Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-JGI_221_v2.0
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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 43 of 168
Found at i:11882120 original size:20 final size:21
Alignment explanation
Indices: 11882065--11882121 Score: 82
Period size: 20 Copynumber: 2.8 Consensus size: 21
11882055 AGAACCCCGT
11882065 GGTATTAATA-TTTTTAAAAA
1 GGTATTAATATTTTTTAAAAA
*
11882085 GGTATTGATATTTTTTAAAAA
1 GGTATTAATATTTTTTAAAAA
*
11882106 -GTATCAATATTTTTTA
1 GGTATTAATATTTTTTA
11882122 GTTGGTATCG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 23 0.70
21 10 0.30
ACGTcount: A:0.39, C:0.02, G:0.11, T:0.49
Consensus pattern (21 bp):
GGTATTAATATTTTTTAAAAA
Found at i:11888524 original size:29 final size:29
Alignment explanation
Indices: 11888410--11888572 Score: 136
Period size: 29 Copynumber: 5.6 Consensus size: 29
11888400 TCGACTATCG
* *
11888410 ATTATGAAAAGGGATGGTGATGGCAATCA
1 ATTATGAAAAGGGATGGTGATGACCATCA
* *
11888439 ACTATAAAAAGGGATGGTGATGACCAT-A
1 ATTATGAAAAGGGATGGTGATGACCATCA
* * * * **
11888467 GAATA-GAAAAGGTATAGCT--TCAGTTATCA
1 -ATTATGAAAAGGGAT-GGTGATGA-CCATCA
11888496 ATTATGAAAAGGGATGGTGATGACCATCA
1 ATTATGAAAAGGGATGGTGATGACCATCA
* * * *
11888525 ACTAAGGAAAGGGATGGTGACGACCATCA
1 ATTATGAAAAGGGATGGTGATGACCATCA
11888554 ATTAATGAAAAGGGATGGT
1 ATT-ATGAAAAGGGATGGT
11888573 TTCGACCATC
Statistics
Matches: 102, Mismatches: 24, Indels: 15
0.72 0.17 0.11
Matches are distributed among these distances:
27 2 0.02
28 16 0.16
29 69 0.68
30 15 0.15
ACGTcount: A:0.40, C:0.10, G:0.28, T:0.23
Consensus pattern (29 bp):
ATTATGAAAAGGGATGGTGATGACCATCA
Found at i:11888568 original size:30 final size:30
Alignment explanation
Indices: 11888492--11888582 Score: 123
Period size: 29 Copynumber: 3.1 Consensus size: 30
11888482 AGCTTCAGTT
*
11888492 ATCAATT-ATGAAAAGGGATGGTGATGACC
1 ATCAATTAATGAAAAGGGATGGTGACGACC
* *
11888521 ATCAACTAA-GGAAAGGGATGGTGACGACC
1 ATCAATTAATGAAAAGGGATGGTGACGACC
**
11888550 ATCAATTAATGAAAAGGGATGGTTTCGACC
1 ATCAATTAATGAAAAGGGATGGTGACGACC
11888580 ATC
1 ATC
11888583 GACTATGAAA
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
29 32 0.60
30 21 0.40
ACGTcount: A:0.37, C:0.14, G:0.26, T:0.22
Consensus pattern (30 bp):
ATCAATTAATGAAAAGGGATGGTGACGACC
Found at i:11888591 original size:29 final size:29
Alignment explanation
Indices: 11888346--11888593 Score: 119
Period size: 29 Copynumber: 8.5 Consensus size: 29
11888336 AATCAATGAT
* * *
11888346 CATCGATTAATGAAAAAGGATAGCTTCGAC
1 CATCGATT-ATGAAAAGGGATGGTTTCGAC
* * * *
11888376 TATCGAATAGGAAAAGGGATAGTTTCGAC
1 CATCGATTATGAAAAGGGATGGTTTCGAC
* * *
11888405 TATCGATTATGAAAAGGGATGGTGAT-GGC
1 CATCGATTATGAAAAGGGATGGT-TTCGAC
* * * * *
11888434 AATCAACTATAAAAAGGGATGGTGAT-GAC
1 CATCGATTATGAAAAGGGATGGT-TTCGAC
* * * * * *
11888463 CATAGAATA-GAAAAGGTATAGCTTC-AGT
1 CATCGATTATGAAAAGGGATGGTTTCGA-C
* * *
11888491 TATCAATTATGAAAAGGGATGGTGAT-GAC
1 CATCGATTATGAAAAGGGATGGT-TTCGAC
* * * * **
11888520 CATCAACTAAGGAAAGGGATGGTGACGAC
1 CATCGATTATGAAAAGGGATGGTTTCGAC
*
11888549 CATCAATTAATGAAAAGGGATGGTTTCGAC
1 CATCGATT-ATGAAAAGGGATGGTTTCGAC
*
11888579 CATCGACTATGAAAA
1 CATCGATTATGAAAA
11888594 TGAACTATAA
Statistics
Matches: 163, Mismatches: 47, Indels: 17
0.72 0.21 0.07
Matches are distributed among these distances:
27 2 0.01
28 14 0.09
29 115 0.71
30 32 0.20
ACGTcount: A:0.39, C:0.12, G:0.25, T:0.23
Consensus pattern (29 bp):
CATCGATTATGAAAAGGGATGGTTTCGAC
Found at i:11893094 original size:51 final size:50
Alignment explanation
Indices: 11892911--11893444 Score: 429
Period size: 51 Copynumber: 10.5 Consensus size: 50
11892901 TTCGACACAT
* * *
11892911 GTAGTAGCCTTCACATAGTACTATACACGTGATAAAG-TTTTACGGTTCAC
1 GTAGTAGCCTTCACATAGTACTACACACGTGACAAAGCTTCT-CGGTTCAC
*
11892961 GTAGTAGCCTTCACATAGTACTACACACGTGATC-AAG-TTTTACGGTTCAC
1 GTAGTAGCCTTCACATAGTACTACACACGTGA-CAAAGCTTCT-CGGTTCAC
* * *
11893011 ATAGCAGCCTTCACATAGTACTACACACGTGACGAAAGCCTT-TCGGTACAC
1 GTAGTAGCCTTCACATAGTACTACACACGTGAC-AAAG-CTTCTCGGTTCAC
* * * * * *
11893062 GTAGTAGCCTTCACTTAGTACTACACATGTGAC-CATCATT-TATGATTCAC
1 GTAGTAGCCTTCACATAGTACTACACACGTGACAAAGC-TTCT-CGGTTCAC
* * *
11893112 GTAGTAGCCTTCACATAGTACTACACACGTGACCAAATCTTCTTGGTACAC
1 GTAGTAGCCTTCACATAGTACTACACACGTGA-CAAAGCTTCTCGGTTCAC
* * * * * * * * *
11893163 ATTGTAGCTTTCACTTAGTACTACACATGTGACCATCA-TTTATCGATTCAC
1 GTAGTAGCCTTCACATAGTACTACACACGTGA-CA-AAGCTTCTCGGTTCAC
* *
11893214 GTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTCGGTACAC
1 GTAGTAGCCTTCACATAGTACTACACACGTGA-CAAAGCTTCTCGGTTCAC
* * * * * * * *
11893265 ATTGTAGCCTTCACTTAGTACTACACATGTGACCATCA-TTTATCGATTCAC
1 GTAGTAGCCTTCACATAGTACTACACACGTGA-CA-AAGCTTCTCGGTTCAC
* * *
11893316 GTAGTAGCCTTCACAGAGTACTACACACGTGACCAAAGCTTCTCGGTACTC
1 GTAGTAGCCTTCACATAGTACTACACACGTGA-CAAAGCTTCTCGGTTCAC
* * * * * * * *
11893367 ATTGTAGCCTTCACTTAGTACTACACATGTGACCATCA-TTTATCGATTCAC
1 GTAGTAGCCTTCACATAGTACTACACACGTGA-CA-AAGCTTCTCGGTTCAC
* *
11893418 GTAGTAGCCTTCACACAGTATTACACA
1 GTAGTAGCCTTCACATAGTACTACACA
11893445 AGTGTTCATC
Statistics
Matches: 391, Mismatches: 78, Indels: 29
0.79 0.16 0.06
Matches are distributed among these distances:
48 1 0.00
49 5 0.01
50 114 0.29
51 261 0.67
52 8 0.02
53 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.30
Consensus pattern (50 bp):
GTAGTAGCCTTCACATAGTACTACACACGTGACAAAGCTTCTCGGTTCAC
Found at i:11893256 original size:102 final size:102
Alignment explanation
Indices: 11892911--11893444 Score: 781
Period size: 102 Copynumber: 5.3 Consensus size: 102
11892901 TTCGACACAT
* * * * * *
11892911 GTAGTAGCCTTCACATAGTACTATACACGTGA-TAAAG-TTTTACGGTTCACGTAGTAGCCTTCA
1 GTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTCT-CGGTACACATTGTAGCCTTCA
* * * *** *
11892974 CATAGTACTACACACGTGATCAAGTTTTA-CGGTTCAC
65 CTTAGTACTACACATGTGACCATCATTTATCGATTCAC
* * * * *
11893011 ATAGCAGCCTTCACATAGTACTACACACGTGACGAAAGCCTT-TCGGTACACGTAGTAGCCTTCA
1 GTAGTAGCCTTCACATAGTACTACACACGTGACCAAAG-CTTCTCGGTACACATTGTAGCCTTCA
11893075 CTTAGTACTACACATGTGACCATCATTTAT-GATTCAC
65 CTTAGTACTACACATGTGACCATCATTTATCGATTCAC
* * *
11893112 GTAGTAGCCTTCACATAGTACTACACACGTGACCAAATCTTCTTGGTACACATTGTAGCTTTCAC
1 GTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTCTCGGTACACATTGTAGCCTTCAC
11893177 TTAGTACTACACATGTGACCATCATTTATCGATTCAC
66 TTAGTACTACACATGTGACCATCATTTATCGATTCAC
*
11893214 GTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCTCGGTACACATTGTAGCCTTCAC
1 GTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTCTCGGTACACATTGTAGCCTTCAC
11893279 TTAGTACTACACATGTGACCATCATTTATCGATTCAC
66 TTAGTACTACACATGTGACCATCATTTATCGATTCAC
* *
11893316 GTAGTAGCCTTCACAGAGTACTACACACGTGACCAAAGCTTCTCGGTACTCATTGTAGCCTTCAC
1 GTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTCTCGGTACACATTGTAGCCTTCAC
11893381 TTAGTACTACACATGTGACCATCATTTATCGATTCAC
66 TTAGTACTACACATGTGACCATCATTTATCGATTCAC
* *
11893418 GTAGTAGCCTTCACACAGTATTACACA
1 GTAGTAGCCTTCACATAGTACTACACA
11893445 AGTGTTCATC
Statistics
Matches: 400, Mismatches: 28, Indels: 10
0.91 0.06 0.02
Matches are distributed among these distances:
100 32 0.08
101 135 0.34
102 231 0.58
103 2 0.00
ACGTcount: A:0.29, C:0.26, G:0.16, T:0.30
Consensus pattern (102 bp):
GTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTTCTCGGTACACATTGTAGCCTTCAC
TTAGTACTACACATGTGACCATCATTTATCGATTCAC
Found at i:11901070 original size:51 final size:53
Alignment explanation
Indices: 11900901--11901331 Score: 418
Period size: 51 Copynumber: 8.5 Consensus size: 53
11900891 CAATACACGC
* * *
11900901 AGTAGCCTTCACATAGTACTACACACGTTATCAAGT-TTTAT-GGTTCAC-GT
1 AGTAGCCTTCACATAGTACTACACACGTGACCAAATCTTTATCGGTTCACAGT
* * *
11900951 AGCAGCCTTCACATAGTACTACACACGTGATCAAGT-TTTA-CGGTTCACA-T
1 AGTAGCCTTCACATAGTACTACACACGTGACCAAATCTTTATCGGTTCACAGT
* *
11901001 AGTAGCCTTCACAGAGTACTACACACGTGACCAAATCTTT-TCGGTACACAG-
1 AGTAGCCTTCACATAGTACTACACACGTGACCAAATCTTTATCGGTTCACAGT
* * *
11901052 AGTAGCCTTCACTTAGTACTACACATGTGACC--ATCATTTATCGATTCA-AGT
1 AGTAGCCTTCACATAGTACTACACACGTGACCAAATC-TTTATCGGTTCACAGT
* * * * *
11901103 AGTAGCCTTCACACAGTACTACACACCTGACCAAAGCTTT-TTGGTACACA-T
1 AGTAGCCTTCACATAGTACTACACACGTGACCAAATCTTTATCGGTTCACAGT
* * * *
11901154 TGTAGCCTTCACTTAGTACTACACATGTGACC--ATCATTTATCGATTCAC-GT
1 AGTAGCCTTCACATAGTACTACACACGTGACCAAATC-TTTATCGGTTCACAGT
* * * * *
11901205 AGTAGCCTTCACACAGTACTACACACATGACCAAAGC-TTCTCGGTACACA-T
1 AGTAGCCTTCACATAGTACTACACACGTGACCAAATCTTTATCGGTTCACAGT
* * * *
11901256 TGTAGCCTTCACTTAGTACTACACATGTGACC--ATCATTTATCGATTCAC-GT
1 AGTAGCCTTCACATAGTACTACACACGTGACCAAATC-TTTATCGGTTCACAGT
*
11901307 AGTAGCCTTCACACAGTACTACACA
1 AGTAGCCTTCACATAGTACTACACA
11901332 AGTGTTCATC
Statistics
Matches: 311, Mismatches: 50, Indels: 39
0.78 0.12 0.10
Matches are distributed among these distances:
49 7 0.02
50 86 0.28
51 210 0.68
52 4 0.01
53 4 0.01
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.29
Consensus pattern (53 bp):
AGTAGCCTTCACATAGTACTACACACGTGACCAAATCTTTATCGGTTCACAGT
Found at i:11901123 original size:102 final size:102
Alignment explanation
Indices: 11900901--11901331 Score: 575
Period size: 102 Copynumber: 4.2 Consensus size: 102
11900891 CAATACACGC
* * * * * *
11900901 AGTAGCCTTCACATAGTACTACACACGTTATC-AAG-TTTTATGGTTCAC-GTAGCAGCCTTCAC
1 AGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTT-CGGTACACAG-AGTAGCCTTCAC
* * * *** *
11900963 ATAGTACTACACACGTGATCAAGTTTTA-CGGTTCACA-T
64 TTAGTACTACACATGTGACCATCATTTATCGATTCA-AGT
* *
11901001 AGTAGCCTTCACAGAGTACTACACACGTGACCAAATCTTTTCGGTACACAGAGTAGCCTTCACTT
1 AGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGGTACACAGAGTAGCCTTCACTT
11901066 AGTACTACACATGTGACCATCATTTATCGATTCAAGT
66 AGTACTACACATGTGACCATCATTTATCGATTCAAGT
* * **
11901103 AGTAGCCTTCACACAGTACTACACACCTGACCAAAGCTTTTTGGTACACATTGTAGCCTTCACTT
1 AGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGGTACACAGAGTAGCCTTCACTT
*
11901168 AGTACTACACATGTGACCATCATTTATCGATTCACGT
66 AGTACTACACATGTGACCATCATTTATCGATTCAAGT
* * **
11901205 AGTAGCCTTCACACAGTACTACACACATGACCAAAGCTTCTCGGTACACATTGTAGCCTTCACTT
1 AGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGGTACACAGAGTAGCCTTCACTT
*
11901270 AGTACTACACATGTGACCATCATTTATCGATTCACGT
66 AGTACTACACATGTGACCATCATTTATCGATTCAAGT
11901307 AGTAGCCTTCACACAGTACTACACA
1 AGTAGCCTTCACACAGTACTACACA
11901332 AGTGTTCATC
Statistics
Matches: 302, Mismatches: 24, Indels: 8
0.90 0.07 0.02
Matches are distributed among these distances:
100 29 0.10
101 42 0.14
102 231 0.76
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.29
Consensus pattern (102 bp):
AGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTTTCGGTACACAGAGTAGCCTTCACTT
AGTACTACACATGTGACCATCATTTATCGATTCAAGT
Found at i:11924532 original size:6 final size:6
Alignment explanation
Indices: 11924514--11924555 Score: 66
Period size: 6 Copynumber: 6.8 Consensus size: 6
11924504 GCAAATGAAT
*
11924514 CATTTC TCATTTC CATTTC TATTTC CATTTC CATTTC CATTT
1 CATTTC -CATTTC CATTTC CATTTC CATTTC CATTTC CATTT
11924556 TGAGCAACTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
6 27 0.82
7 6 0.18
ACGTcount: A:0.17, C:0.29, G:0.00, T:0.55
Consensus pattern (6 bp):
CATTTC
Found at i:11929245 original size:24 final size:25
Alignment explanation
Indices: 11929202--11929249 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
11929192 ATAGAATTTT
11929202 AATTTTAGGATATATATTATTTTAA
1 AATTTTAGGATATATATTATTTTAA
* *
11929227 AATTTTAGTA-ATATGTTATTTTA
1 AATTTTAGGATATATATTATTTTA
11929250 GTAATCTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.54
Consensus pattern (25 bp):
AATTTTAGGATATATATTATTTTAA
Found at i:11929795 original size:19 final size:18
Alignment explanation
Indices: 11929767--11929832 Score: 60
Period size: 20 Copynumber: 3.4 Consensus size: 18
11929757 AACATGATTT
*
11929767 TTATATAATTATAAAAAA
1 TTATAAAATTATAAAAAA
*
11929785 TGTATAAAATTACTCAAAAA
1 T-TATAAAATTA-TAAAAAA
*
11929805 TTATTAAAAATTATAAGAAA
1 TTA-T-AAAATTATAAAAAA
11929825 TTAATAAA
1 TT-ATAAA
11929833 TTAATTAAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
18 1 0.03
19 14 0.36
20 16 0.41
21 8 0.21
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.35
Consensus pattern (18 bp):
TTATAAAATTATAAAAAA
Found at i:11930097 original size:21 final size:20
Alignment explanation
Indices: 11930061--11930105 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
11930051 TGTCTACTGC
*
11930061 AATATGTACCAATTTGAGA-A
1 AATATGTACAAATTTG-GACA
11930081 AATATGTTACAAATTTGGACA
1 AATATG-TACAAATTTGGACA
11930102 AATA
1 AATA
11930106 AATAAAACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.47, C:0.09, G:0.13, T:0.31
Consensus pattern (20 bp):
AATATGTACAAATTTGGACA
Found at i:11930463 original size:3 final size:3
Alignment explanation
Indices: 11930455--11930506 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
11930445 TCTTGATTCT
11930455 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
11930503 TTA T
1 TTA T
11930507 CTATCCAAAC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:11932284 original size:267 final size:269
Alignment explanation
Indices: 11931807--11932338 Score: 908
Period size: 267 Copynumber: 2.0 Consensus size: 269
11931797 TAGTGGCATA
* *
11931807 CCAACATCAGTTTTTAAAGTACAACCATTTAAGGAAGACGTTTGACTATGTCAAAGCATGCGACT
1 CCAACATCAGTCTTTAAAGTACAACCATTTAAGGAAGACATTTGACTATGTCAAAGCATGCGACT
* *
11931872 CACGATGTTGGAACAATGATGATCTCAAGTTTAAGCATCATATGTACAATTATCACTATGAGAAA
66 CACGATGTTGGAACAATGATGATATCAAGTTTAAGCATCATACGTACAATTATCACTATGAGAAA
*
11931937 TGTTATGACTATTACATAATAATACAATAAGCATTCTCAAGGTGGATTAGTCCAGTCTATTGTTC
131 TGTTATGACTATTACATAATAATACAATAAGCATTCTCAAGGTGGATCAGTCCAGTCTATTGTTC
*
11932002 TTTAACATATACTTGTGTTGACTTGATATCACATAT-CTGTAACAACTCTTGTCACCAATCTAGC
196 TTTAACATATACTTGTGTTGACTTGATATCACATATAC-GTAACAACTCTTGTCACCAATCAAGC
11932066 ACATATACAC
260 ACATATACAC
* * *
11932076 CCAACATCAGTCTTTAAAGTACAACCATTTAAGGAAGACATTTGATTGTGTCAAAGCATGTGACT
1 CCAACATCAGTCTTTAAAGTACAACCATTTAAGGAAGACATTTGACTATGTCAAAGCATGCGACT
11932141 CACGATGTTGG-A-AATGATGATATCAAGTTTAAGCATCATACGTACAATTATCACTATGAGAAA
66 CACGATGTTGGAACAATGATGATATCAAGTTTAAGCATCATACGTACAATTATCACTATGAGAAA
* * * * *
11932204 TGTTGTGACTATTACATAATAATCCAATAAGCATTCTCATGGTGGATCAGTCCAGTTTATTTTTC
131 TGTTATGACTATTACATAATAATACAATAAGCATTCTCAAGGTGGATCAGTCCAGTCTATTGTTC
11932269 TTTAACATATACTTGTGTTGACTTGATATCACATATACGTAACAACTCTTGTCACCAATCAAGCA
196 TTTAACATATACTTGTGTTGACTTGATATCACATATACGTAACAACTCTTGTCACCAATCAAGCA
11932334 CATAT
261 CATAT
11932339 TAGCCTCAAT
Statistics
Matches: 248, Mismatches: 14, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
267 175 0.71
268 2 0.01
269 71 0.29
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (269 bp):
CCAACATCAGTCTTTAAAGTACAACCATTTAAGGAAGACATTTGACTATGTCAAAGCATGCGACT
CACGATGTTGGAACAATGATGATATCAAGTTTAAGCATCATACGTACAATTATCACTATGAGAAA
TGTTATGACTATTACATAATAATACAATAAGCATTCTCAAGGTGGATCAGTCCAGTCTATTGTTC
TTTAACATATACTTGTGTTGACTTGATATCACATATACGTAACAACTCTTGTCACCAATCAAGCA
CATATACAC
Found at i:11935338 original size:20 final size:19
Alignment explanation
Indices: 11935309--11935346 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
11935299 CTAAAAATAT
*
11935309 AGAAATTTAAATTAGAAACC
1 AGAAAATTAAATTA-AAACC
11935329 AGAAAATTAAATTAAAAC
1 AGAAAATTAAATTAAAAC
11935347 TGCATAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.61, C:0.08, G:0.08, T:0.24
Consensus pattern (19 bp):
AGAAAATTAAATTAAAACC
Found at i:11943284 original size:26 final size:26
Alignment explanation
Indices: 11943244--11943293 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
11943234 TCTCAAATCT
*
11943244 ATTTTAGCCCCAGTAAATTTTTGATG
1 ATTTTAGCCCCAGTAAAATTTTGATG
11943270 ATTTTA-CCCCTAGTAAAATTTTGA
1 ATTTTAGCCCC-AGTAAAATTTTGA
11943294 GAAAATATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 4 0.18
26 18 0.82
ACGTcount: A:0.30, C:0.16, G:0.12, T:0.42
Consensus pattern (26 bp):
ATTTTAGCCCCAGTAAAATTTTGATG
Found at i:11943627 original size:27 final size:27
Alignment explanation
Indices: 11943551--11943620 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 27
11943541 TGTCCTAGCG
* *
11943551 GACTAGCCTGTATTTAATGTCCCGACA
1 GACTACCCTGTATTTAATGTCTCGACA
* * *
11943578 AACTACCCCGTGTTTAATGTCTCGACA
1 GACTACCCTGTATTTAATGTCTCGACA
11943605 GACTACCCTGTATTTA
1 GACTACCCTGTATTTA
11943621 CTATCTCAAC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.26, C:0.27, G:0.16, T:0.31
Consensus pattern (27 bp):
GACTACCCTGTATTTAATGTCTCGACA
Found at i:11958693 original size:30 final size:30
Alignment explanation
Indices: 11958632--11958694 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
11958622 ACTTATTTTA
*
11958632 TTGTTAATTTTGTTATTATTTTAAGTGCAT
1 TTGTTAATTTTGTTATTATTTTAAGTACAT
11958662 TTGTTAATTTTGTTATTATTTTAAAG-ACAT
1 TTGTTAATTTTGTTATTATTTT-AAGTACAT
11958692 TTG
1 TTG
11958695 CTTGTTAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 28 0.90
31 3 0.10
ACGTcount: A:0.25, C:0.03, G:0.13, T:0.59
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAGTACAT
Found at i:11965885 original size:22 final size:23
Alignment explanation
Indices: 11965858--11965903 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
11965848 TTACATACTA
* *
11965858 ACATATAAATATT-GATTTAATC
1 ACATATAAACATTCAATTTAATC
*
11965880 ACATATTAACATTCAATTTAATC
1 ACATATAAACATTCAATTTAATC
11965903 A
1 A
11965904 AAATTATTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.46, C:0.13, G:0.02, T:0.39
Consensus pattern (23 bp):
ACATATAAACATTCAATTTAATC
Found at i:11968207 original size:25 final size:25
Alignment explanation
Indices: 11968172--11968219 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
11968162 AAAACACGCT
11968172 GCTACCACATTTCCTTTATGCGTCC
1 GCTACCACATTTCCTTTATGCGTCC
*
11968197 GCTACCCCATTTCCTTTATGCGT
1 GCTACCACATTTCCTTTATGCGT
11968220 AGAATCAACC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.15, C:0.35, G:0.12, T:0.38
Consensus pattern (25 bp):
GCTACCACATTTCCTTTATGCGTCC
Found at i:11973565 original size:27 final size:27
Alignment explanation
Indices: 11973520--11973586 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 27
11973510 GTGTAAACCA
* *
11973520 ATGTTTACTTTCCCAATGGACTACCCC
1 ATGTTTACTATCTCAATGGACTACCCC
* * *
11973547 ATGTTTACTATCTCGATGGGCTATCCC
1 ATGTTTACTATCTCAATGGACTACCCC
* *
11973574 GTGGTTACTATCT
1 ATGTTTACTATCT
11973587 TAGCGAGCAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.19, C:0.27, G:0.16, T:0.37
Consensus pattern (27 bp):
ATGTTTACTATCTCAATGGACTACCCC
Found at i:11977244 original size:56 final size:51
Alignment explanation
Indices: 11977178--11977391 Score: 179
Period size: 50 Copynumber: 4.2 Consensus size: 51
11977168 TGAGCCAGTG
* ** *
11977178 TAAGACCATGTTTGGGACATGGCATTGGCATTATTGAAATTATGAGAGGTCCCATC
1 TAAGACCATGTTTGGGACATGGCGTTGGCA--ACCG--A-GATGAGAGGTCCCATC
* * *
11977234 TAAGACCATGTTAGGGACAGGGCGTTGGC-ACCGAGATGAGAGGTCCCATG
1 TAAGACCATGTTTGGGACATGGCGTTGGCAACCGAGATGAGAGGTCCCATC
* *
11977284 TAAGACCATGTCTGGGACATGGCGTTGGC-ACCGAGATGAGAAGTCTCC--C
1 TAAGACCATGTTTGGGACATGGCGTTGGCAACCGAGATGAGAGGTC-CCATC
* * * * ** *
11977333 GTAAGACCATGTCTGGGACATGGC-ATGG-GACCGATATGAGAACTCCCATG
1 -TAAGACCATGTTTGGGACATGGCGTTGGCAACCGAGATGAGAGGTCCCATC
11977383 TAAGACCAT
1 TAAGACCAT
11977392 ATCTGAGATG
Statistics
Matches: 137, Mismatches: 16, Indels: 17
0.81 0.09 0.10
Matches are distributed among these distances:
48 2 0.01
49 26 0.19
50 78 0.57
51 3 0.02
53 2 0.01
56 26 0.19
ACGTcount: A:0.28, C:0.21, G:0.29, T:0.22
Consensus pattern (51 bp):
TAAGACCATGTTTGGGACATGGCGTTGGCAACCGAGATGAGAGGTCCCATC
Found at i:11977294 original size:50 final size:50
Alignment explanation
Indices: 11977219--11977396 Score: 227
Period size: 50 Copynumber: 3.6 Consensus size: 50
11977209 TATTGAAATT
* * *
11977219 ATGAGAGGTCCCATCTAAGACCATGT-TAGGGACAGGGCGTTGGCACCGAG
1 ATGAGAAGTCCCATGTAAGACCATGTCT-GGGACATGGCGTTGGCACCGAG
*
11977269 ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
1 ATGAGAAGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
* * * *
11977319 ATGAGAAGTCTCC-CGTAAGACCATGTCTGGGACATGGC-ATGGGACCGAT
1 ATGAGAAGTC-CCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
* *
11977368 ATGAGAACTCCCATGTAAGACCATATCTG
1 ATGAGAAGTCCCATGTAAGACCATGTCTG
11977397 AGATGTGACA
Statistics
Matches: 115, Mismatches: 10, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
48 2 0.02
49 31 0.27
50 79 0.69
51 3 0.03
ACGTcount: A:0.27, C:0.22, G:0.30, T:0.20
Consensus pattern (50 bp):
ATGAGAAGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAG
Found at i:11978417 original size:27 final size:27
Alignment explanation
Indices: 11978353--11978417 Score: 62
Period size: 25 Copynumber: 2.4 Consensus size: 27
11978343 ATTAAGGGAG
* *
11978353 TTTAGTGTGCTCTCTGATTATTAGCACA
1 TTTA-TGTACTCTCTAATTATTAGCACA
**
11978381 --TCGGTACTCTCTAATTATTAGCACA
1 TTTATGTACTCTCTAATTATTAGCACA
*
11978406 TTTATGTTCTCT
1 TTTATGTACTCT
11978418 GTATAATACT
Statistics
Matches: 28, Mismatches: 7, Indels: 5
0.70 0.17 0.12
Matches are distributed among these distances:
25 20 0.71
26 1 0.04
27 7 0.25
ACGTcount: A:0.22, C:0.20, G:0.14, T:0.45
Consensus pattern (27 bp):
TTTATGTACTCTCTAATTATTAGCACA
Found at i:12004348 original size:43 final size:43
Alignment explanation
Indices: 12004211--12004338 Score: 175
Period size: 43 Copynumber: 3.0 Consensus size: 43
12004201 ACTTCCGAGG
* *
12004211 TGAGATTTCGTGTAAGACCACAGCTGGGTTATTGGCATCGATT
1 TGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGCATCGATT
* * * *
12004254 TGAGATTTCGCGTAAGACCATAGCTGGGCTATTAGCACCAATT
1 TGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGCATCGATT
* * *
12004297 TGAGATTTCGTGTAAGATCATAGTTGAGCTATTGGCATCGAT
1 TGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGCATCGAT
12004339 ACAAGATTTC
Statistics
Matches: 72, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 72 1.00
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (43 bp):
TGAGATTTCGTGTAAGACCATAGCTGGGCTATTGGCATCGATT
Found at i:12014719 original size:14 final size:14
Alignment explanation
Indices: 12014700--12014727 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
12014690 TAAAATTATA
12014700 TTTAATAATTCATT
1 TTTAATAATTCATT
12014714 TTTAATAATTCATT
1 TTTAATAATTCATT
12014728 AATAAATTGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTAATAATTCATT
Found at i:12015206 original size:19 final size:18
Alignment explanation
Indices: 12015180--12015218 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 18
12015170 CCCTCATCCC
12015180 ATCATCTCTC-ACTCATTT
1 ATCATCTCTCAACTC-TTT
12015198 ATCATTCTCTCAACTCTTT
1 ATCA-TCTCTCAACTCTTT
12015217 AT
1 AT
12015219 GCTATTTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.21
19 11 0.58
20 4 0.21
ACGTcount: A:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (18 bp):
ATCATCTCTCAACTCTTT
Found at i:12018226 original size:76 final size:76
Alignment explanation
Indices: 12018098--12018328 Score: 435
Period size: 76 Copynumber: 3.0 Consensus size: 76
12018088 AATGGAGTCA
12018098 AAATTCAATATGTCTATAGTTAGAGTCTGCACCTAAATAAATAGTACTCCAAGATGTACAGAGTA
1 AAATTCAATATGTCTATAGTTAGAGTCTGCACCTAAATAAATAGTACTCCAAGATGTACAGAGTA
12018163 GACTAAGAGAG
66 GACTAAGAGAG
* *
12018174 ACATTCAATATGTCTATAGTTAGAGTCTGCACCTAAATAAATAGTAATCCAAGATGTACAGAGTA
1 AAATTCAATATGTCTATAGTTAGAGTCTGCACCTAAATAAATAGTACTCCAAGATGTACAGAGTA
12018239 GACTAAGAGAG
66 GACTAAGAGAG
*
12018250 AAATTCAATATGTCTATAGTTAGAGTCTGCACCTAAATAAATAGTACTCCAAGATGTACACAGTA
1 AAATTCAATATGTCTATAGTTAGAGTCTGCACCTAAATAAATAGTACTCCAAGATGTACAGAGTA
12018315 GACTAAGAGAG
66 GACTAAGAGAG
12018326 AAA
1 AAA
12018329 GTAGGAAAGT
Statistics
Matches: 150, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 150 1.00
ACGTcount: A:0.42, C:0.15, G:0.18, T:0.26
Consensus pattern (76 bp):
AAATTCAATATGTCTATAGTTAGAGTCTGCACCTAAATAAATAGTACTCCAAGATGTACAGAGTA
GACTAAGAGAG
Found at i:12022330 original size:44 final size:41
Alignment explanation
Indices: 12022236--12022458 Score: 141
Period size: 44 Copynumber: 5.2 Consensus size: 41
12022226 CAGTCTACTT
* * ***
12022236 CACTGCAA-TTTCAGGGAGATAAGACTTGATGCGATCTGCT-
1 CACTGCAACTTT-AGAGAGATAAGACTTGGTTTAATCTGCTC
* *
12022276 CTCTGCAACTTTGGAGAGATAAGATCTGTGGCTTTAATCTGCTC
1 CACTGCAACTTTAGAGAGATAAGA-CT-TGG-TTTAATCTGCTC
* * * *
12022320 CACTGCAACTTTAGGGAAATAGGA-TTGGTTTATTCTGTCTACTC
1 CACTGCAACTTTAGAGAGATAAGACTTGGTTTAATCTG----CTC
* ***
12022364 CACTGCAACTTTAGAAAGATAAGAC-TGGATGCGATCTGCTC
1 CACTGCAACTTTAGAGAGATAAGACTTGG-TTTAATCTGCTC
* *
12022405 TACTGCAACTTTAGAGAGATAAGATCAGTGGTTTTAAT-TCGCTC
1 CACTGCAACTTTAGAGAGATAAGA-C-TTGG-TTTAATCT-GCTC
12022449 CACTGCAACT
1 CACTGCAACT
12022459 GGAGGGAGAT
Statistics
Matches: 140, Mismatches: 28, Indels: 26
0.72 0.14 0.13
Matches are distributed among these distances:
40 25 0.18
41 33 0.24
42 4 0.03
43 9 0.06
44 64 0.46
45 5 0.04
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (41 bp):
CACTGCAACTTTAGAGAGATAAGACTTGGTTTAATCTGCTC
Found at i:12022384 original size:128 final size:127
Alignment explanation
Indices: 12022221--12022650 Score: 432
Period size: 128 Copynumber: 3.4 Consensus size: 127
12022211 CATGATTCAC
* *
12022221 TTATTCAGTCTACTTCACTGCAA-TTTCAGGGAGATAAGACTTGATGCGATCTGCTCTCTGCAAC
1 TTATTCAGTCTACTCCACTGCAACTTT-AGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAAC
* * * *
12022285 TTTGGAGAGATAAGATCTGTGGCTTTAATCTGCTCCACTGCAACTTTAGGGAAATAGGATTGGT
65 TTTAGAGAGATAAGATCTGTGGTTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGATT-GT
* ** *
12022349 TTATTCTGTCTACTCCACTGCAACTTTAGAAAGATAAGACTGGATGCGATCTGCTCTACTGCAAC
1 TTATTCAGTCTACTCCACTGCAACTTTAGGGAGATAAGACTAGATGCGATCTGCTCT-CTGCAAC
* ** *
12022414 TTTAGAGAGATAAGATCAGTGGTTTTAAT-TCGCTCCACTGCAACTGGAGGGAGATAGGATTAT
65 TTTAGAGAGATAAGATCTGTGGTTTTAATCT-GCTCCACTGCAACTTCAGGGAGATAGGATTGT
** * * ** * * * * *
12022477 TGGCTTCAATCGACTCTGCTGCATCTTCAGGGAGATAAGACTAGATGTGATCTACTCTCTACAAC
1 T-TATTCAGTCTACTCCACTGCAACTTTAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAAC
* ** * * * * * *
12022542 TTTAGAGAGATAAGATCTTTCATTTTAGTCCGTTCCGCTACAACTTCAGGGAGATAGGATTAGC
65 TTTAGAGAGATAAGATCTGTGGTTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGATT-GT
* * * * * *
12022606 TTCTTCTGTCTGCTCCATTGCAACTTCAAGGAGATAAGACTAGAT
1 TTATTCAGTCTACTCCACTGCAACTTTAGGGAGATAAGACTAGAT
12022651 AAGATATGTG
Statistics
Matches: 246, Mismatches: 50, Indels: 12
0.80 0.16 0.04
Matches are distributed among these distances:
128 140 0.57
129 106 0.43
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (127 bp):
TTATTCAGTCTACTCCACTGCAACTTTAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACT
TTAGAGAGATAAGATCTGTGGTTTTAATCTGCTCCACTGCAACTTCAGGGAGATAGGATTGT
Found at i:12022425 original size:41 final size:41
Alignment explanation
Indices: 12022236--12022428 Score: 149
Period size: 44 Copynumber: 4.6 Consensus size: 41
12022226 CAGTCTACTT
* *
12022236 CACTGCAA-TTTCAGGGAGATAAGACTTGATGCGATCTGCT-
1 CACTGCAACTTT-AGAGAGATAAGACTGGATGCGATCTGCTC
* * * ***
12022276 CTCTGCAACTTTGGAGAGATAAGATCTGTGGCTTTAATCTGCTC
1 CACTGCAACTTTAGAGAGATAAGA-C--TGGATGCGATCTGCTC
* * * * * *
12022320 CACTGCAACTTTAGGGAAATAGGATTGGTTTATTCTG-TCTACTC
1 CACTGCAACTTTAGAGAGATAAGACTGG---ATGC-GATCTGCTC
*
12022364 CACTGCAACTTTAGAAAGATAAGACTGGATGCGATCTGCTC
1 CACTGCAACTTTAGAGAGATAAGACTGGATGCGATCTGCTC
*
12022405 TACTGCAACTTTAGAGAGATAAGA
1 CACTGCAACTTTAGAGAGATAAGA
12022429 TCAGTGGTTT
Statistics
Matches: 116, Mismatches: 27, Indels: 19
0.72 0.17 0.12
Matches are distributed among these distances:
40 18 0.16
41 38 0.33
43 10 0.09
44 50 0.43
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.30
Consensus pattern (41 bp):
CACTGCAACTTTAGAGAGATAAGACTGGATGCGATCTGCTC
Found at i:12022465 original size:129 final size:127
Alignment explanation
Indices: 12022221--12022558 Score: 401
Period size: 129 Copynumber: 2.6 Consensus size: 127
12022211 CATGATTCAC
* *
12022221 TTATTCAGTCTACTTCACTGCAA-TTTCAGGGAGATAAGACTTGATGCGATCTGCTCTCTGCAAC
1 TTATTCAGTCTACTCCACTGCAACTTT-AGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAAC
* * ** *
12022285 TTTGGAGAGATAAGATCTGTGGCTTTAATCTGCTCCACTGCAACTTTAGGGAAATAGGATTGGT
65 TTTAGAGAGATAAGATCAGTGGCTTTAATCTGCTCCACTGCAACTGGAGGGAAATAGGATT-AT
* ** *
12022349 TTATTCTGTCTACTCCACTGCAACTTTAGAAAGATAAGACTGGATGCGATCTGCTCTACTGCAAC
1 TTATTCAGTCTACTCCACTGCAACTTTAGGGAGATAAGACTAGATGCGATCTGCTCT-CTGCAAC
* *
12022414 TTTAGAGAGATAAGATCAGTGGTTTTAAT-TCGCTCCACTGCAACTGGAGGGAGATAGGATTAT
65 TTTAGAGAGATAAGATCAGTGGCTTTAATCT-GCTCCACTGCAACTGGAGGGAAATAGGATTAT
** * * ** * * * * *
12022477 TGGCTTCAATCGACTCTGCTGCATCTTCAGGGAGATAAGACTAGATGTGATCTACTCTCTACAAC
1 T-TATTCAGTCTACTCCACTGCAACTTTAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAAC
12022542 TTTAGAGAGATAAGATC
65 TTTAGAGAGATAAGATC
12022559 TTTCATTTTA
Statistics
Matches: 179, Mismatches: 27, Indels: 8
0.84 0.13 0.04
Matches are distributed among these distances:
128 74 0.41
129 105 0.59
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.31
Consensus pattern (127 bp):
TTATTCAGTCTACTCCACTGCAACTTTAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACT
TTAGAGAGATAAGATCAGTGGCTTTAATCTGCTCCACTGCAACTGGAGGGAAATAGGATTAT
Found at i:12024918 original size:19 final size:20
Alignment explanation
Indices: 12024883--12024923 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
12024873 ACATACGTAT
12024883 AATAAATAACAAGT-AAATG
1 AATAAATAACAAGTAAAATG
*
12024902 AATAAATAA-TAGATAAAATG
1 AATAAATAACAAG-TAAAATG
12024922 AA
1 AA
12024924 ATAATAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
18 2 0.11
19 10 0.53
20 7 0.37
ACGTcount: A:0.66, C:0.02, G:0.10, T:0.22
Consensus pattern (20 bp):
AATAAATAACAAGTAAAATG
Found at i:12027773 original size:556 final size:555
Alignment explanation
Indices: 12026692--12027789 Score: 1414
Period size: 556 Copynumber: 2.0 Consensus size: 555
12026682 TAAATTGACT
* * *
12026692 AGATAGAGTAAATAAAATAGCTTGTTGTATTGATATAAAGCGCAAATCCACAGAGTTGAATGAGT
1 AGATAGAGTAAATAAAAGAGCCTGTTGTATTGATATAAAGCACAAATCCACAGAGTTGAATGAGT
* * * * * * *
12026757 CCATAATCAAAATCTCTTGAAAGAAAACAATGAACAAATAAATTTAACTCTTAAATCCTATGAAA
66 CCACAATCAAAATCACTTGAAAGAAAACAATGAAAAAATAAACTAAACTCTAAAATCCTAAGAAA
* * * * * *
12026822 GAAAGAAAATAAAACTAAGTTTAATGGAAGAAACTAGGTTAATATAAAAGTGTTTTTAACATGTG
131 GAAAGAAAACAAAACTAAATTTAACGGAAGAAACTAGGTTAATAGAAAAATGTCTTTAACATGTG
* * * **
12026887 CCAAAGGAGCCTATTTATAGCCTTTAGGTGGTCGTCATCCTTAACCCTAGGTCAGCTGATGTTCC
196 CCAAAGAAGCCTATTTATAGCCTTCAGGTGGTCGTCATCCTTAACCCTAGATCAGCTGACATTCC
* *
12026952 CTAGCTTTCAGTTTGATTGTGTAGACCAAAACGCCCCTACTTCATGTCTAATTTCTATCCTAGAG
261 CTAGCTTTAAGTTTGATTGTGTAGACCAAAACGCCCATACTTCATGTCTAATTTCTATCCTAGAG
*
12027017 TCAATGTCGTGACACACCAGGACCTATATCACAACATAGCAACCAGTATGCTCCTCTGTAGCCAT
326 TCAATGTCGTGACACACCAGGACCTATATCACAACATAGCAACCAGTATGCTCCTCTATAGCCAT
* * * * *
12027082 CTTCAGGGGTATATTGTGAAACCCTCAGTTTGTGTCGCAACATCAAAGGCAGACTTGAGTTTTCA
391 CTTCAGGGATATATCGTGAAACACTCAGTCTGTGTCACAACATCAAAGGCAGACTTGAGTTTTCA
* * * * * * *
12027147 TCATTTTCTTCCCTATGCTTCGACATTAGTCCTCCCGTGTTGTGACATAGCATCCAGTATCATTC
456 TCATTATCTTCCCCATGCTTCAACATCAGTCCTCCCGTGTTGCGAAATAGCATACAGTATCATTC
12027212 TAAAATGCCTTCTAATGGTCTCCTACACACTTACA
521 TAAAATGCCTTCTAATGGTCTCCTACACACTTACA
* * * * *
12027247 AGATAGAGTAAATGACAGAGCCTGATTGTGTTGATATTAAGCACAAATCCACAGAGTTGAATTAG
1 AGATAGAGTAAATAAAAGAGCCTG-TTGTATTGATATAAAGCACAAATCCACAGAGTTGAATGAG
* * *
12027312 TCCACAATCAAAATCACTTGAAATAAAATAATGAAAAAATAAACTAAACTCTAAAATCTTAAGAA
65 TCCACAATCAAAATCACTTGAAAGAAAACAATGAAAAAATAAACTAAACTCTAAAATCCTAAGAA
* * * * *
12027377 ATAAATAAAACAAAACTAAATTTAACGGAAGAAACTAGTTTGATGGAAAAATGTCTTTAACATGT
130 AGAAAGAAAACAAAACTAAATTTAACGGAAGAAACTAGGTTAATAGAAAAATGTCTTTAACATGT
* * * *
12027442 GCTAAATAAGCTTATTTATAGCCTTCAGGTGGTTGTCATCCTTAACCCTAGAT-ATGCTGACATT
195 GCCAAAGAAGCCTATTTATAGCCTTCAGGTGGTCGTCATCCTTAACCCTAGATCA-GCTGACATT
* * * * * *
12027506 -CTTGAGCTTTAATTTTGATTGTGTGGACCAAAATGCCCATGC-TCTGTGTCTAATTTCTATCCT
259 CCCT-AGCTTTAAGTTTGATTGTGTAGACCAAAACGCCCATACTTC-ATGTCTAATTTCTATCCT
** * * *
12027569 AGAGTTGATGTTGTGACACACCAGGACCTGTGTCACAACATAGCAACCAGTATGCTCCTCTATAG
322 AGAGTCAATGTCGTGACACACCAGGACCTATATCACAACATAGCAACCAGTATGCTCCTCTATAG
* * * * * *
12027634 CCATTTTTAGGGATATGTCGTGACACACTCAGTCTGTGTCACGACATCGAAGGCAGACTTGAGAT
387 CCATCTTCAGGGATATATCGTGAAACACTCAGTCTGTGTCACAACATCAAAGGCAGACTTGAG-T
* * ** *
12027699 TTTC-TCATTATGTTCCCCATG-TTGCAACATCAGTCCTCCCGTGTTGCGAAATAGCTTATTGTG
451 TTTCATCATTATCTTCCCCATGCTT-CAACATCAGTCCTCCCGTGTTGCGAAATAGCATACAGTA
**
12027762 TTGTTCTAAAATGCCTTCTAATGGTCTC
515 TCATTCTAAAATGCCTTCTAATGGTCTC
12027790 TTGCACGTTT
Statistics
Matches: 460, Mismatches: 77, Indels: 11
0.84 0.14 0.02
Matches are distributed among these distances:
555 27 0.06
556 428 0.93
557 5 0.01
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.31
Consensus pattern (555 bp):
AGATAGAGTAAATAAAAGAGCCTGTTGTATTGATATAAAGCACAAATCCACAGAGTTGAATGAGT
CCACAATCAAAATCACTTGAAAGAAAACAATGAAAAAATAAACTAAACTCTAAAATCCTAAGAAA
GAAAGAAAACAAAACTAAATTTAACGGAAGAAACTAGGTTAATAGAAAAATGTCTTTAACATGTG
CCAAAGAAGCCTATTTATAGCCTTCAGGTGGTCGTCATCCTTAACCCTAGATCAGCTGACATTCC
CTAGCTTTAAGTTTGATTGTGTAGACCAAAACGCCCATACTTCATGTCTAATTTCTATCCTAGAG
TCAATGTCGTGACACACCAGGACCTATATCACAACATAGCAACCAGTATGCTCCTCTATAGCCAT
CTTCAGGGATATATCGTGAAACACTCAGTCTGTGTCACAACATCAAAGGCAGACTTGAGTTTTCA
TCATTATCTTCCCCATGCTTCAACATCAGTCCTCCCGTGTTGCGAAATAGCATACAGTATCATTC
TAAAATGCCTTCTAATGGTCTCCTACACACTTACA
Found at i:12032532 original size:44 final size:44
Alignment explanation
Indices: 12032469--12032557 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
12032459 TTGCGTTGAC
12032469 AAAACGCAAGATTGATTCCTTTAATATCATCAATTGTCCCTCCT
1 AAAACGCAAGATTGATTCCTTTAATATCATCAATTGTCCCTCCT
*
12032513 AAAACGCAGGATTGATTCCTTTAATATCATCAATTGTCCCTCCT
1 AAAACGCAAGATTGATTCCTTTAATATCATCAATTGTCCCTCCT
12032557 A
1 A
12032558 TCGCTTTTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.31, C:0.25, G:0.10, T:0.34
Consensus pattern (44 bp):
AAAACGCAAGATTGATTCCTTTAATATCATCAATTGTCCCTCCT
Found at i:12032548 original size:22 final size:22
Alignment explanation
Indices: 12032479--12032548 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
12032469 AAAACGCAAG
12032479 ATTGATTCCTTTAATATCATCA
1 ATTGATTCCTTTAATATCATCA
* * * *
12032501 ATTG-TCCCTCCTAA-AAC-GCA
1 ATTGATTCCT-TTAATATCATCA
12032521 GGATTGATTCCTTTAATATCATCA
1 --ATTGATTCCTTTAATATCATCA
12032545 ATTG
1 ATTG
12032549 TCCCTCCTAT
Statistics
Matches: 34, Mismatches: 8, Indels: 12
0.63 0.15 0.22
Matches are distributed among these distances:
20 2 0.06
21 6 0.18
22 18 0.53
23 6 0.18
24 2 0.06
ACGTcount: A:0.30, C:0.21, G:0.10, T:0.39
Consensus pattern (22 bp):
ATTGATTCCTTTAATATCATCA
Found at i:12035892 original size:27 final size:27
Alignment explanation
Indices: 12035862--12036146 Score: 225
Period size: 27 Copynumber: 10.6 Consensus size: 27
12035852 CCCTATAAGA
* *
12035862 TAAAATGACCGTAATGCCCTTGTAGGG
1 TAAAATGACCGTAATACCCTTATAGGG
12035889 TAAAATGACCGTAATACACC-TATAGGG
1 TAAAATGACCGTAATAC-CCTTATAGGG
* * * * *
12035916 TAAAATGACTGAAAAACCCCTATAGGT
1 TAAAATGACCGTAATACCCTTATAGGG
* * *
12035943 TAAAATGATCATAATGCCTCTGTA-A-GG
1 TAAAATGACCGTAATACC-CT-TATAGGG
* *
12035970 TAAAATGACCATAATACCCCTATAGGG
1 TAAAATGACCGTAATACCCTTATAGGG
* * * *
12035997 TAAAATGACCGGAAAAACCTCATAGGG
1 TAAAATGACCGTAATACCCTTATAGGG
* * * *
12036024 TAAAATGACCGTAATGCCCCTGTAAGG
1 TAAAATGACCGTAATACCCTTATAGGG
* * *
12036051 TAAAATAACCGTAATACCCCTCTAGGG
1 TAAAATGACCGTAATACCCTTATAGGG
* * * *
12036078 TAAAATGATCGAAAAACTCTTATAGGG
1 TAAAATGACCGTAATACCCTTATAGGG
* * * *
12036105 TTAAATGACTGAAATACCCTTATAAGG
1 TAAAATGACCGTAATACCCTTATAGGG
* *
12036132 TAAAATTACCATAAT
1 TAAAATGACCGTAAT
12036147 GCCCCTGGAG
Statistics
Matches: 199, Mismatches: 53, Indels: 12
0.75 0.20 0.05
Matches are distributed among these distances:
25 2 0.01
26 4 0.02
27 187 0.94
28 4 0.02
29 2 0.01
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.24
Consensus pattern (27 bp):
TAAAATGACCGTAATACCCTTATAGGG
Found at i:12035897 original size:54 final size:53
Alignment explanation
Indices: 12035833--12036152 Score: 212
Period size: 54 Copynumber: 5.9 Consensus size: 53
12035823 CCCCAAAATA
* * * *
12035833 GGTAAAATGACTGAAAAAACCCTATAAGATAAAATGACCGTAATGCCCTTGTAG
1 GGTAAAATGACTG-AAAAACCCTATAAGGTAAAATGACCGTAATACCCCTATAG
* * * * * * *
12035887 GGTAAAATGACCGTAATACACCTATAGGGTAAAATGACTGAAAAACCCCTATAG
1 GGTAAAATGACTGAAAAAC-CCTATAAGGTAAAATGACCGTAATACCCCTATAG
* * ** * *
12035941 GTTAAAATGA-TCATAATGCCTCTGTAAGGTAAAATGACCATAATACCCCTATAG
1 GGTAAAATGACTGA-AAAACC-CTATAAGGTAAAATGACCGTAATACCCCTATAG
* * * * *
12035995 GGTAAAATGACCGGAAAAA-CCTCATAGGGTAAAATGACCGTAATGCCCCTGTAA
1 GGTAAAATGA-CTGAAAAACCCT-ATAAGGTAAAATGACCGTAATACCCCTATAG
* * * * * * * * * * *
12036049 GGTAAAATAACCGTAATACCCCTCTAGGGTAAAATGATCGAAAAACTCTTATAG
1 GGTAAAATGACTG-AAAAACCCTATAAGGTAAAATGACCGTAATACCCCTATAG
* * * * *
12036103 GGTTAAATGACTGAAATACCCTTATAAGGTAAAATTACCATAATGCCCCT
1 GGTAAAATGACTGAAAAACCC-TATAAGGTAAAATGACCGTAATACCCCT
12036153 GGAGGTTAAA
Statistics
Matches: 195, Mismatches: 62, Indels: 18
0.71 0.23 0.07
Matches are distributed among these distances:
53 14 0.07
54 175 0.90
55 5 0.03
56 1 0.01
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.23
Consensus pattern (53 bp):
GGTAAAATGACTGAAAAACCCTATAAGGTAAAATGACCGTAATACCCCTATAG
Found at i:12035972 original size:81 final size:80
Alignment explanation
Indices: 12035833--12036152 Score: 358
Period size: 81 Copynumber: 4.0 Consensus size: 80
12035823 CCCCAAAATA
* * * *
12035833 GGTAAAATGACTGAAAAAACCCTATAAGATAAAATGACCGTAATGCCCTTGTAGGGTAAAATGAC
1 GGTAAAATGACTGAAAAACCCCTATAGGTTAAAATGACCGTAATGCCC-TGTAAGGTAAAATGAC
*
12035898 CGTAATACACCTATAG
65 CGTAATACCCCTATAG
* *
12035914 GGTAAAATGACTGAAAAACCCCTATAGGTTAAAATGATCATAATGCCTCTGTAAGGTAAAATGAC
1 GGTAAAATGACTGAAAAACCCCTATAGGTTAAAATGACCGTAATGCC-CTGTAAGGTAAAATGAC
*
12035979 CATAATACCCCTATAG
65 CGTAATACCCCTATAG
* * * *
12035995 GGTAAAATGACCGGAAAAACCTC-ATAGGGTAAAATGACCGTAATGCCCCTGTAAGGTAAAATAA
1 GGTAAAATGA-CTGAAAAACCCCTATAGGTTAAAATGACCGTAATG-CCCTGTAAGGTAAAATGA
*
12036059 CCGTAATACCCCTCTAG
64 CCGTAATACCCCTATAG
* * * * * * *
12036076 GGTAAAATGA-TCGAAAAACTCTTATAGGGTT-AAATGACTGAAATACCCTTATAAGGTAAAATT
1 GGTAAAATGACT-GAAAAACCCCTATA-GGTTAAAATGACCGTAATGCCC-TGTAAGGTAAAATG
* *
12036139 ACCATAATGCCCCT
63 ACCGTAATACCCCT
12036153 GGAGGTTAAA
Statistics
Matches: 204, Mismatches: 28, Indels: 14
0.83 0.11 0.06
Matches are distributed among these distances:
80 10 0.05
81 178 0.87
82 16 0.08
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.23
Consensus pattern (80 bp):
GGTAAAATGACTGAAAAACCCCTATAGGTTAAAATGACCGTAATGCCCTGTAAGGTAAAATGACC
GTAATACCCCTATAG
Found at i:12036231 original size:24 final size:24
Alignment explanation
Indices: 12036183--12036293 Score: 100
Period size: 24 Copynumber: 4.6 Consensus size: 24
12036173 TCCCCTCGAG
* **
12036183 TGTAAATGATTGATTTGTCCATGA
1 TGTAAATGACTGATTTGTCTGTGA
*
12036207 TGTAAATGACTGATTTGTTTGTGA
1 TGTAAATGACTGATTTGTCTGTGA
* *
12036231 TTTAAATGACTAATTTGTCTGTGA
1 TGTAAATGACTGATTTGTCTGTGA
*
12036255 TTGGT--ATGACTGGTTTGTCTGTGA
1 -T-GTAAATGACTGATTTGTCTGTGA
* **
12036279 TTTGCATGACTGATT
1 TGTAAATGACTGATT
12036294 CTGAGCAAGG
Statistics
Matches: 71, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
22 1 0.01
23 1 0.01
24 67 0.94
25 1 0.01
26 1 0.01
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.45
Consensus pattern (24 bp):
TGTAAATGACTGATTTGTCTGTGA
Found at i:12036441 original size:26 final size:26
Alignment explanation
Indices: 12036412--12036462 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
12036402 GCCACATATT
*
12036412 CTATTACGGGCAGCTTTGGTGCGATA
1 CTATTACGGGCAGCTTTGCTGCGATA
* * *
12036438 CTATTGCTGGTAGCTTTGCTGCGAT
1 CTATTACGGGCAGCTTTGCTGCGAT
12036463 GCTACTGATC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.16, C:0.20, G:0.29, T:0.35
Consensus pattern (26 bp):
CTATTACGGGCAGCTTTGCTGCGATA
Found at i:12036509 original size:32 final size:32
Alignment explanation
Indices: 12036465--12036643 Score: 139
Period size: 32 Copynumber: 5.7 Consensus size: 32
12036455 GCTGCGATGC
* *
12036465 TACTGATCGCTTTGTACCGATCATATTACCGT
1 TACTGATGGCTTTGTACCGATCATATTACTGT
** *
12036497 TACTGATGGCTTTGTGTCGATCATAATACTGT
1 TACTGATGGCTTTGTACCGATCATATTACTGT
* ** * **
12036529 TATTGATGGCTTTGTGTCGATCATAATACCAT
1 TACTGATGGCTTTGTACCGATCATATTACTGT
* * * * * *
12036561 TGCTGATGGCTGTGTGCTGATCATATCACTGC
1 TACTGATGGCTTTGTACCGATCATATTACTGT
* *
12036593 TACTGATGGCTTT-CAGCCAATCATATTACTG-
1 TACTGATGGCTTTGTA-CCGATCATATTACTGT
* *
12036624 TACTTATGGC-TTGTAGCGAT
1 TACTGATGGCTTTGTACCGAT
12036644 TCTGTTTATA
Statistics
Matches: 116, Mismatches: 29, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
30 5 0.04
31 10 0.09
32 101 0.87
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.38
Consensus pattern (32 bp):
TACTGATGGCTTTGTACCGATCATATTACTGT
Found at i:12036583 original size:64 final size:64
Alignment explanation
Indices: 12036462--12036605 Score: 175
Period size: 64 Copynumber: 2.2 Consensus size: 64
12036452 TTTGCTGCGA
* * * *
12036462 TGCTACTGATCGCTTTGTACCGATCATATTACCGTTACTGATGGCTTTGTGTCGATCATAAT-AC
1 TGCTACTGATGGCTTTGTACCGATCATAATACCATTACTGATGGCTGTGTGTCGATCAT-ATCAC
* * ** *
12036526 TGTTATTGATGGCTTTGTGTCGATCATAATACCATTGCTGATGGCTGTGTG-CTGATCATATCAC
1 TGCTACTGATGGCTTTGTACCGATCATAATACCATTACTGATGGCTGTGTGTC-GATCATATCAC
12036590 TGCTACTGATGGCTTT
1 TGCTACTGATGGCTTT
12036606 CAGCCAATCA
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
63 3 0.04
64 64 0.96
ACGTcount: A:0.20, C:0.19, G:0.22, T:0.39
Consensus pattern (64 bp):
TGCTACTGATGGCTTTGTACCGATCATAATACCATTACTGATGGCTGTGTGTCGATCATATCAC
Found at i:12036684 original size:22 final size:22
Alignment explanation
Indices: 12036627--12036678 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
12036617 ATTACTGTAC
* *
12036627 TTATGGCTTGTAGCGATTCTGT
1 TTATGGCTTATAGCGATCCTGT
* *
12036649 TTATAGCTTATAGCTATCCTGT
1 TTATGGCTTATAGCGATCCTGT
12036671 TTATGGCT
1 TTATGGCT
12036679 CTTAGCCATT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.17, C:0.15, G:0.21, T:0.46
Consensus pattern (22 bp):
TTATGGCTTATAGCGATCCTGT
Found at i:12038337 original size:27 final size:27
Alignment explanation
Indices: 12038284--12038344 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 27
12038274 AGCCCACTAC
* * *
12038284 CGAATACCAACTCGCCAGGCCTACTGG
1 CGAACACCAACTCGCAAAGCCTACTGG
* * *
12038311 TGAACACCAACTCGCAAAGCTTTCTGG
1 CGAACACCAACTCGCAAAGCCTACTGG
12038338 CGAACAC
1 CGAACAC
12038345 ACATTCACCA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.30, C:0.34, G:0.20, T:0.16
Consensus pattern (27 bp):
CGAACACCAACTCGCAAAGCCTACTGG
Found at i:12049519 original size:22 final size:22
Alignment explanation
Indices: 12049491--12049535 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
12049481 CTTAAGCTCC
*
12049491 GACGGGTGAACCAACGTGAAAA
1 GACGGGTGAACCAACATGAAAA
12049513 GACGGGTGAACCAACATGAAAA
1 GACGGGTGAACCAACATGAAAA
12049535 G
1 G
12049536 GATGCAGCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.42, C:0.18, G:0.31, T:0.09
Consensus pattern (22 bp):
GACGGGTGAACCAACATGAAAA
Found at i:12054406 original size:108 final size:108
Alignment explanation
Indices: 12054278--12054494 Score: 434
Period size: 108 Copynumber: 2.0 Consensus size: 108
12054268 GATGAGCAAG
12054278 TTACCTTCAGTGTTTTCGAATCTATTCAATGCAAAGATAAAGAAGAATGTCATACTATCGATGTG
1 TTACCTTCAGTGTTTTCGAATCTATTCAATGCAAAGATAAAGAAGAATGTCATACTATCGATGTG
12054343 CTAGATGATTTAACTATAAAATAATTTAATGACCAGAGCACAA
66 CTAGATGATTTAACTATAAAATAATTTAATGACCAGAGCACAA
12054386 TTACCTTCAGTGTTTTCGAATCTATTCAATGCAAAGATAAAGAAGAATGTCATACTATCGATGTG
1 TTACCTTCAGTGTTTTCGAATCTATTCAATGCAAAGATAAAGAAGAATGTCATACTATCGATGTG
12054451 CTAGATGATTTAACTATAAAATAATTTAATGACCAGAGCACAA
66 CTAGATGATTTAACTATAAAATAATTTAATGACCAGAGCACAA
12054494 T
1 T
12054495 ACTTTCTGAG
Statistics
Matches: 109, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
108 109 1.00
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.32
Consensus pattern (108 bp):
TTACCTTCAGTGTTTTCGAATCTATTCAATGCAAAGATAAAGAAGAATGTCATACTATCGATGTG
CTAGATGATTTAACTATAAAATAATTTAATGACCAGAGCACAA
Found at i:12057570 original size:17 final size:16
Alignment explanation
Indices: 12057548--12057579 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
12057538 ATTGGTCGAA
12057548 AAATTTTATTTCTTATG
1 AAATTTTATTT-TTATG
12057565 AAATTTTATTTTTAT
1 AAATTTTATTTTTAT
12057580 TTTATTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.62
Consensus pattern (16 bp):
AAATTTTATTTTTATG
Found at i:12057583 original size:11 final size:11
Alignment explanation
Indices: 12057567--12057592 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
12057557 TTCTTATGAA
12057567 ATTTTATTTTT
1 ATTTTATTTTT
12057578 ATTTTATTTTT
1 ATTTTATTTTT
12057589 ATTT
1 ATTT
12057593 CTGTTCAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (11 bp):
ATTTTATTTTT
Found at i:12059905 original size:17 final size:17
Alignment explanation
Indices: 12059883--12059915 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
12059873 TTTAGTCAAC
*
12059883 ATTGTCGTTGCATTTTT
1 ATTGTCGTCGCATTTTT
12059900 ATTGTCGTCGCATTTT
1 ATTGTCGTCGCATTTT
12059916 AATGTTAGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.12, C:0.15, G:0.18, T:0.55
Consensus pattern (17 bp):
ATTGTCGTCGCATTTTT
Found at i:12062335 original size:8 final size:8
Alignment explanation
Indices: 12062322--12062376 Score: 51
Period size: 8 Copynumber: 7.0 Consensus size: 8
12062312 GTTAGAAAAT
12062322 ATTATTAA
1 ATTATTAA
12062330 ATTATTAA
1 ATTATTAA
12062338 ATT-TTAA
1 ATTATTAA
* *
12062345 TTTGTTAA
1 ATTATTAA
*
12062353 A-TATTAT
1 ATTATTAA
*
12062360 ATTGTTAA
1 ATTATTAA
12062368 CATTATTAA
1 -ATTATTAA
12062377 TTTTATGATT
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
7 11 0.30
8 19 0.51
9 7 0.19
ACGTcount: A:0.42, C:0.02, G:0.04, T:0.53
Consensus pattern (8 bp):
ATTATTAA
Found at i:12064262 original size:27 final size:25
Alignment explanation
Indices: 12064200--12064264 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 25
12064190 AATCTTTCAG
* **
12064200 AGTTTGCCATATGTACTATTCCTTT
1 AGTTTACCATATGTACTATTCCTAA
12064225 AGTGTTCACCATATGTACTATTCTCTCAA
1 AGT-TT-ACCATATGTACTATTC-CT-AA
12064254 AGTTTACCATA
1 AGTTTACCATA
12064265 CCTTCTAGTC
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
25 3 0.09
26 2 0.06
27 21 0.64
28 4 0.12
29 3 0.09
ACGTcount: A:0.26, C:0.22, G:0.11, T:0.42
Consensus pattern (25 bp):
AGTTTACCATATGTACTATTCCTAA
Found at i:12064406 original size:26 final size:26
Alignment explanation
Indices: 12064327--12064408 Score: 83
Period size: 26 Copynumber: 3.1 Consensus size: 26
12064317 CTTACAATTA
12064327 TTCAAAGTTAGCCATGCATATCATTC
1 TTCAAAGTTAGCCATGCATATCATTC
* * * * * * *
12064353 TCCCAAGGTTTGTCATACTTACCATTC
1 T-TCAAAGTTAGCCATGCATATCATTC
*
12064380 TTTAAAGTTAGCCATGCATATCATTC
1 TTCAAAGTTAGCCATGCATATCATTC
12064406 TTC
1 TTC
12064409 TAGGGTTTGT
Statistics
Matches: 39, Mismatches: 16, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
26 20 0.51
27 19 0.49
ACGTcount: A:0.27, C:0.24, G:0.11, T:0.38
Consensus pattern (26 bp):
TTCAAAGTTAGCCATGCATATCATTC
Found at i:12064431 original size:27 final size:27
Alignment explanation
Indices: 12064345--12064436 Score: 96
Period size: 27 Copynumber: 3.4 Consensus size: 27
12064335 TAGCCATGCA
* *
12064345 TATCATTCTCCCAAGGTTTGTCATACT
1 TATCATTCTTCTAAGGTTTGTCATACT
* * * * * *
12064372 TACCATTCTT-TAAAGTTAGCCATGCA
1 TATCATTCTTCTAAGGTTTGTCATACT
*
12064398 TATCATTCTTCTAGGGTTTGTCATACT
1 TATCATTCTTCTAAGGTTTGTCATACT
12064425 TATCATTCTTCT
1 TATCATTCTTCT
12064437 CTTTCAGGGT
Statistics
Matches: 49, Mismatches: 15, Indels: 2
0.74 0.23 0.03
Matches are distributed among these distances:
26 19 0.39
27 30 0.61
ACGTcount: A:0.23, C:0.23, G:0.11, T:0.43
Consensus pattern (27 bp):
TATCATTCTTCTAAGGTTTGTCATACT
Found at i:12064432 original size:53 final size:52
Alignment explanation
Indices: 12064313--12064435 Score: 174
Period size: 53 Copynumber: 2.3 Consensus size: 52
12064303 TAGGGCCTGC
*
12064313 CATACTTACAATTATTCAAAGTTAGCCATGCATATCATTCTCCCAAGGTTTGT
1 CATACTTAC-ATTCTTCAAAGTTAGCCATGCATATCATTCTCCCAAGGTTTGT
* * * *
12064366 CATACTTACCATTCTTTAAAGTTAGCCATGCATATCATTCTTCTAGGGTTTGT
1 CATACTTA-CATTCTTCAAAGTTAGCCATGCATATCATTCTCCCAAGGTTTGT
12064419 CATACTTATCATTCTTC
1 CATACTTA-CATTCTTC
12064436 TCTTTCAGGG
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
53 61 0.98
54 1 0.02
ACGTcount: A:0.27, C:0.23, G:0.11, T:0.40
Consensus pattern (52 bp):
CATACTTACATTCTTCAAAGTTAGCCATGCATATCATTCTCCCAAGGTTTGT
Found at i:12066161 original size:16 final size:16
Alignment explanation
Indices: 12066140--12066172 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
12066130 ATAGCTAATT
*
12066140 AAAGAAAAAGGACTAG
1 AAAGAAAAAAGACTAG
12066156 AAAGAAAAAAGACTAG
1 AAAGAAAAAAGACTAG
12066172 A
1 A
12066173 TTGGAAAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.67, C:0.06, G:0.21, T:0.06
Consensus pattern (16 bp):
AAAGAAAAAAGACTAG
Found at i:12067219 original size:39 final size:40
Alignment explanation
Indices: 12067122--12067269 Score: 178
Period size: 40 Copynumber: 3.8 Consensus size: 40
12067112 AATTATTGAA
*
12067122 TGAATGCACATACGTGTCC-CTGTTTGTACTTTGGTACCCT
1 TGAATGCACATACGTG-CCTCTGTTTGTACTTCGGTACCCT
* * * *
12067162 TGAACGCACATATGTGCCTCTATTGGTACTTCGGTACCC-
1 TGAATGCACATACGTGCCTCTGTTTGTACTTCGGTACCCT
* *
12067201 GGAATGCACATACGTGCCT-TGTTTGTACTTCGATACCCT
1 TGAATGCACATACGTGCCTCTGTTTGTACTTCGGTACCCT
*
12067240 TGAATGCACATACGTGTCCT-TGTTTATACT
1 TGAATGCACATACGTG-CCTCTGTTTGTACT
12067270 CTAATAACTT
Statistics
Matches: 92, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
38 16 0.17
39 33 0.36
40 43 0.47
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.35
Consensus pattern (40 bp):
TGAATGCACATACGTGCCTCTGTTTGTACTTCGGTACCCT
Found at i:12069606 original size:53 final size:53
Alignment explanation
Indices: 12069517--12069660 Score: 195
Period size: 53 Copynumber: 2.7 Consensus size: 53
12069507 TTCAGAGCTG
* *
12069517 GCCATACATATCATTTCTT-T-GGGTTTTATCAGACTTACCATTCCTT-AAAGTTA
1 GCCATGCATATCA-TTCTTCTAGGGTTTT-TCATACTTACCATT-CTTCAAAGTTA
12069570 GCCATGCATATCATTCTTCTAGGGTTTTTCATACTTACCATTCTTCAAAGTTA
1 GCCATGCATATCATTCTTCTAGGGTTTTTCATACTTACCATTCTTCAAAGTTA
* * *
12069623 GTCATGCATATCATTCTTCCAGGGTTTGTCATACTTAC
1 GCCATGCATATCATTCTTCTAGGGTTTTTCATACTTAC
12069661 AATTTTTCTC
Statistics
Matches: 83, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
52 8 0.10
53 68 0.82
54 7 0.08
ACGTcount: A:0.24, C:0.22, G:0.12, T:0.41
Consensus pattern (53 bp):
GCCATGCATATCATTCTTCTAGGGTTTTTCATACTTACCATTCTTCAAAGTTA
Found at i:12069637 original size:26 final size:26
Alignment explanation
Indices: 12069555--12069641 Score: 77
Period size: 26 Copynumber: 3.3 Consensus size: 26
12069545 TCAGACTTAC
*
12069555 CATTCCTT-AAAGTTAGCCATGCATAT
1 CATT-CTTCAAAGTTAGTCATGCATAT
** ** * * *
12069581 CATTCTTCTAGGGTTTTTCATACTTAC
1 CATTCTTC-AAAGTTAGTCATGCATAT
12069608 CATTCTTCAAAGTTAGTCATGCATAT
1 CATTCTTCAAAGTTAGTCATGCATAT
12069634 CATTCTTC
1 CATTCTTC
12069642 CAGGGTTTGT
Statistics
Matches: 44, Mismatches: 15, Indels: 4
0.70 0.24 0.06
Matches are distributed among these distances:
25 3 0.07
26 23 0.52
27 18 0.41
ACGTcount: A:0.25, C:0.23, G:0.10, T:0.41
Consensus pattern (26 bp):
CATTCTTCAAAGTTAGTCATGCATAT
Found at i:12069828 original size:27 final size:27
Alignment explanation
Indices: 12069792--12069917 Score: 146
Period size: 27 Copynumber: 4.7 Consensus size: 27
12069782 TCATATATTG
*
12069792 CCAC-AAGGCTTCGATTTTATAGATTA
1 CCACAAAGGCTTCCATTTTATAGATTA
* * * * *
12069818 CCACTAAGGCTTTCACTTTAAAGATTG
1 CCACAAAGGCTTCCATTTTATAGATTA
*
12069845 CCACAAAGGCTTCCATTTTATAGATTG
1 CCACAAAGGCTTCCATTTTATAGATTA
*
12069872 CAACAAAGGCTTCCATTTTATAGATTA
1 CCACAAAGGCTTCCATTTTATAGATTA
** *
12069899 TTACAAAGGCTTCTATTTT
1 CCACAAAGGCTTCCATTTT
12069918 TCTAGCGTGT
Statistics
Matches: 85, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
26 4 0.05
27 81 0.95
ACGTcount: A:0.31, C:0.20, G:0.13, T:0.36
Consensus pattern (27 bp):
CCACAAAGGCTTCCATTTTATAGATTA
Found at i:12084497 original size:23 final size:23
Alignment explanation
Indices: 12084470--12084591 Score: 163
Period size: 23 Copynumber: 5.3 Consensus size: 23
12084460 ATAAGTGCCA
* * *
12084470 CACTGGTATGTAGCTGAAGCCAC
1 CACTGATATGTAGCCGAAGCTAC
* **
12084493 CACTGATACGTAGCCGTTGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
12084516 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
12084539 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
12084562 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
12084585 CACTGAT
1 CACTGAT
12084592 CAATAACACT
Statistics
Matches: 84, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 84 1.00
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:12084541 original size:46 final size:46
Alignment explanation
Indices: 12084477--12084591 Score: 194
Period size: 46 Copynumber: 2.5 Consensus size: 46
12084467 CCACACTGGT
* * *
12084477 ATGTAGCTGAAGCCACCACTGATACGTAGCCGTTGCTACCACTGAA
1 ATGTAGCCGAAGCTACCACTGATACGTAGCCGTAGCTACCACTGAA
*
12084523 ATGTAGCCGAAGCTACCACTGATATGTAGCCGTAGCTACCACTGAA
1 ATGTAGCCGAAGCTACCACTGATACGTAGCCGTAGCTACCACTGAA
12084569 ATGTAGCCGAAGCTACCACTGAT
1 ATGTAGCCGAAGCTACCACTGAT
12084592 CAATAACACT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 65 1.00
ACGTcount: A:0.30, C:0.27, G:0.22, T:0.22
Consensus pattern (46 bp):
ATGTAGCCGAAGCTACCACTGATACGTAGCCGTAGCTACCACTGAA
Found at i:12084691 original size:8 final size:8
Alignment explanation
Indices: 12084678--12084714 Score: 65
Period size: 8 Copynumber: 4.6 Consensus size: 8
12084668 ACCCAGGACT
12084678 CACTGTAA
1 CACTGTAA
12084686 CACTGTAA
1 CACTGTAA
12084694 CACTGTAA
1 CACTGTAA
*
12084702 CACTGCAA
1 CACTGTAA
12084710 CACTG
1 CACTG
12084715 GTCTCTAGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.35, C:0.30, G:0.14, T:0.22
Consensus pattern (8 bp):
CACTGTAA
Found at i:12084818 original size:18 final size:17
Alignment explanation
Indices: 12084792--12084830 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
12084782 ATTTTCCTTC
12084792 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
12084809 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
12084827 CACA
1 CACA
12084831 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:12088770 original size:16 final size:16
Alignment explanation
Indices: 12088749--12088788 Score: 71
Period size: 16 Copynumber: 2.4 Consensus size: 16
12088739 AATTTGAACT
12088749 TTCTTTCCAATTTATC
1 TTCTTTCCAATTTATC
12088765 TTCTTTCCAATTTATC
1 TTCTTTCCAATTTATC
12088781 TATCTTTC
1 T-TCTTTC
12088789 GCAACAATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 17 0.74
17 6 0.26
ACGTcount: A:0.17, C:0.25, G:0.00, T:0.57
Consensus pattern (16 bp):
TTCTTTCCAATTTATC
Found at i:12089879 original size:23 final size:22
Alignment explanation
Indices: 12089850--12089925 Score: 98
Period size: 23 Copynumber: 3.3 Consensus size: 22
12089840 ATAAGTGCCA
12089850 CACTGATATGTAGTCGAAGCTAC
1 CACTGATATGTAG-CGAAGCTAC
* *
12089873 CACTGATACGTAGCCATAGCTAC
1 CACTGATATGTAGCGA-AGCTAC
*
12089896 CACTGAAATGTAGCTGAAGCTAC
1 CACTGATATGTAGC-GAAGCTAC
12089919 CACTGAT
1 CACTGAT
12089926 CAATAACACT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
22 2 0.04
23 42 0.93
24 1 0.02
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.24
Consensus pattern (22 bp):
CACTGATATGTAGCGAAGCTAC
Found at i:12097555 original size:21 final size:21
Alignment explanation
Indices: 12097529--12097601 Score: 67
Period size: 21 Copynumber: 3.3 Consensus size: 21
12097519 TGATTTTTGG
12097529 ATTAAATTGAATAGTGTGTGA
1 ATTAAATTGAATAGTGTGTGA
* * * *
12097550 ATTAAATACATGTAT-GATTTTTGG
1 ATTAAAT---TGAATAG-TGTGTGA
12097574 ATTAAATTGAATAGTGTGTGA
1 ATTAAATTGAATAGTGTGTGA
12097595 ATTAAAT
1 ATTAAAT
12097602 AGATTGAATT
Statistics
Matches: 39, Mismatches: 8, Indels: 10
0.68 0.14 0.18
Matches are distributed among these distances:
21 22 0.56
22 1 0.03
23 1 0.03
24 15 0.38
ACGTcount: A:0.38, C:0.01, G:0.19, T:0.41
Consensus pattern (21 bp):
ATTAAATTGAATAGTGTGTGA
Found at i:12097571 original size:45 final size:45
Alignment explanation
Indices: 12097516--12097602 Score: 174
Period size: 45 Copynumber: 1.9 Consensus size: 45
12097506 ATTTGTGAAA
12097516 GTATGATTTTTGGATTAAATTGAATAGTGTGTGAATTAAATACAT
1 GTATGATTTTTGGATTAAATTGAATAGTGTGTGAATTAAATACAT
12097561 GTATGATTTTTGGATTAAATTGAATAGTGTGTGAATTAAATA
1 GTATGATTTTTGGATTAAATTGAATAGTGTGTGAATTAAATA
12097603 GATTGAATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.36, C:0.01, G:0.21, T:0.43
Consensus pattern (45 bp):
GTATGATTTTTGGATTAAATTGAATAGTGTGTGAATTAAATACAT
Found at i:12100544 original size:24 final size:26
Alignment explanation
Indices: 12100492--12100545 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 26
12100482 TTTCTCCTAA
*
12100492 ATTTCAATTTTATTTGATTATTTAGT
1 ATTTCAATTTTATTTGATTATTTAAT
12100518 ATTTCAA-TTTA-TTGAATTA-TTAAT
1 ATTTCAATTTTATTTG-ATTATTTAAT
12100542 ATTT
1 ATTT
12100546 TATGCAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 11 0.42
25 8 0.31
26 7 0.27
ACGTcount: A:0.31, C:0.04, G:0.06, T:0.59
Consensus pattern (26 bp):
ATTTCAATTTTATTTGATTATTTAAT
Found at i:12104028 original size:62 final size:62
Alignment explanation
Indices: 12103926--12104051 Score: 198
Period size: 62 Copynumber: 2.0 Consensus size: 62
12103916 ACCTATAAAT
* * *
12103926 ACCCCATTCACCTATTCATATCAACACACCTTTCATTCCTCATATCTCTCTCTCTTTCACTC
1 ACCCAATTCACCTATTCATATCAACACACCTTTCATTCCTCACATCTCTATCTCTTTCACTC
* * *
12103988 ACCCAATTCACCTATTCATTTCAACACACCTTTCATTCCTCACATCTTTATCTCTTTCATTC
1 ACCCAATTCACCTATTCATATCAACACACCTTTCATTCCTCACATCTCTATCTCTTTCACTC
12104050 AC
1 AC
12104052 TTTCTCTTCT
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 58 1.00
ACGTcount: A:0.24, C:0.38, G:0.00, T:0.38
Consensus pattern (62 bp):
ACCCAATTCACCTATTCATATCAACACACCTTTCATTCCTCACATCTCTATCTCTTTCACTC
Found at i:12107895 original size:15 final size:14
Alignment explanation
Indices: 12107872--12107914 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
12107862 TTTTATTTCA
12107872 TTTA-TTTTTAATT
1 TTTATTTTTTAATT
12107885 TTTATTCTTTT-ATT
1 TTTATT-TTTTAATT
12107899 TTTATTTGTTTAATT
1 TTTATTT-TTTAATT
12107914 T
1 T
12107915 CTTTTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 5 0.19
14 13 0.50
15 8 0.31
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (14 bp):
TTTATTTTTTAATT
Found at i:12110893 original size:41 final size:41
Alignment explanation
Indices: 12110830--12110977 Score: 224
Period size: 41 Copynumber: 3.6 Consensus size: 41
12110820 CAACCCCTCA
*
12110830 GGGAATCTGCACTCAGCAACCCCTTTTTGATCAGAGTTTCG
1 GGGAATCTGCACTTAGCAACCCCTTTTTGATCAGAGTTTCG
* *
12110871 GGGAATCTGCACTTAGCGACCCCTTTTTGATCAGAGTTTCC
1 GGGAATCTGCACTTAGCAACCCCTTTTTGATCAGAGTTTCG
* * * *
12110912 AGGAATCTGCACTTAGCAACCCCTTTTTGATTAGTGATTCG
1 GGGAATCTGCACTTAGCAACCCCTTTTTGATCAGAGTTTCG
*
12110953 GGGAATCTACACTTAGCAACCCCTT
1 GGGAATCTGCACTTAGCAACCCCTT
12110978 ACATTCAATG
Statistics
Matches: 96, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 96 1.00
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.30
Consensus pattern (41 bp):
GGGAATCTGCACTTAGCAACCCCTTTTTGATCAGAGTTTCG
Found at i:12112116 original size:11 final size:11
Alignment explanation
Indices: 12112100--12112125 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
12112090 AGGCCATAAA
12112100 AATATAATGAT
1 AATATAATGAT
12112111 AATATAATGAT
1 AATATAATGAT
12112122 AATA
1 AATA
12112126 AAAATCTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.08, T:0.35
Consensus pattern (11 bp):
AATATAATGAT
Found at i:12115212 original size:49 final size:49
Alignment explanation
Indices: 12115155--12115252 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
12115145 TCATAGCTAA
*
12115155 ATCTTTCTTCACACTTTTACTTCTAACTTCACTTCTGGTATTTCTCGGT
1 ATCTTTCTTCACACTTTTACTGCTAACTTCACTTCTGGTATTTCTCGGT
12115204 ATCTTTCTTCACACTTTTACTGCTAACTTCACTTCTGGTATTTCTCGGT
1 ATCTTTCTTCACACTTTTACTGCTAACTTCACTTCTGGTATTTCTCGGT
12115253 GGTCTACCTC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.16, C:0.27, G:0.09, T:0.48
Consensus pattern (49 bp):
ATCTTTCTTCACACTTTTACTGCTAACTTCACTTCTGGTATTTCTCGGT
Found at i:12116822 original size:50 final size:50
Alignment explanation
Indices: 12116756--12116859 Score: 208
Period size: 50 Copynumber: 2.1 Consensus size: 50
12116746 ATATATTTAA
12116756 ATCATACTTAACATTTTAACTATCATCATTAGCATTGTATAAAATAATTT
1 ATCATACTTAACATTTTAACTATCATCATTAGCATTGTATAAAATAATTT
12116806 ATCATACTTAACATTTTAACTATCATCATTAGCATTGTATAAAATAATTT
1 ATCATACTTAACATTTTAACTATCATCATTAGCATTGTATAAAATAATTT
12116856 ATCA
1 ATCA
12116860 AATAACATAT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 54 1.00
ACGTcount: A:0.40, C:0.14, G:0.04, T:0.41
Consensus pattern (50 bp):
ATCATACTTAACATTTTAACTATCATCATTAGCATTGTATAAAATAATTT
Found at i:12117349 original size:41 final size:41
Alignment explanation
Indices: 12117274--12117409 Score: 137
Period size: 41 Copynumber: 3.3 Consensus size: 41
12117264 TATATATCCT
* * * * **
12117274 TTAGCAACACCTTTTTGATCAGAGTTTCGGGGAATCTGCAC
1 TTAGCAACCCCTTTTTGATAAGTGATTCAAGGAATCTGCAC
* * * *
12117315 TTATCAACCTCTTTTTTATCAGTGATTCAAGGAATCTGCAC
1 TTAGCAACCCCTTTTTGATAAGTGATTCAAGGAATCTGCAC
* ** * *
12117356 TTAGCAACCCCTTTTTGATAAGTGATCCTGGGAGTCTACAC
1 TTAGCAACCCCTTTTTGATAAGTGATTCAAGGAATCTGCAC
12117397 TTAGCAACCCCTT
1 TTAGCAACCCCTT
12117410 ACATTCAATG
Statistics
Matches: 78, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 78 1.00
ACGTcount: A:0.25, C:0.24, G:0.17, T:0.34
Consensus pattern (41 bp):
TTAGCAACCCCTTTTTGATAAGTGATTCAAGGAATCTGCAC
Found at i:12121435 original size:10 final size:10
Alignment explanation
Indices: 12121420--12121460 Score: 55
Period size: 10 Copynumber: 3.9 Consensus size: 10
12121410 TAACATGTTG
12121420 AATTTTAATTA
1 AATTTTAA-TA
*
12121431 ATTTTATAATA
1 AATTT-TAATA
12121442 AATTTTAATA
1 AATTTTAATA
12121452 AATTTTAAT
1 AATTTTAAT
12121461 CATTTTCGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
10 14 0.52
11 10 0.37
12 3 0.11
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
AATTTTAATA
Found at i:12135913 original size:15 final size:15
Alignment explanation
Indices: 12135890--12135931 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
12135880 ACCATTCTAA
12135890 CCTCATTGATTCTGAC
1 CCTC-TTGATTCTGAC
* *
12135906 CCTCTTGATTGTTAC
1 CCTCTTGATTCTGAC
12135921 CCTCTTGATTC
1 CCTCTTGATTC
12135932 ATTGCTTGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 19 0.83
16 4 0.17
ACGTcount: A:0.14, C:0.31, G:0.12, T:0.43
Consensus pattern (15 bp):
CCTCTTGATTCTGAC
Found at i:12136776 original size:19 final size:19
Alignment explanation
Indices: 12136739--12136779 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
12136729 ATTAAGCCAT
* **
12136739 ATTAACATTAATCGTAATA
1 ATTAACATTAAGCACAATA
12136758 ATTAACATTAAGCACAATA
1 ATTAACATTAAGCACAATA
12136777 ATT
1 ATT
12136780 CCAAGCATCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.49, C:0.12, G:0.05, T:0.34
Consensus pattern (19 bp):
ATTAACATTAAGCACAATA
Found at i:12142021 original size:23 final size:23
Alignment explanation
Indices: 12141978--12142021 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
12141968 TGTATAATTT
*
12141978 TGATTAAATTGAATGTTAATATG
1 TGATTAAATTGAATGTAAATATG
*
12142001 TGATTATATTGTAAT-TAAATA
1 TGATTAAATTG-AATGTAAATA
12142022 AATATATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 15 0.83
24 3 0.17
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (23 bp):
TGATTAAATTGAATGTAAATATG
Found at i:12142343 original size:23 final size:24
Alignment explanation
Indices: 12142264--12142334 Score: 70
Period size: 27 Copynumber: 2.8 Consensus size: 24
12142254 CGTTCTGACC
* **
12142264 CACAGCTCGTGTGAGCAGGTCCATTT
1 CACAGCTCGTGTGAGCA-TTTGA-TT
12142290 CCACAGCTCGTGTGAGCATTTTGATT
1 -CACAGCTCGTGTGAGCA-TTTGATT
*
12142316 CACAGCTTGTGTGAGCATT
1 CACAGCTCGTGTGAGCATT
12142335 GATGTACAGG
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
24 2 0.05
25 16 0.41
26 2 0.05
27 19 0.49
ACGTcount: A:0.20, C:0.24, G:0.25, T:0.31
Consensus pattern (24 bp):
CACAGCTCGTGTGAGCATTTGATT
Found at i:12148938 original size:41 final size:41
Alignment explanation
Indices: 12148849--12148953 Score: 156
Period size: 41 Copynumber: 2.6 Consensus size: 41
12148839 AAGTGTAAAC
* * *
12148849 AGGGGCAAGTATGTACAATTCAAGGGTACCGAAGTACAAAT
1 AGGGGCACGTATGTGCAATTCAGGGGTACCGAAGTACAAAT
*
12148890 AGGGGCACGTATGTGCAATTCAGGGGTACCTAAGTACAAAT
1 AGGGGCACGTATGTGCAATTCAGGGGTACCGAAGTACAAAT
**
12148931 AGGGGCACACATGTGCAATTCAG
1 AGGGGCACGTATGTGCAATTCAG
12148954 TGAATAATTA
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 58 1.00
ACGTcount: A:0.34, C:0.17, G:0.29, T:0.20
Consensus pattern (41 bp):
AGGGGCACGTATGTGCAATTCAGGGGTACCGAAGTACAAAT
Found at i:12151550 original size:13 final size:15
Alignment explanation
Indices: 12151532--12151563 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
12151522 CTACAACGGA
12151532 CACATGG-C-TGTGT
1 CACATGGCCGTGTGT
12151545 CACATGGCCGTGTGT
1 CACATGGCCGTGTGT
12151560 CACA
1 CACA
12151564 CACGGCTGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 1 0.06
15 9 0.53
ACGTcount: A:0.19, C:0.28, G:0.28, T:0.25
Consensus pattern (15 bp):
CACATGGCCGTGTGT
Found at i:12157043 original size:6 final size:6
Alignment explanation
Indices: 12157032--12157087 Score: 76
Period size: 6 Copynumber: 9.0 Consensus size: 6
12157022 AGACAGAAAA
*
12157032 TAATTT TAATTT TAATTT TAATTT TAATTT CAATTT TAAAATTT TAATTT
1 TAATTT TAATTT TAATTT TAATTT TAATTT TAATTT T--AATTT TAATTT
*
12157082 TTATTT
1 TAATTT
12157088 GTTTATATTT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
6 39 0.87
8 6 0.13
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (6 bp):
TAATTT
Found at i:12164739 original size:46 final size:46
Alignment explanation
Indices: 12164686--12164778 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 46
12164676 TTACGAATAA
12164686 ATTTCCCCATGTAATACGCAGAGGCTAGATTGGATAGGCATTCATC
1 ATTTCCCCATGTAATACGCAGAGGCTAGATTGGATAGGCATTCATC
*
12164732 ATTTCCCCATGTAATATGCAGAGGCTAGATTGGATAGGCATTCATC
1 ATTTCCCCATGTAATACGCAGAGGCTAGATTGGATAGGCATTCATC
12164778 A
1 A
12164779 AAAACATGAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (46 bp):
ATTTCCCCATGTAATACGCAGAGGCTAGATTGGATAGGCATTCATC
Found at i:12184665 original size:25 final size:25
Alignment explanation
Indices: 12184637--12184710 Score: 80
Period size: 25 Copynumber: 3.0 Consensus size: 25
12184627 CATGTACATG
*
12184637 TATGCTCATACGAGCTGTAAATCGA
1 TATGCTCATATGAGCTGTAAATCGA
* *
12184662 TATGCTCATTTGAGTTG-AAGATCGA
1 TATGCTCATATGAGCTGTAA-ATCGA
*
12184687 TATGCTC-TCATGAGCTATAAATCG
1 TATGCTCAT-ATGAGCTGTAAATCG
12184711 GTAACCCTAA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
24 3 0.08
25 35 0.88
26 2 0.05
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (25 bp):
TATGCTCATATGAGCTGTAAATCGA
Found at i:12186106 original size:15 final size:15
Alignment explanation
Indices: 12186083--12186124 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
12186073 ACCATTCTAA
12186083 CCTCATTGATTCTGAC
1 CCTC-TTGATTCTGAC
* *
12186099 CCTCTTGATTGTTAC
1 CCTCTTGATTCTGAC
12186114 CCTCTTGATTC
1 CCTCTTGATTC
12186125 ATTGCTTGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 19 0.83
16 4 0.17
ACGTcount: A:0.14, C:0.31, G:0.12, T:0.43
Consensus pattern (15 bp):
CCTCTTGATTCTGAC
Found at i:12186295 original size:20 final size:22
Alignment explanation
Indices: 12186265--12186305 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
12186255 AATAAAAATT
12186265 ATAACTAAAAATGAAA-TTACA
1 ATAACTAAAAATGAAAGTTACA
12186286 ATAA-TAAAAATGAAAGTTAC
1 ATAACTAAAAATGAAAGTTAC
12186306 CAATTGCCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.61, C:0.07, G:0.07, T:0.24
Consensus pattern (22 bp):
ATAACTAAAAATGAAAGTTACA
Found at i:12189990 original size:7 final size:7
Alignment explanation
Indices: 12189978--12190002 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
12189968 CATGGTTAGG
12189978 TGTAAAT
1 TGTAAAT
12189985 TGTAAAT
1 TGTAAAT
12189992 TGTAAAT
1 TGTAAAT
12189999 TGTA
1 TGTA
12190003 TAGGGTTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.16, T:0.44
Consensus pattern (7 bp):
TGTAAAT
Found at i:12192301 original size:23 final size:23
Alignment explanation
Indices: 12192258--12192301 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
12192248 TGTATAATTT
*
12192258 TGATTAAATTGAATGTTAATATG
1 TGATTAAATTGAATGTAAATATG
*
12192281 TGATTATATTGTAAT-TAAATA
1 TGATTAAATTG-AATGTAAATA
12192302 AATATATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 15 0.83
24 3 0.17
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (23 bp):
TGATTAAATTGAATGTAAATATG
Found at i:12195722 original size:15 final size:15
Alignment explanation
Indices: 12195702--12195730 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
12195692 TGGTGCCTTG
12195702 TTGATATGTGTTAAT
1 TTGATATGTGTTAAT
12195717 TTGATATGTGTTAA
1 TTGATATGTGTTAA
12195731 AGTATGTTTG
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:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTGATATGTGTTAAT
Found at i:12201217 original size:15 final size:15
Alignment explanation
Indices: 12201197--12201227 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
12201187 CCAACCTTCA
12201197 AATTTTACCTCAATT
1 AATTTTACCTCAATT
12201212 AATTTTACCTCAATT
1 AATTTTACCTCAATT
12201227 A
1 A
12201228 TACATAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.19, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTTTACCTCAATT
Found at i:12203487 original size:11 final size:11
Alignment explanation
Indices: 12203471--12203497 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
12203461 TAGAAATTAG
12203471 TTTGTGAAACT
1 TTTGTGAAACT
12203482 TTTGTGAAACT
1 TTTGTGAAACT
12203493 TTTGT
1 TTTGT
12203498 ATTGATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.07, G:0.19, T:0.52
Consensus pattern (11 bp):
TTTGTGAAACT
Found at i:12205354 original size:16 final size:16
Alignment explanation
Indices: 12205333--12205374 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
12205323 ATATTAAATT
*
12205333 ATATATTTTAATTATA
1 ATATATTTTAATAATA
12205349 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
12205364 AT-TATGTTTAA
1 ATATAT-TTTAA
12205375 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:12205359 original size:15 final size:15
Alignment explanation
Indices: 12205323--12205365 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
12205313 GAGTAAATTC
*
12205323 ATATTAAATTAT-AT
1 ATATTTAATTATAAT
12205337 AT-TTTAATTATAAT
1 ATATTTAATTATAAT
*
12205351 ATATTTAATAATAAT
1 ATATTTAATTATAAT
12205366 TATGTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.32
14 6 0.24
15 11 0.44
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATATTTAATTATAAT
Found at i:12205505 original size:18 final size:17
Alignment explanation
Indices: 12205477--12205511 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
12205467 ATTATTAAGA
*
12205477 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
12205494 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
12205512 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:12205553 original size:157 final size:157
Alignment explanation
Indices: 12205324--12205624 Score: 566
Period size: 157 Copynumber: 1.9 Consensus size: 157
12205314 AGTAAATTCA
*
12205324 TATTAAATTATATATTTTAATTATAATATATTTAATAATAATTATGTTTAAATATGATTAAATTA
1 TATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATTAAATTA
*
12205389 TTTATTATTGATATTAATAATCTTATTAAAATTTAAATAACAATAACAATAATAATTTACCAAAA
66 TTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATAATAATTTACCAAAA
12205454 CAAATTTATGCTAATTATTAAGAATTT
131 CAAATTTATGCTAATTATTAAGAATTT
12205481 TATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATTAAATTA
1 TATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATTAAATTA
*
12205546 TTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATAATCATTTACCAAAA
66 TTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATAATAATTTACCAAAA
*
12205611 CAAATTTCTGCTAA
131 CAAATTTATGCTAA
12205625 GGGTATTCTA
Statistics
Matches: 140, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
157 140 1.00
ACGTcount: A:0.48, C:0.05, G:0.03, T:0.44
Consensus pattern (157 bp):
TATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTTAAATATGATTAAATTA
TTTATTATTGATAATAATAATCTTATTAAAATTTAAATAACAATAACAATAATAATTTACCAAAA
CAAATTTATGCTAATTATTAAGAATTT
Found at i:12205776 original size:16 final size:16
Alignment explanation
Indices: 12205757--12205797 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
12205747 ACACAGCTTT
*
12205757 TCCATTACACCTCTAA
1 TCCAATACACCTCTAA
12205773 TCCAATACACCTCTAA
1 TCCAATACACCTCTAA
12205789 TCCAATACA
1 TCCAATACA
12205798 ACGAACCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.37, C:0.37, G:0.00, T:0.27
Consensus pattern (16 bp):
TCCAATACACCTCTAA
Found at i:12208839 original size:41 final size:41
Alignment explanation
Indices: 12208802--12208892 Score: 137
Period size: 41 Copynumber: 2.2 Consensus size: 41
12208792 ATCGAAGTGT
12208802 AAACAGGGGCAAGTATGTGCAATTCAAGGGTACCGAAGTAC
1 AAACAGGGGCAAGTATGTGCAATTCAAGGGTACCGAAGTAC
* * * *
12208843 AAATAGGGGCACGTATGTGCAATTCAGGGGTACCTAAGTAC
1 AAACAGGGGCAAGTATGTGCAATTCAAGGGTACCGAAGTAC
*
12208884 AAATAGGGG
1 AAACAGGGG
12208893 AACACATGTG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.35, C:0.15, G:0.31, T:0.19
Consensus pattern (41 bp):
AAACAGGGGCAAGTATGTGCAATTCAAGGGTACCGAAGTAC
Found at i:12208902 original size:41 final size:41
Alignment explanation
Indices: 12208816--12208910 Score: 136
Period size: 41 Copynumber: 2.3 Consensus size: 41
12208806 AGGGGCAAGT
* * **
12208816 ATGTGCAATTCAAGGGTACCGAAGTACAAATAGGGGCACGT
1 ATGTGCAATTCAGGGGTACCGAAGTACAAATAGGGGAACAC
*
12208857 ATGTGCAATTCAGGGGTACCTAAGTACAAATAGGGGAACAC
1 ATGTGCAATTCAGGGGTACCGAAGTACAAATAGGGGAACAC
*
12208898 ATGTGCAAGTCAG
1 ATGTGCAATTCAG
12208911 TGAATAATTA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.35, C:0.17, G:0.28, T:0.20
Consensus pattern (41 bp):
ATGTGCAATTCAGGGGTACCGAAGTACAAATAGGGGAACAC
Found at i:12217393 original size:20 final size:21
Alignment explanation
Indices: 12217365--12217404 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
12217355 TATGTAATCA
12217365 AAAAGTTTTAATTTTAATTTT
1 AAAAGTTTTAATTTTAATTTT
*
12217386 AAAA-TTTTAATTTTTATTT
1 AAAAGTTTTAATTTTAATTT
12217405 GTTTATATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (21 bp):
AAAAGTTTTAATTTTAATTTT
Found at i:12217469 original size:18 final size:18
Alignment explanation
Indices: 12217446--12217481 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
12217436 CAAGTACTAA
12217446 TCAGTTTATTTTTCTAGT
1 TCAGTTTATTTTTCTAGT
*
12217464 TCAGTTTATTTTTTTAGT
1 TCAGTTTATTTTTCTAGT
12217482 ACAACAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.08, G:0.11, T:0.64
Consensus pattern (18 bp):
TCAGTTTATTTTTCTAGT
Found at i:12251806 original size:5 final size:5
Alignment explanation
Indices: 12251786--12251839 Score: 58
Period size: 5 Copynumber: 10.8 Consensus size: 5
12251776 TTAGTTTAGG
* *
12251786 TTTTC ATTTT- TTTTC TTTTC TCTTC TTTTC -TGTC TTTTTC TTTTC TTTTC
1 TTTTC -TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC -TTTTC TTTTC TTTTC
12251836 TTTT
1 TTTT
12251840 TGTAGTATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
4 7 0.17
5 27 0.66
6 7 0.17
ACGTcount: A:0.02, C:0.19, G:0.02, T:0.78
Consensus pattern (5 bp):
TTTTC
Found at i:12255326 original size:17 final size:17
Alignment explanation
Indices: 12255304--12255341 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
12255294 TATGGTGACC
12255304 ATGGGTATGTGGATGGT
1 ATGGGTATGTGGATGGT
12255321 ATGGGTATGTGGATGGT
1 ATGGGTATGTGGATGGT
12255338 ATGG
1 ATGG
12255342 ATAGTTACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.18, C:0.00, G:0.47, T:0.34
Consensus pattern (17 bp):
ATGGGTATGTGGATGGT
Found at i:12255764 original size:9 final size:9
Alignment explanation
Indices: 12255750--12255780 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
12255740 GTTAAACGAA
12255750 TCGAGTTAT
1 TCGAGTTAT
*
12255759 TCGAGTTAA
1 TCGAGTTAT
12255768 TCGAGTTAT
1 TCGAGTTAT
12255777 TCGA
1 TCGA
12255781 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:12255852 original size:9 final size:9
Alignment explanation
Indices: 12255833--12255869 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
12255823 TGAGTTTTTG
*
12255833 AATTTGAAT
1 AATTCGAAT
*
12255842 AACTCGAAT
1 AATTCGAAT
12255851 AATTCGAAT
1 AATTCGAAT
12255860 AATTCGAAT
1 AATTCGAAT
12255869 A
1 A
12255870 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:12256349 original size:21 final size:20
Alignment explanation
Indices: 12256303--12256350 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
12256293 CCTTTACTCC
*
12256303 CAAATAAAAAATCAAAATAT
1 CAAATAAAAAATCAAAACAT
12256323 CCAAATAAAAAATCACTAAACAT
1 -CAAATAAAAAATCA--AAACAT
12256346 -AAATA
1 CAAATA
12256351 GTAATAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 19 0.79
23 5 0.21
ACGTcount: A:0.67, C:0.15, G:0.00, T:0.19
Consensus pattern (20 bp):
CAAATAAAAAATCAAAACAT
Found at i:12258015 original size:82 final size:82
Alignment explanation
Indices: 12257878--12258042 Score: 224
Period size: 82 Copynumber: 2.0 Consensus size: 82
12257868 TAAATAAATG
* * **
12257878 GGGTCAAAGTCTAAATGATAAGAAGTTAGATTTAGTTCAAGTGAGGGGTTTAAATTGTTAATATG
1 GGGTCAAAGTCTAAATGATAAGAAATTAGATTTAGTTCAACTGAGGAATTTAAATTGTTAATATG
* *
12257943 CTATAAGTACCTTAGTT
66 CCACAAGTACCTTAGTT
* * * *
12257960 GGGTCAATGTCTAAATGGTGAGAAATTAGATTTATTTCATACT-AGGAATTTAAATTGTTAATAT
1 GGGTCAAAGTCTAAATGATAAGAAATTAGATTTAGTTCA-ACTGAGGAATTTAAATTGTTAATAT
12258024 GCCACAAGTACCTTAGTT
65 GCCACAAGTACCTTAGTT
12258042 G
1 G
12258043 TCACATAGTT
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
82 70 0.97
83 2 0.03
ACGTcount: A:0.34, C:0.09, G:0.21, T:0.36
Consensus pattern (82 bp):
GGGTCAAAGTCTAAATGATAAGAAATTAGATTTAGTTCAACTGAGGAATTTAAATTGTTAATATG
CCACAAGTACCTTAGTT
Found at i:12259906 original size:13 final size:13
Alignment explanation
Indices: 12259888--12259914 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12259878 TTCGATATGA
12259888 TGTGTTAGGAGTT
1 TGTGTTAGGAGTT
12259901 TGTGTTAGGAGTT
1 TGTGTTAGGAGTT
12259914 T
1 T
12259915 ATTGGTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.37, T:0.48
Consensus pattern (13 bp):
TGTGTTAGGAGTT
Found at i:12264235 original size:29 final size:25
Alignment explanation
Indices: 12264181--12264231 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
12264171 ACTGGCATCC
12264181 TTAGCATGCATGCAATGGCTGTCAT
1 TTAGCATGCATGCAATGGCTGTCAT
12264206 TTAGCATGCATGCAATGGCTGTCAT
1 TTAGCATGCATGCAATGGCTGTCAT
12264231 T
1 T
12264232 CATTAAAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (25 bp):
TTAGCATGCATGCAATGGCTGTCAT
Found at i:12264710 original size:21 final size:21
Alignment explanation
Indices: 12264662--12264722 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
12264652 ACCAAGTGTT
* *
12264662 TGCCCCAACTCAACAAGAATC
1 TGCCCCAACTCATCAACAATC
*
12264683 TGTCCCAACTCATCAAC-ATAC
1 TGCCCCAACTCATCAACAAT-C
12264704 TGCCCCAACTCATCAACAA
1 TGCCCCAACTCATCAACAA
12264723 GTTACTCCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
20 2 0.06
21 31 0.91
22 1 0.03
ACGTcount: A:0.36, C:0.39, G:0.07, T:0.18
Consensus pattern (21 bp):
TGCCCCAACTCATCAACAATC
Found at i:12266368 original size:16 final size:16
Alignment explanation
Indices: 12266329--12266374 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 16
12266319 GCTTGTTTGT
12266329 TAATTTTAAT-GTAAAG
1 TAATTTT-ATGGTAAAG
*
12266345 TAGTTTTTATGGTAAAG
1 TA-ATTTTATGGTAAAG
12266362 TAATTTT-TGGTAA
1 TAATTTTATGGTAA
12266375 TTTTAATGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 6 0.23
16 8 0.31
17 12 0.46
ACGTcount: A:0.35, C:0.00, G:0.17, T:0.48
Consensus pattern (16 bp):
TAATTTTATGGTAAAG
Found at i:12267336 original size:34 final size:34
Alignment explanation
Indices: 12267298--12267383 Score: 145
Period size: 34 Copynumber: 2.5 Consensus size: 34
12267288 TTACAGTGTT
12267298 ATTTGGTGTGCTGGATGGATTAGCTCATATGAAC
1 ATTTGGTGTGCTGGATGGATTAGCTCATATGAAC
*
12267332 ATTTGGTGTGCTGGATGGATTAGCTCATATGAGC
1 ATTTGGTGTGCTGGATGGATTAGCTCATATGAAC
* *
12267366 ATCTGATGTGCTGGATGG
1 ATTTGGTGTGCTGGATGG
12267384 TTAACCGTGT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.21, C:0.12, G:0.33, T:0.35
Consensus pattern (34 bp):
ATTTGGTGTGCTGGATGGATTAGCTCATATGAAC
Found at i:12268744 original size:9 final size:9
Alignment explanation
Indices: 12268730--12268806 Score: 91
Period size: 9 Copynumber: 8.6 Consensus size: 9
12268720 TTCTCAATAC
*
12268730 CAACAGCTA
1 CAACAGCAA
12268739 CAACAGCAA
1 CAACAGCAA
*
12268748 CAACAACAA
1 CAACAGCAA
*
12268757 CAACAACAA
1 CAACAGCAA
*
12268766 CAACAACAA
1 CAACAGCAA
*
12268775 CAACAACAA
1 CAACAGCAA
*
12268784 CAACAACAA
1 CAACAGCAA
*
12268793 CAACAACAA
1 CAACAGCAA
12268802 CAACA
1 CAACA
12268807 ACAATCACAT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
9 66 1.00
ACGTcount: A:0.62, C:0.34, G:0.03, T:0.01
Consensus pattern (9 bp):
CAACAGCAA
Found at i:12268753 original size:3 final size:3
Alignment explanation
Indices: 12268738--12268810 Score: 137
Period size: 3 Copynumber: 24.3 Consensus size: 3
12268728 ACCAACAGCT
*
12268738 ACA ACA GCA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA
1 ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA ACA
12268786 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
12268811 TCACATAAGC
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.66, C:0.33, G:0.01, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:12269893 original size:3 final size:3
Alignment explanation
Indices: 12269885--12269926 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
12269875 CTCTCGTCTT
12269885 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
12269927 ACGGTTGAAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:12270690 original size:16 final size:16
Alignment explanation
Indices: 12270669--12270701 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
12270659 GGAAAAAAAA
12270669 TTGGATGAATTTTTAT
1 TTGGATGAATTTTTAT
12270685 TTGGATGAATTTTTAT
1 TTGGATGAATTTTTAT
12270701 T
1 T
12270702 GGGGGGAAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.18, T:0.58
Consensus pattern (16 bp):
TTGGATGAATTTTTAT
Found at i:12271785 original size:30 final size:30
Alignment explanation
Indices: 12271721--12271822 Score: 81
Period size: 30 Copynumber: 3.4 Consensus size: 30
12271711 AATTAAAACA
*
12271721 AAAATTAATAAAAGTATTTTAAAATTTAAA---
1 AAAATTAA-AAAAGTATTTTAAAA--AAAATTT
12271751 AAAATTAAAAAAGTATTTTAAAAAAAATTT
1 AAAATTAAAAAAGTATTTTAAAAAAAATTT
*
12271781 AAAATTTAAAAA--A-TTTAAAAAAAGTATTTT
1 AAAATTAAAAAAGTATTTTAAAAAAA--A-TTT
*
12271811 AAAATAAAAAAA
1 AAAATTAAAAAA
12271823 TAAAAATATT
Statistics
Matches: 62, Mismatches: 4, Indels: 12
0.79 0.05 0.15
Matches are distributed among these distances:
27 13 0.21
28 1 0.02
29 16 0.26
30 32 0.52
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (30 bp):
AAAATTAAAAAAGTATTTTAAAAAAAATTT
Found at i:12271793 original size:41 final size:42
Alignment explanation
Indices: 12271738--12271819 Score: 141
Period size: 40 Copynumber: 2.0 Consensus size: 42
12271728 ATAAAAGTAT
12271738 TTTAAAATTTAAAAAAATT-AAAAAAGTATTTTAAAA-AAAA
1 TTTAAAATTTAAAAAAATTAAAAAAAGTATTTTAAAATAAAA
*
12271778 TTTAAAATTTAAAAAATTTAAAAAAAGTATTTTAAAATAAAA
1 TTTAAAATTTAAAAAAATTAAAAAAAGTATTTTAAAATAAAA
12271820 AAATAAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
40 18 0.46
41 17 0.44
42 4 0.10
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (42 bp):
TTTAAAATTTAAAAAAATTAAAAAAAGTATTTTAAAATAAAA
Found at i:12271809 original size:29 final size:27
Alignment explanation
Indices: 12271767--12271823 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 27
12271757 AAAAAAGTAT
*
12271767 TTTAAAAAAAA-TTTAAAATTTAAAAAA
1 TTTAAAAAAAATTTTAAAA-TAAAAAAA
12271794 TTTAAAAAAAGTATTTTAAAATAAAAAAA
1 TTTAAAAAAA--ATTTTAAAATAAAAAAA
12271823 T
1 T
12271824 AAAAATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 10 0.38
29 9 0.35
30 7 0.27
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (27 bp):
TTTAAAAAAAATTTTAAAATAAAAAAA
Done.