGCTCCAAGATTCAAGTTTTAGGGACGTGAC
Found at i:5511951 original size:33 final size:33
Alignment explanation
Indices: 5511913--5511982 Score: 122
Period size: 33 Copynumber: 2.1 Consensus size: 33
5511903 TTAAAATTTT
*
5511913 TAAGGTTTCACATTTGTCACAACAAATAATAAG
1 TAAGGTTTCACATTTGTCACAACAAATAATAAA
*
5511946 TAAGGTTTCACATTTGTCTCAACAAATAATAAA
1 TAAGGTTTCACATTTGTCACAACAAATAATAAA
5511979 TAAG
1 TAAG
5511983 ATTTTCATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.31
Consensus pattern (33 bp):
TAAGGTTTCACATTTGTCACAACAAATAATAAA
Found at i:5512322 original size:30 final size:29
Alignment explanation
Indices: 5512286--5512354 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 29
5512276 TTAAATAAGT
5512286 AATGATAAAATTACACTTTAATCTTTTAAA
1 AATGATAAAATTACA-TTTAATCTTTTAAA
** *
5512316 AATGATAAAAATTTGATTTAATTTTTTAAA
1 AATGAT-AAAATTACATTTAATCTTTTAAA
*
5512346 AATTATAAA
1 AATGATAAA
5512355 GATATAGACT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 3 0.09
30 24 0.71
31 7 0.21
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.42
Consensus pattern (29 bp):
AATGATAAAATTACATTTAATCTTTTAAA
Found at i:5521031 original size:39 final size:39
Alignment explanation
Indices: 5520988--5521087 Score: 146
Period size: 39 Copynumber: 2.6 Consensus size: 39
5520978 TTTGAAACCC
* * *
5520988 AATTACCAATTTGATCATACTTTATATAATAATTAATCT
1 AATTACTAATTTGATCATACTTCATAGAATAATTAATCT
* *
5521027 AATTACTAATTTGGTCATGCTTCATAGAATAATTAATCT
1 AATTACTAATTTGATCATACTTCATAGAATAATTAATCT
*
5521066 AATCACTAATTTGATCATACTT
1 AATTACTAATTTGATCATACTT
5521088 ACAATTGTAA
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 53 1.00
ACGTcount: A:0.38, C:0.14, G:0.06, T:0.42
Consensus pattern (39 bp):
AATTACTAATTTGATCATACTTCATAGAATAATTAATCT
Found at i:5527501 original size:29 final size:29
Alignment explanation
Indices: 5527451--5527507 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
5527441 AAATGTTACA
* * * *
5527451 AATTGAAATATTAGTGATCAAATCGTAAC
1 AATTGAAATATTAATAACCAAAACGTAAC
*
5527480 AATTTAAATATTAATAACCAAAACGTAA
1 AATTGAAATATTAATAACCAAAACGTAA
5527508 ACTTAACCAA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.30
Consensus pattern (29 bp):
AATTGAAATATTAATAACCAAAACGTAAC
Found at i:5527890 original size:17 final size:17
Alignment explanation
Indices: 5527835--5527892 Score: 55
Period size: 17 Copynumber: 3.2 Consensus size: 17
5527825 AAATTTAATA
5527835 AAAAATTAAGGTTATA-TT
1 AAAAATTAA--TTATATTT
*
5527853 AATAATTAAATTATTTATTT
1 AAAAATT-AATTA--TATTT
5527873 AAAAATTAATTATATTT
1 AAAAATTAATTATATTT
5527890 AAA
1 AAA
5527893 TTTTAAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
17 11 0.32
18 6 0.18
19 9 0.26
20 8 0.24
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (17 bp):
AAAAATTAATTATATTT
Found at i:5532756 original size:24 final size:24
Alignment explanation
Indices: 5532729--5532782 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
5532719 CCATCTTATT
5532729 ATATAAAATTATCAAAACTTTCAC
1 ATATAAAATTATCAAAACTTTCAC
* * * *
5532753 ATATAAATTTTTTAATACTTTCAC
1 ATATAAAATTATCAAAACTTTCAC
5532777 ATATAA
1 ATATAA
5532783 TTCATCGATA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (24 bp):
ATATAAAATTATCAAAACTTTCAC
Found at i:5534261 original size:27 final size:26
Alignment explanation
Indices: 5534217--5534267 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
5534207 AACCACTTCG
* *
5534217 TTTTCAATATTTGAATTTGTATTTTC
1 TTTTCAATATATGAATTTATATTTTC
*
5534243 TTTTTAATATATGATATTTATATTT
1 TTTTCAATATATGA-ATTTATATTT
5534268 AAATTTAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 12 0.57
27 9 0.43
ACGTcount: A:0.27, C:0.04, G:0.06, T:0.63
Consensus pattern (26 bp):
TTTTCAATATATGAATTTATATTTTC
Found at i:5534354 original size:16 final size:16
Alignment explanation
Indices: 5534333--5534374 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
5534323 CACTAAATTA
* *
5534333 TTGATAAGTTTTTGTC
1 TTGATAACTTTCTGTC
5534349 TTGATAACTTTCTGTC
1 TTGATAACTTTCTGTC
5534365 TTGATAACTT
1 TTGATAACTT
5534375 GATTGTTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.21, C:0.12, G:0.14, T:0.52
Consensus pattern (16 bp):
TTGATAACTTTCTGTC
Found at i:5538331 original size:15 final size:17
Alignment explanation
Indices: 5538296--5538335 Score: 57
Period size: 15 Copynumber: 2.5 Consensus size: 17
5538286 ATAATAAAAA
*
5538296 TATAATTTCATCATTTT
1 TATAATTTCATCATGTT
5538313 TATAATTT-A-CATGTT
1 TATAATTTCATCATGTT
5538328 TATAATTT
1 TATAATTT
5538336 TTAAAGGATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 13 0.59
16 1 0.05
17 8 0.36
ACGTcount: A:0.33, C:0.07, G:0.03, T:0.57
Consensus pattern (17 bp):
TATAATTTCATCATGTT
Found at i:5563995 original size:22 final size:22
Alignment explanation
Indices: 5563967--5564034 Score: 73
Period size: 22 Copynumber: 3.1 Consensus size: 22
5563957 ATGTTTGTTG
5563967 TTTTGTTACTATTATGTTATTA
1 TTTTGTTACTATTATGTTATTA
* **
5563989 TTTTGTTACCATTGCGTTATTA
1 TTTTGTTACTATTATGTTATTA
* * * *
5564011 TATTATTACTGTTTTGTTATTA
1 TTTTGTTACTATTATGTTATTA
5564033 TT
1 TT
5564035 GTTTAGATAT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.21, C:0.07, G:0.10, T:0.62
Consensus pattern (22 bp):
TTTTGTTACTATTATGTTATTA
Found at i:5564223 original size:12 final size:12
Alignment explanation
Indices: 5564208--5564234 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
5564198 AATTTATTTT
5564208 ATATAAAAAATA
1 ATATAAAAAATA
5564220 ATATAAAAAATA
1 ATATAAAAAATA
5564232 ATA
1 ATA
5564235 CGAGTGAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
ATATAAAAAATA
Found at i:5594873 original size:30 final size:27
Alignment explanation
Indices: 5594815--5594873 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
5594805 TACATATTAC
*
5594815 ATATATAAAGAATTATATTTATTTAAT
1 ATATAAAAAGAATTATATTTATTTAAT
*
5594842 ATATAAAAATAATGTATATATTATTTAA-
1 ATATAAAAAGAAT-TATAT-TTATTTAAT
5594870 ATAT
1 ATAT
5594874 GTACAATTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 11 0.39
28 9 0.32
29 8 0.29
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (27 bp):
ATATAAAAAGAATTATATTTATTTAAT
Found at i:5595939 original size:21 final size:21
Alignment explanation
Indices: 5595899--5595939 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
5595889 TCACCACCAA
* * *
5595899 CTCAATATTTTTTTTTAAAAC
1 CTCAATACTTTTTCTCAAAAC
5595920 CTCAATACTTTTTCTCAAAA
1 CTCAATACTTTTTCTCAAAA
5595940 AAAGTTTTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.20, G:0.00, T:0.46
Consensus pattern (21 bp):
CTCAATACTTTTTCTCAAAAC
Found at i:5618320 original size:23 final size:25
Alignment explanation
Indices: 5618291--5618336 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
5618281 TAATTCATTA
*
5618291 AAATAAT-TTTGA-ATATCAATATC
1 AAATAATATTTGATATATAAATATC
5618314 AAATAATATTTGATATATAAATA
1 AAATAATATTTGATATATAAATA
5618337 CTATAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 7 0.35
24 5 0.25
25 8 0.40
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.39
Consensus pattern (25 bp):
AAATAATATTTGATATATAAATATC
Found at i:5638730 original size:24 final size:25
Alignment explanation
Indices: 5638698--5638746 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
5638688 TAGGTATTAG
* * *
5638698 TATGGTAGG-AATTGTTTGATTATC
1 TATGATAGGAAATCGTTGGATTATC
5638722 TATGATAGGAAATCGTTGGATTATC
1 TATGATAGGAAATCGTTGGATTATC
5638747 ATTATAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.29, C:0.06, G:0.24, T:0.41
Consensus pattern (25 bp):
TATGATAGGAAATCGTTGGATTATC
Found at i:5646540 original size:87 final size:87
Alignment explanation
Indices: 5646346--5646549 Score: 205
Period size: 87 Copynumber: 2.3 Consensus size: 87
5646336 TGTAAAAAAT
* ** * * * *
5646346 CCTCAAATTTTTTCAAAAAATAATTAAGTTTCTGCTTTTATTTTTCACTCATTTGGATATTTAAA
1 CCTCAAAATTTTTCAAAAAGCAATTAAGTTTCTACTTTTATTTTTCACTCAATTGAATACTTAAA
* * *
5646411 TTTTCAAAATGCATCAAAAGGT
66 CTTTCAAAATGCATCAAAAAGA
* *** *
5646433 CCTCAAACTTTAAAAAAAAAAGCAATTAAGTTTCTAC-TTT-TTTTTCACTCAATTGAATACTTG
1 CCTCAAAATTT--TTCAAAAAGCAATTAAGTTTCTACTTTTATTTTTCACTCAATTGAATACTTA
*
5646496 AACTTTCAAAATGCATTAAAAAGA
64 AACTTTCAAAATGCATCAAAAAGA
5646520 CCATCAAAATTTTTCGAAAAAAGCAATTAA
1 CC-TCAAAATTTTTC--AAAAAGCAATTAA
5646550 ACCCTTGAGT
Statistics
Matches: 93, Mismatches: 19, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
87 51 0.55
88 24 0.26
89 18 0.19
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.37
Consensus pattern (87 bp):
CCTCAAAATTTTTCAAAAAGCAATTAAGTTTCTACTTTTATTTTTCACTCAATTGAATACTTAAA
CTTTCAAAATGCATCAAAAAGA
Found at i:5653044 original size:111 final size:111
Alignment explanation
Indices: 5652789--5653016 Score: 456
Period size: 111 Copynumber: 2.1 Consensus size: 111
5652779 AAGAACTGAA
5652789 ATAAGTAATTAAAATTAATAGAATGGTTTTTCAAAACATGAAGCAAAAATTGTTTCCTTTAGTAT
1 ATAAGTAATTAAAATTAATAGAATGGTTTTTCAAAACATGAAGCAAAAATTGTTTCCTTTAGTAT
5652854 TTAAATAACTTGAGTATGATAATAAAATTTAATGGTAAATTTAGTT
66 TTAAATAACTTGAGTATGATAATAAAATTTAATGGTAAATTTAGTT
5652900 ATAAGTAATTAAAATTAATAGAATGGTTTTTCAAAACATGAAGCAAAAATTGTTTCCTTTAGTAT
1 ATAAGTAATTAAAATTAATAGAATGGTTTTTCAAAACATGAAGCAAAAATTGTTTCCTTTAGTAT
5652965 TTAAATAACTTGAGTATGATAATAAAATTTAATGGTAAATTTAGTT
66 TTAAATAACTTGAGTATGATAATAAAATTTAATGGTAAATTTAGTT
5653011 ATAAGT
1 ATAAGT
5653017 GATATTTTTT
Statistics
Matches: 117, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
111 117 1.00
ACGTcount: A:0.43, C:0.05, G:0.13, T:0.39
Consensus pattern (111 bp):
ATAAGTAATTAAAATTAATAGAATGGTTTTTCAAAACATGAAGCAAAAATTGTTTCCTTTAGTAT
TTAAATAACTTGAGTATGATAATAAAATTTAATGGTAAATTTAGTT
Found at i:5653206 original size:21 final size:20
Alignment explanation
Indices: 5653181--5653228 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 20
5653171 TAATATTGTA
5653181 AATTTTTAAAACTTTTTTAAT
1 AATTTTTAAAA-TTTTTTAAT
*
5653202 AATTTATTTAAATTTTTTAAT
1 AATTT-TTAAAATTTTTTAAT
5653223 AATTTT
1 AATTTT
5653229 GTTTATTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 1 0.04
21 19 0.76
22 5 0.20
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (20 bp):
AATTTTTAAAATTTTTTAAT
Found at i:5653211 original size:12 final size:11
Alignment explanation
Indices: 5653183--5653228 Score: 53
Period size: 11 Copynumber: 4.3 Consensus size: 11
5653173 ATATTGTAAA
5653183 TTTTTAA-AACT
1 TTTTTAATAA-T
5653194 TTTTTAATAAT
1 TTTTTAATAAT
5653205 TTATTT-A-AAT
1 TT-TTTAATAAT
5653215 TTTTTAATAAT
1 TTTTTAATAAT
5653226 TTT
1 TTT
5653229 GTTTATTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
9 3 0.10
10 6 0.19
11 17 0.55
12 5 0.16
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (11 bp):
TTTTTAATAAT
Found at i:5655080 original size:73 final size:73
Alignment explanation
Indices: 5654957--5655107 Score: 248
Period size: 73 Copynumber: 2.1 Consensus size: 73
5654947 GGCCGAAAGT
5654957 ATTTTAGAAGTAAAAGCTCAAAATATGTTGCCTCCTCTTTAATGGGATTCACTAAAAACAATGGA
1 ATTTTAGAAGTAAAAGCTCAAAATATGTTGCCTCCTCTTTAATGGGATTCACTAAAAACAATGGA
* *
5655022 ACATGTGC
66 ACACGTAC
* * * *
5655030 ATTTTAGAAGTAAAAGTTCAATATATGTTGCTTCCTCTTTAATGGTATTCACTAAAAACAATGGA
1 ATTTTAGAAGTAAAAGCTCAAAATATGTTGCCTCCTCTTTAATGGGATTCACTAAAAACAATGGA
5655095 ACACGTAC
66 ACACGTAC
5655103 ATTTT
1 ATTTT
5655108 TGTGATTTTG
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (73 bp):
ATTTTAGAAGTAAAAGCTCAAAATATGTTGCCTCCTCTTTAATGGGATTCACTAAAAACAATGGA
ACACGTAC
Found at i:5672247 original size:11 final size:11
Alignment explanation
Indices: 5672233--5672339 Score: 52
Period size: 11 Copynumber: 9.4 Consensus size: 11
5672223 AAATGCCTCT
5672233 AAAATAATAAC
1 AAAATAATAAC
* *
5672244 AAAATTAACAAT
1 AAAA-TAATAAC
* *
5672256 AAAATAAAAAT
1 AAAATAATAAC
* * * *
5672267 TATACAATATC
1 AAAATAATAAC
*
5672278 CAAATAATAAC
1 AAAATAATAAC
*
5672289 AATAAAATAATAAT
1 ---AAAATAATAAC
*
5672303 AATATAATAAC
1 AAAATAATAAC
* *
5672314 AAAATAACAAT
1 AAAATAATAAC
*
5672325 AAAATAATAGC
1 AAAATAATAAC
5672336 AAAA
1 AAAA
5672340 CAATTGATTT
Statistics
Matches: 69, Mismatches: 23, Indels: 8
0.69 0.23 0.08
Matches are distributed among these distances:
11 51 0.74
12 9 0.13
14 9 0.13
ACGTcount: A:0.68, C:0.08, G:0.01, T:0.22
Consensus pattern (11 bp):
AAAATAATAAC
Found at i:5672291 original size:36 final size:33
Alignment explanation
Indices: 5672238--5672331 Score: 116
Period size: 36 Copynumber: 2.7 Consensus size: 33
5672228 CCTCTAAAAT
*
5672238 AATAACAAAATTAACAATAAAATAAAAATTATAC
1 AATAACAAAA-TAACAATAAAATAAAAATAATAC
* * *
5672272 AATATCCAAATAATAACAATAAAATAATAATAATAT
1 AATA-AC-AA-AATAACAATAAAATAAAAATAATAC
5672308 AATAACAAAATAACAATAAAATAA
1 AATAACAAAATAACAATAAAATAA
5672332 TAGCAAAACA
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
33 16 0.31
34 6 0.12
35 2 0.04
36 26 0.50
37 2 0.04
ACGTcount: A:0.68, C:0.09, G:0.00, T:0.23
Consensus pattern (33 bp):
AATAACAAAATAACAATAAAATAAAAATAATAC
Found at i:5672300 original size:3 final size:3
Alignment explanation
Indices: 5672280--5672333 Score: 53
Period size: 3 Copynumber: 19.3 Consensus size: 3
5672270 ACAATATCCA
* * *
5672280 AAT AAT AAC AAT AA- AAT AAT AAT AAT -AT AAT AAC AA- AAT AAC AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5672325 AA- AAT AAT A
1 AAT AAT AAT A
5672334 GCAAAACAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
2 8 0.19
3 34 0.81
ACGTcount: A:0.70, C:0.06, G:0.00, T:0.24
Consensus pattern (3 bp):
AAT
Found at i:5672332 original size:22 final size:22
Alignment explanation
Indices: 5672232--5672339 Score: 87
Period size: 22 Copynumber: 4.7 Consensus size: 22
5672222 TAAATGCCTC
5672232 TAAAATAATAACAAAATTAACAA
1 TAAAATAATAACAAAA-TAACAA
**
5672255 TAAAATAA-AA-ATTAT-ACAA
1 TAAAATAATAACAAAATAACAA
*
5672274 TATCCAAATAATAACAATAAAATAATAA
1 TA---AAATAATAAC---AAAATAACAA
*
5672302 TAATATAATAACAAAATAACAA
1 TAAAATAATAACAAAATAACAA
*
5672324 TAAAATAATAGCAAAA
1 TAAAATAATAACAAAA
5672340 CAATTGATTT
Statistics
Matches: 67, Mismatches: 9, Indels: 19
0.71 0.09 0.20
Matches are distributed among these distances:
19 6 0.09
20 1 0.01
21 2 0.03
22 31 0.46
23 10 0.15
25 9 0.13
27 3 0.04
28 5 0.07
ACGTcount: A:0.68, C:0.08, G:0.01, T:0.23
Consensus pattern (22 bp):
TAAAATAATAACAAAATAACAA
Found at i:5672705 original size:16 final size:16
Alignment explanation
Indices: 5672680--5672716 Score: 56
Period size: 18 Copynumber: 2.2 Consensus size: 16
5672670 TTTTCAGTTT
5672680 ACATATATATATATATCC
1 ACATATAT-TATA-ATCC
5672698 ACATATATTATAATCC
1 ACATATATTATAATCC
5672714 ACA
1 ACA
5672717 ACCACTTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.37
17 4 0.21
18 8 0.42
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (16 bp):
ACATATATTATAATCC
Found at i:5673250 original size:18 final size:19
Alignment explanation
Indices: 5673223--5673266 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
5673213 ACTTTTGTTT
*
5673223 AAATATATAT-GTAAAAAA
1 AAATAAATATCGTAAAAAA
* *
5673241 GAATAAATATCTTAAAAAA
1 AAATAAATATCGTAAAAAA
5673260 AAATAAA
1 AAATAAA
5673267 GAGTCTTTGT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.68, C:0.02, G:0.05, T:0.25
Consensus pattern (19 bp):
AAATAAATATCGTAAAAAA
Found at i:5673273 original size:20 final size:19
Alignment explanation
Indices: 5673234--5673273 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
5673224 AATATATATG
* *
5673234 TAAAAAAGAATAAATATCT
1 TAAAAAAAAATAAAGATCT
5673253 TAAAAAAAAATAAAGAGTCT
1 TAAAAAAAAATAAAGA-TCT
5673273 T
1 T
5673274 TGTTATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.62, C:0.05, G:0.07, T:0.25
Consensus pattern (19 bp):
TAAAAAAAAATAAAGATCT
Found at i:5680786 original size:18 final size:18
Alignment explanation
Indices: 5680751--5680798 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
5680741 ATTTTTTTTT
*
5680751 AATAATTTGTATTATATTA
1 AATAATTTTTA-TATATTA
* *
5680770 TATTATTTTTATATATTA
1 AATAATTTTTATATATTA
5680788 AATAATTTTTA
1 AATAATTTTTA
5680799 ACACATCAAA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (18 bp):
AATAATTTTTATATATTA
Found at i:5681225 original size:74 final size:75
Alignment explanation
Indices: 5681131--5681308 Score: 268
Period size: 74 Copynumber: 2.4 Consensus size: 75
5681121 TGGTACAAAA
* * *
5681131 AGAAGAAAATATAAACTAAACTCTAACTACCCTTTCCTACAAGAATAAACTTGTAAAAGAGGTAG
1 AGAAGAAAATATAGACTAAACTCTAACTACCCCTTCCCACAAGAATAAACTTGTAAAAGAGGTAG
5681196 GAAACTCGTC
66 GAAACTCGTC
* * *
5681206 AGAA-AAAAAATAGACTAAACTCTAACTACCCCTTCCCACAAGAATCAGCTTGTAAAAGAGGTAG
1 AGAAGAAAATATAGACTAAACTCTAACTACCCCTTCCCACAAGAATAAACTTGTAAAAGAGGTAG
* *
5681270 GAGACTCTTC
66 GAAACTCGTC
*
5681280 AGAAGAAAATATAGATTAAACTCTAACTA
1 AGAAGAAAATATAGACTAAACTCTAACTA
5681309 GCTAAATAGG
Statistics
Matches: 92, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
74 66 0.72
75 26 0.28
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (75 bp):
AGAAGAAAATATAGACTAAACTCTAACTACCCCTTCCCACAAGAATAAACTTGTAAAAGAGGTAG
GAAACTCGTC
Found at i:5681441 original size:16 final size:17
Alignment explanation
Indices: 5681407--5681446 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
5681397 TCATGACTCA
*
5681407 TTTAAAGTTTAATTTTT
1 TTTAAAATTTAATTTTT
5681424 TTTAAAATTTAATTTTT
1 TTTAAAATTTAATTTTT
*
5681441 TGTAAA
1 TTTAAA
5681447 TATATTATGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (17 bp):
TTTAAAATTTAATTTTT
Found at i:5694374 original size:17 final size:17
Alignment explanation
Indices: 5694352--5694390 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
5694342 CTCCACCTTG
* *
5694352 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCAACGA
5694369 ACAAGAACTCTCAACGA
1 ACAAGAACTCTCAACGA
5694386 ACAAG
1 ACAAG
5694391 TTCTCCACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.46, C:0.26, G:0.13, T:0.15
Consensus pattern (17 bp):
ACAAGAACTCTCAACGA
Found at i:5701239 original size:17 final size:16
Alignment explanation
Indices: 5701201--5701239 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
5701191 AAATATTAGT
5701201 AAAATA-TTAAAAAAA
1 AAAATATTTAAAAAAA
*
5701216 TAAATATTTAAAAAAA
1 AAAATATTTAAAAAAA
5701232 AAAGATAT
1 AAA-ATAT
5701240 ATGTGATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 5 0.25
16 11 0.55
17 4 0.20
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (16 bp):
AAAATATTTAAAAAAA
Found at i:5702654 original size:22 final size:22
Alignment explanation
Indices: 5702626--5702670 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
5702616 CATCATTAAA
* *
5702626 TTTTAAATTATTTTGATTATAT
1 TTTTAAATTATTCTAATTATAT
5702648 TTTTAAATTATTCTAATTATAT
1 TTTTAAATTATTCTAATTATAT
5702670 T
1 T
5702671 AATCAAATTC
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:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (22 bp):
TTTTAAATTATTCTAATTATAT
Found at i:5703043 original size:17 final size:17
Alignment explanation
Indices: 5703015--5703061 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
5703005 AAATGTTTTA
5703015 TAATTT-TTTTTAATTT
1 TAATTTATTTTTAATTT
*
5703031 TAATTTATTTTTAGTTT
1 TAATTTATTTTTAATTT
**
5703048 TTTTTTATTTTTAA
1 TAATTTATTTTTAA
5703062 AAGTTATGTG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
16 6 0.23
17 20 0.77
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (17 bp):
TAATTTATTTTTAATTT
Found at i:5710532 original size:19 final size:18
Alignment explanation
Indices: 5710505--5710555 Score: 50
Period size: 19 Copynumber: 2.7 Consensus size: 18
5710495 ATTTACTATA
*
5710505 AATTCTTATAATATTTAT
1 AATTTTTATAATATTTAT
*
5710523 AAGTTTTTATGAAT-TTTGT
1 AA-TTTTTAT-AATATTTAT
5710542 AATTTTTAATAATA
1 AATTTTT-ATAATA
5710556 ATCCAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
18 10 0.37
19 14 0.52
20 3 0.11
ACGTcount: A:0.37, C:0.02, G:0.06, T:0.55
Consensus pattern (18 bp):
AATTTTTATAATATTTAT
Found at i:5711084 original size:28 final size:26
Alignment explanation
Indices: 5711041--5711093 Score: 70
Period size: 28 Copynumber: 2.0 Consensus size: 26
5711031 ATGTAAACAA
* *
5711041 TTATAAAATATTTAAAAATATTAATAAT
1 TTATAAAAAATATAAAAA-A-TAATAAT
5711069 TTATAAAAAATATAAAAAATAATAA
1 TTATAAAAAATATAAAAAATAATAA
5711094 AAATGCCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 6 0.26
27 1 0.04
28 16 0.70
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (26 bp):
TTATAAAAAATATAAAAAATAATAAT
Found at i:5711239 original size:2 final size:2
Alignment explanation
Indices: 5711234--5711263 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5711224 GAAAGAAAGA
5711234 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5711264 GGAAAAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5711357 original size:28 final size:28
Alignment explanation
Indices: 5711302--5711357 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
5711292 AATTTTTAGT
* *
5711302 AAATTTTACAATTTTTTTTACATATTTA
1 AAATTTTACAATTTTTTATAAATATTTA
*
5711330 AAATTTTATAATATTTTTATAAAT-TTTA
1 AAATTTTACAAT-TTTTTATAAATATTTA
5711358 TTTTTTTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 15 0.62
29 9 0.38
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (28 bp):
AAATTTTACAATTTTTTATAAATATTTA
Found at i:5711361 original size:15 final size:15
Alignment explanation
Indices: 5711341--5711374 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
5711331 AATTTTATAA
5711341 TATTTTTATAAATTT
1 TATTTTTATAAATTT
* *
5711356 TATTTTTTTTAATTT
1 TATTTTTATAAATTT
5711371 TATT
1 TATT
5711375 GTTTTGCACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TATTTTTATAAATTT
Found at i:5711507 original size:13 final size:13
Alignment explanation
Indices: 5711484--5711515 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
5711474 TCACATCAAC
5711484 ATCAA-ATGTCAT
1 ATCAACATGTCAT
5711496 ATCAACATGTCAT
1 ATCAACATGTCAT
5711509 ATCAACA
1 ATCAACA
5711516 AAATTAACGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.44, C:0.22, G:0.06, T:0.28
Consensus pattern (13 bp):
ATCAACATGTCAT
Found at i:5715688 original size:17 final size:16
Alignment explanation
Indices: 5715651--5715689 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
5715641 TCTCGCAATA
5715651 TTCT-AACCTTTTTAT
1 TTCTAAACCTTTTTAT
*
5715666 TTCTAAACCTTTTTTT
1 TTCTAAACCTTTTTAT
5715682 TTACTAAA
1 TT-CTAAA
5715690 TATTTAAGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 4 0.19
16 12 0.57
17 5 0.24
ACGTcount: A:0.26, C:0.18, G:0.00, T:0.56
Consensus pattern (16 bp):
TTCTAAACCTTTTTAT
Found at i:5723090 original size:14 final size:15
Alignment explanation
Indices: 5723056--5723092 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
5723046 GTGATTGAGT
5723056 TTTATTTTAAATTTA
1 TTTATTTTAAATTTA
5723071 TTTATTTT-AATTT-
1 TTTATTTTAAATTTA
5723084 TTATATTTT
1 TT-TATTTT
5723093 TTTTAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.10
14 11 0.52
15 8 0.38
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTATTTTAAATTTA
Found at i:5725289 original size:25 final size:25
Alignment explanation
Indices: 5725261--5725398 Score: 109
Period size: 25 Copynumber: 5.5 Consensus size: 25
5725251 AAACCATAGT
*
5725261 TAAAGTCC-AAATCACGGTTAAACTC
1 TAAA-TCCTAAATCACGGTTAAACCC
*
5725286 TAAATCCTAAATCACGATTAAACCC
1 TAAATCCTAAATCACGGTTAAACCC
* * *
5725311 TAAATCCTCAATCATGGTTAAACCT
1 TAAATCCTAAATCACGGTTAAACCC
* * ** * *
5725336 TAAATCTTAAACCATAGTTAAATCT
1 TAAATCCTAAATCACGGTTAAACCC
* ** *
5725361 TAAACCCTAAATCACAATTCAACCC
1 TAAATCCTAAATCACGGTTAAACCC
5725386 TAAA-CCATAAATC
1 TAAATCC-TAAATC
5725399 TTAAATCATA
Statistics
Matches: 92, Mismatches: 19, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
24 5 0.05
25 87 0.95
ACGTcount: A:0.43, C:0.25, G:0.05, T:0.27
Consensus pattern (25 bp):
TAAATCCTAAATCACGGTTAAACCC
Found at i:5725390 original size:57 final size:57
Alignment explanation
Indices: 5725329--5725446 Score: 157
Period size: 57 Copynumber: 2.1 Consensus size: 57
5725319 CAATCATGGT
* * * *
5725329 TAAACCTTAAATCTTAAACCATAGTTAAAT-CTTAAACCCTAAATCACAATTCAACCC
1 TAAACCATAAATCTTAAACCATAATTAAATAC-TAAACCCTAAATCACAATTAAACCA
* * *
5725386 TAAACCATAAATCTTAAATCATAATTAAATACTAAACCTTAAATTACAATTAAACCA
1 TAAACCATAAATCTTAAACCATAATTAAATACTAAACCCTAAATCACAATTAAACCA
5725443 TAAA
1 TAAA
5725447 TCCTAAACCA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
57 52 0.98
58 1 0.02
ACGTcount: A:0.49, C:0.21, G:0.01, T:0.29
Consensus pattern (57 bp):
TAAACCATAAATCTTAAACCATAATTAAATACTAAACCCTAAATCACAATTAAACCA
Found at i:5725404 original size:32 final size:32
Alignment explanation
Indices: 5725368--5725429 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
5725358 TCTTAAACCC
* *
5725368 TAAATCACAATTCAACCCTAAACCATAAATCT
1 TAAATCACAATTAAACACTAAACCATAAATCT
* * *
5725400 TAAATCATAATTAAATACTAAACCTTAAAT
1 TAAATCACAATTAAACACTAAACCATAAAT
5725430 TACAATTAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (32 bp):
TAAATCACAATTAAACACTAAACCATAAATCT
Found at i:5725414 original size:25 final size:25
Alignment explanation
Indices: 5725386--5725458 Score: 76
Period size: 25 Copynumber: 2.9 Consensus size: 25
5725376 AATTCAACCC
*
5725386 TAAACCATAAATCTTAAATCATAAT
1 TAAACCATAAATCTTAAATCACAAT
* * *
5725411 TAAA-TACTAAACCTTAAATTACAAT
1 TAAACCA-TAAATCTTAAATCACAAT
* *
5725436 TAAACCATAAATCCTAAACCACA
1 TAAACCATAAATCTTAAATCACA
5725459 GTAAAAACCT
Statistics
Matches: 37, Mismatches: 9, Indels: 4
0.74 0.18 0.08
Matches are distributed among these distances:
24 1 0.03
25 35 0.95
26 1 0.03
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.27
Consensus pattern (25 bp):
TAAACCATAAATCTTAAATCACAAT
Found at i:5725475 original size:50 final size:50
Alignment explanation
Indices: 5725386--5725505 Score: 116
Period size: 50 Copynumber: 2.4 Consensus size: 50
5725376 AATTCAACCC
* * * * **
5725386 TAAACCATAAATCTTAAATCATAATTAAATACTAAACCTTAAATTACAAT
1 TAAACCATAAATCCTAAACCATAAGTAAAAACTAAACCTTAAACCACAAT
* * * *
5725436 TAAACCATAAATCCTAAACCA-CAGTAAAAACCTACACCTTAAACCATATT
1 TAAACCATAAATCCTAAACCATAAGTAAAAA-CTAAACCTTAAACCACAAT
* *
5725486 TAAATCATAAACCCTAAACC
1 TAAACCATAAATCCTAAACC
5725506 CTAAACCATA
Statistics
Matches: 57, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
49 6 0.11
50 51 0.89
ACGTcount: A:0.50, C:0.23, G:0.01, T:0.26
Consensus pattern (50 bp):
TAAACCATAAATCCTAAACCATAAGTAAAAACTAAACCTTAAACCACAAT
Found at i:5725498 original size:18 final size:18
Alignment explanation
Indices: 5725475--5725549 Score: 68
Period size: 18 Copynumber: 4.4 Consensus size: 18
5725465 ACCTACACCT
*
5725475 TAAACCATATTTAAATCA
1 TAAACCATATTTAAACCA
* *
5725493 TAAACC----CTAAACCC
1 TAAACCATATTTAAACCA
5725507 TAAACCATATTTAAACCA
1 TAAACCATATTTAAACCA
* * *
5725525 TAAACCATAGTTAAATCG
1 TAAACCATATTTAAACCA
5725543 TAAACCA
1 TAAACCA
5725550 CGGTTATATC
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
14 11 0.24
18 34 0.76
ACGTcount: A:0.48, C:0.24, G:0.03, T:0.25
Consensus pattern (18 bp):
TAAACCATATTTAAACCA
Found at i:5725511 original size:32 final size:32
Alignment explanation
Indices: 5725466--5725530 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
5725456 ACAGTAAAAA
* * *
5725466 CCTACACCTTAAACCATATTTAAATCATAAAC
1 CCTAAACCCTAAACCATATTTAAACCATAAAC
5725498 CCTAAACCCTAAACCATATTTAAACCATAAAC
1 CCTAAACCCTAAACCATATTTAAACCATAAAC
5725530 C
1 C
5725531 ATAGTTAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.45, C:0.31, G:0.00, T:0.25
Consensus pattern (32 bp):
CCTAAACCCTAAACCATATTTAAACCATAAAC
Found at i:5725624 original size:18 final size:17
Alignment explanation
Indices: 5725575--5725665 Score: 62
Period size: 18 Copynumber: 5.3 Consensus size: 17
5725565 TCCTAAATCA
*
5725575 TAAACCATATTTAAACCCC
1 TAAA-CATAATTAAA-CCC
* *
5725594 AAAACATAGTTAAACCC
1 TAAACATAATTAAACCC
*
5725611 TAAACTATAATTAAACCT
1 TAAAC-ATAATTAAACCC
*
5725629 TAAA-GT--TTAAACCC
1 TAAACATAATTAAACCC
* *
5725643 TAAATTATGATTAAACCC
1 TAAA-CATAATTAAACCC
5725661 TAAAC
1 TAAAC
5725666 CTTGAATCAT
Statistics
Matches: 58, Mismatches: 9, Indels: 12
0.73 0.11 0.15
Matches are distributed among these distances:
14 11 0.19
16 2 0.03
17 7 0.12
18 35 0.60
19 3 0.05
ACGTcount: A:0.47, C:0.22, G:0.03, T:0.27
Consensus pattern (17 bp):
TAAACATAATTAAACCC
Found at i:5725644 original size:32 final size:32
Alignment explanation
Indices: 5725603--5725664 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
5725593 CAAAACATAG
*
5725603 TTAAACCCTAAACTATAATTAAACCTTAAAGT
1 TTAAACCCTAAACTATAATTAAACCCTAAAGT
* *
5725635 TTAAACCCTAAATTATGATTAAACCCTAAA
1 TTAAACCCTAAACTATAATTAAACCCTAAA
5725665 CCTTGAATCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.47, C:0.19, G:0.03, T:0.31
Consensus pattern (32 bp):
TTAAACCCTAAACTATAATTAAACCCTAAAGT
Found at i:5725664 original size:25 final size:24
Alignment explanation
Indices: 5725636--5726350 Score: 219
Period size: 25 Copynumber: 29.5 Consensus size: 24
5725626 CCTTAAAGTT
**
5725636 TAAACCCTAAATTATGATTAAACCC
1 TAAACCCTAAACCAT-ATTAAACCC
* * *
5725661 TAAACCTTGAATCATAATTAAACCC
1 TAAACCCTAAACCAT-ATTAAACCC
* * *
5725686 TAAACACTAAACCATGGTTAAATCC
1 TAAACCCTAAACCAT-ATTAAACCC
*
5725711 T-AACCCTAAACCATAGT------
1 TAAACCCTAAACCATATTAAACCC
5725728 TAAACCCTAAACCATAATTAAACCC
1 TAAACCCTAAACCAT-ATTAAACCC
5725753 TAAACCCTAAACCATAATTAAACCC
1 TAAACCCTAAACCAT-ATTAAACCC
*
5725778 TAAAACCTTAAACCATAGTTAAACCC
1 T-AAACCCTAAACCATA-TTAAACCC
* ** *
5725804 TAAGCTATAAACC---CTAAACCC
1 TAAACCCTAAACCATATTAAACCC
* *
5725825 TAAACCATAAACC---CTAAACCC
1 TAAACCCTAAACCATATTAAACCC
*
5725846 CAAACCCTAAACCATATT------
1 TAAACCCTAAACCATATTAAACCC
* * *
5725864 TAAACCATAAACCATAGTTAAATCG
1 TAAACCCTAAACCATA-TTAAACCC
* * ** *
5725889 TAAACCACGGT-TA-TATCCTAAATCC
1 TAAACC-C--TAAACCATATTAAACCC
* * *
5725914 TAAATCATAAACCATATT-TA---
1 TAAACCCTAAACCATATTAAACCC
*
5725934 -AAACCC-AAAACATAGTTAAACCC
1 TAAACCCTAAACCATA-TTAAACCC
* *
5725957 TAAACCCTAAACTATGGTTAAACCC
1 TAAACCCTAAACCAT-ATTAAACCC
** ***
5725982 TAAACTATAGTTAAACC---TTAAAGTT
1 TAAAC----CCTAAACCATATTAAACCC
* **
5726007 TATACCCTAAATTATGATTAAACCC
1 TAAACCCTAAACCAT-ATTAAACCC
*
5726032 TAAACACTAAACCTTGAATCATAATTAAACCC
1 TAAACCCTAAA-C------CAT-ATTAAACCC
* *
5726064 TAAACACTAAACCATGATTAAATCC
1 TAAACCCTAAACCAT-ATTAAACCC
*
5726089 T-AACCCCAAACCATAGTTAAACCC
1 TAAACCCTAAACCATA-TTAAACCC
* *
5726113 TAAACTCTAAACCATGGTTAAACCC
1 TAAACCCTAAACCAT-ATTAAACCC
* * *
5726138 TAAACCCTAAACCATGGTTAAAACT
1 TAAACCCTAAACCAT-ATTAAACCC
*
5726163 TAAACCCTAAACCATAATTAAACCA
1 TAAACCCTAAACCAT-ATTAAACCC
* * *
5726188 TAAAACCTTAAACCATGGTTAAACAC
1 T-AAACCCTAAACCAT-ATTAAACCC
* * **
5726214 TAAACCTTAAACCCTAAACCACAAACCAC
1 TAAACCCTAAA-CC-ATA--TTAAACC-C
*
5726243 -AAACCCTAAACC---CTAAACCC
1 TAAACCCTAAACCATATTAAACCC
5726263 TAAACCCTAAACC--A-TAAACCC
1 TAAACCCTAAACCATATTAAACCC
* *
5726284 TAAACCCTAAACCATAAACCCTAAACCT
1 TAAACCCTAAACCAT--A--TTAAACCC
5726312 TAAACCCTAAACCATAAACCTTAAACCC
1 TAAACCCTAAACCAT--A--TTAAACCC
5726340 TAAACCCTAAA
1 TAAACCCTAAA
5726351 AATTCACATT
Statistics
Matches: 527, Mismatches: 97, Indels: 129
0.70 0.13 0.17
Matches are distributed among these distances:
17 1 0.00
18 34 0.06
19 10 0.02
20 2 0.00
21 78 0.15
22 1 0.00
23 4 0.01
24 41 0.08
25 220 0.42
26 46 0.09
27 4 0.01
28 57 0.11
29 6 0.01
31 1 0.00
32 22 0.04
ACGTcount: A:0.45, C:0.29, G:0.04, T:0.22
Consensus pattern (24 bp):
TAAACCCTAAACCATATTAAACCC
Found at i:5725735 original size:92 final size:93
Alignment explanation
Indices: 5725635--5725874 Score: 258
Period size: 93 Copynumber: 2.6 Consensus size: 93
5725625 ACCTTAAAGT
** * * * *
5725635 TTAAACCCTAAATTATGATTAAACCCTAAACCTTGAATCATAATTAAACCCT-AAACAC-TAAAC
1 TTAAACCCTAAACCATAATTAAACCCTAAACCCTAAACCATAATTAAACCCTAAAAC-CTTAAAC
* *
5725698 CATGGTTAAATCCTAACCCTAAACCATAG
65 CATAGTTAAACCCTAACCCTAAACCATAG
5725727 TTAAACCCTAAACCATAATTAAACCCTAAACCCTAAACCATAATTAAACCCTAAAACCTTAAACC
1 TTAAACCCTAAACCATAATTAAACCCTAAACCCTAAACCATAATTAAACCCTAAAACCTTAAACC
**
5725792 ATAGTTAAACCCTAAGCTATAAACC----
66 ATAGTTAAACCCTAA-CCCTAAACCATAG
* * * * *
5725817 CTAAACCCTAAACCATAAACCCTAAACCCCAAACCCTAAACCATATTTAAACCATAAA
1 TTAAACCCTAAACCAT-AA--TTAAACCCTAAACCCTAAACCATAATTAAACCCTAAA
5725875 CCATAGTTAA
Statistics
Matches: 127, Mismatches: 15, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
90 15 0.12
91 2 0.02
92 47 0.37
93 56 0.44
94 7 0.06
ACGTcount: A:0.46, C:0.29, G:0.03, T:0.23
Consensus pattern (93 bp):
TTAAACCCTAAACCATAATTAAACCCTAAACCCTAAACCATAATTAAACCCTAAAACCTTAAACC
ATAGTTAAACCCTAACCCTAAACCATAG
Found at i:5725756 original size:7 final size:7
Alignment explanation
Indices: 5725746--5725858 Score: 79
Period size: 7 Copynumber: 15.9 Consensus size: 7
5725736 AAACCATAAT
5725746 TAAACCC
1 TAAACCC
5725753 TAAACCC
1 TAAACCC
*
5725760 TAAACCA
1 TAAACCC
*
5725767 T-AA--T
1 TAAACCC
5725771 TAAACCC
1 TAAACCC
*
5725778 TAAAACCT
1 T-AAACCC
*
5725786 TAAACCATAG
1 TAAACC---C
5725796 TTAAACCC
1 T-AAACCC
* **
5725804 TAAGCTA
1 TAAACCC
5725811 TAAACCC
1 TAAACCC
5725818 TAAACCC
1 TAAACCC
*
5725825 TAAACCA
1 TAAACCC
5725832 TAAACCC
1 TAAACCC
5725839 TAAACCC
1 TAAACCC
*
5725846 CAAACCC
1 TAAACCC
5725853 TAAACC
1 TAAACC
5725859 ATATTTAAAC
Statistics
Matches: 82, Mismatches: 16, Indels: 16
0.72 0.14 0.14
Matches are distributed among these distances:
4 1 0.01
5 2 0.02
6 2 0.02
7 64 0.78
8 7 0.09
10 1 0.01
11 5 0.06
ACGTcount: A:0.46, C:0.35, G:0.02, T:0.18
Consensus pattern (7 bp):
TAAACCC
Found at i:5725781 original size:18 final size:18
Alignment explanation
Indices: 5725712--5725758 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
5725702 GTTAAATCCT
*
5725712 AACCCTAAACCATAGTTA
1 AACCCTAAACCATAATTA
5725730 AACCCTAAACCATAATTA
1 AACCCTAAACCATAATTA
5725748 AACCCTAAACC
1 AACCCTAAACC
5725759 CTAAACCATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.47, C:0.32, G:0.02, T:0.19
Consensus pattern (18 bp):
AACCCTAAACCATAATTA
Found at i:5725823 original size:21 final size:21
Alignment explanation
Indices: 5725728--5725858 Score: 97
Period size: 21 Copynumber: 6.0 Consensus size: 21
5725718 AAACCATAGT
5725728 TAAACCCTAAACCATAATTAAACCC
1 TAAACCCTAAACC---A-TAAACCC
*
5725753 TAAACCCTAAACCAT-AA--T
1 TAAACCCTAAACCATAAACCC
* *
5725771 TAAACCCTAAAACCTTAAACCATAGT
1 TAAACCCT-AAACCATAAACC----C
* *
5725797 TAAACCCTAAGCTATAAACCC
1 TAAACCCTAAACCATAAACCC
5725818 TAAACCCTAAACCATAAACCC
1 TAAACCCTAAACCATAAACCC
* *
5725839 TAAACCCCAAACCCTAAACC
1 TAAACCCTAAACCATAAACC
5725859 ATATTTAAAC
Statistics
Matches: 88, Mismatches: 10, Indels: 20
0.75 0.08 0.17
Matches are distributed among these distances:
18 8 0.09
19 6 0.07
20 4 0.05
21 38 0.43
22 1 0.01
25 22 0.25
26 9 0.10
ACGTcount: A:0.47, C:0.34, G:0.02, T:0.18
Consensus pattern (21 bp):
TAAACCCTAAACCATAAACCC
Found at i:5725874 original size:18 final size:18
Alignment explanation
Indices: 5725847--5725895 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
5725837 CCTAAACCCC
* *
5725847 AAACCCTAAACCATATTT
1 AAACCATAAACCATAGTT
5725865 AAACCATAAACCATAGTT
1 AAACCATAAACCATAGTT
* *
5725883 AAATCGTAAACCA
1 AAACCATAAACCA
5725896 CGGTTATATC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.49, C:0.24, G:0.04, T:0.22
Consensus pattern (18 bp):
AAACCATAAACCATAGTT
Found at i:5725960 original size:43 final size:43
Alignment explanation
Indices: 5725907--5726003 Score: 106
Period size: 43 Copynumber: 2.3 Consensus size: 43
5725897 GGTTATATCC
* * *
5725907 TAAATCCTAAATCATAAACCATATTTAAAACCCAAAAC-ATAGT
1 TAAACCCTAAACCATAAACCATAGTT-AAACCCAAAACTATAGT
* * * *
5725950 TAAACCCTAAACCCTAAACTATGGTTAAACCCTAAACTATAGT
1 TAAACCCTAAACCATAAACCATAGTTAAACCCAAAACTATAGT
*
5725993 TAAACCTTAAA
1 TAAACCCTAAA
5726004 GTTTATACCC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
42 10 0.22
43 35 0.78
ACGTcount: A:0.47, C:0.23, G:0.04, T:0.26
Consensus pattern (43 bp):
TAAACCCTAAACCATAAACCATAGTTAAACCCAAAACTATAGT
Found at i:5725980 original size:18 final size:18
Alignment explanation
Indices: 5725957--5726036 Score: 78
Period size: 18 Copynumber: 4.7 Consensus size: 18
5725947 AGTTAAACCC
5725957 TAAACCCTAAACTATGGT
1 TAAACCCTAAACTATGGT
*
5725975 TAAACCCTAAACTATAGT
1 TAAACCCTAAACTATGGT
* *
5725993 TAAA-CCTTAA--A-GTT
1 TAAACCCTAAACTATGGT
* * *
5726007 TATACCCTAAATTATGAT
1 TAAACCCTAAACTATGGT
5726025 TAAACCCTAAAC
1 TAAACCCTAAAC
5726037 ACTAAACCTT
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
14 4 0.08
15 6 0.12
17 6 0.12
18 33 0.67
ACGTcount: A:0.42, C:0.21, G:0.06, T:0.30
Consensus pattern (18 bp):
TAAACCCTAAACTATGGT
Found at i:5726217 original size:7 final size:7
Alignment explanation
Indices: 5726207--5726350 Score: 193
Period size: 7 Copynumber: 20.6 Consensus size: 7
5726197 AAACCATGGT
*
5726207 TAAACAC
1 TAAACCC
*
5726214 TAAACCT
1 TAAACCC
5726221 TAAACCC
1 TAAACCC
5726228 TAAACCAC
1 TAAACC-C
5726236 -AAACCAC
1 TAAACC-C
5726243 -AAACCC
1 TAAACCC
5726249 TAAACCC
1 TAAACCC
5726256 TAAACCC
1 TAAACCC
5726263 TAAACCC
1 TAAACCC
*
5726270 TAAACCA
1 TAAACCC
5726277 TAAACCC
1 TAAACCC
5726284 TAAACCC
1 TAAACCC
*
5726291 TAAACCA
1 TAAACCC
5726298 TAAACCC
1 TAAACCC
*
5726305 TAAACCT
1 TAAACCC
5726312 TAAACCC
1 TAAACCC
*
5726319 TAAACCA
1 TAAACCC
*
5726326 TAAACCT
1 TAAACCC
5726333 TAAACCC
1 TAAACCC
5726340 TAAACCC
1 TAAACCC
5726347 TAAA
1 TAAA
5726351 AATTCACATT
Statistics
Matches: 123, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
6 1 0.01
7 121 0.98
8 1 0.01
ACGTcount: A:0.48, C:0.37, G:0.00, T:0.15
Consensus pattern (7 bp):
TAAACCC
Found at i:5749355 original size:32 final size:32
Alignment explanation
Indices: 5749307--5749375 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 32
5749297 TTTTCCTCCC
* **
5749307 TTTTTTTTTTCTTTTTTTTTTGGA-TAATATG
1 TTTTTTTTTTCCTTTTTTTGGGGAGTAATATG
5749338 TTTTTATTTTTCCTTTTTTTGGGGAGGTAATATG
1 TTTTT-TTTTTCCTTTTTTTGGGGA-GTAATATG
5749372 TTTT
1 TTTT
5749376 ATTCTTGTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 5 0.16
32 16 0.50
34 11 0.34
ACGTcount: A:0.13, C:0.04, G:0.14, T:0.68
Consensus pattern (32 bp):
TTTTTTTTTTCCTTTTTTTGGGGAGTAATATG
Found at i:5752490 original size:30 final size:30
Alignment explanation
Indices: 5752458--5752650 Score: 228
Period size: 30 Copynumber: 6.5 Consensus size: 30
5752448 AATCTAAAAA
*
5752458 TTATCCTCG-GATTCTCAAGATGTTTGAAAA
1 TTATCC-CGAGATTCTCAAGATGTTTGAAAG
* * *
5752488 TTATCTCGAGATTCTCGAGATGATTGAAAG
1 TTATCCCGAGATTCTCAAGATGTTTGAAAG
* * *
5752518 TTATCCCGGGATTCTCAAGATGTCTGAAAA
1 TTATCCCGAGATTCTCAAGATGTTTGAAAG
** **
5752548 TTATCCCGAGATTCTCGGGATAATTGAAAG
1 TTATCCCGAGATTCTCAAGATGTTTGAAAG
* *
5752578 TTATCCC-AGATTCTCAGGATATTTGAAAG
1 TTATCCCGAGATTCTCAAGATGTTTGAAAG
*
5752607 TTATCCCGAGATTCTCGAGATGTTTGAAAG
1 TTATCCCGAGATTCTCAAGATGTTTGAAAG
*
5752637 TTATCCCGAAATTC
1 TTATCCCGAGATTC
5752651 CTGATTTCTG
Statistics
Matches: 138, Mismatches: 23, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
29 29 0.21
30 109 0.79
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.33
Consensus pattern (30 bp):
TTATCCCGAGATTCTCAAGATGTTTGAAAG
Found at i:5752530 original size:60 final size:59
Alignment explanation
Indices: 5752458--5752644 Score: 275
Period size: 60 Copynumber: 3.1 Consensus size: 59
5752448 AATCTAAAAA
*
5752458 TTATCCTCGGATTCTCAAGATGTTTGAAAATTATCTCGAGATTCTCGAGATGATTGAAAG
1 TTATCC-CGGATTCTCAAGATGTTTGAAAATTATCCCGAGATTCTCGAGATGATTGAAAG
* * *
5752518 TTATCCCGGGATTCTCAAGATGTCTGAAAATTATCCCGAGATTCTCGGGATAATTGAAAG
1 TTATCCC-GGATTCTCAAGATGTTTGAAAATTATCCCGAGATTCTCGAGATGATTGAAAG
* * * * *
5752578 TTATCCCAGATTCTCAGGATATTTGAAAGTTATCCCGAGATTCTCGAGATGTTTGAAAG
1 TTATCCCGGATTCTCAAGATGTTTGAAAATTATCCCGAGATTCTCGAGATGATTGAAAG
5752637 TTATCCCG
1 TTATCCCG
5752645 AAATTCCTGA
Statistics
Matches: 113, Mismatches: 13, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
59 52 0.46
60 61 0.54
ACGTcount: A:0.29, C:0.18, G:0.20, T:0.33
Consensus pattern (59 bp):
TTATCCCGGATTCTCAAGATGTTTGAAAATTATCCCGAGATTCTCGAGATGATTGAAAG
Found at i:5754452 original size:16 final size:17
Alignment explanation
Indices: 5754420--5754455 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
5754410 AATACGTTAT
*
5754420 AAATAAACAAAAGTAAA
1 AAATAAACAAAAATAAA
5754437 AAATAAA-AAAAATAAA
1 AAATAAACAAAAATAAA
5754453 AAA
1 AAA
5754456 CAGTTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.83, C:0.03, G:0.03, T:0.11
Consensus pattern (17 bp):
AAATAAACAAAAATAAA
Found at i:5754474 original size:27 final size:26
Alignment explanation
Indices: 5754444--5754494 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
5754434 AAAAAATAAA
*
5754444 AAAAATAAAAAACAGTTTTAAAAAGTT
1 AAAAAT-AAAAACAGATTTAAAAAGTT
* *
5754471 AAAAATGAACACAGATTTAAAAAG
1 AAAAATAAAAACAGATTTAAAAAG
5754495 AATAAAGGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 15 0.71
27 6 0.29
ACGTcount: A:0.63, C:0.06, G:0.10, T:0.22
Consensus pattern (26 bp):
AAAAATAAAAACAGATTTAAAAAGTT
Found at i:5755354 original size:15 final size:15
Alignment explanation
Indices: 5755334--5755378 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
5755324 CAATTCATAT
*
5755334 TTTATTTTTCTTATA
1 TTTATTTTTCGTATA
5755349 TTTA-TTTTCGTATA
1 TTTATTTTTCGTATA
*
5755363 TTTATTCATTCGTATA
1 TTTATT-TTTCGTATA
5755379 ATTGTTCGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 13 0.50
15 5 0.19
16 8 0.31
ACGTcount: A:0.22, C:0.09, G:0.04, T:0.64
Consensus pattern (15 bp):
TTTATTTTTCGTATA
Found at i:5767193 original size:39 final size:39
Alignment explanation
Indices: 5767149--5767412 Score: 117
Period size: 39 Copynumber: 6.8 Consensus size: 39
5767139 ATTCAACCAT
* ** *
5767149 CCGATCTCTTACCTCGAGCCTAAGGTTGATCACCATTAG
1 CCGATCTCTTACCCCGAGCCTAAGGCAGATCACCATTAA
* * * ** *
5767188 TCGATCTTTTACCCCAAGCCTTGGGCAGATCATCATTAA
1 CCGATCTCTTACCCCGAGCCTAAGGCAGATCACCATTAA
* ** *
5767227 CCGATCTCTTACCCCGAGCTTGGGGCAGATTGTAGCC-TT--
1 CCGATCTCTTACCCCGAGCCTAAGGCAGA-T-CA-CCATTAA
* * ** *
5767266 CTGATCTCTTACCCCGAGCTTGGGGCAGATCACCATTAG
1 CCGATCTCTTACCCCGAGCCTAAGGCAGATCACCATTAA
*** * **
5767305 TTAATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATT--
1 CCGATCTCTTACCCCGAGCCTAAGGCAGA-T-CA-CCATTAA
* * ** * *
5767345 -CGATCTTTTACCTCGAGCCTGGGGCAGATCACCATCAG
1 CCGATCTCTTACCCCGAGCCTAAGGCAGATCACCATTAA
* * **
5767383 CCAATTTCTTACCCCGAGCCTGGGGCAGAT
1 CCGATCTCTTACCCCGAGCCTAAGGCAGAT
5767413 TGCAGCCATC
Statistics
Matches: 182, Mismatches: 31, Indels: 24
0.77 0.13 0.10
Matches are distributed among these distances:
36 6 0.03
37 5 0.03
38 2 0.01
39 156 0.86
40 2 0.01
41 5 0.03
42 6 0.03
ACGTcount: A:0.21, C:0.30, G:0.22, T:0.27
Consensus pattern (39 bp):
CCGATCTCTTACCCCGAGCCTAAGGCAGATCACCATTAA
Found at i:5767272 original size:78 final size:78
Alignment explanation
Indices: 5767188--5767421 Score: 319
Period size: 78 Copynumber: 3.0 Consensus size: 78
5767178 TCACCATTAG
* * * *
5767188 TCGATCTTTTACCCCAAGCCTTGGGCAGATCATCATTAACCGATCTCTTACCCCGAGCTTGGGGC
1 TCGATCTTTTACCCCGAGCCTTGGGCAGATCACCATTAGCCAATCTCTTACCCCGAGCTTGGGGC
*
5767253 AGATTGTAGCC-T
66 AGATTGCAGCCAT
* **
5767265 TCTGATCTCTTACCCCGAG-CTTGGGGCAGATCACCATTAGTTAATCTCTTACCCCGAGCTTGGG
1 TC-GATCTTTTACCCCGAGCCTT-GGGCAGATCACCATTAGCCAATCTCTTACCCCGAGCTTGGG
5767329 GCAGATTGCAGCCAT
64 GCAGATTGCAGCCAT
* * * * *
5767344 TCGATCTTTTACCTCGAGCCTGGGGCAGATCACCATCAGCCAATTTCTTACCCCGAGCCTGGGGC
1 TCGATCTTTTACCCCGAGCCTTGGGCAGATCACCATTAGCCAATCTCTTACCCCGAGCTTGGGGC
5767409 AGATTGCAGCCAT
66 AGATTGCAGCCAT
5767422 CCAATCTCTG
Statistics
Matches: 137, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
77 5 0.04
78 127 0.93
79 5 0.04
ACGTcount: A:0.21, C:0.30, G:0.22, T:0.27
Consensus pattern (78 bp):
TCGATCTTTTACCCCGAGCCTTGGGCAGATCACCATTAGCCAATCTCTTACCCCGAGCTTGGGGC
AGATTGCAGCCAT
Found at i:5767426 original size:39 final size:39
Alignment explanation
Indices: 5767230--5767430 Score: 189
Period size: 39 Copynumber: 5.2 Consensus size: 39
5767220 TCATTAACCG
* * **
5767230 ATCTCTTACCCCGAGCTTGGGGCAGATTGTAGCCTTCTG
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCA
**
5767269 ATCTCTTACCCCGAGCTTGGGGCAGA-T-CA-CCATTAGTTA
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCA-T--CCA
* *
5767308 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATTCG
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCA
* * *
5767347 ATCTTTTACCTCGAGCCTGGGGCAGA-T-CA-CCATCAGCCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCAT---CCA
* *
5767386 ATTTCTTACCCCGAGCCTGGGGCAGATTGCAGCCATCCA
1 ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCA
5767425 ATCTCT
1 ATCTCT
5767431 GAAAAAAATC
Statistics
Matches: 135, Mismatches: 15, Indels: 24
0.78 0.09 0.14
Matches are distributed among these distances:
36 6 0.04
37 4 0.03
38 2 0.01
39 109 0.81
40 2 0.01
41 5 0.04
42 7 0.05
ACGTcount: A:0.20, C:0.31, G:0.22, T:0.27
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCTTGGGGCAGATTGCAGCCATCCA
Found at i:5769608 original size:29 final size:28
Alignment explanation
Indices: 5769538--5769892 Score: 256
Period size: 28 Copynumber: 12.5 Consensus size: 28
5769528 TATTTTCTTT
* *
5769538 AAAAATTATATTTTTCCCTCGAACTTTC
1 AAAAATTACATTTTTCCCTCGAACTTCC
*
5769566 -AAAATTACAATTTTGCCCTCGAACTTCC
1 AAAAATTAC-ATTTTTCCCTCGAACTTCC
* * ** *
5769594 AAAAATCATATTTTTACCCTTAAATTTCTC
1 AAAAATTACATTTTT-CCCTCGAACTTC-C
* * *
5769624 AAAAATTACATTTTGCCCCCGAACTTCT
1 AAAAATTACATTTTTCCCTCGAACTTCC
* * * *
5769652 AAAAATCATATTTTTACCCCCGAACTTCTT
1 AAAAATTACATTTTT-CCCTCGAACTTC-C
* * *
5769682 AAAAATTACA-TTTTCCCCCTAAACTTCT
1 AAAAATTACATTTTTCCCTC-GAACTTCC
*
5769710 AAAAATTACATTTTTACCTCGAACTTCTC
1 AAAAATTACATTTTTCCCTCGAACTTC-C
* * *
5769739 AAAAATCACATTTTACCCT-GAACTTTTC
1 AAAAATTACATTTTTCCCTCGAAC-TTCC
* * * *
5769767 TAAAATTATATTTTACCC-CTGAACTTCT
1 AAAAATTACATTTTTCCCTC-GAACTTCC
*
5769795 AAAAATTACATTTTTACCTCGAACTTCTC
1 AAAAATTACATTTTTCCCTCGAACTTC-C
* *
5769824 AAAAATCACA-TTTTACCTCGAACTTTCC
1 AAAAATTACATTTTTCCCTCGAAC-TTCC
* **
5769852 TAAAATTACA-TTTTCCCTTAAACTTTCC
1 AAAAATTACATTTTTCCCTCGAAC-TTCC
*
5769880 -AAAATTACGTTTT
1 AAAAATTACATTTT
5769893 AACCCCGAAC
Statistics
Matches: 263, Mismatches: 48, Indels: 32
0.77 0.14 0.09
Matches are distributed among these distances:
27 15 0.06
28 139 0.53
29 87 0.33
30 22 0.08
ACGTcount: A:0.34, C:0.25, G:0.03, T:0.38
Consensus pattern (28 bp):
AAAAATTACATTTTTCCCTCGAACTTCC
Found at i:5769800 original size:85 final size:86
Alignment explanation
Indices: 5769537--5769903 Score: 392
Period size: 85 Copynumber: 4.3 Consensus size: 86
5769527 TTATTTTCTT
* * * *
5769537 TAAAAATTATATTTTTCCCTCGAACTT-TC-AAAATTACAATTTTGCCCTCGAAC-TTCCAAAAA
1 TAAAAATTACATTTTTACCTCGAACTTCTCAAAAATCAC-ATTTTACCCTCGAACTTTCCAAAAA
* * * *
5769599 TCATATTTTTACCCTTAAATTTC
65 TTACA-TTTTACCCCTAAACTTC
** * * * *
5769622 TCAAAAATTACATTTTGCCCCCGAACTTCT-AAAAATCATATTTTTACCCCCGAAC-TTCTTAAA
1 T-AAAAATTACATTTTTACCTCGAACTTCTCAAAAATCACA-TTTTACCCTCGAACTTTC-CAAA
*
5769685 AATTACATTTTCCCCCTAAACTTC
63 AATTACATTTTACCCCTAAACTTC
* *
5769709 TAAAAATTACATTTTTACCTCGAACTTCTCAAAAATCACATTTTACCCT-GAACTTTTCTAAAAT
1 TAAAAATTACATTTTTACCTCGAACTTCTCAAAAATCACATTTTACCCTCGAACTTTCCAAAAAT
* *
5769773 TATATTTTACCCCTGAACTTC
66 TACATTTTACCCCTAAACTTC
*
5769794 TAAAAATTACATTTTTACCTCGAACTTCTCAAAAATCACATTTTA-CCTCGAACTTTCCTAAAAT
1 TAAAAATTACATTTTTACCTCGAACTTCTCAAAAATCACATTTTACCCTCGAACTTTCCAAAAAT
*
5769858 TACATTTT-CCCTTAAACTT-
66 TACATTTTACCCCTAAACTTC
* * * *
5769877 TCCAAAATTACGTTTTAACCCCGAACT
1 T-AAAAATTACATTTTTACCTCGAACT
5769904 CTCTGAAACT
Statistics
Matches: 241, Mismatches: 32, Indels: 19
0.83 0.11 0.07
Matches are distributed among these distances:
83 1 0.00
84 33 0.14
85 94 0.39
86 59 0.24
87 46 0.19
88 8 0.03
ACGTcount: A:0.34, C:0.25, G:0.04, T:0.37
Consensus pattern (86 bp):
TAAAAATTACATTTTTACCTCGAACTTCTCAAAAATCACATTTTACCCTCGAACTTTCCAAAAAT
TACATTTTACCCCTAAACTTC
Found at i:5770053 original size:14 final size:14
Alignment explanation
Indices: 5770025--5770059 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
5770015 CTATTCGTAT
*
5770025 TTTATTTTTCTTATA
1 TTTA-TTTTCATATA
5770040 TTTATTTTCATATA
1 TTTATTTTCATATA
5770054 TTTATT
1 TTTATT
5770060 CATTCGTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 15 0.79
15 4 0.21
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTATTTTCATATA
Found at i:5773191 original size:23 final size:23
Alignment explanation
Indices: 5773165--5773365 Score: 209
Period size: 23 Copynumber: 9.0 Consensus size: 23
5773155 TACTGGGTAA
5773165 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
*
5773188 CAGAGAGTACACAAA--G-T-A-
1 CAGAGAGCACACAAAGTGCTAAT
*
5773206 C--TGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
* *
5773227 CAGAGAACACACGAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
** *
5773250 CAGAGAGCACATGAAGTGATAAT
1 CAGAGAGCACACAAAGTGCTAAT
* * *
5773273 AACAGAGAGCACACATAGTTCTAAA
1 --CAGAGAGCACACAAAGTGCTAAT
* *
5773298 CAGAGAGTACACAAAGTACTAAT
1 CAGAGAGCACACAAAGTGCTAAT
*
5773321 CAGAGAGCACACAAAGTACTAAT
1 CAGAGAGCACACAAAGTGCTAAT
*
5773344 CAGAGAGCACACACAGTGCTAA
1 CAGAGAGCACACAAAGTGCTAA
5773366 AAACAGAGAG
Statistics
Matches: 147, Mismatches: 22, Indels: 18
0.79 0.12 0.10
Matches are distributed among these distances:
16 10 0.07
18 2 0.01
19 2 0.01
20 2 0.01
21 2 0.01
23 112 0.76
25 17 0.12
ACGTcount: A:0.45, C:0.20, G:0.20, T:0.14
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAT
Found at i:5773324 original size:71 final size:69
Alignment explanation
Indices: 5773208--5773377 Score: 198
Period size: 71 Copynumber: 2.4 Consensus size: 69
5773198 ACAAAGTACT
* * * * **
5773208 GAGCACACAAAGTGCTAATCAGAGAACACACGAAGTGCTAATCAGAGAGCACATGAAGTGA-TAA
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACTAATCAGAGAGCACACAAAGT-ACTAA
5773272 TAACAGA
65 T--CAGA
* * *
5773279 GAGCACACATAGTTCTAAACAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTACTAAT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACTAATCAGAGAGCACACAAAGTACTAAT
5773344 CAGA
66 CAGA
*
5773348 GAGCACACACAGTGCTAAAAACAGAGAGCA
1 GAGCACACAAAGTGCT--AAACAGAGAGCA
5773378 GGAGACTTGC
Statistics
Matches: 84, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
69 18 0.21
70 1 0.01
71 65 0.77
ACGTcount: A:0.46, C:0.20, G:0.21, T:0.14
Consensus pattern (69 bp):
GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACTAATCAGAGAGCACACAAAGTACTAAT
CAGA
Found at i:5773391 original size:94 final size:94
Alignment explanation
Indices: 5773212--5773398 Score: 243
Period size: 94 Copynumber: 2.0 Consensus size: 94
5773202 AGTACTGAGC
* * * * *
5773212 ACACAAAGTGCTAATCAGAGAACACACGAAGTGCTAATCAGAGAGCACATGAAGTGATAATAACA
1 ACACAAAGTACTAATCAGAGAACACACAAAGTACTAATCAGAGAGCACATCAAGTGATAAAAACA
* *
5773277 GAGAGCACACATAGTTCTAAACAGAGAGT
66 GAGAGCACACAGACTTCTAAACAGAGAGT
* *
5773306 ACACAAAGTACTAATCAGAGAGCACACAAAGTACTAATCAGAGAGCACA-CACAGTGCTAAAAAC
1 ACACAAAGTACTAATCAGAGAACACACAAAGTACTAATCAGAGAGCACATCA-AGTGATAAAAAC
**
5773370 AGAGAGCA-GGAGACTTGCTAAACAGAGAG
65 AGAGAGCACACAGACTT-CTAAACAGAGAG
5773399 CGCGCTAGTG
Statistics
Matches: 80, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
93 5 0.06
94 75 0.94
ACGTcount: A:0.45, C:0.19, G:0.21, T:0.14
Consensus pattern (94 bp):
ACACAAAGTACTAATCAGAGAACACACAAAGTACTAATCAGAGAGCACATCAAGTGATAAAAACA
GAGAGCACACAGACTTCTAAACAGAGAGT
Found at i:5779254 original size:23 final size:23
Alignment explanation
Indices: 5779228--5779428 Score: 202
Period size: 23 Copynumber: 9.0 Consensus size: 23
5779218 TACTGGGTAA
5779228 CAGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
*
5779251 CAGAGAGTACACAAA--G-T-A-
1 CAGAGAGCACACAAAGTGCTAAT
*
5779269 C--TGAGCACACAAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
* *
5779290 CAGAGAACACACGAAGTGCTAAT
1 CAGAGAGCACACAAAGTGCTAAT
** *
5779313 CAGAGAGCACATGAAGTGATAAT
1 CAGAGAGCACACAAAGTGCTAAT
* *
5779336 AACAGAGAGCACACATAGTTCTAAAT
1 --CAGAGAGCACACAAAGTGCT-AAT
* *
5779362 -AGAGAGTACACAAAGTACTAAT
1 CAGAGAGCACACAAAGTGCTAAT
*
5779384 CAGAGAGCACACAAAGTACTAAT
1 CAGAGAGCACACAAAGTGCTAAT
*
5779407 CAGAGAGCACACACAGTGCTAA
1 CAGAGAGCACACAAAGTGCTAA
5779429 AAACAGAGAG
Statistics
Matches: 147, Mismatches: 20, Indels: 22
0.78 0.11 0.12
Matches are distributed among these distances:
16 10 0.07
18 2 0.01
19 2 0.01
20 2 0.01
21 2 0.01
22 3 0.02
23 108 0.73
25 15 0.10
26 3 0.02
ACGTcount: A:0.45, C:0.20, G:0.20, T:0.15
Consensus pattern (23 bp):
CAGAGAGCACACAAAGTGCTAAT
Found at i:5779437 original size:71 final size:70
Alignment explanation
Indices: 5779271--5779440 Score: 191
Period size: 71 Copynumber: 2.4 Consensus size: 70
5779261 ACAAAGTACT
* * * * **
5779271 GAGCACACAAAGTGCTAATCAGAGAACACACGAAGTGCTAATCAGAGAGCACATGAAGTGATAAT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACTAATCAGAGAGCACACAAAGTGATAAT
5779336 AACAGA
66 -ACAGA
* * * *
5779342 GAGCACACATAGTTCTAAATAGAGAGTACACAAAGTACTAATCAGAGAGCACACAAAGT-ACTAA
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACTAATCAGAGAGCACACAAAGTGA-TAA
5779406 T-CAGA
65 TACAGA
*
5779411 GAGCACACACAGTGCTAAAAACAGAGAGCA
1 GAGCACACAAAGTGCT--AAACAGAGAGCA
5779441 GGAGACTTGC
Statistics
Matches: 82, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
69 18 0.22
70 1 0.01
71 63 0.77
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.14
Consensus pattern (70 bp):
GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACTAATCAGAGAGCACACAAAGTGATAAT
ACAGA
Found at i:5779454 original size:94 final size:94
Alignment explanation
Indices: 5779275--5779461 Score: 234
Period size: 94 Copynumber: 2.0 Consensus size: 94
5779265 AGTACTGAGC
* * * * *
5779275 ACACAAAGTGCTAATCAGAGAACACACGAAGTGCTAATCAGAGAGCACATGAAGTGATAATAACA
1 ACACAAAGTACTAATCAGAGAACACACAAAGTACTAATCAGAGAGCACATCAAGTGATAAAAACA
* * *
5779340 GAGAGCACACATAGTTCTAAATAGAGAGT
66 GAGAGCACACAGACTTCTAAACAGAGAGT
* *
5779369 ACACAAAGTACTAATCAGAGAGCACACAAAGTACTAATCAGAGAGCACA-CACAGTGCTAAAAAC
1 ACACAAAGTACTAATCAGAGAACACACAAAGTACTAATCAGAGAGCACATCA-AGTGATAAAAAC
**
5779433 AGAGAGCA-GGAGACTTGCTAAACAGAGAG
65 AGAGAGCACACAGACTT-CTAAACAGAGAG
5779462 CGCGCTAGTG
Statistics
Matches: 79, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
93 5 0.06
94 74 0.94
ACGTcount: A:0.45, C:0.19, G:0.21, T:0.14
Consensus pattern (94 bp):
ACACAAAGTACTAATCAGAGAACACACAAAGTACTAATCAGAGAGCACATCAAGTGATAAAAACA
GAGAGCACACAGACTTCTAAACAGAGAGT
Found at i:5799209 original size:18 final size:18
Alignment explanation
Indices: 5799186--5799221 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
5799176 TAAAATGCCA
5799186 CCGTAAAAACAAAAACCC
1 CCGTAAAAACAAAAACCC
5799204 CCGTAAAAACAAAAACCC
1 CCGTAAAAACAAAAACCC
5799222 TTTAACAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.33, G:0.06, T:0.06
Consensus pattern (18 bp):
CCGTAAAAACAAAAACCC
Found at i:5823349 original size:25 final size:25
Alignment explanation
Indices: 5823333--5823381 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
5823323 AAAATTACTC
*
5823333 GAGAATAAGCTCATTAAGTATAACT
1 GAGAATAAGCTCATTAAGAATAACT
*
5823358 GAGAATAAGCTCATTAAGTATAAC
1 GAGAATAAGCTCATTAAGAATAAC
5823382 AGGAAGCGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.27
Consensus pattern (25 bp):
GAGAATAAGCTCATTAAGAATAACT
Found at i:5829793 original size:39 final size:39
Alignment explanation
Indices: 5829739--5829818 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
5829729 AATGGTTGCC
5829739 CAAGTCATCGCATAAAGTGTAACACCCCTACACCCGGTT
1 CAAGTCATCGCATAAAGTGTAACACCCCTACACCCGGTT
5829778 CAAGTCATCGCATAAAGTGTAACACCCCTACACCCGGTT
1 CAAGTCATCGCATAAAGTGTAACACCCCTACACCCGGTT
5829817 CA
1 CA
5829819 CATGTATAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.31, C:0.34, G:0.15, T:0.20
Consensus pattern (39 bp):
CAAGTCATCGCATAAAGTGTAACACCCCTACACCCGGTT
Found at i:5830820 original size:37 final size:38
Alignment explanation
Indices: 5830777--5830879 Score: 91
Period size: 37 Copynumber: 2.6 Consensus size: 38
5830767 TTCAAAGCAA
*
5830777 TAAAGTGACACCCAGTGTCTCATCG-GCCTAGCCGAAG
1 TAAAGTGACACCCAGTGTCTCATCGAACCTAGCCGAAG
** ** * *
5830814 TAAAGTGGTACCCAGTACCTCATCGAATCTATCCGAAG
1 TAAAGTGACACCCAGTGTCTCATCGAACCTAGCCGAAG
*
5830852 TACAATAATTGACACCCAGTGTCTCATC
1 T---A-AAGTGACACCCAGTGTCTCATC
5830880 AACTCAAGGT
Statistics
Matches: 49, Mismatches: 12, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
37 21 0.43
38 10 0.20
41 1 0.02
42 17 0.35
ACGTcount: A:0.30, C:0.28, G:0.18, T:0.23
Consensus pattern (38 bp):
TAAAGTGACACCCAGTGTCTCATCGAACCTAGCCGAAG
Found at i:5831009 original size:6 final size:6
Alignment explanation
Indices: 5830984--5831040 Score: 87
Period size: 6 Copynumber: 9.5 Consensus size: 6
5830974 ACAATTCATA
* * *
5830984 TCACTT TCAATT CCAATT TCACTT TCACTT TCACTT TCACTT TCACTT
1 TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT TCACTT
5831032 TCACTT TCA
1 TCACTT TCA
5831041 ATTTTGATCA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.21, C:0.32, G:0.00, T:0.47
Consensus pattern (6 bp):
TCACTT
Found at i:5834805 original size:21 final size:21
Alignment explanation
Indices: 5834764--5834805 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5834754 GATATACTGA
*
5834764 ACTAACAGTGAGTACCGAAGT
1 ACTAACAGTGAGTACAGAAGT
* *
5834785 ACTATCAGTGAGTACATAAGT
1 ACTAACAGTGAGTACAGAAGT
5834806 GCTGGGGAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (21 bp):
ACTAACAGTGAGTACAGAAGT
Found at i:5834937 original size:23 final size:23
Alignment explanation
Indices: 5834816--5834937 Score: 140
Period size: 23 Copynumber: 5.3 Consensus size: 23
5834806 GCTGGGGAAA
* * *
5834816 CAGTAAGTACACACAGTGCAAAT
1 CAGTAAGCACACATAGTGCGAAT
* * * *
5834839 TAGTAGGCACACATAGTGCAAAA
1 CAGTAAGCACACATAGTGCGAAT
5834862 CAGTAAGCACACATAGTGCGAAT
1 CAGTAAGCACACATAGTGCGAAT
*
5834885 CAGTAAGCACATATA-TGCGAAT
1 CAGTAAGCACACATAGTGCGAAT
*
5834907 CAGTAAGCACACACAGTGCTGAA-
1 CAGTAAGCACACATAGTGC-GAAT
5834930 CAGTAAGC
1 CAGTAAGC
5834938 GCGCTAATGT
Statistics
Matches: 85, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
22 20 0.24
23 62 0.73
24 3 0.04
ACGTcount: A:0.41, C:0.21, G:0.20, T:0.17
Consensus pattern (23 bp):
CAGTAAGCACACATAGTGCGAAT
Found at i:5840399 original size:111 final size:111
Alignment explanation
Indices: 5840263--5840477 Score: 301
Period size: 111 Copynumber: 1.9 Consensus size: 111
5840253 TATGACGCAG
***
5840263 AATTTTAAACTTTAAAAACACTTAAATATAATTGATGAGATATTGCCATGTAGTAAAAAA-T-AT
1 AATTTTAAACTTTAAAAACACTTAAATATAACCAATGAGATATTGCCATGTAGTAAAAAATTAAT
5840326 TAAAAAATAAAATATAATTAAATAATCAAAACTTAAAAAAAAACCCA
66 TAAAAAATAAAATATAATTAAATAATCAAAAC-TAAAAAAAAACCCA
* *
5840373 AATTTTGAAA-TTCTAAAAACACTTAAATTTAACCAATGAGATATTGTCATGTAGTAAAAAATTA
1 AATTTT-AAACTT-TAAAAACACTTAAATATAACCAATGAGATATTGCCATGTAGTAAAAAATT-
* * *
5840437 AATTAAAAAGTAAATTGTAATTAAATAATCAAAACTAAAAA
63 AATTAAAAAATAAAATATAATTAAATAATCAAAACTAAAAA
5840478 GAGCCATGGC
Statistics
Matches: 92, Mismatches: 8, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
110 8 0.09
111 46 0.50
112 1 0.01
113 6 0.07
114 31 0.34
ACGTcount: A:0.55, C:0.08, G:0.07, T:0.30
Consensus pattern (111 bp):
AATTTTAAACTTTAAAAACACTTAAATATAACCAATGAGATATTGCCATGTAGTAAAAAATTAAT
TAAAAAATAAAATATAATTAAATAATCAAAACTAAAAAAAAACCCA
Found at i:5841412 original size:32 final size:32
Alignment explanation
Indices: 5841363--5841424 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
5841353 TTTTTTGACC
*
5841363 TAATTTGGTACTCAAACTTGACACTTTTTTCT
1 TAATTTAGTACTCAAACTTGACACTTTTTTCT
*
5841395 TAATTTAGTA-TCTAAACTTTACACTTTTTT
1 TAATTTAGTACTC-AAACTTGACACTTTTTT
5841425 TAAGTTGGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 2 0.07
32 25 0.93
ACGTcount: A:0.27, C:0.16, G:0.06, T:0.50
Consensus pattern (32 bp):
TAATTTAGTACTCAAACTTGACACTTTTTTCT
Found at i:5841443 original size:30 final size:32
Alignment explanation
Indices: 5841367--5841444 Score: 90
Period size: 30 Copynumber: 2.5 Consensus size: 32
5841357 TTGACCTAAT
* * *
5841367 TTGGTACTCAAACTTGACACTTTTTTCTTAAT
1 TTGGTACTTAAACTTTACACTTTTTTCTTAAG
*
5841399 TTAGTA-TCTAAACTTTACAC-TTTTT-TTAAG
1 TTGGTACT-TAAACTTTACACTTTTTTCTTAAG
5841429 TTGGTACTTAAACTTT
1 TTGGTACTTAAACTTT
5841445 TTGGGATCCA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
30 17 0.44
31 7 0.18
32 15 0.38
ACGTcount: A:0.27, C:0.15, G:0.09, T:0.49
Consensus pattern (32 bp):
TTGGTACTTAAACTTTACACTTTTTTCTTAAG
Found at i:5843136 original size:14 final size:15
Alignment explanation
Indices: 5843106--5843139 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
5843096 TAGATATGAC
5843106 ATAATCTAATATATT
1 ATAATCTAATATATT
*
5843121 ATAATC-AATTTATT
1 ATAATCTAATATATT
5843135 ATAAT
1 ATAAT
5843140 GTTACCATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (15 bp):
ATAATCTAATATATT
Found at i:5846020 original size:80 final size:80
Alignment explanation
Indices: 5845885--5846032 Score: 203
Period size: 80 Copynumber: 1.9 Consensus size: 80
5845875 AAACCATTGA
* *
5845885 TTAATCCAAATAGAGCTGGGCTCACTTACTGCGGTTTATCCGCTAGGCACTAGGTGCCATGAAAT
1 TTAATCCAAATAGAGCTGAGCTCACTTACTGCGATTTATCCGCTAGGCACTAGGTGCCATGAAAT
5845950 GACAGATTTTGTTGG
66 GACAGATTTTGTTGG
* *
5845965 TTAATCCAACTAGAGCTGAGCTC-CTTTA-TCGCGATTTATTCGCTAGGCA-TCAGGTGCCATGA
1 TTAATCCAAATAGAGCTGAGCTCAC-TTACT-GCGATTTATCCGCTAGGCACT-AGGTGCCATGA
*
5846027 ATTGAC
63 AATGAC
5846033 GAACTTGGTT
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
79 3 0.05
80 57 0.95
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.30
Consensus pattern (80 bp):
TTAATCCAAATAGAGCTGAGCTCACTTACTGCGATTTATCCGCTAGGCACTAGGTGCCATGAAAT
GACAGATTTTGTTGG
Found at i:5862105 original size:58 final size:57
Alignment explanation
Indices: 5861977--5862155 Score: 189
Period size: 58 Copynumber: 3.0 Consensus size: 57
5861967 GGTATCTCTG
* * * * *
5861977 AACTT-ATCATTTTTTTTAATTTGGTATTTAAATTTTTTTTATCCAATTTAATATTTG
1 AACTTAAT-ATTTTTTTTAATTTGGTACTTAAATTTTTTTAATCCAATTTGATACTTA
* *
5862034 AGCTTAACAATTTTTTTTAATTTGGTACTTAAATTTTTTTGAATCCAATTTGATACTTA
1 AACTTAA-TATTTTTTTTAATTTGGTACTTAAATTTTTTT-AATCCAATTTGATACTTA
* * * *
5862093 AACTTAATATTTTTTTCCTAATTTGGTACATAAGCTTTTTTTAGATTCAATTTGATACCTA
1 AACTTAATATTTTTTT--TAATTTGGTACTTAA-ATTTTTTTA-ATCCAATTTGATACTTA
5862154 AA
1 AA
5862156 TTTATAAAAT
Statistics
Matches: 102, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
57 4 0.04
58 39 0.38
59 20 0.20
60 15 0.15
61 24 0.24
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (57 bp):
AACTTAATATTTTTTTTAATTTGGTACTTAAATTTTTTTAATCCAATTTGATACTTA
Found at i:5862354 original size:58 final size:57
Alignment explanation
Indices: 5862292--5862400 Score: 130
Period size: 58 Copynumber: 1.9 Consensus size: 57
5862282 AAATAATATT
* * * *
5862292 AAAAAAATT-AGTTATCAAATTAAGAAAAATAATCAAGTTCAGGTACCAAATTGGATCC
1 AAAAAAATTAAG-TACCAAATTAAAAAAAAT-ATCAAATTCAAGTACCAAATTGGATCC
* * *
5862350 AAAAAATTTAAGTACCAAGTTAAAAAAAATATCAAATTTAAGTACCAAATT
1 AAAAAAATTAAGTACCAAATTAAAAAAAATATCAAATTCAAGTACCAAATT
5862401 AAAAAAATAT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
57 18 0.42
58 23 0.53
59 2 0.05
ACGTcount: A:0.53, C:0.11, G:0.09, T:0.27
Consensus pattern (57 bp):
AAAAAAATTAAGTACCAAATTAAAAAAAATATCAAATTCAAGTACCAAATTGGATCC
Found at i:5862414 original size:29 final size:30
Alignment explanation
Indices: 5862353--5862416 Score: 112
Period size: 30 Copynumber: 2.2 Consensus size: 30
5862343 TGGATCCAAA
*
5862353 AAATTTAAGTACCAAGTTAAAAAAAATATC
1 AAATTTAAGTACCAAATTAAAAAAAATATC
5862383 AAATTTAAGTACCAAATT-AAAAAAATATC
1 AAATTTAAGTACCAAATTAAAAAAAATATC
5862412 AAATT
1 AAATT
5862417 CAAATATTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 16 0.48
30 17 0.52
ACGTcount: A:0.58, C:0.09, G:0.05, T:0.28
Consensus pattern (30 bp):
AAATTTAAGTACCAAATTAAAAAAAATATC
Found at i:5862428 original size:29 final size:29
Alignment explanation
Indices: 5862353--5862422 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
5862343 TGGATCCAAA
* * *
5862353 AAATTTAAGTACCAAGTTAAAAAAAATATC
1 AAATTCAAATACCAAATT-AAAAAAATATC
* *
5862383 AAATTTAAGTACCAAATTAAAAAAATATC
1 AAATTCAAATACCAAATTAAAAAAATATC
5862412 AAATTCAAATA
1 AAATTCAAATA
5862423 TTAAATATGT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
29 20 0.54
30 17 0.46
ACGTcount: A:0.59, C:0.10, G:0.04, T:0.27
Consensus pattern (29 bp):
AAATTCAAATACCAAATTAAAAAAATATC
Found at i:5887752 original size:23 final size:23
Alignment explanation
Indices: 5887678--5887915 Score: 181
Period size: 23 Copynumber: 10.5 Consensus size: 23
5887668 TAAACGGAAC
* * *
5887678 AAACAGAGAGTAC-CGAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
* *
5887700 GAACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
5887722 GGGCAACAGAGAGCACACAAAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
*
5887748 AAACAGAGAGTACACAAA--G-T
1 AAACAGAGAGCACACAAAGTGCT
*
5887768 --AC--TGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
5887787 AATCAGAGAGCACACGAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* * *
5887810 AATCGGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
5887833 AATAACAGAGAGCACA-AGACGTGCT
1 -A-AACAGAGAGCACACA-AAGTGCT
* *
5887858 AAACGGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
5887881 AATCAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
5887904 AATCAGAGAGCA
1 AAACAGAGAGCA
5887916 TGCTAGTGTT
Statistics
Matches: 175, Mismatches: 25, Indels: 31
0.76 0.11 0.13
Matches are distributed among these distances:
16 10 0.06
18 3 0.02
19 1 0.01
20 1 0.01
21 2 0.01
22 17 0.10
23 101 0.58
24 4 0.02
25 29 0.17
26 7 0.04
ACGTcount: A:0.42, C:0.22, G:0.25, T:0.12
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:5887786 original size:39 final size:39
Alignment explanation
Indices: 5887732--5887806 Score: 123
Period size: 39 Copynumber: 1.9 Consensus size: 39
5887722 GGGCAACAGA
*
5887732 GAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
* *
5887771 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGT
1 GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGT
5887807 GCTAATCGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (39 bp):
GAGCACACAAAGTGCTAAACAGAGAGCACACAAAGTACT
Found at i:5887845 original size:48 final size:46
Alignment explanation
Indices: 5887771--5887915 Score: 211
Period size: 46 Copynumber: 3.1 Consensus size: 46
5887761 ACAAAGTACT
*
5887771 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGTGCTAATCGGA
1 GAGCACACACAGTGCTAATCAGAGAGCACACGAAGTGCTAATCGGA
* * *
5887817 GAGCACACACAGTGCTAATAACAGAGAGCACAAGACGTGCTAAACGGA
1 GAGCACACACAGTGCTAAT--CAGAGAGCACACGAAGTGCTAATCGGA
*
5887865 GAGCACACACAGTGCTAATCAGAGAGCACAC-ACAGTGCTAATCAGA
1 GAGCACACACAGTGCTAATCAGAGAGCACACGA-AGTGCTAATCGGA
5887911 GAGCA
1 GAGCA
5887916 TGCTAGTGTT
Statistics
Matches: 88, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
45 1 0.01
46 44 0.50
48 43 0.49
ACGTcount: A:0.40, C:0.23, G:0.25, T:0.12
Consensus pattern (46 bp):
GAGCACACACAGTGCTAATCAGAGAGCACACGAAGTGCTAATCGGA
Found at i:5887890 original size:71 final size:69
Alignment explanation
Indices: 5887782--5887915 Score: 207
Period size: 71 Copynumber: 1.9 Consensus size: 69
5887772 AGCACACAAA
* *
5887782 GTGCTAATCAGAGAGCACACGAAGTGCTAATCGGAGAGCACACACAGTGCTAATAACAGAGAGCA
1 GTGCTAAACAGAGAGCACACGAAGTGCTAATCAGAGAGCACACACAGTGCTAAT--CAGAGAGCA
5887847 CAAGAC
64 CAAGAC
*
5887853 GTGCTAAACGGAGAGCACAC-ACAGTGCTAATCAGAGAGCACACACAGTGCTAATCAGAGAGCA
1 GTGCTAAACAGAGAGCACACGA-AGTGCTAATCAGAGAGCACACACAGTGCTAATCAGAGAGCA
5887916 TGCTAGTGTT
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
69 9 0.15
70 1 0.02
71 49 0.83
ACGTcount: A:0.39, C:0.23, G:0.25, T:0.13
Consensus pattern (69 bp):
GTGCTAAACAGAGAGCACACGAAGTGCTAATCAGAGAGCACACACAGTGCTAATCAGAGAGCACA
AGAC
Done.