Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397254.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_30.0, 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: 15579451
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 73860 characters in sequence are not A, C, G, or T
File 28 of 32
Found at i:13585210 original size:20 final size:20
Alignment explanation
Indices: 13585185--13585223 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
13585175 TGCATAACTT
*
13585185 ACTTTGTACATTGTGTGACG
1 ACTTTGGACATTGTGTGACG
*
13585205 ACTTTGGGCATTGTGTGAC
1 ACTTTGGACATTGTGTGAC
13585224 TTATTTTTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.15, G:0.28, T:0.38
Consensus pattern (20 bp):
ACTTTGGACATTGTGTGACG
Found at i:13585239 original size:22 final size:22
Alignment explanation
Indices: 13585211--13585291 Score: 74
Period size: 22 Copynumber: 3.6 Consensus size: 22
13585201 GACGACTTTG
* **
13585211 GGCATTGTGTGACTTATTTTTA
1 GGCATTGCGTGACTTATTGGTA
*
13585233 GGTATTGCGTGAC-TAGTTGGTA
1 GGCATTGCGTGACTTA-TTGGTA
*
13585255 GGCATTGCGTGACTTATTAGTA
1 GGCATTGCGTGACTTATTGGTA
* *
13585277 AGCTATTGCATGACT
1 GGC-ATTGCGTGACT
13585292 AGTTAATAAG
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
21 2 0.04
22 34 0.71
23 12 0.25
ACGTcount: A:0.21, C:0.12, G:0.27, T:0.40
Consensus pattern (22 bp):
GGCATTGCGTGACTTATTGGTA
Found at i:13585290 original size:23 final size:23
Alignment explanation
Indices: 13585232--13585330 Score: 130
Period size: 23 Copynumber: 4.3 Consensus size: 23
13585222 ACTTATTTTT
*
13585232 AGGTATTGCGTGACTAGTTGGT-
1 AGGTATTGCGTGACTAGTTAGTA
*
13585254 AGGCATTGCGTGACTTA-TTAGTA
1 AGGTATTGCGTGAC-TAGTTAGTA
* * *
13585277 AGCTATTGCATGACTAGTTAATA
1 AGGTATTGCGTGACTAGTTAGTA
13585300 AGGTATTGCGTGACTAGTTAGTA
1 AGGTATTGCGTGACTAGTTAGTA
13585323 AGGTATTG
1 AGGTATTG
13585331 TGTAACTTAG
Statistics
Matches: 65, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
22 19 0.29
23 46 0.71
ACGTcount: A:0.26, C:0.10, G:0.28, T:0.35
Consensus pattern (23 bp):
AGGTATTGCGTGACTAGTTAGTA
Found at i:13585321 original size:46 final size:45
Alignment explanation
Indices: 13585211--13585330 Score: 127
Period size: 46 Copynumber: 2.7 Consensus size: 45
13585201 GACGACTTTG
* * * * * **
13585211 GGCATTGTGTGACTTATT-TTTAGGTATTGCGTGACTAGTTGGTA
1 GGCATTGCGTGACTTATTAGTAAGCTATTGCATGACTAGTTAATA
13585255 GGCATTGCGTGACTTATTAGTAAGCTATTGCATGACTAGTTAATAA
1 GGCATTGCGTGACTTATTAGTAAGCTATTGCATGACTAGTTAAT-A
* *
13585301 GGTATTGCGTGAC-TAGTTAGTAAGGTATTG
1 GGCATTGCGTGACTTA-TTAGTAAGCTATTG
13585331 TGTAACTTAG
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
44 17 0.27
45 21 0.33
46 26 0.41
ACGTcount: A:0.24, C:0.10, G:0.28, T:0.38
Consensus pattern (45 bp):
GGCATTGCGTGACTTATTAGTAAGCTATTGCATGACTAGTTAATA
Found at i:13587584 original size:2 final size:2
Alignment explanation
Indices: 13587577--13587611 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
13587567 GTTCTACTTC
13587577 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13587612 CACATACACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:13594267 original size:33 final size:33
Alignment explanation
Indices: 13594218--13594407 Score: 107
Period size: 33 Copynumber: 5.8 Consensus size: 33
13594208 AATTAAAATA
*
13594218 AAAAATATTAACATAAAATATATAATATAAGAAT
1 AAAAA-ATTAAAATAAAATATATAATATAAGAAT
13594252 AAAAAATTAAAAT-AAA-ATA-AA-AT----AT
1 AAAAAATTAAAATAAAATATATAATATAAGAAT
*
13594277 AAAAAATTAAAAT---TTATATAATATAAGTAA-
1 AAAAAATTAAAATAAAATATATAATATAAG-AAT
* *
13594307 AATAAATTAAAATAAAATATATAATATTAAAAATTATATT
1 AAAAAATTAAAATAAAATATATAATA-T---AA-GA-A-T
* * * *
13594347 AAAGAAATGAAAATAAAATATATAAGATTATAAT
1 AAA-AAATTAAAATAAAATATATAATATAAGAAT
* * *
13594381 AATAAATAAAAATAAAATATATGATAT
1 AAAAAATTAAAATAAAATATATAATAT
13594408 TAAAAATATA
Statistics
Matches: 123, Mismatches: 13, Indels: 41
0.69 0.07 0.23
Matches are distributed among these distances:
24 3 0.02
25 17 0.14
26 2 0.02
29 2 0.02
30 14 0.11
31 4 0.03
32 3 0.02
33 37 0.30
34 9 0.07
35 1 0.01
36 2 0.02
37 4 0.03
38 1 0.01
40 3 0.02
41 21 0.17
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.31
Consensus pattern (33 bp):
AAAAAATTAAAATAAAATATATAATATAAGAAT
Found at i:13594269 original size:5 final size:5
Alignment explanation
Indices: 13594211--13594325 Score: 53
Period size: 5 Copynumber: 23.4 Consensus size: 5
13594201 ATGTTTTAAT
* * * * *
13594211 TAAAA TAAAA -AATAT TAACA TAAAA T-ATA TAATA TAAGAA T-AAA -AAAT
1 TAAAA TAAAA TAA-AA TAAAA TAAAA TAAAA TAAAA TAA-AA TAAAA TAAAA
* ** * *
13594259 TAAAA TAAAA TAAAA TATAAA -AAAT TAAAA T-TTA TATAA TATAAG TAAAA
1 TAAAA TAAAA TAAAA TA-AAA TAAAA TAAAA TAAAA TAAAA TA-AAA TAAAA
*
13594309 TAAAT TAAAA TAAAA TA
1 TAAAA TAAAA TAAAA TA
13594326 TATAATATTA
Statistics
Matches: 82, Mismatches: 18, Indels: 20
0.68 0.15 0.17
Matches are distributed among these distances:
4 13 0.16
5 59 0.72
6 10 0.12
ACGTcount: A:0.69, C:0.01, G:0.02, T:0.29
Consensus pattern (5 bp):
TAAAA
Found at i:13594317 original size:55 final size:57
Alignment explanation
Indices: 13594236--13594342 Score: 166
Period size: 55 Copynumber: 1.9 Consensus size: 57
13594226 TAACATAAAA
13594236 TATATAATATAAGAATAAAAAATTAAAATAAAATA-A-AATATAAAAAATTAAAATT
1 TATATAATATAAGAATAAAAAATTAAAATAAAATATATAATATAAAAAATTAAAATT
* *
13594291 TATATAATATAAGTAA-AATAAATTAAAATAAAATATATAATATTAAAAATTA
1 TATATAATATAAG-AATAAAAAATTAAAATAAAATATATAATATAAAAAATTA
13594343 TATTAAAGAA
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
55 31 0.66
56 3 0.06
57 13 0.28
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (57 bp):
TATATAATATAAGAATAAAAAATTAAAATAAAATATATAATATAAAAAATTAAAATT
Found at i:13594322 original size:50 final size:53
Alignment explanation
Indices: 13594232--13594345 Score: 146
Period size: 50 Copynumber: 2.2 Consensus size: 53
13594222 ATATTAACAT
13594232 AAAA-TATATAATATAAGAATAAAAAATTAAAATAAAATAAAATATAAAAAATTA
1 AAAATTATATAATATAAG-AT-AAAAATTAAAATAAAATAAAATATAAAAAATTA
* * * *
13594286 AAATTTATATAATATAAG-T-AAAA-TAAATTAAAATAAAATATATAATATTA
1 AAAATTATATAATATAAGATAAAAATTAAAATAAAATAAAATATAAAAAATTA
13594336 AAAATTATAT
1 AAAATTATAT
13594346 TAAAGAAATG
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
50 33 0.61
51 4 0.07
53 1 0.02
54 3 0.06
55 13 0.24
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.32
Consensus pattern (53 bp):
AAAATTATATAATATAAGATAAAAATTAAAATAAAATAAAATATAAAAAATTA
Found at i:13594324 original size:15 final size:15
Alignment explanation
Indices: 13594208--13594325 Score: 70
Period size: 15 Copynumber: 8.0 Consensus size: 15
13594198 ATAATGTTTT
13594208 AATTAAAATAAAA-A
1 AATTAAAATAAAATA
*
13594222 ATATTAACATAAAATA
1 A-ATTAAAATAAAATA
* *
13594238 TA-TAATATAAGAATA
1 AATTAAAATAA-AATA
*
13594253 AA--AAATTAAAATA
1 AATTAAAATAAAATA
*
13594266 AAATAAAATATAAA-A
1 AATTAAAATA-AAATA
**
13594281 AATTAAAAT-TTATA
1 AATTAAAATAAAATA
*
13594295 TAA-TATAAGTAAAATA
1 -AATTA-AAATAAAATA
13594311 AATTAAAATAAAATA
1 AATTAAAATAAAATA
13594326 TATAATATTA
Statistics
Matches: 79, Mismatches: 14, Indels: 21
0.69 0.12 0.18
Matches are distributed among these distances:
13 7 0.09
14 16 0.20
15 47 0.59
16 9 0.11
ACGTcount: A:0.69, C:0.01, G:0.02, T:0.29
Consensus pattern (15 bp):
AATTAAAATAAAATA
Found at i:13601072 original size:2 final size:2
Alignment explanation
Indices: 13601065--13601101 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
13601055 CCCTTCTCAG
13601065 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
13601102 TATCCCAGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:13602011 original size:4 final size:4
Alignment explanation
Indices: 13602002--13602028 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
13601992 AAATGTGTAA
13602002 TCTT TCTT TCTT TCTT TCTT TCTT TCT
1 TCTT TCTT TCTT TCTT TCTT TCTT TCT
13602029 ATTTTTGGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (4 bp):
TCTT
Found at i:13610652 original size:24 final size:24
Alignment explanation
Indices: 13610623--13610671 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
13610613 AATGACTCAT
*
13610623 CTGGAAGAAACAGTCATGTCAGCA
1 CTGGAAGAAACAGTCATGGCAGCA
*
13610647 CTGGAAGAAGCAGTCATGGCAGCA
1 CTGGAAGAAACAGTCATGGCAGCA
13610671 C
1 C
13610672 AATTACGCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.35, C:0.22, G:0.29, T:0.14
Consensus pattern (24 bp):
CTGGAAGAAACAGTCATGGCAGCA
Found at i:13623126 original size:860 final size:860
Alignment explanation
Indices: 13621412--13623093 Score: 3364
Period size: 860 Copynumber: 2.0 Consensus size: 860
13621402 TTAATACAAA
13621412 GATACTGGTTCAATATTAGATTTTAAAAGCAGGTTAGTGTGAAAATTGAGTTGCTTTTTAGATAG
1 GATACTGGTTCAATATTAGATTTTAAAAGCAGGTTAGTGTGAAAATTGAGTTGCTTTTTAGATAG
13621477 AGGCTTTCACTAAGGCTTAGTTTTAGGATAGAATTTAAAGCATATTGTAGATATTCTTGAAGATA
66 AGGCTTTCACTAAGGCTTAGTTTTAGGATAGAATTTAAAGCATATTGTAGATATTCTTGAAGATA
13621542 ACATACATTGATGTTAACAAAACAAAATGTTTTTTTAACTTTTAAATTTGATATGAAAGATTTGG
131 ACATACATTGATGTTAACAAAACAAAATGTTTTTTTAACTTTTAAATTTGATATGAAAGATTTGG
13621607 GGGAAGCCAATTTTGTTTTGGGTGTTAAAACCATAAGATGTGATAATGGTCTATTGCTAACACAA
196 GGGAAGCCAATTTTGTTTTGGGTGTTAAAACCATAAGATGTGATAATGGTCTATTGCTAACACAA
13621672 GAGTATTATGTTGAGAAGCTACTTAAAAAGTTTAGACATTTAATGTCACACATATGAGTATTCCT
261 GAGTATTATGTTGAGAAGCTACTTAAAAAGTTTAGACATTTAATGTCACACATATGAGTATTCCT
13621737 TATGTTGCTAATATCCAATTAAAAAAAATAAAGGTGATAGTATGGCTCAACTTAAGTATGCTCAG
326 TATGTTGCTAATATCCAATTAAAAAAAATAAAGGTGATAGTATGGCTCAACTTAAGTATGCTCAG
13621802 ATTATTGGGAGTCTAATGTATTTGATGAGTTATGCTCAACCTGATATAGCTTATGCTATATGTAG
391 ATTATTGGGAGTCTAATGTATTTGATGAGTTATGCTCAACCTGATATAGCTTATGCTATATGTAG
13621867 ACTGAGCAGATATACATAGAGTCCCAATTGGGATCACTGAACTGCCTTGAGCAAAGTAATGAAAT
456 ACTGAGCAGATATACATAGAGTCCCAATTGGGATCACTGAACTGCCTTGAGCAAAGTAATGAAAT
13621932 TGAGAGGTACCATAAACTATGGTATTCTATATAATAGATTTCTCGCTGTATTAGAAGGGTACAAT
521 TGAGAGGTACCATAAACTATGGTATTCTATATAATAGATTTCTCGCTGTATTAGAAGGGTACAAT
13621997 GATGCTAATTGGATTTCAGATTTCGATAAGACAAAATCCACAAGTGGATATGTATTCACTTTTGA
586 GATGCTAATTGGATTTCAGATTTCGATAAGACAAAATCCACAAGTGGATATGTATTCACTTTTGA
13622062 CAGGGGTATTGTAATTTGAAAATTAGCCAAACAAATAATAATTGCTAAATATACAATGGAATTAG
651 CAGGGGTATTGTAATTTGAAAATTAGCCAAACAAATAATAATTGCTAAATATACAATGGAATTAG
13622127 AATTTGTAGCTTTGGAATTAGTTGGCAACGAGGTTGAGTGGTTAAGAAACCTCTTAGCGGATATT
716 AATTTGTAGCTTTGGAATTAGTTGGCAACGAGGTTGAGTGGTTAAGAAACCTCTTAGCGGATATT
13622192 TCGTTAGGAATGAAATTGAAAACTTTCGTGTCTATGCATTGTGATTGCCAAATGGCAATAGCTAT
781 TCGTTAGGAATGAAATTGAAAACTTTCGTGTCTATGCATTGTGATTGCCAAATGGCAATAGCTAT
13622257 TGCAAAGAATGTAGG
846 TGCAAAGAATGTAGG
13622272 GATACTGGTTCAATATTAGATTTTAAAAGCAGGTTAGTGTGAAAATTGAGTTGCTTTTTAGATAG
1 GATACTGGTTCAATATTAGATTTTAAAAGCAGGTTAGTGTGAAAATTGAGTTGCTTTTTAGATAG
13622337 AGGCTTTCACTAAGGCTTAGTTTTAGGATAGAATTTAAAGCATATTGTAGATATTCTTGAAGATA
66 AGGCTTTCACTAAGGCTTAGTTTTAGGATAGAATTTAAAGCATATTGTAGATATTCTTGAAGATA
13622402 ACATACATTGATGTTAACAAAACAAAATGTTTTTTTAACTTTTAAATTTGATATGAAAGATTTGG
131 ACATACATTGATGTTAACAAAACAAAATGTTTTTTTAACTTTTAAATTTGATATGAAAGATTTGG
13622467 GGGAAGCCAATTTTGTTTTGGGTGTTAAAACCATAAGATGTGATAATGGTCTATTGCTAACACAA
196 GGGAAGCCAATTTTGTTTTGGGTGTTAAAACCATAAGATGTGATAATGGTCTATTGCTAACACAA
13622532 GAGTATTATGTTGAGAAGCTACTTAAAAAGTTTAGACATTTAATGTCACACATATGAGTATTCCT
261 GAGTATTATGTTGAGAAGCTACTTAAAAAGTTTAGACATTTAATGTCACACATATGAGTATTCCT
13622597 TATGTTGCTAATATCCAATTAAAAAAAATAAAGGTGATAGTATGGCTCAACTTAAGTATGCTCAG
326 TATGTTGCTAATATCCAATTAAAAAAAATAAAGGTGATAGTATGGCTCAACTTAAGTATGCTCAG
13622662 ATTATTGGGAGTCTAATGTATTTGATGAGTTATGCTCAACCTGATATAGCTTATGCTATATGTAG
391 ATTATTGGGAGTCTAATGTATTTGATGAGTTATGCTCAACCTGATATAGCTTATGCTATATGTAG
13622727 ACTGAGCAGATATACATAGAGTCCCAATTGGGATCACTGAACTGCCTTGAGCAAAGTAATGAAAT
456 ACTGAGCAGATATACATAGAGTCCCAATTGGGATCACTGAACTGCCTTGAGCAAAGTAATGAAAT
13622792 TGAGAGGTACCATAAACTATGGTATTCTATATAATAGATTTCTCGCTGTATTAGAAGGGTACAAT
521 TGAGAGGTACCATAAACTATGGTATTCTATATAATAGATTTCTCGCTGTATTAGAAGGGTACAAT
13622857 GATGCTAATTGGATTTCAGATTTCGATAAGACAAAATCCACAAGTGGATATGTATTCACTTTTGA
586 GATGCTAATTGGATTTCAGATTTCGATAAGACAAAATCCACAAGTGGATATGTATTCACTTTTGA
13622922 CAGGGGTATTGTAATTTGAAAATTAGCCAAACAAATAATAATTGCTAAATATACAATGGAATTAG
651 CAGGGGTATTGTAATTTGAAAATTAGCCAAACAAATAATAATTGCTAAATATACAATGGAATTAG
13622987 AATTTGTAGCTTTGGAATTAGTTGGCAACGAGGTTGAGTGGTTAAGAAACCTCTTAGCGGATATT
716 AATTTGTAGCTTTGGAATTAGTTGGCAACGAGGTTGAGTGGTTAAGAAACCTCTTAGCGGATATT
13623052 TCGTTAGGAATGAAATTGAAAACTTTCGTGTCTATGCATTGT
781 TCGTTAGGAATGAAATTGAAAACTTTCGTGTCTATGCATTGT
13623094 NNNNNNNNNN
Statistics
Matches: 822, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
860 822 1.00
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.34
Consensus pattern (860 bp):
GATACTGGTTCAATATTAGATTTTAAAAGCAGGTTAGTGTGAAAATTGAGTTGCTTTTTAGATAG
AGGCTTTCACTAAGGCTTAGTTTTAGGATAGAATTTAAAGCATATTGTAGATATTCTTGAAGATA
ACATACATTGATGTTAACAAAACAAAATGTTTTTTTAACTTTTAAATTTGATATGAAAGATTTGG
GGGAAGCCAATTTTGTTTTGGGTGTTAAAACCATAAGATGTGATAATGGTCTATTGCTAACACAA
GAGTATTATGTTGAGAAGCTACTTAAAAAGTTTAGACATTTAATGTCACACATATGAGTATTCCT
TATGTTGCTAATATCCAATTAAAAAAAATAAAGGTGATAGTATGGCTCAACTTAAGTATGCTCAG
ATTATTGGGAGTCTAATGTATTTGATGAGTTATGCTCAACCTGATATAGCTTATGCTATATGTAG
ACTGAGCAGATATACATAGAGTCCCAATTGGGATCACTGAACTGCCTTGAGCAAAGTAATGAAAT
TGAGAGGTACCATAAACTATGGTATTCTATATAATAGATTTCTCGCTGTATTAGAAGGGTACAAT
GATGCTAATTGGATTTCAGATTTCGATAAGACAAAATCCACAAGTGGATATGTATTCACTTTTGA
CAGGGGTATTGTAATTTGAAAATTAGCCAAACAAATAATAATTGCTAAATATACAATGGAATTAG
AATTTGTAGCTTTGGAATTAGTTGGCAACGAGGTTGAGTGGTTAAGAAACCTCTTAGCGGATATT
TCGTTAGGAATGAAATTGAAAACTTTCGTGTCTATGCATTGTGATTGCCAAATGGCAATAGCTAT
TGCAAAGAATGTAGG
Found at i:13624269 original size:51 final size:52
Alignment explanation
Indices: 13624164--13624292 Score: 179
Period size: 51 Copynumber: 2.5 Consensus size: 52
13624154 TTTTACCAAA
* *
13624164 ATAGAATTTGATTTGGTCTTTGATTCTGCCAAACATTATAAAATAAACTATT
1 ATAGAACTTGATTTGGTATTTGATTCTGCCAAACATTATAAAATAAACTATT
* * *
13624216 ATAGAACTTGATTTGGTATTTGATTTTG-CTAACATTATAAATTAAACTATT
1 ATAGAACTTGATTTGGTATTTGATTCTGCCAAACATTATAAAATAAACTATT
* *
13624267 ATAGGACATGATTTGGTATTTTGATT
1 ATAGAACTTGATTTGGTA-TTTGATT
13624293 ATTTTTTAGA
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
51 37 0.54
52 32 0.46
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (52 bp):
ATAGAACTTGATTTGGTATTTGATTCTGCCAAACATTATAAAATAAACTATT
Found at i:13626923 original size:30 final size:29
Alignment explanation
Indices: 13626882--13626964 Score: 96
Period size: 30 Copynumber: 2.8 Consensus size: 29
13626872 ATGGAAACAA
* *
13626882 ATATGTTTTCTTCTCTAGATTAAGCTAAAAT
1 ATAT-TTTTCTTCTCTAAATTAAGC-AAAAG
*
13626913 ATATTTTTCTTCTCTTAAATTAAGCCAAAG
1 ATATTTTTCTTCTC-TAAATTAAGCAAAAG
*
13626943 ATA-TTTTCTTGTCTAAATTAAG
1 ATATTTTTCTTCTCTAAATTAAG
13626965 ACTGAACATG
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
28 9 0.19
29 9 0.19
30 16 0.34
31 13 0.28
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (29 bp):
ATATTTTTCTTCTCTAAATTAAGCAAAAG
Found at i:13629663 original size:31 final size:31
Alignment explanation
Indices: 13629628--13629691 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
13629618 AAACCATCCT
13629628 AAGAACGATACTTACCAAATAATTTAGTATG
1 AAGAACGATACTTACCAAATAATTTAGTATG
13629659 AAGAACGATACTTACCAAATAATTTAGTATG
1 AAGAACGATACTTACCAAATAATTTAGTATG
13629690 AA
1 AA
13629692 TCCAAACCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.28
Consensus pattern (31 bp):
AAGAACGATACTTACCAAATAATTTAGTATG
Found at i:13640160 original size:36 final size:36
Alignment explanation
Indices: 13640119--13640203 Score: 116
Period size: 36 Copynumber: 2.4 Consensus size: 36
13640109 AGGATTAGGT
*
13640119 GTAACCTTTACAACATGCCTTTTAACAAGATCAAAC
1 GTAACCTTCACAACATGCCTTTTAACAAGATCAAAC
** **
13640155 GTAACCTTCACAACATGCCTTTTCTCAAGATCACGC
1 GTAACCTTCACAACATGCCTTTTAACAAGATCAAAC
*
13640191 ATAACCTTCACAA
1 GTAACCTTCACAA
13640204 AAACACTTCT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.35, C:0.29, G:0.08, T:0.27
Consensus pattern (36 bp):
GTAACCTTCACAACATGCCTTTTAACAAGATCAAAC
Found at i:13644475 original size:10 final size:10
Alignment explanation
Indices: 13644460--13644485 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
13644450 ATCTATACAA
13644460 TCTTGCACAT
1 TCTTGCACAT
13644470 TCTTGCACAT
1 TCTTGCACAT
13644480 TCTTGC
1 TCTTGC
13644486 CTTGATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.15, C:0.31, G:0.12, T:0.42
Consensus pattern (10 bp):
TCTTGCACAT
Found at i:13647825 original size:52 final size:52
Alignment explanation
Indices: 13647742--13647840 Score: 128
Period size: 52 Copynumber: 1.9 Consensus size: 52
13647732 TTTCTTTTAA
* *
13647742 TAGAACTGATTCGTCAATGTTTCTGTCTGCTAAGAACT-ACTTCTTCTGTTCT
1 TAGAACTAATTCGTCAATATTTCTGTCTGCTAAGAACTGACTT-TTCTGTTCT
* * * *
13647794 TAGAACTAATTCTTCACTATTTTTGTTTGCTAAGAACTGACTTTTCT
1 TAGAACTAATTCGTCAATATTTCTGTCTGCTAAGAACTGACTTTTCT
13647841 CATTTTCAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
52 36 0.90
53 4 0.10
ACGTcount: A:0.23, C:0.19, G:0.13, T:0.44
Consensus pattern (52 bp):
TAGAACTAATTCGTCAATATTTCTGTCTGCTAAGAACTGACTTTTCTGTTCT
Found at i:13648007 original size:20 final size:20
Alignment explanation
Indices: 13647982--13648031 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
13647972 AGAAAACTTA
* *
13647982 AAAGCATATCTTTAAGTTTC
1 AAAGCATATCATTAACTTTC
*
13648002 AAAGCATTATCATTCACTTTC
1 AAAGCA-TATCATTAACTTTC
13648023 AAAGCATAT
1 AAAGCATAT
13648032 TCAATTAATC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (20 bp):
AAAGCATATCATTAACTTTC
Found at i:13656793 original size:18 final size:18
Alignment explanation
Indices: 13656759--13656793 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
13656749 NNNNAATATA
*
13656759 AAAATAAAAAATTAAAAT
1 AAAATAAAAAATAAAAAT
*
13656777 AAAATAAAATATAAAAA
1 AAAATAAAAAATAAAAA
13656794 ATTAACATTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (18 bp):
AAAATAAAAAATAAAAAT
Found at i:13656849 original size:14 final size:14
Alignment explanation
Indices: 13656830--13657077 Score: 60
Period size: 14 Copynumber: 18.2 Consensus size: 14
13656820 ACAAATTAAA
13656830 ATAAAATATATAAT
1 ATAAAATATATAAT
*
13656844 ATAAAAAATAT-AT
1 ATAAAATATATAAT
* *
13656857 -TAAAAAATAAAAT
1 ATAAAATATATAAT
13656870 A-AAAATAT-TAAGATT
1 ATAAAATATAT-A-A-T
* * *
13656885 ATAACATAAACGAA-
1 ATAAAATATA-TAAT
*
13656899 ATAAAATATATGAT
1 ATAAAATATATAAT
13656913 ATTAAAATATAT--T
1 A-TAAAATATATAAT
*
13656926 -TAAGATATGATATTAT
1 ATAA-A-AT-ATATAAT
13656942 ATAAAAT-TAATAAT
1 ATAAAATAT-ATAAT
*
13656956 A-AAAATAAAT-AT
1 ATAAAATATATAAT
13656968 ATTAAAA-ATA-AAT
1 A-TAAAATATATAAT
13656981 AATAAAATATTATAAT
1 -ATAAAATA-TATAAT
*
13656997 A-ATAA-A-A-AA-
1 ATAAAATATATAAT
13657006 ATAAAATATATGACAT
1 ATAAAATATAT-A-AT
13657022 -TAAAA-ATAT-AT
1 ATAAAATATATAAT
*
13657033 -TAGAAATGATATTAT
1 ATA-AAAT-ATATAAT
13657048 ATAAAA-AT-TAAT
1 ATAAAATATATAAT
13657060 AATAAAA-ATATAAAT
1 -ATAAAATATAT-AAT
13657075 ATA
1 ATA
13657078 TTAAACTTGT
Statistics
Matches: 177, Mismatches: 17, Indels: 80
0.65 0.06 0.29
Matches are distributed among these distances:
9 1 0.01
10 5 0.03
11 9 0.05
12 20 0.11
13 43 0.24
14 51 0.29
15 31 0.18
16 13 0.07
17 4 0.02
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.32
Consensus pattern (14 bp):
ATAAAATATATAAT
Found at i:13656860 original size:12 final size:14
Alignment explanation
Indices: 13656830--13656874 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 14
13656820 ACAAATTAAA
*
13656830 ATAAAATATATAAT
1 ATAAAAAATATAAT
13656844 ATAAAAAATAT-AT
1 ATAAAAAATATAAT
13656857 -TAAAAAATA-AA-
1 ATAAAAAATATAAT
13656868 ATAAAAA
1 ATAAAAA
13656875 TATTAAGATT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
12 16 0.57
13 2 0.07
14 10 0.36
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
ATAAAAAATATAAT
Found at i:13656966 original size:13 final size:13
Alignment explanation
Indices: 13656944--13657004 Score: 68
Period size: 15 Copynumber: 4.3 Consensus size: 13
13656934 GATATTATAT
*
13656944 AAAATTAATAATA
1 AAAATAAATAATA
13656957 AAAATAAATATATTA
1 AAAATAAATA-A-TA
13656972 AAAATAAATAATA
1 AAAATAAATAATA
13656985 AAATATTATAATAATA
1 AAA-A-TA-AATAATA
13657001 AAAA
1 AAAA
13657005 AATAAAATAT
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
13 14 0.33
14 3 0.07
15 15 0.36
16 10 0.24
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATAAATAATA
Found at i:13656967 original size:24 final size:24
Alignment explanation
Indices: 13656940--13657015 Score: 72
Period size: 24 Copynumber: 3.2 Consensus size: 24
13656930 ATATGATATT
13656940 ATATAAAATTAATAATAAAAAT-AA
1 ATAT-AAATTAATAATAAAAATAAA
*
13656964 ATAT--ATTAAAAATAAATAATAAA
1 ATATAAATTAATAATAAA-AATAAA
13656987 ATATTATAA-TAATAA-AAAAATAAA
1 ATA-TA-AATTAATAATAAAAATAAA
13657011 ATATA
1 ATATA
13657016 TGACATTAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
21 11 0.25
22 3 0.07
23 7 0.16
24 14 0.32
25 3 0.07
26 5 0.11
27 1 0.02
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (24 bp):
ATATAAATTAATAATAAAAATAAA
Found at i:13656972 original size:21 final size:21
Alignment explanation
Indices: 13656947--13657008 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
13656937 ATTATATAAA
13656947 ATTAATAATAAAAATAAATAT
1 ATTAATAATAAAAATAAATAT
*
13656968 ATTAAAAATAAATAATAAA-AT
1 ATTAATAATAAA-AATAAATAT
*
13656989 ATT-ATAATAATAAAAAAATA
1 ATTAATAATAA-AAATAAATA
13657009 AAATATATGA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
20 11 0.31
21 18 0.51
22 6 0.17
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (21 bp):
ATTAATAATAAAAATAAATAT
Found at i:13656992 original size:52 final size:53
Alignment explanation
Indices: 13656901--13657082 Score: 156
Period size: 52 Copynumber: 3.3 Consensus size: 53
13656891 TAAACGAAAT
* ** *
13656901 AAAATATATGATATTAAAATATATTTAAGATATGATATTATATAAAATTAATAATA
1 AAAATAAAT-ATATTAAAA-ATAAATAAGA-AAGATATTATATAAAATTAATAATA
* *
13656957 AAAATAAATATATTAAAAATAAATAATAAA-ATATTATAATAATAA--AAAAAT-
1 AAAATAAATATATTAAAAATAAATAAGAAAGATATTAT-ATAA-AATTAATAATA
* * * *
13657008 AAAATATATGACATTAAAAATATATTAGAAATGATATTATATAAAAATTAATAATAA
1 AAAATAAAT-ATATTAAAAATAAATAAGAAA-GATATTATAT-AAAATTAATAAT-A
13657065 AAATATAAATATATTAAA
1 AAA-ATAAATATATTAAA
13657083 CTTGTATTTT
Statistics
Matches: 101, Mismatches: 14, Indels: 21
0.74 0.10 0.15
Matches are distributed among these distances:
51 8 0.08
52 29 0.29
53 9 0.09
54 18 0.18
55 14 0.14
56 8 0.08
57 10 0.10
58 5 0.05
ACGTcount: A:0.62, C:0.01, G:0.03, T:0.34
Consensus pattern (53 bp):
AAAATAAATATATTAAAAATAAATAAGAAAGATATTATATAAAATTAATAATA
Found at i:13657251 original size:15 final size:15
Alignment explanation
Indices: 13657231--13657284 Score: 65
Period size: 15 Copynumber: 3.6 Consensus size: 15
13657221 TTTTCCCTGT
*
13657231 AATCACATTGCTTGC
1 AATCACATTACTTGC
13657246 AATCACATTACTTGC
1 AATCACATTACTTGC
* *
13657261 AATCATATTA-TCTGT
1 AATCACATTACT-TGC
13657276 AATCACATT
1 AATCACATT
13657285 GCATTGTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
14 1 0.03
15 33 0.97
ACGTcount: A:0.33, C:0.22, G:0.07, T:0.37
Consensus pattern (15 bp):
AATCACATTACTTGC
Found at i:13659176 original size:21 final size:21
Alignment explanation
Indices: 13659150--13659198 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
13659140 TTTACTACCA
13659150 GCATTATTGTAAACATGCATT
1 GCATTATTGTAAACATGCATT
13659171 GCATTATTGTAAACATGCATT
1 GCATTATTGTAAACATGCATT
13659192 GCATTAT
1 GCATTAT
13659199 AAAAGGCATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (21 bp):
GCATTATTGTAAACATGCATT
Found at i:13669151 original size:32 final size:33
Alignment explanation
Indices: 13669110--13669175 Score: 125
Period size: 32 Copynumber: 2.0 Consensus size: 33
13669100 TATGAGATCG
13669110 ATATTGTCTATTCGATACGTATACTTGC-TAAT
1 ATATTGTCTATTCGATACGTATACTTGCATAAT
13669142 ATATTGTCTATTCGATACGTATACTTGCATAAT
1 ATATTGTCTATTCGATACGTATACTTGCATAAT
13669175 A
1 A
13669176 GAATTTTAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 28 0.85
33 5 0.15
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.42
Consensus pattern (33 bp):
ATATTGTCTATTCGATACGTATACTTGCATAAT
Found at i:13670238 original size:36 final size:36
Alignment explanation
Indices: 13670184--13670289 Score: 140
Period size: 36 Copynumber: 2.9 Consensus size: 36
13670174 TGTATGGAGG
* *
13670184 AAGCCCATGCCCAAAACTTATTAAAAGAAAAGAAAT
1 AAGCCCATGACCAAAACTTATTAAAAGAAAAGAAAC
* * * *
13670220 AAGCCTATGACTATAACTTATTAAAAGAAAAGGAAC
1 AAGCCCATGACCAAAACTTATTAAAAGAAAAGAAAC
* *
13670256 AAGCCCATGCCCAAAACTTGTTAAAAGAAAAGAA
1 AAGCCCATGACCAAAACTTATTAAAAGAAAAGAA
13670290 GTAGTTCTGT
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 58 1.00
ACGTcount: A:0.51, C:0.18, G:0.13, T:0.18
Consensus pattern (36 bp):
AAGCCCATGACCAAAACTTATTAAAAGAAAAGAAAC
Found at i:13670825 original size:2 final size:2
Alignment explanation
Indices: 13670818--13670844 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
13670808 ACTTAGTTTT
13670818 TA TA TA 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 T
13670845 CATCTTCCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13671821 original size:18 final size:17
Alignment explanation
Indices: 13671792--13671839 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
13671782 TTAATTTTTA
13671792 AAAAATAA-TTAAAAAT
1 AAAAATAATTTAAAAAT
* *
13671808 ACAAAATATTTTAATAAT
1 A-AAAATAATTTAAAAAT
*
13671826 AAAATTAATTTAAA
1 AAAAATAATTTAAA
13671840 TGGGTGAGCT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
16 1 0.04
17 16 0.64
18 8 0.32
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAAATAATTTAAAAAT
Found at i:13673945 original size:28 final size:28
Alignment explanation
Indices: 13673883--13673965 Score: 94
Period size: 28 Copynumber: 3.0 Consensus size: 28
13673873 TTTTGCTCAC
*
13673883 CAAAAAATAGATGGATAACTTAACCCAT
1 CAAAAAGTAGATGGATAACTTAACCCAT
* * *
13673911 TAAAAAGTAGATGGAAAACTTAACTCAT
1 CAAAAAGTAGATGGATAACTTAACCCAT
** * *
13673939 CCGAAAGTGGATTGATAACTTAACCCA
1 CAAAAAGTAGATGGATAACTTAACCCA
13673966 CTAGAAATGG
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.23
Consensus pattern (28 bp):
CAAAAAGTAGATGGATAACTTAACCCAT
Found at i:13673972 original size:28 final size:27
Alignment explanation
Indices: 13673892--13673977 Score: 84
Period size: 28 Copynumber: 3.1 Consensus size: 27
13673882 CCAAAAAATA
* *
13673892 GATGGATAACTTAACCCATTAAAAAGTA
1 GATGGATAACTTAACCCA-TAGAAAGTG
* * *
13673920 GATGGAAAACTTAACTCATCCGAAAGTG
1 GATGGATAACTTAACCCAT-AGAAAGTG
*
13673948 GATTGATAACTTAACCCACTAGAAA-TG
1 GATGGATAACTTAACCCA-TAGAAAGTG
13673975 GAT
1 GAT
13673978 AACCCACCAA
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
27 6 0.13
28 40 0.85
29 1 0.02
ACGTcount: A:0.42, C:0.16, G:0.17, T:0.24
Consensus pattern (27 bp):
GATGGATAACTTAACCCATAGAAAGTG
Found at i:13677879 original size:37 final size:38
Alignment explanation
Indices: 13677833--13677918 Score: 156
Period size: 37 Copynumber: 2.3 Consensus size: 38
13677823 ATAATATTAG
13677833 TGTTCAACAAATTCAGTTAAGTGAGAATCTAACATACT
1 TGTTCAACAAATTCAGTTAAGTGAGAATCTAACATACT
13677871 TGTT-AACAAATTCAGTTAAGTGAGAATCTAACATACT
1 TGTTCAACAAATTCAGTTAAGTGAGAATCTAACATACT
*
13677908 TGTTCACCAAA
1 TGTTCAACAAA
13677919 ACCTTTTTTA
Statistics
Matches: 46, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
37 37 0.80
38 9 0.20
ACGTcount: A:0.40, C:0.16, G:0.13, T:0.31
Consensus pattern (38 bp):
TGTTCAACAAATTCAGTTAAGTGAGAATCTAACATACT
Found at i:13680417 original size:17 final size:17
Alignment explanation
Indices: 13680397--13680431 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
13680387 TTTTTAACAT
13680397 TTTATAT-TTATATAATA
1 TTTATATGTTAT-TAATA
13680414 TTTATATGTTATTAATA
1 TTTATATGTTATTAATA
13680431 T
1 T
13680432 AGAGTGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (17 bp):
TTTATATGTTATTAATA
Found at i:13680611 original size:30 final size:29
Alignment explanation
Indices: 13680575--13680667 Score: 107
Period size: 29 Copynumber: 3.2 Consensus size: 29
13680565 AATCATTAGT
*
13680575 TATAAAAATTTATTTGATTAAAAATAAAAA
1 TATAAAAATTTATTTAATT-AAAATAAAAA
*
13680605 TATAAAAATATATTTAATTTAAAAT-AAAA
1 TATAAAAATTTATTTAA-TTAAAATAAAAA
* * * *
13680634 TAAAAAAATTTAATTAAATATAATAAAAA
1 TATAAAAATTTATTTAATTAAAATAAAAA
13680663 TATAA
1 TATAA
13680668 GAGCTATTAT
Statistics
Matches: 53, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
28 5 0.09
29 26 0.49
30 20 0.38
31 2 0.04
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.35
Consensus pattern (29 bp):
TATAAAAATTTATTTAATTAAAATAAAAA
Found at i:13680627 original size:25 final size:24
Alignment explanation
Indices: 13680599--13680666 Score: 73
Period size: 25 Copynumber: 2.8 Consensus size: 24
13680589 TGATTAAAAA
13680599 TAAAAATATAAAAATATATTTAAT
1 TAAAAATATAAAAATATATTTAAT
* * * *
13680623 TTAAAATAAAATAAAAAAATTTAAT
1 TAAAAATATAA-AAATATATTTAAT
*
13680648 TAAATATAATAAAAATATA
1 TAAAAAT-ATAAAAATATA
13680667 AGAGCTATTA
Statistics
Matches: 33, Mismatches: 9, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
24 9 0.27
25 21 0.64
26 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (24 bp):
TAAAAATATAAAAATATATTTAAT
Found at i:13682328 original size:17 final size:18
Alignment explanation
Indices: 13682308--13682343 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
13682298 AATCGAGATG
13682308 AATTAAAAATATT-ATTT
1 AATTAAAAATATTAATTT
*
13682325 AATTAAAATTATTAATTT
1 AATTAAAAATATTAATTT
13682343 A
1 A
13682344 TAAAAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AATTAAAAATATTAATTT
Found at i:13682349 original size:17 final size:17
Alignment explanation
Indices: 13682311--13682373 Score: 51
Period size: 17 Copynumber: 3.6 Consensus size: 17
13682301 CGAGATGAAT
13682311 TAAAAA-TATT-ATTTAA
1 TAAAAATTATTAATTT-A
*
13682327 TTAAAATTATTAATTTA
1 TAAAAATTATTAATTTA
13682344 TAAAAATT-TTACTATATATA
1 TAAAAATTATTA--AT-T-TA
13682364 TAAAAATTAT
1 TAAAAATTAT
13682374 ATTATATTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
16 8 0.21
17 12 0.32
18 6 0.16
19 1 0.03
20 10 0.26
21 1 0.03
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
TAAAAATTATTAATTTA
Found at i:13682379 original size:18 final size:18
Alignment explanation
Indices: 13682329--13682380 Score: 52
Period size: 20 Copynumber: 2.8 Consensus size: 18
13682319 TTATTTAATT
* *
13682329 AAAATTAT-TAATTTATA
1 AAAATTATATTATATATA
*
13682346 AAAATTTTACTATATATATA
1 AAAATTATA-T-TATATATA
13682366 AAAATTATATTATAT
1 AAAATTATATTATAT
13682381 TGAGTATATA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
17 7 0.25
18 5 0.18
19 2 0.07
20 14 0.50
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (18 bp):
AAAATTATATTATATATA
Found at i:13682379 original size:20 final size:20
Alignment explanation
Indices: 13682342--13682380 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
13682332 ATTATTAATT
*
13682342 TATAAAAATTTTACTATATA
1 TATAAAAATTATACTATATA
*
13682362 TATAAAAATTATATTATAT
1 TATAAAAATTATACTATAT
13682381 TGAGTATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (20 bp):
TATAAAAATTATACTATATA
Found at i:13682405 original size:17 final size:17
Alignment explanation
Indices: 13682374--13682407 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
13682364 TAAAAATTAT
*
13682374 ATTATATTGAGTATATA
1 ATTATATTAAGTATATA
*
13682391 ATTATATTAATTATATA
1 ATTATATTAAGTATATA
13682408 TCTCTTTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (17 bp):
ATTATATTAAGTATATA
Found at i:13689315 original size:27 final size:27
Alignment explanation
Indices: 13689285--13689369 Score: 93
Period size: 27 Copynumber: 3.1 Consensus size: 27
13689275 TATGAAGTTT
* *
13689285 AAAGGTCTAGAAGATCCAAAAGACCTA
1 AAAGGTCTAAAAGATCCAAAAGATCTA
13689312 AAAGG-CTTAAAAGATCCAAAAGATCTA
1 AAAGGTC-TAAAAGATCCAAAAGATCTA
** *
13689339 GAAAACT-TAAAAGATCCAAAAGGTCTA
1 -AAAGGTCTAAAAGATCCAAAAGATCTA
13689366 AAAG
1 AAAG
13689370 ATCAAGATTC
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
26 4 0.08
27 42 0.86
28 3 0.06
ACGTcount: A:0.52, C:0.15, G:0.16, T:0.16
Consensus pattern (27 bp):
AAAGGTCTAAAAGATCCAAAAGATCTA
Found at i:13690516 original size:3 final size:3
Alignment explanation
Indices: 13690508--13690533 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
13690498 CCATTGTAAG
13690508 AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AA
13690534 TAATCAGCCA
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:0.69, C:0.31, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:13697277 original size:37 final size:37
Alignment explanation
Indices: 13697173--13697278 Score: 158
Period size: 37 Copynumber: 2.8 Consensus size: 37
13697163 ATAAGGGATG
* *
13697173 TTAATTGATGAAAGTGGCCTTAAATCTACACGCCACAT
1 TTAA-TGATGAAAGTGCCCTTAAATCTACATGCCACAT
* *
13697211 TAAATGATGAAAGTGCCTTTAAATCTACATGCCACAT
1 TTAATGATGAAAGTGCCCTTAAATCTACATGCCACAT
*
13697248 TTAATGATGAAAGTGCCCTTCAATCTACATG
1 TTAATGATGAAAGTGCCCTTAAATCTACATG
13697279 ACAAGAGAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
37 58 0.95
38 3 0.05
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (37 bp):
TTAATGATGAAAGTGCCCTTAAATCTACATGCCACAT
Found at i:13699629 original size:21 final size:20
Alignment explanation
Indices: 13699605--13699656 Score: 50
Period size: 21 Copynumber: 2.5 Consensus size: 20
13699595 AAAAATAAAC
**
13699605 TAAATTAAAAGTAATTCAACA
1 TAAATTAAAA-TAAAACAACA
* *
13699626 TAAAACTAAAATAAAACAACT
1 T-AAATTAAAATAAAACAACA
13699647 TAAATTAAAA
1 TAAATTAAAA
13699657 CAACTTATCA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
20 8 0.32
21 9 0.36
22 8 0.32
ACGTcount: A:0.63, C:0.10, G:0.02, T:0.25
Consensus pattern (20 bp):
TAAATTAAAATAAAACAACA
Found at i:13699655 original size:15 final size:15
Alignment explanation
Indices: 13699632--13699663 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
13699622 AACATAAAAC
13699632 TAAAATAAAACAACT
1 TAAAATAAAACAACT
*
13699647 TAAATTAAAACAACT
1 TAAAATAAAACAACT
13699662 TA
1 TA
13699664 TCATGATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.62, C:0.12, G:0.00, T:0.25
Consensus pattern (15 bp):
TAAAATAAAACAACT
Found at i:13700648 original size:19 final size:18
Alignment explanation
Indices: 13700620--13700657 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
13700610 ATGTTTGAAA
13700620 TTATAAATATCATAATAT
1 TTATAAATATCATAATAT
*
13700638 TTATCAAATATTATAATAT
1 TTAT-AAATATCATAATAT
13700657 T
1 T
13700658 CAAAATCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (18 bp):
TTATAAATATCATAATAT
Found at i:13701654 original size:30 final size:31
Alignment explanation
Indices: 13701600--13701664 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 31
13701590 ATCATTAATC
*
13701600 ATAAAGGGTTTATTAGACTCAAAATAAAAAT
1 ATAAAGGGTTAATTAGACTCAAAATAAAAAT
* *
13701631 ATAAATGGTTAATT-GACTTAAAATAAAAAT
1 ATAAAGGGTTAATTAGACTCAAAATAAAAAT
13701661 ATAA
1 ATAA
13701665 CGGCTTGATT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
30 19 0.61
31 12 0.39
ACGTcount: A:0.54, C:0.05, G:0.11, T:0.31
Consensus pattern (31 bp):
ATAAAGGGTTAATTAGACTCAAAATAAAAAT
Found at i:13712296 original size:117 final size:117
Alignment explanation
Indices: 13712090--13712323 Score: 432
Period size: 117 Copynumber: 2.0 Consensus size: 117
13712080 CGTGGCCATT
*
13712090 AAAAATTTGAGCTCAAGTTGCTAGTAGTGGTGAACTTGGATTATTGTATAGGTCTTAACAATCAT
1 AAAAATTTGAGCTCAAGTTACTAGTAGTGGTGAACTTGGATTATTGTATAGGTCTTAACAATCAT
*
13712155 ATTCACAGCAAATGTAGGATGTTGGGTATCACAATTCCACCCATTCAAATTC
66 ATTCACAGCAAATGTAGGATGTTGGGTATCACAATTCCACCCACTCAAATTC
* *
13712207 AAAAATTTGAGCTTAAGTTACTAGTAGTGGTGGACTTGGATTATTGTATAGGTCTTAACAATCAT
1 AAAAATTTGAGCTCAAGTTACTAGTAGTGGTGAACTTGGATTATTGTATAGGTCTTAACAATCAT
13712272 ATTCACAGCAAATGTAGGATGTTGGGTATCACAATTCCACCCACTCAAATTC
66 ATTCACAGCAAATGTAGGATGTTGGGTATCACAATTCCACCCACTCAAATTC
13712324 TTGATGTCCT
Statistics
Matches: 113, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
117 113 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.32
Consensus pattern (117 bp):
AAAAATTTGAGCTCAAGTTACTAGTAGTGGTGAACTTGGATTATTGTATAGGTCTTAACAATCAT
ATTCACAGCAAATGTAGGATGTTGGGTATCACAATTCCACCCACTCAAATTC
Found at i:13715494 original size:33 final size:33
Alignment explanation
Indices: 13715449--13715518 Score: 124
Period size: 34 Copynumber: 2.1 Consensus size: 33
13715439 AGTTCAACAA
13715449 GGAATGATTAAGGT-GGTAGATTAGGCAATAGT
1 GGAATGATTAAGGTGGGTAGATTAGGCAATAGT
13715481 GGAATGAATTAAGGTGGGTAGATTAGGCAATAGT
1 GGAATG-ATTAAGGTGGGTAGATTAGGCAATAGT
13715515 GGAA
1 GGAA
13715519 AAATGAAGCT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
32 6 0.17
33 8 0.22
34 22 0.61
ACGTcount: A:0.36, C:0.03, G:0.36, T:0.26
Consensus pattern (33 bp):
GGAATGATTAAGGTGGGTAGATTAGGCAATAGT
Found at i:13734394 original size:116 final size:117
Alignment explanation
Indices: 13734250--13735160 Score: 506
Period size: 116 Copynumber: 7.9 Consensus size: 117
13734240 TTAATGAAAA
* * *
13734250 ATATTACTAATTTAATTAATTGCTTAATTATTAAAACATTTTTTCATTTGATTAGCTAAATTATT
1 ATATTACTAATTTAATTAATTGCTTAATTACTAAAACATCTTTTCATTTAATTAGCTAAATTATT
* *
13734315 TCATTAATTTAATAAAACCTTAATTAATTTAAATAATTTTAAATTTGACTAC
66 TAATTAATTTAATAAAACCATAATTAATTTAAATAATTTTAAATTTGACTAC
* * * * * *
13734367 CT-TTACTAAATTAATTAATTCCTTAATTAGC-AATACATGGCCTTT--TTTAATTAGTTAAATT
1 ATATTACTAATTTAATTAATTGCTTAATTA-CTAAAACAT--CTTTTCATTTAATTAGCTAAATT
* ** * * * * * *
13734428 ATGTAATTAATTTTCTCAAATCAGAATTAATTTAAATAA-ATAAAATATT-A-TATA
63 ATTTAATTAATTTAATAAAACCATAATTAATTTAAATAATTTTAAAT-TTGACTA-C
* * * * * *** * *
13734482 ATCTTACTTATTTAATTAATTTCTTAATTACCAACACATCACATCACTTAATTAACTAAATTATT
1 ATATTACTAATTTAATTAATTGCTTAATTACTAAAACATCTTTTCATTTAATTAGCTAAATTATT
* * * * * * * * *
13734547 TAATTAACTCATTACAACCATAATTAATTCAAAAAAATTTAAA-TTAAATA-
66 TAATTAATTTAATAAAACCATAATTAATTTAAATAATTTTAAATTTGACTAC
* * * * * *
13734597 ATATTACTAATTTAATTAATTACTTAATCACTAAAATATTTTTTAATTTGATTAGCTAAATTATT
1 ATATTACTAATTTAATTAATTGCTTAATTACTAAAACATCTTTTCATTTAATTAGCTAAATTATT
* * *
13734662 TCATTAATTTAATAAAATCTTAATTAATTTAAATAATTTTAAATTTGACTAC
66 TAATTAATTTAATAAAACCATAATTAATTTAAATAATTTTAAATTTGACTAC
* * * * * *
13734714 AT-TTACTAATTTATTTAATTGTTTAATTACTAATACATGATTCTT--TTTAATTTGTTAAATTA
1 ATATTACTAATTTAATTAATTGCTTAATTACTAAAACAT-CTT-TTCATTTAATTAGCTAAATTA
* * *** * * * * * * *
13734776 TGTAATTAACTCCCTCAAACCAGAGTTCATTTAAATAA-ATAAAATATT-ATGTA-
64 TTTAATTAATTTAATAAAACCATAATTAATTTAAATAATTTTAAAT-TTGA-CTAC
* * * * * * * * *
13734829 ATATTAATTATTAAATTAATTTCTTACTTACTAACACAT-TACATT-ACTTAATTAACTAAATTA
1 ATATTACTAATTTAATTAATTGCTTAATTACTAAAACATCT--TTTCATTTAATTAGCTAAATTA
* * * * * ** * * * *
13734892 TTTAATTAACTCAGTCACACTTTAATTAAGTTAAATATTTTTAAA-TTAAATA-
64 TTTAATTAATTTAATAAAACCATAATTAATTTAAATAATTTTAAATTTGACTAC
* * * * * * * *
13734944 TTATTACTAATTGAATTAATAGTTTAATTACTAAAACAAT-TTTTAATTT-TTGTAGTTATATTA
1 ATATTACTAATTTAATTAATTGCTTAATTACTAAAAC-ATCTTTTCATTTAAT-TAGCTAAATTA
* * * *
13735007 TTTTATTAATTTAATAAAAGCTTAATTAATTTAAATAGTTTTAAAATTT-AC--C
64 TTTAATTAATTTAATAAAACCATAATTAATTTAAATAATTTT-AAATTTGACTAC
* * * *
13735059 ATATTTACTAATTTAATTAATTGCTTAATTACTAATACAT-TATTCTTTTTAACTT-GTTAAATT
1 ATA-TTACTAATTTAATTAATTGCTTAATTACTAAAACATCTTTTC-ATTTAA-TTAGCTAAATT
* *** ** *
13735122 ATATAATTAATTCCCTCGAACCTTAATTAATTTAAATAA
63 ATTTAATTAATTTAATAAAACCATAATTAATTTAAATAA
13735161 ATAAAGTATT
Statistics
Matches: 592, Mismatches: 168, Indels: 69
0.71 0.20 0.08
Matches are distributed among these distances:
114 8 0.01
115 185 0.31
116 375 0.63
117 18 0.03
118 6 0.01
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.46
Consensus pattern (117 bp):
ATATTACTAATTTAATTAATTGCTTAATTACTAAAACATCTTTTCATTTAATTAGCTAAATTATT
TAATTAATTTAATAAAACCATAATTAATTTAAATAATTTTAAATTTGACTAC
Found at i:13735276 original size:347 final size:346
Alignment explanation
Indices: 13734190--13735285 Score: 1404
Period size: 347 Copynumber: 3.2 Consensus size: 346
13734180 TAAAAATAAA
* * * * * * *
13734190 TAAAGTTATTTAATTAATTCATTAACACCTTAATAAAATTTAATTGTTTTTTAATGAAA-AATAT
1 TAAA-TTATTTAATTAACTCATTAACACCTTAAT-TAATGTAAATATTTTTAAATTAAATAATAT
* * *
13734254 TACTAATTTAATTAATTGCTTAATTATTAAAACATTTTTTCATTTGATTAGCTAAATTATTTCAT
64 TACTAATTTAATTAATAGCTTAATTACTAAAACATTTTTTAATTTGATTAGCTAAATTATTTCAT
* *
13734319 TAATTTAATAAAACCTTAATTAATTTAAATAATTTTAAATTTGACTACCTTTACTAAATTAATTA
129 TAATTTAATAAAACCTTAATTAATTTAAATAATTTTAAATTTGACTACATTTACTAATTTAATTA
* *** **
13734384 ATTCCTTAATTAGC-AATACA-TGGCCTTTTTTAATTAGTTAAATTATGTAATTAATTTTCTCAA
194 ATTGCTTAATTA-CTAATACATTATTC-TTTTTAATT-GTTAAATTATGTAATTAATTCCCTCAA
* *
13734447 ATCAGAATTAATTTAAATAAATAAAATATTATATAATCTTACTTATTTAATTAATTTCTTAATTA
256 ACCAGAATTAATTTAAATAAATAAAATATTATATAATCTTAATTATTTAATTAATTTCTTAATTA
* *
13734512 CCA-ACACATCACATCACTTAATTAAC
321 -CATACACATTACATTACTTAATTAAC
* * **
13734538 TAAATTATTTAATTAACTCATT-ACAACCATAATTAAT-TCAAAAAAATTTAAATTAAATAATAT
1 TAAATTATTTAATTAACTCATTAAC-ACCTTAATTAATGT-AAATATTTTTAAATTAAATAATAT
* *
13734601 TACTAATTTAATTAATTA-CTTAATCACTAAAATATTTTTTAATTTGATTAGCTAAATTATTTCA
64 TACTAATTTAATTAA-TAGCTTAATTACTAAAACATTTTTTAATTTGATTAGCTAAATTATTTCA
* *
13734665 TTAATTTAATAAAATCTTAATTAATTTAAATAATTTTAAATTTGACTACATTTACTAATTTATTT
128 TTAATTTAATAAAACCTTAATTAATTTAAATAATTTTAAATTTGACTACATTTACTAATTTAATT
* * *
13734730 AATTGTTTAATTACTAATACATGATTCTTTTTAATTTGTTAAATTATGTAATTAACTCCCTCAAA
193 AATTGCTTAATTACTAATACATTATTCTTTTTAA-TTGTTAAATTATGTAATTAATTCCCTCAAA
* * * * * *
13734795 CCAGAGTTCATTTAAATAAATAAAATATTATGTAATATTAATTATTAAATTAATTTCTTACTTAC
257 CCAGAATTAATTTAAATAAATAAAATATTATATAATCTTAATTATTTAATTAATTTCTTAATTAC
13734860 -TAACACATTACATTACTTAATTAAC
322 AT-ACACATTACATTACTTAATTAAC
* * * *
13734885 TAAATTATTTAATTAACTCAGTCACACTTTAATTAA-GTTAAATATTTTTAAATTAAATATTATT
1 TAAATTATTTAATTAACTCATTAACACCTTAATTAATG-TAAATATTTTTAAATTAAATAATATT
* * * * * * *
13734949 ACTAATTGAATTAATAGTTTAATTACTAAAACAATTTTTAATTT-TTGTAGTTATATTATTTTAT
65 ACTAATTTAATTAATAGCTTAATTACTAAAACATTTTTTAATTTGAT-TAGCTAAATTATTTCAT
* * * *
13735013 TAATTTAATAAAAGCTTAATTAATTTAAATAGTTTTAAAATTT-ACCATATTTACTAATTTAATT
129 TAATTTAATAAAACCTTAATTAATTTAAATAATTTT-AAATTTGACTACATTTACTAATTTAATT
* *
13735077 AATTGCTTAATTACTAATACATTATTCTTTTTAACTTGTTAAATTATATAATTAATTCCCTCGAA
193 AATTGCTTAATTACTAATACATTATTCTTTTTAA-TTGTTAAATTATGTAATTAATTCCCTCAAA
** * ** *
13735142 CCTTAATTAATTTAAATAAATAAAGTATTATATAATCTTTTTTATTTAATTAATTTTTTAATTAC
257 CCAGAATTAATTTAAATAAATAAAATATTATATAATCTTAATTATTTAATTAATTTCTTAATTAC
* *
13735207 ATACATATTGCATTACTTAATTAAC
322 ATACACATTACATTACTTAATTAAC
13735232 TAAATTATTTAATTAACTCATTAACACCTTAATTAATGTAAATATTTTTAAATT
1 TAAATTATTTAATTAACTCATTAACACCTTAATTAATGTAAATATTTTTAAATT
13735286 GCTTAATTAA
Statistics
Matches: 649, Mismatches: 82, Indels: 35
0.85 0.11 0.05
Matches are distributed among these distances:
345 1 0.00
346 21 0.03
347 608 0.94
348 19 0.03
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.46
Consensus pattern (346 bp):
TAAATTATTTAATTAACTCATTAACACCTTAATTAATGTAAATATTTTTAAATTAAATAATATTA
CTAATTTAATTAATAGCTTAATTACTAAAACATTTTTTAATTTGATTAGCTAAATTATTTCATTA
ATTTAATAAAACCTTAATTAATTTAAATAATTTTAAATTTGACTACATTTACTAATTTAATTAAT
TGCTTAATTACTAATACATTATTCTTTTTAATTGTTAAATTATGTAATTAATTCCCTCAAACCAG
AATTAATTTAAATAAATAAAATATTATATAATCTTAATTATTTAATTAATTTCTTAATTACATAC
ACATTACATTACTTAATTAAC
Found at i:13738329 original size:96 final size:96
Alignment explanation
Indices: 13738165--13738352 Score: 367
Period size: 96 Copynumber: 2.0 Consensus size: 96
13738155 AATTATCTTT
*
13738165 AGCTAATATTATGAAATTTATTGTACCTATTTTCTTTCAAACTTAAACATTTACCTTATAAGCCT
1 AGCTAATATTATGAAATTTATTGTACCTATTTTCTTTCAAACTTAAACACTTACCTTATAAGCCT
13738230 TTAAGAGGCATTTATTCCTATTCTCTTATTC
66 TTAAGAGGCATTTATTCCTATTCTCTTATTC
13738261 AGCTAATATTATGAAATTTATTGTACCTATTTTCTTTCAAACTTAAACACTTACCTTATAAGCCT
1 AGCTAATATTATGAAATTTATTGTACCTATTTTCTTTCAAACTTAAACACTTACCTTATAAGCCT
13738326 TTAAGAGGCATTTATTCCTATTCTCTT
66 TTAAGAGGCATTTATTCCTATTCTCTT
13738353 GTTCTAAACA
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
96 91 1.00
ACGTcount: A:0.30, C:0.18, G:0.07, T:0.44
Consensus pattern (96 bp):
AGCTAATATTATGAAATTTATTGTACCTATTTTCTTTCAAACTTAAACACTTACCTTATAAGCCT
TTAAGAGGCATTTATTCCTATTCTCTTATTC
Found at i:13740218 original size:47 final size:46
Alignment explanation
Indices: 13740167--13740472 Score: 298
Period size: 47 Copynumber: 6.5 Consensus size: 46
13740157 ACAAGGCAGG
*
13740167 GTTCAGAGTTTGGGACATGCCATGGAGGGAATCTGTGACACTCTAGA
1 GTTCAGAGTTTGTGACATGCCATGGAGGGAATCTGTGACA-TCTAGA
* * * * *
13740214 GTTCAGAGTTTATGACATGCCATGGAGGTAATTTGTGGCATGTCAGA
1 GTTCAGAGTTTGTGACATGCCATGGAGGGAATCTGTGACATCT-AGA
* *
13740261 GTTCAGAG-TT-TGACATGCCATGGAGGGAATCTGTGACATGTTAGT
1 GTTCAGAGTTTGTGACATGCCATGGAGGGAATCTGTGACAT-CTAGA
* * * *
13740306 GTTCGGAGTTTGTGACATGCCATTGAGGGAATCTGTGACATGTCAGG
1 GTTCAGAGTTTGTGACATGCCATGGAGGGAATCTGTGACATCT-AGA
* * * * *
13740353 GTTCAGGGTTTGTGACATGCCAGGGTTTAGGGAATTTGTGAGATGTTA-A
1 GTTCAGAGTTTGTGACATGCCATGG---AGGGAATCTGTGACAT-CTAGA
* * * *
13740402 GGTTCAGAGTTTGTGACATGCCATGGAAGGAATCTGTGACACGCCAGT
1 -GTTCAGAGTTTGTGACATGCCATGGAGGGAATCTGTGACA-TCTAGA
13740450 GTTCAGAG-TT-TGACATGCCATGG
1 GTTCAGAGTTTGTGACATGCCATGG
13740473 TGGAAACACC
Statistics
Matches: 215, Mismatches: 32, Indels: 26
0.79 0.12 0.10
Matches are distributed among these distances:
45 48 0.22
46 10 0.05
47 118 0.55
50 38 0.18
51 1 0.00
ACGTcount: A:0.24, C:0.14, G:0.32, T:0.30
Consensus pattern (46 bp):
GTTCAGAGTTTGTGACATGCCATGGAGGGAATCTGTGACATCTAGA
Found at i:13740297 original size:23 final size:23
Alignment explanation
Indices: 13740271--13740347 Score: 73
Period size: 23 Copynumber: 3.3 Consensus size: 23
13740261 GTTCAGAGTT
13740271 TGACATGCCATGGAGGGAATCTG
1 TGACATGCCATGGAGGGAATCTG
** *** * *
13740294 TGACATGTTAGTGTTCGGAGTTTG
1 TGACATGCCA-TGGAGGGAATCTG
*
13740318 TGACATGCCATTGAGGGAATCTG
1 TGACATGCCATGGAGGGAATCTG
13740341 TGACATG
1 TGACATG
13740348 TCAGGGTTCA
Statistics
Matches: 38, Mismatches: 15, Indels: 2
0.69 0.27 0.04
Matches are distributed among these distances:
23 22 0.58
24 16 0.42
ACGTcount: A:0.23, C:0.14, G:0.32, T:0.30
Consensus pattern (23 bp):
TGACATGCCATGGAGGGAATCTG
Found at i:13740315 original size:92 final size:90
Alignment explanation
Indices: 13740153--13740472 Score: 354
Period size: 92 Copynumber: 3.4 Consensus size: 90
13740143 GTGACATGGT
* * * *
13740153 TGTGACAAGGCAGGGTTCAGAGTTTGGGACATGCCATGGAGGGAATCTGTGACACT-CTAGAGTT
1 TGTGACATGTCAGAGTTCAGAGTTT--GACATGCCATGGAGGGAATCTGTGACA-TGTTAG-GTT
* *
13740217 CAGAGTTTATGACATGCCATGGAGGTAATT
62 CAGAGTTTGTGACATGCCATGGAGG-AATC
* *
13740247 TGTGGCATGTCAGAGTTCAGAGTTTGACATGCCATGGAGGGAATCTGTGACATGTTAGTGTTCGG
1 TGTGACATGTCAGAGTTCAGAGTTTGACATGCCATGGAGGGAATCTGTGACATGTTAG-GTTCAG
*
13740312 AGTTTGTGACATGCCATTGAGGGAATC
65 AGTTTGTGACATGCCATGGA-GGAATC
* * * * *
13740339 TGTGACATGTCAGGGTTCAGGGTTTGTGACATGCCAGGGTTTAGGGAATTTGTGAGATGTTAAGG
1 TGTGACATGTCAGAGTTCAGAG-TT-TGACATGCCATGG---AGGGAATCTGTGACATGTT-AGG
13740404 TTCAGAGTTTGTGACATGCCATGGAAGGAATC
60 TTCAGAGTTTGTGACATGCCATGG-AGGAATC
* * *
13740436 TGTGACACGCCAGTGTTCAGAGTTTGACATGCCATGG
1 TGTGACATGTCAGAGTTCAGAGTTTGACATGCCATGG
13740473 TGGAAACACC
Statistics
Matches: 194, Mismatches: 23, Indels: 17
0.83 0.10 0.07
Matches are distributed among these distances:
91 1 0.01
92 75 0.39
93 4 0.02
94 33 0.17
95 12 0.06
96 2 0.01
97 64 0.33
98 3 0.02
ACGTcount: A:0.24, C:0.14, G:0.33, T:0.29
Consensus pattern (90 bp):
TGTGACATGTCAGAGTTCAGAGTTTGACATGCCATGGAGGGAATCTGTGACATGTTAGGTTCAGA
GTTTGTGACATGCCATGGAGGAATC
Found at i:13740370 original size:24 final size:24
Alignment explanation
Indices: 13740339--13740421 Score: 94
Period size: 24 Copynumber: 3.4 Consensus size: 24
13740329 TGAGGGAATC
13740339 TGTGACATGTCAGGGTTCAGGGTT
1 TGTGACATGTCAGGGTTCAGGGTT
* *
13740363 TGTGACATGCCAGGGTTTAGGGAATT
1 TGTGACATGTCAGGGTTCAGGG--TT
* * * *
13740389 TGTGAGATGTTAAGGTTCAGAGTT
1 TGTGACATGTCAGGGTTCAGGGTT
13740413 TGTGACATG
1 TGTGACATG
13740422 CCATGGAAGG
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
24 30 0.62
26 18 0.38
ACGTcount: A:0.22, C:0.10, G:0.35, T:0.34
Consensus pattern (24 bp):
TGTGACATGTCAGGGTTCAGGGTT
Found at i:13740514 original size:59 final size:59
Alignment explanation
Indices: 13740422--13740537 Score: 171
Period size: 59 Copynumber: 2.0 Consensus size: 59
13740412 TTGTGACATG
* * * *
13740422 CCATGGAAGGAATCTGTGACACGCCAGTGTTCAGAGTTTGACATGCCATGGTGGAAACA
1 CCATGGAAGGAATCTATGACACGCCAGGGTTCAGAGTTTGACACGCCATGGAGGAAACA
*
13740481 CCATGG-AGGAAATCTATGACATGCCAGGGTTCAGAGTTTGACACGCCATGGAGGAAA
1 CCATGGAAGG-AATCTATGACACGCCAGGGTTCAGAGTTTGACACGCCATGGAGGAAA
13740538 TCTGTGACAC
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
58 3 0.06
59 48 0.94
ACGTcount: A:0.30, C:0.20, G:0.29, T:0.21
Consensus pattern (59 bp):
CCATGGAAGGAATCTATGACACGCCAGGGTTCAGAGTTTGACACGCCATGGAGGAAACA
Found at i:13740593 original size:23 final size:24
Alignment explanation
Indices: 13740540--13740593 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
13740530 GGAGGAAATC
*
13740540 TGTGACACGCAAACGTTCAGGGTT
1 TGTGACACGCAAACGTTCACGGTT
*
13740564 TGTGACACG-ACAGCGTTCACGG-T
1 TGTGACACGCA-AACGTTCACGGTT
13740587 TGTGACA
1 TGTGACA
13740594 TGCCATAGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
23 9 0.33
24 18 0.67
ACGTcount: A:0.24, C:0.22, G:0.30, T:0.24
Consensus pattern (24 bp):
TGTGACACGCAAACGTTCACGGTT
Found at i:13741255 original size:31 final size:31
Alignment explanation
Indices: 13741219--13741634 Score: 559
Period size: 31 Copynumber: 13.5 Consensus size: 31
13741209 CATGGTTGGT
*
13741219 GTGTAACAACATTTGACTTGTTATGCATGGC
1 GTGTAACAACATTTGACTTGATATGCATGGC
* * **
13741250 ATGTAACAACATTTGACTT-TTCATGGTTGGC
1 GTGTAACAACATTTGACTTGAT-ATGCATGGC
*
13741281 GTGTAGCAACATTTGACTT-ATTATGCATGGC
1 GTGTAACAACATTTGACTTGA-TATGCATGGC
13741312 GTGTAACAACATTTGACTTGATATGCATGGC
1 GTGTAACAACATTTGACTTGATATGCATGGC
* *
13741343 GTGTAACAACATTAGACTTGGTATGCATGGC
1 GTGTAACAACATTTGACTTGATATGCATGGC
* * *
13741374 GTGTAACAACATTGGACTTGTTATGCATGAC
1 GTGTAACAACATTTGACTTGATATGCATGGC
*
13741405 -TGTGACAACATTTGACTTGATATGCATGGC
1 GTGTAACAACATTTGACTTGATATGCATGGC
*
13741435 GTGTAACAATATTTGACTTGATATGCATGGC
1 GTGTAACAACATTTGACTTGATATGCATGGC
* **
13741466 GTGTAACAATATTTGACTTGATATGCATGTT
1 GTGTAACAACATTTGACTTGATATGCATGGC
* * *
13741497 GTGTAATAAAATTTTACTTGATATGCATGGC
1 GTGTAACAACATTTGACTTGATATGCATGGC
*
13741528 GTGTAACAACATTTGACTTGTTATGCATGGC
1 GTGTAACAACATTTGACTTGATATGCATGGC
* * *
13741559 ATGTAACAACATTTTACTTGATATGCATTGC
1 GTGTAACAACATTTGACTTGATATGCATGGC
* *
13741590 GTGTAACAATATTTTACTTGATATGCATGGC
1 GTGTAACAACATTTGACTTGATATGCATGGC
*
13741621 ATGTAACAACATTT
1 GTGTAACAACATTT
13741635 ATTTCTTTCT
Statistics
Matches: 341, Mismatches: 40, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
30 28 0.08
31 311 0.91
32 2 0.01
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.36
Consensus pattern (31 bp):
GTGTAACAACATTTGACTTGATATGCATGGC
Found at i:13744265 original size:28 final size:29
Alignment explanation
Indices: 13744233--13744291 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 29
13744223 TGACAACTTT
*
13744233 AACATATTCA-TTTTAATTTAGACAAAAA
1 AACATATTCAGTCTTAATTTAGACAAAAA
* *
13744261 AACATGTTCAGTCTTAATTTAGACAAGAA
1 AACATATTCAGTCTTAATTTAGACAAAAA
13744290 AA
1 AA
13744292 TATCTTTGGC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 9 0.33
29 18 0.67
ACGTcount: A:0.47, C:0.12, G:0.08, T:0.32
Consensus pattern (29 bp):
AACATATTCAGTCTTAATTTAGACAAAAA
Found at i:13744324 original size:30 final size:30
Alignment explanation
Indices: 13744273--13744355 Score: 98
Period size: 30 Copynumber: 2.8 Consensus size: 30
13744263 CATGTTCAGT
* *
13744273 CTTAATTTAGACAAG-AAAATAT-CTTTGG
1 CTTAATTTAGAGAAGAAAAATATACTTTAG
*
13744301 CTTAATTTAAGAGAAGAAAAATATATTTTAG
1 CTTAATTT-AGAGAAGAAAAATATACTTTAG
*
13744332 CTTAATCTAGAGAAGAAAACATAT
1 CTTAATTTAGAGAAGAAAA-ATAT
13744356 TTGTTTCCAT
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
28 8 0.17
29 6 0.13
30 18 0.38
31 15 0.32
ACGTcount: A:0.46, C:0.08, G:0.13, T:0.33
Consensus pattern (30 bp):
CTTAATTTAGAGAAGAAAAATATACTTTAG
Found at i:13744337 original size:31 final size:29
Alignment explanation
Indices: 13744245--13744355 Score: 100
Period size: 29 Copynumber: 3.8 Consensus size: 29
13744235 CATATTCATT
* * * *
13744245 TTAATTTAGACAA-AAAAACATGTTCAGTC
1 TTAATTTAGAGAAGAAAAATATCTTTAG-C
* *
13744274 TTAATTTAGACAAG-AAAATATCTTTGGC
1 TTAATTTAGAGAAGAAAAATATCTTTAGC
*
13744302 TTAATTTAAGAGAAGAAAAATATATTTTAGC
1 TTAATTT-AGAGAAGAAAAATAT-CTTTAGC
*
13744333 TTAATCTAGAGAAGAAAACATAT
1 TTAATTTAGAGAAGAAAA-ATAT
13744356 TTGTTTCCAT
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
28 8 0.12
29 28 0.41
30 18 0.26
31 15 0.22
ACGTcount: A:0.46, C:0.09, G:0.13, T:0.32
Consensus pattern (29 bp):
TTAATTTAGAGAAGAAAAATATCTTTAGC
Found at i:13745429 original size:22 final size:22
Alignment explanation
Indices: 13745404--13745597 Score: 191
Period size: 22 Copynumber: 8.8 Consensus size: 22
13745394 TCTGTCATGT
*
13745404 TGTTACACGCCATGCTCAAAAA
1 TGTTACACGCCATGTTCAAAAA
*
13745426 TGTTACACG-CAAGTTCAAAAA
1 TGTTACACGCCATGTTCAAAAA
*
13745447 GTGTTACAGGCCATGTTCAAAAA
1 -TGTTACACGCCATGTTCAAAAA
* * *
13745470 TGTTATACG-CAAGTTTAGAAAA
1 TGTTACACGCCATGTTCA-AAAA
* * *
13745492 TGTTACATGCCTTATTCAAAAA
1 TGTTACACGCCATGTTCAAAAA
*
13745514 TGTTACACG-CAAGTTCAAAAA
1 TGTTACACGCCATGTTCAAAAA
13745535 GTGTTACACGCC-TAGTTCAAAAA
1 -TGTTACACGCCAT-GTTCAAAAA
* * *
13745558 TGTTACATG-CAAGTTAAAAAA
1 TGTTACACGCCATGTTCAAAAA
13745579 TTGTTACACGCCATGTTCA
1 -TGTTACACGCCATGTTCA
13745598 CTACGTGTTA
Statistics
Matches: 137, Mismatches: 25, Indels: 19
0.76 0.14 0.10
Matches are distributed among these distances:
21 34 0.25
22 72 0.53
23 31 0.23
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (22 bp):
TGTTACACGCCATGTTCAAAAA
Found at i:13745453 original size:44 final size:44
Alignment explanation
Indices: 13745404--13745597 Score: 266
Period size: 44 Copynumber: 4.4 Consensus size: 44
13745394 TCTGTCATGT
*
13745404 TGTTACACGCCATGCTCAAAAATGTTACACGCAAGTTCAAAAAG
1 TGTTACACGCCATGTTCAAAAATGTTACACGCAAGTTCAAAAAG
* * *
13745448 TGTTACAGGCCATGTTCAAAAATGTTATACGCAAGTTTAGAAAA-
1 TGTTACACGCCATGTTCAAAAATGTTACACGCAAGTTCA-AAAAG
* * *
13745492 TGTTACATGCCTTATTCAAAAATGTTACACGCAAGTTCAAAAAG
1 TGTTACACGCCATGTTCAAAAATGTTACACGCAAGTTCAAAAAG
* * *
13745536 TGTTACACGCC-TAGTTCAAAAATGTTACATGCAAGTTAAAAAAT
1 TGTTACACGCCAT-GTTCAAAAATGTTACACGCAAGTTCAAAAAG
13745580 TGTTACACGCCATGTTCA
1 TGTTACACGCCATGTTCA
13745598 CTACGTGTTA
Statistics
Matches: 132, Mismatches: 14, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
43 5 0.04
44 122 0.92
45 5 0.04
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.28
Consensus pattern (44 bp):
TGTTACACGCCATGTTCAAAAATGTTACACGCAAGTTCAAAAAG
Found at i:13746265 original size:15 final size:15
Alignment explanation
Indices: 13746245--13746282 Score: 76
Period size: 15 Copynumber: 2.5 Consensus size: 15
13746235 GGAAAAGCCT
13746245 GCCCTTTAGGCTCTG
1 GCCCTTTAGGCTCTG
13746260 GCCCTTTAGGCTCTG
1 GCCCTTTAGGCTCTG
13746275 GCCCTTTA
1 GCCCTTTA
13746283 AGACAAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.08, C:0.34, G:0.24, T:0.34
Consensus pattern (15 bp):
GCCCTTTAGGCTCTG
Found at i:13751256 original size:35 final size:35
Alignment explanation
Indices: 13751217--13751315 Score: 125
Period size: 32 Copynumber: 2.9 Consensus size: 35
13751207 TTTTGGATTT
13751217 TGGTTGATCTTGTGAAAAACCATTGTTAAAGGTTG
1 TGGTTGATCTTGTGAAAAACCATTGTTAAAGGTTG
* * *
13751252 TGGTTGAGCCTT-TGAAAAACCATT-TT-GA-GTTT
1 TGGTTGA-TCTTGTGAAAAACCATTGTTAAAGGTTG
*
13751284 TGGTTGATCTTGTGAAAAACCATTGTGAAAGG
1 TGGTTGATCTTGTGAAAAACCATTGTTAAAGG
13751316 GTCTAGCTGA
Statistics
Matches: 53, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
31 3 0.06
32 22 0.42
33 2 0.04
34 3 0.06
35 20 0.38
36 3 0.06
ACGTcount: A:0.28, C:0.10, G:0.25, T:0.36
Consensus pattern (35 bp):
TGGTTGATCTTGTGAAAAACCATTGTTAAAGGTTG
Found at i:13751291 original size:67 final size:67
Alignment explanation
Indices: 13751206--13751338 Score: 196
Period size: 67 Copynumber: 2.0 Consensus size: 67
13751196 GAAAAGTTAG
* * * * * *
13751206 ATTTTGGATTTTGGTTGATCTTGTGAAAAACCATTGTTAAAGGTTGTGGTTGAGCCTTTGAAAAA
1 ATTTTGGATTTTGGTTGATCTTGTGAAAAACCATTGTGAAAGGGTCTAGCTGAGCCTGTGAAAAA
13751271 CC
66 CC
13751273 ATTTT-GAGTTTTGGTTGATCTTGTGAAAAACCATTGTGAAAGGGTCTAGCTGAGCCTGTGAAAA
1 ATTTTGGA-TTTTGGTTGATCTTGTGAAAAACCATTGTGAAAGGGTCTAGCTGAGCCTGTGAAAA
13751337 AC
65 AC
13751339 TATTGCAAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
66 2 0.03
67 57 0.97
ACGTcount: A:0.28, C:0.11, G:0.25, T:0.36
Consensus pattern (67 bp):
ATTTTGGATTTTGGTTGATCTTGTGAAAAACCATTGTGAAAGGGTCTAGCTGAGCCTGTGAAAAA
CC
Found at i:13751300 original size:32 final size:32
Alignment explanation
Indices: 13751206--13751307 Score: 118
Period size: 32 Copynumber: 3.1 Consensus size: 32
13751196 GAAAAGTTAG
13751206 ATTTTG-GATTTTGGTTGATCTTGTGAAAAACC
1 ATTTTGAG-TTTTGGTTGATCTTGTGAAAAACC
* * *
13751238 ATTGTTAAAGGTTGTGGTTGAGCCTT-TGAAAAACC
1 ATT-TT-GA-GTTTTGGTTGA-TCTTGTGAAAAACC
13751273 ATTTTGAGTTTTGGTTGATCTTGTGAAAAACC
1 ATTTTGAGTTTTGGTTGATCTTGTGAAAAACC
13751305 ATT
1 ATT
13751308 GTGAAAGGGT
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
31 3 0.05
32 25 0.43
33 3 0.05
34 2 0.03
35 21 0.36
36 4 0.07
ACGTcount: A:0.26, C:0.10, G:0.23, T:0.41
Consensus pattern (32 bp):
ATTTTGAGTTTTGGTTGATCTTGTGAAAAACC
Found at i:13760600 original size:29 final size:29
Alignment explanation
Indices: 13760564--13760620 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
13760554 GGATATTCAA
* *
13760564 TATATCTTGCTTAGATATTGTGGATATTG
1 TATATCTTACTTAGATACTGTGGATATTG
* *
13760593 TATATCTTATTTAGCTACTGTGGATATT
1 TATATCTTACTTAGATACTGTGGATATT
13760621 ATAAATATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.25, C:0.09, G:0.18, T:0.49
Consensus pattern (29 bp):
TATATCTTACTTAGATACTGTGGATATTG
Found at i:13771124 original size:29 final size:29
Alignment explanation
Indices: 13771082--13771167 Score: 136
Period size: 29 Copynumber: 3.0 Consensus size: 29
13771072 AGATGTTCAA
* * *
13771082 TATAGCTTGCTTAGCTACTATGGATATTG
1 TATATCTTGTTTAGCTACTGTGGATATTG
13771111 TATATCTTGTTTAGCTACTGTGGATATTG
1 TATATCTTGTTTAGCTACTGTGGATATTG
*
13771140 TATATCTTGTTTAGTTACTGTGGATATT
1 TATATCTTGTTTAGCTACTGTGGATATT
13771168 ATAAATAGTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 53 1.00
ACGTcount: A:0.22, C:0.10, G:0.20, T:0.48
Consensus pattern (29 bp):
TATATCTTGTTTAGCTACTGTGGATATTG
Found at i:13771178 original size:27 final size:29
Alignment explanation
Indices: 13771092--13771183 Score: 82
Period size: 29 Copynumber: 3.3 Consensus size: 29
13771082 TATAGCTTGC
* * ** *
13771092 TTAGCTACTATGGATATTGTATATCTTGT
1 TTAGTTACTGTGGATATTGTATAAATAGT
* ** *
13771121 TTAGCTACTGTGGATATTGTATATCTTGT
1 TTAGTTACTGTGGATATTGTATAAATAGT
13771150 TTAGTTACTGTGGATA-T-TATAAATAGT
1 TTAGTTACTGTGGATATTGTATAAATAGT
13771177 TTA-TTAC
1 TTAGTTAC
13771184 AAATCTTTAA
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
26 4 0.07
27 10 0.17
28 1 0.02
29 43 0.74
ACGTcount: A:0.26, C:0.09, G:0.17, T:0.48
Consensus pattern (29 bp):
TTAGTTACTGTGGATATTGTATAAATAGT
Found at i:13775616 original size:32 final size:34
Alignment explanation
Indices: 13775574--13775640 Score: 84
Period size: 32 Copynumber: 2.0 Consensus size: 34
13775564 AAGTTATTTA
*
13775574 TAAATGTTGTGATTGAT-CTTTG-AAAGGCATTG
1 TAAAGGTTGTGATTGATCCTTTGAAAAGGCATTG
* * *
13775606 TAAAGGTTGTGCTTGCTCCTTTGAAAAGTCATTG
1 TAAAGGTTGTGATTGATCCTTTGAAAAGGCATTG
13775640 T
1 T
13775641 GTGAGTTATG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 14 0.48
33 5 0.17
34 10 0.34
ACGTcount: A:0.25, C:0.10, G:0.24, T:0.40
Consensus pattern (34 bp):
TAAAGGTTGTGATTGATCCTTTGAAAAGGCATTG
Found at i:13779662 original size:35 final size:35
Alignment explanation
Indices: 13779623--13779690 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
13779613 GCACTCCATA
* * *
13779623 AATATAGCTAGATGTGAGTGTAAGAATACCACATG
1 AATATAGCCAAATGTGAGGGTAAGAATACCACATG
* *
13779658 AATATAGCCAAATGTGGGGGTGAGAATACCACA
1 AATATAGCCAAATGTGAGGGTAAGAATACCACA
13779691 CGTTGTTCGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.40, C:0.13, G:0.25, T:0.22
Consensus pattern (35 bp):
AATATAGCCAAATGTGAGGGTAAGAATACCACATG
Found at i:13789377 original size:26 final size:25
Alignment explanation
Indices: 13789348--13789406 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 25
13789338 ATTTAAAAAT
13789348 TAATTAAACTATAAATGA-TTAAATTA
1 TAATTAAA-TATAAAT-ATTTAAATTA
*
13789374 TAATTTAAATATTAATATTTAAATTA
1 TAA-TTAAATATAAATATTTAAATTA
13789400 TCAATTA
1 T-AATTA
13789407 TCAATATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
25 1 0.03
26 21 0.72
27 7 0.24
ACGTcount: A:0.51, C:0.03, G:0.02, T:0.44
Consensus pattern (25 bp):
TAATTAAATATAAATATTTAAATTA
Found at i:13789422 original size:26 final size:26
Alignment explanation
Indices: 13789367--13789420 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 26
13789357 TATAAATGAT
*
13789367 TAAATTATAATTTAAATATTAATATT
1 TAAATTATAATTTAAATATTAATATA
* *
13789393 TAAATTATCAATTATCAATATTATTATA
1 TAAATTAT-AATT-TAAATATTAATATA
13789421 AACAGGAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 8 0.35
27 4 0.17
28 11 0.48
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (26 bp):
TAAATTATAATTTAAATATTAATATA
Found at i:13789526 original size:153 final size:151
Alignment explanation
Indices: 13789367--13789718 Score: 404
Period size: 151 Copynumber: 2.3 Consensus size: 151
13789357 TATAAATGAT
* * * *
13789367 TAAATTATAATTTAAATATTAATATTTAAATTATCAATTATCAATATTATTATAAACAGGAAAAA
1 TAAATTATAAATAAAATATTAATATTTAAATTATCAATTATCAATATTATTACAAA-AAGAAAAA
* * * * *
13789432 AGTTTACAATTTAAATTATATATTATATAAGT-TATATTT-AATTTAAAAAATTAATTAAAATTA
65 AGTTTACAATTTAAATAATATATAAAAAAAGTATAT-TTTAAATTT--AAAATTAATTAAAATAA
* * * *
13789495 TTTATATTTTAATCATAATAACATT
127 GTAATATTTTAAGCATAATAACATC
* *
13789520 TCAATTATAAATAAAATATTAATATTTAAATTATCAATT-CCTAATATTATTACAAAAAGAAAAA
1 TAAATTATAAATAAAATATTAATATTTAAATTATCAATTATC-AATATTATTACAAAAAGAAAAA
** * * *
13789584 TTTTTACATTTTTAATAATATATAAAAAAAGTATATTTTAAATTTAAAATTGATTAAAATAAGTA
65 AGTTTACAATTTAAATAATATATAAAAAAAGTATATTTTAAATTTAAAATTAATTAAAATAAGTA
* *
13789649 ATATTTTAAGCATGATATCATC
130 ATATTTTAAGCATAATAACATC
* * * *
13789671 TAAACTATAAATAAAATGTTAATATTTAAATGATCAATTATTAATATT
1 TAAATTATAAATAAAATATTAATATTTAAATTATCAATTATCAATATT
13789719 TTAAATTAAA
Statistics
Matches: 167, Mismatches: 28, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
151 75 0.45
152 35 0.21
153 57 0.34
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.42
Consensus pattern (151 bp):
TAAATTATAAATAAAATATTAATATTTAAATTATCAATTATCAATATTATTACAAAAAGAAAAAA
GTTTACAATTTAAATAATATATAAAAAAAGTATATTTTAAATTTAAAATTAATTAAAATAAGTAA
TATTTTAAGCATAATAACATC
Found at i:13789760 original size:151 final size:150
Alignment explanation
Indices: 13789478--13789761 Score: 333
Period size: 151 Copynumber: 1.9 Consensus size: 150
13789468 TTTAATTTAA
* * * * * * *
13789478 AAAATTAATTAAAATTATTTATATTTTAATCATAATAACATTTCAATTATAAATAAAATATTAAT
1 AAAATTAATTAAAATAAGTAATATTTTAAGCATAATAACATCTAAACTATAAATAAAATATTAAT
* * * * *
13789543 ATTTAAATTATCAATTCCTAATATTATTACAAAAAGAAAAATTTTTACATTTTTAATAATATATA
66 ATTTAAATGATCAATTACTAATATTATTACAAAAAGAAAAATTATTA-ATTTTTAAAAATAAATA
13789608 AAAAAAGTATATTTTAAATTT
130 AAAAAAGTATATTTTAAATTT
* * * *
13789629 AAAATTGATTAAAATAAGTAATATTTTAAGCATGATATCATCTAAACTATAAATAAAATGTTAAT
1 AAAATTAATTAAAATAAGTAATATTTTAAGCATAATAACATCTAAACTATAAATAAAATATTAAT
*
13789694 ATTTAAATGATCAATTATTAATATT-TTA-AATTAAA-AATAAATTATT-ATTATTTAAAAAATA
66 ATTTAAATGATCAATTACTAATATTATTACAA--AAAGAA-AAATTATTAATT-TTT-AAAAATA
13789755 AATAAAA
126 AATAAAA
13789762 TAAAAATAAA
Statistics
Matches: 111, Mismatches: 17, Indels: 10
0.80 0.12 0.07
Matches are distributed among these distances:
149 5 0.05
150 8 0.07
151 98 0.88
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.41
Consensus pattern (150 bp):
AAAATTAATTAAAATAAGTAATATTTTAAGCATAATAACATCTAAACTATAAATAAAATATTAAT
ATTTAAATGATCAATTACTAATATTATTACAAAAAGAAAAATTATTAATTTTTAAAAATAAATAA
AAAAAGTATATTTTAAATTT
Found at i:13789762 original size:27 final size:27
Alignment explanation
Indices: 13789706--13789760 Score: 69
Period size: 26 Copynumber: 2.1 Consensus size: 27
13789696 TTAAATGATC
*
13789706 AATTATTAATATTTTAAATTAAAAATA
1 AATTATTAATATTTTAAATAAAAAATA
*
13789733 AATTATTATTA-TTTAAA-AAATAAATA
1 AATTATTAATATTTTAAATAAA-AAATA
13789759 AA
1 AA
13789761 ATAAAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 2 0.08
26 13 0.52
27 10 0.40
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
AATTATTAATATTTTAAATAAAAAATA
Found at i:13790009 original size:19 final size:19
Alignment explanation
Indices: 13789946--13790010 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
13789936 ATTTAAATTA
13789946 TAAA-AAAATATTAATATTT
1 TAAATAAAATATTAATA-TT
* * *
13789965 TAAAATATTAATGATTAAAATA
1 T-AAATA-AAAT-ATTAATATT
13789987 TAAATAAAATATTAATATT
1 TAAATAAAATATTAATATT
13790006 TAAAT
1 TAAAT
13790011 GATCAATTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
19 13 0.36
20 6 0.17
21 6 0.17
22 5 0.14
23 6 0.17
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (19 bp):
TAAATAAAATATTAATATT
Found at i:13790023 original size:41 final size:41
Alignment explanation
Indices: 13789938--13790023 Score: 113
Period size: 41 Copynumber: 2.1 Consensus size: 41
13789928 TTAATAACAT
* *
13789938 TTAAATTATAAAAAAATATTAATATTTTAAAATATTAATGA
1 TTAAAATATAAAAAAATATTAATATTTTAAAATATCAATGA
*
13789979 TTAAAATATAAATAAAATATTAATA-TTT-AAATGATCAATTA
1 TTAAAATATAAA-AAAATATTAATATTTTAAAAT-ATCAATGA
13790020 TTAA
1 TTAA
13790024 TATTTTAAAC
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
40 4 0.10
41 24 0.60
42 12 0.30
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (41 bp):
TTAAAATATAAAAAAATATTAATATTTTAAAATATCAATGA
Found at i:13790068 original size:25 final size:27
Alignment explanation
Indices: 13790016--13790068 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
13790006 TAAATGATCA
*
13790016 ATTATTAATATTTTAAACAAATTATAT
1 ATTATTAATATTTTAAACAAATAATAT
13790043 ATTATTAATA-TTTAAA-AAATAATAT
1 ATTATTAATATTTTAAACAAATAATAT
13790068 A
1 A
13790069 AAATAAAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 9 0.36
26 6 0.24
27 10 0.40
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (27 bp):
ATTATTAATATTTTAAACAAATAATAT
Found at i:13795030 original size:23 final size:23
Alignment explanation
Indices: 13794986--13795030 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
13794976 TTTATCAATA
* ***
13794986 TAAATATTAAAAAATTTTAATTT
1 TAAAAATTAAAAAATAAAAATTT
13795009 TAAAAATTAAAAAATAAAAATT
1 TAAAAATTAAAAAATAAAAATT
13795031 ATTATTATTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
TAAAAATTAAAAAATAAAAATTT
Found at i:13795307 original size:35 final size:35
Alignment explanation
Indices: 13795258--13795326 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
13795248 ATAATATACA
** *
13795258 GAGAACAATTAAAACAAGTGAAGTGTTACTTCACG
1 GAGAACAACCAAAACAAGTGAAGTGCTACTTCACG
13795293 GAGAACAACCAAAACAAGTGAAGTGCTACTTCAC
1 GAGAACAACCAAAACAAGTGAAGTGCTACTTCAC
13795327 TCACAACAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.43, C:0.19, G:0.19, T:0.19
Consensus pattern (35 bp):
GAGAACAACCAAAACAAGTGAAGTGCTACTTCACG
Found at i:13795335 original size:35 final size:35
Alignment explanation
Indices: 13795268--13795345 Score: 102
Period size: 35 Copynumber: 2.2 Consensus size: 35
13795258 GAGAACAATT
* * *
13795268 AAAACAAGTGAAGTGTTACTTCACGGAGAACAACC
1 AAAACAAGTGAAGTGCTACTTCACGCACAACAACC
* *
13795303 AAAACAAGTGAAGTGCTACTTCACTCACAACAACT
1 AAAACAAGTGAAGTGCTACTTCACGCACAACAACC
*
13795338 AGAACAAG
1 AAAACAAG
13795346 AACAAGTGAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.45, C:0.22, G:0.17, T:0.17
Consensus pattern (35 bp):
AAAACAAGTGAAGTGCTACTTCACGCACAACAACC
Found at i:13802237 original size:35 final size:35
Alignment explanation
Indices: 13802161--13802244 Score: 105
Period size: 35 Copynumber: 2.4 Consensus size: 35
13802151 TATTGTACAA
*** *
13802161 AAAACAACTAAAACAAGTGAAGTGTTATTTTAAGT
1 AAAACAACTAAAACAAGTGAAGCACTACTTTAAGT
* *
13802196 AGAACAACTAAAACAAGTGAAGCACTACTTTACGT
1 AAAACAACTAAAACAAGTGAAGCACTACTTTAAGT
*
13802231 AAAACAATTAAAAC
1 AAAACAACTAAAAC
13802245 TAGAAAAAGT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.51, C:0.14, G:0.12, T:0.23
Consensus pattern (35 bp):
AAAACAACTAAAACAAGTGAAGCACTACTTTAAGT
Found at i:13809473 original size:2 final size:2
Alignment explanation
Indices: 13809466--13809491 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13809456 TCGAATTTTA
13809466 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
13809492 TAAAAAATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13815640 original size:15 final size:15
Alignment explanation
Indices: 13815620--13815669 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
13815610 GAAGCAAAAA
13815620 GAGAAAGGAAGAAGG
1 GAGAAAGGAAGAAGG
* **
13815635 GAGAAAAGAAGAAAA
1 GAGAAAGGAAGAAGG
13815650 GAGAAAGG-AGAAGG
1 GAGAAAGGAAGAAGG
*
13815664 AAGAAA
1 GAGAAA
13815670 TAAGATAAGC
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
14 9 0.32
15 19 0.68
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (15 bp):
GAGAAAGGAAGAAGG
Found at i:13815654 original size:22 final size:23
Alignment explanation
Indices: 13815616--13815669 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 23
13815606 CTTGGAAGCA
* *
13815616 AAAAG-AGAAAGGAAGAAGGGAG
1 AAAAGAAGAAAAGAAGAAAGGAG
13815638 AAAAGAAGAAAAG-AGAAAGGAG
1 AAAAGAAGAAAAGAAGAAAGGAG
*
13815660 -AAGGAAGAAA
1 AAAAGAAGAAA
13815670 TAAGATAAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.32
22 13 0.46
23 6 0.21
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (23 bp):
AAAAGAAGAAAAGAAGAAAGGAG
Found at i:13838497 original size:21 final size:22
Alignment explanation
Indices: 13838471--13838512 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
13838461 CTCTTTTTAA
13838471 AAAAATT-TTATTCTTTAAAAC
1 AAAAATTGTTATTCTTTAAAAC
* *
13838492 AAAAATTGTTTTTTTTTAAAA
1 AAAAATTGTTATTCTTTAAAA
13838513 AGCTTTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.45, C:0.05, G:0.02, T:0.48
Consensus pattern (22 bp):
AAAAATTGTTATTCTTTAAAAC
Found at i:13839048 original size:2 final size:2
Alignment explanation
Indices: 13839041--13839074 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
13839031 TTCCTTTATA
13839041 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
13839075 CATTCAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:13841929 original size:40 final size:42
Alignment explanation
Indices: 13841852--13841932 Score: 103
Period size: 40 Copynumber: 2.0 Consensus size: 42
13841842 TTGAATATTT
* * **
13841852 TTCACCTTAGTGGAGTTTTTTTAACCTTGCCAAGATTGGTGG
1 TTCACCTTAGTGGAGTGTTTCTAACCTCACCAAGATTGGTGG
*
13841894 TTCACCTTAGTGG-G-GTTTCTAACCTCACCATGATTGGTG
1 TTCACCTTAGTGGAGTGTTTCTAACCTCACCAAGATTGGTG
13841933 TCTTTCACAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
40 20 0.59
41 1 0.03
42 13 0.38
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38
Consensus pattern (42 bp):
TTCACCTTAGTGGAGTGTTTCTAACCTCACCAAGATTGGTGG
Found at i:13842970 original size:31 final size:31
Alignment explanation
Indices: 13842932--13843013 Score: 82
Period size: 31 Copynumber: 2.7 Consensus size: 31
13842922 AAATAAATTA
* * *
13842932 TTTTTTATTAT-ATTCAATTAAATTTTTTTAT
1 TTTTTTATTATGAATCAAAT-AAGTTTTTTAT
*
13842963 TTTTTTATTTTGAATCAAATAAGTTTTTTAT
1 TTTTTTATTATGAATCAAATAAGTTTTTTAT
13842994 TTTTATT-TTA--AATCAAATAA
1 TTTT-TTATTATGAATCAAATAA
13843014 ACCCTTATTA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
29 10 0.23
31 26 0.59
32 8 0.18
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (31 bp):
TTTTTTATTATGAATCAAATAAGTTTTTTAT
Found at i:13843001 original size:29 final size:30
Alignment explanation
Indices: 13842929--13843013 Score: 93
Period size: 29 Copynumber: 2.8 Consensus size: 30
13842919 TTTAAATAAA
* * * *
13842929 TTATTTTTTATTAT-ATTCAATTAAATTTTT
1 TTATTTTTTATTTTAAATCAAAT-AAGTTTT
*
13842959 TTATTTTTTTATTTTGAATCAAATAAGTTTT
1 TTA-TTTTTTATTTTAAATCAAATAAGTTTT
13842990 TTA-TTTTTATTTTAAATCAAATAA
1 TTATTTTTTATTTTAAATCAAATAA
13843014 ACCCTTATTA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
29 20 0.42
30 3 0.06
31 19 0.40
32 6 0.12
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (30 bp):
TTATTTTTTATTTTAAATCAAATAAGTTTT
Found at i:13849271 original size:2 final size:2
Alignment explanation
Indices: 13849264--13849294 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
13849254 TCATTCCATC
*
13849264 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
13849295 GCATAGTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13852465 original size:2 final size:2
Alignment explanation
Indices: 13852452--13852481 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
13852442 ATACTAGTAC
*
13852452 AT AT AT AC 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
13852482 CGTGAAGAGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:13865712 original size:41 final size:41
Alignment explanation
Indices: 13865665--13865747 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
13865655 ATGATCATGA
13865665 ACAAAATGTCCTAATGATTGTCTGACATGAAATGATTCACT
1 ACAAAATGTCCTAATGATTGTCTGACATGAAATGATTCACT
13865706 ACAAAATGTCCTAATGATTGTCTGACATGAAATGATTCACT
1 ACAAAATGTCCTAATGATTGTCTGACATGAAATGATTCACT
13865747 A
1 A
13865748 TGTGAATCCC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.31
Consensus pattern (41 bp):
ACAAAATGTCCTAATGATTGTCTGACATGAAATGATTCACT
Found at i:13866070 original size:21 final size:20
Alignment explanation
Indices: 13866028--13866072 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
13866018 ATAAAAAATT
* **
13866028 AATTATTAATTAATTATTAG
1 AATTATTAATTAATCAAAAG
13866048 AATTATTAATCTAATCAAAAG
1 AATTATTAAT-TAATCAAAAG
13866069 AATT
1 AATT
13866073 TAGTCCCATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.42
Consensus pattern (20 bp):
AATTATTAATTAATCAAAAG
Found at i:13869464 original size:34 final size:34
Alignment explanation
Indices: 13869426--13869493 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
13869416 CCTACATTAT
13869426 ACTAAAACACCATTCTTTCCCACTTAATCCTTAC
1 ACTAAAACACCATTCTTTCCCACTTAATCCTTAC
13869460 ACTAAAACACCATTCTTTCCCACTTAATCCTTAC
1 ACTAAAACACCATTCTTTCCCACTTAATCCTTAC
13869494 TCATTCATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.32, C:0.35, G:0.00, T:0.32
Consensus pattern (34 bp):
ACTAAAACACCATTCTTTCCCACTTAATCCTTAC
Found at i:13880655 original size:19 final size:19
Alignment explanation
Indices: 13880620--13880656 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
13880610 GAGAATGTAA
* *
13880620 TTTTTATTTTGTTTTTTGT
1 TTTTTATTTTATGTTTTGT
13880639 TTTTTATTTTATGTTTTG
1 TTTTTATTTTATGTTTTG
13880657 AACATTGATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.11, T:0.81
Consensus pattern (19 bp):
TTTTTATTTTATGTTTTGT
Found at i:13881936 original size:34 final size:34
Alignment explanation
Indices: 13881856--13881958 Score: 118
Period size: 34 Copynumber: 3.0 Consensus size: 34
13881846 AGGAACCATA
* *
13881856 ATGTAGGATCATTAA-CTATATTCCTAGTAGGTTTT
1 ATGTAGGATGATTAATC-ATATTACTAGTAGG-TTT
* *
13881891 ATGAAGGATGATTAATCATATTACTAGTAAGTTT
1 ATGTAGGATGATTAATCATATTACTAGTAGGTTT
* * *
13881925 ATGTAGAATGATTAATTATATTATTAGTAGGTTT
1 ATGTAGGATGATTAATCATATTACTAGTAGGTTT
13881959 TATTATTTTG
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
34 32 0.55
35 25 0.43
36 1 0.02
ACGTcount: A:0.34, C:0.06, G:0.17, T:0.43
Consensus pattern (34 bp):
ATGTAGGATGATTAATCATATTACTAGTAGGTTT
Found at i:13883716 original size:31 final size:30
Alignment explanation
Indices: 13883680--13883758 Score: 85
Period size: 29 Copynumber: 2.7 Consensus size: 30
13883670 AAAATAATTA
13883680 AAATTATTAATATTTAATTA-TAATATCATTT
1 AAATTATTAATATTTAATTATTAATAT--TTT
*
13883711 AAATTA-TAA-ATATAA-TATTAATATTTT
1 AAATTATTAATATTTAATTATTAATATTTT
*
13883738 AAATTATTAATGATTAAATTA
1 AAATTATTAAT-ATTTAATTA
13883759 CAAATTAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
27 9 0.22
28 5 0.12
29 11 0.28
30 7 0.17
31 8 0.20
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (30 bp):
AAATTATTAATATTTAATTATTAATATTTT
Found at i:13883780 original size:25 final size:27
Alignment explanation
Indices: 13883742--13883798 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 27
13883732 TATTTTAAAT
13883742 TATTAATGATTAAATTA-CAA-ATTAA
1 TATTAATGATTAAATTATCAATATTAA
13883767 TATTAAT-ATATAAATTATCAATTATTAA
1 TATTAATGAT-TAAATTATCAA-TATTAA
13883795 TATT
1 TATT
13883799 TAAAAAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
24 2 0.07
25 14 0.50
26 3 0.11
28 9 0.32
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.46
Consensus pattern (27 bp):
TATTAATGATTAAATTATCAATATTAA
Found at i:13883802 original size:47 final size:43
Alignment explanation
Indices: 13883684--13883784 Score: 122
Period size: 42 Copynumber: 2.4 Consensus size: 43
13883674 TAATTAAAAT
* * *
13883684 TATTAATA-TTT-AATTATAATATCATTTAAATTATAAATATAA
1 TATTAATATTTTAAATTATTA-ATGATTTAAATTACAAATATAA
13883726 TATTAATATTTTAAATTATTAATGA-TTAAATTACAAAT-TAA
1 TATTAATATTTTAAATTATTAATGATTTAAATTACAAATATAA
*
13883767 TATTAATA-TATAAATTAT
1 TATTAATATTTTAAATTAT
13883785 CAATTATTAA
Statistics
Matches: 53, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
40 9 0.17
41 11 0.21
42 20 0.38
43 6 0.11
44 7 0.13
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.48
Consensus pattern (43 bp):
TATTAATATTTTAAATTATTAATGATTTAAATTACAAATATAA
Found at i:13884032 original size:27 final size:27
Alignment explanation
Indices: 13883976--13884030 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
13883966 TTTAATTATC
* **
13883976 AATTATTAATATTTTAATTTAAACATA
1 AATTATTAATATTTAAAAATAAACATA
13884003 AATTATTAATATTTAAAAATAAA-ATA
1 AATTATTAATATTTAAAAATAAACATA
13884029 AA
1 AA
13884031 ATAATAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 5 0.20
27 20 0.80
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (27 bp):
AATTATTAATATTTAAAAATAAACATA
Found at i:13884086 original size:202 final size:202
Alignment explanation
Indices: 13883861--13884242 Score: 549
Period size: 202 Copynumber: 1.9 Consensus size: 202
13883851 TTAAATTTAA
*
13883861 AAATTAATTAAAATTAGTAATATTTTAATCATAATAACATTTAAA-TATAAATAAAATATTAATT
1 AAATTAATTAAAATTAGTAATATTTTAATCATAATAA-ATTTAAATTATAAAT-AAATATTAATA
*** * * *
13883925 TTTTAAAATGTT-AAT-A-TAAATTATAAATAAAGTATTAACATTTTAATTATCAATTATTAATA
64 CCCT-AAAT-TTAAATAATTAAATAATAAATAAAATATTAACATTTAAATTATCAATTATTAATA
*
13883987 TTTTAATTTAAACATAAATTATTAATATTT-AAAAATAAAATAAAATAATAAATTTTGATTATAT
127 TTTTAAATTAAACATAAATTATTAATATTTAAAAAATAAAATAAAATAA-AAATTTTGATTATAT
13884051 ATTACAAAAATG
191 ATTACAAAAATG
* *
13884063 AAATTATTTAAAATTATTAATATTTTAATCATAATAAATTTAAATTATAAATAAATATTAATACC
1 AAATTAATTAAAATTAGTAATATTTTAATCATAATAAATTTAAATTATAAATAAATATTAATACC
* * *
13884128 CTAAATTTAAATAATTAAATAATGAATAAAATATTAATATTTAAATTATCAATTATTAATGTTTT
66 CTAAATTTAAATAATTAAATAATAAATAAAATATTAACATTTAAATTATCAATTATTAATATTTT
**
13884193 AAATTAATTATAAATTATTAATATTTAAAAAATAAAATAAAATAAAAATT
131 AAATTAAACATAAATTATTAATATTTAAAAAATAAAATAAAATAAAAATT
13884243 CAAATTCATA
Statistics
Matches: 160, Mismatches: 15, Indels: 10
0.86 0.08 0.05
Matches are distributed among these distances:
199 2 0.01
200 7 0.04
201 19 0.12
202 114 0.71
203 18 0.11
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (202 bp):
AAATTAATTAAAATTAGTAATATTTTAATCATAATAAATTTAAATTATAAATAAATATTAATACC
CTAAATTTAAATAATTAAATAATAAATAAAATATTAACATTTAAATTATCAATTATTAATATTTT
AAATTAAACATAAATTATTAATATTTAAAAAATAAAATAAAATAAAAATTTTGATTATATATTAC
AAAAATG
Found at i:13884186 original size:41 final size:40
Alignment explanation
Indices: 13884071--13884186 Score: 101
Period size: 41 Copynumber: 2.8 Consensus size: 40
13884061 TGAAATTATT
* * *
13884071 TAAAATTATTAATATTTTAATCATAATAAATTTAAATTATAAA
1 TAAAA-TATTAATATTTAAATTATAAT-AA-TTAAATAATAAA
** *
13884114 T-AAATATTAATACCCTAAATT-TAAATAATTAAATAATGAA
1 TAAAATATTAATA-TTTAAATTAT-AATAATTAAATAATAAA
*
13884154 TAAAATATTAATATTTAAATTATCAATTATTAA
1 TAAAATATTAATATTTAAATTAT-AATAATTAA
13884187 TGTTTTAAAT
Statistics
Matches: 59, Mismatches: 10, Indels: 10
0.75 0.13 0.13
Matches are distributed among these distances:
40 17 0.29
41 31 0.53
42 10 0.17
43 1 0.02
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.41
Consensus pattern (40 bp):
TAAAATATTAATATTTAAATTATAATAATTAAATAATAAA
Found at i:13884794 original size:22 final size:21
Alignment explanation
Indices: 13884758--13884798 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
13884748 AAAATTCATA
*
13884758 TAAAAATTATACAAATAAATTC
1 TAAAAATCATACAAA-AAATTC
*
13884780 TAAAAATCATTCAAAAAAT
1 TAAAAATCATACAAAAAAT
13884799 AATCTTAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (21 bp):
TAAAAATCATACAAAAAATTC
Found at i:13885274 original size:16 final size:16
Alignment explanation
Indices: 13885255--13885305 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
13885245 ATTAAATAAG
13885255 AAAAAAATTAAAAATA
1 AAAAAAATTAAAAATA
*
13885271 AAAATTAA-TAAAAATA
1 AAAA-AAATTAAAAATA
* *
13885287 AAATAAATAAATAAATA
1 AAAAAAATTAA-AAATA
13885304 AA
1 AA
13885306 CCAAACTTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
15 2 0.07
16 17 0.61
17 9 0.32
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (16 bp):
AAAAAAATTAAAAATA
Found at i:13885274 original size:32 final size:33
Alignment explanation
Indices: 13885237--13885305 Score: 88
Period size: 32 Copynumber: 2.1 Consensus size: 33
13885227 AGTCACCAAG
* *
13885237 TAAAAATTATTAAATAAGAAAA-AAATTAA-AAA
1 TAAAAATTAATAAA-AAGAAAATAAATAAATAAA
*
13885269 TAAAAATTAATAAAAATAAAATAAATAAATAAA
1 TAAAAATTAATAAAAAGAAAATAAATAAATAAA
13885302 TAAA
1 TAAA
13885306 CCAAACTTAC
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
31 6 0.19
32 19 0.59
33 7 0.22
ACGTcount: A:0.74, C:0.00, G:0.01, T:0.25
Consensus pattern (33 bp):
TAAAAATTAATAAAAAGAAAATAAATAAATAAA
Found at i:13885275 original size:13 final size:14
Alignment explanation
Indices: 13885257--13885301 Score: 56
Period size: 15 Copynumber: 3.2 Consensus size: 14
13885247 TAAATAAGAA
13885257 AAAAATTAA-AAAT
1 AAAAATTAATAAAT
*
13885270 AAAAATTAATAAAA
1 AAAAATTAATAAAT
*
13885284 ATAAAATAAATAAAT
1 A-AAAATTAATAAAT
13885299 AAA
1 AAA
13885302 TAAACCAAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 9 0.33
14 6 0.22
15 12 0.44
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
AAAAATTAATAAAT
Found at i:13885557 original size:10 final size:10
Alignment explanation
Indices: 13885542--13885582 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
13885532 GATAAAATTT
13885542 AAAAATTTAA
1 AAAAATTTAA
13885552 AAAAA-TTAA
1 AAAAATTTAA
* *
13885561 AAATATGTAA
1 AAAAATTTAA
13885571 AAAAATTTAA
1 AAAAATTTAA
13885581 AA
1 AA
13885583 TTTTTATAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
9 8 0.31
10 18 0.69
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (10 bp):
AAAAATTTAA
Found at i:13885573 original size:19 final size:17
Alignment explanation
Indices: 13885535--13885585 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 17
13885525 TTATAAAGAT
*
13885535 AAAATTTAAAAATTTAA
1 AAAAATTAAAAATTTAA
13885552 AAAAATTAAAAATATGTAA
1 AAAAATTAAAAAT-T-TAA
*
13885571 AAAAATTTAAAATTT
1 AAAAATTAAAAATTT
13885586 TTATAAGAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 13 0.43
18 2 0.07
19 15 0.50
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (17 bp):
AAAAATTAAAAATTTAA
Found at i:13885599 original size:37 final size:36
Alignment explanation
Indices: 13885535--13885607 Score: 83
Period size: 37 Copynumber: 2.0 Consensus size: 36
13885525 TTATAAAGAT
*
13885535 AAAATTTAAAAATTTAAAAAAATTAAAAATATGTAAA
1 AAAATTTAAAAATTTAAAAAAAGTAAAAATAT-TAAA
* * * * *
13885572 AAAATTTAAAATTTTTATAAGAGTAAAATTATTAAA
1 AAAATTTAAAAATTTAAAAAAAGTAAAAATATTAAA
13885608 TTTTAAAAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
36 4 0.13
37 26 0.87
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (36 bp):
AAAATTTAAAAATTTAAAAAAAGTAAAAATATTAAA
Found at i:13898736 original size:50 final size:50
Alignment explanation
Indices: 13898661--13898760 Score: 173
Period size: 50 Copynumber: 2.0 Consensus size: 50
13898651 TCCTTTTTTA
* *
13898661 AGATTCTTCTTTTAGCATTAGACATTCAGATCTAAAATGTCTTGGTTTCT
1 AGATTCTTCTTTTAGCATTAGACATTCAGATCTAAAATATCCTGGTTTCT
*
13898711 AGATTCTTCTTTTAGCATTAGACATTCTGATCTAAAATATCCTGGTTTCT
1 AGATTCTTCTTTTAGCATTAGACATTCAGATCTAAAATATCCTGGTTTCT
13898761 TACATTCAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.44
Consensus pattern (50 bp):
AGATTCTTCTTTTAGCATTAGACATTCAGATCTAAAATATCCTGGTTTCT
Found at i:13909764 original size:23 final size:23
Alignment explanation
Indices: 13909738--13909793 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
13909728 CATTATCTAA
*
13909738 ATCTAAGATATAAGAACAAAAAT
1 ATCTAAGATACAAGAACAAAAAT
*
13909761 ATCTACGATACAAGAACAAAAAT
1 ATCTAAGATACAAGAACAAAAAT
13909784 -T-TAAGATACA
1 ATCTAAGATACA
13909794 GGGCTTTGCT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
21 8 0.27
22 1 0.03
23 21 0.70
ACGTcount: A:0.57, C:0.12, G:0.09, T:0.21
Consensus pattern (23 bp):
ATCTAAGATACAAGAACAAAAAT
Done.