Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 19 of 125
Found at i:5932974 original size:20 final size:19
Alignment explanation
Indices: 5932949--5933021 Score: 56
Period size: 20 Copynumber: 3.4 Consensus size: 19
5932939 ACGTAGCAAG
5932949 AAATAAATAAAAAGTATAAA
1 AAATAAATAAAAA-TATAAA
*
5932969 AAATAAAAAATATATATTTATAAA
1 AAATAAATAA-A-A-A--TATAAA
*
5932993 AAATACTATAAAAATATAAA
1 AAATA-AATAAAAATATAAA
5933013 AATATAAAT
1 AA-ATAAAT
5933022 TTTCATTCAA
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
20 19 0.45
21 4 0.10
22 2 0.05
23 2 0.05
24 12 0.29
25 3 0.07
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.27
Consensus pattern (19 bp):
AAATAAATAAAAATATAAA
Found at i:5937813 original size:123 final size:122
Alignment explanation
Indices: 5937300--5937831 Score: 527
Period size: 122 Copynumber: 4.3 Consensus size: 122
5937290 CACACTATTT
* * * *
5937300 TGACCCACTTTTTTGTACCTCATCCA-AAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTTCA
1 TGACCCACTTCTCTGTATCTCAT-CAGGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTTCA
** * * * * * *
5937364 CCTCATTATTTTGGTCCACTTCTCTGTATCTTATCAGGAAGATGACCGCTAT-GTTGTC
65 CCTCATTATTTTGGTATACTTCTCTGTACCTCACCAGGAAGATGACCACT-TCATTATC
* * * * *
5937422 TAACCCACTTTTTTGTATCTCATCAGAAAGATGGGGTTTGGAAGTTTTACTCACA-TGAGC-TCT
1 TGACCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTT-GAAGTTTCACTCACATTGAGCTTC-
* * * * * *
5937485 ACTTCTTTGA-TTTGGTCTACTTCTCTGTACCTCACTAGGAAGATGATCGCTTCATTGTATC
64 ACCTCATT-ATTTTGGTATACTTCTCTGTACCTCACCAGGAAGATGACCACTTCA-T-TATC
* * * *
5937546 TGACTCACTTCTCTGTATCTCATCAAGAAGATGGGGTTTGAAGTTTTACTCACATTGAGCTTCGC
1 TGACCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTTCAC
* * * * * *
5937611 TTCTTTAATTTGGTATACTTCTCTGTACCTTACCAGGAATATGACCACTTCATTGTC
66 CTCATTATTTTGGTATACTTCTCTGTACCTCACCAGGAAGATGACCACTTCATTATC
* * *
5937668 TGACCCACTTCTTTGTATCTCA-CTAGGAAGATGGGATTTGAAGTTTCACTCATATTTGAGCTTC
1 TGACCCACTTCTCTGTATCTCATC-AGGAAGATGGGGTTTGAAGTTTCACTCACA-TTGAGCTTC
* * * *
5937732 ACCTCATTATTTTGGTAAACTTCTCTGTATCTCACCAAGAAGATGACCACTTCATTATT
64 ACCTCATTATTTTGGTATACTTCTCTGTACCTCACCAGGAAGATGACCACTTCATTATC
* ** * * *
5937791 TGACTCGTTTCTCTGTACCTCACCAGGAAGATGAGGTTTGA
1 TGACCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGA
5937832 TGTTGAAGCT
Statistics
Matches: 346, Mismatches: 51, Indels: 25
0.82 0.12 0.06
Matches are distributed among these distances:
121 6 0.02
122 129 0.37
123 122 0.35
124 87 0.25
125 2 0.01
ACGTcount: A:0.23, C:0.22, G:0.17, T:0.37
Consensus pattern (122 bp):
TGACCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTTCAC
CTCATTATTTTGGTATACTTCTCTGTACCTCACCAGGAAGATGACCACTTCATTATC
Found at i:5938068 original size:49 final size:49
Alignment explanation
Indices: 5937991--5938311 Score: 293
Period size: 49 Copynumber: 6.5 Consensus size: 49
5937981 TTCGTTATGG
*
5937991 CCTCGACCTTT-CCTATCATATCTTCATGGTACCGGGTTCACCGTTGCGA
1 CCTCAACCTTTCCCT-TCATATCTTCATGGTACCGGGTTCACCGTTGCGA
* * ** *
5938040 CCTCAACCTTTTCCTTCATATTTTCATGGTACTAGGTTCACCGTTGCAA
1 CCTCAACCTTTCCCTTCATATCTTCATGGTACCGGGTTCACCGTTGCGA
* * * ** * ** *
5938089 CCTCAACCTTTCCCATCACATATTCTAAAGTATCGGGTTCGTCGTTGCGG
1 CCTCAACCTTTCCCTTCATATCTTC-ATGGTACCGGGTTCACCGTTGCGA
* * * * ** * *
5938139 CCTTAACCATTCCCTTCATATCTTAATGGTACTGGGTTTGCCTTTGCGG
1 CCTCAACCTTTCCCTTCATATCTTCATGGTACCGGGTTCACCGTTGCGA
* * *
5938188 CCTCAACTTTTCCCTTCATATCTTCACGGTACCGGGTTCACCATTGCGA
1 CCTCAACCTTTCCCTTCATATCTTCATGGTACCGGGTTCACCGTTGCGA
* * * * * * * *
5938237 CATCAATCTTTCCCATCACATCTTCTAAGGTACCGGGTTAAACGTTGCGG
1 CCTCAACCTTTCCCTTCATATCTTC-ATGGTACCGGGTTCACCGTTGCGA
*
5938287 TCTCAACCTTTCCCTTCATATCTTC
1 CCTCAACCTTTCCCTTCATATCTTC
5938312 GTATTTCCTC
Statistics
Matches: 213, Mismatches: 56, Indels: 5
0.78 0.20 0.02
Matches are distributed among these distances:
49 137 0.64
50 76 0.36
ACGTcount: A:0.19, C:0.31, G:0.15, T:0.35
Consensus pattern (49 bp):
CCTCAACCTTTCCCTTCATATCTTCATGGTACCGGGTTCACCGTTGCGA
Found at i:5938204 original size:148 final size:148
Alignment explanation
Indices: 5937989--5938310 Score: 387
Period size: 148 Copynumber: 2.2 Consensus size: 148
5937979 TTTTCGTTAT
* * *
5937989 GGCCTCGACC-TTTCCTATCATATCTTCATGGTACCGGGTTCACCGTTGCGACCTCAACCTTTTC
1 GGCCTCAACCATTCCCT-TCATATCTTAATGGTACCGGGTTCACCGTTGCGACCTCAACCTTTTC
* * * * *
5938053 CTTCATATTTTCATGGTACTAGGTTCACCGTTGCAACCTCAACCTTTCCCATCACATATTCTAAA
65 CTTCATATCTTCACGGTACCAGGTTCACCATTGCAACATCAACCTTTCCCATCACATATTCTAAA
* ***
5938118 GTATCGGGTTCGTCGTTGC
130 GTACCGGGTTAAACGTTGC
* * ** * *
5938137 GGCCTTAACCATTCCCTTCATATCTTAATGGTACTGGGTTTGCCTTTGCGGCCTCAA-CTTTTCC
1 GGCCTCAACCATTCCCTTCATATCTTAATGGTACCGGGTTCACCGTTGCGACCTCAACCTTTT-C
* * * * *
5938201 CTTCATATCTTCACGGTACCGGGTTCACCATTGCGACATCAATCTTTCCCATCACATCTTCTAAG
65 CTTCATATCTTCACGGTACCAGGTTCACCATTGCAACATCAACCTTTCCCATCACATATTCTAAA
5938266 GTACCGGGTTAAACGTTGC
130 GTACCGGGTTAAACGTTGC
* *
5938285 GGTCTCAACCTTTCCCTTCATATCTT
1 GGCCTCAACCATTCCCTTCATATCTT
5938311 CGTATTTCCT
Statistics
Matches: 146, Mismatches: 26, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
147 5 0.03
148 136 0.93
149 5 0.03
ACGTcount: A:0.19, C:0.30, G:0.16, T:0.35
Consensus pattern (148 bp):
GGCCTCAACCATTCCCTTCATATCTTAATGGTACCGGGTTCACCGTTGCGACCTCAACCTTTTCC
TTCATATCTTCACGGTACCAGGTTCACCATTGCAACATCAACCTTTCCCATCACATATTCTAAAG
TACCGGGTTAAACGTTGC
Found at i:5939279 original size:7 final size:6
Alignment explanation
Indices: 5939266--5939342 Score: 68
Period size: 6 Copynumber: 11.8 Consensus size: 6
5939256 GACCTCTCCT
5939266 TTTTTC TATTTTC TATTTTC TTTTTCC TTTTTTC TTTTTC TTTTT- TTTTTCC
1 TTTTTC T-TTTTC T-TTTTC TTTTT-C -TTTTTC TTTTTC TTTTTC TTTTT-C
5939318 TTTTTTC TTTCTT- TCTTTTC TTTTT
1 -TTTTTC TTT-TTC T-TTTTC TTTTT
5939343 TATTTATTTT
Statistics
Matches: 62, Mismatches: 0, Indels: 18
0.77 0.00 0.22
Matches are distributed among these distances:
5 5 0.08
6 26 0.42
7 21 0.34
8 10 0.16
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTTC
Found at i:5939326 original size:39 final size:39
Alignment explanation
Indices: 5939281--5939355 Score: 98
Period size: 39 Copynumber: 1.9 Consensus size: 39
5939271 CTATTTTCTA
* * *
5939281 TTTTCTTT-TTCCTTTTTTCTTTTTCTTTTTTTTTTCCTT
1 TTTTCTTTCTTCCTTTTCT-TTTTTATTTATTTTTTCCTT
*
5939320 TTTTCTTTCTTTCTTTTCTTTTTTATTTATTTTTTC
1 TTTTCTTTCTTCCTTTTCTTTTTTATTTATTTTTTC
5939356 TTCATTGAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 23 0.74
40 8 0.26
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (39 bp):
TTTTCTTTCTTCCTTTTCTTTTTTATTTATTTTTTCCTT
Found at i:5939337 original size:32 final size:31
Alignment explanation
Indices: 5939266--5939357 Score: 105
Period size: 32 Copynumber: 2.8 Consensus size: 31
5939256 GACCTCTCCT
*
5939266 TTTTTCTATTTTCTATTTTCTTTTTCCTTTTTTC
1 TTTTTCT-TTTT-T-TTTTCTTTTTTCTTTTTTC
5939300 TTTTTCTTTTTTTTTTCCTTTTTTCTTTCTTTC
1 TTTTTCTTTTTTTTTT-CTTTTTTCTTT-TTTC
* *
5939333 -TTTTCTTTTTTATTTATTTTTTCTT
1 TTTTTCTTTTTTTTTTCTTTTTTCTT
5939358 CATTGAATCC
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
31 13 0.25
32 25 0.47
33 8 0.15
34 7 0.13
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.80
Consensus pattern (31 bp):
TTTTTCTTTTTTTTTTCTTTTTTCTTTTTTC
Found at i:5939343 original size:7 final size:7
Alignment explanation
Indices: 5939264--5939357 Score: 86
Period size: 7 Copynumber: 13.4 Consensus size: 7
5939254 TCGACCTCTC
5939264 CTTTTTT
1 CTTTTTT
*
5939271 CTATTTT
1 CTTTTTT
*
5939278 CTATTTT
1 CTTTTTT
*
5939285 CTTTTTC
1 CTTTTTT
5939292 CTTTTTT
1 CTTTTTT
5939299 C-TTTTT
1 CTTTTTT
5939305 C-TTTTT
1 CTTTTTT
*
5939311 -TTTTTC
1 CTTTTTT
5939317 CTTTTTT
1 CTTTTTT
5939324 CTTTCTTT
1 CTTT-TTT
5939332 CTTTTCTT
1 CTTTT-TT
*
5939340 TTTTATTT
1 CTTT-TTT
*
5939348 ATTTTTT
1 CTTTTTT
5939355 CTT
1 CTT
5939358 CATTGAATCC
Statistics
Matches: 73, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
6 15 0.21
7 40 0.55
8 17 0.23
9 1 0.01
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (7 bp):
CTTTTTT
Found at i:5945646 original size:20 final size:20
Alignment explanation
Indices: 5945589--5945650 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
5945579 CAATTATTTG
5945589 TGTTTTGTTTTCTTGCTATT
1 TGTTTTGTTTTCTTGCTATT
*
5945609 T-TTTTCTTTGTC-T--T-TT
1 TGTTTTGTTT-TCTTGCTATT
5945625 TGTTTTGTTTTCTTGCTATT
1 TGTTTTGTTTTCTTGCTATT
5945645 TGTTTT
1 TGTTTT
5945651 CTTTATCTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
16 5 0.15
17 9 0.26
19 9 0.26
20 11 0.32
ACGTcount: A:0.03, C:0.10, G:0.13, T:0.74
Consensus pattern (20 bp):
TGTTTTGTTTTCTTGCTATT
Found at i:5946503 original size:25 final size:23
Alignment explanation
Indices: 5946470--5946526 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 23
5946460 TGTATTTAAA
5946470 ATAATTATTTGAAATATTATATATAT
1 ATAA-TATTTGAAATATT-TAT-TAT
*
5946496 ATAATATTTGAAATATTTATTTT
1 ATAATATTTGAAATATTTATTAT
5946519 ATAATATT
1 ATAATATT
5946527 AGAATTTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
23 10 0.33
24 3 0.10
25 13 0.43
26 4 0.13
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (23 bp):
ATAATATTTGAAATATTTATTAT
Found at i:5946570 original size:28 final size:28
Alignment explanation
Indices: 5946501--5946562 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
5946491 TATATATAAT
*
5946501 ATTTGAAATATTTATTTTATAATATTAGA
1 ATTT-AAATAATTATTTTATAATATTAGA
*
5946530 ATTTAAATAATTATTTTTTAATATTAGA
1 ATTTAAATAATTATTTTATAATATTAGA
5946558 ATTTA
1 ATTTA
5946563 CTATATTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
28 27 0.87
29 4 0.13
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (28 bp):
ATTTAAATAATTATTTTATAATATTAGA
Found at i:5948060 original size:13 final size:13
Alignment explanation
Indices: 5948042--5948090 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
5948032 CTTAACCCAA
5948042 ACTTTTTAAAAAT
1 ACTTTTTAAAAAT
*
5948055 AC-TTTTCAAAAT
1 ACTTTTTAAAAAT
* *
5948067 CACTTTTTCAAAAC
1 -ACTTTTTAAAAAT
5948081 ACTTTTTAAA
1 ACTTTTTAAA
5948091 GCGCTTCTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
12 9 0.29
13 13 0.42
14 9 0.29
ACGTcount: A:0.41, C:0.16, G:0.00, T:0.43
Consensus pattern (13 bp):
ACTTTTTAAAAAT
Found at i:5948699 original size:13 final size:13
Alignment explanation
Indices: 5948681--5948706 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5948671 AATTTTACAT
5948681 TCTATTCAGTTTA
1 TCTATTCAGTTTA
5948694 TCTATTCAGTTTA
1 TCTATTCAGTTTA
5948707 GTCCCTAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.08, T:0.54
Consensus pattern (13 bp):
TCTATTCAGTTTA
Found at i:5950117 original size:30 final size:30
Alignment explanation
Indices: 5950083--5950155 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 30
5950073 TTTGATATAT
*
5950083 AAACTTTAATTTGGTGTAATTATACACATG
1 AAACTTTAATTTGGTGTAAATATACACATG
* * * *
5950113 AAACTTTGATTGTGGTTTAAATGTATACATG
1 AAACTTTAATT-TGGTGTAAATATACACATG
*
5950144 AAACATTAATTT
1 AAACTTTAATTT
5950156 TGATTCAATC
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
30 11 0.31
31 24 0.69
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.41
Consensus pattern (30 bp):
AAACTTTAATTTGGTGTAAATATACACATG
Found at i:5953327 original size:30 final size:30
Alignment explanation
Indices: 5953264--5953331 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 30
5953254 TAGGGTTTTG
5953264 ATTT-TTTACCAAAATAAAATATAAAAAAAT
1 ATTTATTTACCAAAAT-AAATATAAAAAAAT
* *
5953294 ATTTATTTACTAAAAT-AATATACAAAAATT
1 ATTTATTTACCAAAATAAATATA-AAAAAAT
5953324 ATTTATTT
1 ATTTATTT
5953332 TATTTGACTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
29 6 0.18
30 18 0.53
31 10 0.29
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (30 bp):
ATTTATTTACCAAAATAAATATAAAAAAAT
Found at i:5953357 original size:36 final size:34
Alignment explanation
Indices: 5953268--5953368 Score: 100
Period size: 31 Copynumber: 3.0 Consensus size: 34
5953258 GTTTTGATTT
* * *
5953268 TTTACCAAAATAAAATATAAAAA--AATA-TTTA
1 TTTACTAAAATAAAATACAAAAATTATTATTTTA
*
5953299 TTTACTAAAATAATATACAAAAATTATTTATTTTA
1 TTTACTAAAATAAAATACAAAAATTA-TTATTTTA
* **
5953334 TTTGACTAAAGTAAAATTTAAAAATTATTATTTTA
1 TTT-ACTAAAATAAAATACAAAAATTATTATTTTA
5953369 ATAAAAATAA
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
31 20 0.35
33 1 0.02
34 2 0.04
35 15 0.26
36 19 0.33
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (34 bp):
TTTACTAAAATAAAATACAAAAATTATTATTTTA
Found at i:5953365 original size:35 final size:35
Alignment explanation
Indices: 5953295--5953368 Score: 96
Period size: 36 Copynumber: 2.1 Consensus size: 35
5953285 TAAAAAAATA
*
5953295 TTTATTTACTAAAATAATATACAAAAATTATTTAT
1 TTTATTTACTAAAATAAAATACAAAAATTATTTAT
* **
5953330 TTTATTTGACTAAAGTAAAATTTAAAAATTA-TTAT
1 TTTATTT-ACTAAAATAAAATACAAAAATTATTTAT
5953365 TTTA
1 TTTA
5953369 ATAAAAATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
35 15 0.44
36 19 0.56
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (35 bp):
TTTATTTACTAAAATAAAATACAAAAATTATTTAT
Found at i:5954171 original size:24 final size:24
Alignment explanation
Indices: 5954144--5954190 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
5954134 TGTGGAACTT
5954144 GTAGAAAATGAAGATCCAACTCCA
1 GTAGAAAATGAAGATCCAACTCCA
5954168 GTAGAAAATGAAGATCCAACTCC
1 GTAGAAAATGAAGATCCAACTCC
5954191 GTGTATGGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.45, C:0.21, G:0.17, T:0.17
Consensus pattern (24 bp):
GTAGAAAATGAAGATCCAACTCCA
Found at i:5956688 original size:7 final size:7
Alignment explanation
Indices: 5956658--5956712 Score: 51
Period size: 7 Copynumber: 7.7 Consensus size: 7
5956648 TGGTTTCTAA
5956658 TTTAAGG
1 TTTAAGG
5956665 -TTAAGGG
1 TTTAA-GG
5956672 TTT-AGAG
1 TTTAAG-G
5956679 TTTAAGG
1 TTTAAGG
5956686 TTTAAGG
1 TTTAAGG
5956693 TTTATAGG
1 TTTA-AGG
* *
5956701 TATAAAG
1 TTTAAGG
5956708 TTTAA
1 TTTAA
5956713 ATAAATGATC
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
6 5 0.12
7 25 0.62
8 10 0.25
ACGTcount: A:0.33, C:0.00, G:0.25, T:0.42
Consensus pattern (7 bp):
TTTAAGG
Found at i:5956701 original size:15 final size:14
Alignment explanation
Indices: 5956658--5956712 Score: 51
Period size: 15 Copynumber: 3.9 Consensus size: 14
5956648 TGGTTTCTAA
5956658 TTTAAGG-TTAAGGG
1 TTTAAGGTTTAA-GG
5956672 TTT-AGAGTTTAAGG
1 TTTAAG-GTTTAAGG
5956686 TTTAAGGTTTATAGG
1 TTTAAGGTTTA-AGG
* *
5956701 TATAAAGTTTAA
1 TTTAAGGTTTAA
5956713 ATAAATGATC
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
13 2 0.06
14 15 0.43
15 18 0.51
ACGTcount: A:0.33, C:0.00, G:0.25, T:0.42
Consensus pattern (14 bp):
TTTAAGGTTTAAGG
Found at i:5957024 original size:45 final size:45
Alignment explanation
Indices: 5956960--5957050 Score: 173
Period size: 45 Copynumber: 2.0 Consensus size: 45
5956950 GGAGGAGTAC
5956960 AGTATTGCGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTTG
1 AGTATTGCGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTTG
*
5957005 AGTATTGCGGTGGCTCGTCAAACTGAGGCTGATATCTTTGGCTTG
1 AGTATTGCGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTTG
5957050 A
1 A
5957051 TAAGCTAGAC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.19, C:0.19, G:0.31, T:0.32
Consensus pattern (45 bp):
AGTATTGCGGTGGCTCGTCAAACTGAGGCTGATATCCTTGGCTTG
Found at i:5957124 original size:6 final size:6
Alignment explanation
Indices: 5957113--5957159 Score: 85
Period size: 6 Copynumber: 7.8 Consensus size: 6
5957103 TCATCCAATG
*
5957113 CCTCTT CTTCTT CCTCTT CCTCTT CCTCTT CCTCTT CCTCTT CCTCT
1 CCTCTT CCTCTT CCTCTT CCTCTT CCTCTT CCTCTT CCTCTT CCTCT
5957160 GGGTTTGGGG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (6 bp):
CCTCTT
Found at i:5959052 original size:4 final size:4
Alignment explanation
Indices: 5959043--5959122 Score: 74
Period size: 4 Copynumber: 19.5 Consensus size: 4
5959033 TCTCCTTCTC
* * *
5959043 CTTT CTTT CTTCT CCTTT CTTT CTTCT CCTT C-TT CCTT C-TT CCTT CTTT
1 CTTT CTTT CTT-T -CTTT CTTT CTT-T CTTT CTTT CTTT CTTT CTTT CTTT
*
5959092 CTTT CTTT CTTTT CTTT ATTT CTTT CTTT CT
1 CTTT CTTT C-TTT CTTT CTTT CTTT CTTT CT
5959123 AAACCCGTTG
Statistics
Matches: 66, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
3 6 0.09
4 48 0.73
5 9 0.14
6 3 0.05
ACGTcount: A:0.01, C:0.31, G:0.00, T:0.68
Consensus pattern (4 bp):
CTTT
Found at i:5959054 original size:14 final size:14
Alignment explanation
Indices: 5959024--5959103 Score: 89
Period size: 14 Copynumber: 5.9 Consensus size: 14
5959014 TATGTTACCT
*
5959024 TTCTCTCTTTC-TCC
1 TTCTC-CTTTCTTTC
5959038 TTCTCCTTTCTTTC
1 TTCTCCTTTCTTTC
5959052 TTCTCCTTTCTTTC
1 TTCTCCTTTCTTTC
*
5959066 TTCTCC-TTCTTCC
1 TTCTCCTTTCTTTC
5959079 TTCTTCC-TTCTTTC
1 TTC-TCCTTTCTTTC
5959093 TT-T-CTTTCTTT
1 TTCTCCTTTCTTT
5959104 TCTTTATTTC
Statistics
Matches: 60, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
11 1 0.02
12 7 0.12
13 14 0.23
14 38 0.63
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (14 bp):
TTCTCCTTTCTTTC
Found at i:5964203 original size:4 final size:4
Alignment explanation
Indices: 5964194--5964220 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
5964184 TCAAGCCAGA
5964194 GAGG GAGG GAGG GAGG GAGG GAGG GAG
1 GAGG GAGG GAGG GAGG GAGG GAGG GAG
5964221 TGGGTGTGTT
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:0.26, C:0.00, G:0.74, T:0.00
Consensus pattern (4 bp):
GAGG
Found at i:5968112 original size:16 final size:17
Alignment explanation
Indices: 5968091--5968122 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
5968081 GGAATGAAGC
5968091 AAAGAAAAATA-AAAGG
1 AAAGAAAAATAGAAAGG
5968107 AAAGAAAAATAGAAAG
1 AAAGAAAAATAGAAAG
5968123 TTTGGAGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06
Consensus pattern (17 bp):
AAAGAAAAATAGAAAGG
Found at i:5969478 original size:9 final size:9
Alignment explanation
Indices: 5969466--5969503 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
5969456 TTTTTAGAAT
5969466 TTTTAAAAA
1 TTTTAAAAA
5969475 TTTTAAAAA
1 TTTTAAAAA
*
5969484 TATTT-TAAA
1 T-TTTAAAAA
5969493 TTTTAAAAA
1 TTTTAAAAA
5969502 TT
1 TT
5969504 AAAATAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
8 3 0.12
9 19 0.76
10 3 0.12
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:5973282 original size:2 final size:2
Alignment explanation
Indices: 5973275--5973307 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5973265 AAATTGTCAC
5973275 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5973308 AATTCACTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5973498 original size:22 final size:22
Alignment explanation
Indices: 5973473--5973514 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
5973463 GCTGTTAATA
* *
5973473 ATTTTTAATACTTTTTTAAATT
1 ATTTTTAATAATTATTTAAATT
5973495 ATTTTTAATAATTATTTAAA
1 ATTTTTAATAATTATTTAAA
5973515 AATCACATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (22 bp):
ATTTTTAATAATTATTTAAATT
Found at i:5975656 original size:26 final size:25
Alignment explanation
Indices: 5975597--5975656 Score: 68
Period size: 25 Copynumber: 2.4 Consensus size: 25
5975587 AACTCGATTC
*
5975597 AATTTGATTAAAAATTATTTAACTT
1 AATTTGATTAAAAATTATTTAAATT
* *
5975622 GATTCGATTCAAAAATT-TTTAAATT
1 AATTTGATT-AAAAATTATTTAAATT
5975647 AAATTTGATT
1 -AATTTGATT
5975657 GTTAAAATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
25 14 0.50
26 14 0.50
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.47
Consensus pattern (25 bp):
AATTTGATTAAAAATTATTTAAATT
Found at i:5975712 original size:14 final size:14
Alignment explanation
Indices: 5975693--5975722 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
5975683 TAAATCGAAA
5975693 TCTTTTGACTTGAT
1 TCTTTTGACTTGAT
5975707 TCTTTTGACTTGAT
1 TCTTTTGACTTGAT
5975721 TC
1 TC
5975723 GATTAGATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.17, G:0.13, T:0.57
Consensus pattern (14 bp):
TCTTTTGACTTGAT
Found at i:5981708 original size:14 final size:14
Alignment explanation
Indices: 5981685--5981717 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5981675 ACGTGTTTTA
5981685 TTTA-TTTAATATT
1 TTTATTTTAATATT
*
5981698 TTTATTTTAATTTT
1 TTTATTTTAATATT
5981712 TTTATT
1 TTTATT
5981718 ATATGTATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTATTTTAATATT
Found at i:5984406 original size:17 final size:18
Alignment explanation
Indices: 5984384--5984426 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
5984374 TAATTAATTA
5984384 AATTAAATTAA-ATTCTC
1 AATTAAATTAATATTCTC
*
5984401 AATTAAA-TAATTTTCTC
1 AATTAAATTAATATTCTC
*
5984418 AATCAAATT
1 AATTAAATT
5984427 CTAATTCCGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 3 0.14
17 18 0.82
18 1 0.05
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.42
Consensus pattern (18 bp):
AATTAAATTAATATTCTC
Found at i:5984958 original size:16 final size:17
Alignment explanation
Indices: 5984934--5984966 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
5984924 ATTTTAGTTG
5984934 AAATAATTTTTTGAAAA
1 AAATAATTTTTTGAAAA
5984951 AAAT-ATTTTTTGAAAA
1 AAATAATTTTTTGAAAA
5984967 GCAAATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (17 bp):
AAATAATTTTTTGAAAA
Found at i:5990121 original size:6 final size:6
Alignment explanation
Indices: 5990112--5990138 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5990102 ATGTTGGAGT
5990112 AGGTGA AGGTGA AGGTGA AGGTGA AGG
1 AGGTGA AGGTGA AGGTGA AGGTGA AGG
5990139 CGTGATTCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.52, T:0.15
Consensus pattern (6 bp):
AGGTGA
Found at i:5993649 original size:120 final size:122
Alignment explanation
Indices: 5993445--5993728 Score: 334
Period size: 120 Copynumber: 2.4 Consensus size: 122
5993435 TTTAGAAAAA
* *** * *
5993445 AAATTCAAAATTTTTT-GGTGTT-GCCATTGCATGGTCGACACCCCCTGTTTCAGAAAAAAAAAT
1 AAATTCCAAATTTTTTGGGTGTTGGCCATCAAATGGCCGACACCCCCTATTTCAGAAAAAAAAAT
5993508 TTAAATTTTTTTGGTGTTGGCCATCAAATAG-CTGACA-CCTCTTTTTCTCGAA-AAAT
66 TTAAATTTTTTTGGTGTTGGCCATCAAATAGAC-GACATCCTC-TTTTCTCGAATAAAT
***
5993564 -AATT-TGTA-TTTTTGGGTGTTGGCCATCAAATGGCCGACACCCTCCTATTCTC-GAGAAAAAA
1 AAATTCCAAATTTTTTGGGTGTTGGCCATCAAATGGCCGACACCC-CCTATT-TCAGA-AAAAAA
* *
5993625 ATTTTAAATTTTTTTGGTGTTGGCCATCAAATGGACGACATCCTCTTTTCTCGAATAAAT
63 AATTTAAATTTTTTTGGTGTTGGCCATCAAATAGACGACATCCTCTTTTCTCGAATAAAT
** *
5993685 AAATTCCAAATTTTTTTTGTGTTGGCCATCAAATGACCGACACC
1 AAATTCCAAATTTTTTGGGTGTTGGCCATCAAATGGCCGACACC
5993729 AACTTCTTTT
Statistics
Matches: 138, Mismatches: 16, Indels: 17
0.81 0.09 0.10
Matches are distributed among these distances:
116 5 0.04
117 7 0.05
118 21 0.15
119 7 0.05
120 54 0.39
121 9 0.07
122 4 0.03
123 1 0.01
124 30 0.22
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (122 bp):
AAATTCCAAATTTTTTGGGTGTTGGCCATCAAATGGCCGACACCCCCTATTTCAGAAAAAAAAAT
TTAAATTTTTTTGGTGTTGGCCATCAAATAGACGACATCCTCTTTTCTCGAATAAAT
Found at i:5993652 original size:62 final size:62
Alignment explanation
Indices: 5993438--5993728 Score: 280
Period size: 62 Copynumber: 4.8 Consensus size: 62
5993428 GCCTTGTTTT
* * * *** * *
5993438 AGAAAAAAAATTCAAAATTTTTTGGTGTT-GCCATTGCATGGTCGACACCC-CCTGTT-TC-
1 AGAAAAAAATTTTAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCTCCTTTTCTCG
* * * *
5993496 AGAAAAAAAAATTTAAATTTTTTTGGTGTTGGCCATCAAATAGCTGACA-CCTCTTTTTCTCG
1 AG-AAAAAAATTTTAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCTCCTTTTCTCG
* * *
5993558 A-AAAATAATTTGT--A-TTTTTGGGTGTTGGCCATCAAATGGCCGACACCCTCCTATTCTCG
1 AGAAAAAAATTT-TAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCTCCTTTTCTCG
* *
5993617 AGAAAAAAATTTTAAATTTTTTTGGTGTTGGCCATCAAATGGACGACATCCT-CTTTTCTCG
1 AGAAAAAAATTTTAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCTCCTTTTCTCG
** * *
5993678 A-ATAAATAAATTCCAAATTTTTTTTGTGTTGGCCATCAAATGACCGACACC
1 AGA-AAA-AAATTTTAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACC
5993729 AACTTCTTTT
Statistics
Matches: 192, Mismatches: 28, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
58 30 0.16
59 41 0.21
60 34 0.18
61 16 0.08
62 71 0.37
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (62 bp):
AGAAAAAAATTTTAAATTTTTTTGGTGTTGGCCATCAAATGGCCGACACCCTCCTTTTCTCG
Found at i:5994610 original size:30 final size:30
Alignment explanation
Indices: 5994550--5994641 Score: 89
Period size: 30 Copynumber: 3.1 Consensus size: 30
5994540 TAATAATTAG
* * ** *
5994550 AATATACATGAAATTAGAAAGAAAAATTAA
1 AATATACAAGAAATTCGAAATTAAATTTAA
5994580 AATATACAAGAAATTCGAAATTAAATTTAA
1 AATATACAAGAAATTCGAAATTAAATTTAA
* *
5994610 AATA-AAAACAAAATTAC-AAATTAAATTTAA
1 AATATACAA-GAAATT-CGAAATTAAATTTAA
5994640 AA
1 AA
5994642 AGTAAAGGGA
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
29 3 0.06
30 49 0.92
31 1 0.02
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.26
Consensus pattern (30 bp):
AATATACAAGAAATTCGAAATTAAATTTAA
Found at i:5997182 original size:83 final size:83
Alignment explanation
Indices: 5997052--5997396 Score: 507
Period size: 83 Copynumber: 4.1 Consensus size: 83
5997042 AATTGTAATA
*
5997052 TAATAATAATAATAAATTTTATTTAAAGATATAAAATTAATAAATAATGTATTGTCAAATCAACA
1 TAAT-ATAATAAAAAATTTTATTTAAAGATATAAAATTAATAAATAATGTATTGTCAAATCAACA
5997117 CATTATATGATAAAAATTG
65 CATTATATGATAAAAATTG
5997136 TAATATAATAAAAAATTTTATTTAAAGATATAAAATTAATAAATAATGTATTGTCAAATCAACAC
1 TAATATAATAAAAAATTTTATTTAAAGATATAAAATTAATAAATAATGTATTGTCAAATCAACAC
5997201 ATTATATGATAAAAATTG
66 ATTATATGATAAAAATTG
* ***
5997219 TAAAATAATAAATTTTTTTATTTAAAGATATAAAATTAATAAATAATGTATTGTCAAATCAACAC
1 TAATATAATAAAAAATTTTATTTAAAGATATAAAATTAATAAATAATGTATTGTCAAATCAACAC
*
5997284 ATTATATGATAAAAATTA
66 ATTATATGATAAAAATTG
* * * *
5997302 TAATATAAT-AATAATTTGTACTTT-AA-ATATGAAAATTTGATAAATAATGTACTGTCAAATTA
1 TAATATAATAAAAAATTT-TA-TTTAAAGATAT-AAAA-TTAATAAATAATGTATTGTCAAATCA
* * *
5997364 ACACAATATTTGATATAAATTG
62 ACACATTATATGATAAAAATTG
5997386 TAATATAATAA
1 TAATATAATAA
5997397 CTATCTTTTT
Statistics
Matches: 240, Mismatches: 16, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
82 10 0.04
83 172 0.72
84 57 0.24
85 1 0.00
ACGTcount: A:0.51, C:0.05, G:0.06, T:0.38
Consensus pattern (83 bp):
TAATATAATAAAAAATTTTATTTAAAGATATAAAATTAATAAATAATGTATTGTCAAATCAACAC
ATTATATGATAAAAATTG
Found at i:5997217 original size:45 final size:45
Alignment explanation
Indices: 5997162--5997310 Score: 120
Period size: 45 Copynumber: 3.4 Consensus size: 45
5997152 TTTATTTAAA
5997162 GATATAAAATTAATAAATAATGTATTGTCAAATCAACACATTATAT
1 GATATAAAATT-ATAAATAATGTATTGTCAAATCAACACATTATAT
* ** *** * *
5997208 GATA-AAAATTGTAAAATAATAAATT-T----T-TTTA-TTTA-AA
1 GATATAAAATTAT-AAATAATGTATTGTCAAATCAACACATTATAT
5997245 GATATAAAATTAATAAATAATGTATTGTCAAATCAACACATTATAT
1 GATATAAAATT-ATAAATAATGTATTGTCAAATCAACACATTATAT
5997291 GATA-AAAATTATAATATAAT
1 GATATAAAATTATAA-ATAAT
5997311 AATAATTTGT
Statistics
Matches: 75, Mismatches: 16, Indels: 25
0.65 0.14 0.22
Matches are distributed among these distances:
37 5 0.07
38 19 0.25
39 3 0.04
40 1 0.01
43 1 0.01
44 7 0.09
45 30 0.40
46 9 0.12
ACGTcount: A:0.52, C:0.05, G:0.06, T:0.37
Consensus pattern (45 bp):
GATATAAAATTATAAATAATGTATTGTCAAATCAACACATTATAT
Found at i:5997544 original size:12 final size:12
Alignment explanation
Indices: 5997527--5997574 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 12
5997517 AAACATGTTC
5997527 ATTAATTTCCAA
1 ATTAATTTCCAA
5997539 ATTAATTTCAACTTAA
1 ATTAATTTC--C--AA
*
5997555 ATTAATTTTCAA
1 ATTAATTTCCAA
5997567 ATTAATTT
1 ATTAATTT
5997575 TTACACAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
12 19 0.61
14 2 0.06
16 10 0.32
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTAATTTCCAA
Found at i:5997573 original size:16 final size:16
Alignment explanation
Indices: 5997537--5997571 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
5997527 ATTAATTTCC
*
5997537 AAATTAATTTCAACTT
1 AAATTAATTTCAAATT
5997553 AAATTAATTTTCAAATT
1 AAATTAA-TTTCAAATT
5997570 AA
1 AA
5997572 TTTTTACACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.43
Consensus pattern (16 bp):
AAATTAATTTCAAATT
Found at i:5997584 original size:28 final size:28
Alignment explanation
Indices: 5997527--5997584 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
5997517 AAACATGTTC
**
5997527 ATTAATTTCCAAATTAATTTCAACTTAA
1 ATTAATTTCCAAATTAATTTCAACACAA
* **
5997555 ATTAATTTTCAAATTAATTTTTACACAA
1 ATTAATTTCCAAATTAATTTCAACACAA
5997583 AT
1 AT
5997585 ATATTTCGTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.45
Consensus pattern (28 bp):
ATTAATTTCCAAATTAATTTCAACACAA
Found at i:5999760 original size:19 final size:19
Alignment explanation
Indices: 5999724--5999769 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
5999714 TAATATTTTC
5999724 ACAA-CAAAA-TATTTAAT
1 ACAATCAAAATTATTTAAT
5999741 A-AATCAAAATTATATTAAT
1 ACAATCAAAATTAT-TTAAT
5999760 ACAAT-AAAAT
1 ACAATCAAAAT
5999770 ATAAATCTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 2 0.08
17 6 0.24
18 3 0.12
19 11 0.44
20 3 0.12
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (19 bp):
ACAATCAAAATTATTTAAT
Found at i:6000476 original size:61 final size:59
Alignment explanation
Indices: 6000409--6000631 Score: 265
Period size: 61 Copynumber: 3.8 Consensus size: 59
6000399 AGGAGAAGTT
6000409 GGTGTCGGCCATTTGATGGCCAACACAAAAAAAATTTGAAATTTTTTTATTCGAGAAAAGG
1 GGTGTCGGCCATTTGATGGCCAACACAAAAAAAATTTG-AATTTTTTT-TTCGAGAAAAGG
* * * * *
6000470 GGTGTCGGCCATTTGATGGCTAACACGAAAAAAATTTGAATTCTTTTCTCGAGAATAGGG
1 GGTGTCGGCCATTTGATGGCCAACACAAAAAAAATTTGAATTTTTTTTTCGAGAA-AAGG
** ** * *
6000530 GGTGTCGGCCATTTGATGATCAACAC-CTAAAAA--TGTATTTTTTTTT-GAAAAAAGG
1 GGTGTCGGCCATTTGATGGCCAACACAAAAAAAATTTGAATTTTTTTTTCGAGAAAAGG
** *
6000585 GGTGTCGATCATTTGATGGCCAACATAAAAAAAATTTGAATTTTTTT
1 GGTGTCGGCCATTTGATGGCCAACACAAAAAAAATTTGAATTTTTTT
6000632 CCGAAACAGA
Statistics
Matches: 135, Mismatches: 23, Indels: 11
0.80 0.14 0.07
Matches are distributed among these distances:
55 24 0.18
56 9 0.07
57 10 0.07
58 10 0.07
59 12 0.09
60 34 0.25
61 36 0.27
ACGTcount: A:0.33, C:0.13, G:0.21, T:0.33
Consensus pattern (59 bp):
GGTGTCGGCCATTTGATGGCCAACACAAAAAAAATTTGAATTTTTTTTTCGAGAAAAGG
Found at i:6000715 original size:85 final size:84
Alignment explanation
Indices: 6000558--6000725 Score: 239
Period size: 86 Copynumber: 2.0 Consensus size: 84
6000548 ATCAACACCT
* * * *
6000558 AAAAATGTATTTTTTTTTGAAAAAAGGGGTGTCGATCATTTGATGGCCAACATAAAAAAAATTTG
1 AAAAATGAATTTTTTTTCGAAAAAAGGGGTGTCGACCATTTGATGGCCAACACAAAAAAAATTTG
6000623 AATTTTTTTCCGAAACAGA
66 AATTTTTTTCCGAAACAGA
* *
6000642 AAAAATGCAATTTTTTTTCGAGAAAAGGGGGTGTCGACCATTTGATGGCCAACACCAAAAAAATT
1 AAAAATG-AATTTTTTTTCGA-AAAAAGGGGTGTCGACCATTTGATGGCCAACACAAAAAAAATT
**
6000707 T-AATTTTTTTTTGAAACAG
64 TGAATTTTTTTCCGAAACAG
6000726 GGGATTTCGG
Statistics
Matches: 74, Mismatches: 8, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
84 7 0.09
85 27 0.36
86 40 0.54
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.33
Consensus pattern (84 bp):
AAAAATGAATTTTTTTTCGAAAAAAGGGGTGTCGACCATTTGATGGCCAACACAAAAAAAATTTG
AATTTTTTTCCGAAACAGA
Found at i:6002213 original size:16 final size:16
Alignment explanation
Indices: 6002192--6002226 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
6002182 ATATTTCGGT
*
6002192 TTAACTCGAATATTAA
1 TTAACTCGAATATGAA
6002208 TTAACTCGAATATGAA
1 TTAACTCGAATATGAA
6002224 TTA
1 TTA
6002227 CATAATTCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.43, C:0.11, G:0.09, T:0.37
Consensus pattern (16 bp):
TTAACTCGAATATGAA
Found at i:6004319 original size:21 final size:21
Alignment explanation
Indices: 6004293--6004336 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
6004283 ATATGGGTTT
6004293 TAATATTCAATTTCACTATAA
1 TAATATTCAATTTCACTATAA
6004314 TAATATTCAATTTCACTATAA
1 TAATATTCAATTTCACTATAA
6004335 TA
1 TA
6004337 TAAATATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (21 bp):
TAATATTCAATTTCACTATAA
Found at i:6013253 original size:6 final size:6
Alignment explanation
Indices: 6013244--6013277 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
6013234 TAAAAAAATA
*
6013244 TGAGTA TGAGTG TGAGTG TGAGTG TGAGTG TGAG
1 TGAGTG TGAGTG TGAGTG TGAGTG TGAGTG TGAG
6013278 AGCTCCTAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.21, C:0.00, G:0.47, T:0.32
Consensus pattern (6 bp):
TGAGTG
Found at i:6027296 original size:2 final size:2
Alignment explanation
Indices: 6027289--6027331 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
6027279 TTTAATGGTA
6027289 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6027331 A
1 A
6027332 CACAATAGAA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6028439 original size:16 final size:16
Alignment explanation
Indices: 6028418--6028463 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 16
6028408 GTTGGAATAG
6028418 AATAGAGCTGTAATGA
1 AATAGAGCTGTAATGA
* *
6028434 AATAGAGTTGTAATGG
1 AATAGAGCTGTAATGA
6028450 AATAGAGCTGTAAT
1 AATAGAGCTGTAAT
6028464 CAGTAATTCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.41, C:0.04, G:0.26, T:0.28
Consensus pattern (16 bp):
AATAGAGCTGTAATGA
Found at i:6028686 original size:58 final size:57
Alignment explanation
Indices: 6028619--6028778 Score: 184
Period size: 58 Copynumber: 2.8 Consensus size: 57
6028609 AATTATTGTT
*
6028619 ATTAAATTTTAATA-AGATTATTATTAAATGTAATTTAATAAAAATAATAAATAATTTA
1 ATTAAATTTTAATATA-ATTATTATTAAATATAATTTAATAAAAATAA-AAATAATTTA
* * * * *
6028677 ATTATATTTTAACATAATTATTATTAAATACAATTTAAT-AATATAAATATAATTTA
1 ATTAAATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAAAAATAATTTA
6028733 A-TAACATTTTTAATATAATTATTATTAAAATATGAA-TTAATAAAAA
1 ATTAA-A-TTTTAATATAATTATTATT-AAATAT-AATTTAATAAAAA
6028779 ATATAATATA
Statistics
Matches: 86, Mismatches: 10, Indels: 11
0.80 0.09 0.10
Matches are distributed among these distances:
55 2 0.02
56 11 0.13
57 24 0.28
58 43 0.50
59 6 0.07
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (57 bp):
ATTAAATTTTAATATAATTATTATTAAATATAATTTAATAAAAATAAAAATAATTTA
Found at i:6028764 original size:29 final size:29
Alignment explanation
Indices: 6028683--6028761 Score: 90
Period size: 29 Copynumber: 2.8 Consensus size: 29
6028673 TTTAATTATA
*
6028683 TTTTAACATAATTATTATTAAAT-ACAAT
1 TTTTAATATAATTATTATTAAATAACAAT
* * * *
6028711 TTAATAATATAAATATAATTTAATAAC-AT
1 TT-TTAATATAATTATTATTAAATAACAAT
6028740 TTTTAATATAATTATTATTAAA
1 TTTTAATATAATTATTATTAAA
6028762 ATATGAATTA
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
28 18 0.45
29 20 0.50
30 2 0.05
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (29 bp):
TTTTAATATAATTATTATTAAATAACAAT
Found at i:6032746 original size:48 final size:44
Alignment explanation
Indices: 6032669--6032844 Score: 156
Period size: 48 Copynumber: 3.8 Consensus size: 44
6032659 AAACGAAACA
* * * *
6032669 AACAGAGAGTAC-CGAAGTACTGAACAGAGAGCACATAAGTGCTGGG
1 AACAGAGAGCACACAAAGTGCTAAACAGAGAGCACA-AAGTGCT--G
* *
6032715 CAACAGAAAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACTG
1 -AACAGAGAGCACACAAAGTGCTAAACAGAGAG--CACAAAGTGCTG
* * *
6032762 ATCAGAGAGCACACAAAGTGCTAATAACAGAGAGCACGAGACGTGCTA
1 AACAGAGAGCACACAAAGTGCT-A-AACAGAGAGCAC-A-AAGTGCTG
* *
6032810 AACAGAGAGCACACACAGTGCTAATCAGAGAGCAC
1 AACAGAGAGCACACAAAGTGCTAAACAGAGAGCAC
6032845 GCTAGTGTTC
Statistics
Matches: 108, Mismatches: 14, Indels: 15
0.79 0.10 0.11
Matches are distributed among these distances:
46 34 0.31
47 14 0.13
48 50 0.46
49 6 0.06
50 4 0.04
ACGTcount: A:0.43, C:0.21, G:0.24, T:0.11
Consensus pattern (44 bp):
AACAGAGAGCACACAAAGTGCTAAACAGAGAGCACAAAGTGCTG
Found at i:6032752 original size:23 final size:23
Alignment explanation
Indices: 6032668--6032844 Score: 144
Period size: 23 Copynumber: 7.6 Consensus size: 23
6032658 TAAACGAAAC
* * *
6032668 AAACAGAGAGTAC-CGAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
* *
6032690 GAACAGAGAGCACA-TAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
6032712 GGGCAACAGAAAGCACACAAAGTGCT
1 ---AAACAGAGAGCACACAAAGTGCT
* *
6032738 AAACAGAGAGTACACAAAGTACT
1 AAACAGAGAGCACACAAAGTGCT
* *
6032761 GATCAGAGAGCACACAAAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
* *
6032784 AATAACAGAGAGCACGA-GACGTGCT
1 -A-AACAGAGAGCAC-ACAAAGTGCT
*
6032809 AAACAGAGAGCACACACAGTGCT
1 AAACAGAGAGCACACAAAGTGCT
*
6032832 AATCAGAGAGCAC
1 AAACAGAGAGCAC
6032845 GCTAGTGTTC
Statistics
Matches: 123, Mismatches: 23, Indels: 17
0.75 0.14 0.10
Matches are distributed among these distances:
22 18 0.15
23 67 0.54
24 1 0.01
25 29 0.24
26 8 0.07
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.11
Consensus pattern (23 bp):
AAACAGAGAGCACACAAAGTGCT
Found at i:6032791 original size:71 final size:71
Alignment explanation
Indices: 6032668--6032844 Score: 198
Period size: 71 Copynumber: 2.5 Consensus size: 71
6032658 TAAACGAAAC
* * * **
6032668 AAACAGAGAGTAC-CGAAGTACTGAACAGAGAGCACATAAGTGCTGGGCAACAGAAAGCAC-ACA
1 AAACAGAGAGTACACAAAGTACTGATCAGAGAGCACAAAAGTGCTGAACAACAGAAAGCACGA-A
6032731 AAGTGCT
65 AAGTGCT
* * *
6032738 AAACAGAGAGTACACAAAGTACTGATCAGAGAGCACACAAAGTGCT-AATAACAGAGAGCACGAG
1 AAACAGAGAGTACACAAAGTACTGATCAGAGAGCACA-AAAGTGCTGAACAACAGAAAGCACGAA
*
6032802 ACGTGCT
65 AAGTGCT
* * * *
6032809 AAACAGAGAGCACACACAGTGCTAATCAGAGAGCAC
1 AAACAGAGAGTACACAAAGTACTGATCAGAGAGCAC
6032845 GCTAGTGTTC
Statistics
Matches: 91, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
70 13 0.14
71 70 0.77
72 8 0.09
ACGTcount: A:0.44, C:0.21, G:0.24, T:0.11
Consensus pattern (71 bp):
AAACAGAGAGTACACAAAGTACTGATCAGAGAGCACAAAAGTGCTGAACAACAGAAAGCACGAAA
AGTGCT
Found at i:6034980 original size:24 final size:25
Alignment explanation
Indices: 6034929--6034980 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 25
6034919 CGATTATTCA
* * *
6034929 AATAATAAAATTATATTTTTACTAT
1 AATAATAAAATTATAATTTAAATAT
*
6034954 AATAA-AAAATTATAATTTAAATTT
1 AATAATAAAATTATAATTTAAATAT
6034978 AAT
1 AAT
6034981 CTTTTTAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 18 0.78
25 5 0.22
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (25 bp):
AATAATAAAATTATAATTTAAATAT
Found at i:6036187 original size:12 final size:12
Alignment explanation
Indices: 6036153--6036250 Score: 52
Period size: 12 Copynumber: 7.8 Consensus size: 12
6036143 ATAACATCTA
* *
6036153 AACAACCAAAAT
1 AACAACAAAAAC
*
6036165 AATAACAAAAAAC
1 AACAAC-AAAAAC
*
6036178 AACAGCAAAAATAAC
1 AACA--ACAAA-AAC
*
6036193 AACAACAAAAAT
1 AACAACAAAAAC
* *
6036205 AATAACAAAAAT
1 AACAACAAAAAC
* *
6036217 AGCAACAAAAAT
1 AACAACAAAAAC
**
6036229 AACAGTAAAAAC
1 AACAACAAAAAC
*
6036241 AACACCAAAA
1 AACAACAAAA
6036251 CAGTAAAAAA
Statistics
Matches: 66, Mismatches: 16, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
12 44 0.67
13 11 0.17
14 3 0.05
15 8 0.12
ACGTcount: A:0.70, C:0.18, G:0.03, T:0.08
Consensus pattern (12 bp):
AACAACAAAAAC
Found at i:6036195 original size:15 final size:15
Alignment explanation
Indices: 6036171--6036212 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
6036161 AAATAATAAC
*
6036171 AAAA-AACAACAGCA
1 AAAATAACAACAACA
6036185 AAAATAACAACAACA
1 AAAATAACAACAACA
*
6036200 AAAATAATAACAA
1 AAAATAACAACAA
6036213 AAATAGCAAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 4 0.16
15 21 0.84
ACGTcount: A:0.74, C:0.17, G:0.02, T:0.07
Consensus pattern (15 bp):
AAAATAACAACAACA
Found at i:6036249 original size:24 final size:24
Alignment explanation
Indices: 6036190--6036250 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
6036180 CAGCAAAAAT
*
6036190 AACAACAACAAAAATAATAACAAA
1 AACAACAACAAAAATAACAACAAA
* * **
6036214 AATAGCAACAAAAATAACAGTAAA
1 AACAACAACAAAAATAACAACAAA
*
6036238 AACAACACCAAAA
1 AACAACAACAAAA
6036251 CAGTAAAAAA
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.70, C:0.18, G:0.03, T:0.08
Consensus pattern (24 bp):
AACAACAACAAAAATAACAACAAA
Found at i:6036268 original size:19 final size:20
Alignment explanation
Indices: 6036229--6036271 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
6036219 CAACAAAAAT
*
6036229 AACAGTAAAAACAACACCAA
1 AACAGTAAAAACAAAACCAA
*
6036249 AACAGTAAAAA-AAAATCAA
1 AACAGTAAAAACAAAACCAA
6036268 AACA
1 AACA
6036272 ACAATCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.70, C:0.19, G:0.05, T:0.07
Consensus pattern (20 bp):
AACAGTAAAAACAAAACCAA
Found at i:6036309 original size:29 final size:29
Alignment explanation
Indices: 6036236--6036321 Score: 84
Period size: 29 Copynumber: 2.9 Consensus size: 29
6036226 AATAACAGTA
*
6036236 AAAACAAC-ACCAAAACAGTAAAAAAAAATC
1 AAAACAACAACCAAAACA--ATAAAAAAATC
* *
6036266 AAAACAACAATCAAAACAATAAAAAATTC
1 AAAACAACAACCAAAACAATAAAAAAATC
** * *
6036295 AAAACAGTAACCAAAATAGTAAAAAAA
1 AAAACAACAACCAAAACAATAAAAAAA
6036322 CAACATCAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
29 30 0.65
30 8 0.17
31 8 0.17
ACGTcount: A:0.70, C:0.16, G:0.03, T:0.10
Consensus pattern (29 bp):
AAAACAACAACCAAAACAATAAAAAAATC
Found at i:6039345 original size:18 final size:17
Alignment explanation
Indices: 6039315--6039348 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
6039305 ATAATTAAGG
*
6039315 ATATTAAATTAAATTAT
1 ATATTAAAATAAATTAT
6039332 ATATGTAAAATAAATTA
1 ATAT-TAAAATAAATTA
6039349 GTGTAGTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (17 bp):
ATATTAAAATAAATTAT
Found at i:6046722 original size:15 final size:15
Alignment explanation
Indices: 6046702--6046731 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6046692 TTACAAAAAA
6046702 AAAAAAAACTAAATT
1 AAAAAAAACTAAATT
*
6046717 AAAAAAAATTAAATT
1 AAAAAAAACTAAATT
6046732 TGGGGGGACC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAAAAAACTAAATT
Found at i:6047218 original size:25 final size:25
Alignment explanation
Indices: 6047190--6047238 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
6047180 AATAAGGCTA
*
6047190 AATTAGTCACATATG-TTGTTTTTTT
1 AATTAGTCAAATA-GATTGTTTTTTT
*
6047215 AATTGGTCAAATAGATTGTTTTTT
1 AATTAGTCAAATAGATTGTTTTTT
6047239 GAAGATTTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.27, C:0.06, G:0.14, T:0.53
Consensus pattern (25 bp):
AATTAGTCAAATAGATTGTTTTTTT
Found at i:6052876 original size:33 final size:33
Alignment explanation
Indices: 6052839--6052902 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
6052829 ACAAAAAATT
6052839 TTTTTTTAAAAAAATATAAAAAAGCTTAATTGG
1 TTTTTTTAAAAAAATATAAAAAAGCTTAATTGG
* * *
6052872 TTTTTTTAAAAGATTATAAAAGAGCTTAATT
1 TTTTTTTAAAAAAATATAAAAAAGCTTAATT
6052903 ATAAACGAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.42
Consensus pattern (33 bp):
TTTTTTTAAAAAAATATAAAAAAGCTTAATTGG
Found at i:6072620 original size:33 final size:33
Alignment explanation
Indices: 6072583--6072648 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
6072573 TCGAGTCTCA
*
6072583 TCTTTGTTG-CTAAATATCTTCCTTGAAATTAAT
1 TCTTTGTTGCCT-AATATCTTCCTTAAAATTAAT
* *
6072616 TCTTTTTTGCCTAATTTCTTCCTTAAAATTAAT
1 TCTTTGTTGCCTAATATCTTCCTTAAAATTAAT
6072649 GCCTTTATGG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 27 0.93
34 2 0.07
ACGTcount: A:0.26, C:0.17, G:0.06, T:0.52
Consensus pattern (33 bp):
TCTTTGTTGCCTAATATCTTCCTTAAAATTAAT
Found at i:6074434 original size:11 final size:12
Alignment explanation
Indices: 6074394--6074456 Score: 67
Period size: 12 Copynumber: 5.4 Consensus size: 12
6074384 TTATGGTTCA
*
6074394 TTTATTAGCTCG
1 TTTATAAGCTCG
* *
6074406 TTTATTAGCTCA
1 TTTATAAGCTCG
*
6074418 TATA-AAGCTCG
1 TTTATAAGCTCG
*
6074429 TTTA-AAGCCCG
1 TTTATAAGCTCG
6074440 TTTATAAGCTCG
1 TTTATAAGCTCG
6074452 TTTAT
1 TTTAT
6074457 TGGACCCATC
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
11 18 0.42
12 25 0.58
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.43
Consensus pattern (12 bp):
TTTATAAGCTCG
Found at i:6075686 original size:22 final size:23
Alignment explanation
Indices: 6075652--6075694 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
6075642 AATTATGAAA
*
6075652 AATATAACATATTATAAAATTAT
1 AATAAAACATATTATAAAATTAT
*
6075675 AATAAAAC-TATTTTAAAATT
1 AATAAAACATATTATAAAATT
6075695 TACAACAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (23 bp):
AATAAAACATATTATAAAATTAT
Found at i:6079352 original size:19 final size:19
Alignment explanation
Indices: 6079316--6079356 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
6079306 CAACTAAGTT
*
6079316 TTTTATTTAGTTGGTTTTG
1 TTTTATTTAATTGGTTTTG
**
6079335 TTTTATTTAATTTTTTTTG
1 TTTTATTTAATTGGTTTTG
6079354 TTT
1 TTT
6079357 GTTTGGATAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.12, T:0.76
Consensus pattern (19 bp):
TTTTATTTAATTGGTTTTG
Found at i:6079427 original size:23 final size:24
Alignment explanation
Indices: 6079371--6079428 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
6079361 GGATAGTTAA
*
6079371 CATAAACGAACATGTTCGCGAACG
1 CATAAATGAACATGTTCGCGAACG
6079395 CATAAATGAACATGTTCGCGAACG
1 CATAAATGAACATGTTCGCGAACG
*
6079419 -TTAAATGAAC
1 CATAAATGAAC
6079429 GTTAAACGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
23 9 0.28
24 23 0.72
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (24 bp):
CATAAATGAACATGTTCGCGAACG
Found at i:6079430 original size:11 final size:11
Alignment explanation
Indices: 6079413--6079463 Score: 59
Period size: 11 Copynumber: 4.5 Consensus size: 11
6079403 AACATGTTCG
6079413 CGAACGTTAAA
1 CGAACGTTAAA
*
6079424 TGAACGTTAAA
1 CGAACGTTAAA
*
6079435 CGAACATGTT-CA
1 CGAAC--GTTAAA
6079447 CGAACGTTAAA
1 CGAACGTTAAA
6079458 CGAACG
1 CGAACG
6079464 AGCACAAACA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
10 3 0.09
11 21 0.64
12 6 0.18
13 3 0.09
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.20
Consensus pattern (11 bp):
CGAACGTTAAA
Found at i:6079440 original size:34 final size:34
Alignment explanation
Indices: 6079397--6079463 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
6079387 CGCGAACGCA
* * *
6079397 TAAATGAACATGTTCGCGAACGTTAAATGAACGT
1 TAAACGAACATGTTCACGAACGTTAAACGAACGT
6079431 TAAACGAACATGTTCACGAACGTTAAACGAACG
1 TAAACGAACATGTTCACGAACGTTAAACGAACG
6079464 AGCACAAACA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.22
Consensus pattern (34 bp):
TAAACGAACATGTTCACGAACGTTAAACGAACGT
Found at i:6081646 original size:3 final size:3
Alignment explanation
Indices: 6081638--6081667 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
6081628 TTCTATTAAG
*
6081638 ATC ATC ATC ATC ATC ATC ATC GTC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
6081668 GGCAGCATGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.33, G:0.03, T:0.33
Consensus pattern (3 bp):
ATC
Found at i:6086726 original size:29 final size:30
Alignment explanation
Indices: 6086674--6086730 Score: 89
Period size: 29 Copynumber: 1.9 Consensus size: 30
6086664 ATTTGATTAC
* *
6086674 TAAATTATTCGAATTATTCGAAAGTTTTCA
1 TAAATTATTCGAACTATTCAAAAGTTTTCA
6086704 TAAATTATT-GAACTATTCAAAAGTTTT
1 TAAATTATTCGAACTATTCAAAAGTTTT
6086731 TAAAAGTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.44
Consensus pattern (30 bp):
TAAATTATTCGAACTATTCAAAAGTTTTCA
Found at i:6090973 original size:18 final size:18
Alignment explanation
Indices: 6090950--6090985 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
6090940 GACAGTGTAA
*
6090950 AAGTTGTTGAGTAGAATT
1 AAGTTGTGGAGTAGAATT
*
6090968 AAGTTGTGGAGTTGAATT
1 AAGTTGTGGAGTAGAATT
6090986 TCGGGCTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.31, T:0.39
Consensus pattern (18 bp):
AAGTTGTGGAGTAGAATT
Found at i:6094448 original size:89 final size:89
Alignment explanation
Indices: 6094282--6094448 Score: 199
Period size: 89 Copynumber: 1.9 Consensus size: 89
6094272 GCATTTCATG
* * * * *
6094282 TTTTGTCCAAGTTAGGCTTTGAACTTGATAATTGTCCTCACATTAGGGCCTAAACTAGGCAATCG
1 TTTTGTCCAAATTAGGCCTTGAACTTGACAATTGTCCTCACATGAGGGCCTAAACTAGGCAATCA
*
6094347 CTCTTACATTGGGGTTTGAATTTT
66 CTCTCACATTGGGGTTTGAATTTT
* * ** * * *
6094371 TTTTGTCCAAATTAGTCCTTGAACTTGGCAATTGTTTTCATATGAGGGCCTAAACTTGGCAATTA
1 TTTTGTCCAAATTAGGCCTTGAACTTGACAATTGTCCTCACATGAGGGCCTAAACTAGGCAATCA
* *
6094436 TTCTCACTTTGGG
66 CTCTCACATTGGG
6094449 ATTTAAACTT
Statistics
Matches: 63, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
89 63 1.00
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (89 bp):
TTTTGTCCAAATTAGGCCTTGAACTTGACAATTGTCCTCACATGAGGGCCTAAACTAGGCAATCA
CTCTCACATTGGGGTTTGAATTTT
Found at i:6096026 original size:37 final size:36
Alignment explanation
Indices: 6095984--6096125 Score: 110
Period size: 37 Copynumber: 3.9 Consensus size: 36
6095974 AAAGGCAAAA
* *
6095984 ATGAACAGAAGTGATTCTCTGTAAAGAAAATACGGAG
1 ATGAACA-AAGAGATTCTCTGTAAAGAAAAAACGGAG
* *
6096021 ATGAACAATAAAGATTCTCTACG-AAA-AAAAAACAGAG
1 ATGAACAA-AGAGATTCTCT--GTAAAGAAAAAACGGAG
* * ** *
6096058 ATGAACAAAGTGATTCTTTACAAAGAAAAAACGAAG
1 ATGAACAAAGAGATTCTCTGTAAAGAAAAAACGGAG
* *
6096094 ATAAATAGTAA-AGATTCTCTGTAAAGAAAAAA
1 ATGAACA--AAGAGATTCTCTGTAAAGAAAAAA
6096126 AAAAAACAAA
Statistics
Matches: 82, Mismatches: 16, Indels: 14
0.73 0.14 0.12
Matches are distributed among these distances:
35 3 0.04
36 23 0.28
37 50 0.61
38 5 0.06
39 1 0.01
ACGTcount: A:0.52, C:0.11, G:0.17, T:0.20
Consensus pattern (36 bp):
ATGAACAAAGAGATTCTCTGTAAAGAAAAAACGGAG
Found at i:6098334 original size:18 final size:20
Alignment explanation
Indices: 6098283--6098341 Score: 95
Period size: 19 Copynumber: 3.0 Consensus size: 20
6098273 CAACAAATTA
6098283 TTTTAAAATATTAAAATTATT
1 TTTTAAAATA-TAAAATTATT
6098304 TTTTAAAATAT-AAATTATT
1 TTTTAAAATATAAAATTATT
6098323 TTTTAAAA-ATAAAATTATT
1 TTTTAAAATATAAAATTATT
6098342 AAAATTATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
18 2 0.05
19 24 0.65
20 1 0.03
21 10 0.27
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TTTTAAAATATAAAATTATT
Found at i:6098346 original size:28 final size:29
Alignment explanation
Indices: 6098307--6098382 Score: 99
Period size: 31 Copynumber: 2.7 Consensus size: 29
6098297 AATTATTTTT
6098307 TAAAA-TA-TAAATTATTTTTT-AAA-AA
1 TAAAATTATTAAATTATTTTTTGAAATAA
6098332 TAAAATTATTAAAATTATTTTTTTGAAATAA
1 TAAAATTATT-AAATTA-TTTTTTGAAATAA
6098363 TAAAATTATTAAA-TATTTTT
1 TAAAATTATTAAATTATTTTT
6098383 AATTTTCAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
25 5 0.11
26 2 0.04
27 1 0.02
28 11 0.24
29 8 0.18
30 6 0.13
31 12 0.27
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (29 bp):
TAAAATTATTAAATTATTTTTTGAAATAA
Found at i:6098368 original size:31 final size:28
Alignment explanation
Indices: 6098307--6098382 Score: 97
Period size: 29 Copynumber: 2.8 Consensus size: 28
6098297 AATTATTTTT
6098307 TAAAA-TA-TAAATTA-TTTTTTAAAAA
1 TAAAATTATTAAATTATTTTTTTAAAAA
6098332 TAAAATTATTAAAATTATTTTTTTGAAATAA
1 TAAAATTATT-AAATTATTTTTTT-AAA-AA
6098363 TAAAATTATTAAA-TATTTTT
1 TAAAATTATTAAATTATTTTT
6098383 AATTTTCAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
25 5 0.11
26 2 0.04
27 1 0.02
28 6 0.13
29 13 0.29
30 6 0.13
31 12 0.27
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (28 bp):
TAAAATTATTAAATTATTTTTTTAAAAA
Found at i:6099401 original size:32 final size:32
Alignment explanation
Indices: 6099329--6099401 Score: 78
Period size: 32 Copynumber: 2.3 Consensus size: 32
6099319 GAAAATCTCC
* * *
6099329 AAACCTAAATCTCGAAAATCCTCAAAATTTTG
1 AAACCTAAAACCCGAAAATCCTCAAAATTTTA
*
6099361 AAATCTAAAACCCGAAAAT-CTCCGAAAA-TTTA
1 AAACCTAAAACCCGAAAATCCT-C-AAAATTTTA
6099393 AAACCTAAA
1 AAACCTAAA
6099402 TTAAAATCCT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
31 2 0.06
32 28 0.82
33 4 0.12
ACGTcount: A:0.49, C:0.22, G:0.05, T:0.23
Consensus pattern (32 bp):
AAACCTAAAACCCGAAAATCCTCAAAATTTTA
Found at i:6100291 original size:37 final size:37
Alignment explanation
Indices: 6100250--6100392 Score: 133
Period size: 37 Copynumber: 3.8 Consensus size: 37
6100240 CTTGGAAGAC
* *
6100250 AAAAGACAGAGATGAACATGAGTGATTCTCTACAAAG
1 AAAAGACAGAGATGAACAGGAATGATTCTCTACAAAG
* *
6100287 AAAAGACAAAGATGAACAGGAATGATTCTCTGCAAAG
1 AAAAGACAGAGATGAACAGGAATGATTCTCTACAAAG
* * ** * * * *
6100324 AAAAGAAAGAGCTGAGTAGTAAAGATTCTTTACAAAAAA
1 AAAAGACAGAGATGAACAGGAATGATTCTCTAC--AAAG
* *
6100363 AGAAAGAAAGAGATGAACAGTAATGATTCT
1 A-AAAGACAGAGATGAACAGGAATGATTCT
6100393 TGAGTAAAGC
Statistics
Matches: 85, Mismatches: 18, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
37 57 0.67
39 4 0.05
40 24 0.28
ACGTcount: A:0.50, C:0.10, G:0.21, T:0.19
Consensus pattern (37 bp):
AAAAGACAGAGATGAACAGGAATGATTCTCTACAAAG
Found at i:6103858 original size:3 final size:3
Alignment explanation
Indices: 6103850--6103875 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
6103840 ATTTTACCTT
6103850 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
6103876 TTTGCCTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:6110054 original size:2 final size:2
Alignment explanation
Indices: 6110047--6110092 Score: 83
Period size: 2 Copynumber: 23.0 Consensus size: 2
6110037 ATATTTGTTA
*
6110047 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6110089 AT AT
1 AT AT
6110093 GATGTGCAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6110870 original size:31 final size:31
Alignment explanation
Indices: 6110835--6110897 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
6110825 ATGGATGATA
6110835 TGATGAGAAGGATCCATAAAATAATTTCTCT
1 TGATGAGAAGGATCCATAAAATAATTTCTCT
* * * *
6110866 TGATGGGAAGGGTCTATAAAGTAATTTCTCT
1 TGATGAGAAGGATCCATAAAATAATTTCTCT
6110897 T
1 T
6110898 TTTTATTTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.35
Consensus pattern (31 bp):
TGATGAGAAGGATCCATAAAATAATTTCTCT
Found at i:6117489 original size:20 final size:20
Alignment explanation
Indices: 6117395--6117491 Score: 56
Period size: 20 Copynumber: 4.9 Consensus size: 20
6117385 TCTTGTATGG
*
6117395 GTTTGCACTTCGGTGCCTCT
1 GTTTGCACTACGGTGCCTCT
*
6117415 G-TT-CA-TACTTGGTGTCTCT
1 GTTTGCACTAC--GGTGCCTCT
* ** *
6117434 TTTTGCACTTTGATGCCTCT
1 GTTTGCACTACGGTGCCTCT
** * **
6117454 AATTGCACAATTGTGCCTCT
1 GTTTGCACTACGGTGCCTCT
6117474 GTTTGCACTACGGTGCCT
1 GTTTGCACTACGGTGCCT
6117492 TTGCATAGCA
Statistics
Matches: 54, Mismatches: 18, Indels: 10
0.66 0.22 0.12
Matches are distributed among these distances:
17 2 0.04
18 2 0.04
19 10 0.19
20 37 0.69
21 2 0.04
22 1 0.02
ACGTcount: A:0.12, C:0.26, G:0.21, T:0.41
Consensus pattern (20 bp):
GTTTGCACTACGGTGCCTCT
Found at i:6117491 original size:40 final size:39
Alignment explanation
Indices: 6117395--6117491 Score: 97
Period size: 40 Copynumber: 2.5 Consensus size: 39
6117385 TCTTGTATGG
* * * *
6117395 GTTTGCACTTCGGTGCCTCTGTTCATACTTGGTGTCTCT
1 GTTTGCACTTCGGTGCCTCTATTCACAATTGGTGCCTCT
* * *
6117434 TTTTGCACTTTGATGCCTCTAATTGCACAATT-GTGCCTCT
1 GTTTGCACTTCGGTGCCTCT-ATT-CACAATTGGTGCCTCT
*
6117474 GTTTGCACTACGGTGCCT
1 GTTTGCACTTCGGTGCCT
6117492 TTGCATAGCA
Statistics
Matches: 45, Mismatches: 11, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
39 17 0.38
40 23 0.51
41 5 0.11
ACGTcount: A:0.12, C:0.26, G:0.21, T:0.41
Consensus pattern (39 bp):
GTTTGCACTTCGGTGCCTCTATTCACAATTGGTGCCTCT
Found at i:6126814 original size:3 final size:3
Alignment explanation
Indices: 6126795--6126835 Score: 64
Period size: 3 Copynumber: 13.3 Consensus size: 3
6126785 AGACATGGTA
*
6126795 TAT TCAT TAT CAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
6126836 TTTAATTCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.32, C:0.05, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:6127983 original size:3 final size:3
Alignment explanation
Indices: 6127975--6128011 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
6127965 ATTTCATTTA
*
6127975 AAT AAT AAT AAT AAT AAT AAT CAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
6128012 GTGATGTCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:6128696 original size:24 final size:24
Alignment explanation
Indices: 6128660--6128705 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
6128650 GTGGAACCAG
*
6128660 TAGAAAATGAAGATCTAACTCCAA
1 TAGAAAATAAAGATCTAACTCCAA
*
6128684 TAGAAATTAAAGATCTAACTCC
1 TAGAAAATAAAGATCTAACTCC
6128706 GTGTATGGTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.48, C:0.17, G:0.11, T:0.24
Consensus pattern (24 bp):
TAGAAAATAAAGATCTAACTCCAA
Found at i:6131793 original size:6 final size:6
Alignment explanation
Indices: 6131784--6131817 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
6131774 CTTCCTCTTA
*
6131784 CTCTGG CTCTGG CTCTGG CTTTGG CTCTGG CTCT
1 CTCTGG CTCTGG CTCTGG CTCTGG CTCTGG CTCT
6131818 AGGGTAAGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.32, G:0.29, T:0.38
Consensus pattern (6 bp):
CTCTGG
Found at i:6131799 original size:18 final size:18
Alignment explanation
Indices: 6131778--6131817 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
6131768 ATGCCTCTTC
*
6131778 CTCTTACTCTGGCTCTGG
1 CTCTGACTCTGGCTCTGG
* *
6131796 CTCTGGCTTTGGCTCTGG
1 CTCTGACTCTGGCTCTGG
6131814 CTCT
1 CTCT
6131818 AGGGTAAGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.03, C:0.33, G:0.25, T:0.40
Consensus pattern (18 bp):
CTCTGACTCTGGCTCTGG
Found at i:6137595 original size:4 final size:4
Alignment explanation
Indices: 6137586--6137632 Score: 60
Period size: 4 Copynumber: 11.8 Consensus size: 4
6137576 CTTTCTCTTA
* *
6137586 TTCT TTCT TTCCT CTCT TT-A TTCT TTCT TTCT TTCT TTCT TTCT TTC
1 TTCT TTCT TT-CT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTC
6137633 CTCTCTCTAC
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
3 2 0.05
4 32 0.86
5 3 0.08
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (4 bp):
TTCT
Found at i:6140395 original size:28 final size:28
Alignment explanation
Indices: 6140336--6140421 Score: 81
Period size: 28 Copynumber: 3.1 Consensus size: 28
6140326 GACATTTTTC
*
6140336 ATTTGAAATTAATTATGTTTATGAA--TGA
1 ATTTGAAATTAATTATGTTTA--AATTTGT
6140364 ATTTGAAATTAATTATGTTTAAATTTGT
1 ATTTGAAATTAATTATGTTTAAATTTGT
* * **
6140392 ATTT--AATTAATAATTTTTATGTTTGT
1 ATTTGAAATTAATTATGTTTAAATTTGT
6140418 ATTT
1 ATTT
6140422 TGGTTTAGGG
Statistics
Matches: 51, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
26 24 0.47
28 27 0.53
ACGTcount: A:0.35, C:0.00, G:0.10, T:0.55
Consensus pattern (28 bp):
ATTTGAAATTAATTATGTTTAAATTTGT
Found at i:6140410 original size:26 final size:26
Alignment explanation
Indices: 6140370--6140421 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
6140360 ATGAATTTGA
*
6140370 AATTAATTATGTTTAAATTTGTATTT
1 AATTAATAATGTTTAAATTTGTATTT
* **
6140396 AATTAATAATTTTTATGTTTGTATTT
1 AATTAATAATGTTTAAATTTGTATTT
6140422 TGGTTTAGGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.60
Consensus pattern (26 bp):
AATTAATAATGTTTAAATTTGTATTT
Found at i:6140608 original size:16 final size:16
Alignment explanation
Indices: 6140589--6140646 Score: 91
Period size: 16 Copynumber: 3.7 Consensus size: 16
6140579 GGTTTATGAT
6140589 TTTTTAAGGTTTAAGG
1 TTTTTAAGGTTTAAGG
*
6140605 TTTTTAAGGTTTAATG
1 TTTTTAAGGTTTAAGG
*
6140621 -TTTTAAGGTTTTAGG
1 TTTTTAAGGTTTAAGG
6140636 TTTTTAAGGTT
1 TTTTTAAGGTT
6140647 ATGATTTTAG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
15 13 0.34
16 25 0.66
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.55
Consensus pattern (16 bp):
TTTTTAAGGTTTAAGG
Found at i:6140639 original size:7 final size:8
Alignment explanation
Indices: 6140590--6140646 Score: 66
Period size: 7 Copynumber: 7.2 Consensus size: 8
6140580 GTTTATGATT
6140590 TTTTAAGG
1 TTTTAAGG
6140598 -TTTAAGG
1 TTTTAAGG
6140605 TTTTTAAGG
1 -TTTTAAGG
*
6140614 -TTTAATG
1 TTTTAAGG
6140621 TTTTAAGG
1 TTTTAAGG
6140629 TTTT-AGG
1 TTTTAAGG
6140636 TTTTTAAGG
1 -TTTTAAGG
6140645 TT
1 TT
6140647 ATGATTTTAG
Statistics
Matches: 42, Mismatches: 2, Indels: 10
0.78 0.04 0.19
Matches are distributed among these distances:
7 16 0.38
8 16 0.38
9 10 0.24
ACGTcount: A:0.23, C:0.00, G:0.23, T:0.54
Consensus pattern (8 bp):
TTTTAAGG
Found at i:6141680 original size:16 final size:17
Alignment explanation
Indices: 6141651--6141683 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
6141641 AATTACATTT
*
6141651 CTCTCCTTTTTTCTTTC
1 CTCTCCTTTCTTCTTTC
6141668 CTCTCC-TTCTTCTTTC
1 CTCTCCTTTCTTCTTTC
6141684 TTTCTTTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.00, C:0.39, G:0.00, T:0.61
Consensus pattern (17 bp):
CTCTCCTTTCTTCTTTC
Found at i:6141926 original size:15 final size:16
Alignment explanation
Indices: 6141906--6141943 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
6141896 CCAGTGTCAA
*
6141906 GTATTTT-TTCTTCGT
1 GTATTTTATACTTCGT
6141921 GTATTTTATACTTCGT
1 GTATTTTATACTTCGT
6141937 GTATTTT
1 GTATTTT
6141944 GTACGTTTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.13, C:0.11, G:0.13, T:0.63
Consensus pattern (16 bp):
GTATTTTATACTTCGT
Found at i:6142537 original size:18 final size:18
Alignment explanation
Indices: 6142501--6142540 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
6142491 ATTACTTCTC
* **
6142501 AAAAGTACTTTTGGGATA
1 AAAAATACTTTTGAAATA
6142519 AAAAATACTTTTGAAATA
1 AAAAATACTTTTGAAATA
6142537 AAAA
1 AAAA
6142541 CATTGCTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.53, C:0.05, G:0.12, T:0.30
Consensus pattern (18 bp):
AAAAATACTTTTGAAATA
Found at i:6142764 original size:25 final size:27
Alignment explanation
Indices: 6142736--6142791 Score: 75
Period size: 25 Copynumber: 2.2 Consensus size: 27
6142726 TTACTCAACT
*
6142736 AAATAAAAAAATTAAA-T-AACAAATC
1 AAATAAAAAAATTAAATTAAACAAAAC
6142761 AAAT--AAAAATTAAATTAAACAAAAC
1 AAATAAAAAAATTAAATTAAACAAAAC
6142786 AAATAA
1 AAATAA
6142792 CTTAAAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 10 0.38
24 1 0.04
25 15 0.58
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (27 bp):
AAATAAAAAAATTAAATTAAACAAAAC
Found at i:6143078 original size:24 final size:23
Alignment explanation
Indices: 6143041--6143087 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
6143031 TAAAAAATTA
6143041 CCTTTTTTTCCTTTCTTTCCTCT
1 CCTTTTTTTCCTTTCTTTCCTCT
* *
6143064 CCTTTTTCTTTCTTTCTTTTCTCT
1 CCTTTTT-TTCCTTTCTTTCCTCT
6143088 TTTTGTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (23 bp):
CCTTTTTTTCCTTTCTTTCCTCT
Found at i:6143261 original size:26 final size:27
Alignment explanation
Indices: 6143231--6143288 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 27
6143221 GAAAACACCC
6143231 TTTGGCACCGCCATTCAAT-CCCCTCA
1 TTTGGCACCGCCATTCAATCCCCCTCA
* * *
6143257 TTTGGTACTGCCATTCAATCCCCCTCT
1 TTTGGCACCGCCATTCAATCCCCCTCA
6143284 TTTGG
1 TTTGG
6143289 TGTCGCCATT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 17 0.61
27 11 0.39
ACGTcount: A:0.16, C:0.36, G:0.14, T:0.34
Consensus pattern (27 bp):
TTTGGCACCGCCATTCAATCCCCCTCA
Found at i:6143288 original size:27 final size:26
Alignment explanation
Indices: 6143231--6143299 Score: 84
Period size: 27 Copynumber: 2.6 Consensus size: 26
6143221 GAAAACACCC
*
6143231 TTTGGCACCGCCATTCAATCCCCTCA
1 TTTGGTACCGCCATTCAATCCCCTCA
* *
6143257 TTTGGTACTGCCATTCAATCCCCCTCT
1 TTTGGTACCGCCATTCAAT-CCCCTCA
**
6143284 TTTGGTGTCGCCATTC
1 TTTGGTACCGCCATTC
6143300 TGTGTTCTTC
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
26 17 0.47
27 19 0.53
ACGTcount: A:0.14, C:0.36, G:0.14, T:0.35
Consensus pattern (26 bp):
TTTGGTACCGCCATTCAATCCCCTCA
Found at i:6146370 original size:2 final size:2
Alignment explanation
Indices: 6146363--6146392 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6146353 TATTGCTTTT
6146363 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
6146393 GAAAATGGGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:6147336 original size:39 final size:40
Alignment explanation
Indices: 6147268--6147360 Score: 129
Period size: 39 Copynumber: 2.4 Consensus size: 40
6147258 TTAAATGATT
* *
6147268 TTAAAATT-A-TTACAATTATTTTTAAAAAATATAAAATTA
1 TTAAAATTAATTTAAAATTATTTTT-AAAAATATAAAAATA
6147307 TTAAAATTAATTTAAAATTATTTTT-AAAATATAAAAATA
1 TTAAAATTAATTTAAAATTATTTTTAAAAATATAAAAATA
*
6147346 TTAAAATTATTTTAA
1 TTAAAATTAATTTAA
6147361 TATTTTAATC
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
39 35 0.71
40 1 0.02
41 13 0.27
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (40 bp):
TTAAAATTAATTTAAAATTATTTTTAAAAATATAAAAATA
Found at i:6151740 original size:25 final size:24
Alignment explanation
Indices: 6151687--6151732 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
6151677 GTTGGATCCA
6151687 AATTAAATTCTAAAAAGATAATTTG
1 AATTAAA-TCTAAAAAGATAATTTG
*
6151712 AATTAAATCTAAACA-ATAATT
1 AATTAAATCTAAAAAGATAATT
6151733 CCTTAATTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 7 0.35
25 7 0.35
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (24 bp):
AATTAAATCTAAAAAGATAATTTG
Found at i:6151971 original size:24 final size:24
Alignment explanation
Indices: 6151944--6151991 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
6151934 TTTTTGCTCC
*
6151944 TTTCGCTTTCAAATGCTTTCCTAA
1 TTTCACTTTCAAATGCTTTCCTAA
*
6151968 TTTCACTTTCAAATGTTTTCCTAA
1 TTTCACTTTCAAATGCTTTCCTAA
6151992 GTATAGAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.23, C:0.23, G:0.06, T:0.48
Consensus pattern (24 bp):
TTTCACTTTCAAATGCTTTCCTAA
Found at i:6154621 original size:13 final size:13
Alignment explanation
Indices: 6154605--6154640 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
6154595 TTTCTCTCAA
6154605 TTTTCTTTTTTTT
1 TTTTCTTTTTTTT
6154618 TTTTCTTTTTTTT
1 TTTTCTTTTTTTT
6154631 TCTTT-TTTTT
1 T-TTTCTTTTT
6154641 AAACAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 19 0.86
14 3 0.14
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (13 bp):
TTTTCTTTTTTTT
Found at i:6154626 original size:10 final size:10
Alignment explanation
Indices: 6154613--6154640 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
6154603 AATTTTCTTT
6154613 TTTTTTTTTC
1 TTTTTTTTTC
6154623 TTTTTTTTTC
1 TTTTTTTTTC
6154633 TTTTTTTT
1 TTTTTTTT
6154641 AAACAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:6154630 original size:22 final size:22
Alignment explanation
Indices: 6154571--6154640 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 22
6154561 CTCAGACATA
* * *
6154571 TTTTTGTCTTTTTCTTCTTATT
1 TTTTTCTCTTTTTTTTCTTTTT
***
6154593 TTTTTCTCTCAATTTTCTTTTT
1 TTTTTCTCTTTTTTTTCTTTTT
*
6154615 TTTTTTTCTTTTTTTTTCTTTTT
1 TTTTTCTC-TTTTTTTTCTTTTT
6154638 TTT
1 TTT
6154641 AAACAATAAA
Statistics
Matches: 37, Mismatches: 10, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
22 23 0.62
23 14 0.38
ACGTcount: A:0.04, C:0.13, G:0.01, T:0.81
Consensus pattern (22 bp):
TTTTTCTCTTTTTTTTCTTTTT
Found at i:6155615 original size:21 final size:21
Alignment explanation
Indices: 6155591--6155634 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
6155581 TAAATATAAT
6155591 AATTTTTTTTCAAATTTTTTA
1 AATTTTTTTTCAAATTTTTTA
*
6155612 AATTTTTTTTCAATTTTTTTA
1 AATTTTTTTTCAAATTTTTTA
6155633 AA
1 AA
6155635 AACATGAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.66
Consensus pattern (21 bp):
AATTTTTTTTCAAATTTTTTA
Found at i:6157738 original size:12 final size:12
Alignment explanation
Indices: 6157723--6157767 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
6157713 AAGAACCTAT
6157723 AAAATAAAATTA
1 AAAATAAAATTA
*
6157735 AAAATTAAATTA
1 AAAATAAAATTA
*
6157747 AAAATTAAATTA
1 AAAATAAAATTA
*
6157759 AAAACAAAA
1 AAAATAAAA
6157768 AATATATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (12 bp):
AAAATAAAATTA
Found at i:6157740 original size:7 final size:7
Alignment explanation
Indices: 6157728--6157797 Score: 58
Period size: 7 Copynumber: 10.1 Consensus size: 7
6157718 CCTATAAAAT
6157728 AAAATTA
1 AAAATTA
6157735 AAAATT-
1 AAAATTA
6157741 -AAATTA
1 AAAATTA
6157747 AAAATT-
1 AAAATTA
6157753 -AAATTA
1 AAAATTA
**
6157759 AAAACAA
1 AAAATTA
6157766 AAAATATA
1 AAAAT-TA
*
6157774 TAAAAATA
1 -AAAATTA
6157782 AAAATTA
1 AAAATTA
6157789 ATAAATTA
1 A-AAATTA
6157797 A
1 A
6157798 TAAAAATAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 13
0.72 0.09 0.19
Matches are distributed among these distances:
5 10 0.20
7 26 0.52
8 10 0.20
9 4 0.08
ACGTcount: A:0.71, C:0.01, G:0.00, T:0.27
Consensus pattern (7 bp):
AAAATTA
Found at i:6157744 original size:17 final size:17
Alignment explanation
Indices: 6157723--6157804 Score: 62
Period size: 18 Copynumber: 4.6 Consensus size: 17
6157713 AAGAACCTAT
6157723 AAAAT-AAAATTAAA-A
1 AAAATAAAAATTAAATA
6157738 ATTAAATTAAAAATTAAATTA
1 A--AAA-TAAAAATTAAA-TA
* * *
6157759 AAAACAAAAAATATATA
1 AAAATAAAAATTAAATA
6157776 AAAATAAAAATT-AATA
1 AAAATAAAAATTAAATA
6157792 AATTAATAAAAAT
1 AA--AATAAAAAT
6157805 AAAGTTTTCC
Statistics
Matches: 53, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
15 1 0.02
16 5 0.09
17 15 0.28
18 18 0.34
19 12 0.23
21 2 0.04
ACGTcount: A:0.72, C:0.01, G:0.00, T:0.27
Consensus pattern (17 bp):
AAAATAAAAATTAAATA
Found at i:6169463 original size:31 final size:32
Alignment explanation
Indices: 6169401--6169464 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
6169391 TTTTTTGTCC
** *
6169401 AATTAGGTACTTGAACTTAGCTTTTTGGTTCA
1 AATTAGGTACTTGAACTTAGCTTCATAGTTCA
*
6169433 AATTA-GTACTTGAACTTGGCTTCATAGTTCA
1 AATTAGGTACTTGAACTTAGCTTCATAGTTCA
6169464 A
1 A
6169465 GTTGATTCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 23 0.82
32 5 0.18
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (32 bp):
AATTAGGTACTTGAACTTAGCTTCATAGTTCA
Found at i:6170232 original size:13 final size:13
Alignment explanation
Indices: 6170216--6170245 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
6170206 CAATTTTAAT
6170216 TTAAAATTAAAAA
1 TTAAAATTAAAAA
*
6170229 TTAAAATTAAAAT
1 TTAAAATTAAAAA
6170242 TTAA
1 TTAA
6170246 TTATAAATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
TTAAAATTAAAAA
Found at i:6171246 original size:31 final size:31
Alignment explanation
Indices: 6171187--6171247 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
6171177 TACAATTTAG
* *
6171187 TCATTGAATTATTCGAAAGTTTTCATTTAAA
1 TCATTGAATTATTCAAAAATTTTCATTTAAA
*
6171218 TCATTGAATTGTTCAAAAAATTTT-ATTTAA
1 TCATTGAATTATTC-AAAAATTTTCATTTAA
6171248 GTCACTGGGC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
31 19 0.73
32 7 0.27
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (31 bp):
TCATTGAATTATTCAAAAATTTTCATTTAAA
Found at i:6182171 original size:9 final size:9
Alignment explanation
Indices: 6182157--6182190 Score: 68
Period size: 9 Copynumber: 3.8 Consensus size: 9
6182147 GTTAATCAAA
6182157 TCAAGTTAT
1 TCAAGTTAT
6182166 TCAAGTTAT
1 TCAAGTTAT
6182175 TCAAGTTAT
1 TCAAGTTAT
6182184 TCAAGTT
1 TCAAGTT
6182191 TTGAGTTAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.44
Consensus pattern (9 bp):
TCAAGTTAT
Done.