Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168159.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_4, 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: 33012953
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 65000 characters in sequence are not A, C, G, or T
File 109 of 160
Found at i:20692094 original size:12 final size:11
Alignment explanation
Indices: 20692056--20692127 Score: 58
Period size: 12 Copynumber: 6.4 Consensus size: 11
20692046 TTTAGTACTT
20692056 TTTTA-TTTTA
1 TTTTATTTTTA
**
20692066 TTCCATTTTTA
1 TTTTATTTTTA
*
20692077 TCTTTATCTTTA
1 T-TTTATTTTTA
20692089 TTTTTATTTTTA
1 -TTTTATTTTTA
20692101 TTCTTATTTTT-
1 TT-TTATTTTTA
*
20692112 TTATTTTTTTTA
1 TT-TTATTTTTA
20692124 TTTT
1 TTTT
20692128 TTTGTCTTCT
Statistics
Matches: 49, Mismatches: 8, Indels: 9
0.74 0.12 0.14
Matches are distributed among these distances:
10 3 0.06
11 19 0.39
12 26 0.53
13 1 0.02
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTATTTTTA
Found at i:20692102 original size:6 final size:6
Alignment explanation
Indices: 20692070--20692128 Score: 68
Period size: 6 Copynumber: 10.0 Consensus size: 6
20692060 ATTTTATTCC
* * *
20692070 ATTTTT ATCTTT ATCTTT ATTTTT ATTTTT ATTCTT ATTTTT -TTATTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATT-TTT
20692118 -TTTTT ATTTTT
1 ATTTTT ATTTTT
20692129 TTGTCTTCTT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
5 5 0.11
6 42 0.89
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.80
Consensus pattern (6 bp):
ATTTTT
Found at i:20692124 original size:35 final size:34
Alignment explanation
Indices: 20692055--20692128 Score: 87
Period size: 35 Copynumber: 2.1 Consensus size: 34
20692045 ATTTAGTACT
*
20692055 TTTTTATTTTATTCCATTTTTATCTTTATCTTTA
1 TTTTTATTTTATTCCATTTTTATATTTATCTTTA
* * *
20692089 TTTTTATTTTTATTCTTATTTTTTTATTT-TTTTTA
1 TTTTTA-TTTTATTC-CATTTTTATATTTATCTTTA
20692124 TTTTT
1 TTTTT
20692129 TTGTCTTCTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
34 6 0.18
35 18 0.53
36 10 0.29
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (34 bp):
TTTTTATTTTATTCCATTTTTATATTTATCTTTA
Found at i:20692129 original size:18 final size:18
Alignment explanation
Indices: 20692071--20692130 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 18
20692061 TTTTATTCCA
20692071 TTTTTATCTTTATCTTTATTT
1 TTTTTAT-TTT-T-TTTATTT
* *
20692092 TTATTT-TTATTCTTA-TT
1 TT-TTTATTTTTTTTATTT
20692109 TTTTTATTTTTTTTATTT
1 TTTTTATTTTTTTTATTT
20692127 TTTT
1 TTTT
20692131 GTCTTCTTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 9
0.71 0.09 0.20
Matches are distributed among these distances:
16 3 0.09
17 11 0.34
18 9 0.28
19 1 0.03
20 2 0.06
21 3 0.09
22 3 0.09
ACGTcount: A:0.13, C:0.05, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTTATTTTTTTTATTT
Found at i:20692297 original size:119 final size:115
Alignment explanation
Indices: 20692136--20692485 Score: 501
Period size: 119 Copynumber: 3.0 Consensus size: 115
20692126 TTTTTGTCTT
*
20692136 CTTAAAATAAA--TTCAAAAAAATATTTTTGG-GAAAAGTTGAAAGTATCAATTTTCCTTAAAAA
1 CTTAAAATAAATTTTCAAAAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTTTTCTTAAAAA
*
20692198 TAAATTTTCAAAAAAAAAGGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTC
66 TAAATTTTCAAAAAAAAA---TTTTTGGGGAAAAGTTGAAAGTATCAATTTTC
20692251 CTTAGAAATAAATTTTCAAAAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTTTTCTTAAAA
1 CTTA-AAATAAATTTTCAAAAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTTTTCTTAAAA
* *
20692316 ATAAATTTCCAAAAAAAATATTTTTGGGGAAAAATTGAAAGTATCAATTTTC
65 ATAAATTTTCAAAAAAAA-ATTTTTGGGGAAAAGTTGAAAGTATCAATTTTC
** *
20692368 CTTATAAATAAATTTTCAAAAAAAGGGTTTTT-GAGGAAAAGTTGAAAGTATCAATTTTTCTTGA
1 CTTA-AAATAAATTTTCAAAAAAA-TATTTTTGGA-GAAAAGTTGAAAGTATCAATTTTTCTTAA
* *
20692432 AAATCAAAATTTCACAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
63 AAAT-AAATTTTCA-AAAAAAAATTTTTGGGGAAAAGTTGAAAGTATCAATTTT
20692486 TCCTACACAA
Statistics
Matches: 214, Mismatches: 12, Indels: 14
0.89 0.05 0.06
Matches are distributed among these distances:
115 4 0.02
116 7 0.03
117 55 0.26
118 56 0.26
119 85 0.40
120 7 0.03
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.35
Consensus pattern (115 bp):
CTTAAAATAAATTTTCAAAAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTTTTCTTAAAAA
TAAATTTTCAAAAAAAAATTTTTGGGGAAAAGTTGAAAGTATCAATTTTC
Found at i:20692340 original size:59 final size:59
Alignment explanation
Indices: 20692134--20692487 Score: 456
Period size: 59 Copynumber: 6.1 Consensus size: 59
20692124 TTTTTTTGTC
20692134 TTCTT-AAAATAAA--TTC-AAAAAAATATTTTTGG-GAAAAGTTGAAAGTATCAATTT
1 TTCTTAAAAATAAATTTTCAAAAAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTT
*
20692188 TCCTTAAAAATAAATTTTCAAAAAAAA-AGGGTTTTT-GAGGAAAAGTTGAAAGTATCAATTT
1 TTCTTAAAAATAAATTTTCAAAAAAAATA---TTTTTGGA-GAAAAGTTGAAAGTATCAATTT
* *
20692249 TCCTTAGAAATAAATTTTC-AAAAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTT
1 TTCTTAAAAATAAATTTTCAAAAAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTT
* * *
20692307 TTCTTAAAAATAAATTTCCAAAAAAAATATTTTTGGGGAAAAATTGAAAGTATCAATTT
1 TTCTTAAAAATAAATTTTCAAAAAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTT
* * ***
20692366 TCCTTATAAATAAATTTTCAAAAAAAGGGTTTTT-GAGGAAAAGTTGAAAGTATCAATTT
1 TTCTTAAAAATAAATTTTCAAAAAAAATATTTTTGGA-GAAAAGTTGAAAGTATCAATTT
* * * *
20692425 TTCTTGAAAATCAAAATTTCACAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTT
1 TTCTTAAAAAT-AAATTTTCAAAAAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTT
20692485 TTC
1 TTC
20692488 CTACACAAGA
Statistics
Matches: 261, Mismatches: 24, Indels: 24
0.84 0.08 0.08
Matches are distributed among these distances:
54 4 0.02
55 8 0.03
57 4 0.02
58 51 0.20
59 97 0.37
60 55 0.21
61 42 0.16
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.36
Consensus pattern (59 bp):
TTCTTAAAAATAAATTTTCAAAAAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTT
Found at i:20692453 original size:178 final size:172
Alignment explanation
Indices: 20692134--20692487 Score: 568
Period size: 178 Copynumber: 2.0 Consensus size: 172
20692124 TTTTTTTGTC
*
20692134 TTCTTAAAATAAATTCAAAAAAATATTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT
1 TTCTTAAAATAAATTCAAAAAAATATTTTTGGGAAAAATTGAAAGTATCAATTTTCCTTAAAAAT
*
20692199 AAATTTTCAAAAAAAAAGGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAAT
66 AAATTTTC-AAAAAAAAGGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAAA
20692264 TTTCAAAAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTT
130 TTTCAAAAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTT
20692307 TTCTTAAAAATAAATTTCCAAAAAAAATATTTTTGGGGAAAAATTGAAAGTATCAATTTTCCTTA
1 TTCTT-AAAATAAA-TT-C-AAAAAAATATTTTT-GGGAAAAATTGAAAGTATCAATTTTCCTTA
* *
20692372 TAAATAAATTTTC-AAAAAAAGGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTT-GAAAA
61 AAAATAAATTTTCAAAAAAAAGGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAG-AAA
*
20692435 TCAAAATTTCACAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTT
125 T-AAAATTTCA-AAAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTT
20692485 TTC
1 TTC
20692488 CTACACAAGA
Statistics
Matches: 168, Mismatches: 5, Indels: 11
0.91 0.03 0.06
Matches are distributed among these distances:
173 5 0.03
174 8 0.05
175 3 0.02
176 49 0.29
177 22 0.13
178 81 0.48
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.36
Consensus pattern (172 bp):
TTCTTAAAATAAATTCAAAAAAATATTTTTGGGAAAAATTGAAAGTATCAATTTTCCTTAAAAAT
AAATTTTCAAAAAAAAGGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAATAAAAT
TTCAAAAAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTT
Found at i:20702608 original size:533 final size:537
Alignment explanation
Indices: 20701761--20702762 Score: 1458
Period size: 534 Copynumber: 1.9 Consensus size: 537
20701751 ATAAAATTCA
* *
20701761 AAACAAACGAGAGCTAATGAATTACCTTTTTATTTATTTTTTTCTCTAACCAAGCTTTATATTTA
1 AAACAAACAAGAGCTAATGAATTACCTTCTTATTTATTTTTTTCTCTAACCAAGCTTTATATTTA
* * * * *
20701826 GGGCACTTATATTTCATATGACCTTTTTTCTTATAGGAAAATCACTTGATATCTTTCTTAATGAT
66 GAGCACTTATATTTCATATGACCTTTCTTCTTATAGGAAAAACACTTGATATCTTTCGTAATGAC
** * * * *
20701891 AGTTTTAGGACCTCCTACCCCTTTTGTCTAACCATAACCCTATCTTTTGTTATCCTAAACTTTCT
131 AACTTTAGAACCTCCTACCCCTTTAGTCTAACCACAACCCTATCATTTGTTATCCTAAACTTTCT
* *
20701956 TATGAGCATTAAAAACAAATCTCACAAGTTTCCCATAATTCCTTTGGTAATTAGGTTTGGAATGG
196 TATGAGCATTAAAAACAAATCTCACAAGTTTCCCATAATTCATTTGGTAATTAGATTTGGAATGG
* *
20702021 GTAATAAGATAGGCACTCTCACTCTTTTCTTTCTTGAGTTTTTCTTCCTCAAAAACATA-TTTTG
261 ATAATAAGATAGGCACTCTCACTCTTTTCTTTCTTAAGTTTTTCTTCCTCAAAAACATATTTTTG
* * ** *
20702085 AGATAAGAACATTAACATTCCAAACCTCATTCATAGCATTATAGGCAATTTTTATCTAGGTGAAC
326 AGATAAGAACATTAACACTCCAAACCTCATTCATAACATTATAAACAATTTTGATCTAGGTGAAC
* * *
20702150 TCAATAGGTAAGGAATTAA-GGGCATGGTGAATAATGAA-TTTGTCAGGGAGGACAATTTTATGG
391 TCAATAGGTAAGGAATTAAGGGGCATGATGAACAATGAATTTTGTCAGGGAGGACAATTTCATGG
20702213 GAGGTCAATTTAGTAGACCATTCTCTTAATAAAATCTCTAACACCCCATACACTGTCATACCTTA
456 GAGGTCAATTTAGTAGACCATTCTCTTAATAAAATCTCTAACACCCCATACACTGTCATACCTTA
20702278 TGCTCATAAGCTCACTC
521 TGCTCATAAGCTCACTC
* *
20702295 AAACAAACAAGAGCTAGTGAGTTACCTTCTTATTTATTTTTTTCTCTAACCAAGCTTTATATTTA
1 AAACAAACAAGAGCTAATGAATTACCTTCTTATTTATTTTTTTCTCTAACCAAGCTTTATATTTA
* * *
20702360 GAGCACTTATGTTTCATATGACCTTTCTTCTTATAGGAAAAACATTTGATATCTTTCGTAATGGC
66 GAGCACTTATATTTCATATGACCTTTCTTCTTATAGGAAAAACACTTGATATCTTTCGTAATGAC
** * * *
20702425 AACTTTAGAACCTTTTA-CCCTTTAGTTTGACCACAACCCTATCATTTGTTATCTTAAACTTTCT
131 AACTTTAGAACCTCCTACCCCTTTAGTCTAACCACAACCCTATCATTTGTTATCCTAAACTTTCT
* ** * * * **
20702489 TATGAGTATTAGGAATAGATCTCACAGGTTTCTTATAATTCATTTGGTAATT-GAATTT-GAAGT
196 TATGAGCATTAAAAACAAATCTCACAAGTTTCCCATAATTCATTTGGTAATTAG-ATTTGGAA-T
* * * *
20702552 GGATAGTAAGATGGGTACTCTCACTCTTTTCTTTCTTAAGTTTTTCTTCTTCAAAAACATATTTT
259 GGATAATAAGATAGGCACTCTCACTCTTTTCTTTCTTAAGTTTTTCTTCCTCAAAAACATATTTT
* * *
20702617 TGAGATAAGATCATTAACACTCCAAACCTCATTCATAACATTATAAATAATTTTGATTTAGGTGA
324 TGAGATAAGAACATTAACACTCCAAACCTCATTCATAACATTATAAACAATTTTGATCTAGGTGA
* * * *
20702682 ACTTAATAGGTAAGGAATTAAGGGGTATGATGAACAATGAATTTTGTTAGGGAGGATAATTTCAT
389 ACTCAATAGGTAAGGAATTAAGGGGCATGATGAACAATGAATTTTGTCAGGGAGGACAATTTCAT
20702747 GGGAGGTCAATTTAGT
454 GGGAGGTCAATTTAGT
20702763 TTGAATGTGA
Statistics
Matches: 409, Mismatches: 54, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
532 4 0.01
533 143 0.35
534 210 0.51
535 16 0.04
536 36 0.09
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (537 bp):
AAACAAACAAGAGCTAATGAATTACCTTCTTATTTATTTTTTTCTCTAACCAAGCTTTATATTTA
GAGCACTTATATTTCATATGACCTTTCTTCTTATAGGAAAAACACTTGATATCTTTCGTAATGAC
AACTTTAGAACCTCCTACCCCTTTAGTCTAACCACAACCCTATCATTTGTTATCCTAAACTTTCT
TATGAGCATTAAAAACAAATCTCACAAGTTTCCCATAATTCATTTGGTAATTAGATTTGGAATGG
ATAATAAGATAGGCACTCTCACTCTTTTCTTTCTTAAGTTTTTCTTCCTCAAAAACATATTTTTG
AGATAAGAACATTAACACTCCAAACCTCATTCATAACATTATAAACAATTTTGATCTAGGTGAAC
TCAATAGGTAAGGAATTAAGGGGCATGATGAACAATGAATTTTGTCAGGGAGGACAATTTCATGG
GAGGTCAATTTAGTAGACCATTCTCTTAATAAAATCTCTAACACCCCATACACTGTCATACCTTA
TGCTCATAAGCTCACTC
Found at i:20711396 original size:37 final size:37
Alignment explanation
Indices: 20711340--20711412 Score: 92
Period size: 37 Copynumber: 2.0 Consensus size: 37
20711330 TTTTATTTTG
* *
20711340 GACCTTAAATCTTGATTATTATGGCATAACAATTGTC
1 GACCTTAAACCATGATTATTATGGCATAACAATTGTC
* * * *
20711377 GACCTTAAACCATGGTTATTATTGTATAATAATTGT
1 GACCTTAAACCATGATTATTATGGCATAACAATTGT
20711413 GCAACTAGTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.40
Consensus pattern (37 bp):
GACCTTAAACCATGATTATTATGGCATAACAATTGTC
Found at i:20718559 original size:264 final size:263
Alignment explanation
Indices: 20718081--20718863 Score: 1192
Period size: 256 Copynumber: 3.0 Consensus size: 263
20718071 ATTTGATGAA
* * * ** *
20718081 TAGTTTGTAAATAAATATGATTTTTATTTATTTATATTTATTTATTAAATTTAATAAACGATTAC
1 TAGTTTATGAATAAATTTGATTTTTATTTGCTTATATTTATTTATTAAATTTAATAAATGATTAC
* * * * *
20718146 AAACAACATTTTAGATTTCATTTATTAAATAAACCAAT-ACGAACAAACAAGTTCAGCTAA-ATA
66 AAATAACATTTTAGATTTTATTTATTAAATAAACTAATCTCGAACAAACAAGTTCAGTTAAGA-A
* * * **
20718209 TTGTTTAAAATTTATTCGTTTATGGATTGTTAAAATTTGTTTGTTGTTTGATAATAACAAAATAA
130 TTGTTTAAAATTTGTTCGTATATGGATTTTTAAAATTCATTTGTTGTTTGATAATAACAAAATAA
20718274 TATTATTATCTTTTTACCCTAATATTACTTTAAACCTAAAC-GATCTAACATTCTCACTCACTCA
195 TATTATTATCTTTTTACCCTAATATTACTTTAAACCT-AACGGATCTAACATTCTCA-TCACTCA
20718338 CTCACT
258 CTCACT
20718344 TAGTTTATGAATAAATTT-AGTTTTTATTTGCTTATATTTATTTATTAAATTTAATAAATGATTA
1 TAGTTTATGAATAAATTTGA-TTTTTATTTGCTTATATTTATTTATTAAATTTAATAAATGATTA
20718408 CAAATAACATTTTAGATTTTATTTATTAAATAAACTAATCTCGAACAAACAAGTTCAGTTAAGAA
65 CAAATAACATTTTAGATTTTATTTATTAAATAAACTAATCTCGAACAAACAAGTTCAGTTAAGAA
*
20718473 TTGTTTAAAATTTGTTCGTATATGAATTTTTAAAATTCATTTGTTGTTTGATAATAACAAAATAA
130 TTGTTTAAAATTTGTTCGTATATGGATTTTTAAAATTCATTTGTTGTTTGATAATAACAAAATAA
*
20718538 TATTATTATCTTTTTACCCTAAAATTACTTTAAACCTAACGGATCTAACA---T--T--CTCACT
195 TATTATTATCTTTTTACCCTAATATTACTTTAAACCTAACGGATCTAACATTCTCATCACTCACT
20718596 CACT
260 CACT
*
20718600 TAGTTTATGAATAAATTTGATTTTTATTTGCTTATATTTATTTATTAAATTTAACAAATGATTAC
1 TAGTTTATGAATAAATTTGATTTTTATTTGCTTATATTTATTTATTAAATTTAATAAATGATTAC
* * *
20718665 AAATAATATTTCAGATTTTATTTATTAAATAAACTAATCTCGAACAAATAAGTTCAGTTAAGAAT
66 AAATAACATTTTAGATTTTATTTATTAAATAAACTAATCTCGAACAAACAAGTTCAGTTAAGAAT
* *
20718730 TGTTTAAAATTTGTTGGTATATGGATTTTTAAAATTCATTTGTTGTTTGATAATAGCAAAATAAT
131 TGTTTAAAATTTGTTCGTATATGGATTTTTAAAATTCATTTGTTGTTTGATAATAACAAAATAAT
* * * *
20718795 AATATTATCTTTTTACCCTAATATTACTTTAAACCTACCTGATATAACATTCTCATTCACTCACT
196 ATTATTATCTTTTTACCCTAATATTACTTTAAACCTAACGGATCTAACATTCTCA-TCACTCACT
20718860 CACT
260 CACT
20718864 CACTCATGTT
Statistics
Matches: 477, Mismatches: 30, Indels: 25
0.90 0.06 0.05
Matches are distributed among these distances:
256 240 0.50
257 1 0.00
258 1 0.00
259 1 0.00
261 1 0.00
262 2 0.00
263 95 0.20
264 135 0.28
265 1 0.00
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.44
Consensus pattern (263 bp):
TAGTTTATGAATAAATTTGATTTTTATTTGCTTATATTTATTTATTAAATTTAATAAATGATTAC
AAATAACATTTTAGATTTTATTTATTAAATAAACTAATCTCGAACAAACAAGTTCAGTTAAGAAT
TGTTTAAAATTTGTTCGTATATGGATTTTTAAAATTCATTTGTTGTTTGATAATAACAAAATAAT
ATTATTATCTTTTTACCCTAATATTACTTTAAACCTAACGGATCTAACATTCTCATCACTCACTC
ACT
Found at i:20719795 original size:28 final size:28
Alignment explanation
Indices: 20719737--20719796 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
20719727 TATTTAATTA
**
20719737 AAAAGTAAAAATAAAAACAAAAAATTGT
1 AAAAGTAAAAATAAAAACAAAAAATAAT
20719765 AAAAGTAAAAATGAAAAA-AAACAAA-AAT
1 AAAAGTAAAAAT-AAAAACAAA-AAATAAT
20719793 AAAA
1 AAAA
20719797 TAATATAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 20 0.71
29 8 0.29
ACGTcount: A:0.77, C:0.03, G:0.07, T:0.13
Consensus pattern (28 bp):
AAAAGTAAAAATAAAAACAAAAAATAAT
Found at i:20721919 original size:18 final size:19
Alignment explanation
Indices: 20721881--20721919 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
20721871 AGTAAATGGC
**
20721881 AAGAGCATGATATTGAAAT
1 AAGAGCATGATATCAAAAT
20721900 AAGAGCATGA-ATCAAAAT
1 AAGAGCATGATATCAAAAT
20721918 AA
1 AA
20721920 ACATGAAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.54, C:0.08, G:0.18, T:0.21
Consensus pattern (19 bp):
AAGAGCATGATATCAAAAT
Found at i:20728820 original size:11 final size:10
Alignment explanation
Indices: 20728790--20728833 Score: 63
Period size: 11 Copynumber: 4.3 Consensus size: 10
20728780 AATAATAATA
20728790 AAATTAATTT
1 AAATTAATTT
20728800 -AATTAATTT
1 AAATTAATTT
20728809 AAATTAAATTT
1 AAATT-AATTT
20728820 AAATTTAATTT
1 AAA-TTAATTT
20728831 AAA
1 AAA
20728834 ATATAAAGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
9 9 0.29
10 4 0.13
11 16 0.52
12 2 0.06
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (10 bp):
AAATTAATTT
Found at i:20729187 original size:23 final size:23
Alignment explanation
Indices: 20729143--20729187 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
20729133 ATCATAAAAC
* *
20729143 ACTCAAAATCCTAAATCTTAAAT
1 ACTCAAAATCCTAAACCCTAAAT
20729166 ACTCAAAA-CCTTAAACCCTAAA
1 ACTCAAAATCC-TAAACCCTAAA
20729188 ACTTGAAACC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 17 0.89
ACGTcount: A:0.49, C:0.27, G:0.00, T:0.24
Consensus pattern (23 bp):
ACTCAAAATCCTAAACCCTAAAT
Found at i:20729204 original size:23 final size:21
Alignment explanation
Indices: 20729171--20729258 Score: 79
Period size: 22 Copynumber: 4.0 Consensus size: 21
20729161 TAAATACTCA
*
20729171 AAACCTTAAACCCTAAAACTTG
1 AAACC-TAAAACCTAAAACTTG
*
20729193 AAACCCTAAAACCAAAAACCTTG
1 AAA-CCTAAAACCTAAAA-CTTG
**
20729216 AAACCTCAAAATCCTAAAAC-AA
1 AAACCT-AAAA-CCTAAAACTTG
20729238 AAATCCTAAAACCTAAAACTT
1 AAA-CCTAAAACCTAAAACTT
20729259 TAAAATCTTG
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
21 8 0.15
22 23 0.43
23 17 0.31
24 6 0.11
ACGTcount: A:0.52, C:0.27, G:0.02, T:0.18
Consensus pattern (21 bp):
AAACCTAAAACCTAAAACTTG
Found at i:20729211 original size:15 final size:15
Alignment explanation
Indices: 20729178--20729256 Score: 61
Period size: 15 Copynumber: 5.3 Consensus size: 15
20729168 TCAAAACCTT
***
20729178 AAACCCTAAAACTTG
1 AAACCCTAAAACCAA
20729193 AAACCCTAAAACCAA
1 AAACCCTAAAACCAA
* * *
20729208 AAACCTTGAAACCTCA
1 AAACCCTAAAACC-AA
*
20729224 AAATCCTAAAA-CAA
1 AAACCCTAAAACCAA
* *
20729238 AAATCCTAAAACCTA
1 AAACCCTAAAACCAA
20729253 AAAC
1 AAAC
20729257 TTTAAAATCT
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
14 12 0.24
15 29 0.58
16 9 0.18
ACGTcount: A:0.54, C:0.28, G:0.03, T:0.15
Consensus pattern (15 bp):
AAACCCTAAAACCAA
Found at i:20729220 original size:45 final size:44
Alignment explanation
Indices: 20729170--20729300 Score: 111
Period size: 45 Copynumber: 2.9 Consensus size: 44
20729160 TTAAATACTC
20729170 AAAACCTTAAACCCTAAAACTTGAAACCCTAAAACCAAAAACCTT
1 AAAACCTTAAACCCTAAAAC-TGAAACCCTAAAACCAAAAACCTT
* * * ** * * *
20729215 GAAACCTCAAAATCCTAAAACAAAAATCCTAAAACCTAAAACTTT
1 AAAACCT-TAAACCCTAAAACTGAAACCCTAAAACCAAAAACCTT
* * * *
20729260 AAAATCTTGAAACCCTTAAA-TGAGACCCTAAATCCTAAAAA
1 AAAACCTT-AAACCCTAAAACTGAAACCCTAAAACC-AAAAA
20729301 TCCACCAAGA
Statistics
Matches: 64, Mismatches: 19, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
44 10 0.16
45 43 0.67
46 11 0.17
ACGTcount: A:0.51, C:0.25, G:0.04, T:0.20
Consensus pattern (44 bp):
AAAACCTTAAACCCTAAAACTGAAACCCTAAAACCAAAAACCTT
Found at i:20729242 original size:14 final size:14
Alignment explanation
Indices: 20729223--20729249 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
20729213 TTGAAACCTC
20729223 AAAATCCTAAAACA
1 AAAATCCTAAAACA
20729237 AAAATCCTAAAAC
1 AAAATCCTAAAAC
20729250 CTAAAACTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.22, G:0.00, T:0.15
Consensus pattern (14 bp):
AAAATCCTAAAACA
Found at i:20729254 original size:7 final size:7
Alignment explanation
Indices: 20729170--20729256 Score: 59
Period size: 8 Copynumber: 11.7 Consensus size: 7
20729160 TTAAATACTC
20729170 AAAACCTT
1 AAAACC-T
*
20729178 AAACCCT
1 AAAACCT
*
20729185 AAAACTT
1 AAAACCT
*
20729192 GAAACCCT
1 -AAAACCT
*
20729200 AAAACCA
1 AAAACCT
20729207 AAAACCTT
1 AAAACC-T
*
20729215 GAAACCT
1 AAAACCT
20729222 CAAAATCCT
1 -AAAA-CCT
*
20729231 AAAA-CA
1 AAAACCT
20729237 AAAATCCT
1 AAAA-CCT
20729245 AAAACCT
1 AAAACCT
20729252 AAAAC
1 AAAAC
20729257 TTTAAAATCT
Statistics
Matches: 61, Mismatches: 12, Indels: 13
0.71 0.14 0.15
Matches are distributed among these distances:
6 5 0.08
7 26 0.43
8 27 0.44
9 3 0.05
ACGTcount: A:0.54, C:0.28, G:0.02, T:0.16
Consensus pattern (7 bp):
AAAACCT
Found at i:20735609 original size:13 final size:13
Alignment explanation
Indices: 20735588--20735626 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
20735578 ATGTAATGTA
*
20735588 AAAAAAATAAAAT
1 AAAAAAATAAAAG
*
20735601 AAAAGAATAAAAG
1 AAAAAAATAAAAG
20735614 AAAATAAATAAAA
1 AAAA-AAATAAAA
20735627 AAATAATGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
13 15 0.68
14 7 0.32
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.13
Consensus pattern (13 bp):
AAAAAAATAAAAG
Found at i:20735622 original size:22 final size:22
Alignment explanation
Indices: 20735586--20735632 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
20735576 GCATGTAATG
*
20735586 TAAAAAAAATAAAATAAAAGAA
1 TAAAAAAAATAAAATAAAAAAA
20735608 TAAAAGAAAAT-AAATAAAAAAA
1 TAAAA-AAAATAAAATAAAAAAA
20735630 TAA
1 TAA
20735633 TGATTGTGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.81, C:0.00, G:0.04, T:0.15
Consensus pattern (22 bp):
TAAAAAAAATAAAATAAAAAAA
Found at i:20737212 original size:30 final size:29
Alignment explanation
Indices: 20737148--20737210 Score: 117
Period size: 29 Copynumber: 2.2 Consensus size: 29
20737138 CATTTTAGTG
20737148 AAAAATAAGAAAACTATGTTTGGGTGTAA
1 AAAAATAAGAAAACTATGTTTGGGTGTAA
*
20737177 AAAAATAAGAAAACTGTGTTTGGGTGTAA
1 AAAAATAAGAAAACTATGTTTGGGTGTAA
20737206 AAAAA
1 AAAAA
20737211 ATTCTCGAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.51, C:0.03, G:0.21, T:0.25
Consensus pattern (29 bp):
AAAAATAAGAAAACTATGTTTGGGTGTAA
Found at i:20737717 original size:36 final size:37
Alignment explanation
Indices: 20737671--20737743 Score: 112
Period size: 36 Copynumber: 2.0 Consensus size: 37
20737661 TCTATGTTTA
20737671 GGCATATGCATCCTAAAAGT-TTTATATTTGCATTAG
1 GGCATATGCATCCTAAAAGTCTTTATATTTGCATTAG
* * *
20737707 GGCATCTGCATCTTAAAAGTCTTTATATTTGTATTAG
1 GGCATATGCATCCTAAAAGTCTTTATATTTGCATTAG
20737744 AACTTTTGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
36 18 0.55
37 15 0.45
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.41
Consensus pattern (37 bp):
GGCATATGCATCCTAAAAGTCTTTATATTTGCATTAG
Found at i:20738260 original size:30 final size:27
Alignment explanation
Indices: 20738208--20738265 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 27
20738198 AATAAAGAAG
20738208 AAAAAAAAAGAAAAAGTCTGTCAAAAA
1 AAAAAAAAAGAAAAAGTCTGTCAAAAA
*
20738235 AAAAAAGAAAGAAAGAAAGTTTGTCAAAAA
1 AAAAAA-AAAG-AA-AAAGTCTGTCAAAAA
20738265 A
1 A
20738266 GAGAAGAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
27 6 0.22
28 4 0.15
29 2 0.07
30 15 0.56
ACGTcount: A:0.69, C:0.05, G:0.14, T:0.12
Consensus pattern (27 bp):
AAAAAAAAAGAAAAAGTCTGTCAAAAA
Found at i:20738521 original size:29 final size:29
Alignment explanation
Indices: 20738483--20738717 Score: 152
Period size: 29 Copynumber: 8.2 Consensus size: 29
20738473 CAAGATAAGA
* **
20738483 TTTAAGCCTAGTTTAGCTGGCACTTAGAT
1 TTTAAGCCCAGTTTAGCTGGCACACAGAT
* * * * * *** *
20738512 TTTAAGCCTAATTTAACTAGTATTTATAT
1 TTTAAGCCCAGTTTAGCTGGCACACAGAT
* ** *
20738541 TTTAAGCCTAGTTTAATTGGCACACA-AA
1 TTTAAGCCCAGTTTAGCTGGCACACAGAT
* * * *
20738569 TTTAAGCCCAGCTTAGTTGGCACTCAAAT
1 TTTAAGCCCAGTTTAGCTGGCACACAGAT
* * *
20738598 TTTAAGCCCAGTTTAACTAGCACACAAAT
1 TTTAAGCCCAGTTTAGCTGGCACACAGAT
* * * **
20738627 TTTCA-CCAAGTTTAGCTAGCACTTAGAT
1 TTTAAGCCCAGTTTAGCTGGCACACAGAT
* * *
20738655 TTTAAGCCCAATTTAGTTGGCACACGGA-
1 TTTAAGCCCAGTTTAGCTGGCACACAGAT
* *
20738683 TTTAAGCCAAGTTTAGTTGGCACACAGAT
1 TTTAAGCCCAGTTTAGCTGGCACACAGAT
20738712 TTTAAG
1 TTTAAG
20738718 ACCAATTTGG
Statistics
Matches: 162, Mismatches: 41, Indels: 6
0.78 0.20 0.03
Matches are distributed among these distances:
28 70 0.43
29 92 0.57
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (29 bp):
TTTAAGCCCAGTTTAGCTGGCACACAGAT
Found at i:20738588 original size:28 final size:28
Alignment explanation
Indices: 20738541--20738713 Score: 141
Period size: 28 Copynumber: 6.1 Consensus size: 28
20738531 GTATTTATAT
* *
20738541 TTTAAGCCTAGTTTAATTGGCACACAAA
1 TTTAAGCCCAGTTTAGTTGGCACACAAA
* *
20738569 TTTAAGCCCAGCTTAGTTGGCACTCAAA
1 TTTAAGCCCAGTTTAGTTGGCACACAAA
** *
20738597 TTTTAAGCCCAGTTTAACTAGCACACAAA
1 -TTTAAGCCCAGTTTAGTTGGCACACAAA
* * * * ** *
20738626 TTTTCA-CCAAGTTTAGCTAGCACTTAGAT
1 -TTTAAGCCCAGTTTAGTTGGCACACA-AA
* **
20738655 TTTAAGCCCAATTTAGTTGGCACACGGA
1 TTTAAGCCCAGTTTAGTTGGCACACAAA
* *
20738683 TTTAAGCCAAGTTTAGTTGGCACACAGA
1 TTTAAGCCCAGTTTAGTTGGCACACAAA
20738711 TTT
1 TTT
20738714 TAAGACCAAT
Statistics
Matches: 114, Mismatches: 28, Indels: 6
0.77 0.19 0.04
Matches are distributed among these distances:
28 72 0.63
29 42 0.37
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (28 bp):
TTTAAGCCCAGTTTAGTTGGCACACAAA
Found at i:20738605 original size:57 final size:57
Alignment explanation
Indices: 20738539--20738717 Score: 207
Period size: 57 Copynumber: 3.1 Consensus size: 57
20738529 TAGTATTTAT
* * * *
20738539 ATTTTAAGCCTAGTTTAATTGGCACACAAATTTAAGCCCAGCTTAGTTGGCACTCAA
1 ATTTTAAGCCCAGTTTAATTGGCACACAAATTTAAGCCAAGTTTAGTTGGCACTCAG
* * * * * *
20738596 ATTTTAAGCCCAGTTTAACTAGCACACAAATTTTCA-CCAAGTTTAGCTAGCACTTAG
1 ATTTTAAGCCCAGTTTAATTGGCACACAAA-TTTAAGCCAAGTTTAGTTGGCACTCAG
* * ** *
20738653 ATTTTAAGCCCAATTTAGTTGGCACACGGATTTAAGCCAAGTTTAGTTGGCACACAG
1 ATTTTAAGCCCAGTTTAATTGGCACACAAATTTAAGCCAAGTTTAGTTGGCACTCAG
20738710 ATTTTAAG
1 ATTTTAAG
20738718 ACCAATTTGG
Statistics
Matches: 99, Mismatches: 21, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
56 4 0.04
57 91 0.92
58 4 0.04
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (57 bp):
ATTTTAAGCCCAGTTTAATTGGCACACAAATTTAAGCCAAGTTTAGTTGGCACTCAG
Found at i:20738686 original size:114 final size:114
Alignment explanation
Indices: 20738521--20738790 Score: 301
Period size: 114 Copynumber: 2.4 Consensus size: 114
20738511 TTTTAAGCCT
* * * * * *
20738521 AATTTAACTAGTATTTATATTTTAAGCCTAGTTTAATTGGCACACAAATTTAAGCCCAGCTTAGT
1 AATTTAGCTAGCACTTAGATTTTAAGCCTAGTTTAGTTGGCACACAAATTTAAGCCAAGCTTAGT
* * * **
20738586 TGGCACTCAAATTTTAAGCCCAGTTTAACTAGCACACAAATTTTCA-CC
66 TGGCACACAAATTTTAAGACCAATTTAACTAGCACACAAATTTGAACCC
* * ** *
20738634 AAGTTTAGCTAGCACTTAGATTTTAAGCCCAATTTAGTTGGCACACGGATTTAAGCCAAGTTTAG
1 AA-TTTAGCTAGCACTTAGATTTTAAGCCTAGTTTAGTTGGCACACAAATTTAAGCCAAGCTTAG
* ** * *
20738699 TTGGCACACAGATTTTAAGACCAATTTGGCTAGGACGCAAATTTGAACCC
65 TTGGCACACAAATTTTAAGACCAATTTAACTAGCACACAAATTTGAACCC
* * *
20738749 AATTTAGCTTGTACTTTGA-TTTAAGCCTAGTTTAGTTGGCAC
1 AATTTAGCTAGCACTTAGATTTTAAGCCTAGTTTAGTTGGCAC
20738791 CCAACCCAAA
Statistics
Matches: 129, Mismatches: 26, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
113 23 0.18
114 102 0.79
115 4 0.03
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (114 bp):
AATTTAGCTAGCACTTAGATTTTAAGCCTAGTTTAGTTGGCACACAAATTTAAGCCAAGCTTAGT
TGGCACACAAATTTTAAGACCAATTTAACTAGCACACAAATTTGAACCC
Found at i:20741685 original size:39 final size:40
Alignment explanation
Indices: 20741641--20741754 Score: 96
Period size: 39 Copynumber: 3.0 Consensus size: 40
20741631 CCAAAATCAT
20741641 AAAACCCTAAAAACCAT-AAATCCTAAATA-CTTAAAA-CCC
1 AAAACCCTAAAAACC-TCAAATCCTAAA-ACCTTAAAATCCC
* * * *
20741680 TAAACCTTCAAAATCTCAAATCCTAAAACCTTAAAATCCC
1 AAAACCCTAAAAACCTCAAATCCTAAAACCTTAAAATCCC
* * * *
20741720 AAAA-CC-AAAATCCT-AAAACCAAAAACTTTAAAATC
1 AAAACCCTAAAAACCTCAAATCCTAAAACCTTAAAATC
20741755 TTAAAACCTT
Statistics
Matches: 60, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
37 18 0.30
38 7 0.12
39 29 0.48
40 6 0.10
ACGTcount: A:0.53, C:0.27, G:0.00, T:0.20
Consensus pattern (40 bp):
AAAACCCTAAAAACCTCAAATCCTAAAACCTTAAAATCCC
Found at i:20741731 original size:14 final size:14
Alignment explanation
Indices: 20741697--20741743 Score: 67
Period size: 14 Copynumber: 3.2 Consensus size: 14
20741687 TCAAAATCTC
20741697 AAATCCTAAAACCTTA
1 AAATCCTAAAACC--A
*
20741713 AAATCCCAAAACCA
1 AAATCCTAAAACCA
20741727 AAATCCTAAAACCA
1 AAATCCTAAAACCA
20741741 AAA
1 AAA
20741744 ACTTTAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 17 0.59
16 12 0.41
ACGTcount: A:0.57, C:0.28, G:0.00, T:0.15
Consensus pattern (14 bp):
AAATCCTAAAACCA
Found at i:20743645 original size:29 final size:28
Alignment explanation
Indices: 20743581--20743646 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 28
20743571 CCAATAAGCC
* *
20743581 CTCTATCTCAATTTCCTCTTGTTTTTAT
1 CTCTCTCTCAATTTCCTCTTGTCTTTAT
* * * *
20743609 CTTTCTCTCAATTTTGCTTTTGTCTTTCT
1 CTCTCTCTCAA-TTTCCTCTTGTCTTTAT
20743638 CTCTCTCTC
1 CTCTCTCTC
20743647 TCAATTTTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
28 9 0.30
29 21 0.70
ACGTcount: A:0.09, C:0.29, G:0.05, T:0.58
Consensus pattern (28 bp):
CTCTCTCTCAATTTCCTCTTGTCTTTAT
Found at i:20745701 original size:51 final size:51
Alignment explanation
Indices: 20745646--20745748 Score: 197
Period size: 51 Copynumber: 2.0 Consensus size: 51
20745636 TGACATGTGG
*
20745646 ATAACTAATTCGGTCTCATATTCTTATAAAACTTGTTTAATAAATTTTTTT
1 ATAACTAATTCGGTCTCATATTCTTATAAAACTTATTTAATAAATTTTTTT
20745697 ATAACTAATTCGGTCTCATATTCTTATAAAACTTATTTAATAAATTTTTTT
1 ATAACTAATTCGGTCTCATATTCTTATAAAACTTATTTAATAAATTTTTTT
20745748 A
1 A
20745749 AAAAAAATTT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 51 1.00
ACGTcount: A:0.35, C:0.12, G:0.05, T:0.49
Consensus pattern (51 bp):
ATAACTAATTCGGTCTCATATTCTTATAAAACTTATTTAATAAATTTTTTT
Found at i:20745813 original size:22 final size:22
Alignment explanation
Indices: 20745778--20745819 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
20745768 AAAAATAAAT
*
20745778 AAAAATAAAGAAATGGAAAAGG
1 AAAAATAAAGAAATGAAAAAGG
20745800 AAAAATGAAA-AAATGAAAAA
1 AAAAAT-AAAGAAATGAAAAA
20745820 ATGAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.10
Consensus pattern (22 bp):
AAAAATAAAGAAATGAAAAAGG
Found at i:20745830 original size:9 final size:8
Alignment explanation
Indices: 20745800--20745828 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
20745790 ATGGAAAAGG
20745800 AAAAATGA
1 AAAAATGA
20745808 AAAAATGA
1 AAAAATGA
20745816 AAAAATGA
1 AAAAATGA
20745824 AAAAA
1 AAAAA
20745829 ATCATAGAGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.79, C:0.00, G:0.10, T:0.10
Consensus pattern (8 bp):
AAAAATGA
Found at i:20745915 original size:21 final size:22
Alignment explanation
Indices: 20745891--20745933 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
20745881 TTAAACTGTG
20745891 TTTAA-AAT-ATATAAATATAAA
1 TTTAATAATAATA-AAATATAAA
20745912 TTTAATTAATAATAAAATATAA
1 TTTAA-TAATAATAAAATATAA
20745934 TGTTATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 5 0.26
23 11 0.58
24 3 0.16
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAATAATAATAAAATATAAA
Found at i:20747295 original size:9 final size:9
Alignment explanation
Indices: 20747281--20747310 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
20747271 GATAGTTTAT
20747281 TAATTAAAA
1 TAATTAAAA
20747290 TAATTAAAA
1 TAATTAAAA
20747299 TAAATTAAAA
1 T-AATTAAAA
20747309 TA
1 TA
20747311 TAAAAGCTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (9 bp):
TAATTAAAA
Found at i:20747306 original size:10 final size:10
Alignment explanation
Indices: 20747282--20747310 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
20747272 ATAGTTTATT
20747282 AATTAAAAT-
1 AATTAAAATA
20747291 AATTAAAATA
1 AATTAAAATA
20747301 AATTAAAATA
1 AATTAAAATA
20747311 TAAAAGCTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.47
10 10 0.53
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (10 bp):
AATTAAAATA
Found at i:20747538 original size:21 final size:19
Alignment explanation
Indices: 20747499--20747535 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
20747489 CCTAATTAGG
20747499 TCTCACTTTTTAAATATAA
1 TCTCACTTTTTAAATATAA
20747518 TCTCACTTTTTAAATATA
1 TCTCACTTTTTAAATATA
20747536 TAAAAAGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.35, C:0.16, G:0.00, T:0.49
Consensus pattern (19 bp):
TCTCACTTTTTAAATATAA
Found at i:20747955 original size:20 final size:18
Alignment explanation
Indices: 20747930--20747971 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 18
20747920 GAATTTTAAA
20747930 TTATTTAATATGTATAAAAT
1 TTATTT-ATAT-TATAAAAT
*
20747950 TTATTTATCTTATAAAAT
1 TTATTTATATTATAAAAT
20747968 TTAT
1 TTAT
20747972 CAATAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 12 0.57
19 3 0.14
20 6 0.29
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (18 bp):
TTATTTATATTATAAAAT
Found at i:20748823 original size:8 final size:8
Alignment explanation
Indices: 20748806--20748862 Score: 66
Period size: 8 Copynumber: 7.5 Consensus size: 8
20748796 AAATAAATAG
20748806 AAAAAATT
1 AAAAAATT
*
20748814 AAAAATTT
1 AAAAAATT
*
20748822 AAAAAA-G
1 AAAAAATT
*
20748829 GAAAAATT
1 AAAAAATT
20748837 --AAAATT
1 AAAAAATT
20748843 AAAAAATT
1 AAAAAATT
20748851 AAAAAATT
1 AAAAAATT
20748859 AAAA
1 AAAA
20748863 TTGAGAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
6 6 0.15
7 5 0.12
8 30 0.73
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.23
Consensus pattern (8 bp):
AAAAAATT
Found at i:20748824 original size:22 final size:22
Alignment explanation
Indices: 20748799--20748862 Score: 67
Period size: 23 Copynumber: 2.9 Consensus size: 22
20748789 CAATAAAAAA
*
20748799 TAAATAGAAAAAATTAAAAATT
1 TAAAAAGAAAAAATTAAAAATT
*
20748821 TAAAAAAGGAAAAATT-AAAATT
1 T-AAAAAGAAAAAATTAAAAATT
* *
20748843 AAAAAATTAAAAAATTAAAA
1 TAAAAA-GAAAAAATTAAAA
20748863 TTGAGAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
21 5 0.15
22 14 0.41
23 15 0.44
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (22 bp):
TAAAAAGAAAAAATTAAAAATT
Found at i:20748824 original size:29 final size:28
Alignment explanation
Indices: 20748792--20748863 Score: 74
Period size: 29 Copynumber: 2.5 Consensus size: 28
20748782 ATTTATCCAA
*
20748792 TAAAAAATAAATAGA-AAAAATTAAAAATT
1 TAAAAAATAAA-A-ATAAAAATTAAAAAAT
* *
20748821 TAAAAAAGGAAAAATTAAAATTAAAAAAT
1 TAAAAAA-TAAAAATAAAAATTAAAAAAT
*
20748850 TAAAAAATTAAAAT
1 TAAAAAATAAAAAT
20748864 TGAGAAAAAA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
28 6 0.17
29 27 0.75
30 3 0.08
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (28 bp):
TAAAAAATAAAAATAAAAATTAAAAAAT
Found at i:20748863 original size:22 final size:22
Alignment explanation
Indices: 20748804--20748873 Score: 77
Period size: 22 Copynumber: 3.0 Consensus size: 22
20748794 AAAAATAAAT
*
20748804 AGAAAAAATTAAAAATTTAAAAA
1 AGAAAAAATT-AAAATTAAAAAA
*
20748827 AGGAAAAATTAAAATTAAAAAA
1 AGAAAAAATTAAAATTAAAAAA
**
20748849 TTAAAAAATTAAAATTGAGAAAAA
1 AGAAAAAATTAAAATT-A-AAAAA
20748873 A
1 A
20748874 ATGCTTACAT
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
22 24 0.62
23 10 0.26
24 5 0.13
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.21
Consensus pattern (22 bp):
AGAAAAAATTAAAATTAAAAAA
Found at i:20750881 original size:23 final size:24
Alignment explanation
Indices: 20750855--20750909 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
20750845 ACTAAAAATT
* *
20750855 AAAAAAACGAAAAAATGAAA-GAG
1 AAAAAAACAAAAAAATAAAATGAG
*
20750878 AAAAAAATAAAAAAATAAAATTGAG
1 AAAAAAACAAAAAAATAAAA-TGAG
20750903 AAAAAAA
1 AAAAAAA
20750910 GCTTATTGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 17 0.63
25 10 0.37
ACGTcount: A:0.78, C:0.02, G:0.11, T:0.09
Consensus pattern (24 bp):
AAAAAAACAAAAAAATAAAATGAG
Found at i:20751245 original size:18 final size:20
Alignment explanation
Indices: 20751224--20751267 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
20751214 AAAAAAAAAT
*
20751224 AAAAAATGA-TAAAA-AAGA
1 AAAAAAAGATTAAAAGAAGA
20751242 AAAAAAAGATTAAAAGGAAGA
1 AAAAAAAGATTAAAA-GAAGA
20751263 AAAAA
1 AAAAA
20751268 CTTGATACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 8 0.36
19 5 0.23
21 9 0.41
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (20 bp):
AAAAAAAGATTAAAAGAAGA
Found at i:20751518 original size:23 final size:22
Alignment explanation
Indices: 20751492--20751535 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
20751482 CTTTAACAGA
* *
20751492 TAAATTTTATAAAAAATATTTAT
1 TAAATATTAAAAAAAAT-TTTAT
20751515 TAAATATTAAAAAAAATTTTA
1 TAAATATTAAAAAAAATTTTA
20751536 AAAAAGGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TAAATATTAAAAAAAATTTTAT
Found at i:20751572 original size:18 final size:17
Alignment explanation
Indices: 20751534--20751590 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
20751524 AAAAAAATTT
*
20751534 TAAAAAAGGA-AAAAAA
1 TAAAAAAGAATAAAAAA
* *
20751550 -CAAAAAGAACTAAAAAT
1 TAAAAAAGAA-TAAAAAA
*
20751567 TAAAAAAGCATAAAAAA
1 TAAAAAAGAATAAAAAA
20751584 TAAAAAA
1 TAAAAAA
20751591 TAATGGACAC
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
15 7 0.22
17 18 0.56
18 7 0.22
ACGTcount: A:0.77, C:0.05, G:0.07, T:0.11
Consensus pattern (17 bp):
TAAAAAAGAATAAAAAA
Found at i:20758885 original size:16 final size:18
Alignment explanation
Indices: 20758854--20758892 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
20758844 ACAATTTATT
20758854 TTTTTATTATATTTATCA
1 TTTTTATTATATTTATCA
*
20758872 TTTTTA-TA-ATTTATTA
1 TTTTTATTATATTTATCA
20758888 TTTTT
1 TTTTT
20758893 TAGCAAAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 12 0.60
17 2 0.10
18 6 0.30
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTTTATTATATTTATCA
Found at i:20758893 original size:17 final size:17
Alignment explanation
Indices: 20758846--20758894 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
20758836 TCATTTAAAC
*
20758846 AATTTATTTTTTTATTAT
1 AATTTATTATTTT-TTAT
*
20758864 -ATTTATCA-TTTTTAT
1 AATTTATTATTTTTTAT
20758879 AATTTATTATTTTTTA
1 AATTTATTATTTTTTA
20758895 GCAAAAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 4 0.15
16 10 0.38
17 12 0.46
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (17 bp):
AATTTATTATTTTTTAT
Found at i:20759080 original size:3 final size:3
Alignment explanation
Indices: 20759074--20759099 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
20759064 TTATTACTAG
20759074 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
20759100 TCATAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:20760239 original size:178 final size:180
Alignment explanation
Indices: 20759984--20760330 Score: 522
Period size: 178 Copynumber: 1.9 Consensus size: 180
20759974 AATAATAATA
*
20759984 ATAATAAGATAAAATTGGTGCCTACAGTTGCCTCTCTTTGCTTATTTATGAGAATTAAGAATAAA
1 ATAATAAGACAAAATTGGTGCCTACAGTTGCCTCTCTTTGCTTATTTATGAGAATTAAGAATAAA
* * *
20760049 GCAAAGACAAAAAGACACTAATTTTGTTCAGGTAAACACATACAAAA-AATGAAACATTGAACAT
66 GCAAAAACAAAAAAACACCAATTTTGTTCAGGTAAACACATA-AAAACAATGAAACATTGAACAT
* *
20760113 AAAG-TTTTTTTTTGAAAGAAACTTTGAAAGGC-TCTTTTAAACCAAAATT
130 AAAGATTTTTTTTTGAAAAAAAATTTGAAAGGCTTCTTTTAAACCAAAATT
* ** * * *
20760162 ATAATAGGACAAAATTGGTGTTTACAGTTGCCTTTCTTTGTTTATTTTTGAGAA-TAAGAAATAA
1 ATAATAAGACAAAATTGGTGCCTACAGTTGCCTCTCTTTGCTTATTTATGAGAATTAAG-AATAA
*
20760226 AGCAAAAACAAAAAAACACCAATTTTGTTTAGGTAAACACATAAAAACAATGAAACATTGAACAT
65 AGCAAAAACAAAAAAACACCAATTTTGTTCAGGTAAACACATAAAAACAATGAAACATTGAACAT
20760291 AAAGATTTTTTTTTTGAAAAAAAATTTGAAAGGCTTCTTT
130 AAAGA-TTTTTTTTTGAAAAAAAATTTGAAAGGCTTCTTT
20760331 AAATAGAGGT
Statistics
Matches: 151, Mismatches: 13, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
177 8 0.05
178 112 0.74
180 26 0.17
181 5 0.03
ACGTcount: A:0.43, C:0.12, G:0.13, T:0.32
Consensus pattern (180 bp):
ATAATAAGACAAAATTGGTGCCTACAGTTGCCTCTCTTTGCTTATTTATGAGAATTAAGAATAAA
GCAAAAACAAAAAAACACCAATTTTGTTCAGGTAAACACATAAAAACAATGAAACATTGAACATA
AAGATTTTTTTTTGAAAAAAAATTTGAAAGGCTTCTTTTAAACCAAAATT
Found at i:20760430 original size:40 final size:39
Alignment explanation
Indices: 20760377--20760637 Score: 245
Period size: 39 Copynumber: 6.6 Consensus size: 39
20760367 TTTTCATTAG
*
20760377 AGGCAACGAACTTTAAATGTTAAAAAGTTCCTCTTACTAA
1 AGGCAACGAACTTTAAAT-TTAAAAAGTTCCTCTCACTAA
* * * * * * *
20760417 ATGCAATGAACTTTAAATATTAAAAGGTTCATCTTATTAG
1 AGGCAACGAACTTTAAAT-TTAAAAAGTTCCTCTCACTAA
* * *
20760457 AGGCAACAAACTTTAAATTCAAAAAGTTCCTCTCACTAG
1 AGGCAACGAACTTTAAATTTAAAAAGTTCCTCTCACTAA
* * *
20760496 AGGCAACGAACTTTAAATTTAAAAAGCTCTTCTCACCAA
1 AGGCAACGAACTTTAAATTTAAAAAGTTCCTCTCACTAA
* * * * *
20760535 AGGCAACGAACTTTAAA-TTCAAAAGTCCCTTTTCACCAG
1 AGGCAACGAACTTTAAATTTAAAAAGTTCC-TCTCACTAA
* * * * * *
20760574 AGGCAACGAACCTTAAATTCAAAAAGCTCCTATAACCAA
1 AGGCAACGAACTTTAAATTTAAAAAGTTCCTCTCACTAA
*
20760613 AGGCAACAAACTTTAAATGTTAAAA
1 AGGCAACGAACTTTAAAT-TTAAAA
20760638 TCTGAAAGGA
Statistics
Matches: 180, Mismatches: 38, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
38 8 0.04
39 111 0.62
40 61 0.34
ACGTcount: A:0.42, C:0.20, G:0.11, T:0.27
Consensus pattern (39 bp):
AGGCAACGAACTTTAAATTTAAAAAGTTCCTCTCACTAA
Found at i:20760558 original size:78 final size:78
Alignment explanation
Indices: 20760349--20760630 Score: 278
Period size: 78 Copynumber: 3.6 Consensus size: 78
20760339 GTTATGAAAT
* * ** * * * *
20760349 TTTAAATTCAAAAGGCTCTTTTCATTAGAGGCAACGAACTTTAAATGTTAAAAAGTTCCTCTTAC
1 TTTAAATTCAAAAAGCTCTTCTCACCAAAGGCAACAAACTTTAAAT-TCAAAAAGTTCCTCTCAC
* * *
20760414 TAAATGCAATGAAC
65 TAGAGGCAACGAAC
* * * * * ** *
20760428 TTTAAATATTAAAAGGTTCATCTTATTAGAGGCAACAAACTTTAAATTCAAAAAGTTCCTCTCAC
1 TTTAAAT-TCAAAAAGCTCTTCTCACCAAAGGCAACAAACTTTAAATTCAAAAAGTTCCTCTCAC
20760493 TAGAGGCAACGAAC
65 TAGAGGCAACGAAC
* * * *
20760507 TTTAAATTTAAAAAGCTCTTCTCACCAAAGGCAACGAACTTTAAATTC-AAAAGTCCCTTTTCAC
1 TTTAAATTCAAAAAGCTCTTCTCACCAAAGGCAACAAACTTTAAATTCAAAAAGTTCC-TCTCAC
*
20760571 CAGAGGCAACGAAC
65 TAGAGGCAACGAAC
* * * *
20760585 CTTAAATTCAAAAAGCTCCTATAACCAAAGGCAACAAACTTTAAAT
1 TTTAAATTCAAAAAGCTCTTCTCACCAAAGGCAACAAACTTTAAAT
20760631 GTTAAAATCT
Statistics
Matches: 173, Mismatches: 28, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
77 8 0.05
78 91 0.53
79 41 0.24
80 33 0.19
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.28
Consensus pattern (78 bp):
TTTAAATTCAAAAAGCTCTTCTCACCAAAGGCAACAAACTTTAAATTCAAAAAGTTCCTCTCACT
AGAGGCAACGAAC
Found at i:20760800 original size:40 final size:40
Alignment explanation
Indices: 20760753--20760852 Score: 132
Period size: 39 Copynumber: 2.5 Consensus size: 40
20760743 AAAGCTATGT
*
20760753 AACTTTAAATGTTAAAAGGCT-TTTCTAACCAGAGGCAACA
1 AACTTTAAATGTTAAAAGGCTCTTT-TAACCAAAGGCAACA
* * * *
20760793 AATTTTAAAT-TCAAAATGCTCTTTTAACCAAAGGCAACG
1 AACTTTAAATGTTAAAAGGCTCTTTTAACCAAAGGCAACA
20760832 AACTTTAAATGTTAAAAGGCT
1 AACTTTAAATGTTAAAAGGCT
20760853 GAGAGGTAAT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
39 30 0.60
40 20 0.40
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.30
Consensus pattern (40 bp):
AACTTTAAATGTTAAAAGGCTCTTTTAACCAAAGGCAACA
Found at i:20773445 original size:21 final size:22
Alignment explanation
Indices: 20773410--20773459 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 22
20773400 ATATCATAAA
*
20773410 AAAATAAATATAAAAATCAATA-C
1 AAAAT-AATAT-AAAATCAAAATC
20773433 AAAATAA-ATAAAATCAAAATC
1 AAAATAATATAAAATCAAAATC
20773454 AAAATA
1 AAAATA
20773460 GAAAATAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 9 0.36
21 9 0.36
22 2 0.08
23 5 0.20
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.20
Consensus pattern (22 bp):
AAAATAATATAAAATCAAAATC
Found at i:20773469 original size:12 final size:11
Alignment explanation
Indices: 20773438--20773486 Score: 55
Period size: 10 Copynumber: 4.3 Consensus size: 11
20773428 AATACAAAAT
*
20773438 AAATAAAATCA
1 AAATAAAATGA
20773449 AAATCAAAATAGA
1 AAAT-AAAAT-GA
20773462 AAATAAAAATGA
1 AAAT-AAAATGA
20773474 AAA-AAAATGA
1 AAATAAAATGA
20773484 AAA
1 AAA
20773487 ACTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
10 10 0.29
11 4 0.12
12 10 0.29
13 10 0.29
ACGTcount: A:0.76, C:0.04, G:0.06, T:0.14
Consensus pattern (11 bp):
AAATAAAATGA
Found at i:20773470 original size:13 final size:12
Alignment explanation
Indices: 20773438--20773486 Score: 50
Period size: 11 Copynumber: 4.2 Consensus size: 12
20773428 AATACAAAAT
*
20773438 AAAT-AAAATCA
1 AAATAAAAATGA
*
20773449 AAATCAAAATAGA
1 AAATAAAAAT-GA
20773462 AAATAAAAATG-
1 AAATAAAAATGA
20773473 AAA-AAAAATGA
1 AAATAAAAATGA
20773484 AAA
1 AAA
20773487 ACTTACAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
10 7 0.21
11 10 0.30
12 6 0.18
13 10 0.30
ACGTcount: A:0.76, C:0.04, G:0.06, T:0.14
Consensus pattern (12 bp):
AAATAAAAATGA
Found at i:20774307 original size:3 final size:3
Alignment explanation
Indices: 20774299--20774330 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
20774289 TTTTCTAGAT
*
20774299 TAA TAA TAA TAA TAA TAA TAA TTA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
20774331 TAAACAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:20780608 original size:10 final size:10
Alignment explanation
Indices: 20780593--20780617 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
20780583 GTTAGAGGAA
20780593 AAATATATAT
1 AAATATATAT
20780603 AAATATATAT
1 AAATATATAT
20780613 AAATA
1 AAATA
20780618 GCAGCTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
AAATATATAT
Found at i:20786817 original size:2 final size:2
Alignment explanation
Indices: 20786810--20786837 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
20786800 AGAGTTAAAA
20786810 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
20786838 GAGGGGCTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:20787788 original size:2 final size:2
Alignment explanation
Indices: 20787781--20787821 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
20787771 CATGGTACTA
*
20787781 AT AT AT AT AT AT AT AT AT AT AT GT 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 AT AT AT A
20787822 AAAGGAAGAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20789554 original size:22 final size:22
Alignment explanation
Indices: 20789499--20789581 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 22
20789489 TTATTATATT
* *
20789499 AATAAATAATATTTTTATTATATA
1 AATAAATAATA-TTATATTA-ACA
20789523 ATTATAAATAATATTATATTAACA
1 A--ATAAATAATATTATATTAACA
*
20789547 AATAAAT-A-A-TATATTAACG
1 AATAAATAATATTATATTAACA
*
20789566 AATAACTAATATTATA
1 AATAAATAATATTATA
20789582 CTAATATTAT
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
19 15 0.30
20 2 0.04
21 2 0.04
22 10 0.20
24 4 0.08
25 7 0.14
26 10 0.20
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (22 bp):
AATAAATAATATTATATTAACA
Found at i:20792968 original size:165 final size:164
Alignment explanation
Indices: 20792675--20792991 Score: 390
Period size: 165 Copynumber: 1.9 Consensus size: 164
20792665 TTTTGATAAA
* * *
20792675 AAATGCCTTGAATAACCCCATTTAATTTTTTGTAAGAGATTATTCAAGACATTTTCTGATAAAAA
1 AAATGCCTTGAATAACCCCATTCAATTTTTTGTAAAAGATTATTAAAGACATTTTCTGATAAAAA
*
20792740 ATGTCTTGAATAATCCCTAAAAAAAAAGAGAAGATTATTGAAGGCATTTTTGATAAAAAAAACAC
66 ATGCCTTGAATAATCCCTAAAAAAAAAGAGAAGATTATTGAAGGCATTTTTGA-AAAAAAAACAC
*
20792805 CTTGAATAATCCTTTCATAAAAATTAAAGGAGATT
130 ATTGAATAATCCTTTCATAAAAATTAAAGGAGATT
* * *
20792840 AAATGCCTTGAATAATCCCATTCAATTTTTTGTAAAAGATTATTTAAAG-TATTTT-TGGTAAAA
1 AAATGCCTTGAATAACCCCATTCAATTTTTTGTAAAAGATTA-TTAAAGACATTTTCTGATAAAA
* * * * *** ***
20792903 AATGCCTTGAATAATTCCCTCCAAAAAAAAG-GATGTGGTTATTTAAGTTGTTTTTG-GCCAAAA
65 AATGCCTTGAATAA-TCCCT-AAAAAAAAAGAGA--AGATTATTGAAGGCATTTTTGAAAAAAAA
20792966 ACACATTGAATAATCCTTTCATAAAA
126 ACACATTGAATAATCCTTTCATAAAA
20792992 CTTGAAAAGG
Statistics
Matches: 129, Mismatches: 18, Indels: 10
0.82 0.11 0.06
Matches are distributed among these distances:
164 20 0.16
165 80 0.62
166 14 0.11
167 15 0.12
ACGTcount: A:0.41, C:0.13, G:0.12, T:0.34
Consensus pattern (164 bp):
AAATGCCTTGAATAACCCCATTCAATTTTTTGTAAAAGATTATTAAAGACATTTTCTGATAAAAA
ATGCCTTGAATAATCCCTAAAAAAAAAGAGAAGATTATTGAAGGCATTTTTGAAAAAAAAACACA
TTGAATAATCCTTTCATAAAAATTAAAGGAGATT
Found at i:20793364 original size:131 final size:130
Alignment explanation
Indices: 20793131--20793392 Score: 445
Period size: 131 Copynumber: 2.0 Consensus size: 130
20793121 AATGCATTTT
* * *
20793131 TGGGCAAAAATGCTTTGAATAATACCTTCACAAAAATTAGAGGAATTATTCAAGGTGTTTTTTGC
1 TGGGCAAAAATACCTTGAATAATACCTTCACAAAAATTAGAGGAATTATTCAAGGTATTTTTTGC
* * *
20793196 TAGAAAATGCCTTGAATAACCTCATTAATTATTAATTGAATGGGATTATTTAAATTACTATCATA
66 TAGAAAATACCTTGAATAACCTCATTAATTATTAATTGAATGGCATTATTTAAATTACCATCATA
20793261 TGGGCAAAAATACCTTGAATAATACCTTCACAAAAATTAGAGAGAATTATTCAA-GTCATTTTTT
1 TGGGCAAAAATACCTTGAATAATACCTTCACAAAAATTAGAG-GAATTATTCAAGGT-ATTTTTT
20793325 GCTAGAAAATACCTTGAATAACCTCATTAATTATTAATTGAATGGCATTATTTAAATTACCATCA
64 GCTAGAAAATACCTTGAATAACCTCATTAATTATTAATTGAATGGCATTATTTAAATTACCATCA
20793390 TA
129 TA
20793392 T
1 T
20793393 ATACCAAGAA
Statistics
Matches: 124, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
130 42 0.34
131 82 0.66
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (130 bp):
TGGGCAAAAATACCTTGAATAATACCTTCACAAAAATTAGAGGAATTATTCAAGGTATTTTTTGC
TAGAAAATACCTTGAATAACCTCATTAATTATTAATTGAATGGCATTATTTAAATTACCATCATA
Found at i:20793892 original size:13 final size:13
Alignment explanation
Indices: 20793874--20793899 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20793864 TTATCAGGTA
20793874 AAGTTTTCTATTC
1 AAGTTTTCTATTC
20793887 AAGTTTTCTATTC
1 AAGTTTTCTATTC
20793900 GTGCCCACTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.08, T:0.54
Consensus pattern (13 bp):
AAGTTTTCTATTC
Found at i:20795769 original size:15 final size:15
Alignment explanation
Indices: 20795751--20795785 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
20795741 TGTCATCATT
20795751 GTAAGGTCCATCTTG
1 GTAAGGTCCATCTTG
20795766 GTAAGGTCCATCTTG
1 GTAAGGTCCATCTTG
20795781 GTAAG
1 GTAAG
20795786 AACAAGGATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (15 bp):
GTAAGGTCCATCTTG
Found at i:20798566 original size:24 final size:25
Alignment explanation
Indices: 20798507--20798566 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 25
20798497 GTTTGGTTAG
*
20798507 AGTTTATTTAT-TGTTCATGAATAT
1 AGTTTATTTATATGTTCATGAACAT
* *
20798531 AATTTA-TAATATGTTCATGAACAT
1 AGTTTATTTATATGTTCATGAACAT
20798555 -GTTTATTTATAT
1 AGTTTATTTATAT
20798567 ATATTTGTGA
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
23 7 0.24
24 22 0.76
ACGTcount: A:0.33, C:0.05, G:0.10, T:0.52
Consensus pattern (25 bp):
AGTTTATTTATATGTTCATGAACAT
Found at i:20801827 original size:2 final size:2
Alignment explanation
Indices: 20801820--20801845 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
20801810 AAGAAAAACA
20801820 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
20801846 TGTATACACA
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:20802908 original size:23 final size:23
Alignment explanation
Indices: 20802867--20802911 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
20802857 AATAAATGAT
*
20802867 AAATAAAAAAAAAAGATAAAAAC
1 AAATAAAAAAAAAACATAAAAAC
**
20802890 AAATAAAAAATCAACATAAAAA
1 AAATAAAAAAAAAACATAAAAA
20802912 GTTGAATTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.80, C:0.07, G:0.02, T:0.11
Consensus pattern (23 bp):
AAATAAAAAAAAAACATAAAAAC
Found at i:20803574 original size:9 final size:10
Alignment explanation
Indices: 20803553--20803578 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
20803543 AGTGTGCATA
20803553 TTTTATAATT
1 TTTTATAATT
20803563 TTTTATAATT
1 TTTTATAATT
20803573 TTTTAT
1 TTTTAT
20803579 CTTAATTCTT
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:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (10 bp):
TTTTATAATT
Found at i:20808802 original size:29 final size:27
Alignment explanation
Indices: 20808704--20808802 Score: 66
Period size: 25 Copynumber: 3.7 Consensus size: 27
20808694 GTATTGTATT
*
20808704 ATTTATTA-TTATTATTATGTA--TTA
1 ATTTATTATTTATTATTATTTATGTTA
* *
20808728 ATATATGTATATATT-TTATTTAT-TT-
1 ATTTAT-TATTTATTATTATTTATGTTA
* * *
20808753 ATTTATTTTTTTGTTAATATTTATGTGTA
1 ATTTA-TTATTTATTATTATTTATGT-TA
20808782 ATTTATTATTTATGTATTATT
1 ATTTATTATTTAT-TATTATT
20808803 ACTAATATGT
Statistics
Matches: 55, Mismatches: 11, Indels: 13
0.70 0.14 0.16
Matches are distributed among these distances:
24 5 0.09
25 17 0.31
26 14 0.25
27 1 0.02
28 7 0.13
29 11 0.20
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (27 bp):
ATTTATTATTTATTATTATTTATGTTA
Found at i:20809354 original size:31 final size:31
Alignment explanation
Indices: 20809295--20809361 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
20809285 AATTTCCAGA
* ** *
20809295 TTCCGACGAAAATTCCGACGAAGTTTGAATT
1 TTCCGACGAAAATTCCGACCAACCTTGAAGT
* *
20809326 TTCCGATGAAAATTCCGGCCAACCTTGAAGT
1 TTCCGACGAAAATTCCGACCAACCTTGAAGT
20809357 TTCCG
1 TTCCG
20809362 GCCACCAACC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.28
Consensus pattern (31 bp):
TTCCGACGAAAATTCCGACCAACCTTGAAGT
Found at i:20812908 original size:16 final size:16
Alignment explanation
Indices: 20812887--20812918 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
20812877 AGAATCAATG
20812887 TCACAATAGGGTTTTA
1 TCACAATAGGGTTTTA
20812903 TCACAATAGGGTTTTA
1 TCACAATAGGGTTTTA
20812919 CCAAAACCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (16 bp):
TCACAATAGGGTTTTA
Found at i:20816791 original size:22 final size:22
Alignment explanation
Indices: 20816749--20816792 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
20816739 AATAAATGAT
*
20816749 AAATAAAAAAAAAGATAAAAAA
1 AAATAAAAAAAAACATAAAAAA
*
20816771 AAATAAAAAATCAACATAAAAA
1 AAATAAAAAA-AAACATAAAAA
20816793 GTTGAATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.82, C:0.05, G:0.02, T:0.11
Consensus pattern (22 bp):
AAATAAAAAAAAACATAAAAAA
Found at i:20817344 original size:16 final size:16
Alignment explanation
Indices: 20817325--20817364 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
20817315 TTTTATTATG
* *
20817325 TTTTTATTTTGATAAT
1 TTTTTAATTTCATAAT
*
20817341 TTTTTAATTTCTTAAT
1 TTTTTAATTTCATAAT
20817357 TTTTTAAT
1 TTTTTAAT
20817365 CATGATTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.25, C:0.03, G:0.03, T:0.70
Consensus pattern (16 bp):
TTTTTAATTTCATAAT
Found at i:20824955 original size:16 final size:16
Alignment explanation
Indices: 20824934--20824965 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
20824924 AGAATCAATG
20824934 TCACAATAGGGTTTTA
1 TCACAATAGGGTTTTA
20824950 TCACAATAGGGTTTTA
1 TCACAATAGGGTTTTA
20824966 CCAAAACCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.12, G:0.19, T:0.38
Consensus pattern (16 bp):
TCACAATAGGGTTTTA
Found at i:20830484 original size:36 final size:36
Alignment explanation
Indices: 20830420--20830490 Score: 90
Period size: 36 Copynumber: 2.0 Consensus size: 36
20830410 GAAGAACAAC
*
20830420 AAGAACAAGAACATGAAGATGAAAAAGATGTTGAAG
1 AAGAACAAGAACATGAAGATGAAAAAGATGATGAAG
* * *
20830456 AAGAATAAGAACATG-ATATGGAAGAAGATGATGAA
1 AAGAACAAGAACATGAAGAT-GAAAAAGATGATGAA
20830491 AAAAATGATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 3 0.10
36 27 0.90
ACGTcount: A:0.55, C:0.04, G:0.25, T:0.15
Consensus pattern (36 bp):
AAGAACAAGAACATGAAGATGAAAAAGATGATGAAG
Found at i:20832650 original size:18 final size:18
Alignment explanation
Indices: 20832601--20832701 Score: 62
Period size: 18 Copynumber: 5.2 Consensus size: 18
20832591 TTATTTAGTG
*
20832601 ATTTCTTATATATGAATATA
1 ATTT-TTAT-TATGATTATA
20832621 ATATTTTATTATGATTATA
1 AT-TTTTATTATGATTATA
* *
20832640 ATTTTTCTTAT-ACTTGTA
1 ATTTTTATTATGA-TTATA
20832658 ATTTTTTATGATTATGATTATA
1 A--TTTT-T-ATTATGATTATA
* *
20832680 ATTTCTCTTAT-ATTTATA
1 ATTTTTATTATGA-TTATA
20832698 ATTT
1 ATTT
20832702 CATAAAAAAT
Statistics
Matches: 66, Mismatches: 7, Indels: 18
0.73 0.08 0.20
Matches are distributed among these distances:
17 2 0.03
18 26 0.39
19 12 0.18
20 13 0.20
21 3 0.05
22 9 0.14
23 1 0.02
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (18 bp):
ATTTTTATTATGATTATA
Found at i:20835003 original size:42 final size:42
Alignment explanation
Indices: 20834905--20835072 Score: 162
Period size: 42 Copynumber: 4.0 Consensus size: 42
20834895 AAAAAACTTC
* * * * * *
20834905 TCTAAACAGAGGCTCAATGACTTTTG-GAAATAAATTAAGCTCC
1 TCTAAACAGAGGCACCATAACTTTTGAAAAATAAA--ATGCTCA
** *
20834948 TCTAAGTAGAGGCACCGTAACTTTTGAAAAATAAAATGCTCA
1 TCTAAACAGAGGCACCATAACTTTTGAAAAATAAAATGCTCA
* *
20834990 TCTAAACAGAGGCACCACAA-TTTTGGAAAAGTAAAATGCTCA
1 TCTAAACAGAGGCACCATAACTTTT-GAAAAATAAAATGCTCA
* *
20835032 TTTAAACAGAGGCACCATAAC-TTTGAAAAAATAAAAAGCTC
1 TCTAAACAGAGGCACCATAACTTTTG-AAAAATAAAATGCTC
20835073 CTTGACGATC
Statistics
Matches: 103, Mismatches: 18, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
41 5 0.05
42 71 0.69
43 20 0.19
44 7 0.07
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.24
Consensus pattern (42 bp):
TCTAAACAGAGGCACCATAACTTTTGAAAAATAAAATGCTCA
Found at i:20835267 original size:23 final size:22
Alignment explanation
Indices: 20835241--20835291 Score: 66
Period size: 23 Copynumber: 2.3 Consensus size: 22
20835231 GTTCAATAAG
*
20835241 GATTCAAATTTGCAAGATTTCAA
1 GATTCAAATTTGCAA-ATTGCAA
**
20835264 GATTCGCATTTGCAAATTGCAA
1 GATTCAAATTTGCAAATTGCAA
20835286 GATTCA
1 GATTCA
20835292 CATCCAACAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 11 0.46
23 13 0.54
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (22 bp):
GATTCAAATTTGCAAATTGCAA
Found at i:20835310 original size:43 final size:42
Alignment explanation
Indices: 20835257--20835350 Score: 109
Period size: 43 Copynumber: 2.2 Consensus size: 42
20835247 AATTTGCAAG
* *
20835257 ATTTCAAGATTCGCATTTGCAA-ATTGCAAGATTCACATCCAAC
1 ATTTAAAGATTCGCATTTG-AATATTG-AAGATTCACATCCAAA
* * *
20835300 ATTTAAAGATTCTCATTTGAATTTTGGAGATTCACATCCAAA
1 ATTTAAAGATTCGCATTTGAATATTGAAGATTCACATCCAAA
20835342 ATTTCAAAG
1 ATTT-AAAG
20835351 CTTCTTATTC
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
42 20 0.45
43 24 0.55
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (42 bp):
ATTTAAAGATTCGCATTTGAATATTGAAGATTCACATCCAAA
Found at i:20835495 original size:79 final size:79
Alignment explanation
Indices: 20835404--20835580 Score: 291
Period size: 79 Copynumber: 2.2 Consensus size: 79
20835394 GTTTCACACC
* * * *
20835404 TCAAAAATTCTCATTTGAGTTCAAAGATTCATATTCAACAAATTTTGGGTTTTACACCTCAAAGA
1 TCAAAGATTCTCATTTGAGTTCAAAGATTCACATTCAACAAATTTTGAGTTTCACACCTCAAAGA
20835469 TTCTCATTTGAAAT
66 TTCTCATTTGAAAT
* *
20835483 TCAAAGCTTCTCATTTGAGTTCAAAGATTCACATTCGACAAATTTTGAGTTTCACACCTCAAAGA
1 TCAAAGATTCTCATTTGAGTTCAAAGATTCACATTCAACAAATTTTGAGTTTCACACCTCAAAGA
*
20835548 TTCTCATTTGGAAT
66 TTCTCATTTGAAAT
20835562 TCAAAGATTCTCATTTGAG
1 TCAAAGATTCTCATTTGAG
20835581 AACTTAAAAA
Statistics
Matches: 90, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
79 90 1.00
ACGTcount: A:0.33, C:0.18, G:0.12, T:0.37
Consensus pattern (79 bp):
TCAAAGATTCTCATTTGAGTTCAAAGATTCACATTCAACAAATTTTGAGTTTCACACCTCAAAGA
TTCTCATTTGAAAT
Found at i:20835507 original size:20 final size:21
Alignment explanation
Indices: 20835462--20835579 Score: 79
Period size: 21 Copynumber: 5.9 Consensus size: 21
20835452 GTTTTACACC
20835462 TCAAAGATTCTCATTTGAAAT
1 TCAAAGATTCTCATTTGAAAT
* *
20835483 TCAAAGCTTCTCATTTG-AGT
1 TCAAAGATTCTCATTTGAAAT
* *
20835503 TCAAAGATTCACATTCG--A-
1 TCAAAGATTCTCATTTGAAAT
* * * **
20835521 -C-AA-ATTTTGAGTTTCACACC
1 TCAAAGATTCTCA-TTTGA-AAT
*
20835541 TCAAAGATTCTCATTTGGAAT
1 TCAAAGATTCTCATTTGAAAT
20835562 TCAAAGATTCTCATTTGA
1 TCAAAGATTCTCATTTGA
20835580 GAACTTAAAA
Statistics
Matches: 70, Mismatches: 19, Indels: 16
0.67 0.18 0.15
Matches are distributed among these distances:
15 4 0.06
16 4 0.06
17 1 0.01
20 16 0.23
21 35 0.50
22 5 0.07
23 5 0.07
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.36
Consensus pattern (21 bp):
TCAAAGATTCTCATTTGAAAT
Found at i:20836861 original size:19 final size:17
Alignment explanation
Indices: 20836835--20836979 Score: 92
Period size: 19 Copynumber: 8.5 Consensus size: 17
20836825 AATTTGAGTA
* *
20836835 TTCA-TTTTCTCTCATT
1 TTCATTTTTTTCTCTTT
20836851 TTCATTTTTTT-TCCATTCT
1 TTCATTTTTTTCT-C-TT-T
*
20836870 TTCATTTTTTT-TGTTT
1 TTCATTTTTTTCTCTTT
*
20836886 TT--TTTTTTT-TGTTT
1 TTCATTTTTTTCTCTTT
20836900 TTCA-TTTTTTCTCTTTGT
1 TTCATTTTTTTCTC-TT-T
20836918 TTCATTTTTTTCTCTTTTT
1 TTCATTTTTTTCTC--TTT
20836937 TTC-TTTTTTTCT-TTT
1 TTCATTTTTTTCTCTTT
* *
20836952 TTCTTTTTTTTTTTCTTT
1 TTC-ATTTTTTTCTCTTT
20836970 TTCATCTTTT
1 TTCAT-TTTT
20836980 CCTATCCATT
Statistics
Matches: 108, Mismatches: 6, Indels: 28
0.76 0.04 0.20
Matches are distributed among these distances:
14 14 0.13
15 12 0.11
16 9 0.08
17 19 0.18
18 25 0.23
19 26 0.24
20 3 0.03
ACGTcount: A:0.06, C:0.14, G:0.02, T:0.78
Consensus pattern (17 bp):
TTCATTTTTTTCTCTTT
Found at i:20836878 original size:1 final size:1
Alignment explanation
Indices: 20836874--20836971 Score: 61
Period size: 1 Copynumber: 98.0 Consensus size: 1
20836864 CATTCTTTCA
* * ** * * * ** * *
20836874 TTTTTTTTGTTTTTTTTTTTTTGTTTTTCATTTTTTCTCTTTGTTTCATTTTTTTCTCTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * *
20836939 CTTTTTTTCTTTTTTCTTTTTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
20836972 CATCTTTTCC
Statistics
Matches: 69, Mismatches: 28, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 69 1.00
ACGTcount: A:0.02, C:0.10, G:0.03, T:0.85
Consensus pattern (1 bp):
T
Found at i:20836979 original size:18 final size:17
Alignment explanation
Indices: 20836849--20836979 Score: 87
Period size: 18 Copynumber: 7.7 Consensus size: 17
20836839 TTTTCTCTCA
*
20836849 TTTTCATTTTTTTTCCAT
1 TTTTCATTTTTTTTTC-T
*
20836867 TCTTTCA-TTTTTTTT-G
1 T-TTTCATTTTTTTTTCT
*
20836883 TTTT--TTTTTTTTTGT
1 TTTTCATTTTTTTTTCT
20836898 TTTTCATTTTTTCTCTT-T
1 TTTTCATTTTTT-T-TTCT
* *
20836916 GTTTCATTTTTTTCTCT
1 TTTTCATTTTTTTTTCT
20836933 TTTT--TTCTTTTTTTCTT
1 TTTTCATT-TTTTTTTC-T
*
20836950 TTTTCTTTTTTTTTTTCT
1 TTTTC-ATTTTTTTTTCT
*
20836968 TTTTCATCTTTT
1 TTTTCATTTTTT
20836980 CCTATCCATT
Statistics
Matches: 91, Mismatches: 9, Indels: 27
0.72 0.07 0.21
Matches are distributed among these distances:
14 8 0.09
15 9 0.10
16 9 0.10
17 21 0.23
18 27 0.30
19 15 0.16
20 2 0.02
ACGTcount: A:0.05, C:0.13, G:0.02, T:0.80
Consensus pattern (17 bp):
TTTTCATTTTTTTTTCT
Found at i:20841024 original size:55 final size:57
Alignment explanation
Indices: 20840964--20841070 Score: 164
Period size: 55 Copynumber: 1.9 Consensus size: 57
20840954 TTTTTTTTAA
* *
20840964 TTTTTAAATTTTTCACCATTTGGGCCTATTT-AGAA-ATTCTCTCTTTTTTTGTTGG
1 TTTTTAAATTTTTCACCATTTGGGCCAATTTAAAAATATTCTCTCTTTTTTTGTTGG
* *
20841019 TTTTTAAATTTTTCACCATTTGGGTCAATTTAAAAATATTTTCTCTTTTTTT
1 TTTTTAAATTTTTCACCATTTGGGCCAATTTAAAAATATTCTCTCTTTTTTT
20841071 TTTGTCTTCG
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
55 29 0.63
56 3 0.07
57 14 0.30
ACGTcount: A:0.21, C:0.13, G:0.09, T:0.56
Consensus pattern (57 bp):
TTTTTAAATTTTTCACCATTTGGGCCAATTTAAAAATATTCTCTCTTTTTTTGTTGG
Found at i:20841912 original size:21 final size:20
Alignment explanation
Indices: 20841888--20841933 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
20841878 TTTAAAAAGT
*
20841888 TTTTTTGACTGCTTTCTCTAA
1 TTTTTTGACT-CTCTCTCTAA
*
20841909 -TTTTTGCCTCTCTCTCTAA
1 TTTTTTGACTCTCTCTCTAA
20841928 TTTTTT
1 TTTTTT
20841934 TTTATGTGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.11, C:0.22, G:0.07, T:0.61
Consensus pattern (20 bp):
TTTTTTGACTCTCTCTCTAA
Found at i:20841914 original size:20 final size:19
Alignment explanation
Indices: 20841889--20841932 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
20841879 TTAAAAAGTT
*
20841889 TTTTTGACTGCTTTCTCTAA
1 TTTTTGACT-CTCTCTCTAA
*
20841909 TTTTTGCCTCTCTCTCTAA
1 TTTTTGACTCTCTCTCTAA
20841928 TTTTT
1 TTTTT
20841933 TTTTATGTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.11, C:0.23, G:0.07, T:0.59
Consensus pattern (19 bp):
TTTTTGACTCTCTCTCTAA
Found at i:20842106 original size:8 final size:8
Alignment explanation
Indices: 20842093--20842126 Score: 54
Period size: 7 Copynumber: 4.5 Consensus size: 8
20842083 CTCAATTAAC
20842093 TATTTTTT
1 TATTTTTT
20842101 TA-TTTTT
1 TATTTTTT
20842108 TA-TTTTT
1 TATTTTTT
20842115 TATTTTTT
1 TATTTTTT
20842123 TATT
1 TATT
20842127 AACAAAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 14 0.56
8 11 0.44
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (8 bp):
TATTTTTT
Found at i:20843924 original size:18 final size:16
Alignment explanation
Indices: 20843903--20843947 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 16
20843893 AGCTGAATGG
20843903 TGTATTTTTTTTAGTATT
1 TGTATTTTTTTTA-T-TT
*
20843921 TGTATTTTTATTATTT
1 TGTATTTTTTTTATTT
*
20843937 TTTATTTTTTT
1 TGTATTTTTTT
20843948 CATGATCATG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 11 0.46
17 1 0.04
18 12 0.50
ACGTcount: A:0.16, C:0.00, G:0.07, T:0.78
Consensus pattern (16 bp):
TGTATTTTTTTTATTT
Found at i:20845277 original size:15 final size:15
Alignment explanation
Indices: 20845257--20845286 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
20845247 TCTCTTAAAT
20845257 TTTTAATCTTATTTA
1 TTTTAATCTTATTTA
*
20845272 TTTTAATCTTTTTTA
1 TTTTAATCTTATTTA
20845287 CTTGTTTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTAATCTTATTTA
Found at i:20847260 original size:3 final size:3
Alignment explanation
Indices: 20847254--20847320 Score: 120
Period size: 3 Copynumber: 23.0 Consensus size: 3
20847244 AAATAGAAGA
20847254 AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AAT AA- AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
20847300 AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT
20847321 TTATGATTAT
Statistics
Matches: 62, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
2 4 0.06
3 58 0.94
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:20847284 original size:23 final size:23
Alignment explanation
Indices: 20847254--20847318 Score: 121
Period size: 23 Copynumber: 2.8 Consensus size: 23
20847244 AAATAGAAGA
20847254 AATAATAATAATAATAATATAAT
1 AATAATAATAATAATAATATAAT
*
20847277 AATAATAATAATAATAAAATAAT
1 AATAATAATAATAATAATATAAT
20847300 AATAATAATAATAATAATA
1 AATAATAATAATAATAATA
20847319 ATTTATGATT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (23 bp):
AATAATAATAATAATAATATAAT
Found at i:20850444 original size:24 final size:25
Alignment explanation
Indices: 20850417--20850463 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
20850407 AAAAATGAGA
*
20850417 AAAAATGAAAATA-AAATAAAAATC
1 AAAAATGAAAATAGAAAGAAAAATC
20850441 AAAAATGAAAATAGAAAGAAAAA
1 AAAAATGAAAATAGAAAGAAAAA
20850464 GAAAAGTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 13 0.62
25 8 0.38
ACGTcount: A:0.77, C:0.02, G:0.09, T:0.13
Consensus pattern (25 bp):
AAAAATGAAAATAGAAAGAAAAATC
Found at i:20850462 original size:18 final size:18
Alignment explanation
Indices: 20850391--20850468 Score: 51
Period size: 18 Copynumber: 4.5 Consensus size: 18
20850381 AACAACAATT
*
20850391 AAATGATAAATAGCAA-AA
1 AAATGA-AAATAGAAAGAA
*
20850409 AAATGAGAAA-A-AATG-A
1 AAATGA-AAATAGAAAGAA
* *
20850425 AAAT-AAAATAAAAATCAA
1 AAATGAAAATAGAAA-GAA
20850443 AAATGAAAATAGAAAGAA
1 AAATGAAAATAGAAAGAA
20850461 AAA-GAAAA
1 AAATGAAAA
20850469 GTCAAAACCT
Statistics
Matches: 47, Mismatches: 7, Indels: 13
0.70 0.10 0.19
Matches are distributed among these distances:
14 3 0.06
15 2 0.04
16 8 0.17
17 6 0.13
18 19 0.40
19 9 0.19
ACGTcount: A:0.73, C:0.03, G:0.12, T:0.13
Consensus pattern (18 bp):
AAATGAAAATAGAAAGAA
Found at i:20850468 original size:24 final size:23
Alignment explanation
Indices: 20850391--20850468 Score: 68
Period size: 24 Copynumber: 3.1 Consensus size: 23
20850381 AACAACAATT
20850391 AAATGATAAATAGCAAAAAAATGAGAAA
1 AAATGA-AAATAG-AAAAAAA--AG-AA
*
20850419 AAATGAAAATA-AAATAAAAATCAA
1 AAATGAAAATAGAAA-AAAAA-GAA
20850443 AAATGAAAATAGAAAGAAAAAGAA
1 AAATGAAAATAGAAA-AAAAAGAA
20850467 AA
1 AA
20850469 GTCAAAACCT
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
24 18 0.41
25 11 0.25
26 4 0.09
27 5 0.11
28 6 0.14
ACGTcount: A:0.73, C:0.03, G:0.12, T:0.13
Consensus pattern (23 bp):
AAATGAAAATAGAAAAAAAAGAA
Found at i:20851791 original size:17 final size:17
Alignment explanation
Indices: 20851769--20851801 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
20851759 CACAAGGTTC
*
20851769 CAAAGATTTGCAAGACA
1 CAAAGATTCGCAAGACA
20851786 CAAAGATTCGCAAGAC
1 CAAAGATTCGCAAGAC
20851802 TTTCAAATTC
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:0.45, C:0.21, G:0.18, T:0.15
Consensus pattern (17 bp):
CAAAGATTCGCAAGACA
Found at i:20851916 original size:17 final size:16
Alignment explanation
Indices: 20851863--20852022 Score: 94
Period size: 17 Copynumber: 9.7 Consensus size: 16
20851853 TTTATGTTCA
20851863 CAAGAA-TTCATATTTG
1 CAAGAATTTCA-ATTTG
20851879 CAAGAA-TTCAAATTTG
1 CAAGAATTTC-AATTTG
* *
20851895 TAAGAATTTCAGACTTG
1 CAAGAATTTCA-ATTTG
*
20851912 CAAGAACTTCAATTTTG
1 CAAGAATTTCAA-TTTG
* * *
20851929 CAAGATTTTTAGATTCG
1 CAAGAATTTCA-ATTTG
* * *
20851946 TAAGAATTTTAAATTCG
1 CAAGAA-TTTCAATTTG
20851963 CAAGAA-TTCAACTTTG
1 CAAGAATTTCAA-TTTG
**
20851979 CAATTATTT-AGATTTG
1 CAAGAATTTCA-ATTTG
* *
20851995 CATGAATTTCAAATTAG
1 CAAGAATTTC-AATTTG
20852012 CAAGAATTTCA
1 CAAGAATTTCA
20852023 GTTTCATAAA
Statistics
Matches: 111, Mismatches: 22, Indels: 22
0.72 0.14 0.14
Matches are distributed among these distances:
15 4 0.04
16 40 0.36
17 61 0.55
18 6 0.05
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (16 bp):
CAAGAATTTCAATTTG
Found at i:20851948 original size:100 final size:99
Alignment explanation
Indices: 20851839--20852086 Score: 248
Period size: 100 Copynumber: 2.5 Consensus size: 99
20851829 TAAAAATGGA
* *
20851839 AGATTCGTAAGATTTTTATGTTCACAAGAATTCATATTTGCAAGAATTCAAATTTGTAAGAATTT
1 AGATTCGTAAGATTTTTATGTTCGCAAGAATTCA-ATTTGCAAGAATTCAAATTTGCAAGAATTT
* ** *
20851904 CAGACTT-GCAAGAACTTCAATTTTGCAAGATTTTT
65 CA-AATTAGCAAGAACTTCAATTTCACAAAATTTTT
* ** ** * * *
20851939 AGATTCGTAAGAATTTTAAATTCGCAAGAATTCAACTTTGCAATTATTTAGATTTGCATGAATTT
1 AGATTCGTAAGATTTTTATGTTCGCAAGAATTCAA-TTTGCAAGAATTCAAATTTGCAAGAATTT
* * *
20852004 CAAATTAGCAAGAATTTCAGTTTCATAAAATTTTT
65 CAAATTAGCAAGAACTTCAATTTCACAAAATTTTT
** * *
20852039 AGATTTATAAGAATTTTT-TGTTTGCAAGAATTCAGATTCGCAAGAATT
1 AGATTCGTAAG-ATTTTTATGTTCGCAAGAATTCA-ATTTGCAAGAATT
20852087 TTATAATTTC
Statistics
Matches: 118, Mismatches: 26, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
99 4 0.03
100 108 0.92
101 6 0.05
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.40
Consensus pattern (99 bp):
AGATTCGTAAGATTTTTATGTTCGCAAGAATTCAATTTGCAAGAATTCAAATTTGCAAGAATTTC
AAATTAGCAAGAACTTCAATTTCACAAAATTTTT
Found at i:20858640 original size:20 final size:21
Alignment explanation
Indices: 20858597--20858654 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 21
20858587 TGCAATACTT
*
20858597 ATGC-AAT-AATATAA-TATC
1 ATGCAAATAAATATAATTATG
*
20858615 ATGCAAATATAT-TAATTATG
1 ATGCAAATAAATATAATTATG
*
20858635 ATGCAATTAAATATAATTAT
1 ATGCAAATAAATATAATTAT
20858655 TTAATTATGC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
18 4 0.12
19 6 0.19
20 15 0.47
21 7 0.22
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (21 bp):
ATGCAAATAAATATAATTATG
Found at i:20858766 original size:10 final size:9
Alignment explanation
Indices: 20858746--20858785 Score: 53
Period size: 9 Copynumber: 4.2 Consensus size: 9
20858736 ATTAAATGAT
20858746 AAATAACAAA
1 AAATAA-AAA
20858756 AAATAGAAAA
1 AAATA-AAAA
20858766 AAATAAAAA
1 AAATAAAAA
*
20858775 AATTAAAAA
1 AAATAAAAA
20858784 AA
1 AA
20858786 TGAAAATAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
9 14 0.50
10 13 0.46
11 1 0.04
ACGTcount: A:0.82, C:0.03, G:0.03, T:0.12
Consensus pattern (9 bp):
AAATAAAAA
Found at i:20858773 original size:17 final size:17
Alignment explanation
Indices: 20858753--20858802 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
20858743 GATAAATAAC
20858753 AAAAAATAGAAAAAAAT
1 AAAAAATAGAAAAAAAT
*
20858770 AAAAAA-ATTAAAAAAAT
1 AAAAAATA-GAAAAAAAT
*
20858787 -GAAAATAGAAAGAAAA
1 AAAAAATAGAAA-AAAA
20858803 AGGAAAGCCA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
16 8 0.30
17 19 0.70
ACGTcount: A:0.80, C:0.00, G:0.08, T:0.12
Consensus pattern (17 bp):
AAAAAATAGAAAAAAAT
Found at i:20859224 original size:22 final size:22
Alignment explanation
Indices: 20859199--20859244 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
20859189 TTAAACCTAG
*
20859199 AAATTCA-AATAAAATTCCCAAA
1 AAATTCACAATAAAAAT-CCAAA
*
20859221 AAATTTACAATAAAAATCCAAA
1 AAATTCACAATAAAAATCCAAA
20859243 AA
1 AA
20859245 TCCCAAATCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.63, C:0.15, G:0.00, T:0.22
Consensus pattern (22 bp):
AAATTCACAATAAAAATCCAAA
Found at i:20859780 original size:22 final size:22
Alignment explanation
Indices: 20859732--20859781 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
20859722 CAATAATCCC
20859732 ACTTTTTTTTATTTCTCTTTTT
1 ACTTTTTTTTATTTCTCTTTTT
*
20859754 TCTTTTTTTTACTTT-T-TTTTT
1 ACTTTTTTTTA-TTTCTCTTTTT
20859775 GACTTTT
1 -ACTTTT
20859782 GACTAAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 5 0.21
22 16 0.67
23 3 0.12
ACGTcount: A:0.08, C:0.12, G:0.02, T:0.78
Consensus pattern (22 bp):
ACTTTTTTTTATTTCTCTTTTT
Found at i:20859814 original size:22 final size:22
Alignment explanation
Indices: 20859786--20859844 Score: 84
Period size: 22 Copynumber: 2.6 Consensus size: 22
20859776 ACTTTTGACT
20859786 AAATTAAACA-AAAAGCAAAGTC
1 AAATTAAA-ATAAAAGCAAAGTC
*
20859808 AAATTAAAATAAAATCAAAGTC
1 AAATTAAAATAAAAGCAAAGTC
20859830 AAATTAAAATTAAAA
1 AAATTAAAA-TAAAA
20859845 TTAAAAAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
21 1 0.03
22 28 0.82
23 5 0.15
ACGTcount: A:0.66, C:0.08, G:0.05, T:0.20
Consensus pattern (22 bp):
AAATTAAAATAAAAGCAAAGTC
Found at i:20862625 original size:14 final size:15
Alignment explanation
Indices: 20862595--20862628 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
20862585 GTAATTTATT
20862595 ATAAAAATATTAATTA
1 ATAAAAATA-TAATTA
20862611 ATAAAAATA-AATTA
1 ATAAAAATATAATTA
20862625 ATAA
1 ATAA
20862629 TTGATAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.50
16 9 0.50
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
ATAAAAATATAATTA
Found at i:20862670 original size:25 final size:25
Alignment explanation
Indices: 20862609--20862671 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 25
20862599 AAATATTAAT
* *
20862609 TAATAAA-AATAAATTAATAATTGA
1 TAATAAATATTAATTTAATAATTGA
*
20862633 TAATAAATATTAATTTAATAATATTA
1 TAATAAATATTAATTTAATAAT-TGA
*
20862659 TAATATAT-TTAAT
1 TAATAAATATTAAT
20862672 ATATTTACTA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
24 7 0.21
25 17 0.52
26 9 0.27
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (25 bp):
TAATAAATATTAATTTAATAATTGA
Found at i:20862686 original size:10 final size:9
Alignment explanation
Indices: 20862645--20862696 Score: 59
Period size: 10 Copynumber: 5.3 Consensus size: 9
20862635 ATAAATATTA
20862645 ATTTAATAAT
1 ATTTAAT-AT
20862655 ATTATAATAT
1 ATT-TAATAT
20862665 ATTTAATAT
1 ATTTAATAT
*
20862674 ATTTACTATT
1 ATTTAATA-T
20862684 ATTTAATAAT
1 ATTTAAT-AT
20862694 ATT
1 ATT
20862697 CAAATTTAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
9 13 0.35
10 19 0.51
11 5 0.14
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (9 bp):
ATTTAATAT
Found at i:20862710 original size:21 final size:21
Alignment explanation
Indices: 20862636--20862959 Score: 216
Period size: 21 Copynumber: 16.0 Consensus size: 21
20862626 TAATTGATAA
20862636 TAAATATTAATTTAATAATAT
1 TAAATATTAATTTAATAATAT
20862657 TATAATA-T-ATTTAAT-ATAT
1 TA-AATATTAATTTAATAATAT
* *
20862676 TTACTATT-ATTTAATAATAT
1 TAAATATTAATTTAATAATAT
20862696 TCAAAT-TTAATTTAATAATAT
1 T-AAATATTAATTTAATAATAT
* * *
20862717 TCAATATTAATGTAATAAGAT
1 TAAATATTAATTTAATAATAT
* ** *
20862738 TAAATAGTAA-TCCATATTAT
1 TAAATATTAATTTAATAATAT
*
20862758 TTAATATTAATTTAATAATAT
1 TAAATATTAATTTAATAATAT
* * * *
20862779 TAACTATT-TTTTAAGAATGT
1 TAAATATTAATTTAATAATAT
* **
20862799 TAAAT-TTTATTGGAT-A-A-
1 TAAATATTAATTTAATAATAT
*
20862816 TAAATATTACTTTAAT-A-A-
1 TAAATATTAATTTAATAATAT
20862834 TAAATATTAATTTAAT-ATAT
1 TAAATATTAATTTAATAATAT
*
20862854 TAAATTTTAATTTACA-AATAT
1 TAAATATTAATTTA-ATAATAT
* * *
20862875 TCAATATTGATTTATTAATAT
1 TAAATATTAATTTAATAATAT
* * * *
20862896 TAAATACTAATATGATAACAAT
1 TAAATATTAATTTAATAA-TAT
* *
20862918 T-AATCTAAATTTAATAATAT
1 TAAATATTAATTTAATAATAT
*
20862938 TTAATATT-ATGTTAATAATAT
1 TAAATATTAAT-TTAATAATAT
20862959 T
1 T
20862960 TCAATATTGT
Statistics
Matches: 231, Mismatches: 55, Indels: 34
0.72 0.17 0.11
Matches are distributed among these distances:
17 5 0.02
18 27 0.12
19 17 0.07
20 64 0.28
21 111 0.48
22 7 0.03
ACGTcount: A:0.46, C:0.04, G:0.03, T:0.47
Consensus pattern (21 bp):
TAAATATTAATTTAATAATAT
Found at i:20862960 original size:21 final size:20
Alignment explanation
Indices: 20862638--20862998 Score: 170
Period size: 21 Copynumber: 17.7 Consensus size: 20
20862628 ATTGATAATA
20862638 AATATTAATTTAATAATATTAT
1 AATATT-ATTTAATAATATT-T
20862660 AATA-TATTTAAT-ATATTT
1 AATATTATTTAATAATATTT
* *
20862678 ACTATTATTTAATAATATTC
1 AATATTATTTAATAATATTT
*
20862698 AA-ATTTAATTTAATAATATTC
1 AATA-TT-ATTTAATAATATTT
* * *
20862719 AATATTAATGTAATAAGATTA
1 AATATT-ATTTAATAATATTT
* * ** *
20862740 AATAGTAATCCATATTATTT
1 AATATTATTTAATAATATTT
20862760 AATATTAATTTAATAATA-TT
1 AATATT-ATTTAATAATATTT
* * * *
20862780 AACTATTTTTTAAGAATGTTA
1 AA-TATTATTTAATAATATTT
* **
20862801 AATTTTATTGGATAATA---
1 AATATTATTTAATAATATTT
20862818 AATATTACTTTAATAATA---
1 AATATTA-TTTAATAATATTT
*
20862836 AATATTAATTTAAT-ATATTA
1 AATATT-ATTTAATAATATTT
* *
20862856 AATTTTAATTTACA-AATATTC
1 AATATT-ATTTA-ATAATATTT
* *
20862877 AATATTGATTTATTAATATTA
1 AATATT-ATTTAATAATATTT
* * * * *
20862898 AATACTAATATGATAACAATT
1 AATA-TTATTTAATAATATTT
* *
20862919 AATCTAAATTTAATAATATTT
1 AATAT-TATTTAATAATATTT
20862940 AATATTATGTTAATAATATTT
1 AATATTAT-TTAATAATATTT
* *
20862961 CAATATTGTTTGAATATTATTTT
1 -AATATTATTT-AATAATA-TTT
*
20862984 AATAATATTTTAATA
1 AATATTA-TTTAATA
20862999 CGCTTTTTAT
Statistics
Matches: 260, Mismatches: 56, Indels: 46
0.72 0.15 0.13
Matches are distributed among these distances:
17 9 0.03
18 24 0.09
19 15 0.06
20 62 0.24
21 116 0.45
22 28 0.11
23 6 0.02
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (20 bp):
AATATTATTTAATAATATTT
Found at i:20863011 original size:33 final size:33
Alignment explanation
Indices: 20862940--20863029 Score: 110
Period size: 33 Copynumber: 2.7 Consensus size: 33
20862930 AATAATATTT
* * *
20862940 AATATTATGTTAATAATATTTCAATATTGTTTG
1 AATATTATTTTAATAATATTTTAATATCGTTTG
*
20862973 AATATTATTTTAATAATATTTTAATA-CGCTTTT
1 AATATTATTTTAATAATATTTTAATATCG-TTTG
* *
20863006 TATATTATTTTAATAATTTTTTAA
1 AATATTATTTTAATAATATTTTAA
20863030 AATGAAATGT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
32 1 0.02
33 49 0.98
ACGTcount: A:0.37, C:0.03, G:0.04, T:0.56
Consensus pattern (33 bp):
AATATTATTTTAATAATATTTTAATATCGTTTG
Found at i:20863016 original size:11 final size:11
Alignment explanation
Indices: 20862927--20863029 Score: 84
Period size: 11 Copynumber: 9.5 Consensus size: 11
20862917 TTAATCTAAA
*
20862927 TTTAATAATA-
1 TTTAATATTAT
20862937 TTTAATATTAT
1 TTTAATATTAT
* *
20862948 GTTAATAATAT
1 TTTAATATTAT
* *
20862959 TTCAATATTGT
1 TTTAATATTAT
*
20862970 TTGAATATTAT
1 TTTAATATTAT
*
20862981 TTTAATAATAT
1 TTTAATATTAT
***
20862992 TTTAATACGCT
1 TTTAATATTAT
*
20863003 TTTTATATTAT
1 TTTAATATTAT
20863014 TTTAATAATT-T
1 TTTAAT-ATTAT
20863025 TTTAA
1 TTTAA
20863030 AATGAAATGT
Statistics
Matches: 72, Mismatches: 19, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
10 9 0.12
11 60 0.83
12 3 0.04
ACGTcount: A:0.37, C:0.03, G:0.04, T:0.56
Consensus pattern (11 bp):
TTTAATATTAT
Found at i:20864025 original size:176 final size:175
Alignment explanation
Indices: 20863702--20864140 Score: 516
Period size: 176 Copynumber: 2.5 Consensus size: 175
20863692 TGCCTTTATG
* * ** * *
20863702 CAAGAAAAATTGATACTTTCAACTTTTCCT-TAAAGCATTTTTGAA-ATTTTATCTTTAAAAAAA
1 CAAGAGAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTGAAGATTTTATTTTTAAGAAAA
* *
20863765 ATTGATATTTTCAACTTTTCTCCAAAAATGTCTATTTTTATTGAAATTTTATTTTCAAGGAGAAT
66 ATTGATACTTTCAACTTTTCTCCAAAAA--T-TATTTTTATTGAAATTTTATTTTCAAGGAAAAT
* ** *
20863830 TGATACTTTCAAATTTTTCTCGAAGATCTATTTTTTT-AATTTTTATTTT
128 TAATACTTTCAAATTTTTCTC-AA-AAATATTTTTTTAAAATTTTATTTT
* *
20863879 CAAGAGAAATTGATACTTTCAACTTTCCCTCAAAAATATTTTTTGAAGTTTTTATTTTTAAGAAA
1 CAAGAGAAATTGATACTTTCAACTTTTCCTCAAAAATA-TTTTTGAAGATTTTATTTTTAAGAAA
* *
20863944 AATTGATACTTTCAACTTTTC-CTCAAAAA-TATTTTT-TTGAAGTTATTATTTTTAAGGAAAAT
65 AATTGATACTTTCAACTTTTCTC-CAAAAATTATTTTTATTGAAATT-TTATTTTCAAGGAAAAT
*
20864006 TAATACTTTCAATTTTTTCTCAAAAATATTTTTTTGAAAATTTTATTTT
128 TAATACTTTCAAATTTTTCTCAAAAATATTTTTTT-AAAATTTTATTTT
* *
20864055 CAAG-GAAAATTGATACTTTCAACTTTTTCTCAAAAATACCCTTTTTGAAGCTTTTATTTTTAAG
1 CAAGAG-AAATTGATACTTTCAACTTTTCCTCAAAAATA---TTTTTGAAGATTTTATTTTTAAG
* *
20864119 AAAAATTAATACTCTCAA-TTTT
62 AAAAATTGATACTTTCAACTTTT
20864141 AAACCAAATC
Statistics
Matches: 229, Mismatches: 23, Indels: 20
0.84 0.08 0.07
Matches are distributed among these distances:
174 10 0.04
175 10 0.04
176 86 0.38
177 32 0.14
178 42 0.18
179 9 0.04
180 40 0.17
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.47
Consensus pattern (175 bp):
CAAGAGAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTGAAGATTTTATTTTTAAGAAAA
ATTGATACTTTCAACTTTTCTCCAAAAATTATTTTTATTGAAATTTTATTTTCAAGGAAAATTAA
TACTTTCAAATTTTTCTCAAAAATATTTTTTTAAAATTTTATTTT
Found at i:20864087 original size:118 final size:117
Alignment explanation
Indices: 20863702--20864140 Score: 451
Period size: 118 Copynumber: 3.7 Consensus size: 117
20863692 TGCCTTTATG
* ** * * *
20863702 CAAGAAAAATTGATACTTTCAACTTTTCCT-TAAAGCA--TTTTTGAAATTTTATCTTTAAAAAA
1 CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAGTTTTATTTTTAAGAAA
* * *
20863764 AATTGATATTTTCAA-CTTTTCTCCAAAAATGTCTATTTTTATTG-AAATTTTATTTT
66 AATTAATACTTTCAATTTTTTCT-CAAAAA----TATTTTT-TTGAAAATTTTATTTT
* * * * ** * *
20863820 CAAGGAGAATTGATACTTTCAAATTTTTCTCGAAGATCTATTTTTTT-AATTTTTATTTTCAAGA
1 CAAGAAAAATTGATACTTTCAACTTTTCCTC-AA-AAATATTTTTTTGAAGTTTTATTTTTAAGA
* * * ** **
20863884 GAAATTGATACTTTCAACTTTCCCTCAAAAATA-TTTTTTGAAGTTTTTATTTT
64 AAAATTAATACTTTCAATTTTTTCTCAAAAATATTTTTTTGAAAATTTTATTTT
* *
20863937 TAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAGTTATTATTTTTAAGGA
1 CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAGTT-TTATTTTTAAGAA
20864002 AAATTAATACTTTCAATTTTTTCTCAAAAATATTTTTTTGAAAATTTTATTTT
65 AAATTAATACTTTCAATTTTTTCTCAAAAATATTTTTTTGAAAATTTTATTTT
* * **
20864055 CAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATACCCTTTTTGAAGCTTTTATTTTTAAGA
1 CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATA-TTTTTTTGAAG-TTTTATTTTTAAGA
*
20864120 AAAATTAATACTCTCAATTTT
64 AAAATTAATACTTTCAATTTT
20864141 AAACCAAATC
Statistics
Matches: 266, Mismatches: 43, Indels: 23
0.80 0.13 0.07
Matches are distributed among these distances:
115 10 0.04
116 9 0.03
117 78 0.29
118 81 0.30
119 40 0.15
120 3 0.01
121 2 0.01
122 34 0.13
123 9 0.03
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.47
Consensus pattern (117 bp):
CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAGTTTTATTTTTAAGAAA
AATTAATACTTTCAATTTTTTCTCAAAAATATTTTTTTGAAAATTTTATTTT
Found at i:20864122 original size:59 final size:59
Alignment explanation
Indices: 20863702--20864140 Score: 407
Period size: 59 Copynumber: 7.5 Consensus size: 59
20863692 TGCCTTTATG
* * * ** *
20863702 CAAGAAAAATTGATACTTTCAACTTTTCCT-TAAAGCA--TTTTTGAA-ATTTTATCTTT
1 CAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAGTTTTTAT-TTT
** * *
20863758 -AAAAAAAATTGATATTTTCAAC-TTTTCTCCAAAAATGTCTATTTTTATTGAA-ATTTTATTTT
1 CAAGGAAAATTGATACTTTCAACTTTTTCT-CAAAAA----TATTTTT-TTGAAGTTTTTATTTT
* * **
20863820 CAAGGAGAATTGATACTTTCAAATTTTTCTCGAAGATCTATTTTTTT-AA-TTTTTATTTT
1 CAAGGAAAATTGATACTTTCAACTTTTTCTC-AA-AAATATTTTTTTGAAGTTTTTATTTT
**
20863879 CAA-GAGAAATTGATACTTTCAACTTTCCCTCAAAAATA-TTTTTTGAAGTTTTTATTTT
1 CAAGGA-AAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAGTTTTTATTTT
* * * *
20863937 TAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTGAAGTTATTATTTT
1 CAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAGTTTTTATTTT
* * * **
20863996 TAAGGAAAATTAATACTTTCAATTTTTTCTCAAAAATATTTTTTTGAAAATTTTATTTT
1 CAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAGTTTTTATTTT
** *
20864055 CAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATACCCTTTTTGAAGCTTTTATTTT
1 CAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATA-TTTTTTTGAAGTTTTTATTTT
* * * *
20864115 TAAGAAAAATTAATACTCTCAA-TTTT
1 CAAGGAAAATTGATACTTTCAACTTTT
20864141 AAACCAAATC
Statistics
Matches: 322, Mismatches: 42, Indels: 35
0.81 0.11 0.09
Matches are distributed among these distances:
54 5 0.02
55 20 0.06
56 9 0.03
57 5 0.02
58 47 0.15
59 146 0.45
60 38 0.12
61 7 0.02
62 6 0.02
63 30 0.09
64 8 0.02
65 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.47
Consensus pattern (59 bp):
CAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTGAAGTTTTTATTTT
Found at i:20864711 original size:17 final size:17
Alignment explanation
Indices: 20864691--20864754 Score: 74
Period size: 17 Copynumber: 3.8 Consensus size: 17
20864681 GGATTCAAAA
20864691 ATTCACAAGAATTTCAG
1 ATTCACAAGAATTTCAG
* **
20864708 ATTCGCAAGAATTGGAG
1 ATTCACAAGAATTTCAG
** *
20864725 ATTCGTAAGATTTTCAG
1 ATTCACAAGAATTTCAG
20864742 ATTCACAAGAATT
1 ATTCACAAGAATT
20864755 GGAGTTGGAT
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.31
Consensus pattern (17 bp):
ATTCACAAGAATTTCAG
Found at i:20864745 original size:34 final size:34
Alignment explanation
Indices: 20864697--20864785 Score: 119
Period size: 34 Copynumber: 2.6 Consensus size: 34
20864687 AAAAATTCAC
* *
20864697 AAGAATTTCAGATTCGCAAGAATTGGAGATTCG-T
1 AAGATTTTCAGATTCACAAGAATTGGAG-TTCGAT
*
20864731 AAGATTTTCAGATTCACAAGAATTGGAGTTGGAT
1 AAGATTTTCAGATTCACAAGAATTGGAGTTCGAT
20864765 AAGACTTTT-AGATTCACAAGA
1 AAGA-TTTTCAGATTCACAAGA
20864786 CATTCAAATT
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
33 3 0.06
34 43 0.86
35 4 0.08
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.30
Consensus pattern (34 bp):
AAGATTTTCAGATTCACAAGAATTGGAGTTCGAT
Found at i:20864824 original size:51 final size:51
Alignment explanation
Indices: 20864737--20864836 Score: 130
Period size: 51 Copynumber: 2.0 Consensus size: 51
20864727 TCGTAAGATT
* *
20864737 TTCAGATTCACAAGAATTGGAGTTGGATAAGACTTTTAGATTCACAAGACA
1 TTCAAATTCACAAGAATTGGAGTTGGACAAGACTTTTAGATTCACAAGACA
* * * *
20864788 TTCAAATTCGCAAGAATTGGAGATTTG-CAAGCCTTTTATATTCACAAGA
1 TTCAAATTCACAAGAATTGGAG-TTGGACAAGACTTTTAGATTCACAAGA
20864837 AATAAAGATT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
51 39 0.93
52 3 0.07
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (51 bp):
TTCAAATTCACAAGAATTGGAGTTGGACAAGACTTTTAGATTCACAAGACA
Found at i:20866203 original size:14 final size:14
Alignment explanation
Indices: 20866184--20866217 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
20866174 TTTTTTAATC
20866184 TTTTTTATTTTTC-A
1 TTTTTTA-TTTTCAA
20866198 TTTTTTATTTTCAA
1 TTTTTTATTTTCAA
20866212 TTTTTT
1 TTTTTT
20866218 TTGCTTTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.26
14 14 0.74
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTTATTTTCAA
Done.