Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012480.1 Kokia drynarioides strain JFW-HI SEQ_127484, 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: 230415
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:2290 original size:17 final size:16
Alignment explanation
Indices: 2249--2292 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
2239 AGCAACTCAT
2249 ATTTATTT-A-TTTTA
1 ATTTATTTAATTTTTA
2263 ATTTATTTAATTTTTA
1 ATTTATTTAATTTTTA
2279 ATTTAGTTTAATTT
1 ATTTA-TTTAATTT
2293 ATGTTGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 8 0.30
15 1 0.04
16 10 0.37
17 8 0.30
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (16 bp):
ATTTATTTAATTTTTA
Found at i:2659 original size:12 final size:12
Alignment explanation
Indices: 2642--2669 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
2632 GATATTCCTT
2642 AATTTGTTTTGA
1 AATTTGTTTTGA
2654 AATTTGTTTTGA
1 AATTTGTTTTGA
2666 AATT
1 AATT
2670 GAACCTTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.14, T:0.57
Consensus pattern (12 bp):
AATTTGTTTTGA
Found at i:7383 original size:24 final size:23
Alignment explanation
Indices: 7343--7400 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
7333 TATATATTTC
*
7343 AATTAA-ATTTTATAAATAATTAA
1 AATTAATA-TTTAGAAATAATTAA
* *
7366 TATTAATTATTTAGAAATATTTAA
1 AATTAA-TATTTAGAAATAATTAA
7390 AATTAATATTT
1 AATTAATATTT
7401 CATATATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 10 0.34
24 18 0.62
25 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
AATTAATATTTAGAAATAATTAA
Found at i:7990 original size:17 final size:17
Alignment explanation
Indices: 7973--8005 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
7963 TAATTTCAAT
7973 TTTA-ATTCAATTATAA
1 TTTACATTCAATTATAA
7989 TTTACATTCAATTATAA
1 TTTACATTCAATTATAA
8006 ATATGTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTACATTCAATTATAA
Found at i:8740 original size:29 final size:30
Alignment explanation
Indices: 8698--8756 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
8688 GAATTGGATC
*
8698 AAATCAAAATTTCATATATAAAATTACACA
1 AAATCAAAAATTCATATATAAAATTACACA
* *
8728 AAAT-AAAAATTCATGTATACAATTACACA
1 AAATCAAAAATTCATATATAAAATTACACA
8757 TCAAACCATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 22 0.85
30 4 0.15
ACGTcount: A:0.56, C:0.14, G:0.02, T:0.29
Consensus pattern (30 bp):
AAATCAAAAATTCATATATAAAATTACACA
Found at i:9372 original size:140 final size:140
Alignment explanation
Indices: 9120--9402 Score: 530
Period size: 140 Copynumber: 2.0 Consensus size: 140
9110 TTTGGTACCG
9120 TTTCGTTATTATGTTTCTATTATTTTGTTGTTATTGTTTGAATATTGTATAACTCTTGTTTTATT
1 TTTCGTTATTATGTTTCTATTATTTTGTTGTTATTGTTTGAATATTGTATAACTCTTGTTTTATT
* * *
9185 GTTAATCTTGCTACTATTTTAGAGGTATTTGTTTGCTAAATTGCACATATCTTAATGTTATTTAA
66 GTTAATCTCGCTACTATTTTAGAGATATTTGTTTGCTAAATTACACATATCTTAATGTTATTTAA
9250 GTATAAATAT
131 GTATAAATAT
9260 TTTCGTTATTATGTTTCTATTATTTTGTTGTTATTGTTTGAATATTGTATAACTCTTGTTTTATT
1 TTTCGTTATTATGTTTCTATTATTTTGTTGTTATTGTTTGAATATTGTATAACTCTTGTTTTATT
*
9325 GTTAATCTCGTTACTATTTTAGAGATATTTGTTTGCTAAATTACACATATCTTAATGTTATTTAA
66 GTTAATCTCGCTACTATTTTAGAGATATTTGTTTGCTAAATTACACATATCTTAATGTTATTTAA
9390 GTATAAATAT
131 GTATAAATAT
9400 TTT
1 TTT
9403 TTAAATTTAT
Statistics
Matches: 139, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 139 1.00
ACGTcount: A:0.25, C:0.08, G:0.12, T:0.55
Consensus pattern (140 bp):
TTTCGTTATTATGTTTCTATTATTTTGTTGTTATTGTTTGAATATTGTATAACTCTTGTTTTATT
GTTAATCTCGCTACTATTTTAGAGATATTTGTTTGCTAAATTACACATATCTTAATGTTATTTAA
GTATAAATAT
Found at i:10277 original size:32 final size:27
Alignment explanation
Indices: 10193--10278 Score: 75
Period size: 28 Copynumber: 3.0 Consensus size: 27
10183 GAACTTGACA
10193 TTTTTCTTAATTTGGTACTTAAACTTT
1 TTTTTCTTAATTTGGTACTTAAACTTT
* * *
10220 TTTTGGTC-CAATTTGATACTCAAACTTAAT
1 TTTT--TCTTAATTTGGTACTTAAACTT--T
10250 ACGTTTTTCTTAATTTGGTACTTAAACTT
1 ---TTTTTCTTAATTTGGTACTTAAACTT
10279 GACACTTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
27 4 0.09
28 16 0.36
29 2 0.04
30 1 0.02
31 2 0.04
32 16 0.36
33 4 0.09
ACGTcount: A:0.26, C:0.14, G:0.09, T:0.51
Consensus pattern (27 bp):
TTTTTCTTAATTTGGTACTTAAACTTT
Found at i:10278 original size:90 final size:90
Alignment explanation
Indices: 10172--10363 Score: 248
Period size: 90 Copynumber: 2.1 Consensus size: 90
10162 TTAATTTAAC
* * *
10172 ATTTGGTACCTGAACTTGACA-TTTTTCTT-AATTTGGTACTTAAACTTTTTTTG-GTCCAATTT
1 ATTTGGTACCTAAACTTGACACTTTTT-TTAAAGTTGGTACTTAAA-TTTTTTGGAGTCCAATTT
* *
10234 GATA-CTCAAACTTAATACGTTTTTCTTA
64 GATACCT-AAACTTAACAC-TTTTTCCTA
* * *
10262 ATTTGGTACTTAAACTTGACACTTTTTTTAAAGTTGGTATTTAAATTTTTTGGAGTCCAATTTGG
1 ATTTGGTACCTAAACTTGACACTTTTTTTAAAGTTGGTACTTAAATTTTTTGGAGTCCAATTTGA
10327 TACCTAAACTTAACACTTTTTCCTA
66 TACCTAAACTTAACACTTTTTCCTA
10352 ATTTGGTACCTA
1 ATTTGGTACCTA
10364 CTTTTTTTAA
Statistics
Matches: 89, Mismatches: 9, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
90 47 0.53
91 40 0.45
92 2 0.02
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (90 bp):
ATTTGGTACCTAAACTTGACACTTTTTTTAAAGTTGGTACTTAAATTTTTTGGAGTCCAATTTGA
TACCTAAACTTAACACTTTTTCCTA
Found at i:10289 original size:32 final size:31
Alignment explanation
Indices: 10172--10306 Score: 86
Period size: 32 Copynumber: 4.5 Consensus size: 31
10162 TTAATTTAAC
* *
10172 ATTTGGTACCTGAACTTGACA-TTTTTCTTA
1 ATTTGGTACTTAAACTTGACATTTTTTCTTA
*
10202 ATTTGGTACTTAAACTT----TTTTTGGTC-CA
1 ATTTGGTACTTAAACTTGACATTTTT--TCTTA
* * * * *
10230 ATTTGATACTCAAACTTAATACGTTTTTCTTA
1 ATTTGGTACTTAAACTTGACA-TTTTTTCTTA
*
10262 ATTTGGTACTTAAACTTGACACTTTTTT-TAA
1 ATTTGGTACTTAAACTTGACA-TTTTTTCTTA
* *
10293 AGTTGGTATTTAAA
1 ATTTGGTACTTAAA
10307 TTTTTTGGAG
Statistics
Matches: 81, Mismatches: 15, Indels: 17
0.72 0.13 0.15
Matches are distributed among these distances:
27 4 0.05
28 16 0.20
29 2 0.02
30 15 0.19
31 16 0.20
32 24 0.30
33 4 0.05
ACGTcount: A:0.27, C:0.13, G:0.12, T:0.47
Consensus pattern (31 bp):
ATTTGGTACTTAAACTTGACATTTTTTCTTA
Found at i:10614 original size:59 final size:60
Alignment explanation
Indices: 10528--10643 Score: 162
Period size: 59 Copynumber: 1.9 Consensus size: 60
10518 CCAAATTTAA
* * * * *
10528 TCTAAAAAAAGCTTAGGTGCCAAATTAGGAAAAAATACCCAGTTCTAGTACTAAATTGGG
1 TCTAAAAAAAGCTTAGATACCAAATTAGGAAAAAATACCAAGTTCAAGTACCAAATTGGG
* *
10588 TCTAAAAAAA-TTTAGATACCAAATTAGGAAAAAATATCAAGTTCAAGTACCAAATT
1 TCTAAAAAAAGCTTAGATACCAAATTAGGAAAAAATACCAAGTTCAAGTACCAAATT
10644 AAAAAAATAT
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
59 39 0.80
60 10 0.20
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.26
Consensus pattern (60 bp):
TCTAAAAAAAGCTTAGATACCAAATTAGGAAAAAATACCAAGTTCAAGTACCAAATTGGG
Found at i:10639 original size:31 final size:30
Alignment explanation
Indices: 10604--10673 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 30
10594 AAAATTTAGA
10604 TACCAAATTAGGAAAAAATA-TCAAGTTCAAG
1 TACCAAATTA--AAAAAATAGTCAAGTTCAAG
10635 TACCAAATTAAAAAAATATGTCAAGTTCAAG
1 TACCAAATTAAAAAAATA-GTCAAGTTCAAG
10666 TACCAAAT
1 TACCAAAT
10674 ATTATATTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
29 8 0.22
31 29 0.78
ACGTcount: A:0.51, C:0.14, G:0.10, T:0.24
Consensus pattern (30 bp):
TACCAAATTAAAAAAATAGTCAAGTTCAAG
Found at i:13029 original size:19 final size:20
Alignment explanation
Indices: 12992--13044 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 20
12982 AAAAATATTT
12992 AAAATTATAAAAATATTCAAA
1 AAAATTAT-AAAATATTCAAA
* *
13013 AAAATTATAAAA-CTTCATA
1 AAAATTATAAAATATTCAAA
13032 AAAATT-TAAAATA
1 AAAATTATAAAATA
13045 ATTAGCATGA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 4 0.14
21 8 0.29
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (20 bp):
AAAATTATAAAATATTCAAA
Found at i:13042 original size:29 final size:29
Alignment explanation
Indices: 12981--13048 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 29
12971 TATGCCATGC
*
12981 TAAAAATATT-TAAAATTATAAAAATATT
1 TAAAAAAATTATAAAATTATAAAAATATT
*
13009 CAAAAAAATTATAAAACTTCAT-AAAA-ATT
1 TAAAAAAATTATAAAA-TT-ATAAAAATATT
*
13038 TAAAATAATTA
1 TAAAAAAATTA
13049 GCATGAAAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
28 8 0.24
29 17 0.52
30 6 0.18
31 2 0.06
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (29 bp):
TAAAAAAATTATAAAATTATAAAAATATT
Found at i:13721 original size:146 final size:146
Alignment explanation
Indices: 13457--13750 Score: 588
Period size: 146 Copynumber: 2.0 Consensus size: 146
13447 GATTACAAAA
13457 ATCAGAAAAACAAAACTTGTTAACTTTAAGAACCATAGTTTTCCAATCATATTTGTAAATAGAAG
1 ATCAGAAAAACAAAACTTGTTAACTTTAAGAACCATAGTTTTCCAATCATATTTGTAAATAGAAG
13522 AAAGTAAAAAAGCAATTTTCTTTTGGCTAATTTGATAATTTCACATTTCCTTTGTAAAAGATTAT
66 AAAGTAAAAAAGCAATTTTCTTTTGGCTAATTTGATAATTTCACATTTCCTTTGTAAAAGATTAT
13587 CAGTAAGGTTAGACCC
131 CAGTAAGGTTAGACCC
13603 ATCAGAAAAACAAAACTTGTTAACTTTAAGAACCATAGTTTTCCAATCATATTTGTAAATAGAAG
1 ATCAGAAAAACAAAACTTGTTAACTTTAAGAACCATAGTTTTCCAATCATATTTGTAAATAGAAG
13668 AAAGTAAAAAAGCAATTTTCTTTTGGCTAATTTGATAATTTCACATTTCCTTTGTAAAAGATTAT
66 AAAGTAAAAAAGCAATTTTCTTTTGGCTAATTTGATAATTTCACATTTCCTTTGTAAAAGATTAT
13733 CAGTAAGGTTAGACCC
131 CAGTAAGGTTAGACCC
13749 AT
1 AT
13751 TTGGAAATTC
Statistics
Matches: 148, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
146 148 1.00
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (146 bp):
ATCAGAAAAACAAAACTTGTTAACTTTAAGAACCATAGTTTTCCAATCATATTTGTAAATAGAAG
AAAGTAAAAAAGCAATTTTCTTTTGGCTAATTTGATAATTTCACATTTCCTTTGTAAAAGATTAT
CAGTAAGGTTAGACCC
Found at i:24556 original size:19 final size:19
Alignment explanation
Indices: 24532--24570 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
24522 AACATCATCT
24532 ACAGCTTTAGAGCTAACAG
1 ACAGCTTTAGAGCTAACAG
24551 ACAGCTTTAGAGCTAACAG
1 ACAGCTTTAGAGCTAACAG
24570 A
1 A
24571 AGGTTAGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (19 bp):
ACAGCTTTAGAGCTAACAG
Found at i:28426 original size:39 final size:41
Alignment explanation
Indices: 28383--28464 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 41
28373 AGGGGTGGTG
* *
28383 AGTGAGAGGAAGGC-C-TGATCAACATGGACTAGGTTCTAT
1 AGTGAGAAGAAGGCTCTTGATCAACATGGACTAAGTTCTAT
*
28422 AGTGAGAAGAAGGCTTCTTGGTCAACATGGACTAAGTTCTAT
1 AGTGAGAAGAAGGC-TCTTGATCAACATGGACTAAGTTCTAT
28464 A
1 A
28465 CACCTCTTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
39 13 0.35
41 1 0.03
42 23 0.62
ACGTcount: A:0.32, C:0.15, G:0.28, T:0.26
Consensus pattern (41 bp):
AGTGAGAAGAAGGCTCTTGATCAACATGGACTAAGTTCTAT
Found at i:29348 original size:31 final size:31
Alignment explanation
Indices: 29312--29377 Score: 132
Period size: 31 Copynumber: 2.1 Consensus size: 31
29302 CAACATTATC
29312 ACTATCATTTTACATATTTAATATGCCAAGA
1 ACTATCATTTTACATATTTAATATGCCAAGA
29343 ACTATCATTTTACATATTTAATATGCCAAGA
1 ACTATCATTTTACATATTTAATATGCCAAGA
29374 ACTA
1 ACTA
29378 ACACATTCAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.38
Consensus pattern (31 bp):
ACTATCATTTTACATATTTAATATGCCAAGA
Found at i:34286 original size:30 final size:30
Alignment explanation
Indices: 34252--34335 Score: 150
Period size: 30 Copynumber: 2.8 Consensus size: 30
34242 AAATGCTAAG
34252 TTTGTTTAGAAGTGCTGAAACATGTACCAT
1 TTTGTTTAGAAGTGCTGAAACATGTACCAT
* *
34282 TTTGTTTAGAAGTGTTGAAACATGTACTAT
1 TTTGTTTAGAAGTGCTGAAACATGTACCAT
34312 TTTGTTTAGAAGTGCTGAAACATG
1 TTTGTTTAGAAGTGCTGAAACATG
34336 CATCATTTGG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.39
Consensus pattern (30 bp):
TTTGTTTAGAAGTGCTGAAACATGTACCAT
Found at i:38436 original size:27 final size:27
Alignment explanation
Indices: 38405--38467 Score: 90
Period size: 27 Copynumber: 2.3 Consensus size: 27
38395 CTCATGGATG
**
38405 AAATTAAAGAAGGGGGTGTGATGAATA
1 AAATTAAAGAAGACGGTGTGATGAATA
*
38432 AAATTAAAGAAGACGGTGTGATGAATG
1 AAATTAAAGAAGACGGTGTGATGAATA
*
38459 AAATGAAAG
1 AAATTAAAG
38468 GGACTTCTGC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.48, C:0.02, G:0.30, T:0.21
Consensus pattern (27 bp):
AAATTAAAGAAGACGGTGTGATGAATA
Found at i:49136 original size:30 final size:28
Alignment explanation
Indices: 49097--49170 Score: 69
Period size: 29 Copynumber: 2.6 Consensus size: 28
49087 AACAACTGAA
*
49097 ATTATATTTTGAAATTTAAAAAGTAGAGGG
1 ATTAAATTTT-AAATTT-AAAAGTAGAGGG
** *
49127 ATTAAATTTTTAAAAATAAAAGTATAGGG
1 ATTAAA-TTTTAAATTTAAAAGTAGAGGG
*
49156 -TTAAATTCTAAATTT
1 ATTAAATTTTAAATTT
49171 GTGAAACTTA
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
27 7 0.19
28 5 0.14
29 11 0.31
30 9 0.25
31 4 0.11
ACGTcount: A:0.46, C:0.01, G:0.14, T:0.39
Consensus pattern (28 bp):
ATTAAATTTTAAATTTAAAAGTAGAGGG
Found at i:54870 original size:20 final size:19
Alignment explanation
Indices: 54840--54880 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
54830 GTGTTTGGAC
54840 TTAGGTAAAATTAAGCATT
1 TTAGGTAAAATTAAGCATT
*
54859 TTAGGATAAAATTTAGCATT
1 TTAGG-TAAAATTAAGCATT
54879 TT
1 TT
54881 TCATGCATGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.39, C:0.05, G:0.15, T:0.41
Consensus pattern (19 bp):
TTAGGTAAAATTAAGCATT
Found at i:55818 original size:26 final size:26
Alignment explanation
Indices: 55782--55840 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
55772 TACCATTTAC
*
55782 AGTTTACCATTTA-TCTTTCAGTACTT
1 AGTTTATCATTTACT-TTTCAGTACTT
55808 AGTTTATCATTTACTTTTCAGTACTT
1 AGTTTATCATTTACTTTTCAGTACTT
*
55834 GGTTTAT
1 AGTTTAT
55841 TTTAGTTCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 29 0.97
27 1 0.03
ACGTcount: A:0.22, C:0.15, G:0.10, T:0.53
Consensus pattern (26 bp):
AGTTTATCATTTACTTTTCAGTACTT
Found at i:57360 original size:30 final size:33
Alignment explanation
Indices: 57290--57362 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 33
57280 TTGAAAAGGT
*
57290 TGAAAAGGTTATTACCCTATAATGGTTATCAAC
1 TGAAAAGGTTATTACCCTATAATGGATATCAAC
* *
57323 TGGAAAGGTT-TTATCC-A-AATGGATATCAAAC
1 TGAAAAGGTTATTACCCTATAATGGATATC-AAC
57354 -GAAAAGGTT
1 TGAAAAGGTT
57363 GAAAAGGATA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
30 17 0.49
31 4 0.11
32 5 0.14
33 9 0.26
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.30
Consensus pattern (33 bp):
TGAAAAGGTTATTACCCTATAATGGATATCAAC
Found at i:58278 original size:21 final size:21
Alignment explanation
Indices: 58236--58280 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
58226 ATATAGGAGC
*
58236 GTGGGAAAACCACACAAGCGT
1 GTGGGAAAACCACACAACCGT
* * *
58257 GTGGGAGAGCCACACACCCGT
1 GTGGGAAAACCACACAACCGT
58278 GTG
1 GTG
58281 ACCCATGTAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.27, G:0.33, T:0.11
Consensus pattern (21 bp):
GTGGGAAAACCACACAACCGT
Found at i:59085 original size:23 final size:22
Alignment explanation
Indices: 59066--59120 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
59056 AACTTAATCA
59066 AACATGTTCACGAACATTAAATG
1 AACATGTTCACGAACATT-AATG
* *
59089 AATATGTTCATGAACATATAATTG
1 AACATGTTCACGAACAT-TAA-TG
59113 AACATGTT
1 AACATGTT
59121 AATGAACCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 17 0.63
24 10 0.37
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.33
Consensus pattern (22 bp):
AACATGTTCACGAACATTAATG
Found at i:59119 original size:24 final size:23
Alignment explanation
Indices: 59066--59127 Score: 79
Period size: 24 Copynumber: 2.7 Consensus size: 23
59056 AACTTAATCA
*
59066 AACATGTTCACGAACATTAAATG
1 AACATGTTCATGAACATTAAATG
* *
59089 AATATGTTCATGAACATATAATTG
1 AACATGTTCATGAACAT-TAAATG
*
59113 AACATGTTAATGAAC
1 AACATGTTCATGAAC
59128 CATGTTAATG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
23 15 0.45
24 18 0.55
ACGTcount: A:0.44, C:0.13, G:0.13, T:0.31
Consensus pattern (23 bp):
AACATGTTCATGAACATTAAATG
Found at i:59131 original size:13 final size:12
Alignment explanation
Indices: 59066--59139 Score: 62
Period size: 12 Copynumber: 6.2 Consensus size: 12
59056 AACTTAATCA
* *
59066 AACATGTTCACG
1 AACATGTTAATG
*
59078 AACAT-TAAATG
1 AACATGTTAATG
* *
59089 AATATGTTCATG
1 AACATGTTAATG
*
59101 AACAT-ATAATTG
1 AACATGTTAA-TG
59113 AACATGTTAATG
1 AACATGTTAATG
59125 AACCATGTTAATG
1 AA-CATGTTAATG
59138 AA
1 AA
59140 TCATAAACAA
Statistics
Matches: 48, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
11 9 0.19
12 24 0.50
13 15 0.31
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (12 bp):
AACATGTTAATG
Found at i:59397 original size:11 final size:11
Alignment explanation
Indices: 59383--59414 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
59373 AACTTTATAT
59383 GAACGGTTCAC
1 GAACGGTTCAC
*
59394 GAACAGTTCAC
1 GAACGGTTCAC
59405 GAACGGTTCA
1 GAACGGTTCA
59415 TTGAATGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.19
Consensus pattern (11 bp):
GAACGGTTCAC
Found at i:62138 original size:28 final size:24
Alignment explanation
Indices: 62081--62143 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
62071 AAAAATAATC
* *
62081 TTTCAGTTAAATTCTATTTATTTG
1 TTTCAATTAAACTCTATTTATTTG
62105 TTTCAATTAAACTCTATTTATTTG
1 TTTCAATTAAACTCTATTTATTTG
* *
62129 TTTAAATCAAACTCT
1 TTTCAATTAAACTCT
62144 TATTACTCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.30, C:0.13, G:0.05, T:0.52
Consensus pattern (24 bp):
TTTCAATTAAACTCTATTTATTTG
Found at i:63250 original size:12 final size:13
Alignment explanation
Indices: 63207--63262 Score: 51
Period size: 12 Copynumber: 4.2 Consensus size: 13
63197 TGCTTTTTAA
63207 TTTTTTATATATT
1 TTTTTTATATATT
* * *
63220 TATATATTTTTTTAGT
1 T-T-T-TTTATATATT
63236 TTTTTTATA-ATT
1 TTTTTTATATATT
63248 TTTTTTATATATT
1 TTTTTTATATATT
63261 TT
1 TT
63263 AATTGCATTT
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
12 11 0.33
13 10 0.30
14 2 0.06
15 2 0.06
16 8 0.24
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (13 bp):
TTTTTTATATATT
Found at i:63284 original size:12 final size:12
Alignment explanation
Indices: 63235--63286 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
63225 ATTTTTTTAG
*
63235 TTTTTTTATAAT
1 TTTTTTTATATT
63247 TTTTTTTATATAT
1 TTTTTTTATAT-T
** **
63260 TTTAATTGCATT
1 TTTTTTTATATT
63272 TTTTTTTATATT
1 TTTTTTTATATT
63284 TTT
1 TTT
63287 ATATATTTTT
Statistics
Matches: 30, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
12 22 0.73
13 8 0.27
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (12 bp):
TTTTTTTATATT
Found at i:63308 original size:17 final size:17
Alignment explanation
Indices: 63284--63320 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
63274 TTTTTATATT
63284 TTTATATATTTTTTATAAA
1 TTTATA-ATTTTTTA-AAA
63303 TTTATAATTTTTTAAAA
1 TTTATAATTTTTTAAAA
63320 T
1 T
63321 AATAATAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 8 0.44
19 6 0.33
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTATAATTTTTTAAAA
Found at i:65361 original size:173 final size:174
Alignment explanation
Indices: 65072--65434 Score: 683
Period size: 173 Copynumber: 2.1 Consensus size: 174
65062 TGTGAGAATT
*
65072 ATTAAACTAGAAAATTTGATTAAAGAATTTTCTTAAGAAATTAATTTGGAAAATCTTAGTGATTT
1 ATTAAACTTGAAAATTTGATTAAAGAATTTTCTTAAGAAATTAATTTGGAAAATCTTAGTGATTT
*
65137 TTTAGAAAACTAATTTTGATCCAGTAAAATTAAATTAATCAAATTAATTAAAATAAATATGATA-
66 TTGAGAAAACTAATTTTGATCCAGTAAAATTAAATTAATCAAATTAATTAAAATAAATATGATAT
65201 TTTTGAAAATTAATTTTCAAATTAGATAATTGGCTCAATGGGCA
131 TTTTGAAAATTAATTTTCAAATTAGATAATTGGCTCAATGGGCA
*
65245 ATTAAACTTGAAAATTTGATTAAAGAATTTTCTTAATAAATTAATTTGGAAAATCTTAGTGATTT
1 ATTAAACTTGAAAATTTGATTAAAGAATTTTCTTAAGAAATTAATTTGGAAAATCTTAGTGATTT
*
65310 TTGAGAAAATTAATTTTGATCCAGTAAAATTAAATTAATCAAATTAATTAAAATAAATATGATAT
66 TTGAGAAAACTAATTTTGATCCAGTAAAATTAAATTAATCAAATTAATTAAAATAAATATGATAT
65375 TTTTGAAAATTAATTTTCAAATTAGATAATTGGCTCAATGGGCA
131 TTTTGAAAATTAATTTTCAAATTAGATAATTGGCTCAATGGGCA
65419 ATTAAACTTGAAAATT
1 ATTAAACTTGAAAATT
65435 AGACCTGAGA
Statistics
Matches: 185, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
173 125 0.68
174 60 0.32
ACGTcount: A:0.44, C:0.06, G:0.11, T:0.39
Consensus pattern (174 bp):
ATTAAACTTGAAAATTTGATTAAAGAATTTTCTTAAGAAATTAATTTGGAAAATCTTAGTGATTT
TTGAGAAAACTAATTTTGATCCAGTAAAATTAAATTAATCAAATTAATTAAAATAAATATGATAT
TTTTGAAAATTAATTTTCAAATTAGATAATTGGCTCAATGGGCA
Found at i:66421 original size:13 final size:13
Alignment explanation
Indices: 66403--66427 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
66393 TAAAATTTTG
66403 AGGGAAAGTAAAT
1 AGGGAAAGTAAAT
66416 AGGGAAAGTAAA
1 AGGGAAAGTAAA
66428 ATTTTGAAGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.32, T:0.12
Consensus pattern (13 bp):
AGGGAAAGTAAAT
Found at i:69170 original size:45 final size:45
Alignment explanation
Indices: 69106--69200 Score: 190
Period size: 45 Copynumber: 2.1 Consensus size: 45
69096 TTTTACCTCA
69106 TCCCTAGTGTTGTTGAGATTCATGATCACATGGTCCCTCGATTGT
1 TCCCTAGTGTTGTTGAGATTCATGATCACATGGTCCCTCGATTGT
69151 TCCCTAGTGTTGTTGAGATTCATGATCACATGGTCCCTCGATTGT
1 TCCCTAGTGTTGTTGAGATTCATGATCACATGGTCCCTCGATTGT
69196 TCCCT
1 TCCCT
69201 CAAGTCATCT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.17, C:0.24, G:0.21, T:0.38
Consensus pattern (45 bp):
TCCCTAGTGTTGTTGAGATTCATGATCACATGGTCCCTCGATTGT
Found at i:76038 original size:29 final size:30
Alignment explanation
Indices: 75980--76050 Score: 117
Period size: 29 Copynumber: 2.4 Consensus size: 30
75970 TTGCATTATG
*
75980 TCATTAATGGCTATTATATATCTCTCCTTTA
1 TCATTATTGGCTATTATATA-CTCTCCTTTA
76011 TCATTATTGGCTATTATATA-TCTCCTTTA
1 TCATTATTGGCTATTATATACTCTCCTTTA
76040 TCATTATTGGC
1 TCATTATTGGC
76051 ATGACTTTAC
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
29 20 0.51
31 19 0.49
ACGTcount: A:0.24, C:0.18, G:0.08, T:0.49
Consensus pattern (30 bp):
TCATTATTGGCTATTATATACTCTCCTTTA
Found at i:79140 original size:20 final size:21
Alignment explanation
Indices: 79095--79149 Score: 60
Period size: 20 Copynumber: 2.7 Consensus size: 21
79085 CTTTTTCAAC
*
79095 AAAAATTACAAAATGATTTTC
1 AAAAATTACAAAATGATTTTA
*
79116 GAAAATT-CAAAAT-ATTTATA
1 AAAAATTACAAAATGATTT-TA
*
79136 AAAAATTCCAAAAT
1 AAAAATTACAAAAT
79150 TTCATAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 4 0.14
20 13 0.45
21 12 0.41
ACGTcount: A:0.56, C:0.09, G:0.04, T:0.31
Consensus pattern (21 bp):
AAAAATTACAAAATGATTTTA
Found at i:79156 original size:20 final size:20
Alignment explanation
Indices: 79117--79156 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
79107 ATGATTTTCG
*
79117 AAAATTCAAAATATTTATAA
1 AAAATTCAAAATATTCATAA
79137 AAAATTCCAAAAT-TTCATAA
1 AAAATT-CAAAATATTCATAA
79157 TTTTTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.57, C:0.10, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAATTCAAAATATTCATAA
Found at i:83782 original size:71 final size:71
Alignment explanation
Indices: 83619--83806 Score: 234
Period size: 71 Copynumber: 2.6 Consensus size: 71
83609 TAAATGAAGT
* * * * * * * *
83619 ATCGGTAGAAGTATAGGGGAAAGGAGAACTTAGCTACTAACTTGAGTTGTTTTGGAACAACTCAA
1 ATCGGTAGAAGTTTAAGGGAAAAGATATCTTGGCTACTGACTTGAGTTGTTTCGGAACAACTCAA
*
83684 CAAAGT
66 CAAAGC
* *
83690 ATCGATAGAAG-TTCAGAGGAAAAGATATCTTGGCTACTGACTTGAGTTGTTTCGGAACAACTCA
1 ATCGGTAGAAGTTTAAG-GGAAAAGATATCTTGGCTACTGACTTGAGTTGTTTCGGAACAACTCA
*
83754 ACAATGC
65 ACAAAGC
* *
83761 ATCGGTAGATGTTTAAGGGAAAAGATATCTTGGCTACTGGCTTGAG
1 ATCGGTAGAAGTTTAAGGGAAAAGATATCTTGGCTACTGACTTGAG
83807 AGGTTTCAGT
Statistics
Matches: 99, Mismatches: 16, Indels: 4
0.83 0.13 0.03
Matches are distributed among these distances:
70 2 0.02
71 93 0.94
72 4 0.04
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.27
Consensus pattern (71 bp):
ATCGGTAGAAGTTTAAGGGAAAAGATATCTTGGCTACTGACTTGAGTTGTTTCGGAACAACTCAA
CAAAGC
Found at i:97026 original size:13 final size:13
Alignment explanation
Indices: 96994--97025 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
96984 TCAAATAGTG
96994 AATAAAATAAATA
1 AATAAAATAAATA
97007 AATAAAATAAAT-
1 AATAAAATAAATA
97019 AATAAAA
1 AATAAAA
97026 AAGAAACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (13 bp):
AATAAAATAAATA
Found at i:100577 original size:27 final size:27
Alignment explanation
Indices: 100539--100602 Score: 128
Period size: 27 Copynumber: 2.4 Consensus size: 27
100529 TCCTTTTGTA
100539 TCATATTTAGCATGCATTACTAGCATT
1 TCATATTTAGCATGCATTACTAGCATT
100566 TCATATTTAGCATGCATTACTAGCATT
1 TCATATTTAGCATGCATTACTAGCATT
100593 TCATATTTAG
1 TCATATTTAG
100603 TATTTACATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.42
Consensus pattern (27 bp):
TCATATTTAGCATGCATTACTAGCATT
Found at i:105328 original size:19 final size:19
Alignment explanation
Indices: 105301--105338 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
105291 AATCTGCTAG
*
105301 GTACAAAATCGACAGATCA
1 GTACAAAATCGACAAATCA
*
105320 GTACGAAATCGACAAATCA
1 GTACAAAATCGACAAATCA
105339 AACTCCCTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.21, G:0.16, T:0.16
Consensus pattern (19 bp):
GTACAAAATCGACAAATCA
Found at i:107644 original size:50 final size:50
Alignment explanation
Indices: 107581--108039 Score: 454
Period size: 50 Copynumber: 9.2 Consensus size: 50
107571 CCTTTTTTAT
* * **
107581 AGCTTTAGCGGTGTAAGATTCACCTTTACGGAATCAATCTGCCCCTCTAC
1 AGCTTTAGGGGTGTAAGATTCGCCTTTACGGCTTCAATCTGCCCCTCTAC
* * * * *
107631 AACTTTAGGGGTGTACGATTTGCCTTTACGGCTTTAATCTGCCACTCTAC
1 AGCTTTAGGGGTGTAAGATTCGCCTTTACGGCTTCAATCTGCCCCTCTAC
* * *
107681 AGCTTTAGGGGTGTAAGATTCACCTTTGCGGCTTCAATCTGCCCTTCTAC
1 AGCTTTAGGGGTGTAAGATTCGCCTTTACGGCTTCAATCTGCCCCTCTAC
* * * * * * * *
107731 AGCTTTAGAGATATAATATTCACCTTTATGGCTTCAATCTACCCCTCTAT
1 AGCTTTAGGGGTGTAAGATTCGCCTTTACGGCTTCAATCTGCCCCTCTAC
*** * * * *
107781 AGCTTTAGCAATGTAGGATTCACCTTTACGACTTCAATCTGACCCTCTAC
1 AGCTTTAGGGGTGTAAGATTCGCCTTTACGGCTTCAATCTGCCCCTCTAC
* * * *
107831 AGGTTTAGGGGTGTACGATTCGCCTTTACGGCTTCAATTTGCCCCTCTAT
1 AGCTTTAGGGGTGTAAGATTCGCCTTTACGGCTTCAATCTGCCCCTCTAC
* * * * * **
107881 AACTTTAGGGGTGTATGATTCGTCTTTGCGACTTCAATCTGCCCCTCTTTT
1 AGCTTTAGGGGTGTAAGATTCGCCTTTACGGCTTCAATCTGCCCCTC-TAC
* * * * *
107932 A-CTTTAGGGGTGTACGATTCGCCTTTACGGCTTCAATATGCTCCTTTTC
1 AGCTTTAGGGGTGTAAGATTCGCCTTTACGGCTTCAATCTGCCCCTCTAC
* * * *
107981 AGCTTTAGGGTTGCAAGATTCGCCTTTGCAGCTTCAA-CTTGCCCCTCTAC
1 AGCTTTAGGGGTGTAAGATTCGCCTTTACGGCTTCAATC-TGCCCCTCTAC
*
108031 AACTTTAGG
1 AGCTTTAGG
108040 ATTTGGTGTG
Statistics
Matches: 334, Mismatches: 72, Indels: 6
0.81 0.17 0.01
Matches are distributed among these distances:
49 3 0.01
50 328 0.98
51 3 0.01
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.35
Consensus pattern (50 bp):
AGCTTTAGGGGTGTAAGATTCGCCTTTACGGCTTCAATCTGCCCCTCTAC
Found at i:109246 original size:61 final size:61
Alignment explanation
Indices: 109058--109245 Score: 313
Period size: 61 Copynumber: 3.1 Consensus size: 61
109048 CTCCCTTTTA
* * *
109058 TTTTTACCAATTTGAGCCACCCTTTACAGGTTTTCAACTCAAACTTTTGAGTTTTGAGAGT
1 TTTTTACCAGTTTGAGCCGCCCTTTACGGGTTTTCAACTCAAACTTTTGAGTTTTGAGAGT
* *
109119 TTTTTACCAGTTTGAGTCGCCCTTTATGGGTTTTCAACTCAAACTTTTGAGTTTTGAGAGT
1 TTTTTACCAGTTTGAGCCGCCCTTTACGGGTTTTCAACTCAAACTTTTGAGTTTTGAGAGT
* *
109180 TTTTTTCCAGTTTGAGCCGCCCTTTACGGGTTTTCAAATCAAACTTTTGAGTTTTGAGAGT
1 TTTTTACCAGTTTGAGCCGCCCTTTACGGGTTTTCAACTCAAACTTTTGAGTTTTGAGAGT
109241 TTTTT
1 TTTTT
109246 TAGGCGAAGT
Statistics
Matches: 118, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
61 118 1.00
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.44
Consensus pattern (61 bp):
TTTTTACCAGTTTGAGCCGCCCTTTACGGGTTTTCAACTCAAACTTTTGAGTTTTGAGAGT
Found at i:118406 original size:39 final size:39
Alignment explanation
Indices: 118352--118437 Score: 163
Period size: 39 Copynumber: 2.2 Consensus size: 39
118342 TGAATAAAAG
118352 ACACTCCAATGTGAGTGCATTATGACTTTTCAAGGGAGA
1 ACACTCCAATGTGAGTGCATTATGACTTTTCAAGGGAGA
*
118391 ACACTCTAATGTGAGTGCATTATGACTTTTCAAGGGAGA
1 ACACTCCAATGTGAGTGCATTATGACTTTTCAAGGGAGA
118430 ACACTCCA
1 ACACTCCA
118438 CTGCAGGTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.28
Consensus pattern (39 bp):
ACACTCCAATGTGAGTGCATTATGACTTTTCAAGGGAGA
Found at i:123924 original size:11 final size:11
Alignment explanation
Indices: 123910--123939 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
123900 ACGAATAGCA
123910 AATAAATAAAT
1 AATAAATAAAT
*
123921 AATAAAAAAAT
1 AATAAATAAAT
123932 AATAAATA
1 AATAAATA
123940 TATGAAATAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (11 bp):
AATAAATAAAT
Found at i:124117 original size:15 final size:15
Alignment explanation
Indices: 124099--124140 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
124089 AAATGTCATG
124099 AAAATAAATAACAACA
1 AAAATAAATAACAA-A
*
124115 AAAATAAA-CACACAA
1 AAAATAAATAACA-AA
124130 AAAATAAATAA
1 AAAATAAATAA
124141 AAATTAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.76, C:0.12, G:0.00, T:0.12
Consensus pattern (15 bp):
AAAATAAATAACAAA
Found at i:125215 original size:18 final size:19
Alignment explanation
Indices: 125183--125220 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
125173 GTAAAAACAA
125183 TTGGGTCTTA-TTTTTATT
1 TTGGGTCTTATTTTTTATT
125201 TTGGGT-TTATTTTTTTATT
1 TTGGGTCTTA-TTTTTTATT
125220 T
1 T
125221 ATTGGTTATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 3 0.17
18 6 0.33
19 9 0.50
ACGTcount: A:0.11, C:0.03, G:0.16, T:0.71
Consensus pattern (19 bp):
TTGGGTCTTATTTTTTATT
Found at i:129424 original size:15 final size:14
Alignment explanation
Indices: 129404--129448 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 14
129394 GGATCACCCA
129404 ATCTTCATAATACTC
1 ATCTTCATAATA-TC
129419 ATCTTCATAGATATC
1 ATCTTCATA-ATATC
*
129434 ATCATCATAAATATC
1 ATCTTCAT-AATATC
129449 CTTATAAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
15 23 0.85
16 4 0.15
ACGTcount: A:0.38, C:0.22, G:0.02, T:0.38
Consensus pattern (14 bp):
ATCTTCATAATATC
Found at i:142800 original size:24 final size:24
Alignment explanation
Indices: 142751--142848 Score: 126
Period size: 24 Copynumber: 4.1 Consensus size: 24
142741 CTAAACAATA
*
142751 TTAGCTCTCACGAGCCC-GAATGG
1 TTAGCTCTTACGAGCCCAGAATGG
* *
142774 TTAGCTCTTATGAGCCTAGAATGG
1 TTAGCTCTTACGAGCCCAGAATGG
*
142798 TTAGCTCTTACAAGCCCAGAATGG
1 TTAGCTCTTACGAGCCCAGAATGG
* * *
142822 TTAACTCTTATGAGCCCAAAATGG
1 TTAGCTCTTACGAGCCCAGAATGG
142846 TTA
1 TTA
142849 ACCAATATAT
Statistics
Matches: 64, Mismatches: 10, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
23 14 0.22
24 50 0.78
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (24 bp):
TTAGCTCTTACGAGCCCAGAATGG
Found at i:142820 original size:48 final size:47
Alignment explanation
Indices: 142751--142848 Score: 142
Period size: 48 Copynumber: 2.1 Consensus size: 47
142741 CTAAACAATA
* * * *
142751 TTAGCTCTCACGAGCCCGAATGGTTAGCTCTTATGAGCCTAGAATGG
1 TTAGCTCTCACAAGCCCGAATGGTTAACTCTTATGAGCCCAAAATGG
*
142798 TTAGCTCTTACAAGCCCAGAATGGTTAACTCTTATGAGCCCAAAATGG
1 TTAGCTCTCACAAGCCC-GAATGGTTAACTCTTATGAGCCCAAAATGG
142846 TTA
1 TTA
142849 ACCAATATAT
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
47 15 0.33
48 30 0.67
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (47 bp):
TTAGCTCTCACAAGCCCGAATGGTTAACTCTTATGAGCCCAAAATGG
Found at i:143013 original size:82 final size:82
Alignment explanation
Indices: 142863--143013 Score: 178
Period size: 82 Copynumber: 1.8 Consensus size: 82
142853 ATATATGATG
* * * * * * *
142863 CTGCTTACACAAGCTGATGAGAATTTGCGACATACGCGAAGACTCAGTCATCGATACGGTCTAGA
1 CTGCTCACACAAGCTGATGAGAATTCGCAACATACGCAAAGACTCAGCCATCGATACGGTCCACA
142928 ATTTCCCACTCTCAATT
66 ATTTCCCACTCTCAATT
* * * * *
142945 CTGCTCACACTAGCTTATGAGAATTCGTAACATACGTAAAGACTCAGCCATC-ATAGGGGTCCAC
1 CTGCTCACACAAGCTGATGAGAATTCGCAACATACGCAAAGACTCAGCCATCGATA-CGGTCCAC
143009 AATTT
65 AATTT
143014 AGTATTCGTT
Statistics
Matches: 56, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
81 3 0.05
82 53 0.95
ACGTcount: A:0.30, C:0.25, G:0.18, T:0.26
Consensus pattern (82 bp):
CTGCTCACACAAGCTGATGAGAATTCGCAACATACGCAAAGACTCAGCCATCGATACGGTCCACA
ATTTCCCACTCTCAATT
Found at i:147474 original size:20 final size:20
Alignment explanation
Indices: 147449--147487 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
147439 GAAATTTCTT
147449 TCTAATTAAAACCCCTATTG
1 TCTAATTAAAACCCCTATTG
147469 TCTAATTAAAACCCCTATT
1 TCTAATTAAAACCCCTATT
147488 ATCGCATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.26, G:0.03, T:0.36
Consensus pattern (20 bp):
TCTAATTAAAACCCCTATTG
Found at i:147496 original size:20 final size:20
Alignment explanation
Indices: 147452--147497 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
147442 ATTTCTTTCT
* *
147452 AATTAAAACCCCTATTGTCT
1 AATTAAAACCCCTATTATCG
147472 AATTAAAACCCCTATTATCG
1 AATTAAAACCCCTATTATCG
*
147492 CATTAA
1 AATTAA
147498 TTCGATCTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.39, C:0.24, G:0.04, T:0.33
Consensus pattern (20 bp):
AATTAAAACCCCTATTATCG
Found at i:148973 original size:25 final size:25
Alignment explanation
Indices: 148945--149022 Score: 59
Period size: 26 Copynumber: 3.0 Consensus size: 25
148935 TCAAACACAT
148945 ATTTGTCTTTTTCTTCTTTTTTTCA
1 ATTTGTCTTTTTCTTCTTTTTTTCA
* * **
148970 ATTT-TATTTTTTTTCACTTTTTTTTT
1 ATTTGTCTTTTTCTT--CTTTTTTTCA
* *
148996 CTTTCGACTTTTTCTTCTGTTTTTTCA
1 ATTT-GTCTTTTTCTTCT-TTTTTTCA
149023 TTAAAATTCA
Statistics
Matches: 38, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
24 8 0.21
25 4 0.11
26 13 0.34
27 6 0.16
28 7 0.18
ACGTcount: A:0.09, C:0.15, G:0.04, T:0.72
Consensus pattern (25 bp):
ATTTGTCTTTTTCTTCTTTTTTTCA
Found at i:149005 original size:17 final size:15
Alignment explanation
Indices: 148961--149008 Score: 60
Period size: 16 Copynumber: 3.0 Consensus size: 15
148951 CTTTTTCTTC
*
148961 TTTTTTTCAATTTTAT
1 TTTTTTTCACTTTT-T
148977 TTTTTTTCACTTTTT
1 TTTTTTTCACTTTTT
148992 TTTTCTTTCGACTTTTT
1 TTTT-TTTC-ACTTTTT
149009 CTTCTGTTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
15 5 0.17
16 17 0.59
17 7 0.24
ACGTcount: A:0.10, C:0.12, G:0.02, T:0.75
Consensus pattern (15 bp):
TTTTTTTCACTTTTT
Found at i:151748 original size:15 final size:14
Alignment explanation
Indices: 151724--151784 Score: 56
Period size: 15 Copynumber: 4.3 Consensus size: 14
151714 GACTAAAAAG
151724 TAAATCAAAATGAAA
1 TAAAT-AAAATGAAA
*
151739 TAAATTAAAAAGAAA
1 TAAA-TAAAATGAAA
151754 T-AATAAAA-GAAA
1 TAAATAAAATGAAA
151766 GTACAATAAAAT-AAA
1 -TA-AATAAAATGAAA
151781 TAAA
1 TAAA
151785 ATAAGAAGGG
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
12 4 0.10
13 8 0.20
14 4 0.10
15 23 0.57
16 1 0.03
ACGTcount: A:0.70, C:0.03, G:0.07, T:0.20
Consensus pattern (14 bp):
TAAATAAAATGAAA
Found at i:151799 original size:42 final size:43
Alignment explanation
Indices: 151720--151802 Score: 107
Period size: 42 Copynumber: 2.0 Consensus size: 43
151710 AGCAGACTAA
*
151720 AAAGTAAATCAAAATGAAATAAATTAAAAAGAAATAATAAAAG
1 AAAGTAAATCAAAATGAAATAAAATAAAAAGAAATAATAAAAG
* **
151763 AAAGTACAAT-AAAAT-AAATAAAATAAGAAGGGATAATAAA
1 AAAGTA-AATCAAAATGAAATAAAATAAAAAGAAATAATAAA
151803 GGTCGAACGG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
42 21 0.60
43 11 0.31
44 3 0.09
ACGTcount: A:0.69, C:0.02, G:0.11, T:0.18
Consensus pattern (43 bp):
AAAGTAAATCAAAATGAAATAAAATAAAAAGAAATAATAAAAG
Found at i:157332 original size:17 final size:18
Alignment explanation
Indices: 157299--157349 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
157289 TCATTCTCCT
157299 AATT-TTTAAATTGTTTA
1 AATTATTTAAATTGTTTA
*
157316 AATTATTTAACTT-TTTA
1 AATTATTTAAATTGTTTA
*
157333 ATTTATTTTAAATTGTT
1 AATTA-TTTAAATTGTT
157350 AATATTTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
17 12 0.43
18 14 0.50
19 2 0.07
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (18 bp):
AATTATTTAAATTGTTTA
Found at i:161246 original size:24 final size:24
Alignment explanation
Indices: 161209--161254 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
161199 TGGTTAAACT
161209 CTATCTAGGATCGTAAGAGCTAAC
1 CTATCTAGGATCGTAAGAGCTAAC
* *
161233 CTATCTGGGCTCGTAAGAGCTA
1 CTATCTAGGATCGTAAGAGCTA
161255 TTTCTGTCTA
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:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (24 bp):
CTATCTAGGATCGTAAGAGCTAAC
Found at i:161983 original size:21 final size:21
Alignment explanation
Indices: 161950--162027 Score: 63
Period size: 21 Copynumber: 3.7 Consensus size: 21
161940 TGGAGATTTT
*
161950 TGTATCAGTAGAAG-CATGACA
1 TGTATCGGTAGAAGTCAT-ACA
* *
161971 TGTTTCGGTAGAAGTCATACT
1 TGTATCGGTAGAAGTCATACA
* *
161992 TGTATCGGTA-ATACTGCCT-CA
1 TGTATCGGTAGA-AGT-CATACA
162013 TGTATCGGTAGAAGT
1 TGTATCGGTAGAAGT
162028 TTGCACTATT
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
20 1 0.02
21 38 0.84
22 6 0.13
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.32
Consensus pattern (21 bp):
TGTATCGGTAGAAGTCATACA
Found at i:165113 original size:3 final size:3
Alignment explanation
Indices: 165105--165157 Score: 58
Period size: 3 Copynumber: 17.7 Consensus size: 3
165095 GGGGCAATTC
165105 CTT CTT CTT CTT CCTT C-T CTT CTT -TT CTCT CTT CTT C-T CTT GCTT
1 CTT CTT CTT CTT -CTT CTT CTT CTT CTT CT-T CTT CTT CTT CTT -CTT
165150 CTT CTT CT
1 CTT CTT CT
165158 ACTACAATAC
Statistics
Matches: 44, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
2 6 0.14
3 29 0.66
4 9 0.20
ACGTcount: A:0.00, C:0.36, G:0.02, T:0.62
Consensus pattern (3 bp):
CTT
Found at i:184839 original size:15 final size:15
Alignment explanation
Indices: 184808--184855 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
184798 AAATCTCCCA
184808 ATCTTCATAG-TATTC
1 ATCTTCATAGATA-TC
184823 ATCTTCATAGATATC
1 ATCTTCATAGATATC
* * *
184838 ATCCTCGTAGATGTC
1 ATCTTCATAGATATC
184853 ATC
1 ATC
184856 ATCGTAATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 27 0.93
16 2 0.07
ACGTcount: A:0.27, C:0.23, G:0.10, T:0.40
Consensus pattern (15 bp):
ATCTTCATAGATATC
Found at i:187033 original size:71 final size:71
Alignment explanation
Indices: 186958--187139 Score: 229
Period size: 71 Copynumber: 2.6 Consensus size: 71
186948 GAAGTACATT
* * * * * * *
186958 TAGAAGTACAGGGGAAAGGAGACCTTAGCTACTGACTTGAGTTGTTTCAGAACAACTCAACAAAG
1 TAGAAGTTCAAGGGAAAAGATATCTTGGCTACTGACTTGAGCTGTTTCAGAACAACTCAACAAAG
187023 TATCAG
66 TATCAG
* * ** * *
187029 TAGAAGTTCAAGGGAAAAGATATTTTGGCGACTGACTTGAGCTGTTTTGGAACAACTTAACAATG
1 TAGAAGTTCAAGGGAAAAGATATCTTGGCTACTGACTTGAGCTGTTTCAGAACAACTCAACAAAG
*
187094 TATCGG
66 TATCAG
*
187100 TAGATGTTCAAGGGAAAAGATATCTTGGCTACTGACTTGA
1 TAGAAGTTCAAGGGAAAAGATATCTTGGCTACTGACTTGA
187140 AAGGTTTCAG
Statistics
Matches: 94, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
71 94 1.00
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (71 bp):
TAGAAGTTCAAGGGAAAAGATATCTTGGCTACTGACTTGAGCTGTTTCAGAACAACTCAACAAAG
TATCAG
Found at i:196225 original size:24 final size:25
Alignment explanation
Indices: 196168--196226 Score: 77
Period size: 26 Copynumber: 2.4 Consensus size: 25
196158 AGAAGAATAC
*
196168 TGGAAGCTTGAAGATGGTAGAAGCAG
1 TGGAAGCTTGAAGATGATAGAAG-AG
196194 TGGAAGCTTGAAGATGATA-AATG-G
1 TGGAAGCTTGAAGATGATAGAA-GAG
196218 TGGAAGCTT
1 TGGAAGCTT
196227 AGTAGTTGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 10 0.32
25 2 0.06
26 19 0.61
ACGTcount: A:0.34, C:0.07, G:0.36, T:0.24
Consensus pattern (25 bp):
TGGAAGCTTGAAGATGATAGAAGAG
Found at i:203786 original size:17 final size:16
Alignment explanation
Indices: 203731--203791 Score: 61
Period size: 16 Copynumber: 3.8 Consensus size: 16
203721 TATTTGAAAA
* *
203731 AAAAATATTTTTCTTT
1 AAAAATATTTTTATTC
*
203747 AAAAA-ATAATTTATTC
1 AAAAATAT-TTTTATTC
*
203763 AAGAATATTTTTATCTC
1 AAAAATATTTTTAT-TC
203780 AAAAATATTTTT
1 AAAAATATTTTT
203792 TAAAAGTAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
15 2 0.06
16 19 0.53
17 15 0.42
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
AAAAATATTTTTATTC
Found at i:215512 original size:39 final size:39
Alignment explanation
Indices: 215468--215564 Score: 194
Period size: 39 Copynumber: 2.5 Consensus size: 39
215458 CTTTAACACA
215468 GAGTTATAAATTCTTATTTTTTTTGGTTATTAACATATT
1 GAGTTATAAATTCTTATTTTTTTTGGTTATTAACATATT
215507 GAGTTATAAATTCTTATTTTTTTTGGTTATTAACATATT
1 GAGTTATAAATTCTTATTTTTTTTGGTTATTAACATATT
215546 GAGTTATAAATTCTTATTT
1 GAGTTATAAATTCTTATTT
215565 CTTTACCTCA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 58 1.00
ACGTcount: A:0.29, C:0.05, G:0.10, T:0.56
Consensus pattern (39 bp):
GAGTTATAAATTCTTATTTTTTTTGGTTATTAACATATT
Found at i:226631 original size:97 final size:96
Alignment explanation
Indices: 226446--226638 Score: 225
Period size: 97 Copynumber: 2.0 Consensus size: 96
226436 TTTTTGAGAA
** *
226446 AAGGATATTCGATTATCTTGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGCAATATTTCA
1 AAGGATATTCGATTATCTTGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
* *
226511 GAATCGAAGATTAGGAAACATTGCCTCGATT
66 GAATCGAAGATAAAGAAACATTGCCTCGATT
* *
226542 AAGGGTATTCGATTAT-TTCGGTTTGAAGAAAAAATTGCACCTAGTAAGTTAAGGCACAA-ATTT
1 AAGGATATTCGATTATCTT-GATTTGAAG-AAAAATTGCACCTAGTAAGTTAAGGCACAATA-TT
*
226605 TC-GAAACTCGAA-ATAAA-AGAATATTGCCTCGATT
63 TCAG-AA-TCGAAGATAAAGA-AACATTGCCTCGATT
226639 TTAAAGTTTT
Statistics
Matches: 83, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
95 2 0.02
96 26 0.31
97 50 0.60
98 5 0.06
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.30
Consensus pattern (96 bp):
AAGGATATTCGATTATCTTGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
GAATCGAAGATAAAGAAACATTGCCTCGATT
Found at i:226998 original size:29 final size:30
Alignment explanation
Indices: 226966--227176 Score: 141
Period size: 29 Copynumber: 7.2 Consensus size: 30
226956 GTAAAAGGGT
* *
226966 AATTTTAAG-AGTTTTGAGGTCGAAAATGG
1 AATTTTAAGAAGTTTAGAGGTCAAAAATGG
** *
226995 AATTTTTGGAAGTTTAGCGGTCAAAAATGG
1 AATTTTAAGAAGTTTAGAGGTCAAAAATGG
** *
227025 AATTTTTGGAAGTTTAGGGGT-AAAAATGG
1 AATTTTAAGAAGTTTAGAGGTCAAAAATGG
**
227054 AATTTTTGGAAGTTTAG-GAGT-AAATAAT-G
1 AATTTTAAGAAGTTTAGAG-GTCAAA-AATGG
** *
227083 AATTTTTGGAAGTTTCGAGGTCAAAAATGG
1 AATTTTAAGAAGTTTAGAGGTCAAAAATGG
** * * *
227113 AATTTTTGGAAG-TTCGAGGGT-AAATATGA
1 AATTTTAAGAAGTTTAGA-GGTCAAAAATGG
** * *
227142 AATTTTTGGAAGTTTTGGGGT-AAAAATGG
1 AATTTTAAGAAGTTTAGAGGTCAAAAATGG
227171 AATTTT
1 AATTTT
227177 TTGGATAGTT
Statistics
Matches: 161, Mismatches: 13, Indels: 16
0.85 0.07 0.08
Matches are distributed among these distances:
28 1 0.01
29 97 0.60
30 63 0.39
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.36
Consensus pattern (30 bp):
AATTTTAAGAAGTTTAGAGGTCAAAAATGG
Found at i:227029 original size:59 final size:57
Alignment explanation
Indices: 226975--227191 Score: 274
Period size: 59 Copynumber: 3.7 Consensus size: 57
226965 TAATTTTAAG
*
226975 AGTTTTGAGGTCGAAAATGGAATTTTTGGAAGTTTAGCGGTCAAAAATGGAATTTTTGGA
1 AGTTTTGAGGT-AAAAATGGAATTTTTGGAAGTTTAG-GGT-AAAAATGGAATTTTTGGA
* *
227035 AGTTTAGGGGTAAAAATGGAATTTTTGGAAGTTTAGGAGTAAATAAT-GAATTTTTGGA
1 AGTTTTGAGGTAAAAATGGAATTTTTGGAAGTTTAGG-GTAAA-AATGGAATTTTTGGA
* * * *
227093 AGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTCGAGGGTAAATATGAAATTTTTGGA
1 AGTTTTGAGGT-AAAAATGGAATTTTTGGAAGTT-TAGGGTAAAAATGGAATTTTTGGA
*
227152 AGTTTTGGGGTAAAAATGGAATTTTTTGGATAGTTTAGGG
1 AGTTTTGAGGTAAAAATGGAA-TTTTTGGA-AGTTTAGGG
227192 ACCTCCCGGG
Statistics
Matches: 139, Mismatches: 11, Indels: 15
0.84 0.07 0.09
Matches are distributed among these distances:
58 36 0.26
59 87 0.63
60 16 0.12
ACGTcount: A:0.33, C:0.03, G:0.29, T:0.36
Consensus pattern (57 bp):
AGTTTTGAGGTAAAAATGGAATTTTTGGAAGTTTAGGGTAAAAATGGAATTTTTGGA
Found at i:227134 original size:88 final size:88
Alignment explanation
Indices: 226988--227189 Score: 291
Period size: 88 Copynumber: 2.3 Consensus size: 88
226978 TTTGAGGTCG
* *
226988 AAAATGGAATTTTTGGAAGTTTAGCGGTCAAAAATGGAATTTTTGGAAGTTTAGGGGTAAAAATG
1 AAAATGGAATTTTTGGAAGTTTAGAGGTCAAAAATGGAATTTTTGGAAGTTGAGGGGTAAAAATG
*
227053 GAATTTTTGGAAGTTTAGGAGTA
66 AAATTTTTGGAAGTTTAGGAGTA
* *
227076 AATAAT-GAATTTTTGGAAGTTTCGAGGTCAAAAATGGAATTTTTGGAAGTTCGA-GGGTAAATA
1 AA-AATGGAATTTTTGGAAGTTTAGAGGTCAAAAATGGAATTTTTGGAAGTT-GAGGGGTAAAAA
* *
227139 TGAAATTTTTGGAAGTTTTGGGGTA
64 TGAAATTTTTGGAAGTTTAGGAGTA
227164 AAAATGGAATTTTTTGGATAGTTTAG
1 AAAATGGAA-TTTTTGGA-AGTTTAG
227190 GGACCTCCCG
Statistics
Matches: 101, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
87 3 0.03
88 80 0.79
89 12 0.12
90 6 0.06
ACGTcount: A:0.34, C:0.02, G:0.27, T:0.36
Consensus pattern (88 bp):
AAAATGGAATTTTTGGAAGTTTAGAGGTCAAAAATGGAATTTTTGGAAGTTGAGGGGTAAAAATG
AAATTTTTGGAAGTTTAGGAGTA
Found at i:227177 original size:29 final size:29
Alignment explanation
Indices: 226988--227191 Score: 268
Period size: 29 Copynumber: 6.9 Consensus size: 29
226978 TTTGAGGTCG
*
226988 AAAATGGAATTTTTGGAAGTTTAGCGGTCA
1 AAAATGGAATTTTTGGAAGTTTAGGGGT-A
227018 AAAATGGAATTTTTGGAAGTTTAGGGGTA
1 AAAATGGAATTTTTGGAAGTTTAGGGGTA
*
227047 AAAATGGAATTTTTGGAAGTTTAGGAGTA
1 AAAATGGAATTTTTGGAAGTTTAGGGGTA
* *
227076 AATAAT-GAATTTTTGGAAGTTTCGAGGTCA
1 AA-AATGGAATTTTTGGAAGTTTAGGGGT-A
*
227106 AAAATGGAATTTTTGGAAG-TTCGAGGGTA
1 AAAATGGAATTTTTGGAAGTTTAG-GGGTA
* * *
227135 AATATGAAATTTTTGGAAGTTTTGGGGTA
1 AAAATGGAATTTTTGGAAGTTTAGGGGTA
227164 AAAATGGAATTTTTTGGATAGTTTAGGG
1 AAAATGGAA-TTTTTGGA-AGTTTAGGG
227192 ACCTCCCGGG
Statistics
Matches: 155, Mismatches: 12, Indels: 13
0.86 0.07 0.07
Matches are distributed among these distances:
29 87 0.56
30 60 0.39
31 8 0.05
ACGTcount: A:0.34, C:0.02, G:0.28, T:0.36
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTTAGGGGTA
Found at i:228307 original size:7 final size:7
Alignment explanation
Indices: 228295--228419 Score: 75
Period size: 7 Copynumber: 18.0 Consensus size: 7
228285 TATTACTAAA
228295 TATTAAT
1 TATTAAT
228302 TATTAAT
1 TATTAAT
228309 TATTAA-
1 TATTAAT
*
228315 TAGGT-AT
1 TA-TTAAT
228322 TATTAAT
1 TATTAAT
*
228329 TACTGTTAT
1 TA-T-TAAT
* *
228338 TAATACT
1 TATTAAT
228345 TATTAAT
1 TATTAAT
228352 ATCATT-AT
1 -T-ATTAAT
*
228360 TATAAATT
1 TATTAA-T
*
228368 TATTATT
1 TATTAAT
228375 TATT-AT
1 TATTAAT
228381 TATT-AT
1 TATTAAT
228387 TATTAA-
1 TATTAAT
228393 TATTAAT
1 TATTAAT
228400 TATTAAT
1 TATTAAT
* *
228407 GA-TACT
1 TATTAAT
228413 TATTAAT
1 TATTAAT
228420 AAGTTATGAA
Statistics
Matches: 90, Mismatches: 16, Indels: 24
0.69 0.12 0.18
Matches are distributed among these distances:
6 27 0.30
7 46 0.51
8 9 0.10
9 8 0.09
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.54
Consensus pattern (7 bp):
TATTAAT
Found at i:228313 original size:3 final size:3
Alignment explanation
Indices: 228295--228404 Score: 60
Period size: 3 Copynumber: 34.7 Consensus size: 3
228285 TATTACTAAA
* * * * *
228295 TAT TAAT TAT TAAT TAT TAA TAGG TAT TAT TAAT TAC TGT TAT TAA TACT
1 TAT T-AT TAT T-AT TAT TAT TA-T TAT TAT T-AT TAT TAT TAT TAT TA-T
* * * *
228345 TAT TAA TAT CAT TAT TAT AAA T-T TAT TATT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT
*
228390 TAA TAT TAAT TAT TA
1 TAT TAT T-AT TAT TA
228405 ATGATACTTA
Statistics
Matches: 80, Mismatches: 19, Indels: 16
0.70 0.17 0.14
Matches are distributed among these distances:
2 1 0.01
3 60 0.75
4 19 0.24
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (3 bp):
TAT
Found at i:228405 original size:13 final size:12
Alignment explanation
Indices: 228295--228420 Score: 76
Period size: 13 Copynumber: 9.7 Consensus size: 12
228285 TATTACTAAA
228295 TATTAATTATTAAT
1 TATTAA-TATT-AT
*
228309 TATTAATAGGTAT
1 TATTAATA-TTAT
* *
228322 TATTAATTACTGT
1 TATTAA-TATTAT
228335 TATTAATACTTAT
1 TATTAATA-TTAT
*
228348 TAAT-ATCATTAT
1 TATTAAT-ATTAT
*
228360 TATAAATTTATTATT
1 TATTAA--TATTA-T
*
228375 TATTATTATTAT
1 TATTAATATTAT
228387 TATTAATATTAAT
1 TATTAATATT-AT
228400 TATTAATGA-TACT
1 TATTAAT-ATTA-T
228413 TATTAATA
1 TATTAATA
228421 AGTTATGAAA
Statistics
Matches: 90, Mismatches: 11, Indels: 24
0.72 0.09 0.19
Matches are distributed among these distances:
12 22 0.24
13 48 0.53
14 14 0.16
15 6 0.07
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.54
Consensus pattern (12 bp):
TATTAATATTAT
Found at i:229100 original size:17 final size:17
Alignment explanation
Indices: 229072--229134 Score: 74
Period size: 17 Copynumber: 3.7 Consensus size: 17
229062 ATTTTAAAGT
* *
229072 TTTAAGTTTAAAAT-TA
1 TTTAAATTTAAAATAAA
*
229088 TTTCAAATTTAAACTAAA
1 TTT-AAATTTAAAATAAA
*
229106 TTTAAATTTAAAATGAA
1 TTTAAATTTAAAATAAA
229123 TTTAAATTTAAA
1 TTTAAATTTAAA
229135 TTTAAAGTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
16 3 0.08
17 33 0.82
18 4 0.10
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.44
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:229108 original size:11 final size:11
Alignment explanation
Indices: 229108--229151 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
229098 AAACTAAATT
229108 TAAATTTAAAA
1 TAAATTTAAAA
* *
229119 TGAATTTAAATT
1 TAAATTTAAA-A
*
229131 TAAATTTAAAG
1 TAAATTTAAAA
229142 TAAATTTAAA
1 TAAATTTAAA
229152 TTTAGAAATG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 19 0.68
12 9 0.32
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.41
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:229113 original size:6 final size:6
Alignment explanation
Indices: 229087--229155 Score: 72
Period size: 6 Copynumber: 11.8 Consensus size: 6
229077 GTTTAAAATT
* * *
229087 ATTTCAA ATTTAA A-CTAA ATTTAA ATTTAA A-ATGA ATTTAA ATTTAA
1 ATTT-AA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
*
229134 ATTTAA A-GTAA ATTTAA ATTTA
1 ATTTAA ATTTAA ATTTAA ATTTA
229156 GAAATGAATC
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
5 11 0.22
6 36 0.71
7 4 0.08
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (6 bp):
ATTTAA
Found at i:229116 original size:34 final size:35
Alignment explanation
Indices: 229072--229151 Score: 94
Period size: 34 Copynumber: 2.3 Consensus size: 35
229062 ATTTTAAAGT
* *
229072 TTTAAGTTTAAAAT-TATTTCAAATTTAAA-CTAAA
1 TTTAAATTTAAAATGAATTT-AAATTTAAATCTAAA
*
229106 TTTAAATTTAAAATGAATTTAAATTTAAATTTAAA
1 TTTAAATTTAAAATGAATTTAAATTTAAATCTAAA
*
229141 -GTAAATTTAAA
1 TTTAAATTTAAA
229152 TTTAGAAATG
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
34 32 0.80
35 8 0.20
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.44
Consensus pattern (35 bp):
TTTAAATTTAAAATGAATTTAAATTTAAATCTAAA
Found at i:229132 original size:23 final size:23
Alignment explanation
Indices: 229102--229155 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
229092 AAATTTAAAC
*
229102 TAAATTTAAATTTAAAATGAATT
1 TAAATTTAAATTTAAAATAAATT
*
229125 TAAATTTAAATTTAAAGTAAATT
1 TAAATTTAAATTTAAAATAAATT
229148 TAAATTTA
1 TAAATTTA
229156 GAAATGAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (23 bp):
TAAATTTAAATTTAAAATAAATT
Found at i:229145 original size:17 final size:17
Alignment explanation
Indices: 229087--229155 Score: 66
Period size: 17 Copynumber: 3.6 Consensus size: 17
229077 GTTTAAAATT
*
229087 ATTTCAAATTTAAACTAA
1 ATTT-AAATTTAAAGTAA
229105 ATTTAAATTTAAAATGAATTTAA
1 ATTTAAATTT-AAA-G----TAA
229128 ATTTAAATTTAAAGTAA
1 ATTTAAATTTAAAGTAA
229145 ATTTAAATTTA
1 ATTTAAATTTA
229156 GAAATGAATC
Statistics
Matches: 44, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
17 20 0.45
18 7 0.16
21 1 0.02
22 3 0.07
23 13 0.30
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (17 bp):
ATTTAAATTTAAAGTAA
Found at i:230138 original size:196 final size:199
Alignment explanation
Indices: 229541--230168 Score: 775
Period size: 206 Copynumber: 3.1 Consensus size: 199
229531 TAACTTGGCC
* * * ** * *
229541 TTCTTCTCAGTATCTCATCAGGAAGACGACCATATCACTTGTTTTGAT-CAACTTCTCTGTGTTT
1 TTCTTCTCTGTATCTCATCAGGAAGATGACC--GTC-CTTGTTTCAATCCAACTTCTCTGTATCT
* * * *
229605 CATCAGGAAGACGGATTTGGTTCACTTCTCAGTATTTCAATAAGAAGCTAACCATTTTATTGCTT
63 CATCAGGAAGACGAATTTGGTCCACTTCTCAGTATTTCATTAGGAAGCTAACCATTTTATTGCTT
* * *
229670 CGACTTGCTTCTCAGTATCTTATCAGGAAGCT-AGGGTTCGAAGATTTGCTCACATCGAG-CGTG
128 CGACATGCTTCTCAGTATCTCATCAGGAAGCTGA-GGTTCGAAGATTTGCTCACATCGAGCCCTG
*
229733 AGTTTGATTTGGTC
192 A----G--TTGGTA
** * *
229747 TTCTTCTCAATATCTCATCAGGAAGATGACCGTATTGCTTGTTTCAATCC-GCTTCTCTGTATCT
1 TTCTTCTCTGTATCTCATCAGGAAGATGACCG---TCCTTGTTTCAATCCAACTTCTCTGTATCT
* *
229811 CATCAGGAAGACGAATTTGGTCCACTTCTCAGTTTTTCATCAGGAAGCTAACCATTTTATTGCTT
63 CATCAGGAAGACGAATTTGGTCCACTTCTCAGTATTTCATTAGGAAGCTAACCATTTTATTGCTT
* * * *
229876 CAACATGCTTCTCAATATCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCGATCCCTGA
128 CGACATGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCACATCGAGCCCTGA
229941 GTTGGTA
193 GTTGGTA
* * *
229948 TTCTTCTCTGTATCTCATTAGGAAGATGACCG-CCTTGTTTCAA-CCAACTTCTCTGTACCTCAC
1 TTCTTCTCTGTATCTCATCAGGAAGATGACCGTCCTTGTTTCAATCCAACTTCTCTGTATCTCAT
* *
230011 CAGGAAGACGAATTTGGTCCACTTCTCAGTATCTCATTAGGAAGCTAACC-TTTTATTGCTTCGC
66 CAGGAAGACGAATTTGGTCCACTTCTCAGTATTTCATTAGGAAGCTAACCATTTTATTGCTTCGA
* * * *
230075 CCTGCTTCTCAGTATCTCATCAAGAAGCTGAGATTCGAAGATTTGCTCATATCGAGCCCTGAGTT
131 CATGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCACATCGAGCCCTGAGTT
230140 GGTA
196 GGTA
*
230144 TACTTCTCTGTATCTCATCAGGAAG
1 TTCTTCTCTGTATCTCATCAGGAAG
230169 CTAACCATTT
Statistics
Matches: 371, Mismatches: 44, Indels: 24
0.85 0.10 0.05
Matches are distributed among these distances:
196 99 0.27
197 71 0.19
201 34 0.09
203 1 0.00
206 160 0.43
207 6 0.02
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.35
Consensus pattern (199 bp):
TTCTTCTCTGTATCTCATCAGGAAGATGACCGTCCTTGTTTCAATCCAACTTCTCTGTATCTCAT
CAGGAAGACGAATTTGGTCCACTTCTCAGTATTTCATTAGGAAGCTAACCATTTTATTGCTTCGA
CATGCTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTTGCTCACATCGAGCCCTGAGTT
GGTA
Found at i:230247 original size:115 final size:114
Alignment explanation
Indices: 230031--230237 Score: 342
Period size: 115 Copynumber: 1.8 Consensus size: 114
230021 AATTTGGTCC
* * *
230031 ACTTCTCAGTATCTCATTAGGAAGCTAACCTTTTATTGCTTCGCCCTGCTTCTCAGTATCTCATC
1 ACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTACTTCGACCTGCTTCTCAGTATCTCATC
230096 AAGAAGCTGAGATTCGAAGATTTGCTCATATCGAGCCCTGAGTTGGTAT
66 AAGAAGCTGAGATTCGAAGATTTGCTCATATCGAGCCCTGAGTTGGTAT
*
230145 ACTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTACTTCGACCTGCTTCTCAGTATCTCAT
1 ACTTCTCAGTATCTCATCAGGAAGCTAACC-TTTTATTACTTCGACCTGCTTCTCAGTATCTCAT
* * *
230210 CAGGAAGCTGCGGTTCGAAGATTTGCTC
65 CAAGAAGCTGAGATTCGAAGATTTGCTC
230238 GCTTTGAGCC
Statistics
Matches: 85, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
114 28 0.33
115 57 0.67
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (114 bp):
ACTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTACTTCGACCTGCTTCTCAGTATCTCATC
AAGAAGCTGAGATTCGAAGATTTGCTCATATCGAGCCCTGAGTTGGTAT
Done.