Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008309.1 Hibiscus syriacus cultivar Beakdansim tig00110999_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 111767
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:5388 original size:21 final size:21
Alignment explanation
Indices: 5344--5403 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
5334 CCCCCCCTGA
***
5344 GGGAACCGATTCCCCCTTTGAG
1 GGGAACCGATTCCCCC-CACAG
5366 GGGAACCGATTCCCCCCACAG
1 GGGAACCGATTCCCCCCACAG
* *
5387 GGGAATCGATACCCCCC
1 GGGAACCGATTCCCCCC
5404 TGGGGTTCTG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
21 17 0.52
22 16 0.48
ACGTcount: A:0.22, C:0.38, G:0.25, T:0.15
Consensus pattern (21 bp):
GGGAACCGATTCCCCCCACAG
Found at i:8067 original size:75 final size:74
Alignment explanation
Indices: 7942--8143 Score: 232
Period size: 75 Copynumber: 2.8 Consensus size: 74
7932 TCAAGCCAAA
* * * **
7942 AATTCCAGATTGCTCAGA-GGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGGT
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCATAGGAGGAACCGATT-CCCCCTAAACAGT
8006 TTGGCTCCGAG
64 TTGGCTCCGAG
* *
8017 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATATGAGGAACCGATTCCCCCTAAACAGTTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTTT
* *
8082 TGTTCCGAG
66 GGCTCCGAG
* ** * *
8091 AATTCCAGTATG--CGGAGGGAACCGA-TCCCCCCCAGGGGGTACCGATTCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCT
8144 GTTCAACGGT
Statistics
Matches: 110, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
71 23 0.21
72 13 0.12
74 29 0.26
75 35 0.32
76 10 0.09
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.21
Consensus pattern (74 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTTT
GGCTCCGAG
Found at i:9504 original size:147 final size:148
Alignment explanation
Indices: 9088--9537 Score: 778
Period size: 147 Copynumber: 3.0 Consensus size: 148
9078 GAGTCGAGGG
* * * * * *
9088 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATTTATGAGGTCTT-TGAGACACAT
1 TCTACGCGGTCCTTCGGGA-ATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
* *
9152 ACTTGGTCCTTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
65 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
9217 TATGGCACTACGGTGTAAT
130 TATGGCACTACGGTGTAAT
*
9236 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGTAGTCTTGTAAGACACAT
1 TCTACGCGGTCCTTCGGGA-ATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
9301 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
65 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
*
9366 TATGGCACTACGGTGCAAT
130 TATGGCACTACGGTGTAAT
9385 TCTACGCGGTCCTTCGGG-ATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACATA
1 TCTACGCGGTCCTTCGGGAATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACATA
9449 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTAT
66 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTAT
9514 ATGGCACTACGGTGTAAT
131 ATGGCACTACGGTGTAAT
9532 TCTACG
1 TCTACG
9538 TGCACTTCGG
Statistics
Matches: 288, Mismatches: 13, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
147 133 0.46
148 47 0.16
149 108 0.38
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (148 bp):
TCTACGCGGTCCTTCGGGAATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACATA
CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTAT
ATGGCACTACGGTGTAAT
Found at i:9771 original size:21 final size:21
Alignment explanation
Indices: 9747--9807 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
9737 ATAAATAATT
*
9747 TGATGATAATGATAGA-GATAA
1 TGATAATAAT-ATAGATGATAA
*
9768 TGATAATAATATATATGATAA
1 TGATAATAATATAGATGATAA
* * *
9789 TGCTAAGAAAATAGATGAT
1 TGATAATAATATAGATGAT
9808 GATATGTACA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
20 4 0.12
21 29 0.88
ACGTcount: A:0.49, C:0.02, G:0.18, T:0.31
Consensus pattern (21 bp):
TGATAATAATATAGATGATAA
Found at i:10451 original size:17 final size:17
Alignment explanation
Indices: 10422--10463 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
10412 TTAATTTTAT
*
10422 TTTTAT-ATTTATATAA
1 TTTTATAATATATATAA
*
10438 TTTTATAATATATATGA
1 TTTTATAATATATATAA
10455 -TTTATAATA
1 TTTTATAATA
10464 AAAATAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 15 0.65
17 8 0.35
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
TTTTATAATATATATAA
Found at i:13254 original size:30 final size:30
Alignment explanation
Indices: 13218--13353 Score: 173
Period size: 30 Copynumber: 4.5 Consensus size: 30
13208 GTAACAGTAT
*
13218 ACCAGATAATAGTAGAACAAATAATAATAG
1 ACCAGATAATAGTAGAACAGATAATAATAG
* * *
13248 ATCAGATAACAGTAGAACAGATAATAGTAG
1 ACCAGATAATAGTAGAACAGATAATAATAG
* * *
13278 ACCAGATAATATTATAATAGATAATAATAG
1 ACCAGATAATAGTAGAACAGATAATAATAG
* * *
13308 ACCAGATAATAGTATAATAGATAATAGTAG
1 ACCAGATAATAGTAGAACAGATAATAATAG
*
13338 ACCATATAATAGTAGA
1 ACCAGATAATAGTAGA
13354 CCTGATAGCA
Statistics
Matches: 92, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 92 1.00
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (30 bp):
ACCAGATAATAGTAGAACAGATAATAATAG
Found at i:13286 original size:60 final size:60
Alignment explanation
Indices: 13193--13353 Score: 196
Period size: 60 Copynumber: 2.7 Consensus size: 60
13183 ATCATAACAA
* * * * * *
13193 ATAACAGTAGACCTGGTAACAGTATACCAGATAATAGTAGAACAAATAATAATAGATCAG
1 ATAACAGTAGAACAGATAATAGTAGACCAGATAATAGTAGAACAAATAATAATAGACCAG
* * * *
13253 ATAACAGTAGAACAGATAATAGTAGACCAGATAATATTATAATAGATAATAATAGACCAG
1 ATAACAGTAGAACAGATAATAGTAGACCAGATAATAGTAGAACAAATAATAATAGACCAG
* * * *
13313 ATAATAGTATAATAGATAATAGTAGACCATATAATAGTAGA
1 ATAACAGTAGAACAGATAATAGTAGACCAGATAATAGTAGA
13354 CCTGATAGCA
Statistics
Matches: 85, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 85 1.00
ACGTcount: A:0.50, C:0.10, G:0.16, T:0.24
Consensus pattern (60 bp):
ATAACAGTAGAACAGATAATAGTAGACCAGATAATAGTAGAACAAATAATAATAGACCAG
Found at i:13354 original size:15 final size:15
Alignment explanation
Indices: 13193--13360 Score: 147
Period size: 15 Copynumber: 11.2 Consensus size: 15
13183 ATCATAACAA
* *
13193 ATAACAGTAGACCTG
1 ATAATAGTAGACCAG
* * *
13208 GTAACAGTATACCAG
1 ATAATAGTAGACCAG
* *
13223 ATAATAGTAGAACAA
1 ATAATAGTAGACCAG
* *
13238 ATAATAATAGATCAG
1 ATAATAGTAGACCAG
* *
13253 ATAACAGTAGAACAG
1 ATAATAGTAGACCAG
13268 ATAATAGTAGACCAG
1 ATAATAGTAGACCAG
* * **
13283 ATAATATTATAATAG
1 ATAATAGTAGACCAG
*
13298 ATAATAATAGACCAG
1 ATAATAGTAGACCAG
* **
13313 ATAATAGTATAATAG
1 ATAATAGTAGACCAG
*
13328 ATAATAGTAGACCAT
1 ATAATAGTAGACCAG
*
13343 ATAATAGTAGACCTG
1 ATAATAGTAGACCAG
13358 ATA
1 ATA
13361 GCATTAGATC
Statistics
Matches: 119, Mismatches: 34, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
15 119 1.00
ACGTcount: A:0.49, C:0.11, G:0.15, T:0.24
Consensus pattern (15 bp):
ATAATAGTAGACCAG
Found at i:13374 original size:30 final size:30
Alignment explanation
Indices: 13335--13391 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
13325 TAGATAATAG
*
13335 TAGACCATATAATAGTAGACCTGATAGCAT
1 TAGACCATATAACAGTAGACCTGATAGCAT
* * *
13365 TAGATCATATAGCAGTAGACTTGATAG
1 TAGACCATATAACAGTAGACCTGATAG
13392 TTTGAGCATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (30 bp):
TAGACCATATAACAGTAGACCTGATAGCAT
Found at i:13902 original size:14 final size:14
Alignment explanation
Indices: 13883--13913 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
13873 AATACATTTG
*
13883 TTTATGTTTGTTTA
1 TTTATGTTCGTTTA
13897 TTTATGTTCGTTTA
1 TTTATGTTCGTTTA
13911 TTT
1 TTT
13914 CATTTGTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.03, G:0.13, T:0.71
Consensus pattern (14 bp):
TTTATGTTCGTTTA
Found at i:14688 original size:21 final size:22
Alignment explanation
Indices: 14638--14690 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
14628 TTTAAAATAA
*
14638 ATTTTAAAATATGTATTGATTT
1 ATTTTAAAATATGGATTGATTT
14660 ATTTTAAAATATGGATTGATTT
1 ATTTTAAAATATGGATTGATTT
*
14682 ATTTAAAAA
1 ATTTTAAAA
14691 AAATTATTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.42, C:0.00, G:0.09, T:0.49
Consensus pattern (22 bp):
ATTTTAAAATATGGATTGATTT
Found at i:14752 original size:31 final size:31
Alignment explanation
Indices: 14714--14803 Score: 162
Period size: 31 Copynumber: 2.9 Consensus size: 31
14704 AGTTGTATGG
14714 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATTTCAGTATTGTAAAACTAAA
14745 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATTTCAGTATTGTAAAACTAAA
* *
14776 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATTTCAGTATTGTAAAACT
14804 CTTTTAAAAT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 57 1.00
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATTTCAGTATTGTAAAACTAAA
Found at i:14840 original size:22 final size:22
Alignment explanation
Indices: 14812--14871 Score: 111
Period size: 22 Copynumber: 2.7 Consensus size: 22
14802 CTCTTTTAAA
14812 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
*
14834 ATTTATTTTTAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
14856 ATTTATTTTAAAATAT
1 ATTTATTTTAAAATAT
14872 TTATTATTAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.53
Consensus pattern (22 bp):
ATTTATTTTAAAATATGGATTG
Found at i:14912 original size:31 final size:31
Alignment explanation
Indices: 14877--14935 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
14867 AATATTTATT
* *
14877 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGCAAAACTAAA
14908 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCAGTATTGCAAAACT
14936 CTTTTAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAACTAAA
Found at i:15137 original size:31 final size:31
Alignment explanation
Indices: 15080--15138 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
15070 AGTTGTATGG
* **
15080 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATTTCAGCATTACAAAACTAAA
15111 ATTATTTAAATTTCAGCATTACAAAACT
1 ATTATTTAAATTTCAGCATTACAAAACT
15139 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATTTCAGCATTACAAAACTAAA
Found at i:16667 original size:29 final size:29
Alignment explanation
Indices: 16624--16706 Score: 130
Period size: 29 Copynumber: 2.8 Consensus size: 29
16614 CTCACCTAAC
16624 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
16654 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
* *
16683 TAAATGATGTAGGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
16707 ATTTAGTTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 45 0.92
30 4 0.08
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:21430 original size:29 final size:29
Alignment explanation
Indices: 21387--21469 Score: 130
Period size: 29 Copynumber: 2.8 Consensus size: 29
21377 CTCACCTAAC
21387 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
21417 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
* *
21446 TAAATGATGTAGGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
21470 ATTTAGTTTG
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 45 0.92
30 4 0.08
ACGTcount: A:0.42, C:0.10, G:0.16, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:24504 original size:58 final size:58
Alignment explanation
Indices: 24430--24547 Score: 227
Period size: 58 Copynumber: 2.0 Consensus size: 58
24420 ATTATCAGGT
*
24430 TTGATCTGTTTTACTATCTAAATTTTTAATATTTTTTAAAATTATGCCTAAAGTTTAA
1 TTGATCTGTTTCACTATCTAAATTTTTAATATTTTTTAAAATTATGCCTAAAGTTTAA
24488 TTGATCTGTTTCACTATCTAAATTTTTAATATTTTTTAAAATTATGCCTAAAGTTTAA
1 TTGATCTGTTTCACTATCTAAATTTTTAATATTTTTTAAAATTATGCCTAAAGTTTAA
24546 TT
1 TT
24548 TTTGTTTTAT
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 59 1.00
ACGTcount: A:0.32, C:0.09, G:0.07, T:0.52
Consensus pattern (58 bp):
TTGATCTGTTTCACTATCTAAATTTTTAATATTTTTTAAAATTATGCCTAAAGTTTAA
Found at i:24544 original size:29 final size:29
Alignment explanation
Indices: 24454--24550 Score: 87
Period size: 29 Copynumber: 3.4 Consensus size: 29
24444 TATCTAAATT
24454 TTTAATATTTTTTAAAATTATGCCTAAAG
1 TTTAATATTTTTTAAAATTATGCCTAAAG
* * * *
24483 TTTAATTGATCTGTTT--CACTAT--CTAAATT
1 TTTAA-T-AT-TTTTTAAAATTATGCCTAAA-G
24512 TTTAATATTTTTTAAAATTATGCCTAAAG
1 TTTAATATTTTTTAAAATTATGCCTAAAG
24541 TTTAAT-TTTT
1 TTTAATATTTT
24551 GTTTTATTTT
Statistics
Matches: 52, Mismatches: 8, Indels: 17
0.68 0.10 0.22
Matches are distributed among these distances:
26 4 0.08
27 2 0.04
28 14 0.27
29 16 0.31
30 10 0.19
31 2 0.04
32 4 0.08
ACGTcount: A:0.33, C:0.08, G:0.06, T:0.53
Consensus pattern (29 bp):
TTTAATATTTTTTAAAATTATGCCTAAAG
Found at i:25138 original size:423 final size:422
Alignment explanation
Indices: 24515--25368 Score: 1512
Period size: 423 Copynumber: 2.0 Consensus size: 422
24505 CTAAATTTTT
24515 AATATTTTTTAAAATTATGCCTAAAGTTTAATTTTTGTTTTATTTTAATACCCCATTGTTAAAAA
1 AATATTTTTTAAAATTATGCCTAAAGTTTAATTTTTGTTTTATTTTAATACCCCATTGTTAAAAA
*
24580 CTTCGATTTTTGTTTAATTTCAATACCTCATTAAAAATATGACGTTAAATTTTGAAAGAAATAAC
66 CTTCGATTTTTGTTTAATTTCAATACCTCATTAAAAATATGACGTTAAATTTTGAAAGAAATAAA
* * *
24645 AAAAATTAAAGTTTAGGTACTAAAACGGATCAAAACTAATAAATTAGGTACTAAACGTGCTAAGT
131 AAAAATAAAAGTTTAGGTACTAAAACGGACCAAAACTAATAAATTAGATACTAAACGTGCTAAGT
* *
24710 TTTTAACGGCGGGTACAAAAATAAAATGAAACCTAAATGTTAGGTATGATTTTGAAAAAAATTTG
196 TTTTAACGGCGGGTACAAAAATAAAATGAAACCTAAATGTTAGATATGATTTTG-AAAAAA-TTA
*
24775 AAATTTTAGATACTAAAACTGATATTTTAGGTAACAAATGTGTAGTTTACCCTGAACCCAATATT
259 AAATTTTAGATACTAAAACTGATATTTTAAGTAACAAATGTGTAGTTTACCCTGAACCCAATATT
*
24840 AAAGGTTTAAGGTTGACAATTTAATCACTAAGAGATTAATTAATTAATTAAGAGGTTAAAAATGT
324 AAAGGTTTAAGGTTAACAATTTAATCACTAAGAGATTAATTAATTAATTAAGAGGTTAAAAATGT
* *
24905 TCATATTATCCCATTTTGTATACGTTCGAATTTC
389 TCATATTATCCCATTTTGTATACGCTCGAATCTC
*
24939 AATATTTTTTAAAATTATGCCTAAAGTTTAATTTTTGTTTTATTTTAATACTCCATTGTT-AAAA
1 AATATTTTTTAAAATTATGCCTAAAGTTTAATTTTTGTTTTATTTTAATACCCCATTGTTAAAAA
*
25003 CTTCGGTTTTTGTTTAATTTCAATACCTCATTAAAAATATGACGTTAAATTTTGAAAGAAATAAA
66 CTTCGATTTTTGTTTAATTTCAATACCTCATTAAAAATATGACGTTAAATTTTGAAAGAAATAAA
25068 AAAAATAAAAGTTTAGGTACTAAAACGGACCAAAACTAATAAATTAGATACTAAACGTGCTAAGT
131 AAAAATAAAAGTTTAGGTACTAAAACGGACCAAAACTAATAAATTAGATACTAAACGTGCTAAGT
* * *
25133 TTTTAACGGCGGGTACTAAAATGAAATGAAACCTAAATGTTAGATATGGTTTTGAAAAAATTAAA
196 TTTTAACGGCGGGTACAAAAATAAAATGAAACCTAAATGTTAGATATGATTTTGAAAAAATTAAA
* *
25198 ATTTTAGTTACTAAAACTGATATTTTAAGTACCAAATGTGTAGTTTACCCTGAACCCAATATTAA
261 ATTTTAGATACTAAAACTGATATTTTAAGTAACAAATGTGTAGTTTACCCTGAACCCAATATTAA
*
25263 AGGTTTAAGGTTAACAATTTAATCACTAAGAGATTCATTAATTAATTAAGAGGTTAAAAATGTTC
326 AGGTTTAAGGTTAACAATTTAATCACTAAGAGATTAATTAATTAATTAAGAGGTTAAAAATGTTC
*
25328 ATATTATCCCATTTTGTATATGCTCGAATCTC
391 ATATTATCCCATTTTGTATACGCTCGAATCTC
25360 AATATTTTT
1 AATATTTTT
25369 CTTAAAGATA
Statistics
Matches: 411, Mismatches: 19, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
421 167 0.41
422 6 0.01
423 179 0.44
424 59 0.14
ACGTcount: A:0.40, C:0.11, G:0.12, T:0.37
Consensus pattern (422 bp):
AATATTTTTTAAAATTATGCCTAAAGTTTAATTTTTGTTTTATTTTAATACCCCATTGTTAAAAA
CTTCGATTTTTGTTTAATTTCAATACCTCATTAAAAATATGACGTTAAATTTTGAAAGAAATAAA
AAAAATAAAAGTTTAGGTACTAAAACGGACCAAAACTAATAAATTAGATACTAAACGTGCTAAGT
TTTTAACGGCGGGTACAAAAATAAAATGAAACCTAAATGTTAGATATGATTTTGAAAAAATTAAA
ATTTTAGATACTAAAACTGATATTTTAAGTAACAAATGTGTAGTTTACCCTGAACCCAATATTAA
AGGTTTAAGGTTAACAATTTAATCACTAAGAGATTAATTAATTAATTAAGAGGTTAAAAATGTTC
ATATTATCCCATTTTGTATACGCTCGAATCTC
Found at i:26351 original size:15 final size:14
Alignment explanation
Indices: 26327--26385 Score: 64
Period size: 14 Copynumber: 4.1 Consensus size: 14
26317 GTAATTAGTT
26327 TTCTGGAAATTGAA
1 TTCTGGAAATTGAA
*
26341 TTCTGGAAAATGAA
1 TTCTGGAAATTGAA
*
26355 TTACTGGAATTTGAA
1 TT-CTGGAAATTGAA
* * *
26370 TTTTGAAAAATGAA
1 TTCTGGAAATTGAA
26384 TT
1 TT
26386 ACATTTCTGG
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
14 25 0.68
15 12 0.32
ACGTcount: A:0.39, C:0.05, G:0.19, T:0.37
Consensus pattern (14 bp):
TTCTGGAAATTGAA
Found at i:26371 original size:29 final size:29
Alignment explanation
Indices: 26329--26387 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
26319 AATTAGTTTT
*
26329 CTGGAAATTGAATTCTGGAAAATGAATTA
1 CTGGAAATTGAATTCTGAAAAATGAATTA
* *
26358 CTGGAATTTGAATTTTGAAAAATGAATTA
1 CTGGAAATTGAATTCTGAAAAATGAATTA
26387 C
1 C
26388 ATTTCTGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.41, C:0.07, G:0.19, T:0.34
Consensus pattern (29 bp):
CTGGAAATTGAATTCTGAAAAATGAATTA
Found at i:26711 original size:92 final size:86
Alignment explanation
Indices: 26591--26762 Score: 195
Period size: 92 Copynumber: 1.9 Consensus size: 86
26581 TTCTTATTTT
* * * *
26591 TAAAATATTAAAATAATTTATTTATTATTAAA-TATTATTTTTATAATTTTATTA-ATAAAAATA
1 TAAAATATTAAAATAATTTAATTATTATTAAAGTAATAGTTTTAT-ATTATATTATA-AAAAATA
*
26654 TTAATATTGGTATATTTTATTCAAA
64 TT-A-ATTAGTATATTTTATTCAAA
* *
26679 TAAATATATTATAAATTATATTAATTATTTATTAAAGTAATAGTTTTATATTATATTTTAAAAAA
1 TAAA-ATATTA-AAATAAT-TTAATTA-TTATTAAAGTAATAGTTTTATATTATATTATAAAAAA
26744 TATTAATTAGTATATTTTA
62 TATTAATTAGTATATTTTA
26763 AATATCTTTA
Statistics
Matches: 71, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
88 4 0.06
89 6 0.08
90 19 0.27
91 7 0.10
92 24 0.34
93 11 0.15
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (86 bp):
TAAAATATTAAAATAATTTAATTATTATTAAAGTAATAGTTTTATATTATATTATAAAAAATATT
AATTAGTATATTTTATTCAAA
Found at i:26807 original size:30 final size:30
Alignment explanation
Indices: 26770--26899 Score: 121
Period size: 30 Copynumber: 4.4 Consensus size: 30
26760 TTAAATATCT
*
26770 TTATTAAA-ATATTAATAGATTATTATATTA
1 TTATTAAATATATAAATA-ATTATTATATTA
* *
26800 ATATTAAATATATAAATAA-TATTAT-TCA
1 TTATTAAATATATAAATAATTATTATATTA
26828 TTATTAAATATATAAATAATTTATTATA-TA
1 TTATTAAATATATAAATAA-TTATTATATTA
* *
26858 TTATTAAA-ATAAAAAT-A-TAATATAATTGA
1 TTATTAAATATATAAATAATTATTAT-ATT-A
26887 TTATTATAATATA
1 TTATTA-AATATA
26900 ATTGTTTATT
Statistics
Matches: 84, Mismatches: 7, Indels: 17
0.78 0.06 0.16
Matches are distributed among these distances:
26 5 0.06
27 1 0.01
28 22 0.26
29 20 0.24
30 25 0.30
31 11 0.13
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.46
Consensus pattern (30 bp):
TTATTAAATATATAAATAATTATTATATTA
Found at i:26821 original size:24 final size:26
Alignment explanation
Indices: 26794--26874 Score: 78
Period size: 28 Copynumber: 3.0 Consensus size: 26
26784 ATAGATTATT
26794 ATATTA-A-TATTAAATATATAAATA
1 ATATTATATTATTAAATATATAAATA
26818 ATATTATTCATTATTAAATATATAAATA
1 ATATTA-T-ATTATTAAATATATAAATA
*
26846 ATTTATTATATATTATTAAA-ATAAAAATA
1 A--TA-T-TATATTATTAAATATATAAATA
26875 TAATATAATT
Statistics
Matches: 48, Mismatches: 1, Indels: 11
0.80 0.02 0.18
Matches are distributed among these distances:
24 6 0.12
27 1 0.02
28 18 0.38
29 8 0.17
30 11 0.23
31 2 0.04
32 2 0.04
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (26 bp):
ATATTATATTATTAAATATATAAATA
Found at i:26878 original size:59 final size:59
Alignment explanation
Indices: 26770--26899 Score: 151
Period size: 59 Copynumber: 2.2 Consensus size: 59
26760 TTAAATATCT
* * *
26770 TTATTAAA-ATATTAATAGATTATTATATTAATATTAAATATATAAATAATATTATTCA
1 TTATTAAATATATAAATAGATTATTATATTAATATTAAATATAAAAATAATATAATTCA
* *
26828 TTATTAAATATATAAATA-ATTTATTATA-TATTATTAAA-ATAAAAATATAATATAATTGA
1 TTATTAAATATATAAATAGA-TTATTATATTAATATTAAATAT-AAAA-ATAATATAATTCA
26887 TTATTATAATATA
1 TTATTA-AATATA
26900 ATTGTTTATT
Statistics
Matches: 62, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
57 2 0.03
58 21 0.34
59 33 0.53
60 6 0.10
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.46
Consensus pattern (59 bp):
TTATTAAATATATAAATAGATTATTATATTAATATTAAATATAAAAATAATATAATTCA
Found at i:26896 original size:18 final size:18
Alignment explanation
Indices: 26873--26919 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
26863 AAAATAAAAA
26873 TATAATATAATTGATTAT
1 TATAATATAATTGATTAT
*
26891 TATAATATAATTGTTTAT
1 TATAATATAATTGATTAT
* *
26909 TTTAGTATAAT
1 TATAATATAAT
26920 ATTAAAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.53
Consensus pattern (18 bp):
TATAATATAATTGATTAT
Found at i:26981 original size:23 final size:25
Alignment explanation
Indices: 26952--27002 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
26942 ATTAGAAATA
26952 TTAATAAAT-ATATTTT-AAATATT
1 TTAATAAATAATATTTTAAAATATT
*
26975 TTAATAATTAATATTTTAAAATATT
1 TTAATAAATAATATTTTAAAATATT
27000 TTA
1 TTA
27003 TTAATATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 8 0.32
24 7 0.28
25 10 0.40
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (25 bp):
TTAATAAATAATATTTTAAAATATT
Found at i:27248 original size:42 final size:42
Alignment explanation
Indices: 27183--27264 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
27173 AAACTCTAGA
* * *
27183 AAAACATTTTTCGGGAAACGAATTACGTGAAACAAACACGGG
1 AAAACATTTTCCGGAAAACGAATTACATGAAACAAACACGGG
*
27225 AAAACATTTTCCGGAAAATGAATTACATGAAACAAACACG
1 AAAACATTTTCCGGAAAACGAATTACATGAAACAAACACG
27265 AGATTTCGGG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.46, C:0.17, G:0.17, T:0.20
Consensus pattern (42 bp):
AAAACATTTTCCGGAAAACGAATTACATGAAACAAACACGGG
Found at i:28060 original size:23 final size:23
Alignment explanation
Indices: 28033--28088 Score: 112
Period size: 23 Copynumber: 2.4 Consensus size: 23
28023 TCAAGTTCAA
28033 AGTTAAGTTTGAGGCTTCAATCG
1 AGTTAAGTTTGAGGCTTCAATCG
28056 AGTTAAGTTTGAGGCTTCAATCG
1 AGTTAAGTTTGAGGCTTCAATCG
28079 AGTTAAGTTT
1 AGTTAAGTTT
28089 AAGATTATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.27, C:0.11, G:0.25, T:0.38
Consensus pattern (23 bp):
AGTTAAGTTTGAGGCTTCAATCG
Found at i:39124 original size:21 final size:20
Alignment explanation
Indices: 39100--39154 Score: 78
Period size: 19 Copynumber: 2.8 Consensus size: 20
39090 TGTCACAATC
39100 AATTAACCATTTCGTCACGAG
1 AATTAA-CATTTCGTCACGAG
39121 AATT-ACATTTCGTCACGAG
1 AATTAACATTTCGTCACGAG
*
39140 AATT-ACATTTTGTCA
1 AATTAACATTTCGTCA
39155 TAACTAACTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
19 28 0.85
20 1 0.03
21 4 0.12
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.35
Consensus pattern (20 bp):
AATTAACATTTCGTCACGAG
Found at i:39131 original size:19 final size:19
Alignment explanation
Indices: 39107--39154 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
39097 ATCAATTAAC
39107 CATTTCGTCACGAGAATTA
1 CATTTCGTCACGAGAATTA
39126 CATTTCGTCACGAGAATTA
1 CATTTCGTCACGAGAATTA
*
39145 CATTTTGTCA
1 CATTTCGTCA
39155 TAACTAACTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (19 bp):
CATTTCGTCACGAGAATTA
Found at i:39589 original size:31 final size:33
Alignment explanation
Indices: 39519--39589 Score: 83
Period size: 31 Copynumber: 2.2 Consensus size: 33
39509 TTATAAATGA
* *
39519 GAAATTAATATTTGTTACAAATTGTTATTTTGAT
1 GAAA-TAATATTTGTCACAAATTGTTATTTTGAC
* *
39553 TAAATAA-ATTTGTCAC-AATTTTTATTTTGAC
1 GAAATAATATTTGTCACAAATTGTTATTTTGAC
39584 GAAATA
1 GAAATA
39590 TGGAGACGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
31 18 0.56
32 8 0.25
33 3 0.09
34 3 0.09
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.46
Consensus pattern (33 bp):
GAAATAATATTTGTCACAAATTGTTATTTTGAC
Found at i:39761 original size:97 final size:95
Alignment explanation
Indices: 39640--39941 Score: 268
Period size: 97 Copynumber: 3.2 Consensus size: 95
39630 AAATTTAACG
* * * * *
39640 TGTTATTGTGAATAAATCATTTTGTTACAATTTGTTATTGTGAAAGAATATTACTTGTCACAATT
1 TGTTATTGTGACTAAATAAATTTGTTACAATTTGTTATTATGAAAGAATATTATTTGTCACAATT
39705 CTTTATGATGAGAAATTAATATTTATATAAAT
66 -TTTAT-ATGAGAAATTAATATTTATATAAAT
* * * * * * * * *
39737 TATTATTTTGATTAAATAAATTTGTCAGAATTTTTTATTTTGACAA-AATA-AATTTGACACAAA
1 TGTTATTGTGACTAAATAAATTTGTTACAATTTGTTATTATGA-AAGAATATTATTTGTCAC-AA
**
39800 TTTTTAT-TTTG-AA-TAA-ATTTAT-T--A-
64 TTTTTATATGAGAAATTAATATTTATATAAAT
* * *
39824 CGTTATTGTAACTAAATAAATTTGTTACAATTTGTTATTATGAAAGAATATT-TTTGTCATAATT
1 TGTTATTGTGACTAAATAAATTTGTTACAATTTGTTATTATGAAAGAATATTATTTGTCACAA-T
39888 TTTTATATTGAGAAATTAATAATTGT-TATAAAT
65 TTTTATA-TGAGAAATTAAT-ATT-TATATAAAT
*
39921 TGTTATTATGACTAAATAAAT
1 TGTTATTGTGACTAAATAAAT
39942 ATCGAAATCC
Statistics
Matches: 158, Mismatches: 31, Indels: 32
0.71 0.14 0.14
Matches are distributed among these distances:
86 4 0.03
87 51 0.32
88 1 0.01
89 2 0.01
90 3 0.02
91 9 0.06
92 3 0.02
93 6 0.04
94 4 0.03
96 13 0.08
97 60 0.38
98 2 0.01
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.47
Consensus pattern (95 bp):
TGTTATTGTGACTAAATAAATTTGTTACAATTTGTTATTATGAAAGAATATTATTTGTCACAATT
TTTATATGAGAAATTAATATTTATATAAAT
Found at i:39775 original size:32 final size:32
Alignment explanation
Indices: 39733--39817 Score: 109
Period size: 32 Copynumber: 2.7 Consensus size: 32
39723 ATATTTATAT
* * * *
39733 AAATTATTATTTTGATTAAATAAATTTGTCAG
1 AAATTTTTATTTTGAATAAATAAATTTGACAC
*
39765 AATTTTTTATTTTGACA-AAATAAATTTGACAC
1 AAATTTTTATTTTGA-ATAAATAAATTTGACAC
39797 AAATTTTTATTTTGAATAAAT
1 AAATTTTTATTTTGAATAAAT
39818 TTATTACGTT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
31 1 0.02
32 44 0.98
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.47
Consensus pattern (32 bp):
AAATTTTTATTTTGAATAAATAAATTTGACAC
Found at i:39851 original size:184 final size:183
Alignment explanation
Indices: 39598--39941 Score: 464
Period size: 184 Copynumber: 1.9 Consensus size: 183
39588 TATGGAGACG
* * * * *
39598 AAATAAATTTGACATAACTGTTTACTTTGACTAAATTTAACGTGTTATTGTGAATAAATCATTTT
1 AAATAAATTTGACACAAATGTTTACTTTGAATAAATTTAACG-GTTATTGTGAATAAATAAATTT
*
39663 GTTACAATTTGTTATTGTGAAAGAATATTACTTGTCACAATTCTTTATGA-TGAGAAATTAAT-A
65 GTTACAATTTGTTATTATGAAAGAATATT-CTTGTCACAATTCTTTAT-ATTGAGAAATTAATAA
* *
39726 TT-TATATAAATTATTATTTTGATTAAATAAATTTGTCAGAATTTTTTATTTTGACA
128 TTGT-TATAAATTATTATTATGACTAAATAAATTTGTCAGAATTTTTTATTTTGACA
* *
39782 AAATAAATTTGACACAAATTTTTATTTTGAATAAATTTATTAC-GTTATTGT-AACTAAATAAAT
1 AAATAAATTTGACACAAATGTTTACTTTGAATAAATTTA--ACGGTTATTGTGAA-TAAATAAAT
* * *
39845 TTGTTACAATTTGTTATTATGAAAGAATATTTTTGTCATAATTTTTTATATTGAGAAATTAATAA
63 TTGTTACAATTTGTTATTATGAAAGAATATTCTTGTCACAATTCTTTATATTGAGAAATTAATAA
*
39910 TTGTTATAAATTGTTATTATGACTAAATAAAT
128 TTGTTATAAATTATTATTATGACTAAATAAAT
39942 ATCGAAATCC
Statistics
Matches: 140, Mismatches: 14, Indels: 12
0.84 0.08 0.07
Matches are distributed among these distances:
182 1 0.01
183 29 0.21
184 107 0.76
185 1 0.01
186 2 0.01
ACGTcount: A:0.38, C:0.06, G:0.10, T:0.46
Consensus pattern (183 bp):
AAATAAATTTGACACAAATGTTTACTTTGAATAAATTTAACGGTTATTGTGAATAAATAAATTTG
TTACAATTTGTTATTATGAAAGAATATTCTTGTCACAATTCTTTATATTGAGAAATTAATAATTG
TTATAAATTATTATTATGACTAAATAAATTTGTCAGAATTTTTTATTTTGACA
Found at i:41836 original size:3 final size:3
Alignment explanation
Indices: 41828--41853 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
41818 TTTTCTTAAG
41828 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
41854 TAAAGCATAA
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:49439 original size:21 final size:20
Alignment explanation
Indices: 49400--49441 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
49390 TGATGTTTAG
*
49400 TATATATATATAAT-ATATA
1 TATATATATATAATGTTATA
49419 TATATATATATATATGTTATA
1 TATATATATATA-ATGTTATA
49440 TA
1 TA
49442 GTTAAATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 12 0.60
20 2 0.10
21 6 0.30
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
TATATATATATAATGTTATA
Found at i:49441 original size:2 final size:2
Alignment explanation
Indices: 49400--49433 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
49390 TGATGTTTAG
49400 TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
49434 GTTATATAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:52347 original size:24 final size:23
Alignment explanation
Indices: 52280--52361 Score: 56
Period size: 24 Copynumber: 3.4 Consensus size: 23
52270 TTTAAATATT
* *
52280 TAATTATTATTAAATCATTATTAG
1 TAATCATTA-TAAATCATTATTAC
* * * *
52304 TACTTATTATAATTTTATTATTAC
1 TAATCATTATAA-ATCATTATTAC
*
52328 TAATCATTACTAAATCATTAGTATC
1 TAATCATTA-TAAATCATTATTA-C
*
52353 AAATCATTA
1 TAATCATTA
52362 AATATTAGTA
Statistics
Matches: 45, Mismatches: 10, Indels: 5
0.75 0.17 0.08
Matches are distributed among these distances:
23 3 0.07
24 30 0.67
25 12 0.27
ACGTcount: A:0.40, C:0.10, G:0.02, T:0.48
Consensus pattern (23 bp):
TAATCATTATAAATCATTATTAC
Found at i:52369 original size:21 final size:22
Alignment explanation
Indices: 52338--52382 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
52328 TAATCATTAC
**
52338 TAAATCATTAGTATCAAATCAT
1 TAAATCATTAGTAAAAAATCAT
52360 TAAAT-ATTAGTAAAAAATCAT
1 TAAATCATTAGTAAAAAATCAT
52381 TA
1 TA
52383 TTAGTAATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.36
Consensus pattern (22 bp):
TAAATCATTAGTAAAAAATCAT
Found at i:52418 original size:15 final size:15
Alignment explanation
Indices: 52398--52426 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
52388 AATCATTACT
52398 AAATCATTAAATATC
1 AAATCATTAAATATC
52413 AAATCATTAAATAT
1 AAATCATTAAATAT
52427 TAATAATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (15 bp):
AAATCATTAAATATC
Found at i:52530 original size:21 final size:22
Alignment explanation
Indices: 52488--52530 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
52478 AATTCGATTT
* *
52488 GATAAAATCGATTAACATATTA
1 GATAAAATCGATTAAAAAATTA
52510 GATAAAAT-GATTAAAAAATTA
1 GATAAAATCGATTAAAAAATTA
52531 CCAATAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.56, C:0.05, G:0.09, T:0.30
Consensus pattern (22 bp):
GATAAAATCGATTAAAAAATTA
Found at i:57213 original size:9 final size:9
Alignment explanation
Indices: 57199--57231 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
57189 AGTAGGTTCT
57199 GGAGGAGGG
1 GGAGGAGGG
57208 GGAGGAGGG
1 GGAGGAGGG
*
57217 GGAGGAGGA
1 GGAGGAGGG
57226 GGAGGA
1 GGAGGA
57232 ACTGCACTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.27, C:0.00, G:0.73, T:0.00
Consensus pattern (9 bp):
GGAGGAGGG
Found at i:59682 original size:28 final size:27
Alignment explanation
Indices: 59626--59682 Score: 69
Period size: 28 Copynumber: 2.1 Consensus size: 27
59616 AAAGTTATCT
* *
59626 TTTTAGTTCAAATAGGTACCTAGATTA
1 TTTTAGTTCAAATAGGTACCTAAACTA
* *
59653 TTTTATTTCAAAATAGGTACTTAAACTA
1 TTTTAGTTC-AAATAGGTACCTAAACTA
59681 TT
1 TT
59683 CAATTTTTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 8 0.32
28 17 0.68
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.44
Consensus pattern (27 bp):
TTTTAGTTCAAATAGGTACCTAAACTA
Found at i:59866 original size:31 final size:29
Alignment explanation
Indices: 59764--59895 Score: 194
Period size: 29 Copynumber: 4.5 Consensus size: 29
59754 AAAAGAAATT
* *
59764 AAATGCTTTAGGTACATATTTTGATCAAA
1 AAATACTTTAGGTACCTATTTTGATCAAA
59793 AAATACTTTAGGTACCTATTTTGATCAAA
1 AAATACTTTAGGTACCTATTTTGATCAAA
*
59822 AAAGACTTTAGGTACCTATTTTGATCAAA
1 AAATACTTTAGGTACCTATTTTGATCAAA
* *
59851 AATATACTTTTAGGTACTTATTTTGA-CCAA
1 AA-ATAC-TTTAGGTACCTATTTTGATCAAA
59881 AAATACTTTAGGTAC
1 AAATACTTTAGGTAC
59896 TTAAATGAAA
Statistics
Matches: 95, Mismatches: 6, Indels: 5
0.90 0.06 0.05
Matches are distributed among these distances:
28 9 0.09
29 61 0.64
30 8 0.08
31 17 0.18
ACGTcount: A:0.37, C:0.13, G:0.12, T:0.38
Consensus pattern (29 bp):
AAATACTTTAGGTACCTATTTTGATCAAA
Found at i:61185 original size:79 final size:81
Alignment explanation
Indices: 61026--61186 Score: 206
Period size: 79 Copynumber: 2.0 Consensus size: 81
61016 AATAAAAATA
* * * * *
61026 TTAACATTTTCAGTAAAGCGTTACCTAAAATATTATTTTTTTTCTACCGAAAATGTTAATATTGT
1 TTAACATTTTCAGTAAAGCGCTACCTAAAACATTATTTTTTTTCTACAGAAAATATTAATATTGG
*
61091 GCGCTACCTATAATGT
66 GCGCTACCTAAAATGT
61107 TTAACA-TTTCAGGTAAA-CGCTACCTAAAACATTA-TTTTTTTCTACA-AGAAATATTAATATT
1 TTAACATTTTCA-GTAAAGCGCTACCTAAAACATTATTTTTTTTCTACAGA-AAATATTAATATT
61168 GGGCG-TCACCTAAAATGT
64 GGGCGCT-ACCTAAAATGT
61186 T
1 T
61187 ATTTTTCTAC
Statistics
Matches: 71, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
78 2 0.03
79 38 0.54
80 20 0.28
81 11 0.15
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (81 bp):
TTAACATTTTCAGTAAAGCGCTACCTAAAACATTATTTTTTTTCTACAGAAAATATTAATATTGG
GCGCTACCTAAAATGT
Found at i:65235 original size:28 final size:27
Alignment explanation
Indices: 65186--65243 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 27
65176 CCTAAACTCT
* *
65186 TTTTAGTCAAAATAGATTCTTAAAGTA
1 TTTTAGTCAAAATAGATACTTAAACTA
65213 TTTTATGTCAAAATATG-TACTTAAACTA
1 TTTTA-GTCAAAATA-GATACTTAAACTA
65241 TTT
1 TTT
65244 GAATTTTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 5 0.19
28 21 0.78
29 1 0.04
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.45
Consensus pattern (27 bp):
TTTTAGTCAAAATAGATACTTAAACTA
Found at i:65363 original size:29 final size:30
Alignment explanation
Indices: 65300--65366 Score: 118
Period size: 29 Copynumber: 2.3 Consensus size: 30
65290 TAAAGAATAA
65300 TTTAGGTATTTAGATTAAAAAATTGAAAAC
1 TTTAGGTATTTAGATTAAAAAATTGAAAAC
*
65330 TTTAGGTATTTAGATT-AAAGATTGAAAAC
1 TTTAGGTATTTAGATTAAAAAATTGAAAAC
65359 TTTAGGTA
1 TTTAGGTA
65367 CCTATTTTGA
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
29 20 0.56
30 16 0.44
ACGTcount: A:0.42, C:0.03, G:0.16, T:0.39
Consensus pattern (30 bp):
TTTAGGTATTTAGATTAAAAAATTGAAAAC
Found at i:68758 original size:15 final size:16
Alignment explanation
Indices: 68732--68762 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
68722 TTATAAATAT
68732 AATAATATTTTTAAAA
1 AATAATATTTTTAAAA
68748 AATAA-ATTTTTAAAA
1 AATAATATTTTTAAAA
68763 TACCAGATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AATAATATTTTTAAAA
Found at i:73599 original size:29 final size:29
Alignment explanation
Indices: 73557--73612 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
73547 TGTTTGTCGT
**
73557 AGGTCGCTGGGAGGGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
73586 AGGTCGCCCGGAGGGCATGGCGACCTA
1 AGGTCGCCCGGAGGGCATGGCGACCTA
73613 TGTGTTGGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.20, C:0.27, G:0.41, T:0.12
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCATGGCGACCTACA
Found at i:73722 original size:10 final size:11
Alignment explanation
Indices: 73709--73757 Score: 50
Period size: 10 Copynumber: 4.6 Consensus size: 11
73699 ACACGGTGGG
73709 CATCCGAG-GC
1 CATCCGAGAGC
73719 CATCCGAGAAGC
1 CATCCGAG-AGC
* *
73731 TATGCGAGAG-
1 CATCCGAGAGC
73741 CATCCGAG-GC
1 CATCCGAGAGC
73751 CATCCGA
1 CATCCGA
73758 CCAAGGGCAT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
9 1 0.03
10 21 0.66
11 2 0.06
12 8 0.25
ACGTcount: A:0.27, C:0.33, G:0.29, T:0.12
Consensus pattern (11 bp):
CATCCGAGAGC
Found at i:73788 original size:14 final size:14
Alignment explanation
Indices: 73744--73789 Score: 74
Period size: 14 Copynumber: 3.3 Consensus size: 14
73734 GCGAGAGCAT
73744 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
* *
73758 CCAAGGGCATCCGA
1 CCGAGGCCATCCGA
73772 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
73786 CCGA
1 CCGA
73790 ATTATGTGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.24, C:0.41, G:0.28, T:0.07
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:73903 original size:29 final size:29
Alignment explanation
Indices: 73858--73942 Score: 134
Period size: 29 Copynumber: 2.9 Consensus size: 29
73848 GAGCAAGGGT
73858 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
* * *
73887 AGGTCGCCAGGATTGCATTGCGACCTACA
1 AGGTCGCCCGGAGTGCATGGCGACCTACA
*
73916 AGGTCGCCCGGAGGGCATGGCGACCTA
1 AGGTCGCCCGGAGTGCATGGCGACCTA
73943 TGCTTGGGGA
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.21, C:0.29, G:0.34, T:0.15
Consensus pattern (29 bp):
AGGTCGCCCGGAGTGCATGGCGACCTACA
Found at i:86936 original size:26 final size:26
Alignment explanation
Indices: 86900--86961 Score: 115
Period size: 26 Copynumber: 2.4 Consensus size: 26
86890 CTCGCAAGTT
86900 TTCGAGTCGAGCTCCATTTCAGAGTG
1 TTCGAGTCGAGCTCCATTTCAGAGTG
*
86926 TTCGAGTCGAGCTCCATTTCAGAGTT
1 TTCGAGTCGAGCTCCATTTCAGAGTG
86952 TTCGAGTCGA
1 TTCGAGTCGA
86962 ACTCAGCAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.32
Consensus pattern (26 bp):
TTCGAGTCGAGCTCCATTTCAGAGTG
Found at i:91076 original size:2 final size:2
Alignment explanation
Indices: 91069--91100 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
91059 CATATTCAAA
91069 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
91101 CACATTTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:109792 original size:15 final size:14
Alignment explanation
Indices: 109764--109822 Score: 59
Period size: 15 Copynumber: 4.2 Consensus size: 14
109754 ACTCATTAAT
109764 TTTTAA-TTTTTTA
1 TTTTAATTTTTTTA
109777 TTTTAATTTCTTTTA
1 TTTTAATTT-TTTTA
* **
109792 TTTCAA-TTTTAAA
1 TTTTAATTTTTTTA
109805 TTTTAAATTTTTTTA
1 TTTT-AATTTTTTTA
109820 TTT
1 TTT
109823 GTTTGCTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
13 12 0.33
14 6 0.17
15 18 0.50
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTAATTTTTTTA
Done.