Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000761.1 Hibiscus syriacus cultivar Beakdansim tig00001478_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 5609167
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 10 of 23
Found at i:2581915 original size:28 final size:27
Alignment explanation
Indices: 2581884--2581958 Score: 71
Period size: 29 Copynumber: 2.6 Consensus size: 27
2581874 TTATATATAT
*
2581884 ATATATTAATATAGTATAATTTTTTAAA
1 ATATATTAATATA-TATAAGTTTTTAAA
2581912 ATATA-TATATATATAATATAGTTTTTAAA
1 ATATATTA-ATATAT-ATA-AGTTTTTAAA
* *
2581941 ACATTTTGAATATATATA
1 ATATATT-AATATATATA
2581959 TATATATATA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
27 3 0.08
28 13 0.33
29 15 0.38
30 7 0.18
31 1 0.03
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.48
Consensus pattern (27 bp):
ATATATTAATATATATAAGTTTTTAAA
Found at i:2581916 original size:30 final size:29
Alignment explanation
Indices: 2581880--2581941 Score: 79
Period size: 29 Copynumber: 2.0 Consensus size: 29
2581870 TTTGTTATAT
* *
2581880 ATATATATATTAATATAGTATAATTTTTTAAA
1 ATATATATA-T-ATATAATAT-AGTTTTTAAA
2581912 ATATATATATATATAATATAGTTTTTAAA
1 ATATATATATATATAATATAGTTTTTAAA
2581941 A
1 A
2581942 CATTTTGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 10 0.36
30 8 0.29
31 1 0.04
32 9 0.32
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (29 bp):
ATATATATATATATAATATAGTTTTTAAA
Found at i:2582001 original size:37 final size:37
Alignment explanation
Indices: 2581958--2582369 Score: 272
Period size: 37 Copynumber: 11.2 Consensus size: 37
2581948 GAATATATAT
*
2581958 ATATATATATATAATATAGTTTTTGAAAACATTATGAAA
1 ATATATATATAT-ATATAGTTTTT-AAAACATTTTGAAA
*
2581997 ATATATATATAATATATAGTTTTTTAAACATTTTGAAA
1 ATATATATAT-ATATATAGTTTTTAAAACATTTTGAAA
2582035 ACT-TATATA-ATATATAGTTTTTAAAAACATTTTGAAA
1 A-TATATATATATATATAGTTTTT-AAAACATTTTGAAA
* * *
2582072 ACT-TATATA-ATATATAGTTTTTAAAAAATATAT-ATA
1 A-TATATATATATATATAGTTTTTAAAACAT-TTTGAAA
* * * * * * *
2582108 TTATGA-ATATATATATA-TATATATATATATATAT-ATAT
1 ATAT-ATATATATATATAGTTTTTA-AAACAT-TTTGA-AA
* *
2582146 ATATATATATAATATATAGTTGTTCAAAGCATTTTGAAA
1 ATATATATAT-ATATATAGTT-TTTAAAACATTTTGAAA
*
2582185 AAATATATATAATATATAGTTTTTAAAACATTTTGAAA
1 ATATATATAT-ATATATAGTTTTTAAAACATTTTGAAA
****
2582223 ATATATATA-ATATATAG-TTTTAATTTGTTTTG-AA
1 ATATATATATATATATAGTTTTTAAAACATTTTGAAA
*
2582257 A-ATATATA-ATATATAGTTTTGAAAACATTTT-AAA
1 ATATATATATATATATAGTTTTTAAAACATTTTGAAA
* * *
2582291 ACA-ATA-ATATACAT--TTTTTAAAAAATATTTTTGAAA
1 ATATATATATATATATAGTTTTT--AAAACA-TTTTGAAA
* * *
2582327 ATGTATATA-ATATA-A-TTTTGAAAATATTTTTGAAA
1 ATATATATATATATATAGTTTTTAAAACA-TTTTGAAA
*
2582362 GTATATAT
1 ATATATAT
2582370 TAGTTTTAAA
Statistics
Matches: 304, Mismatches: 44, Indels: 54
0.76 0.11 0.13
Matches are distributed among these distances:
32 4 0.01
33 16 0.05
34 28 0.09
35 38 0.12
36 41 0.13
37 66 0.22
38 50 0.16
39 52 0.17
40 7 0.02
41 2 0.01
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.45
Consensus pattern (37 bp):
ATATATATATATATATAGTTTTTAAAACATTTTGAAA
Found at i:2582104 original size:2 final size:2
Alignment explanation
Indices: 2582099--2582163 Score: 100
Period size: 2 Copynumber: 33.5 Consensus size: 2
2582089 TTTTTAAAAA
2582099 AT AT AT AT AT -T AT GA- AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2582140 AT AT AT AT AT AT AT AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2582164 GTTGTTCAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
1 3 0.05
2 55 0.93
3 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2582494 original size:28 final size:28
Alignment explanation
Indices: 2582461--2582519 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
2582451 TAAAATGTTA
* *
2582461 TTTATTTATTA-TTATTATTTTTATTTAT
1 TTTATTTATCATTTA-TATATTTATTTAT
*
2582489 TTTATTTGTCATTTATATATTTATTTAT
1 TTTATTTATCATTTATATATTTATTTAT
2582517 TTT
1 TTT
2582520 TTCCTTCTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 24 0.89
29 3 0.11
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73
Consensus pattern (28 bp):
TTTATTTATCATTTATATATTTATTTAT
Found at i:2583690 original size:9 final size:8
Alignment explanation
Indices: 2583671--2583747 Score: 52
Period size: 8 Copynumber: 9.6 Consensus size: 8
2583661 ATAATTTAAC
2583671 ATTTTTTT
1 ATTTTTTT
2583679 ATTTTATTT
1 ATTTT-TTT
*
2583688 ATTTTTTCC
1 ATTTTTT-T
**
2583697 ATTGATTT
1 ATTTTTTT
2583705 ATTTCTTTT
1 ATTT-TTTT
*
2583714 -TTTTATT
1 ATTTTTTT
*
2583721 ATTATTTT
1 ATTTTTTT
2583729 A--TTTTT
1 ATTTTTTT
*
2583735 ATGTTTTT
1 ATTTTTTT
2583743 ATTTT
1 ATTTT
2583748 ATATCTAACA
Statistics
Matches: 52, Mismatches: 11, Indels: 12
0.69 0.15 0.16
Matches are distributed among these distances:
6 5 0.10
7 3 0.06
8 28 0.54
9 16 0.31
ACGTcount: A:0.17, C:0.04, G:0.03, T:0.77
Consensus pattern (8 bp):
ATTTTTTT
Found at i:2585255 original size:24 final size:25
Alignment explanation
Indices: 2585211--2585274 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
2585201 AATATTTATA
**
2585211 AATATATAAATAATAAAATTAAATGAT
1 AATATATAAATAAT--AATTAAAAAAT
2585238 AATATATAAATAAT-ATTAAAAAAT
1 AATATATAAATAATAATTAAAAAAT
*
2585262 AACATAT-AATAAT
1 AATATATAAATAAT
2585275 TTAGTCAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 6 0.18
24 14 0.41
27 14 0.41
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (25 bp):
AATATATAAATAATAATTAAAAAAT
Found at i:2589959 original size:92 final size:92
Alignment explanation
Indices: 2589802--2589985 Score: 368
Period size: 92 Copynumber: 2.0 Consensus size: 92
2589792 TCAAGAATGT
2589802 GTTATTTATATCAATCTGACGCAGCTGCCACCGCCTTGCTACAGCTAACGACAAGACCACATAAA
1 GTTATTTATATCAATCTGACGCAGCTGCCACCGCCTTGCTACAGCTAACGACAAGACCACATAAA
2589867 TTATATGGAACTTAATTACTGGGCTAA
66 TTATATGGAACTTAATTACTGGGCTAA
2589894 GTTATTTATATCAATCTGACGCAGCTGCCACCGCCTTGCTACAGCTAACGACAAGACCACATAAA
1 GTTATTTATATCAATCTGACGCAGCTGCCACCGCCTTGCTACAGCTAACGACAAGACCACATAAA
2589959 TTATATGGAACTTAATTACTGGGCTAA
66 TTATATGGAACTTAATTACTGGGCTAA
2589986 AGGTTTCAGT
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
92 92 1.00
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (92 bp):
GTTATTTATATCAATCTGACGCAGCTGCCACCGCCTTGCTACAGCTAACGACAAGACCACATAAA
TTATATGGAACTTAATTACTGGGCTAA
Found at i:2594470 original size:77 final size:76
Alignment explanation
Indices: 2594318--2594470 Score: 254
Period size: 77 Copynumber: 2.0 Consensus size: 76
2594308 GAAATGTGTG
*
2594318 TATATATATATATATTCATTAATAACAAACATATATATTATCATGAATGAGAATATTATTATTTT
1 TATATATATATATATTCATTAAAAACAAACATATATATTATCATGAATGAGAATATTATTATTTT
*
2594383 ATTATATGATA
66 ATAATATGATA
2594394 TATATATATATATATTCATTAAAAACAAACACGTATATA-TATCATGAATGAGAATATTATTATT
1 TATATATATATATATTCATTAAAAACAAACA--TATATATTATCATGAATGAGAATATTATTATT
*
2594458 TTCTAATATGATA
64 TTATAATATGATA
2594471 CTTTTAAATA
Statistics
Matches: 72, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
76 30 0.42
77 36 0.50
78 6 0.08
ACGTcount: A:0.45, C:0.07, G:0.06, T:0.42
Consensus pattern (76 bp):
TATATATATATATATTCATTAAAAACAAACATATATATTATCATGAATGAGAATATTATTATTTT
ATAATATGATA
Found at i:2599408 original size:24 final size:25
Alignment explanation
Indices: 2599381--2599427 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
2599371 TTTAAGTACT
2599381 TAAAGTA-TTTTTGGTCAAAATACC
1 TAAAGTATTTTTTGGTCAAAATACC
2599405 TAAAGTATTTTTTGGTCAAAATA
1 TAAAGTATTTTTTGGTCAAAATA
2599428 GGTACCTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (25 bp):
TAAAGTATTTTTTGGTCAAAATACC
Found at i:2599434 original size:29 final size:26
Alignment explanation
Indices: 2599374--2599442 Score: 88
Period size: 29 Copynumber: 2.6 Consensus size: 26
2599364 TTTTTTATTT
*
2599374 AAGTACTTAAAGTA-TTTTTGGTCAA
1 AAGTACCTAAAGTATTTTTTGGTCAA
2599399 AA-TACCTAAAGTATTTTTTGGTCAAA
1 AAGTACCTAAAGTATTTTTTGGTC-AA
2599425 ATAGGTACCTAAAGTATT
1 A-A-GTACCTAAAGTATT
2599443 CAATTTTTTC
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
24 10 0.26
25 11 0.29
26 3 0.08
27 1 0.03
29 13 0.34
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (26 bp):
AAGTACCTAAAGTATTTTTTGGTCAA
Found at i:2601827 original size:21 final size:20
Alignment explanation
Indices: 2601790--2601828 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
2601780 TCAAAATCAT
* *
2601790 TTTTCAAAATTTCATTTTCA
1 TTTTCAAAATCTAATTTTCA
2601810 TTTTCAAAAATCTAATTTT
1 TTTTC-AAAATCTAATTTT
2601829 GCTTTCAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.33, C:0.13, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTTCAAAATCTAATTTTCA
Found at i:2604757 original size:30 final size:30
Alignment explanation
Indices: 2604723--2604789 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
2604713 GGGCTGACAA
* *
2604723 TGAACTAGCTGAAAACTGGTAAAACCGGGG
1 TGAACCAGCTGAAAACTGGCAAAACCGGGG
* * **
2604753 TGAACCGGTTGAAAACTGGCAAAACCGGTT
1 TGAACCAGCTGAAAACTGGCAAAACCGGGG
2604783 TGAACCA
1 TGAACCA
2604790 CCGGTTCACC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.36, C:0.19, G:0.27, T:0.18
Consensus pattern (30 bp):
TGAACCAGCTGAAAACTGGCAAAACCGGGG
Found at i:2606152 original size:22 final size:23
Alignment explanation
Indices: 2606092--2606153 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 23
2606082 AGTATACAAA
* *
2606092 TAATATTATTTATTAAAAATAAT
1 TAATATAATTTATTTAAAATAAT
2606115 TAATATAA-TTATTTTAAAAT-AT
1 TAATATAATTTA-TTTAAAATAAT
2606137 TGAA-ATAATTTATTTAA
1 T-AATATAATTTATTTAA
2606154 TATTATTTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
22 15 0.44
23 19 0.56
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
TAATATAATTTATTTAAAATAAT
Found at i:2606304 original size:29 final size:28
Alignment explanation
Indices: 2606270--2606325 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
2606260 ATAATTTATT
*
2606270 ATATATTGTTAAAATAAAAATTTAATATC
1 ATATATTATTAAAAT-AAAATTTAATATC
* *
2606299 ATATATTATTATAATATAATTTAATAT
1 ATATATTATTAAAATAAAATTTAATAT
2606326 GTTATTATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 11 0.46
29 13 0.54
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (28 bp):
ATATATTATTAAAATAAAATTTAATATC
Found at i:2606651 original size:72 final size:73
Alignment explanation
Indices: 2606549--2606743 Score: 286
Period size: 72 Copynumber: 2.6 Consensus size: 73
2606539 ATATGATAGT
* * *
2606549 ATATAATATATAGGTTTGAAAAATGGTTTTGAAAACATATAATATATAGTTTTTAAAAGA-CTAT
1 ATATAATATATA-GTTTTAAAAATGGTTTTGAAAACATATAATATATAGTGTTTAAAA-ATCGAT
2606613 TTTTGAAAA-
64 TTTTGAAAAC
2606622 ATATAATATATAGTTTTAAAAATGGTTTTGAAAACATATAATATATAGTGTTTAAAAATCGATTT
1 ATATAATATATAGTTTTAAAAATGGTTTTGAAAACATATAATATATAGTGTTTAAAAATCGATTT
2606687 TTGAAAAC
66 TTGAAAAC
*
2606695 ATATAATATATAGTTTTTAAAAACGGTTTTTGAAAACGTATATAATATA
1 ATATAATATATAG-TTTTAAAAATGG-TTTTGAAAAC--ATATAATATA
2606744 GGTTTGAAAA
Statistics
Matches: 112, Mismatches: 4, Indels: 8
0.90 0.03 0.06
Matches are distributed among these distances:
71 1 0.01
72 55 0.49
73 25 0.22
74 11 0.10
75 10 0.09
77 10 0.09
ACGTcount: A:0.45, C:0.04, G:0.11, T:0.40
Consensus pattern (73 bp):
ATATAATATATAGTTTTAAAAATGGTTTTGAAAACATATAATATATAGTGTTTAAAAATCGATTT
TTGAAAAC
Found at i:2606743 original size:110 final size:108
Alignment explanation
Indices: 2606549--2606753 Score: 290
Period size: 110 Copynumber: 1.9 Consensus size: 108
2606539 ATATGATAGT
*
2606549 ATATAATATATAGGTTTGAAAAATGGTTTTGAAAACATATAATATATAGTTTTTAAAAGACTATT
1 ATATAATATATAGGTTTGAAAAATGGTTTTGAAAACATATAATATATAGTTTTTAAAAGACGATT
*
2606614 TTTGAAAAATATAATATATAGTTTTAAAAATGGTTTTGAAAAC
66 TTTGAAAAATATAATATATAGGTTTAAAAATGGTTTTGAAAAC
*
2606657 ATATAATATATAGTGTTT-AAAAATCGATTTTTGAAAACATATAATATATAGTTTTTAAAA-ACG
1 ATATAATATATAG-GTTTGAAAAAT-G-GTTTTGAAAACATATAATATATAGTTTTTAAAAGACG
* * *
2606720 GTTTTTGAAAACGTAT-ATAATATAGGTTTGAAAA
63 ATTTTTGAAAA-ATATAAT-ATATAGGTTTAAAAA
2606754 CATATATACA
Statistics
Matches: 86, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
108 19 0.22
109 19 0.22
110 48 0.56
ACGTcount: A:0.45, C:0.03, G:0.12, T:0.40
Consensus pattern (108 bp):
ATATAATATATAGGTTTGAAAAATGGTTTTGAAAACATATAATATATAGTTTTTAAAAGACGATT
TTTGAAAAATATAATATATAGGTTTAAAAATGGTTTTGAAAAC
Found at i:2606744 original size:37 final size:37
Alignment explanation
Indices: 2606549--2606743 Score: 254
Period size: 38 Copynumber: 5.3 Consensus size: 37
2606539 ATATGATAGT
* * *
2606549 ATATAATATATAGGTTTGAAAAATGG-TTTTGAAAAC
1 ATATAATATATAGTTTTTAAAAACGGTTTTTGAAAAC
**
2606585 ATATAATATATAGTTTTTAAAAGACTATTTTTGAAAA-
1 ATATAATATATAGTTTTTAAAA-ACGGTTTTTGAAAAC
*
2606622 ATATAATATATAG-TTTTAAAAATGG-TTTTGAAAAC
1 ATATAATATATAGTTTTTAAAAACGGTTTTTGAAAAC
* *
2606657 ATATAATATATAGTGTTTAAAAATCGATTTTTGAAAAC
1 ATATAATATATAGTTTTTAAAAA-CGGTTTTTGAAAAC
2606695 ATATAATATATAGTTTTTAAAAACGGTTTTTGAAAAC
1 ATATAATATATAGTTTTTAAAAACGGTTTTTGAAAAC
2606732 GTATATAATATA
1 --ATATAATATA
2606744 GGTTTGAAAA
Statistics
Matches: 138, Mismatches: 13, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
34 9 0.07
35 14 0.10
36 36 0.26
37 28 0.20
38 41 0.30
39 10 0.07
ACGTcount: A:0.45, C:0.04, G:0.11, T:0.40
Consensus pattern (37 bp):
ATATAATATATAGTTTTTAAAAACGGTTTTTGAAAAC
Found at i:2606751 original size:23 final size:24
Alignment explanation
Indices: 2606723--2606777 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 24
2606713 AAAAACGGTT
*
2606723 TTTGAAAACGTATATA-ATATAGG
1 TTTGAAAACATATATACATATAGG
*
2606746 TTTGAAAACATATATACATATAGT
1 TTTGAAAACATATATACATATAGG
*
2606770 TTTTAAAA
1 TTTGAAAA
2606778 TGGTTTTTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 15 0.54
24 13 0.46
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.38
Consensus pattern (24 bp):
TTTGAAAACATATATACATATAGG
Found at i:2606754 original size:60 final size:60
Alignment explanation
Indices: 2606686--2606803 Score: 193
Period size: 60 Copynumber: 2.0 Consensus size: 60
2606676 AAAATCGATT
* *
2606686 TTTGAAAACATATA-ATATATAGTTTTTAAAAACGGTTTTTGAAAACGTATATAATATAGG
1 TTTGAAAACATATATACATATAGTTTTT-AAAACGGTTTTTGAAAACATATATAATATAGG
*
2606746 TTTGAAAACATATATACATATAGTTTTTAAAATGGTTTTTGAAAACATATATAATATA
1 TTTGAAAACATATATACATATAGTTTTTAAAACGGTTTTTGAAAACATATATAATATA
2606804 TATAATTTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
60 42 0.78
61 12 0.22
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.40
Consensus pattern (60 bp):
TTTGAAAACATATATACATATAGTTTTTAAAACGGTTTTTGAAAACATATATAATATAGG
Found at i:2606777 original size:24 final size:23
Alignment explanation
Indices: 2606720--2606777 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 23
2606710 TTTAAAAACG
*
2606720 GTTTTTGAAAACGTATATAATATA
1 GTTTTT-AAAACATATATAATATA
* *
2606744 GGTTTGAAAACATATATACATATA
1 GTTTTTAAAACATATATA-ATATA
2606768 GTTTTTAAAA
1 GTTTTTAAAA
2606778 TGGTTTTTGA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
23 11 0.39
24 17 0.61
ACGTcount: A:0.43, C:0.05, G:0.12, T:0.40
Consensus pattern (23 bp):
GTTTTTAAAACATATATAATATA
Found at i:2606852 original size:28 final size:26
Alignment explanation
Indices: 2606820--2606877 Score: 64
Period size: 29 Copynumber: 2.2 Consensus size: 26
2606810 TTTTGAAAAC
2606820 ATATTATA-AAAGTTTTTGAAAATATAAT
1 ATATTATATAAAGTTTTT--AAATA-AAT
* *
2606848 ATATTCTATATAGTTTTTAAATAAAT
1 ATATTATATAAAGTTTTTAAATAAAT
2606874 ATAT
1 ATAT
2606878 AGTATGTGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 7 0.26
27 5 0.19
28 7 0.26
29 8 0.30
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (26 bp):
ATATTATATAAAGTTTTTAAATAAAT
Found at i:2606902 original size:12 final size:11
Alignment explanation
Indices: 2606887--2606926 Score: 55
Period size: 12 Copynumber: 3.5 Consensus size: 11
2606877 TAGTATGTGT
2606887 TATATTATATTA
1 TATATTAT-TTA
2606899 TATATTATTTA
1 TATATTATTTA
2606910 TAGTATTATTTA
1 TA-TATTATTTA
2606922 T-TATT
1 TATATT
2606927 TTATTCATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 4 0.15
11 5 0.19
12 18 0.67
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (11 bp):
TATATTATTTA
Found at i:2609261 original size:15 final size:15
Alignment explanation
Indices: 2609241--2609272 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2609231 GTAGGAATTT
2609241 TTATTTTCATTATTA
1 TTATTTTCATTATTA
*
2609256 TTATTTTGATTATTA
1 TTATTTTCATTATTA
2609271 TT
1 TT
2609273 TTTATCTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.69
Consensus pattern (15 bp):
TTATTTTCATTATTA
Found at i:2611957 original size:24 final size:23
Alignment explanation
Indices: 2611930--2611983 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 23
2611920 ATCTTCCACA
*
2611930 AAAGAACAAGCTTCATCTGTTGC
1 AAAGAACAAGCTTCATCGGTTGC
*
2611953 GAAAGAATAAGCTTCATCGGTTGC
1 -AAAGAACAAGCTTCATCGGTTGC
2611977 AAA-AACA
1 AAAGAACA
2611984 TAAGCTTCTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 3 0.11
23 3 0.11
24 21 0.78
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (23 bp):
AAAGAACAAGCTTCATCGGTTGC
Found at i:2611986 original size:24 final size:24
Alignment explanation
Indices: 2611937--2611991 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
2611927 ACAAAAGAAC
* *
2611937 AAGCTTCATCTGTTGCGAAAGAAT
1 AAGCTTCATCGGTTGCGAAAAAAT
2611961 AAGCTTCATCGGTTGC-AAAAACAT
1 AAGCTTCATCGGTTGCGAAAAA-AT
2611985 AAGCTTC
1 AAGCTTC
2611992 TGTAACTAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 4 0.14
24 24 0.86
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (24 bp):
AAGCTTCATCGGTTGCGAAAAAAT
Found at i:2612840 original size:192 final size:194
Alignment explanation
Indices: 2612489--2612878 Score: 766
Period size: 192 Copynumber: 2.0 Consensus size: 194
2612479 TATATGTTGG
2612489 GACCGTCGGCGCACCCTACGACGCAGCGGAAACAAAACTTGATGGTCTCACAAGGGATCCAAGTA
1 GACCGTCGGCGCACCCTACGACGCAGCGGAAACAAAACTTGATGGTCTCACAAGGGATCCAAGTA
2612554 CGTAAAATCGAAATCGGGAGGAATTGATGCAAATACTTACAGCGGGTTCCTTGAAAAACAACAAG
66 CGTAAAATCGAAATCGGGAGGAATTGATGCAAATACTTACAGCGGGTTCCTTGAAAAACAACAAG
2612619 GACAACAATGATTGATGATGGTGTCGATCGGTTCGAATCGCAAGCCTCCATGAAATCACGTCTT
131 GACAACAATGATTGATGATGGTGTCGATCGGTTCGAATCGCAAGCCTCCATGAAATCACGTCTT
2612683 GACCGTCGGCGCACCCTACGACGCAGCGGAAACAAAACTTGATGGTCTCACAAGGGATCCAAGTA
1 GACCGTCGGCGCACCCTACGACGCAGCGGAAACAAAACTTGATGGTCTCACAAGGGATCCAAGTA
2612748 CGT-AAATCGAAATCGGGAGGAA-TGATGCAAATACTTACAGCGGGTTCCTTGAAAAACAACAAG
66 CGTAAAATCGAAATCGGGAGGAATTGATGCAAATACTTACAGCGGGTTCCTTGAAAAACAACAAG
2612811 GACAACAATGATTGATGATGGTGTCGATCGGTTCGAATCGCAAGCCTCCATGAAATCACGTCTT
131 GACAACAATGATTGATGATGGTGTCGATCGGTTCGAATCGCAAGCCTCCATGAAATCACGTCTT
2612875 GACC
1 GACC
2612879 TCTACTCAGT
Statistics
Matches: 196, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
192 109 0.56
193 19 0.10
194 68 0.35
ACGTcount: A:0.33, C:0.23, G:0.24, T:0.20
Consensus pattern (194 bp):
GACCGTCGGCGCACCCTACGACGCAGCGGAAACAAAACTTGATGGTCTCACAAGGGATCCAAGTA
CGTAAAATCGAAATCGGGAGGAATTGATGCAAATACTTACAGCGGGTTCCTTGAAAAACAACAAG
GACAACAATGATTGATGATGGTGTCGATCGGTTCGAATCGCAAGCCTCCATGAAATCACGTCTT
Found at i:2624542 original size:15 final size:15
Alignment explanation
Indices: 2624510--2624538 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2624500 CATAATTAGT
2624510 AAAAAATAACCTCAC
1 AAAAAATAACCTCAC
2624525 AAAAAA-AACCTCAC
1 AAAAAATAACCTCAC
2624539 CAAACACTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.62, C:0.28, G:0.00, T:0.10
Consensus pattern (15 bp):
AAAAAATAACCTCAC
Found at i:2624897 original size:15 final size:15
Alignment explanation
Indices: 2624852--2624890 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
2624842 TCTTTAAACC
2624852 ATTTTTTCTTTCTTTT
1 ATTTTTT-TTTCTTTT
*
2624868 GTTTTTTTTTCTTTT
1 ATTTTTTTTTCTTTT
2624883 ATTTTTTT
1 ATTTTTTT
2624891 ATTTTTTTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.05, C:0.08, G:0.03, T:0.85
Consensus pattern (15 bp):
ATTTTTTTTTCTTTT
Found at i:2624899 original size:8 final size:8
Alignment explanation
Indices: 2624853--2624899 Score: 51
Period size: 8 Copynumber: 5.9 Consensus size: 8
2624843 CTTTAAACCA
*
2624853 TTTTTTCT
1 TTTTTTAT
*
2624861 TTCTTTTGT
1 TT-TTTTAT
2624870 TTTTTT-T
1 TTTTTTAT
*
2624877 TCTTTTAT
1 TTTTTTAT
2624885 TTTTTTAT
1 TTTTTTAT
2624893 TTTTTTA
1 TTTTTTA
2624900 CTGACCCGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
7 6 0.18
8 21 0.62
9 7 0.21
ACGTcount: A:0.06, C:0.06, G:0.02, T:0.85
Consensus pattern (8 bp):
TTTTTTAT
Found at i:2626238 original size:17 final size:17
Alignment explanation
Indices: 2626216--2626251 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
2626206 TAAGAGTTAA
2626216 TTTAATAAATGAACTAG
1 TTTAATAAATGAACTAG
*
2626233 TTTAATGAATGAACTAG
1 TTTAATAAATGAACTAG
2626250 TT
1 TT
2626252 GATTTAAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.42, C:0.06, G:0.14, T:0.39
Consensus pattern (17 bp):
TTTAATAAATGAACTAG
Found at i:2626258 original size:21 final size:21
Alignment explanation
Indices: 2626210--2626258 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 21
2626200 CACAATTAAG
*
2626210 AGTTAATTTAATAAATGAACT
1 AGTTGATTTAATAAATGAACT
*
2626231 A---G-TTTAATGAATGAACT
1 AGTTGATTTAATAAATGAACT
2626248 AGTTGATTTAA
1 AGTTGATTTAA
2626259 ATGCAATGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 8
0.69 0.06 0.25
Matches are distributed among these distances:
17 15 0.68
20 1 0.05
21 6 0.27
ACGTcount: A:0.43, C:0.04, G:0.14, T:0.39
Consensus pattern (21 bp):
AGTTGATTTAATAAATGAACT
Found at i:2631875 original size:21 final size:20
Alignment explanation
Indices: 2631834--2631887 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 20
2631824 CAAACATTTC
* *
2631834 TTCATTTTTTT-TATCTTAT
1 TTCATTTTTTTCTATATAAT
2631853 TTCATTTTTTTCGTATATAAT
1 TTCATTTTTTTC-TATATAAT
*
2631874 TTTATTTCTTTTCT
1 TTCATTT-TTTTCT
2631888 TCATTCTATG
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 11 0.38
21 13 0.45
22 5 0.17
ACGTcount: A:0.17, C:0.11, G:0.02, T:0.70
Consensus pattern (20 bp):
TTCATTTTTTTCTATATAAT
Found at i:2636924 original size:23 final size:23
Alignment explanation
Indices: 2636895--2636939 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
2636885 ATATGGTAGT
2636895 ATATAATATATAGTTTTTAAAAC
1 ATATAATATATAGTTTTTAAAAC
2636918 ATATAATATATAGTTTTTAAAA
1 ATATAATATATAGTTTTTAAAA
2636940 ATGGTTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.44
Consensus pattern (23 bp):
ATATAATATATAGTTTTTAAAAC
Found at i:2636954 original size:36 final size:38
Alignment explanation
Indices: 2636906--2636999 Score: 138
Period size: 36 Copynumber: 2.5 Consensus size: 38
2636896 TATAATATAT
* *
2636906 AGTTTTTAAAACATATAATATATAGTTTTTAAAA-ATG
1 AGTTTTAAAAACATATAATATATAGTTTTTAAAAGACG
2636943 -GTTTTAAAAACATATAATATATAGTTTTTAAAAGACG
1 AGTTTTAAAAACATATAATATATAGTTTTTAAAAGACG
* *
2636980 ATTTTTGAAAACATATAATA
1 AGTTTTAAAAACATATAATA
2637000 CAGTTTTGAA
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
36 32 0.63
37 2 0.04
38 17 0.33
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.40
Consensus pattern (38 bp):
AGTTTTAAAAACATATAATATATAGTTTTTAAAAGACG
Found at i:2637008 original size:21 final size:21
Alignment explanation
Indices: 2636982--2637064 Score: 123
Period size: 21 Copynumber: 4.0 Consensus size: 21
2636972 AAAAGACGAT
*
2636982 TTTTGAAAACATATAATACAG
1 TTTTGAAAACATATAATATAG
2637003 TTTTGAAAACATATAATATAG
1 TTTTGAAAACATATAATATAG
*
2637024 TTTTGAAAACATATTATATAG
1 TTTTGAAAACATATAATATAG
*
2637045 TTTTTTAAAA-ATATAATATA
1 -TTTTGAAAACATATAATATA
2637065 TATTATATAG
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
21 49 0.86
22 8 0.14
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Consensus pattern (21 bp):
TTTTGAAAACATATAATATAG
Found at i:2637068 original size:30 final size:33
Alignment explanation
Indices: 2637034--2637105 Score: 114
Period size: 30 Copynumber: 2.3 Consensus size: 33
2637024 TTTTGAAAAC
*
2637034 ATATTATATAGTTTTTTAA-AAATATA-A-TAT
1 ATATTATATAGTTTTTAAATAAATATATAGTAT
2637064 ATATTATATAGTTTTTAAATAAATATATAGTAT
1 ATATTATATAGTTTTTAAATAAATATATAGTAT
2637097 ATATTATAT
1 ATATTATAT
2637106 TATATCATAT
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
30 18 0.47
31 7 0.18
32 1 0.03
33 12 0.32
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (33 bp):
ATATTATATAGTTTTTAAATAAATATATAGTAT
Found at i:2637078 original size:28 final size:27
Alignment explanation
Indices: 2637034--2637099 Score: 89
Period size: 26 Copynumber: 2.4 Consensus size: 27
2637024 TTTTGAAAAC
2637034 ATATTATATAGTTTTTTAAAAATATAATAT
1 ATATTATATAG-TTTTT-AAAATA-AATAT
2637064 ATATTATATAGTTTTT-AAATAAATAT
1 ATATTATATAGTTTTTAAAATAAATAT
*
2637090 ATAGTATATA
1 ATATTATATA
2637100 TTATATTATA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
26 14 0.40
27 5 0.14
29 5 0.14
30 11 0.31
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (27 bp):
ATATTATATAGTTTTTAAAATAAATAT
Found at i:2643081 original size:18 final size:17
Alignment explanation
Indices: 2643019--2643084 Score: 55
Period size: 17 Copynumber: 3.8 Consensus size: 17
2643009 AGAGTTAGTC
*
2643019 TAATAAATGAAC-AAGTT
1 TAATTAATGAACTAA-TT
* *
2643036 TGATGAATGAACTAATT
1 TAATTAATGAACTAATT
*
2643053 TAATTATTGAACTAACTT
1 TAATTAATGAACTAA-TT
2643071 T-ATTCAATGAACTA
1 TAATT-AATGAACTA
2643085 GATTCATGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
17 27 0.68
18 13 0.32
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (17 bp):
TAATTAATGAACTAATT
Found at i:2649360 original size:36 final size:36
Alignment explanation
Indices: 2649217--2649340 Score: 187
Period size: 36 Copynumber: 3.4 Consensus size: 36
2649207 TTCATTCAAG
* * *
2649217 ATTTTATATCTCTTAAGATTATTTT-TCTTAAAACAT
1 ATTTTATTTCACTTGAGATTATTTTCT-TTAAAACAT
*
2649253 ATTTTATCTCACTTGAGATTATTTTCTTTAAAACAT
1 ATTTTATTTCACTTGAGATTATTTTCTTTAAAACAT
2649289 ATTTTATTTCACTTGAGATTATTTTCTTTAAAACAT
1 ATTTTATTTCACTTGAGATTATTTTCTTTAAAACAT
*
2649325 ATTTTATTTCAATTGA
1 ATTTTATTTCACTTGA
2649341 AAGTGTTTAT
Statistics
Matches: 82, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
36 81 0.99
37 1 0.01
ACGTcount: A:0.31, C:0.11, G:0.05, T:0.52
Consensus pattern (36 bp):
ATTTTATTTCACTTGAGATTATTTTCTTTAAAACAT
Found at i:2652639 original size:38 final size:40
Alignment explanation
Indices: 2652594--2652685 Score: 125
Period size: 38 Copynumber: 2.4 Consensus size: 40
2652584 TGAATATTTT
**
2652594 TCCCGAAGGACCACTATGTCCTGAAGGACCACT-GAT-TG
1 TCCCGAAGGACCACTATGTCCCAAAGGACCACTAGATATG
* * *
2652632 TTCCGAAGAACCACTATGTCCCAAAGGACCACTATATATG
1 TCCCGAAGGACCACTATGTCCCAAAGGACCACTAGATATG
2652672 TCCCGAAGGACCAC
1 TCCCGAAGGACCAC
2652686 ACCTTAAGAA
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
38 29 0.64
39 2 0.04
40 14 0.31
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.20
Consensus pattern (40 bp):
TCCCGAAGGACCACTATGTCCCAAAGGACCACTAGATATG
Found at i:2652644 original size:20 final size:17
Alignment explanation
Indices: 2652596--2652666 Score: 79
Period size: 18 Copynumber: 3.9 Consensus size: 17
2652586 AATATTTTTC
2652596 CCGAAGGACCACTATGT
1 CCGAAGGACCACTATGT
2652613 CCTGAAGGACCACTGATTGTT
1 CC-GAAGGACCACT-A-TG-T
*
2652634 CCGAAGAACCACTATGT
1 CCGAAGGACCACTATGT
*
2652651 CCCAAAGGACCACTAT
1 -CCGAAGGACCACTAT
2652667 ATATGTCCCG
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
17 3 0.07
18 26 0.57
19 2 0.04
20 12 0.26
21 3 0.07
ACGTcount: A:0.31, C:0.30, G:0.20, T:0.20
Consensus pattern (17 bp):
CCGAAGGACCACTATGT
Found at i:2652940 original size:24 final size:21
Alignment explanation
Indices: 2652884--2652941 Score: 55
Period size: 24 Copynumber: 2.5 Consensus size: 21
2652874 ATATCTTCTC
2652884 ATCACTTTTCATATAAACATGT
1 ATCAC-TTTCATATAAACATGT
2652906 ATTTCAC-TTCATATACACACATGT
1 A--TCACTTTCATATA-A-ACATGT
2652930 GATCACTTTCAT
1 -ATCACTTTCAT
2652942 TATTTCACAT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
22 9 0.30
23 5 0.17
24 15 0.50
25 1 0.03
ACGTcount: A:0.33, C:0.22, G:0.05, T:0.40
Consensus pattern (21 bp):
ATCACTTTCATATAAACATGT
Found at i:2659658 original size:18 final size:19
Alignment explanation
Indices: 2659610--2659687 Score: 86
Period size: 20 Copynumber: 3.9 Consensus size: 19
2659600 CACTAAATAT
*
2659610 TTGTCCCGAAGGACCACCGA
1 TTGTCCCGAAGGACCA-CTA
* *
2659630 TTGTTCCGAAGAACCACTA
1 TTGTCCCGAAGGACCACTA
2659649 -TGTCCCGAAGGACCACTGTA
1 TTGTCCCGAAGGACCAC--TA
2659669 TATGTCCCGAAGGACCACT
1 T-TGTCCCGAAGGACCACT
2659688 CCTTAAAAAC
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
18 14 0.29
19 2 0.04
20 17 0.35
22 16 0.33
ACGTcount: A:0.27, C:0.31, G:0.22, T:0.21
Consensus pattern (19 bp):
TTGTCCCGAAGGACCACTA
Found at i:2659662 original size:38 final size:40
Alignment explanation
Indices: 2659611--2659687 Score: 113
Period size: 38 Copynumber: 2.0 Consensus size: 40
2659601 ACTAAATATT
*
2659611 TGTCCCGAAGGACCACCG-AT-TGTTCCGAAGAACCACTA
1 TGTCCCGAAGGACCACCGTATATGTCCCGAAGAACCACTA
* *
2659649 TGTCCCGAAGGACCACTGTATATGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACCGTATATGTCCCGAAGAACCACT
2659688 CCTTAAAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 17 0.50
39 2 0.06
40 15 0.44
ACGTcount: A:0.27, C:0.31, G:0.22, T:0.19
Consensus pattern (40 bp):
TGTCCCGAAGGACCACCGTATATGTCCCGAAGAACCACTA
Found at i:2659675 original size:22 final size:21
Alignment explanation
Indices: 2659611--2659687 Score: 90
Period size: 22 Copynumber: 3.8 Consensus size: 21
2659601 ACTAAATATT
*
2659611 TGTCCCGAAGGACCACCGAT-
1 TGTCCCGAAGGACCACTGATA
* *
2659631 TGTTCCGAAGAACCAC---TA
1 TGTCCCGAAGGACCACTGATA
2659649 TGTCCCGAAGGACCACTGTATA
1 TGTCCCGAAGGACCACTG-ATA
2659671 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
2659688 CCTTAAAAAC
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
17 1 0.02
18 14 0.29
20 14 0.29
22 19 0.40
ACGTcount: A:0.27, C:0.31, G:0.22, T:0.19
Consensus pattern (21 bp):
TGTCCCGAAGGACCACTGATA
Found at i:2667335 original size:6 final size:6
Alignment explanation
Indices: 2667326--2667374 Score: 53
Period size: 6 Copynumber: 7.5 Consensus size: 6
2667316 TTCTATTTTC
*
2667326 TTTATT TTTATTT TTTATT ATGTTATT TTTATT TTTATT CTTGATT TTT
1 TTTATT TTTA-TT TTTATT -T-TTATT TTTATT TTTATT -TTTATT TTT
2667375 TGGAGTAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
6 19 0.51
7 13 0.35
8 5 0.14
ACGTcount: A:0.16, C:0.02, G:0.04, T:0.78
Consensus pattern (6 bp):
TTTATT
Found at i:2667983 original size:18 final size:18
Alignment explanation
Indices: 2667956--2667991 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
2667946 ATTTTTGAAA
2667956 AAAAAAACAAGTATGCTT
1 AAAAAAACAAGTATGCTT
*
2667974 AAAAACACAAGTATGCTT
1 AAAAAAACAAGTATGCTT
2667992 TAGTTCTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.14, G:0.11, T:0.22
Consensus pattern (18 bp):
AAAAAAACAAGTATGCTT
Found at i:2669680 original size:18 final size:16
Alignment explanation
Indices: 2669633--2669681 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 16
2669623 GATACACAGG
2669633 CAGGGGTATCGGTACC
1 CAGGGGTATCGGTACC
2669649 C--GGGTAT-GGATACC
1 CAGGGGTATCGG-TACC
2669663 CATAGGGGTATCGGTACC
1 C--AGGGGTATCGGTACC
2669681 C
1 C
2669682 TTTTTGCATT
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
13 2 0.07
14 11 0.41
16 1 0.04
18 11 0.41
19 2 0.07
ACGTcount: A:0.20, C:0.24, G:0.35, T:0.20
Consensus pattern (16 bp):
CAGGGGTATCGGTACC
Found at i:2669734 original size:22 final size:22
Alignment explanation
Indices: 2669706--2669747 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
2669696 GTTTGAGCAG
2669706 TCATAGGGGTATCGATACCCGT
1 TCATAGGGGTATCGATACCCGT
*
2669728 TCATAGGGGTATCGGTACCC
1 TCATAGGGGTATCGATACCC
2669748 AAGGTATTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.21, C:0.24, G:0.29, T:0.26
Consensus pattern (22 bp):
TCATAGGGGTATCGATACCCGT
Found at i:2669792 original size:37 final size:37
Alignment explanation
Indices: 2669713--2669784 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 37
2669703 CAGTCATAGG
* *
2669713 GGTATCGATACCCGTTCATAGGGGTATCGGTACCCAA
1 GGTATTGATACCCGTTCATAGGGGTATCGCTACCCAA
2669750 GGTATTGATACCC-TTCATAGGGGTATCGCTACCCA
1 GGTATTGATACCCGTTCATAGGGGTATCGCTACCCA
2669785 TTTGTATTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
36 21 0.64
37 12 0.36
ACGTcount: A:0.24, C:0.25, G:0.25, T:0.26
Consensus pattern (37 bp):
GGTATTGATACCCGTTCATAGGGGTATCGCTACCCAA
Found at i:2672229 original size:66 final size:66
Alignment explanation
Indices: 2672121--2672250 Score: 206
Period size: 66 Copynumber: 2.0 Consensus size: 66
2672111 AGTATGAAGA
* * *
2672121 CTCTGGCAGGTTCAGTCGCTGCTGGTAATTCCTCGTAAAGGTTCTGCACCGGCTGGTAATTCCTA
1 CTCTGGCAGGTTCAGTCGCTGCTAGTAATTCCTCGTAAAGGTTCAGCACCGACTGGTAATTCCTA
2672186 T
66 T
** *
2672187 CTCTGGCAGGTTCAGTCGCTGCTAGTAATTCCTTTTATAGGTTCAGCACCGACTGGTAATTCCT
1 CTCTGGCAGGTTCAGTCGCTGCTAGTAATTCCTCGTAAAGGTTCAGCACCGACTGGTAATTCCT
2672251 TATAGACCTA
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
66 58 1.00
ACGTcount: A:0.18, C:0.25, G:0.24, T:0.33
Consensus pattern (66 bp):
CTCTGGCAGGTTCAGTCGCTGCTAGTAATTCCTCGTAAAGGTTCAGCACCGACTGGTAATTCCTA
T
Found at i:2673272 original size:36 final size:36
Alignment explanation
Indices: 2673225--2673295 Score: 142
Period size: 36 Copynumber: 2.0 Consensus size: 36
2673215 GGACAAAATA
2673225 ATTGGGTTGCCTCTCTTTCAGCAATGTCAGTTTTCC
1 ATTGGGTTGCCTCTCTTTCAGCAATGTCAGTTTTCC
2673261 ATTGGGTTGCCTCTCTTTCAGCAATGTCAGTTTTC
1 ATTGGGTTGCCTCTCTTTCAGCAATGTCAGTTTTC
2673296 AGATATGCGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.14, C:0.24, G:0.20, T:0.42
Consensus pattern (36 bp):
ATTGGGTTGCCTCTCTTTCAGCAATGTCAGTTTTCC
Found at i:2673947 original size:19 final size:18
Alignment explanation
Indices: 2673901--2673954 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 18
2673891 TGCATTTATC
* *
2673901 TTAAAATTTATTTTTTAA
1 TTAAAATTTATTTATGAA
*
2673919 ATAAATATTTACTTTATGAA
1 TTAAA-ATTTA-TTTATGAA
2673939 TTAAAATTTTATTTAT
1 TTAAAA-TTTATTTAT
2673955 TTCTATTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
18 4 0.14
19 11 0.38
20 14 0.48
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (18 bp):
TTAAAATTTATTTATGAA
Found at i:2676209 original size:16 final size:17
Alignment explanation
Indices: 2676184--2676220 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
2676174 TTGTATTTAA
2676184 ATTAACTTTAATAACTT
1 ATTAACTTTAATAACTT
2676201 ATTAA-TTTAATAACTT
1 ATTAACTTTAATAACTT
2676217 ATTA
1 ATTA
2676221 TAAAAATCAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTAACTTTAATAACTT
Found at i:2676307 original size:70 final size:73
Alignment explanation
Indices: 2676207--2676344 Score: 160
Period size: 70 Copynumber: 1.9 Consensus size: 73
2676197 ACTTATTAAT
* *
2676207 TTAATAACTTATTATAAAAATCACTAAATATCT-AATATAAATATT-T-TTAATCTTATTATAAT
1 TTAATAACTTATTATAAAAATCACTAAATATATAAATATAAATATTATATTAATCTTATAATAAT
2676269 ATTTAAAA
66 ATTTAAAA
* * *
2676277 TTAA-AACTATATTAT-AAAATTATCTTAATATATAAAATATTAATATTATAATTAATCTTATAA
1 TTAATAACT-TATTATAAAAATCA-CTAAATATAT-AAATATAAATATTAT-ATTAATCTTATAA
2676340 TAATA
62 TAATA
2676345 AGTAATGATT
Statistics
Matches: 56, Mismatches: 5, Indels: 9
0.80 0.07 0.13
Matches are distributed among these distances:
69 10 0.18
70 18 0.32
72 11 0.20
73 1 0.02
75 16 0.29
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (73 bp):
TTAATAACTTATTATAAAAATCACTAAATATATAAATATAAATATTATATTAATCTTATAATAAT
ATTTAAAA
Found at i:2676370 original size:22 final size:23
Alignment explanation
Indices: 2676335--2676377 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
2676325 TAATTAATCT
2676335 TATAATAATAAGTAATGATTAAAA
1 TATAATAATAAGTAAT-ATTAAAA
2676359 TATAA-AAT-AGTAATATTAA
1 TATAATAATAAGTAATATTAA
2676378 TTATTATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 6 0.32
23 3 0.16
24 5 0.26
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.35
Consensus pattern (23 bp):
TATAATAATAAGTAATATTAAAA
Found at i:2677111 original size:16 final size:16
Alignment explanation
Indices: 2677092--2677134 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
2677082 GTGTTTTTGT
*
2677092 TTCTTATTGTTCGTCG
1 TTCTTATTGCTCGTCG
*
2677108 TTCTTGTTGCTCGTCG
1 TTCTTATTGCTCGTCG
*
2677124 TTCTTGTTGCT
1 TTCTTATTGCT
2677135 TCCTCTTGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.02, C:0.21, G:0.21, T:0.56
Consensus pattern (16 bp):
TTCTTATTGCTCGTCG
Found at i:2678159 original size:5 final size:5
Alignment explanation
Indices: 2678149--2678195 Score: 51
Period size: 5 Copynumber: 9.4 Consensus size: 5
2678139 TATTTATATG
* * *
2678149 ATAAA ATAAA A-AAA ATAAA ATAGA AGAAA ATAAAA AGAAA ATAAA AT
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA AT-AAA ATAAA ATAAA AT
2678196 CACTTAAATG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
4 4 0.12
5 26 0.76
6 4 0.12
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (5 bp):
ATAAA
Found at i:2678168 original size:14 final size:15
Alignment explanation
Indices: 2678149--2678189 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 15
2678139 TATTTATATG
2678149 ATAAAATA-AAAAAA
1 ATAAAATAGAAAAAA
*
2678163 ATAAAATAGAAGAAA
1 ATAAAATAGAAAAAA
2678178 ATAAAA-AGAAAA
1 ATAAAATAGAAAA
2678190 TAAAATCACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.12
Consensus pattern (15 bp):
ATAAAATAGAAAAAA
Found at i:2679165 original size:20 final size:20
Alignment explanation
Indices: 2679118--2679168 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
2679108 TATTGTATTG
* *
2679118 TGTGAATAGTATCGGTACTG
1 TGTGAATAGTATCGATACTA
* *
2679138 TATAAATAGTATCGATACTA
1 TGTGAATAGTATCGATACTA
2679158 TGTGAATAGTA
1 TGTGAATAGTA
2679169 ATGAACATAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.08, G:0.22, T:0.35
Consensus pattern (20 bp):
TGTGAATAGTATCGATACTA
Found at i:2679383 original size:20 final size:20
Alignment explanation
Indices: 2679358--2679405 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
2679348 TAGAAAATGA
2679358 ATCCCCAATGGCTCCAAAAC
1 ATCCCCAATGGCTCCAAAAC
2679378 ATCCCCAATGGCTCCAAAAC
1 ATCCCCAATGGCTCCAAAAC
*
2679398 GTCCCCAA
1 ATCCCCAA
2679406 CAGCTATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.42, G:0.10, T:0.15
Consensus pattern (20 bp):
ATCCCCAATGGCTCCAAAAC
Found at i:2682379 original size:18 final size:18
Alignment explanation
Indices: 2682356--2682412 Score: 69
Period size: 18 Copynumber: 3.0 Consensus size: 18
2682346 TATATTTTCC
*
2682356 AACAATTGGTATCTTTTT
1 AACAATTGATATCTTTTT
2682374 AACAATTGATATCCTTTAGTT
1 AACAATTGATAT-CTTT--TT
*
2682395 AATAATTGATATCTTTTT
1 AACAATTGATATCTTTTT
2682413 CATTAAACAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
18 13 0.38
19 4 0.12
20 4 0.12
21 13 0.38
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.49
Consensus pattern (18 bp):
AACAATTGATATCTTTTT
Found at i:2682663 original size:20 final size:20
Alignment explanation
Indices: 2682624--2682693 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
2682614 AAAATGTTTT
**
2682624 TATGAATAGTATTG-TACTG
1 TATGAATAGTACAGATACTG
*
2682643 TATGAATAGTACCGATACTG
1 TATGAATAGTACAGATACTG
* *
2682663 TATAAATAGTACATATACTG
1 TATGAATAGTACAGATACTG
* *
2682683 TGTGAAAAGTA
1 TATGAATAGTA
2682694 ATGAACATTA
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 12 0.29
20 30 0.71
ACGTcount: A:0.39, C:0.09, G:0.19, T:0.34
Consensus pattern (20 bp):
TATGAATAGTACAGATACTG
Found at i:2685532 original size:23 final size:23
Alignment explanation
Indices: 2685501--2685545 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
2685491 ACGATATCAT
*
2685501 ATATCAAAATCATATTATTATATA
1 ATATCAAAATAATATTA-TATATA
2685525 ATAT-AAAATAATATTATATAT
1 ATATCAAAATAATATTATATAT
2685546 GATTTCATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 5 0.25
23 11 0.55
24 4 0.20
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.42
Consensus pattern (23 bp):
ATATCAAAATAATATTATATATA
Found at i:2687573 original size:6 final size:6
Alignment explanation
Indices: 2687553--2687595 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
2687543 TCTCGTCTCG
*
2687553 GGTCG- GGTC-T GGTCGT GGTCGT GGTCAT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
2687596 AATACGTGTC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
5 8 0.24
6 26 0.76
ACGTcount: A:0.02, C:0.16, G:0.49, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:2687585 original size:18 final size:17
Alignment explanation
Indices: 2687553--2687595 Score: 70
Period size: 18 Copynumber: 2.5 Consensus size: 17
2687543 TCTCGTCTCG
2687553 GGTCG-GGTCTGGTCGT
1 GGTCGTGGTCTGGTCGT
2687569 GGTCGTGGTCATGGTCGT
1 GGTCGTGGTC-TGGTCGT
2687587 GGTCGTGGT
1 GGTCGTGGT
2687596 AATACGTGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
16 5 0.20
17 4 0.16
18 16 0.64
ACGTcount: A:0.02, C:0.16, G:0.49, T:0.33
Consensus pattern (17 bp):
GGTCGTGGTCTGGTCGT
Found at i:2687737 original size:21 final size:21
Alignment explanation
Indices: 2687713--2687870 Score: 182
Period size: 21 Copynumber: 7.6 Consensus size: 21
2687703 TTTGGAATAA
*
2687713 ATCGCAACGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
*
2687734 ATCGCAATGCGAACTTGGACT
1 ATCGCAATGCGAACTTCGACT
*
2687755 ATCGCAATGCGAA-TAT-GTA-A
1 ATCGCAATGCGAACT-TCG-ACT
*
2687775 ATCGCAATGCGATAGTCTC--CT
1 ATCGCAATGCGA-ACT-TCGACT
*
2687796 ATCGCAATGCGAACTTGGACT
1 ATCGCAATGCGAACTTCGACT
*
2687817 ATCGCAACGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
*
2687838 ATCGCAATGCGAACTTGGACT
1 ATCGCAATGCGAACTTCGACT
2687859 ATCGCAATGCGA
1 ATCGCAATGCGA
2687871 TTTACATATT
Statistics
Matches: 118, Mismatches: 11, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
19 1 0.01
20 16 0.14
21 99 0.84
22 2 0.02
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.23
Consensus pattern (21 bp):
ATCGCAATGCGAACTTCGACT
Found at i:2687884 original size:83 final size:82
Alignment explanation
Indices: 2687713--2687871 Score: 221
Period size: 83 Copynumber: 1.9 Consensus size: 82
2687703 TTTGGAATAA
* * *
2687713 ATCGCAACGCGAACTTCGACTATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATC
1 ATCGCAACGCGAACTTCGACTATCGCAACGCGAACTTCGACTATCGCAATGCGAATATGGAAATC
*
2687778 GCAATGCGATAGTCTCCT
66 GCAATGCGATA-TCTCAT
* * *
2687796 ATCGCAATGCGAACTTGGACTATCGCAACGCGAACTTCGACTATCGCAATGCGAACT-TGGACTA
1 ATCGCAACGCGAACTTCGACTATCGCAACGCGAACTTCGACTATCGCAATGCGAA-TATGGA-AA
2687860 TCGCAATGCGAT
64 TCGCAATGCGAT
2687872 TTACATATTC
Statistics
Matches: 68, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
83 54 0.79
84 14 0.21
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (82 bp):
ATCGCAACGCGAACTTCGACTATCGCAACGCGAACTTCGACTATCGCAATGCGAATATGGAAATC
GCAATGCGATATCTCAT
Found at i:2687893 original size:20 final size:20
Alignment explanation
Indices: 2687860--2687908 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
2687850 ACTTGGACTA
* *
2687860 TCGCAATGCGATTTACATAT
1 TCGCATTGCAATTTACATAT
2687880 TCGCATTGCAATTTACATAT
1 TCGCATTGCAATTTACATAT
2687900 TCGCATTGC
1 TCGCATTGC
2687909 GATAGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (20 bp):
TCGCATTGCAATTTACATAT
Found at i:2687925 original size:21 final size:21
Alignment explanation
Indices: 2687899--2688077 Score: 238
Period size: 21 Copynumber: 8.6 Consensus size: 21
2687889 AATTTACATA
2687899 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
2687920 TTCGCATTGCAATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
2687941 TTCGTATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
2687962 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
2687983 TTCGCATTGCGATAGT-CGAC
1 TTCGCATTGCGATAGTCCAAG
* *
2688003 TATCGCATTGCGAT-TTACATA-
1 T-TCGCATTGCGATAGTCCA-AG
2688024 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
2688045 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
2688066 TTCGCGTTGCGA
1 TTCGCATTGCGA
2688078 ATATGGAAAT
Statistics
Matches: 139, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
20 17 0.12
21 121 0.87
22 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.31
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:2688099 original size:62 final size:62
Alignment explanation
Indices: 2687879--2688077 Score: 274
Period size: 62 Copynumber: 3.2 Consensus size: 62
2687869 GATTTACATA
* * * *
2687879 TTCGCATTGCAATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCAATAGTCGAAG
1 TTCGCATTGCGATATACAAATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGAAG
* * * *
2687941 TTCGTATTGCGATAGTCCAAGTTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCG-AC
1 TTCGCATTGCGATA-TACAAATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGAAG
* *
2688003 TATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGAAG
1 T-TCGCATTGCGATATACAAATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGAAG
*
2688066 TTCGCGTTGCGA
1 TTCGCATTGCGA
2688078 ATATGGAAAT
Statistics
Matches: 119, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
62 65 0.55
63 54 0.45
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.32
Consensus pattern (62 bp):
TTCGCATTGCGATATACAAATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGAAG
Found at i:2689325 original size:21 final size:21
Alignment explanation
Indices: 2689301--2689345 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
2689291 AAATTACGTA
*
2689301 TTTAGTACCTAAACTATCAGT
1 TTTAGTACCTAAACTATCAAT
*
2689322 TTTAGTACCTAAACTTTCAAT
1 TTTAGTACCTAAACTATCAAT
2689343 TTT
1 TTT
2689346 TTCAAATCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.31, C:0.18, G:0.07, T:0.44
Consensus pattern (21 bp):
TTTAGTACCTAAACTATCAAT
Found at i:2692299 original size:4 final size:4
Alignment explanation
Indices: 2692292--2692318 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
2692282 GTATGTATAT
2692292 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
2692319 CATAGTTGAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:2698988 original size:29 final size:30
Alignment explanation
Indices: 2698939--2698996 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
2698929 AAGCATTTAA
*
2698939 AAAAAATTAAAATACATCACTACACATGAC
1 AAAAAATTAAAATACATCACTAAACATGAC
2698969 AAAAAATGTAAAA-ACA-CACTAAACATGA
1 AAAAAAT-TAAAATACATCACTAAACATGA
2698997 AAGGACTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 11 0.42
30 10 0.38
31 5 0.19
ACGTcount: A:0.60, C:0.17, G:0.05, T:0.17
Consensus pattern (30 bp):
AAAAAATTAAAATACATCACTAAACATGAC
Found at i:2701476 original size:22 final size:22
Alignment explanation
Indices: 2701448--2701496 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
2701438 AACAGTAGAA
2701448 GAATTTCACTATGAGAAAATAG
1 GAATTTCACTATGAGAAAATAG
2701470 GAATTTCACTATGAGAAAATAG
1 GAATTTCACTATGAGAAAATAG
2701492 GAATT
1 GAATT
2701497 ACAACTTCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.45, C:0.08, G:0.18, T:0.29
Consensus pattern (22 bp):
GAATTTCACTATGAGAAAATAG
Found at i:2706198 original size:34 final size:34
Alignment explanation
Indices: 2706153--2706219 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 34
2706143 AATAGGAATT
*
2706153 ACAACTTCTCTC-GATCTAACAAGGAGAAAACAATA
1 ACAACTTCTCTCTGA--TAAAAAGGAGAAAACAATA
2706188 ACAA-TTCTCTCTTGATAAAAAGGAGAAAACAA
1 ACAACTTCTCTC-TGATAAAAAGGAGAAAACAA
2706220 CTCTAAAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 23 0.79
35 4 0.14
36 2 0.07
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.21
Consensus pattern (34 bp):
ACAACTTCTCTCTGATAAAAAGGAGAAAACAATA
Found at i:2706438 original size:23 final size:23
Alignment explanation
Indices: 2706385--2706439 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 23
2706375 CTATGTCACA
* * *
2706385 TTTCAACCATTTTTGGTGTCAAC
1 TTTCAACCATTATTAGTGCCAAC
* * *
2706408 TATGAACCATTATTATTGCCAAC
1 TTTCAACCATTATTAGTGCCAAC
2706431 TTTCAACCA
1 TTTCAACCA
2706440 CCTAATGTTT
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.29, C:0.24, G:0.09, T:0.38
Consensus pattern (23 bp):
TTTCAACCATTATTAGTGCCAAC
Found at i:2706790 original size:3 final size:3
Alignment explanation
Indices: 2706778--2707181 Score: 99
Period size: 3 Copynumber: 131.3 Consensus size: 3
2706768 ATATAATTTT
* * *
2706778 ATA ATAA ATA ATA ATA ATA A-A TTA ATA TACA ATTA ATA ATAA ATA TTA
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA -ATA A-TA ATA AT-A ATA ATA
* * * * *
2706826 ATA TTA CATA ATG AT- ATA ATA CTA ATA ATA GTA ATA ATA GACA ATA
1 ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA
* * * * * * *
2706872 ATA TTGA ATA TATA ATT ACA ACA TTTA ATA CTA ATGA ATA A-A AAA GATA
1 ATA AT-A ATA -ATA ATA ATA ATA -ATA ATA ATA AT-A ATA ATA ATA -ATA
* * *
2706921 GATA ATA ATA ATA GAGTA ATA ATA AT- ATA A-A ATA ATA TTA CTTA TTA
1 -ATA ATA ATA ATA -A-TA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA
* * * * *
2706968 ATA ATAA ATA CT- ATA ATA GTA TATA ATT ATA TGTA ATA AT- TTA ATA
1 ATA AT-A ATA ATA ATA ATA ATA -ATA ATA ATA -ATA ATA ATA ATA ATA
* * *
2707014 ATA TATA AT- ATA AGTA GTA A-C ATA A-A A-A AT- GTA ACGTA TATA
1 ATA -ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA A--TA -ATA
* * * * *
2707056 ATA ATA ATGT ATA ATA ATA TTG ATA CTA ATA ATA GTA A-A AT- ATA
1 ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
2707100 A-A ATTA ATA GATA ATA ATA GTT A-A AT- ATA AAA ATA ATA GATA ATA
1 ATA A-TA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA
*
2707145 ATA ATAA ACA ATGA ATA AT- ATA ATA A-A ATA ATA ATA A
1 ATA AT-A ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA A
2707182 CTAAATAAAA
Statistics
Matches: 293, Mismatches: 62, Indels: 92
0.66 0.14 0.21
Matches are distributed among these distances:
2 32 0.11
3 193 0.66
4 63 0.22
5 4 0.01
6 1 0.00
ACGTcount: A:0.57, C:0.03, G:0.05, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2706796 original size:13 final size:13
Alignment explanation
Indices: 2706778--2707189 Score: 82
Period size: 13 Copynumber: 30.8 Consensus size: 13
2706768 ATATAATTTT
2706778 ATAATAAATAATA
1 ATAATAAATAATA
2706791 ATAATAAATTAATA
1 ATAATAAA-TAATA
* *
2706805 TACAATTAATAATA
1 -ATAATAAATAATA
* *
2706819 A-ATATTAATATTA
1 ATA-ATAAATAATA
*
2706832 CATAATGATATAATA
1 -ATAAT-AAATAATA
* *
2706847 CTAAT-AATAGTA
1 ATAATAAATAATA
* *
2706859 ATAATAGACAATA
1 ATAATAAATAATA
* *
2706872 ATATTGAATATATA
1 ATAATAAATA-ATA
* *
2706886 ATTACAACATTTAATA
1 ATAATAA-A--TAATA
* *
2706902 CTAATGAATAA-A
1 ATAATAAATAATA
* *
2706914 AAAGATAGATAATA
1 ATA-ATAAATAATA
*
2706928 ATAATAGAGTAATA
1 ATAATA-AATAATA
2706942 ATAATATAA-AATA
1 ATAATA-AATAATA
* ** *
2706955 ATATTACTTATTA
1 ATAATAAATAATA
2706968 ATAATAAATACTATA
1 ATAATAAATA--ATA
* * *
2706983 ATAGTATATAATT
1 ATAATAAATAATA
*
2706996 AT-ATGTAATAAT-
1 ATAAT-AAATAATA
*
2707008 TTAAT-AATATATA
1 ATAATAAATA-ATA
* *
2707021 AT-ATAAGTAGTA
1 ATAATAAATAATA
* *
2707033 A-CATAAAAAAT-
1 ATAATAAATAATA
* *
2707044 GTAACGTATATAATA
1 ATAA--TAAATAATA
**
2707059 ATAATGTATAATA
1 ATAATAAATAATA
* *
2707072 ATATTGATACTAATA
1 ATAAT-A-AATAATA
*
2707087 ATAGTAAA-ATATA
1 ATAATAAATA-ATA
*
2707100 A-AATTAATAGATA
1 ATAATAAATA-ATA
**
2707113 ATAATAGTTAA-A
1 ATAATAAATAATA
2707125 TATAA-AAATAATA
1 -ATAATAAATAATA
2707138 GATAAT-AATAATAA
1 -ATAATAAATAAT-A
* *
2707152 ACAATGAATAAT-
1 ATAATAAATAATA
2707164 ATAATAAAATAATA
1 ATAAT-AAATAATA
2707178 ATAACTAAATAA
1 ATAA-TAAATAA
2707190 AAACATATAA
Statistics
Matches: 280, Mismatches: 79, Indels: 79
0.64 0.18 0.18
Matches are distributed among these distances:
11 4 0.01
12 42 0.15
13 122 0.44
14 67 0.24
15 37 0.13
16 6 0.02
17 2 0.01
ACGTcount: A:0.58, C:0.03, G:0.05, T:0.34
Consensus pattern (13 bp):
ATAATAAATAATA
Found at i:2706846 original size:24 final size:23
Alignment explanation
Indices: 2706768--2706852 Score: 59
Period size: 24 Copynumber: 3.6 Consensus size: 23
2706758 TTAGTTATAT
* *
2706768 ATATAAT-TTTATAATAAATAATA
1 ATATAATATTAAT-ATACATAATA
*
2706791 ATA-ATAAATTAATATACAATTAATA
1 ATATA-ATATTAATATAC-A-TAATA
*
2706816 ATA-AATATTAATATTACATAATG
1 ATATAATATTAATA-TACATAATA
*
2706839 ATATAATACTAATA
1 ATATAATATTAATA
2706853 ATAGTAATAA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
22 1 0.02
23 14 0.28
24 23 0.46
25 12 0.24
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.39
Consensus pattern (23 bp):
ATATAATATTAATATACATAATA
Found at i:2707120 original size:29 final size:29
Alignment explanation
Indices: 2707082--2707152 Score: 115
Period size: 29 Copynumber: 2.4 Consensus size: 29
2707072 ATATTGATAC
*
2707082 TAATAATAGTAAAATATAAAATTAATAGA
1 TAATAATAGTAAAATATAAAAATAATAGA
*
2707111 TAATAATAGTTAAATATAAAAATAATAGA
1 TAATAATAGTAAAATATAAAAATAATAGA
*
2707140 TAATAATAATAAA
1 TAATAATAGTAAA
2707153 CAATGAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (29 bp):
TAATAATAGTAAAATATAAAAATAATAGA
Found at i:2707148 original size:19 final size:19
Alignment explanation
Indices: 2707112--2707192 Score: 53
Period size: 20 Copynumber: 4.1 Consensus size: 19
2707102 ATTAATAGAT
*
2707112 AATAATAGTTAA-ATATAAA
1 AATAATAGATAATA-ATAAA
2707131 AATAATAGATAATAATAATA
1 AATAATAGATAATAATAA-A
*
2707151 AACAAT-GAATAAT-ATAATAA
1 AATAATAG-ATAATAAT-A-AA
2707171 AATAATA-ATAACTAAATAAA
1 AATAATAGATAA-T-AATAAA
2707191 AA
1 AA
2707193 CATATAATAA
Statistics
Matches: 50, Mismatches: 3, Indels: 17
0.71 0.04 0.24
Matches are distributed among these distances:
19 22 0.44
20 24 0.48
21 2 0.04
22 2 0.04
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (19 bp):
AATAATAGATAATAATAAA
Found at i:2707651 original size:36 final size:36
Alignment explanation
Indices: 2707585--2707666 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 36
2707575 GTATTTATGG
* * *
2707585 GTTAAGTCTGATTTGTGGGCGACTCTTACATTGCAA
1 GTTAAGTCTGATTTATGGGCGACGCTTACATTACAA
* * *
2707621 GTTAAGTTTGATTTATGGGTGACAGC-TACATTACGA
1 GTTAAGTCTGATTTATGGGCGAC-GCTTACATTACAA
2707657 GTTAAGTCTG
1 GTTAAGTCTG
2707667 GTGGGAAATA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
36 37 0.97
37 1 0.03
ACGTcount: A:0.24, C:0.13, G:0.26, T:0.37
Consensus pattern (36 bp):
GTTAAGTCTGATTTATGGGCGACGCTTACATTACAA
Found at i:2709724 original size:53 final size:53
Alignment explanation
Indices: 2709629--2710013 Score: 423
Period size: 53 Copynumber: 7.2 Consensus size: 53
2709619 AGGATGTTTT
* * * *
2709629 AAAAGGTGAGTCTTTCATTTATGTATGATGATGTATGCGGGAAATAAATTAGG
1 AAAATGTGAGTCTTTCATTTATGGATGATGATGTATGTGGGAAAGAAATTAGG
* * * *
2709682 AAAATGTTAGTATTTCATTTATGGATAATGATGTATGTGGGAAAGAAATTAGA
1 AAAATGTGAGTCTTTCATTTATGGATGATGATGTATGTGGGAAAGAAATTAGG
** * *
2709735 AAAATGTGAGTCTTTCATTTATGGATGATGATGTATACGAGCATA-AAATTAGG
1 AAAATGTGAGTCTTTCATTTATGGATGATGATGTATGTG-GGAAAGAAATTAGG
* * * * **
2709788 AAAAGGTGAATCTTTTATTTATGGATGATGATGTATGTAGTCAAGAAATTAGG
1 AAAATGTGAGTCTTTCATTTATGGATGATGATGTATGTGGGAAAGAAATTAGG
* * * * * *
2709841 AAAAAGTAAGTCTTTCATTTATAGATGATGATGTAAGAGGGCAAGAAATTAGG
1 AAAATGTGAGTCTTTCATTTATGGATGATGATGTATGTGGGAAAGAAATTAGG
* * * *
2709894 AATATGTGATTCTTTTATTTATGGATGATGATGTATGTGGGTAAGAAATTAGG
1 AAAATGTGAGTCTTTCATTTATGGATGATGATGTATGTGGGAAAGAAATTAGG
* * * * *
2709947 AAAAAGGTAAGTCTTTAATTTATGGATGATGATTTATGTAGGCAAA-AAATTAGG
1 -AAAATGTGAGTCTTTCATTTATGGATGATGATGTATGT-GGGAAAGAAATTAGG
*
2710001 AAAAGGTGAGTCT
1 AAAATGTGAGTCT
2710014 CCCCCTCATT
Statistics
Matches: 276, Mismatches: 52, Indels: 8
0.82 0.15 0.02
Matches are distributed among these distances:
52 2 0.01
53 227 0.82
54 43 0.16
55 4 0.01
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.34
Consensus pattern (53 bp):
AAAATGTGAGTCTTTCATTTATGGATGATGATGTATGTGGGAAAGAAATTAGG
Found at i:2709918 original size:159 final size:160
Alignment explanation
Indices: 2709629--2710013 Score: 472
Period size: 159 Copynumber: 2.4 Consensus size: 160
2709619 AGGATGTTTT
* * * * * * *
2709629 AAAAGGTGAGTCTTTCATTTATGTATGATGATGTATG-CGGGAAATAAATTAGGAAAATGTTAGT
1 AAAAGGTGAATCTTTAATTTATGGATGATGATGTATGTAGGCAAA-AAATTAGGAAAAAGTAAGT
* * * *
2709693 ATTTCATTTATGGATAATGATGTATGTGGGAAAGAAATTAGAAAAATGTGAGTCTTTCATTTATG
65 CTTTCATTTATAGATAATGATGTAAGAGGGAAAGAAATTAGAAAAATGTGAGTCTTTCATTTATG
2709758 GATGATGATGTATACGAGCATA-AAATTAGG-
130 GATGATGATGTATACGAGCA-AGAAATTAGGA
* * *
2709788 AAAAGGTGAATCTTTTATTTATGGATGATGATGTATGTAGTCAAGAAATTAGGAAAAAGTAAGTC
1 AAAAGGTGAATCTTTAATTTATGGATGATGATGTATGTAGGCAAAAAATTAGGAAAAAGTAAGTC
* * * * * *
2709853 TTTCATTTATAGATGATGATGTAAGAGGGCAAGAAATTAGGAATATGTGATTCTTTTATTTATGG
66 TTTCATTTATAGATAATGATGTAAGAGGGAAAGAAATTAGAAAAATGTGAGTCTTTCATTTATGG
** * *
2709918 ATGATGATGTATGTGGGTAAGAAATTAGGA
131 ATGATGATGTATACGAGCAAGAAATTAGGA
* * *
2709948 AAAAGGT-AAGTCTTTAATTTATGGATGATGATTTATGTAGGCAAAAAATTAGGAAAAGGTGAGT
1 AAAAGGTGAA-TCTTTAATTTATGGATGATGATGTATGTAGGCAAAAAATTAGGAAAAAGTAAGT
2710012 CT
65 CT
2710014 CCCCCTCATT
Statistics
Matches: 193, Mismatches: 29, Indels: 7
0.84 0.13 0.03
Matches are distributed among these distances:
158 1 0.01
159 132 0.68
160 60 0.31
ACGTcount: A:0.37, C:0.04, G:0.24, T:0.34
Consensus pattern (160 bp):
AAAAGGTGAATCTTTAATTTATGGATGATGATGTATGTAGGCAAAAAATTAGGAAAAAGTAAGTC
TTTCATTTATAGATAATGATGTAAGAGGGAAAGAAATTAGAAAAATGTGAGTCTTTCATTTATGG
ATGATGATGTATACGAGCAAGAAATTAGGA
Found at i:2716127 original size:22 final size:22
Alignment explanation
Indices: 2716099--2716142 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
2716089 TAGTTGGGTT
2716099 TGGGGTTAATTTGGTTTTGAGA
1 TGGGGTTAATTTGGTTTTGAGA
2716121 TGGGGTTAATTTGGTTTTGAGA
1 TGGGGTTAATTTGGTTTTGAGA
2716143 CTGTTTGAGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.36, T:0.45
Consensus pattern (22 bp):
TGGGGTTAATTTGGTTTTGAGA
Found at i:2716927 original size:74 final size:74
Alignment explanation
Indices: 2716821--2717178 Score: 517
Period size: 73 Copynumber: 4.9 Consensus size: 74
2716811 AGGGCGTTGT
*
2716821 TTGTTTTAAGAAAAA-AATATCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCG
1 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCG
2716885 AGATAAATC
66 AGATAAATC
* * * *
2716894 TTGTTTTATGAAAAATAATCTCAAGTGAGATAAATCTTCTGTTTTGAGTGAAACTATCTCAAGTG
1 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCG
* *
2716959 AGGT-GATC
66 AGATAAATC
* * *
2716967 TTGTTTTAAGAAAAACAATCTCAAGTGAGCTAAATCTTCTATTTCGACTGAAACTATCTCAAGCG
1 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCG
2717032 -GCATAAATC
66 AG-ATAAATC
* * *
2717041 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTTTGTTT-TAGTGAAACTATCTCAAGTG
1 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCG
*
2717105 AGATGAATC
66 AGATAAATC
* * * *
2717114 TTGTTTTAAGAAAAACAATATCAAGTGAGATAAATCATCTGTCTCAAGTGAAACTATCTCAAGCG
1 TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCG
2717179 TCTTCTGTTT
Statistics
Matches: 252, Mismatches: 28, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
72 1 0.00
73 139 0.55
74 112 0.44
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (74 bp):
TTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCG
AGATAAATC
Found at i:2717003 original size:147 final size:147
Alignment explanation
Indices: 2716821--2717178 Score: 578
Period size: 147 Copynumber: 2.4 Consensus size: 147
2716811 AGGGCGTTGT
2716821 TTGTTTTAAGAAAAA-AATATCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCG
1 TTGTTTTAAGAAAAACAATATCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCG
* *
2716885 AG-ATAAATCTTGTTTTATGAAAAATAATCTCAAGTGAGATAAATCTTCTGTTTTGAGTGAAACT
66 -GCATAAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTT-AGTGAAACT
*
2716949 ATCTCAAGTGAGGTG-ATC
129 ATCTCAAGTGAGATGAATC
* * * *
2716967 TTGTTTTAAGAAAAACAATCTCAAGTGAGCTAAATCTTCTATTTCGACTGAAACTATCTCAAGCG
1 TTGTTTTAAGAAAAACAATATCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCG
*
2717032 GCATAAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTTTGTTTTAGTGAAACTAT
66 GCATAAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTTAGTGAAACTAT
2717097 CTCAAGTGAGATGAATC
131 CTCAAGTGAGATGAATC
* * *
2717114 TTGTTTTAAGAAAAACAATATCAAGTGAGATAAATCATCTGTCTCAAGTGAAACTATCTCAAGCG
1 TTGTTTTAAGAAAAACAATATCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCG
2717179 TCTTCTGTTT
Statistics
Matches: 194, Mismatches: 15, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
146 39 0.20
147 155 0.80
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (147 bp):
TTGTTTTAAGAAAAACAATATCAAGTGAGATAAATCTTCTGTTTCGAGTGAAACTATCTCAAGCG
GCATAAATCTTGTTTTAAGAAAAACAATCTCAAGTGAGATAAATCTTCTGTTTTAGTGAAACTAT
CTCAAGTGAGATGAATC
Found at i:2717195 original size:31 final size:31
Alignment explanation
Indices: 2717151--2717209 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
2717141 AGATAAATCA
2717151 TCTGTCTCAAGTGAAACTATCTCAAGCGTCT
1 TCTGTCTCAAGTGAAACTATCTCAAGCGTCT
* *
2717182 TCTGTTTCGAGTGAAACTATCTCAAGCG
1 TCTGTCTCAAGTGAAACTATCTCAAGCG
2717210 AGATGAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (31 bp):
TCTGTCTCAAGTGAAACTATCTCAAGCGTCT
Found at i:2726065 original size:17 final size:17
Alignment explanation
Indices: 2726040--2726074 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
2726030 TTCCTTAGCC
*
2726040 GAATAGGCTTAGGAGTG
1 GAATAGGCTAAGGAGTG
*
2726057 GAATCGGCTAAGGAGTG
1 GAATAGGCTAAGGAGTG
2726074 G
1 G
2726075 TTATTTTACT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.09, G:0.43, T:0.20
Consensus pattern (17 bp):
GAATAGGCTAAGGAGTG
Found at i:2727831 original size:90 final size:87
Alignment explanation
Indices: 2727675--2727847 Score: 265
Period size: 90 Copynumber: 2.0 Consensus size: 87
2727665 CCTAACACAC
* * *
2727675 CCTTTTATAGCCAAGTTACCTTATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTGTAT
1 CCTTTTATAGCCAAGTTACCTAATCATATTAGGGTTTTATTATTTCAAATTAATCAAATCTATAT
*
2727740 TTAATTAATTTGAATTTAATAAT
66 TTAATTAA-TTGAAATTAATAAT
* *
2727763 CCTTTTATATCCAAGTTACTCTAATTATATTAGGGATTTTATTATTTCAAATTAATCAAATCTAT
1 CCTTTTATAGCCAAGTTAC-CTAATCATATTAGGG-TTTTATTATTTCAAATTAATCAAATCTAT
2727828 ATTTAATTAATTGAAATTAA
64 ATTTAATTAATTGAAATTAA
2727848 ATATTCGAGT
Statistics
Matches: 77, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
88 18 0.23
89 22 0.29
90 37 0.48
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.47
Consensus pattern (87 bp):
CCTTTTATAGCCAAGTTACCTAATCATATTAGGGTTTTATTATTTCAAATTAATCAAATCTATAT
TTAATTAATTGAAATTAATAAT
Found at i:2728598 original size:20 final size:20
Alignment explanation
Indices: 2728573--2728619 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
2728563 TATAATCATG
2728573 TATCAATTCTGACATCTCTA
1 TATCAATTCTGACATCTCTA
2728593 TATCAATTCTGACATCTCTA
1 TATCAATTCTGACATCTCTA
*
2728613 TGTCAAT
1 TATCAAT
2728620 AGTGGCAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.30, C:0.23, G:0.06, T:0.40
Consensus pattern (20 bp):
TATCAATTCTGACATCTCTA
Found at i:2734453 original size:89 final size:89
Alignment explanation
Indices: 2734302--2734466 Score: 287
Period size: 89 Copynumber: 1.9 Consensus size: 89
2734292 CCTAACACAC
2734302 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
2734367 TTTAATTAATTGGAATTTAATAAT
66 TTTAATTAATTGGAATTTAATAAT
* *
2734391 CCTTTTATATCCAAGTTA-CCTAATCATATTAGGGATTTTATTATTTTAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTAT
*
2734455 ATTTATTTAATT
65 ATTTAATTAATT
2734467 AAAATTAAAT
Statistics
Matches: 72, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
88 16 0.22
89 56 0.78
ACGTcount: A:0.35, C:0.11, G:0.07, T:0.47
Consensus pattern (89 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
TTTAATTAATTGGAATTTAATAAT
Found at i:2739073 original size:23 final size:23
Alignment explanation
Indices: 2739039--2739094 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
2739029 TCTTCTTATT
2739039 AAAA-AAAAAAGTAGCAATTCAA
1 AAAAGAAAAAAGTAGCAATTCAA
*
2739061 AAAAGAAAAAAGTAGCAGTTCAA
1 AAAAGAAAAAAGTAGCAATTCAA
2739084 AAAAGAAAAAA
1 AAAAGAAAAAA
2739095 TAAAAGAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 4 0.12
23 28 0.88
ACGTcount: A:0.70, C:0.07, G:0.12, T:0.11
Consensus pattern (23 bp):
AAAAGAAAAAAGTAGCAATTCAA
Found at i:2739123 original size:12 final size:12
Alignment explanation
Indices: 2739084--2739115 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
2739074 AGCAGTTCAA
*
2739084 AAAAGAAAAAAT
1 AAAAGAAAAAAG
2739096 AAAAGAAAAAAG
1 AAAAGAAAAAAG
2739108 AAAAGAAA
1 AAAAGAAA
2739116 TCAGAAAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.12, T:0.03
Consensus pattern (12 bp):
AAAAGAAAAAAG
Found at i:2740237 original size:12 final size:12
Alignment explanation
Indices: 2740199--2740244 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
2740189 CTTCTTTTCC
2740199 TTATTTTCAAGTT
1 TTATTTT-AAGTT
*
2740212 TTCATTTTCA-TT
1 TT-ATTTTAAGTT
2740224 TTATTTTAAGTT
1 TTATTTTAAGTT
2740236 TTATTTTAA
1 TTATTTTAA
2740245 ACATGCTAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
11 6 0.21
12 15 0.52
13 3 0.10
14 5 0.17
ACGTcount: A:0.24, C:0.07, G:0.04, T:0.65
Consensus pattern (12 bp):
TTATTTTAAGTT
Found at i:2741233 original size:53 final size:53
Alignment explanation
Indices: 2741151--2741688 Score: 582
Period size: 53 Copynumber: 10.1 Consensus size: 53
2741141 TTTTAAAAGT
* * * * *
2741151 TGAGTCTTTCATTCATGGATGATGATGTATGAGAGAAAAAAATTAGGAAAATG
1 TGAGTCTTTCATTTATGGATGATGATGTATGCGGGCAAGAAATTAGGAAAATG
* ** * *
2741204 TGAGTCTTTCATTTATGGATGATGGTGTATGCATGTAAGAAATTAAG-AAATCG
1 TGAGTCTTTCATTTATGGATGATGATGTATGCGGGCAAGAAATTAGGAAAAT-G
* * * * * * * *
2741257 GGAGTTTTTTATTTATGGATAATAATGTATACGAGCAAGAAATTAGGAAAGTG
1 TGAGTCTTTCATTTATGGATGATGATGTATGCGGGCAAGAAATTAGGAAAATG
* * * *
2741310 AGAGTGTTTCATTTATAGACT-ATGATGTATGTGGGCAAGAAATTAGGAAAATG
1 TGAGTCTTTCATTTATGGA-TGATGATGTATGCGGGCAAGAAATTAGGAAAATG
* * * * * *
2741363 TGAGTCTTTCTTTTATGAATAATGAAGTATGCGAGCAAGAAATTAGGAAAAAG
1 TGAGTCTTTCATTTATGGATGATGATGTATGCGGGCAAGAAATTAGGAAAATG
* *
2741416 TGAGTATTTCATTTATGGATGATGATGTATGCGGGCAAGAAACTAGGAAAATG
1 TGAGTCTTTCATTTATGGATGATGATGTATGCGGGCAAGAAATTAGGAAAATG
* *
2741469 TGAGTCTTTCATTTATGGATGATGATGTATGCGGGCAAGAAATTAGAAAAATA
1 TGAGTCTTTCATTTATGGATGATGATGTATGCGGGCAAGAAATTAGGAAAATG
* * * *
2741522 TGAGTCTTTAATTTTTGGATGATGATATATGCGGGAAAGAAATTAGGAAAATG
1 TGAGTCTTTCATTTATGGATGATGATGTATGCGGGCAAGAAATTAGGAAAATG
* * *
2741575 TTAGTCTTTCATTTGCT-GATGAT-AGTGTATGCGGGCTAGAAATTAGGAAAATG
1 TGAGTCTTTCATTT-ATGGATGATGA-TGTATGCGGGCAAGAAATTAGGAAAATG
** ** * *
2741628 AAAACCTTTCATTTATGGATGATGATGTATGAGGG-AAAAGAATTAGGAAAATGG
1 TGAGTCTTTCATTTATGGATGATGATGTATGCGGGCAAGA-AATTAGGAAAAT-G
2741682 TGAGTCT
1 TGAGTCT
2741689 CCCCCATAAT
Statistics
Matches: 401, Mismatches: 74, Indels: 19
0.81 0.15 0.04
Matches are distributed among these distances:
52 9 0.02
53 382 0.95
54 10 0.02
ACGTcount: A:0.36, C:0.07, G:0.25, T:0.32
Consensus pattern (53 bp):
TGAGTCTTTCATTTATGGATGATGATGTATGCGGGCAAGAAATTAGGAAAATG
Found at i:2759426 original size:33 final size:32
Alignment explanation
Indices: 2759372--2759447 Score: 91
Period size: 33 Copynumber: 2.3 Consensus size: 32
2759362 CATTGAGCAT
* *
2759372 AAGAGCCAACCTAAGAGAGTACCCTGGGGCCT
1 AAGAGCCTACCTAAGAGAGTACCCTGGGGCCC
* *
2759404 TAGAGCCTACACTAAG-GAAGTACCTTGGGGCCC
1 AAGAGCCTAC-CTAAGAG-AGTACCCTGGGGCCC
2759437 AAGAGCCTACC
1 AAGAGCCTACC
2759448 CAAGGGTCAC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
32 10 0.27
33 27 0.73
ACGTcount: A:0.30, C:0.29, G:0.26, T:0.14
Consensus pattern (32 bp):
AAGAGCCTACCTAAGAGAGTACCCTGGGGCCC
Found at i:2761913 original size:59 final size:59
Alignment explanation
Indices: 2761841--2762043 Score: 253
Period size: 59 Copynumber: 3.4 Consensus size: 59
2761831 AGTGTATATA
*
2761841 GTGGGCATAACCTTATGTGTCATATTTGGGACTGTACTTAAGTATACCTAGTAAAGAGG
1 GTGGACATAACCTTATGTGTCATATTTGGGACTGTACTTAAGTATACCTAGTAAAGAGG
* ** ** * * ** * **
2761900 GTGGACATGACCTTATGTGTCATACTCGGGAGACTACACTAAAGTATAGCTAGTGTATATA
1 GTGGACATAACCTTATGTGTCATA-TTTGG-GACTGTACTTAAGTATACCTAGTAAAGAGG
*
2761961 GTGGGCATAACCTTATGTGTCATATTTGGGACTGTACTTAAGTATACCTAGTAAAGAGG
1 GTGGACATAACCTTATGTGTCATATTTGGGACTGTACTTAAGTATACCTAGTAAAGAGG
*
2762020 GTGGACATGACCTTATGTGTCATA
1 GTGGACATAACCTTATGTGTCATA
2762044 CTCGGTATAG
Statistics
Matches: 114, Mismatches: 28, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
59 65 0.57
60 6 0.05
61 43 0.38
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.32
Consensus pattern (59 bp):
GTGGACATAACCTTATGTGTCATATTTGGGACTGTACTTAAGTATACCTAGTAAAGAGG
Found at i:2761974 original size:61 final size:60
Alignment explanation
Indices: 2761809--2761985 Score: 221
Period size: 59 Copynumber: 3.0 Consensus size: 60
2761799 CTGCATATTC
**
2761809 GAGACTACACTAAAGTATAGCTAGTGTATATAGTGGGCATAACCTTATGTGTCATATTTG
1 GAGACTACACTAAAGTATAGCTAGTGTATATAGTGGGCATAACCTTATGTGTCATATCGG
** * * ** * ** * *
2761869 G-GACTGTACTTAAGTATACCTAGTAAAGAGGGTGGACATGACCTTATGTGTCATACTCGG
1 GAGACTACACTAAAGTATAGCTAGTGTATATAGTGGGCATAACCTTATGTGTCATA-TCGG
2761929 GAGACTACACTAAAGTATAGCTAGTGTATATAGTGGGCATAACCTTATGTGTCATAT
1 GAGACTACACTAAAGTATAGCTAGTGTATATAGTGGGCATAACCTTATGTGTCATAT
2761986 TTGGGACTGT
Statistics
Matches: 91, Mismatches: 24, Indels: 4
0.76 0.20 0.03
Matches are distributed among these distances:
59 43 0.47
60 5 0.05
61 43 0.47
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (60 bp):
GAGACTACACTAAAGTATAGCTAGTGTATATAGTGGGCATAACCTTATGTGTCATATCGG
Found at i:2762022 original size:120 final size:120
Alignment explanation
Indices: 2761809--2762048 Score: 480
Period size: 120 Copynumber: 2.0 Consensus size: 120
2761799 CTGCATATTC
2761809 GAGACTACACTAAAGTATAGCTAGTGTATATAGTGGGCATAACCTTATGTGTCATATTTGGGACT
1 GAGACTACACTAAAGTATAGCTAGTGTATATAGTGGGCATAACCTTATGTGTCATATTTGGGACT
2761874 GTACTTAAGTATACCTAGTAAAGAGGGTGGACATGACCTTATGTGTCATACTCGG
66 GTACTTAAGTATACCTAGTAAAGAGGGTGGACATGACCTTATGTGTCATACTCGG
2761929 GAGACTACACTAAAGTATAGCTAGTGTATATAGTGGGCATAACCTTATGTGTCATATTTGGGACT
1 GAGACTACACTAAAGTATAGCTAGTGTATATAGTGGGCATAACCTTATGTGTCATATTTGGGACT
2761994 GTACTTAAGTATACCTAGTAAAGAGGGTGGACATGACCTTATGTGTCATACTCGG
66 GTACTTAAGTATACCTAGTAAAGAGGGTGGACATGACCTTATGTGTCATACTCGG
2762049 TATAGCACTA
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
120 120 1.00
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (120 bp):
GAGACTACACTAAAGTATAGCTAGTGTATATAGTGGGCATAACCTTATGTGTCATATTTGGGACT
GTACTTAAGTATACCTAGTAAAGAGGGTGGACATGACCTTATGTGTCATACTCGG
Found at i:2776286 original size:167 final size:169
Alignment explanation
Indices: 2776010--2776348 Score: 646
Period size: 167 Copynumber: 2.0 Consensus size: 169
2776000 GCCTAGGAAT
2776010 GACACCTCCTTCTGATCAAACAAGCATTTTTCCTCTCAAGTGCTCAATGTGTTCCTCTAAGGTCT
1 GACACCTCCTTCTGATCAAACAAGCATTTTTCCTCTCAAGTGCTCAATGTGTTCCTCTAAGGTCT
2776075 TACTATACACCACAATGTCATCAAGGTAAACTATAACAAAATGATCAGGAAATGGTTGTACTACC
66 TACTATACACCACAATGTCATCAAGGTAAACTATAACAAAATGATCAGGAAATGGTTGTACTACC
2776140 TTATTCATCAA-TGTAGAAGGT-AAGGGGAATTTGTGAG
131 TTATTCATCAAGTGTAGAAGGTAAAGGGGAATTTGTGAG
2776177 GACACCTCCTTCTGATCAAACAAGCATTTTTCCTCTCAAGTGCTCAATGTGTTCCTCTAAGGTCT
1 GACACCTCCTTCTGATCAAACAAGCATTTTTCCTCTCAAGTGCTCAATGTGTTCCTCTAAGGTCT
2776242 TACTATACACCACAATGTCATCAAGGTAAACTATAACAAAATGATCAGGAAATGGTTGTACTACC
66 TACTATACACCACAATGTCATCAAGGTAAACTATAACAAAATGATCAGGAAATGGTTGTACTACC
2776307 TTATTCATCAATGTGTAGAAGGTAGAAGGGGAATTTGTGAG
131 TTATTCATCAA-GTGTAGAAGGTA-AAGGGGAATTTGTGAG
2776348 G
1 G
2776349 CTAAAGGGCA
Statistics
Matches: 168, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
167 141 0.84
169 10 0.06
171 17 0.10
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.30
Consensus pattern (169 bp):
GACACCTCCTTCTGATCAAACAAGCATTTTTCCTCTCAAGTGCTCAATGTGTTCCTCTAAGGTCT
TACTATACACCACAATGTCATCAAGGTAAACTATAACAAAATGATCAGGAAATGGTTGTACTACC
TTATTCATCAAGTGTAGAAGGTAAAGGGGAATTTGTGAG
Found at i:2783805 original size:21 final size:21
Alignment explanation
Indices: 2783776--2783882 Score: 121
Period size: 20 Copynumber: 5.2 Consensus size: 21
2783766 GATTCTGACT
2783776 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGAGTATCCGTAAA
* *
2783797 ATCGTAACGCGTATCCGT-AA
1 ATCGCAACGAGTATCCGTAAA
** *
2783817 ATCGCAACGACAATACGTAAA
1 ATCGCAACGAGTATCCGTAAA
*
2783838 ATCGCAACGCGTATCCGT-AA
1 ATCGCAACGAGTATCCGTAAA
* *
2783858 ATCGCAACGAGAATACGT-AA
1 ATCGCAACGAGTATCCGTAAA
2783878 ATCGC
1 ATCGC
2783883 CATGTCAAGA
Statistics
Matches: 71, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
20 39 0.55
21 32 0.45
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (21 bp):
ATCGCAACGAGTATCCGTAAA
Found at i:2783821 original size:41 final size:41
Alignment explanation
Indices: 2783735--2783882 Score: 171
Period size: 41 Copynumber: 3.7 Consensus size: 41
2783725 AATTTTCCAG
* *
2783735 AATCGCAACGCA-AATATG-AAAATCGCAACGCG-ATTC-TGA
1 AATCGCAACG-AGAATACGTAAAATCGCAACGCGTATCCGT-A
* * * *
2783774 CTATCGCAACGAGTATCCGTAAAATCGTAACGCGTATCCGTA
1 -AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTA
*
2783816 AATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTA
2783857 AATCGCAACGAGAATACGT-AAATCGC
1 AATCGCAACGAGAATACGTAAAATCGC
2783883 CATGTCAAGA
Statistics
Matches: 92, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
39 1 0.01
40 19 0.21
41 67 0.73
42 4 0.04
43 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (41 bp):
AATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTA
Found at i:2785239 original size:33 final size:34
Alignment explanation
Indices: 2785182--2785277 Score: 140
Period size: 33 Copynumber: 2.9 Consensus size: 34
2785172 AAATCTTTCG
2785182 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
*
2785216 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
* ** *
2785249 CGTTGCTATAGTCATTTTCGCGTTGCGAT
1 CGTTGCGATTTTCATTTTCGCATTGCGAT
2785278 AGTCTGTTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 29 0.52
34 27 0.48
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.44
Consensus pattern (34 bp):
CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
Found at i:2785397 original size:14 final size:14
Alignment explanation
Indices: 2785378--2785414 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
2785368 CATCAATTAA
2785378 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
2785392 ACAAATCATCTTTT
1 ACAAATCAACATTT
2785406 ACAAATCAA
1 ACAAATCAA
2785415 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:2786368 original size:98 final size:98
Alignment explanation
Indices: 2786199--2786394 Score: 392
Period size: 98 Copynumber: 2.0 Consensus size: 98
2786189 CCATTAGGCA
2786199 ACACATATGATTACTGTCGTTGATTCTTCAAGTGAACCACGTGAAAAGACGTCGGCATAATTGTA
1 ACACATATGATTACTGTCGTTGATTCTTCAAGTGAACCACGTGAAAAGACGTCGGCATAATTGTA
2786264 TATCACGTTTTTTTAATATTTTTCTTCAATTTC
66 TATCACGTTTTTTTAATATTTTTCTTCAATTTC
2786297 ACACATATGATTACTGTCGTTGATTCTTCAAGTGAACCACGTGAAAAGACGTCGGCATAATTGTA
1 ACACATATGATTACTGTCGTTGATTCTTCAAGTGAACCACGTGAAAAGACGTCGGCATAATTGTA
2786362 TATCACGTTTTTTTAATATTTTTCTTCAATTTC
66 TATCACGTTTTTTTAATATTTTTCTTCAATTTC
2786395 CTTACAATTA
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 98 1.00
ACGTcount: A:0.29, C:0.17, G:0.14, T:0.40
Consensus pattern (98 bp):
ACACATATGATTACTGTCGTTGATTCTTCAAGTGAACCACGTGAAAAGACGTCGGCATAATTGTA
TATCACGTTTTTTTAATATTTTTCTTCAATTTC
Found at i:2787467 original size:20 final size:20
Alignment explanation
Indices: 2787441--2787563 Score: 201
Period size: 20 Copynumber: 6.2 Consensus size: 20
2787431 GAAACTTAAA
*
2787441 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
*
2787461 ATGGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
2787481 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
2787501 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
2787521 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
* **
2787541 ATCGCAATACGAATTTGACT
1 ATCGCAATGCGAAAATGACT
2787561 ATC
1 ATC
2787564 ACAACGAGAG
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 97 1.00
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.21
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:2787624 original size:19 final size:19
Alignment explanation
Indices: 2787611--2787711 Score: 132
Period size: 19 Copynumber: 5.8 Consensus size: 19
2787601 CGCGATTATA
2787611 GTTTCGCGTTGCGATTTTG
1 GTTTCGCGTTGCGATTTTG
2787630 GTTTCGCGTTGCGATTTT-
1 GTTTCGCGTTGCGATTTTG
2787648 G--T--CGTTGCGATTTTG
1 GTTTCGCGTTGCGATTTTG
2787663 GTTTCGCGTTGCGATTTT-
1 GTTTCGCGTTGCGATTTTG
2787681 G--T--CGTTGCGATTTTG
1 GTTTCGCGTTGCGATTTTG
2787696 GTTTCGCGTTGCGATT
1 GTTTCGCGTTGCGATT
2787712 CTCTTGTTGC
Statistics
Matches: 72, Mismatches: 0, Indels: 20
0.78 0.00 0.22
Matches are distributed among these distances:
14 24 0.33
15 2 0.03
16 2 0.03
17 2 0.03
18 2 0.03
19 40 0.56
ACGTcount: A:0.06, C:0.16, G:0.31, T:0.48
Consensus pattern (19 bp):
GTTTCGCGTTGCGATTTTG
Found at i:2787655 original size:14 final size:14
Alignment explanation
Indices: 2787636--2787695 Score: 75
Period size: 14 Copynumber: 3.9 Consensus size: 14
2787626 TTTGGTTTCG
2787636 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
2787650 CGTTGCGATTTTGGTTT
1 CGTTGCGATTTT-G--T
2787667 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
2787683 CGTTGCGATTTTG
1 CGTTGCGATTTTG
2787696 GTTTCGCGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
14 25 0.61
15 1 0.02
16 1 0.02
17 1 0.02
18 1 0.02
19 12 0.29
ACGTcount: A:0.07, C:0.15, G:0.30, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:2787659 original size:33 final size:33
Alignment explanation
Indices: 2787617--2787744 Score: 202
Period size: 33 Copynumber: 3.9 Consensus size: 33
2787607 TATAGTTTCG
2787617 CGTTGCGATTTTGGTTTCGCGTTGCGATTTTGT
1 CGTTGCGATTTTGGTTTCGCGTTGCGATTTTGT
2787650 CGTTGCGATTTTGGTTTCGCGTTGCGATTTTGT
1 CGTTGCGATTTTGGTTTCGCGTTGCGATTTTGT
* *
2787683 CGTTGCGATTTTGGTTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTGGTTTCGCGTTGCGATTTTGT
* ** *
2787716 TGTTGCGATTTTTATTTCTCGTTGCGATT
1 CGTTGCGATTTTGGTTTCGCGTTGCGATT
2787745 CATTTCGCGT
Statistics
Matches: 89, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 89 1.00
ACGTcount: A:0.07, C:0.16, G:0.27, T:0.49
Consensus pattern (33 bp):
CGTTGCGATTTTGGTTTCGCGTTGCGATTTTGT
Found at i:2787994 original size:94 final size:94
Alignment explanation
Indices: 2787848--2788227 Score: 640
Period size: 94 Copynumber: 4.1 Consensus size: 94
2787838 ATGGATTGCA
* *
2787848 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
2787912 TTAGCAGAATTGGCAGCAACCAAACAAAT
66 TTAGCAGAATTGGCAGCAACCAAATAAAT
2787941 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
2788006 TTAGCAGAATTGGCAGCAACCGAAA-AAAT
66 TTAGCAGAATTGGCAGCAACC-AAATAAAT
*
2788035 TTACTTTCAACCAAAAGATAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
2788100 TTAGCAGAATTGGCAACAACCGAATAAAT
66 TTAGCAGAATTGGCAGCAACCAAATAAAT
*
2788129 TTAC-TTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAG
* *
2788193 TTTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTTAGCAGAATTGGCAGCAACCAAATAAAT
2788223 TTACT
1 TTACT
2788228 AAGAATCTAA
Statistics
Matches: 273, Mismatches: 9, Indels: 8
0.94 0.03 0.03
Matches are distributed among these distances:
93 24 0.09
94 246 0.90
95 3 0.01
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.21
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
TTAGCAGAATTGGCAGCAACCAAATAAAT
Found at i:2789948 original size:20 final size:20
Alignment explanation
Indices: 2789925--2789980 Score: 80
Period size: 20 Copynumber: 2.8 Consensus size: 20
2789915 TGAAATGAAA
2789925 ATCGCAACGAGAGAATGACT
1 ATCGCAACGAGAGAATGACT
2789945 ATCGCAATACGA-A-AATGACT
1 ATCGC-A-ACGAGAGAATGACT
2789965 ATCGCAACGAGAGAAT
1 ATCGCAACGAGAGAAT
2789981 CGCAACGCGA
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
18 4 0.12
19 2 0.06
20 20 0.62
21 2 0.06
22 4 0.12
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.16
Consensus pattern (20 bp):
ATCGCAACGAGAGAATGACT
Found at i:2790040 original size:14 final size:14
Alignment explanation
Indices: 2790021--2790077 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
2790011 TTTGGTTTCG
2790021 CGTTGCGATTATCT
1 CGTTGCGATTATCT
*
2790035 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TT-A--TCT
*
2790054 CGTTGCGATTCTCT
1 CGTTGCGATTATCT
2790068 CGTTGCGATT
1 CGTTGCGATT
2790078 TTCATTTCGT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 2 0.06
17 3 0.09
19 10 0.29
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTATCT
Found at i:2790053 original size:33 final size:33
Alignment explanation
Indices: 2790005--2790130 Score: 171
Period size: 33 Copynumber: 3.8 Consensus size: 33
2789995 AAAATCGCAA
** *
2790005 TGCGATTTTGGTTTCGCGTTGCGATTATCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
2790038 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
* *
2790071 TGCGATTTTCATTTCGTGTTGCAATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
** *
2790104 TGCGATAGTCATTTTCGTGTTGCGATT
1 TGCGATTTTCA-TTTCGCGTTGCGATT
2790131 TTCATTTTCA
Statistics
Matches: 84, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
33 70 0.83
34 14 0.17
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:2790150 original size:20 final size:20
Alignment explanation
Indices: 2790102--2790152 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
2790092 CAATTCTCTC
** *
2790102 GTTGCGATAGTCATTTTCGT
1 GTTGCGATTTTCATTTTCAT
2790122 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCAT
2790142 GTTGCGATTTT
1 GTTGCGATTTT
2790153 AAGTTTAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.14, C:0.14, G:0.22, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAT
Found at i:2790747 original size:21 final size:21
Alignment explanation
Indices: 2790713--2790803 Score: 98
Period size: 21 Copynumber: 4.4 Consensus size: 21
2790703 TTAAAAATCG
2790713 CGTTGCGA-TTTACGGATTGT
1 CGTTGCGATTTTACGGATTGT
*
2790733 CGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTTACGGATTGT
* *
2790754 CGTTACGA-TTTACGGATACG-
1 CGTTGCGATTTTACGGAT-TGT
* **
2790774 CGTTGCGATTTTACAGATACT
1 CGTTGCGATTTTACGGATTGT
2790795 CGTTGCGAT
1 CGTTGCGAT
2790804 AGTCAGAATC
Statistics
Matches: 59, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
20 23 0.39
21 36 0.61
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (21 bp):
CGTTGCGATTTTACGGATTGT
Found at i:2790798 original size:41 final size:41
Alignment explanation
Indices: 2790713--2790803 Score: 114
Period size: 41 Copynumber: 2.2 Consensus size: 41
2790703 TTAAAAATCG
* **
2790713 CGTTGCGATTTACGGATTGTCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATCGTCGTTGCGATTTTACGTATACT
*
2790754 CGTTACGATTTACGGATACG-CGTTGCGATTTTACAG-ATACT
1 CGTTGCGATTTACGGAT-CGTCGTTGCGATTTTAC-GTATACT
2790795 CGTTGCGAT
1 CGTTGCGAT
2790804 AGTCAGAATC
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
41 41 0.95
42 2 0.05
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (41 bp):
CGTTGCGATTTACGGATCGTCGTTGCGATTTTACGTATACT
Found at i:2790835 original size:20 final size:20
Alignment explanation
Indices: 2790710--2790864 Score: 91
Period size: 20 Copynumber: 7.7 Consensus size: 20
2790700 GCTTTAAAAA
* **
2790710 TCGCGTTGCGATTTACGGAT
1 TCGCGTTGCGATTTTCATAT
*
2790730 T-GTCGTTGCGATTTTACGTAT
1 TCG-CGTTGCGATTTT-CATAT
* * **
2790751 T-GTCGTTACGATTTACGGAT
1 TCG-CGTTGCGATTTTCATAT
* *
2790771 ACGCGTTGCGATTTTACAGAT
1 TCGCGTTGCGATTTT-CATAT
* * ** * *
2790792 ACTCGTTGCGATAGTCAGAA
1 TCGCGTTGCGATTTTCATAT
*
2790812 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
2790832 TCGCGTTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
2790852 TCGCGTTGCGATT
1 TCGCGTTGCGATT
2790865 CTGGAAAATC
Statistics
Matches: 108, Mismatches: 21, Indels: 12
0.77 0.15 0.09
Matches are distributed among these distances:
19 2 0.02
20 71 0.66
21 35 0.32
ACGTcount: A:0.18, C:0.18, G:0.25, T:0.39
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Done.