Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009229.1 Hibiscus syriacus cultivar Beakdansim tig00112835_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: 219427
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1057 original size:23 final size:23
Alignment explanation
Indices: 1030--1080 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
1020 TGTTTAATAT
* * *
1030 TAATAAAATATTTTATTTTATTA
1 TAATAAAATACTTAATTATATTA
*
1053 TAATAATATACTTAATTATATTA
1 TAATAAAATACTTAATTATATTA
1076 TAATA
1 TAATA
1081 TATGATATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (23 bp):
TAATAAAATACTTAATTATATTA
Found at i:2037 original size:23 final size:23
Alignment explanation
Indices: 2011--2066 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
2001 ACCGGTCATA
2011 ACCCGACCCGACCCGACCCGTTG
1 ACCCGACCCGACCCGACCCGTTG
* *
2034 ACCCGACCAGACCTGACCCGTTG
1 ACCCGACCCGACCCGACCCGTTG
2057 ACCCGACCCG
1 ACCCGACCCG
2067 TTGACCGTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.20, C:0.50, G:0.21, T:0.09
Consensus pattern (23 bp):
ACCCGACCCGACCCGACCCGTTG
Found at i:2038 original size:13 final size:13
Alignment explanation
Indices: 2020--2072 Score: 67
Period size: 13 Copynumber: 4.3 Consensus size: 13
2010 AACCCGACCC
2020 GACCCGACCCGTT
1 GACCCGACCCGTT
*
2033 GACCCGA-CC--A
1 GACCCGACCCGTT
*
2043 GACCTGACCCGTT
1 GACCCGACCCGTT
2056 GACCCGACCCGTT
1 GACCCGACCCGTT
2069 GACC
1 GACC
2073 GTTGACCGGC
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
10 6 0.18
11 2 0.06
12 2 0.06
13 23 0.70
ACGTcount: A:0.19, C:0.45, G:0.23, T:0.13
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:4413 original size:47 final size:48
Alignment explanation
Indices: 4346--4462 Score: 175
Period size: 47 Copynumber: 2.4 Consensus size: 48
4336 TTTTCGATTT
4346 GATTTCTGATATGATACTTGACATGGATTCTGATCTGATA-TCTGACATG
1 GATTT-TGATATGATACTTGACATGGATTCTGATCTGATACT-TGACATG
* * *
4395 GA-TTTGATCTGATACTTGACTTGGATTCTGATCTGATACTTGACCTG
1 GATTTTGATATGATACTTGACATGGATTCTGATCTGATACTTGACATG
4442 GATTTTGATATGATACTTGAC
1 GATTTTGATATGATACTTGAC
4463 GTGAATTATG
Statistics
Matches: 62, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
47 40 0.65
48 20 0.32
49 2 0.03
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.40
Consensus pattern (48 bp):
GATTTTGATATGATACTTGACATGGATTCTGATCTGATACTTGACATG
Found at i:4479 original size:24 final size:24
Alignment explanation
Indices: 4349--4462 Score: 160
Period size: 24 Copynumber: 4.8 Consensus size: 24
4339 TCGATTTGAT
*
4349 TTCTGATATGATACTTGACATGGA
1 TTCTGATCTGATACTTGACATGGA
4373 TTCTGATCTGATA-TCTGACATGGA
1 TTCTGATCTGATACT-TGACATGGA
*
4397 TT-TGATCTGATACTTGACTTGGA
1 TTCTGATCTGATACTTGACATGGA
*
4420 TTCTGATCTGATACTTGACCTGGA
1 TTCTGATCTGATACTTGACATGGA
* *
4444 TTTTGATATGATACTTGAC
1 TTCTGATCTGATACTTGAC
4463 GTGAATTATG
Statistics
Matches: 82, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
23 21 0.26
24 61 0.74
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.40
Consensus pattern (24 bp):
TTCTGATCTGATACTTGACATGGA
Found at i:4614 original size:31 final size:32
Alignment explanation
Indices: 4548--4614 Score: 82
Period size: 34 Copynumber: 2.1 Consensus size: 32
4538 AATACCTGGA
*
4548 GGTTCCTCGGCTGTGTGCTCAGGCCTTACTTACT
1 GGTTCCTCGACTGTGTGCTCAGGCC-T-CTTACT
* *
4582 GGTTCTTCGACTGTGTGCTCAGGGC-CTTACT
1 GGTTCCTCGACTGTGTGCTCAGGCCTCTTACT
4613 GG
1 GG
4615 ACGTGACAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
31 8 0.27
34 22 0.73
ACGTcount: A:0.09, C:0.27, G:0.30, T:0.34
Consensus pattern (32 bp):
GGTTCCTCGACTGTGTGCTCAGGCCTCTTACT
Found at i:4681 original size:2 final size:2
Alignment explanation
Indices: 4674--4716 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
4664 CGGATGGGGG
4674 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
4716 T
1 T
4717 GTTTTAAAAG
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:12711 original size:22 final size:21
Alignment explanation
Indices: 12682--12729 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 21
12672 AGCCTTTCTC
*
12682 TTTT-ATATAAAAATATTATT
1 TTTTAATATAAAAATAATATT
* *
12702 TATTTAATATTAATATAATATT
1 T-TTTAATATAAAAATAATATT
12724 TTTTAA
1 TTTTAA
12730 AAATATTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 8 0.35
22 14 0.61
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TTTTAATATAAAAATAATATT
Found at i:12847 original size:19 final size:20
Alignment explanation
Indices: 12800--12847 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
12790 AAGTTTATTT
12800 ATTAATAATTTTAATATAACA
1 ATTAAT-ATTTTAATATAACA
* *
12821 A-TATTATTTTAATA-AATA
1 ATTAATATTTTAATATAACA
12839 ATTAATATT
1 ATTAATATT
12848 ATTATTTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
18 4 0.17
19 15 0.65
20 3 0.13
21 1 0.04
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
ATTAATATTTTAATATAACA
Found at i:12882 original size:27 final size:25
Alignment explanation
Indices: 12799--12883 Score: 65
Period size: 27 Copynumber: 3.5 Consensus size: 25
12789 AAAGTTTATT
12799 TATTAATAATTTTAAT--ATAAC-AA
1 TATTAAT-ATTTTAATAAATAACTAA
*
12822 TA-T--TATTTTAATAAATAATTAA
1 TATTAATATTTTAATAAATAACTAA
*
12844 TATTATTATTTTAATAAAATATACTAA
1 TATTAATATTTTAAT-AAATA-ACTAA
* *
12871 TCTTAATGTTTTA
1 TATTAATATTTTA
12884 TTTATAAGAT
Statistics
Matches: 49, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
19 8 0.16
20 1 0.02
21 4 0.08
22 5 0.10
23 3 0.06
25 9 0.18
26 5 0.10
27 14 0.29
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.49
Consensus pattern (25 bp):
TATTAATATTTTAATAAATAACTAA
Found at i:13819 original size:76 final size:75
Alignment explanation
Indices: 13729--13892 Score: 233
Period size: 75 Copynumber: 2.2 Consensus size: 75
13719 TAAACTCAAA
*
13729 TTTT-GGATAATATTTTAAACATTATAT-TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGT
1 TTTTAGGATATTATTTT-AACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGG-TTTTAGT
13792 ATTTTAATTAAG
64 ATTTTAATTAAG
* * *
13804 TTTTAGGATATTATTTTTATATTTTATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
1 TTTTAGGATATTATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
*
13869 TTTAATTAGG
66 TTTAATTAAG
* *
13879 ATTTAGAATATTAT
1 TTTTAGGATATTAT
13893 ATTATTTTTT
Statistics
Matches: 80, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
75 41 0.51
76 39 0.49
ACGTcount: A:0.29, C:0.02, G:0.11, T:0.57
Consensus pattern (75 bp):
TTTTAGGATATTATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTAT
TTTAATTAAG
Found at i:13878 original size:19 final size:19
Alignment explanation
Indices: 13850--13912 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
13840 TGTATTTTAG
*
13850 TTTAAATAGGTTTTAGTAT
1 TTTAATTAGGTTTTAGTAT
* *
13869 TTTAATTAGGATTTAGAAT
1 TTTAATTAGGTTTTAGTAT
* **
13888 ATTATATTATTTTTTAGGTAT
1 TTTA-ATTAGGTTTTA-GTAT
13909 TTTA
1 TTTA
13913 GTTTAAATAG
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 19 0.58
20 8 0.24
21 6 0.18
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.56
Consensus pattern (19 bp):
TTTAATTAGGTTTTAGTAT
Found at i:14566 original size:21 final size:22
Alignment explanation
Indices: 14541--14581 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
14531 CTTTAATTTG
14541 TTTATTTAATTATT-TTTTTCT
1 TTTATTTAATTATTATTTTTCT
*
14562 TTTATTTAATTCTTATTTTT
1 TTTATTTAATTATTATTTTT
14582 TATTTTAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTATTTAATTATTATTTTTCT
Found at i:14654 original size:16 final size:19
Alignment explanation
Indices: 14621--14661 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
14611 CCTTTTATAT
14621 TTATTACTATTAATATTTA
1 TTATTACTATTAATATTTA
*
14640 TTATTA-TATTAAT-TTTT
1 TTATTACTATTAATATTTA
14657 TTATT
1 TTATT
14662 TTTTTTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.38
18 7 0.33
19 6 0.29
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (19 bp):
TTATTACTATTAATATTTA
Found at i:20271 original size:9 final size:9
Alignment explanation
Indices: 20257--20296 Score: 62
Period size: 9 Copynumber: 4.3 Consensus size: 9
20247 TATATTTTTG
20257 TTTTTATTT
1 TTTTTATTT
20266 TTTTTATTT
1 TTTTTATTT
*
20275 TCGTTTATTT
1 T-TTTTATTT
20285 TTTTTATTT
1 TTTTTATTT
20294 TTT
1 TTT
20297 AGCGAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
9 20 0.71
10 8 0.29
ACGTcount: A:0.10, C:0.03, G:0.03, T:0.85
Consensus pattern (9 bp):
TTTTTATTT
Found at i:22292 original size:75 final size:76
Alignment explanation
Indices: 22136--22300 Score: 253
Period size: 76 Copynumber: 2.2 Consensus size: 76
22126 TTAAACTCAA
*
22136 ATTTAGGATAATATTTTAAACATTATATTTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTA
1 ATTTAGGATATTATTTTAAACATTATATTTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTA
22201 TTTTAATTAAG
66 TTTTAATTAAG
* * *
22212 TTTTAGGATATTATTTT-TACATTTTATCTTTATCTTTGTATTTTAGTTTAAATAGG-TTTTAGT
1 ATTTAGGATATTATTTTAAACATTATAT-TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGT
*
22275 ATTTTAATTAGG
65 ATTTTAATTAAG
*
22287 ATTTAGAATATTAT
1 ATTTAGGATATTAT
22301 ATTATTTTTT
Statistics
Matches: 81, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
75 38 0.47
76 43 0.53
ACGTcount: A:0.30, C:0.03, G:0.11, T:0.56
Consensus pattern (76 bp):
ATTTAGGATATTATTTTAAACATTATATTTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTA
TTTTAATTAAG
Found at i:24467 original size:12 final size:13
Alignment explanation
Indices: 24445--24476 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
24435 CGTTTGTTGT
24445 GCTTGCTCCTCGG
1 GCTTGCTCCTCGG
24458 GCTT-CTCCTCGG
1 GCTTGCTCCTCGG
24470 GC-TGCTC
1 GCTTGCTC
24477 AGGCTCATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 1 0.06
12 13 0.72
13 4 0.22
ACGTcount: A:0.00, C:0.41, G:0.28, T:0.31
Consensus pattern (13 bp):
GCTTGCTCCTCGG
Found at i:25717 original size:24 final size:25
Alignment explanation
Indices: 25690--25739 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
25680 CAAAACACAA
25690 TAATTT-GAAAA-TTAACATTTTTTT
1 TAATTTCGAAAATTTAA-ATTTTTTT
25714 TAATTTCGAAAATTTAAATTTTTTT
1 TAATTTCGAAAATTTAAATTTTTTT
25739 T
1 T
25740 TGGAAAATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 6 0.25
25 14 0.58
26 4 0.17
ACGTcount: A:0.36, C:0.04, G:0.04, T:0.56
Consensus pattern (25 bp):
TAATTTCGAAAATTTAAATTTTTTT
Found at i:26173 original size:22 final size:23
Alignment explanation
Indices: 26134--26182 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
26124 TGTGTTGTGG
26134 GGGGGAATCGGTTCCCCTTCAA-A
1 GGGGGAATCGGTTCCCC-TCAAGA
26157 GGGGGAATCGGTT-CCCTCAAGA
1 GGGGGAATCGGTTCCCCTCAAGA
26179 GGGG
1 GGGG
26183 ATCGATTCCC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 4 0.16
22 8 0.32
23 13 0.52
ACGTcount: A:0.20, C:0.22, G:0.39, T:0.18
Consensus pattern (23 bp):
GGGGGAATCGGTTCCCCTCAAGA
Found at i:26182 original size:21 final size:21
Alignment explanation
Indices: 26134--26194 Score: 72
Period size: 20 Copynumber: 2.9 Consensus size: 21
26124 TGTGTTGTGG
26134 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
26157 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
*
26177 GAGGGG-ATCGATTCCCTC
1 G-GGGGAATCGGTTCCCTC
26195 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
20 14 0.39
21 6 0.17
22 3 0.08
23 13 0.36
ACGTcount: A:0.20, C:0.26, G:0.33, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:32561 original size:21 final size:22
Alignment explanation
Indices: 32536--32576 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
32526 CTTTAATTTG
32536 TTTATTTAATTATT-TTTTTCT
1 TTTATTTAATTATTATTTTTCT
*
32557 TTTATTTAATTCTTATTTTT
1 TTTATTTAATTATTATTTTT
32577 TATTTTAACC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTATTTAATTATTATTTTTCT
Found at i:33126 original size:31 final size:31
Alignment explanation
Indices: 33090--33157 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
33080 TCAAAATATA
*
33090 TAAGATATGATCACATTTATTTTTATTTAAT
1 TAAGATATGAACACATTTATTTTTATTTAAT
* * *
33121 TAAGATATGAACACTTTTGTTTTTATTTATT
1 TAAGATATGAACACATTTATTTTTATTTAAT
33152 TAAGAT
1 TAAGAT
33158 GTGGTCACCA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.34, C:0.06, G:0.09, T:0.51
Consensus pattern (31 bp):
TAAGATATGAACACATTTATTTTTATTTAAT
Found at i:38122 original size:20 final size:20
Alignment explanation
Indices: 38097--38167 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
38087 TTCTAGCTGT
38097 TTGGAGCCGTTGGTGGTTGA
1 TTGGAGCCGTTGGTGGTTGA
*
38117 TTGGAGCCATTGGTGGTTGA
1 TTGGAGCCGTTGGTGGTTGA
38137 TTGGAGCCGTTGGTGGTTGA
1 TTGGAGCCGTTGGTGGTTGA
*
38157 TTAGAGCCGTT
1 TTGGAGCCGTT
38168 TGATTCATTA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.13, C:0.11, G:0.41, T:0.35
Consensus pattern (20 bp):
TTGGAGCCGTTGGTGGTTGA
Found at i:41744 original size:27 final size:27
Alignment explanation
Indices: 41709--41809 Score: 145
Period size: 27 Copynumber: 3.9 Consensus size: 27
41699 ATAAAAAGTT
*
41709 AAAAAAATGAATTGAGAGGATTTGATA
1 AAAAAAATGAATTGAGAGAATTTGATA
41736 AAAAAAATGAATTGAGAGAATTTGAT-
1 AAAAAAATGAATTGAGAGAATTTGATA
* *
41762 -AAAAAATGAATTGAAAGGATTTGATA
1 AAAAAAATGAATTGAGAGAATTTGATA
*
41788 AAAAAAA-GAATTTAGAGAATTT
1 AAAAAAATGAATTGAGAGAATTT
41810 AGAGGAATGC
Statistics
Matches: 66, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
25 23 0.35
26 12 0.18
27 31 0.47
ACGTcount: A:0.54, C:0.00, G:0.19, T:0.27
Consensus pattern (27 bp):
AAAAAAATGAATTGAGAGAATTTGATA
Found at i:41772 original size:52 final size:51
Alignment explanation
Indices: 41710--41809 Score: 173
Period size: 52 Copynumber: 1.9 Consensus size: 51
41700 TAAAAAGTTA
*
41710 AAAAAATGAATTGAGAGGATTTGATAAAAAAAATGAATTGAGAGAATTTGAT
1 AAAAAATGAATTGAAAGGATTTGATAAAAAAAA-GAATTGAGAGAATTTGAT
*
41762 AAAAAATGAATTGAAAGGATTTGATAAAAAAAAGAATTTAGAGAATTT
1 AAAAAATGAATTGAAAGGATTTGATAAAAAAAAGAATTGAGAGAATTT
41810 AGAGGAATGC
Statistics
Matches: 46, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
51 14 0.30
52 32 0.70
ACGTcount: A:0.54, C:0.00, G:0.19, T:0.27
Consensus pattern (51 bp):
AAAAAATGAATTGAAAGGATTTGATAAAAAAAAGAATTGAGAGAATTTGAT
Found at i:46316 original size:21 final size:21
Alignment explanation
Indices: 46292--46331 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
46282 TTGGTTTTCC
46292 GGAAAATGAATTACTGGAACT
1 GGAAAATGAATTACTGGAACT
46313 GGAAAATGAATTACTGGAA
1 GGAAAATGAATTACTGGAA
46332 TTTAAATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.45, C:0.07, G:0.25, T:0.23
Consensus pattern (21 bp):
GGAAAATGAATTACTGGAACT
Found at i:46353 original size:14 final size:15
Alignment explanation
Indices: 46310--46355 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
46300 AATTACTGGA
46310 ACTGGAAAATGAATT
1 ACTGGAAAATGAATT
** *
46325 ACTGGAATTTAAATT
1 ACTGGAAAATGAATT
46340 A-TGGAAAATGAATT
1 ACTGGAAAATGAATT
46354 AC
1 AC
46356 ATTTCTGGAA
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.46, C:0.07, G:0.17, T:0.30
Consensus pattern (15 bp):
ACTGGAAAATGAATT
Found at i:46566 original size:22 final size:23
Alignment explanation
Indices: 46510--46594 Score: 63
Period size: 22 Copynumber: 3.9 Consensus size: 23
46500 ATAACAAATA
*
46510 TTAAATATAATAATATTATTTATC
1 TTAAA-ATATTAATATTATTTATC
* * *
46534 ATAAAA-CTTAATATTA-TTATT
1 TTAAAATATTAATATTATTTATC
* *
46555 TTAAAATATTAAAATAATTTAT-
1 TTAAAATATTAATATTATTTATC
*
46577 TT--ATTATTAATATTATTT
1 TTAAAATATTAATATTATTT
46595 TTATAATTTT
Statistics
Matches: 48, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
20 13 0.27
21 9 0.19
22 17 0.35
23 5 0.10
24 4 0.08
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
TTAAAATATTAATATTATTTATC
Found at i:46791 original size:23 final size:24
Alignment explanation
Indices: 46738--46815 Score: 70
Period size: 25 Copynumber: 3.0 Consensus size: 24
46728 TTTATTAAAA
46738 TATTATTTAAATATATAAAATATAT
1 TATTA-TTAAATATATAAAATATAT
46763 TCATTATTAAATATATAAGAATTTTATTAT
1 T-ATTATTAAATATATAA-AA---TA-TAT
46793 ATATTATTAAA-ATA-AAAATATAT
1 -TATTATTAAATATATAAAATATAT
46816 ATCTTATATT
Statistics
Matches: 46, Mismatches: 0, Indels: 16
0.74 0.00 0.26
Matches are distributed among these distances:
23 3 0.07
24 2 0.04
25 13 0.28
26 6 0.13
27 2 0.04
28 2 0.04
29 5 0.11
30 12 0.26
31 1 0.02
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (24 bp):
TATTATTAAATATATAAAATATAT
Found at i:46831 original size:25 final size:24
Alignment explanation
Indices: 46797--46885 Score: 60
Period size: 25 Copynumber: 3.7 Consensus size: 24
46787 TATTATATAT
*
46797 TATTAAAATAAAAATATATATCTTA
1 TATTATAATAAAAATATATAT-TTA
* *
46822 TATTATAATATAATTGAT-TATTTTA
1 TATTATAATAAAAAT-ATATA-TTTA
* **
46847 TATAATTTTAAAAATATAATATTT-
1 TATTATAATAAAAATAT-ATATTTA
46871 TATTAT--TAAAAATAT
1 TATTATAATAAAAATAT
46886 TAATAAATAA
Statistics
Matches: 51, Mismatches: 9, Indels: 11
0.72 0.13 0.15
Matches are distributed among these distances:
22 9 0.18
24 7 0.14
25 30 0.59
26 5 0.10
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (24 bp):
TATTATAATAAAAATATATATTTA
Found at i:48345 original size:180 final size:181
Alignment explanation
Indices: 48098--48440 Score: 562
Period size: 180 Copynumber: 1.9 Consensus size: 181
48088 TTTCTGTAAC
* *
48098 TAAAATAATTTTGTTAAAATTTGTTATTGTGAAAGAATATTATTTGTCACAATTTTTTATAATGA
1 TAAAATAATTTTGTTAAAATTTGTTATAGTGAAAGAATATTACTTGTCACAATTTTTTATAATGA
*
48163 GAAATTAATATTTGTTATAAATTGTTA-TTTTGATTAAATAAATTTATCACAATTTTTTATTTTG
66 GAAATTAATATTTGTTATAAATTATTATTTTTGATTAAATAAATTTATCACAATTTTTTATTTTG
* *
48227 ACAAAATATTAGGACGAAGTAAATTTGACATAATTGTTTACTTTGATTAAA
131 ACAAAATATTAGGACAAAATAAATTTGACATAATTGTTTACTTTGATTAAA
* ** *
48278 TAAAATCATTTTGTTGCAATTTGTTATAGTGAAAGAATATTACTTGTCACAATTTTTTATGATGA
1 TAAAATAATTTTGTTAAAATTTGTTATAGTGAAAGAATATTACTTGTCACAATTTTTTATAATGA
* *
48343 GAAATTAATATTTGTTATAAATTATTATTTTTGATTAAATAAATTTGTCAGAATTTTTTATTTTG
66 GAAATTAATATTTGTTATAAATTATTATTTTTGATTAAATAAATTTATCACAATTTTTTATTTTG
* *
48408 ACAAAATATTATGACAAAATAAATTTGATATAA
131 ACAAAATATTAGGACAAAATAAATTTGACATAA
48441 ATTTTTGTAG
Statistics
Matches: 149, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
180 85 0.57
181 64 0.43
ACGTcount: A:0.39, C:0.05, G:0.10, T:0.46
Consensus pattern (181 bp):
TAAAATAATTTTGTTAAAATTTGTTATAGTGAAAGAATATTACTTGTCACAATTTTTTATAATGA
GAAATTAATATTTGTTATAAATTATTATTTTTGATTAAATAAATTTATCACAATTTTTTATTTTG
ACAAAATATTAGGACAAAATAAATTTGACATAATTGTTTACTTTGATTAAA
Found at i:51242 original size:183 final size:181
Alignment explanation
Indices: 50989--51331 Score: 442
Period size: 183 Copynumber: 1.9 Consensus size: 181
50979 AATTTGTCAC
* * * * *
50989 AAAAACGTGAATATCATTATTTTTTTTGACAATGTTTTTTGTAATAATTATTAACACTTATAGTT
1 AAAAACGTGAATATCATTATTTGTTGTGACAATGTTTTTTGTAACAATAATTAACACTTATAATT
**
51054 ACAAAATTTGTCACTATATGAATTTT-TTTGGATTA-AAGAAATATGGAGAGAAATC-TTTGTGA
66 ACAAAACATGTCACTATATG-ATTTTGTTT-GATTACAA-AAAT-TGGAGA-AAATCATTTGTGA
*
51116 CAATATATTTTGTCACTATAATTAAAACATATAACGACAAATATTTTTTTTTTACT
126 CAATACATTTTGTCACTATAATTAAAACATATAACGACAAATATTTTTTTTTTACT
* * * *
51172 AAAAACTTGAATCTCATTATTTGTTGTGACAATTTTTTTTGTAACAATAATTATA-GCTTATAAT
1 AAAAACGTGAATATCATTATTTGTTGTGACAATGTTTTTTGTAACAATAATTA-ACACTTATAAT
** * *
51236 TACAAAACATGTCACTATATGATTTTGTTTTTTTACCAAAAATTGGAGATAATCATTTGTGACTA
65 TACAAAACATGTCACTATATGATTTTGTTTGATTA-CAAAAATTGGAGAAAATCATTTGTGACAA
*
51301 TACATTTTGTCACTATAATTAAAATATATAA
129 TACATTTTGTCACTATAATTAAAACATATAA
51332 TTACAAACAA
Statistics
Matches: 138, Mismatches: 17, Indels: 11
0.83 0.10 0.07
Matches are distributed among these distances:
181 4 0.03
182 52 0.38
183 79 0.57
184 3 0.02
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.43
Consensus pattern (181 bp):
AAAAACGTGAATATCATTATTTGTTGTGACAATGTTTTTTGTAACAATAATTAACACTTATAATT
ACAAAACATGTCACTATATGATTTTGTTTGATTACAAAAATTGGAGAAAATCATTTGTGACAATA
CATTTTGTCACTATAATTAAAACATATAACGACAAATATTTTTTTTTTACT
Found at i:53891 original size:27 final size:27
Alignment explanation
Indices: 53861--53916 Score: 62
Period size: 27 Copynumber: 2.0 Consensus size: 27
53851 AATATGACTT
53861 TTTTAATATA-AAAAAATTATATAC-ATA
1 TTTTAATA-ACAAAAAA-TATATACTATA
*
53888 TTTTCATAACGAAAAAATATATACTATA
1 TTTTAATAAC-AAAAAATATATACTATA
53916 T
1 T
53917 ACATAATAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
26 1 0.04
27 14 0.56
28 10 0.40
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (27 bp):
TTTTAATAACAAAAAATATATACTATA
Found at i:55948 original size:26 final size:29
Alignment explanation
Indices: 55919--55974 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
55909 AATATGACTT
*
55919 TTTTAAT-A-TAAAAAATTATATAC-ATA
1 TTTTAATAACTAAAAAAATATATACTATA
*
55945 TTTTCATAACTAAAAAAATATATACTATA
1 TTTTAATAACTAAAAAAATATATACTATA
55974 T
1 T
55975 ACATAATAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 6 0.24
27 1 0.04
28 14 0.56
29 4 0.16
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (29 bp):
TTTTAATAACTAAAAAAATATATACTATA
Found at i:56026 original size:14 final size:15
Alignment explanation
Indices: 56007--56037 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
55997 AATATGACTT
56007 AAACATAACA-AATA
1 AAACATAACACAATA
56021 AAACATAACACAATA
1 AAACATAACACAATA
56036 AA
1 AA
56038 TTTTGGAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.71, C:0.16, G:0.00, T:0.13
Consensus pattern (15 bp):
AAACATAACACAATA
Found at i:62777 original size:24 final size:23
Alignment explanation
Indices: 62696--62778 Score: 69
Period size: 24 Copynumber: 3.4 Consensus size: 23
62686 GGAGTACACA
*
62696 AATGCACTATTACTAGAGTGTTAC
1 AATGCACTAATACTAGAGTG-TAC
* *
62720 AAGGCACTAA-AGCAAGAGTGTAAC
1 AATGCACTAATA-CTAGAGTGT-AC
* *
62744 AAATGAACTAATACTGGAGTGTAC
1 -AATGCACTAATACTAGAGTGTAC
62768 GAATGCACTAA
1 -AATGCACTAA
62779 ACATGACATA
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
23 2 0.04
24 28 0.61
25 15 0.33
26 1 0.02
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (23 bp):
AATGCACTAATACTAGAGTGTAC
Found at i:70304 original size:21 final size:19
Alignment explanation
Indices: 70276--70321 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
70266 TCATTGAATC
70276 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
70296 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
70315 ACTTAGT
1 A-TTAGT
70322 AGGATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Found at i:71890 original size:21 final size:21
Alignment explanation
Indices: 71861--71904 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
71851 TTATCCTTGC
71861 AAGAATTCATGGCCTCGACAA
1 AAGAATTCATGGCCTCGACAA
* * *
71882 AAGATTTCATGGCGTCTACAA
1 AAGAATTCATGGCCTCGACAA
71903 AA
1 AA
71905 ACCTTGATGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.23
Consensus pattern (21 bp):
AAGAATTCATGGCCTCGACAA
Found at i:78332 original size:21 final size:19
Alignment explanation
Indices: 78304--78349 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
78294 TCATTGAATC
78304 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
78324 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
78343 ACTTAGT
1 A-TTAGT
78350 AGGATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Found at i:85802 original size:22 final size:22
Alignment explanation
Indices: 85774--85818 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
85764 TGCATGACAG
*
85774 ACGAAAACAAAGAAAATCGTTA
1 ACGAAAACAAAGAAAATCATTA
85796 ACGAAAACAAAGAAAATCATTA
1 ACGAAAACAAAGAAAATCATTA
85818 A
1 A
85819 ATTTTGTGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.62, C:0.13, G:0.11, T:0.13
Consensus pattern (22 bp):
ACGAAAACAAAGAAAATCATTA
Found at i:88325 original size:22 final size:22
Alignment explanation
Indices: 88290--88332 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
88280 CATAATTATT
88290 TAAAAAATTAAATAA-AAATAC
1 TAAAAAATTAAATAATAAATAC
*
88311 TAAAAATATTTAATAATAAATA
1 TAAAAA-ATTAAATAATAAATA
88333 ATTTTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 8 0.42
23 5 0.26
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (22 bp):
TAAAAAATTAAATAATAAATAC
Found at i:91554 original size:26 final size:26
Alignment explanation
Indices: 91502--91555 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
91492 ATCATTCGTA
**
91502 ATAAACATCATATATACATATTCATG
1 ATAAACATCATATATACATAACCATG
91528 ATAAACATCATATATA-ATAACCAATG
1 ATAAACATCATATATACATAACC-ATG
91554 AT
1 AT
91556 CAATGCATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 4 0.16
26 21 0.84
ACGTcount: A:0.50, C:0.15, G:0.04, T:0.31
Consensus pattern (26 bp):
ATAAACATCATATATACATAACCATG
Found at i:93269 original size:20 final size:22
Alignment explanation
Indices: 93221--93269 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 22
93211 AATGATTCTA
93221 CAACATCAATATCATCAAAATC
1 CAACATCAATATCATCAAAATC
*
93243 CATCATCAAT-TCAT-AAAA-C
1 CAACATCAATATCATCAAAATC
93262 CTAACATC
1 C-AACATC
93270 TTCTTCATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 2 0.08
20 9 0.38
21 4 0.17
22 9 0.38
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (22 bp):
CAACATCAATATCATCAAAATC
Found at i:97546 original size:21 final size:22
Alignment explanation
Indices: 97522--97562 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
97512 ATCATTGTTT
*
97522 ATTATATATGATG-TTATCAGG
1 ATTACATATGATGTTTATCAGG
97543 ATTACATATGATGTTTATCA
1 ATTACATATGATGTTTATCA
97563 TAAATGTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.34, C:0.07, G:0.15, T:0.44
Consensus pattern (22 bp):
ATTACATATGATGTTTATCAGG
Found at i:100581 original size:33 final size:34
Alignment explanation
Indices: 100544--100607 Score: 87
Period size: 35 Copynumber: 1.9 Consensus size: 34
100534 AAATGAAAAT
*
100544 GGATTTTGAA-TATC-AAAATGAAATCTTGAAGAA
1 GGATTTAGAACTATCAAAAATGAAAT-TTGAAGAA
*
100577 GGATTTAGAACTCTCAAAAATGAAATTTGAA
1 GGATTTAGAACTATCAAAAATGAAATTTGAA
100608 AGTATTGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
33 9 0.33
34 8 0.30
35 10 0.37
ACGTcount: A:0.45, C:0.08, G:0.17, T:0.30
Consensus pattern (34 bp):
GGATTTAGAACTATCAAAAATGAAATTTGAAGAA
Found at i:104581 original size:21 final size:21
Alignment explanation
Indices: 104555--104594 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
104545 CCCCCTTTGA
*
104555 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
104576 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
104595 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:119505 original size:17 final size:19
Alignment explanation
Indices: 119483--119530 Score: 64
Period size: 17 Copynumber: 2.6 Consensus size: 19
119473 TCCCTTTTAT
*
119483 TCTCTTTTTT-T-TTCTCC
1 TCTCTTTTTTCTCTCCTCC
119500 TCTCTTTTTTCTCTCCTCC
1 TCTCTTTTTTCTCTCCTCC
119519 TCTACTTTTTTC
1 TCT-CTTTTTTC
119531 GTGTCCTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
17 10 0.37
18 1 0.04
19 8 0.30
20 8 0.30
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65
Consensus pattern (19 bp):
TCTCTTTTTTCTCTCCTCC
Found at i:127429 original size:34 final size:33
Alignment explanation
Indices: 127379--127472 Score: 100
Period size: 35 Copynumber: 2.8 Consensus size: 33
127369 ATTTCAAGAG
* *
127379 AAAATGTTTCAAGTGAGATGCAATT-CTTTAGAC
1 AAAATGTCTCAAGTGAGATGAAATTGCTTTA-AC
* *
127412 AAAATTGTCTCAAGTGAGATGAAATTTGTTTTAAG
1 AAAA-TGTCTCAAGTGAGATGAAA-TTGCTTTAAC
*
127447 AAAACTATCTCAAGTGAGATGAAATT
1 AAAA-TGTCTCAAGTGAGATGAAATT
127473 ATTGTTTTGA
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
33 4 0.08
34 19 0.37
35 25 0.48
36 4 0.08
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.33
Consensus pattern (33 bp):
AAAATGTCTCAAGTGAGATGAAATTGCTTTAAC
Found at i:127510 original size:39 final size:36
Alignment explanation
Indices: 127379--127518 Score: 126
Period size: 39 Copynumber: 3.9 Consensus size: 36
127369 ATTTCAAGAG
* * * *
127379 AAAATGTTTCAAGTGAGATGCAA--TT-CTTTAGACA
1 AAAATGTCTCAAGTGAGATGAAATTTTGTTTTA-AAA
* *
127413 AAATTGTCTCAAGTGAGATGAAA-TTTGTTTTAAGA
1 AAAATGTCTCAAGTGAGATGAAATTTTGTTTTAAAA
* *
127448 AAACTATCTCAAGTGAGATGAAATTATTGTTTTGAGAAA
1 AAAATGTCTCAAGTGAGATGAAATT-TTGTTTT-A-AAA
*
127487 AAAATGTCTCAAGTGAGACGAAATTTGTGTTT
1 AAAATGTCTCAAGTGAGATGAAATTT-TGTTT
127519 CAAGTGAAAA
Statistics
Matches: 88, Mismatches: 11, Indels: 9
0.81 0.10 0.08
Matches are distributed among these distances:
34 20 0.23
35 25 0.28
36 5 0.06
37 7 0.08
38 2 0.02
39 29 0.33
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (36 bp):
AAAATGTCTCAAGTGAGATGAAATTTTGTTTTAAAA
Found at i:136300 original size:21 final size:21
Alignment explanation
Indices: 136274--136343 Score: 61
Period size: 21 Copynumber: 3.2 Consensus size: 21
136264 TTGTGCATAA
136274 TGCATCGATACACTATGAAAG
1 TGCATCGATACACTATGAAAG
* * *
136295 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGAT--A-CACTATGAAAG
*
136319 TGCATCGATACA-TCATGAAAA
1 TGCATCGATACACT-ATGAAAG
136340 TGCA
1 TGCA
136344 CTGATGCACT
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
20 1 0.03
21 18 0.47
22 1 0.03
23 1 0.03
24 17 0.45
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (21 bp):
TGCATCGATACACTATGAAAG
Found at i:136338 original size:45 final size:44
Alignment explanation
Indices: 136274--136371 Score: 130
Period size: 45 Copynumber: 2.2 Consensus size: 44
136264 TTGTGCATAA
*
136274 TGCATCGATACACTATGAAAGTGCA-TCGATGCA-TCCCTTTGAATG
1 TGCATCGATACACTATGAAAATGCACT-GATGCACT-CC-TTGAATG
136319 TGCATCGATACA-TCATGAAAATGCACTGATGCACTCCTTGAATG
1 TGCATCGATACACT-ATGAAAATGCACTGATGCACTCCTTGAATG
136363 TGCATCGAT
1 TGCATCGAT
136372 GCACAAGGCC
Statistics
Matches: 49, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
44 17 0.35
45 30 0.61
46 2 0.04
ACGTcount: A:0.30, C:0.22, G:0.19, T:0.29
Consensus pattern (44 bp):
TGCATCGATACACTATGAAAATGCACTGATGCACTCCTTGAATG
Found at i:140136 original size:39 final size:39
Alignment explanation
Indices: 140091--140201 Score: 143
Period size: 39 Copynumber: 2.9 Consensus size: 39
140081 ATAAATGTAT
* *
140091 AATGCAAAGATGAAAGTGCAAAGGTAAATACATATGCAA
1 AATGCAAAGATGAAAGTGCAAAGGTAAATACAAATCCAA
* * *
140130 AATGCAAAGTTGAAAGTGCAAATGTAAATACAAATCCAG
1 AATGCAAAGATGAAAGTGCAAAGGTAAATACAAATCCAA
* * *
140169 AATGCAAAGATGAAAATGC-TATGTAAATACAAA
1 AATGCAAAGATGAAAGTGCAAAGGTAAATACAAA
140202 ATGCAAATAT
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
38 13 0.20
39 51 0.80
ACGTcount: A:0.51, C:0.11, G:0.18, T:0.20
Consensus pattern (39 bp):
AATGCAAAGATGAAAGTGCAAAGGTAAATACAAATCCAA
Found at i:148422 original size:45 final size:45
Alignment explanation
Indices: 148358--148459 Score: 170
Period size: 45 Copynumber: 2.2 Consensus size: 45
148348 GTTTCATTAT
148358 ATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAATGG-TGCC
1 ATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAA-GGATGCC
*
148403 ATAAATGAAATGCATAACGGTGCATTTAAGGCATGAAAGGATGCC
1 ATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCC
148448 ATAAATGGAAAT
1 ATAAAT-GAAAT
148460 AATGAATAAT
Statistics
Matches: 54, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
44 2 0.04
45 47 0.87
46 5 0.09
ACGTcount: A:0.42, C:0.12, G:0.24, T:0.23
Consensus pattern (45 bp):
ATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGCC
Found at i:148424 original size:24 final size:24
Alignment explanation
Indices: 148358--148425 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 24
148348 GTTTCATTAT
148358 ATAAATGAAATGCATAACGGTG-C
1 ATAAATGAAATGCATAACGGTGCC
** *
148381 ATTAAA-GGCATG-A-AATGGTGCC
1 A-TAAATGAAATGCATAACGGTGCC
148403 ATAAATGAAATGCATAACGGTGC
1 ATAAATGAAATGCATAACGGTGC
148426 ATTTAAGGCA
Statistics
Matches: 34, Mismatches: 6, Indels: 9
0.69 0.12 0.18
Matches are distributed among these distances:
21 10 0.29
22 7 0.21
23 6 0.18
24 11 0.32
ACGTcount: A:0.41, C:0.13, G:0.24, T:0.22
Consensus pattern (24 bp):
ATAAATGAAATGCATAACGGTGCC
Found at i:155111 original size:45 final size:45
Alignment explanation
Indices: 155041--155323 Score: 424
Period size: 45 Copynumber: 6.3 Consensus size: 45
155031 TGTTTCATTG
*
155041 CATAAATGAAATGCATAACGATGCATTAAAGGCATGAAAGGATGT
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGT
* *
155086 CATAAATGAAATGCATAACAGTGCATTAAAGGCATGAAATGATGT
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGT
* *
155131 CATAAATGAAATGCATAACGGTACATTAAAGGCATGAAATGATGT
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGT
* * *
155176 CATAAATGAAATACATAACGGTGCATTAAAGGCATGAAAGAATGC
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGT
* *
155221 CATAAATGAAATGCATAACAGTGCATTAAAGGCATGAAAGAATGT
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGT
* * *
155266 CATAAATGAAATGCATAACGGTTCATTAAAGCCATTAAAGGATG-
1 CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGT
155310 CTATAAATGGAAAT
1 C-ATAAAT-GAAAT
155324 AATGAATAAT
Statistics
Matches: 218, Mismatches: 18, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
44 1 0.00
45 212 0.97
46 5 0.02
ACGTcount: A:0.45, C:0.12, G:0.20, T:0.23
Consensus pattern (45 bp):
CATAAATGAAATGCATAACGGTGCATTAAAGGCATGAAAGGATGT
Found at i:156543 original size:24 final size:24
Alignment explanation
Indices: 156502--156568 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
156492 ACATAGGTCT
* * *
156502 CGTTCGTTCACGTACGTTC-GTGAA
1 CGTTCGTTTATGTTCGTTCGGT-AA
156526 CGTTCGTTTATGTTCGTTCGGTAA
1 CGTTCGTTTATGTTCGTTCGGTAA
* *
156550 TGTTCGTTTATGTTTGTTC
1 CGTTCGTTTATGTTCGTTC
156569 ATTTATGTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 35 0.95
25 2 0.05
ACGTcount: A:0.12, C:0.18, G:0.24, T:0.46
Consensus pattern (24 bp):
CGTTCGTTTATGTTCGTTCGGTAA
Found at i:157097 original size:34 final size:32
Alignment explanation
Indices: 157020--157083 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
157010 AAATATATAG
157020 AATTTG-CAAAAAACAAAACAAAGGTTTCTAT
1 AATTTGCCAAAAAACAAAACAAAGGTTTCTAT
*
157051 AATTTGCCAAAAAACAAAACAAATGTTTCTAT
1 AATTTGCCAAAAAACAAAACAAAGGTTTCTAT
157083 A
1 A
157084 CAATTTCTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 6 0.19
32 25 0.81
ACGTcount: A:0.52, C:0.14, G:0.08, T:0.27
Consensus pattern (32 bp):
AATTTGCCAAAAAACAAAACAAAGGTTTCTAT
Found at i:157798 original size:16 final size:16
Alignment explanation
Indices: 157777--157809 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
157767 AAAAAAAAAT
157777 TGTTCGTTTATATTCG
1 TGTTCGTTTATATTCG
*
157793 TGTTCGTTTATGTTCG
1 TGTTCGTTTATATTCG
157809 T
1 T
157810 TTATTTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATATTCG
Found at i:159658 original size:11 final size:11
Alignment explanation
Indices: 159642--159704 Score: 60
Period size: 11 Copynumber: 5.9 Consensus size: 11
159632 AAAATTATAT
159642 TATTAAAAATA
1 TATTAAAAATA
159653 TATTAAAAATA
1 TATTAAAAATA
* ***
159664 CATTATTGATA
1 TATTAAAAATA
159675 -ATTATAAAAT-
1 TATTA-AAAATA
159685 T-TTAAAAATA
1 TATTAAAAATA
159695 TATTAAAAAT
1 TATTAAAAAT
159705 TCTATAATAT
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
9 5 0.12
10 8 0.20
11 28 0.68
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:159828 original size:7 final size:7
Alignment explanation
Indices: 159813--159912 Score: 62
Period size: 7 Copynumber: 14.3 Consensus size: 7
159803 ATTTGTAATT
159813 AACCTTA
1 AACCTTA
*
159820 AACCCTA
1 AACCTTA
*
159827 AA-ATCTA
1 AACCT-TA
*
159834 AACCATA
1 AACCTTA
*
159841 AACCCTA
1 AACCTTA
*
159848 AATCATT-
1 AA-CCTTA
159855 AACCTTA
1 AACCTTA
159862 AACCTTA
1 AACCTTA
159869 AACCTTA
1 AACCTTA
*
159876 AACCTTG
1 AACCTTA
*
159883 AA-TTATA
1 AACCT-TA
*
159890 AATCTTA
1 AACCTTA
* *
159897 ATCCCTA
1 AACCTTA
159904 AACCTTA
1 AACCTTA
159911 AA
1 AA
159913 TTCAATTATG
Statistics
Matches: 69, Mismatches: 18, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
6 4 0.06
7 62 0.90
8 3 0.04
ACGTcount: A:0.45, C:0.26, G:0.01, T:0.28
Consensus pattern (7 bp):
AACCTTA
Found at i:159891 original size:28 final size:28
Alignment explanation
Indices: 159813--159914 Score: 80
Period size: 28 Copynumber: 3.6 Consensus size: 28
159803 ATTTGTAATT
* * * * *
159813 AACCTTAAACCCTAAAATCTAAACCATA
1 AACCCTAAACCTTAAATTATAAACCTTA
* **
159841 AACCCTAAATCATTAACCT-TAAACCTTA
1 AACCCTAAA-CCTTAAATTATAAACCTTA
* * *
159869 AACCTTAAACCTTGAATTATAAATCTTA
1 AACCCTAAACCTTAAATTATAAACCTTA
*
159897 ATCCCTAAACCTTAAATT
1 AACCCTAAACCTTAAATT
159915 CAATTATGTG
Statistics
Matches: 57, Mismatches: 15, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
27 5 0.09
28 47 0.82
29 5 0.09
ACGTcount: A:0.44, C:0.25, G:0.01, T:0.29
Consensus pattern (28 bp):
AACCCTAAACCTTAAATTATAAACCTTA
Found at i:159912 original size:21 final size:20
Alignment explanation
Indices: 159811--159913 Score: 82
Period size: 21 Copynumber: 5.0 Consensus size: 20
159801 GTATTTGTAA
*
159811 TTAACCTTAAACCCTAAAATC
1 TTAACCTTAAA-CCTTAAATC
* * *
159832 TAAACCATAAACCCTAAATC
1 TTAACCTTAAACCTTAAATC
*
159852 ATTAACCTTAAACCTTAAACC
1 -TTAACCTTAAACCTTAAATC
* *
159873 TTAAACCTTGAA-TTATAAATC
1 TT-AACCTTAAACCT-TAAATC
*
159894 TTAATCCCTAAACCTTAAAT
1 TTAA-CCTTAAACCTTAAAT
159914 TCAATTATGT
Statistics
Matches: 63, Mismatches: 14, Indels: 10
0.72 0.16 0.11
Matches are distributed among these distances:
20 12 0.19
21 50 0.79
22 1 0.02
ACGTcount: A:0.44, C:0.25, G:0.01, T:0.30
Consensus pattern (20 bp):
TTAACCTTAAACCTTAAATC
Found at i:162517 original size:18 final size:17
Alignment explanation
Indices: 162472--162526 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 17
162462 CACCGGTCAA
162472 CGGTCAACGGGTCGGGT
1 CGGTCAACGGGTCGGGT
162489 CGGTCAACGGGTCGGGTT
1 CGGTCAACGGGTCGGG-T
* * *
162507 GGGTTAACGGGTCAGGT
1 CGGTCAACGGGTCGGGT
162524 CGG
1 CGG
162527 GTCGTGACCG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
17 19 0.58
18 14 0.42
ACGTcount: A:0.13, C:0.20, G:0.47, T:0.20
Consensus pattern (17 bp):
CGGTCAACGGGTCGGGT
Found at i:162528 original size:18 final size:18
Alignment explanation
Indices: 162473--162529 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
162463 ACCGGTCAAC
162473 GGTCAACGGGTCGGGTC-
1 GGTCAACGGGTCGGGTCG
*
162490 GGTCAACGGGTCGGGTTG
1 GGTCAACGGGTCGGGTCG
* *
162508 GGTTAACGGGTCAGGTCG
1 GGTCAACGGGTCGGGTCG
162526 GGTC
1 GGTC
162530 GTGACCGGTT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 16 0.47
18 18 0.53
ACGTcount: A:0.12, C:0.19, G:0.47, T:0.21
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:169759 original size:18 final size:17
Alignment explanation
Indices: 169707--169760 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
169697 CACCGGTCTA
*
169707 CGGTCAACAGGTCGGGT
1 CGGTCAACGGGTCGGGT
*
169724 CGGTCAACGGGTCAGGT
1 CGGTCAACGGGTCGGGT
* *
169741 CAGGTTAATGGGTCGGGT
1 C-GGTCAACGGGTCGGGT
169759 CG
1 CG
169761 TGACCGGTTA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
17 17 0.55
18 14 0.45
ACGTcount: A:0.17, C:0.20, G:0.43, T:0.20
Consensus pattern (17 bp):
CGGTCAACGGGTCGGGT
Found at i:171822 original size:20 final size:21
Alignment explanation
Indices: 171781--171831 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
171771 TGCATATACT
* *
171781 ATATCATATTATTAAAACCTA
1 ATATCATATTATCAAAAACTA
171802 ATATCATA-TATCAAAAACTA
1 ATATCATATTATCAAAAACTA
171822 ATA--ATATTAT
1 ATATCATATTAT
171832 AAAGTATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 3 0.11
19 3 0.11
20 13 0.48
21 8 0.30
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (21 bp):
ATATCATATTATCAAAAACTA
Found at i:175763 original size:15 final size:14
Alignment explanation
Indices: 175726--175761 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
175716 ATGGAAATTA
175726 TTTTAAAATTTATT
1 TTTTAAAATTTATT
*
175740 TTTTAAAATTTTTT
1 TTTTAAAATTTATT
175754 TTTTAAAA
1 TTTTAAAA
175762 ATAATATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTAAAATTTATT
Found at i:177731 original size:20 final size:21
Alignment explanation
Indices: 177689--177732 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
177679 TGATTTGTTT
*
177689 TGATGTGGAATTGATTGAGAA
1 TGATGTGGAATTGATGGAGAA
177710 TGAT-TGGAATTGAATGGA-AA
1 TGATGTGGAATTG-ATGGAGAA
177730 TGA
1 TGA
177733 ATTTTAGGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 13 0.62
21 8 0.38
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (21 bp):
TGATGTGGAATTGATGGAGAA
Found at i:183088 original size:260 final size:260
Alignment explanation
Indices: 182623--183357 Score: 907
Period size: 260 Copynumber: 2.8 Consensus size: 260
182613 AAATGAGCAC
* * *
182623 CAGATTGA-AGCTGATTCAAC-TCTTTCTGTGAAGAACCAAGCGAAATATTTTCACTGATCCAAC
1 CAGATTGACA-CTGATTCGACTTCTTT-TATGAAGAACCAAGTGAAATATTTTCACTGATCCAAC
* * ** * *
182686 TCATTCTCTTAAGAATTGAGTGAAAGGTTGTTACTAATCCAACTCCTTCTATGAATA-ACCGAGT
64 TCATTCTGTAAAGAATCAAGTGAAAGGTTGTTACTGATCCAACTCCTTCTGTGAA-AGACCGAGT
*
182750 AACATGACAAATGTTGATCCAACTCCTTATGTAAAGAATCAAACAAAATGTCGAT-CTTGATCTA
128 AACATGACAAATGTTGATCCAACTCCTTATGTGAAGAATCAAACAAAATGTCGATGC-TGATCTA
** *
182814 TCTC-TTTCTGTGATAGAATCAAGCAATATGGTGATACTGTTTCGAC-TCATTCTGTGAGGAAAC
192 -CTCATTTCTGTGATAGAATCAAGCAATATAATGATACTGTTTCGACTTCA-TCTGTGAAGAAAC
182877 AAACAT
255 AAACAT
* *
182883 CAGATTGACACTGATTCGACTTCTTTTATTAAGAACCAAATGAAATATTTTCACTGATCCAACTC
1 CAGATTGACACTGATTCGACTTCTTTTATGAAGAACCAAGTGAAATATTTTCACTGATCCAACTC
* * * *
182948 ATTCTGTAAAGAATCAAGTGAAAGGTTGTTATTGATCCAACTCCTTTTGTGAAAGATCAAGTAAC
66 ATTCTGTAAAGAATCAAGTGAAAGGTTGTTACTGATCCAACTCCTTCTGTGAAAGACCGAGTAAC
* * * * *
183013 ATGACAAATGTTGATCTAACTCCTTCTGTGATGAATCAAACAAAATGCCAATGCTGATCTACCTC
131 ATGACAAATGTTGATCCAACTCCTTATGTGAAGAATCAAACAAAATGTCGATGCTGATCTA-CTC
* * ** * * *
183078 ATTT-TGTGATAGAATTAAGAAATATAATGATGTTGTTTTGACTTCATCTGTGAAGAAATAAGCA
195 ATTTCTGTGATAGAATCAAGCAATATAATGATACTGTTTCGACTTCATCTGTGAAGAAACAAACA
183142 T
260 T
* ** * * * * *
183143 CAGATTAACGTTGATTCGACTCCTTCTATGAAGAGCCAAGTG--ATAGGTTTAACTGATCCAACT
1 CAGATTGACACTGATTCGACTTCTTTTATGAAGAACCAAGTGAAATA-TTTTCACTGATCCAACT
* * *
183206 -ACTTCTGTGAAGAATCAAGTGAAAGGTTGTTAGTGATCCAACTCCTTCTGTGAAGGACCGAGTA
65 CA-TTCTGTAAAGAATCAAGTGAAAGGTTGTTACTGATCCAACTCCTTCTGTGAAAGACCGAGTA
* *
183270 ACATGACAAATGTTGATCCAACTCATTATGTGAAGAATCAAACAAAATGTCGATGATGATCTACT
129 ACATGACAAATGTTGATCCAACTCCTTATGTGAAGAATCAAACAAAATGTCGATGCTGATCTACT
*
183335 -ATTTCTGTGATAAAATCAAGCAA
194 CATTTCTGTGATAGAATCAAGCAA
183358 AAGGTTGAAC
Statistics
Matches: 408, Mismatches: 58, Indels: 20
0.84 0.12 0.04
Matches are distributed among these distances:
257 4 0.01
258 21 0.05
259 128 0.31
260 242 0.59
261 13 0.03
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (260 bp):
CAGATTGACACTGATTCGACTTCTTTTATGAAGAACCAAGTGAAATATTTTCACTGATCCAACTC
ATTCTGTAAAGAATCAAGTGAAAGGTTGTTACTGATCCAACTCCTTCTGTGAAAGACCGAGTAAC
ATGACAAATGTTGATCCAACTCCTTATGTGAAGAATCAAACAAAATGTCGATGCTGATCTACTCA
TTTCTGTGATAGAATCAAGCAATATAATGATACTGTTTCGACTTCATCTGTGAAGAAACAAACAT
Found at i:183257 original size:43 final size:42
Alignment explanation
Indices: 183161--183260 Score: 128
Period size: 42 Copynumber: 2.4 Consensus size: 42
183151 CGTTGATTCG
* * *
183161 ACTCCTTCTATGAAGAGCCAAGTGATAGGTTTAACTGATCCA
1 ACTCCTTCTGTGAAGAACCAAGTGAAAGGTTTAACTGATCCA
* * * *
183203 ACTACTTCTGTGAAGAATCAAGTGAAAGGTTGTTAGTGATCCA
1 ACTCCTTCTGTGAAGAACCAAGTGAAAGGTT-TAACTGATCCA
183246 ACTCCTTCTGTGAAG
1 ACTCCTTCTGTGAAG
183261 GACCGAGTAA
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 26 0.53
43 23 0.47
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (42 bp):
ACTCCTTCTGTGAAGAACCAAGTGAAAGGTTTAACTGATCCA
Found at i:184720 original size:17 final size:18
Alignment explanation
Indices: 184698--184744 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
184688 TCATTTCAAA
184698 TTTCTTTTTATTA-TATT
1 TTTCTTTTTATTATTATT
*
184715 TTTCTTTTTCTTATTATT
1 TTTCTTTTTATTATTATT
*
184733 TTTATTTTTATT
1 TTTCTTTTTATT
184745 TTTTTCTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTCTTTTTATTATTATT
Found at i:184725 original size:23 final size:24
Alignment explanation
Indices: 184698--184747 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
184688 TCATTTCAAA
* *
184698 TTTCTTTTTA-TTATATTTTTCTT
1 TTTCTTATTATTTATATTTTTATT
*
184721 TTTCTTATTATTTTTATTTTTATT
1 TTTCTTATTATTTATATTTTTATT
184745 TTT
1 TTT
184748 TTCTTCAAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 9 0.39
24 14 0.61
ACGTcount: A:0.14, C:0.06, G:0.00, T:0.80
Consensus pattern (24 bp):
TTTCTTATTATTTATATTTTTATT
Found at i:188307 original size:23 final size:23
Alignment explanation
Indices: 188261--188304 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
188251 AAATTTATGA
188261 AATGAATATAAAGAATGAGAAAT
1 AATGAATATAAAGAATGAGAAAT
* *
188284 AATGAATGTAAA-AATGTGAAA
1 AATGAATATAAAGAATGAGAAA
188305 ATATACAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.59, C:0.00, G:0.18, T:0.23
Consensus pattern (23 bp):
AATGAATATAAAGAATGAGAAAT
Found at i:206342 original size:20 final size:21
Alignment explanation
Indices: 206292--206342 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 21
206282 ATATACATAT
206292 TATATATA-TTATATATGTAA
1 TATATATATTTATATATGTAA
206312 TAT-TATTATTTAT-TAATG-AA
1 TATATA-TATTTATAT-ATGTAA
206332 TATATATATTT
1 TATATATATTT
206343 TGACATTTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
19 2 0.07
20 16 0.59
21 9 0.33
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (21 bp):
TATATATATTTATATATGTAA
Found at i:207750 original size:2 final size:2
Alignment explanation
Indices: 207737--207770 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
207727 ACTTATATGT
*
207737 TA TA TCA TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA T
207771 GTACACATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:207974 original size:195 final size:203
Alignment explanation
Indices: 207620--208024 Score: 562
Period size: 194 Copynumber: 2.0 Consensus size: 203
207610 TGGATTTTAA
*
207620 TTTTAATTATCTTTCTATATTACATTATAATATTTGTATATATTTTATATCCTTATTAGTTTTTT
1 TTTTAATTATCTTTCTATATTACATTATAATA--T-TATATATTTTATATCATTATTAG-TTTTT
*
207685 TTATACACTCGTATATATGTATTATTAGAATAGTATTATTTCACTTATATGTTATATCATATATA
62 TTATACACTCGTATACA-GTATTATTAGAATAGTATTATTTCACTTATATG-T-TAT-ATATATA
207750 TATATATATATATGTATATATGTACACATTTTGTATTTTACCCTATTTGTTTACTTCTTTATTAT
123 TATATATATATATGTATATATGTACACA-TTTGTATTTTACCCTATTTGTTTACTTCTTTATTAT
207815 TATATTTATTTACATTAG
187 TATATTTA-TTACATTAG
*
207833 TTTTAATTATCTTTTTATATTACA-TATAATA-TATATATTTTATA-CTATTATTAG-TTTTTTA
1 TTTTAATTATCTTTCTATATTACATTATAATATTATATATTTTATATC-ATTATTAGTTTTTTTA
** * *
207894 TACGTTCGTATACA-T-TTATTAGTATAGTA-TATTTCA-TT-TATG-TGT-TATATATATATAT
65 TACACTCGTATACAGTATTATTAGAATAGTATTATTTCACTTATATGTTATATATATATATATAT
*
207952 ATATATGTATATATGTACACATTTGTATTTTACCCTATTTTTTTACTTCTTTATTATTATATTTA
130 ATATATGTATATATGTACACATTTGTATTTTACCCTATTTGTTTACTTCTTTATTATTATATTTA
208017 TTACATTA
195 TTACATTA
208025 TTATTTTTTT
Statistics
Matches: 183, Mismatches: 8, Indels: 22
0.86 0.04 0.10
Matches are distributed among these distances:
193 8 0.04
194 43 0.23
195 34 0.19
197 2 0.01
200 4 0.02
201 2 0.01
202 7 0.04
203 13 0.07
204 1 0.01
206 18 0.10
207 1 0.01
208 20 0.11
212 7 0.04
213 23 0.13
ACGTcount: A:0.31, C:0.08, G:0.05, T:0.56
Consensus pattern (203 bp):
TTTTAATTATCTTTCTATATTACATTATAATATTATATATTTTATATCATTATTAGTTTTTTTAT
ACACTCGTATACAGTATTATTAGAATAGTATTATTTCACTTATATGTTATATATATATATATATA
TATATGTATATATGTACACATTTGTATTTTACCCTATTTGTTTACTTCTTTATTATTATATTTAT
TACATTAG
Found at i:208025 original size:20 final size:19
Alignment explanation
Indices: 207998--208055 Score: 70
Period size: 17 Copynumber: 3.2 Consensus size: 19
207988 ATTTTTTTAC
207998 TTCT-TTATTATTATATTT
1 TTCTATTATTATTATATTT
208016 ATTAC-ATTATTATT-T-TTT
1 -TT-CTATTATTATTATATTT
208034 TTCTATTATTATTATATTT
1 TTCTATTATTATTATATTT
208053 TTC
1 TTC
208056 CTCCCTCTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
16 1 0.03
17 11 0.32
18 4 0.12
19 9 0.26
20 9 0.26
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (19 bp):
TTCTATTATTATTATATTT
Done.