Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168270.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_5, 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: 27802247
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 124000 characters in sequence are not A, C, G, or T
File 120 of 147
Found at i:21517213 original size:3 final size:3
Alignment explanation
Indices: 21517205--21517258 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
21517195 CGAACTCAAG
21517205 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
21517253 AAT AAT
1 AAT AAT
21517259 TTGGTGTGGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:21517494 original size:86 final size:85
Alignment explanation
Indices: 21517361--21517699 Score: 333
Period size: 86 Copynumber: 4.0 Consensus size: 85
21517351 ATAAACAACA
* * * *
21517361 TGGACTAAGTTGAAAAGGATTTGGCATAAGCTAAAATTCGAAAACAAAATGACCTAGATTGAACC
1 TGGACTAAGTTGAAAAGGATTTGACGTAAGCCAAAATCCGAAAACAAAATGACCTAGATTGAACC
* *
21517426 GAAGTCTGAAATGAATAACT
66 AAAGTCTGAAATGAATAAAT
* * * *
21517446 TGAACTAAGTTGAAGAAGGATTTGACGCAAGCCGAAATCCCAAAACAAAATGACCTAGATTGAAC
1 TGGACTAAGTTGAA-AAGGATTTGACGTAAGCCAAAATCCGAAAACAAAATGACCTAGATTGAAC
* * * *
21517511 TAAAATTTGAAA-GTATACAAT
65 CAAAGTCTGAAATGAATA-AAT
*** * * * *
21517532 CTGGACTAAACCGAAATGGATTT-AGCGTAAGCCCAAATCCGAAAATAAAATGACCTGGATTGAA
1 -TGGACTAAGTTGAAAAGGATTTGA-CGTAAGCCAAAATCCGAAAACAAAATGACCTAGATTGAA
* * *
21517596 CCAAAGTCTGAGAGTAAATAATT
64 CCAAAGTCTGA-AATGAATAAAT
* * * * * *
21517619 TGGACTAAGTTGAAATGGATTTGGCGTAAGCTAAAATACGAAAACAAAATAACCTTGATTGAACC
1 TGGACTAAGTTGAAAAGGATTTGACGTAAGCCAAAATCCGAAAACAAAATGACCTAGATTGAACC
21517684 AAAGTCT-AAGATGAAT
66 AAAGTCTGAA-ATGAAT
21517700 TATCTAGTCT
Statistics
Matches: 203, Mismatches: 43, Indels: 16
0.77 0.16 0.06
Matches are distributed among these distances:
84 1 0.00
85 23 0.11
86 163 0.80
87 13 0.06
88 3 0.01
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.23
Consensus pattern (85 bp):
TGGACTAAGTTGAAAAGGATTTGACGTAAGCCAAAATCCGAAAACAAAATGACCTAGATTGAACC
AAAGTCTGAAATGAATAAAT
Found at i:21529351 original size:58 final size:56
Alignment explanation
Indices: 21529289--21529505 Score: 199
Period size: 57 Copynumber: 3.8 Consensus size: 56
21529279 AAAAATTTTT
* *
21529289 ATTTTTAA-AGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTGAAATTGTC
1 ATTTTTAAGA-AAAATTGATACTTTCAACTTTTCCT-AAAAATATTTTTTGAAATT-TA
**
21529347 ATTTTTAAGAAAAATTGATAC-TTCAACTTTT-CTTTAAATCCATTTTTTGAAATATTA
1 ATTTTTAAGAAAAATTGATACTTTCAACTTTTCCTAAAAAT--ATTTTTTGAAAT-TTA
* * * * * *
21529404 AATTTTATGAAAAATTAATGCTTTTAACTTTTCCTAAAAAAATAGTTTTTTGAAAATTTT
1 ATTTTTAAGAAAAATTGATACTTTCAACTTTTCCT--AAAAATA-TTTTTTG-AAATTTA
* * *
21529464 ACTTTCAAG-AAAATTGATACTTTCAACTTATCCTAAAAATAT
1 ATTTTTAAGAAAAATTGATACTTTCAACTTTTCCTAAAAATAT
21529506 ATATTTTTTC
Statistics
Matches: 131, Mismatches: 18, Indels: 22
0.77 0.11 0.13
Matches are distributed among these distances:
55 4 0.03
56 3 0.02
57 47 0.36
58 29 0.22
59 25 0.19
60 15 0.11
61 8 0.06
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.45
Consensus pattern (56 bp):
ATTTTTAAGAAAAATTGATACTTTCAACTTTTCCTAAAAATATTTTTTGAAATTTA
Found at i:21529408 original size:17 final size:17
Alignment explanation
Indices: 21529388--21529421 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
21529378 CTTTAAATCC
* *
21529388 ATTTTTTGAAATATTAA
1 ATTTTATGAAAAATTAA
21529405 ATTTTATGAAAAATTAA
1 ATTTTATGAAAAATTAA
21529422 TGCTTTTAAC
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:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (17 bp):
ATTTTATGAAAAATTAA
Found at i:21530470 original size:16 final size:16
Alignment explanation
Indices: 21530449--21530487 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
21530439 TCTGTTTTTA
* * *
21530449 TTTATTTTTTATTCTT
1 TTTATTTTTCATTATC
21530465 TTTATTTTTCATTATC
1 TTTATTTTTCATTATC
21530481 TTTATTT
1 TTTATTT
21530488 GAAACACATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTATTTTTCATTATC
Found at i:21532586 original size:23 final size:23
Alignment explanation
Indices: 21532558--21532649 Score: 78
Period size: 23 Copynumber: 4.0 Consensus size: 23
21532548 TAAAATTAAT
* *
21532558 AAAATATAAAAATTAGAAAAGAG
1 AAAATAAAAAAAATAGAAAAGAG
* *
21532581 AAAATAAAAAAAATAGGAAAGGG
1 AAAATAAAAAAAATAGAAAAGAG
* * *
21532604 GAAATAAAGAAGAAAGAGAAAAGAA
1 AAAATAAA-AA-AAATAGAAAAGAG
* *
21532629 AAAAAAAAAAAAACA-AAAAGA
1 AAAATAAAAAAAATAGAAAAGA
21532650 TGAGAATGAG
Statistics
Matches: 55, Mismatches: 12, Indels: 5
0.76 0.17 0.07
Matches are distributed among these distances:
22 6 0.11
23 30 0.55
24 4 0.07
25 15 0.27
ACGTcount: A:0.75, C:0.01, G:0.16, T:0.08
Consensus pattern (23 bp):
AAAATAAAAAAAATAGAAAAGAG
Found at i:21532922 original size:7 final size:7
Alignment explanation
Indices: 21532889--21532922 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
21532879 TAGATTTTTA
*
21532889 TCATTGG
1 TCATTTG
*
21532896 TCATTGG
1 TCATTTG
21532903 TCATTTG
1 TCATTTG
21532910 TCATTTG
1 TCATTTG
21532917 TCATTT
1 TCATTT
21532923 TTTATTTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.15, C:0.15, G:0.18, T:0.53
Consensus pattern (7 bp):
TCATTTG
Found at i:21533313 original size:95 final size:93
Alignment explanation
Indices: 21533161--21533331 Score: 297
Period size: 95 Copynumber: 1.8 Consensus size: 93
21533151 AAAATAAAAC
21533161 TGACAAAGAATAAATGTCGACATTACCGGAAAGCTTGGCTAGTAACCAGCTTTTGAGTACAGCCA
1 TGACAAAGAATAAATGTCGACATTACCGGAAAGCTTGGCTAGTAACCAGCTTTTGAGTACAGCCA
21533226 GGACCCTGGACCTGGCTGGAAAATGAAGG
66 GG-CCCTGGACCTGGCTGGAAAATGAAGG
* * *
21533255 TGACAAAAGAATCAATGTCGACATTGCTGGAAAGCTTGGCTAGTAACCAGCTTTTGAGTACAGCC
1 TGAC-AAAGAATAAATGTCGACATTACCGGAAAGCTTGGCTAGTAACCAGCTTTTGAGTACAGCC
21533320 AGGCCCTGGACC
65 AGGCCCTGGACC
21533332 CTCCTCCGTA
Statistics
Matches: 73, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
94 13 0.18
95 60 0.82
ACGTcount: A:0.32, C:0.22, G:0.26, T:0.21
Consensus pattern (93 bp):
TGACAAAGAATAAATGTCGACATTACCGGAAAGCTTGGCTAGTAACCAGCTTTTGAGTACAGCCA
GGCCCTGGACCTGGCTGGAAAATGAAGG
Found at i:21537022 original size:15 final size:15
Alignment explanation
Indices: 21536984--21537013 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
21536974 TAGCTTGTAA
*
21536984 AAAATTAAATTGGAT
1 AAAATTAAATTAGAT
21536999 AAAATTAAATTAGAT
1 AAAATTAAATTAGAT
21537014 TTAATTAAAA
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:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (15 bp):
AAAATTAAATTAGAT
Found at i:21538748 original size:19 final size:19
Alignment explanation
Indices: 21538712--21538748 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
21538702 AGAAAAGGAA
* *
21538712 TGAAATTTTTTTTGTGAAC
1 TGAAATTTTGTTTCTGAAC
21538731 TGAAATTTTGTTTCTGAA
1 TGAAATTTTGTTTCTGAA
21538749 TAATATTCCA
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:0.27, C:0.05, G:0.16, T:0.51
Consensus pattern (19 bp):
TGAAATTTTGTTTCTGAAC
Found at i:21540046 original size:52 final size:52
Alignment explanation
Indices: 21539968--21540165 Score: 263
Period size: 52 Copynumber: 3.8 Consensus size: 52
21539958 ATAACCATAC
*
21539968 AAACTTGCCCATTAAGAATCCCTCTCCTCTTAGAATTCTTTTCCTGTAAGTT
1 AAACTTGCCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGTAAGTT
*
21540020 AAACTTGCCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTATAAGTT
1 AAACTTGCCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGTAAGTT
* * * * * *
21540072 AAACTTGCCTATTAAGAATCCCTTTCCTTTTAGAATTCTTCTCTTGCAAGTC
1 AAACTTGCCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGTAAGTT
** * * *
21540124 AAACTTATCTATTAAGAATCCC-CTTTCTCTTGGAATTCTTCT
1 AAACTTGCCCATTAAGAATCCCTC-TCCTCTTAGAATTCTTCT
21540166 TTTGCAAGTC
Statistics
Matches: 130, Mismatches: 15, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
52 130 1.00
ACGTcount: A:0.26, C:0.26, G:0.09, T:0.39
Consensus pattern (52 bp):
AAACTTGCCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGTAAGTT
Found at i:21540509 original size:25 final size:25
Alignment explanation
Indices: 21540435--21540509 Score: 73
Period size: 25 Copynumber: 3.1 Consensus size: 25
21540425 TCTGGACTTG
* * *
21540435 CTTCCCATGTCTCAAATCATGGGCT
1 CTTCCCATGTCTCGAACCATCGGCT
* * **
21540460 -TT-CCATATCTCGAACTATCAACT
1 CTTCCCATGTCTCGAACCATCGGCT
21540483 CTTCCCATGTCTCGAACCATCGGCT
1 CTTCCCATGTCTCGAACCATCGGCT
21540508 CT
1 CT
21540510 GATACCACTT
Statistics
Matches: 37, Mismatches: 11, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
23 14 0.38
24 4 0.11
25 19 0.51
ACGTcount: A:0.21, C:0.35, G:0.12, T:0.32
Consensus pattern (25 bp):
CTTCCCATGTCTCGAACCATCGGCT
Found at i:21541132 original size:52 final size:52
Alignment explanation
Indices: 21541042--21541198 Score: 208
Period size: 52 Copynumber: 3.0 Consensus size: 52
21541032 TATAACCATA
* *
21541042 CAAACTTGCCTATTAAGAATCCCTCTCCTCTTAAAATTCTTCTCCTGTAAGT
1 CAAACTTGCCTATTAAGAATCCCTTTCCTCTTAAAATTCTTCTCCTGCAAGT
* * * *
21541094 CAAACTTGCCTATTAAGAATCCCTTTCCTTTTAGAATTCTTTTCTTGCAAGT
1 CAAACTTGCCTATTAAGAATCCCTTTCCTCTTAAAATTCTTCTCCTGCAAGT
* * **
21541146 CAAACTTACCTATTAAGAATCTCCTTT-CTCTTGAAATTCTTCTTTTGCAAGT
1 CAAACTTGCCTATTAAGAATC-CCTTTCCTCTTAAAATTCTTCTCCTGCAAGT
21541198 C
1 C
21541199 TTCTTGTCCA
Statistics
Matches: 92, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
52 87 0.95
53 5 0.05
ACGTcount: A:0.26, C:0.25, G:0.08, T:0.40
Consensus pattern (52 bp):
CAAACTTGCCTATTAAGAATCCCTTTCCTCTTAAAATTCTTCTCCTGCAAGT
Found at i:21541238 original size:11 final size:11
Alignment explanation
Indices: 21541222--21541264 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
21541212 AGCAATATCT
21541222 AACAAATCTCA
1 AACAAATCTCA
*
21541233 AACAAATCTCT
1 AACAAATCTCA
21541244 AACAAATCTCA
1 AACAAATCTCA
*
21541255 AATAAATCTC
1 AACAAATCTC
21541265 TTATGAGATT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (11 bp):
AACAAATCTCA
Found at i:21541244 original size:22 final size:22
Alignment explanation
Indices: 21541219--21541265 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
21541209 TCAAGCAATA
21541219 TCTAACAAATCTCAAACAAATC
1 TCTAACAAATCTCAAACAAATC
*
21541241 TCTAACAAATCTCAAATAAATC
1 TCTAACAAATCTCAAACAAATC
21541263 TCT
1 TCT
21541266 TATGAGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.28
Consensus pattern (22 bp):
TCTAACAAATCTCAAACAAATC
Found at i:21542299 original size:2 final size:2
Alignment explanation
Indices: 21542292--21542316 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
21542282 GATACTAATA
21542292 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 A
21542317 AAAAACAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:21547644 original size:18 final size:20
Alignment explanation
Indices: 21547610--21547646 Score: 60
Period size: 18 Copynumber: 1.9 Consensus size: 20
21547600 AATATTTTAT
21547610 TAATTAAAATAATAAAAATA
1 TAATTAAAATAATAAAAATA
21547630 TAATT-AAAT-ATAAAAAT
1 TAATTAAAATAATAAAAAT
21547647 TCGATTAGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 4 0.24
20 5 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
TAATTAAAATAATAAAAATA
Found at i:21550473 original size:32 final size:32
Alignment explanation
Indices: 21550416--21550508 Score: 107
Period size: 32 Copynumber: 2.9 Consensus size: 32
21550406 TGCGTGTGCG
*
21550416 TGTTGATTTTTTCAACAAGTGGTATCAGAGCTA
1 TGTTGATTTTCT-AACAAGTGGTATCAGAGCTA
* * * *
21550449 TGTTGATTTTCTAATAAGTGGTATCAAAGTTG
1 TGTTGATTTTCTAACAAGTGGTATCAGAGCTA
* *
21550481 TGGTGA-TCTCTAACAAGTGGTATCAGAG
1 TGTTGATTTTCTAACAAGTGGTATCAGAG
21550509 TGAAGTTCGA
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
31 19 0.37
32 21 0.41
33 11 0.22
ACGTcount: A:0.28, C:0.11, G:0.24, T:0.38
Consensus pattern (32 bp):
TGTTGATTTTCTAACAAGTGGTATCAGAGCTA
Found at i:21552399 original size:196 final size:194
Alignment explanation
Indices: 21552063--21552443 Score: 629
Period size: 196 Copynumber: 2.0 Consensus size: 194
21552053 TTTTTATTTA
*
21552063 TTAAAAAAAAATTATTCTCGAGAAAAATAAATCAAAACCTTTTTATTGAAATAATTCTTAAAATG
1 TTAAAAAAAAATTATTCTCGAGAAAAATAAATCAAAACCTTTTTATTGAAATAATTATTAAAATG
21552128 TTTCAGTACGTTGGTAACATTAAAAGAACTCTTTCTCACCTAGAGATTTCTTAAAACATCTCTAC
66 TTTCAGTACGTTGGTAACATTAAAAGAACTCTTTCTCACCTAGAGATTTCTTAAAACATCTCTAC
* * *
21552193 TTAGAATACTTTTAGAATCTCATCTTTGGAGGCTCGAATTTATTTTTCGTAAGAAAATGTCATGT
131 TCAGAATACTTTTAGAATCTCATCTTT-GAGGCTCAAATTTACTTTTCGTAAGAAAATGTCATGT
* * *
21552258 TTAAAAAAAATTTTATTCTCGAGAAAAATAAATTAAAACTTTTTTATTGAAATAATTATTAAAAT
1 TTAAAAAAAA-ATTATTCTCGAGAAAAATAAATCAAAACCTTTTTATTGAAATAATTATTAAAAT
*
21552323 G-TTCTAGTACGTTGGTAACATTAAAAGAACTCTTTCTCACCTAGAGATTTCTTAAAGCATCTCT
65 GTTTC-AGTACGTTGGTAACATTAAAAGAACTCTTTCTCACCTAGAGATTTCTTAAAACATCTCT
* * *
21552387 ACTCGGAATACTTTTAGAATCTCATCTTTGAGGTTTAAATTTACTTTTCGTAAGAAA
129 ACTCAGAATACTTTTAGAATCTCATCTTTGAGGCTCAAATTTACTTTTCGTAAGAAA
21552444 TTATATCATG
Statistics
Matches: 173, Mismatches: 11, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
195 37 0.21
196 136 0.79
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.38
Consensus pattern (194 bp):
TTAAAAAAAAATTATTCTCGAGAAAAATAAATCAAAACCTTTTTATTGAAATAATTATTAAAATG
TTTCAGTACGTTGGTAACATTAAAAGAACTCTTTCTCACCTAGAGATTTCTTAAAACATCTCTAC
TCAGAATACTTTTAGAATCTCATCTTTGAGGCTCAAATTTACTTTTCGTAAGAAAATGTCATGT
Found at i:21559531 original size:25 final size:26
Alignment explanation
Indices: 21559484--21559543 Score: 79
Period size: 25 Copynumber: 2.3 Consensus size: 26
21559474 TGTGTAAGTT
21559484 TTTTTTTATTTTTGATTTGTTTTG-C
1 TTTTTTTATTTTTGATTTGTTTTGAC
*
21559509 TTTTTTTATTTTT-TTTTGTTTTTGACC
1 TTTTTTTATTTTTGATTTG-TTTTGA-C
21559536 TTTTTTTA
1 TTTTTTTA
21559544 CTAAAAGTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 4 0.13
25 18 0.58
27 9 0.29
ACGTcount: A:0.08, C:0.05, G:0.08, T:0.78
Consensus pattern (26 bp):
TTTTTTTATTTTTGATTTGTTTTGAC
Found at i:21560270 original size:12 final size:12
Alignment explanation
Indices: 21560253--21560287 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
21560243 CTCATTCAAA
21560253 ATTTTATTAATT
1 ATTTTATTAATT
21560265 ATTTTATTAATT
1 ATTTTATTAATT
*
21560277 TTTTTAATTAA
1 ATTTT-ATTAA
21560288 AATTTTGAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 16 0.76
13 5 0.24
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
ATTTTATTAATT
Found at i:21560696 original size:206 final size:205
Alignment explanation
Indices: 21560314--21560684 Score: 441
Period size: 206 Copynumber: 1.8 Consensus size: 205
21560304 AATTTAATCA
* * * *
21560314 TATTGAAGATTTTCTATAAACATTCCAATACGCTGGTAATATTTTATAAAAAATCTTTTCACCTA
1 TATTGAAAATTTTCTATAAACACTCCAATACGCTGGTAATATTTAAAAAAAAATCTTTTCACCTA
* * * * * ** *
21560379 GAGATTTCTTAAAGCATCTCTACTCGGAATACTTTTAGAATCCCATTATTGGATTGAATTTCTTT
66 GAGATTTCGTAAAGCATCACTACTCGGAATACCTTTAGAATCCCATCATAGGATAAAATTTCTCT
* *
21560444 TATTCCTATTTTTATTACTTATTTTTAATTTATTAATCAATTTTTATTTATTATTAGAAAAGAAA
131 TATTCCTATTTTTATTACTTAGTATTAATTTATTAATCAATTTTTATTTATTATTAGAAAAGAAA
21560509 ATTTTTACTG
196 ATTTTTACTG
* * * *
21560519 TATTGAAAATTTTTTTATAAATACTCTAATACGCTGGTAGTATTTAAAAAAAAATCTTCTT-ACC
1 TATTGAAAA-TTTTCTATAAACACTCCAATACGCTGGTAATATTTAAAAAAAAATCTT-TTCACC
* * *
21560583 TAGAGATTTCGT-AGGCATCACTACTCGGAATACCTTT-GAATCTCATCGTAGGATAAAAATTT-
64 TAGAGATTTCGTAAAGCATCACTACTCGGAATACCTTTAGAATCCCATCATAGGAT-AAAATTTC
21560645 TCTT-TTCCTATATTTTTTATTACTTTAGTATT-A-TTATTAA
128 TCTTATTCC--TA-TTTTTATTAC-TTAGTATTAATTTATTAA
21560685 ATTTATTTTT
Statistics
Matches: 138, Mismatches: 21, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
203 4 0.03
204 16 0.12
205 44 0.32
206 66 0.48
207 8 0.06
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.45
Consensus pattern (205 bp):
TATTGAAAATTTTCTATAAACACTCCAATACGCTGGTAATATTTAAAAAAAAATCTTTTCACCTA
GAGATTTCGTAAAGCATCACTACTCGGAATACCTTTAGAATCCCATCATAGGATAAAATTTCTCT
TATTCCTATTTTTATTACTTAGTATTAATTTATTAATCAATTTTTATTTATTATTAGAAAAGAAA
ATTTTTACTG
Found at i:21560914 original size:13 final size:13
Alignment explanation
Indices: 21560896--21560927 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
21560886 AATAAACGTT
*
21560896 CGGTTCGGTTCGA
1 CGGTTCGGTCCGA
21560909 CGGTTCGGTCCGA
1 CGGTTCGGTCCGA
21560922 CGGTTC
1 CGGTTC
21560928 AACTCGGTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.06, C:0.28, G:0.38, T:0.28
Consensus pattern (13 bp):
CGGTTCGGTCCGA
Found at i:21561801 original size:22 final size:22
Alignment explanation
Indices: 21561757--21561802 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
21561747 GGGGGATCTA
* *
21561757 GGTGGCTGTAGGGTAGTTAGTC
1 GGTGGCTATAGGGTAGCTAGTC
* *
21561779 GGTGGCTATAGGGTGGCTGGTC
1 GGTGGCTATAGGGTAGCTAGTC
21561801 GG
1 GG
21561803 GAGGCTGGTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.11, C:0.11, G:0.50, T:0.28
Consensus pattern (22 bp):
GGTGGCTATAGGGTAGCTAGTC
Found at i:21561921 original size:11 final size:11
Alignment explanation
Indices: 21561900--21561933 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
21561890 TTTTCGTTTC
21561900 TTTTGTTTGTT
1 TTTTGTTTGTT
21561911 TATTT-TTTGTT
1 T-TTTGTTTGTT
21561922 TTTTGTTTGTT
1 TTTTGTTTGTT
21561933 T
1 T
21561934 GGTTAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
10 3 0.14
11 15 0.71
12 3 0.14
ACGTcount: A:0.03, C:0.00, G:0.15, T:0.82
Consensus pattern (11 bp):
TTTTGTTTGTT
Found at i:21571267 original size:3 final size:3
Alignment explanation
Indices: 21571259--21571313 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
21571249 GCATTTAACC
21571259 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
21571307 TTA TTA T
1 TTA TTA T
21571314 CTCCCATTCT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:21575227 original size:3 final size:3
Alignment explanation
Indices: 21575219--21575255 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
21575209 ATAACATTTA
21575219 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
21575256 CTTTGTGAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:21575291 original size:11 final size:11
Alignment explanation
Indices: 21575277--21575302 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
21575267 TGTTGTTTCA
21575277 TTTTATTTTAT
1 TTTTATTTTAT
21575288 TTTTATTTTAT
1 TTTTATTTTAT
21575299 TTTT
1 TTTT
21575303 GAATTTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (11 bp):
TTTTATTTTAT
Found at i:21575655 original size:16 final size:16
Alignment explanation
Indices: 21575634--21575698 Score: 53
Period size: 16 Copynumber: 4.1 Consensus size: 16
21575624 TAGAATTATG
*
21575634 TAAATAAATTTTAGTT
1 TAAATAAATTTTAATT
* *
21575650 TAAAT-ATTTTTATTT
1 TAAATAAATTTTAATT
*
21575665 TATAA-ATATTTTATATT
1 TA-AATAAATTTTA-ATT
*
21575682 TTAATAAATTTTAATT
1 TAAATAAATTTTAATT
21575698 T
1 T
21575699 TTTATTTTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
15 10 0.26
16 18 0.47
17 10 0.26
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (16 bp):
TAAATAAATTTTAATT
Found at i:21575666 original size:15 final size:15
Alignment explanation
Indices: 21575642--21575714 Score: 58
Period size: 17 Copynumber: 4.7 Consensus size: 15
21575632 TGTAAATAAA
*
21575642 TTTTAGTTTAAATAT
1 TTTTATTTTAAATAT
21575657 TTTTATTTTATAAATAT
1 TTTTA-TTT-TAAATAT
*
21575674 TTTATATTTTAATAAAT
1 TTT-TATTTTAA-ATAT
* **
21575691 TTTAATTTTTTAT-T
1 TTTTATTTTAAATAT
21575705 TTTTATTTTA
1 TTTTATTTTA
21575715 TAAATATAAA
Statistics
Matches: 46, Mismatches: 8, Indels: 9
0.73 0.13 0.14
Matches are distributed among these distances:
14 9 0.20
15 6 0.13
16 10 0.22
17 19 0.41
18 2 0.04
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (15 bp):
TTTTATTTTAAATAT
Found at i:21575690 original size:19 final size:17
Alignment explanation
Indices: 21575650--21575721 Score: 73
Period size: 17 Copynumber: 4.4 Consensus size: 17
21575640 AATTTTAGTT
21575650 TAAATATTTTTATTTTA
1 TAAATATTTTTATTTTA
21575667 TAAATATTTTATATTTTA
1 TAAATATTTT-TATTTTA
*
21575685 -ATAA-ATTTTAATTTT-
1 TA-AATATTTTTATTTTA
*
21575700 T-TAT-TTTTTATTTTA
1 TAAATATTTTTATTTTA
21575715 TAAATAT
1 TAAATAT
21575722 AAAACATAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 14
0.71 0.06 0.23
Matches are distributed among these distances:
14 10 0.23
15 1 0.02
16 7 0.16
17 17 0.39
18 9 0.20
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TAAATATTTTTATTTTA
Found at i:21575745 original size:13 final size:13
Alignment explanation
Indices: 21575729--21575753 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
21575719 TATAAAACAT
21575729 AAAAAATTAAAAG
1 AAAAAATTAAAAG
21575742 AAAAAATTAAAA
1 AAAAAATTAAAA
21575754 ATAAAAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (13 bp):
AAAAAATTAAAAG
Found at i:21576507 original size:20 final size:19
Alignment explanation
Indices: 21576484--21576528 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
21576474 TTTTTAGTTT
* *
21576484 TTTTTTAATTTTTTGTTGGG
1 TTTTTT-ATTCTTTGATGGG
*
21576504 TTTTTTCTTCTTTGATGGG
1 TTTTTTATTCTTTGATGGG
21576523 TTTTTT
1 TTTTTT
21576529 TTTTTTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 16 0.73
20 6 0.27
ACGTcount: A:0.07, C:0.04, G:0.18, T:0.71
Consensus pattern (19 bp):
TTTTTTATTCTTTGATGGG
Found at i:21576952 original size:11 final size:11
Alignment explanation
Indices: 21576919--21576968 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
21576909 TTGAGTGTAC
21576919 TATTTATCTTCTA
1 TATTTAT-TT-TA
* *
21576932 CATTTGTTTTA
1 TATTTATTTTA
21576943 TATTTATTTTA
1 TATTTATTTTA
*
21576954 TATTTATTTTT
1 TATTTATTTTA
21576965 TATT
1 TATT
21576969 AAGTGTATGA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
11 25 0.78
12 2 0.06
13 5 0.16
ACGTcount: A:0.22, C:0.06, G:0.02, T:0.70
Consensus pattern (11 bp):
TATTTATTTTA
Found at i:21579882 original size:26 final size:26
Alignment explanation
Indices: 21579853--21579908 Score: 94
Period size: 26 Copynumber: 2.2 Consensus size: 26
21579843 TCCACAAAGC
21579853 TAATAGATAATTAAATATTCCATTTT
1 TAATAGATAATTAAATATTCCATTTT
* *
21579879 TAATGGATAATTAAATATTTCATTTT
1 TAATAGATAATTAAATATTCCATTTT
21579905 TAAT
1 TAAT
21579909 TGTCACATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.48
Consensus pattern (26 bp):
TAATAGATAATTAAATATTCCATTTT
Found at i:21604025 original size:1 final size:1
Alignment explanation
Indices: 21604019--21604046 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
21604009 ATTGAAACAT
21604019 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
21604047 TTTGTGAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:21605775 original size:22 final size:21
Alignment explanation
Indices: 21605746--21605788 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
21605736 TCAAATAAGC
*
21605746 TATTT-AAATTTAATCTAATTT
1 TATTTAAAAATTAAT-TAATTT
21605767 TATTCTAAAAATTAATTAATTT
1 TATT-TAAAAATTAATTAATTT
21605789 AACCTGAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 4 0.21
22 7 0.37
23 8 0.42
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (21 bp):
TATTTAAAAATTAATTAATTT
Found at i:21616801 original size:25 final size:25
Alignment explanation
Indices: 21616750--21616801 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
21616740 TTCCGAATTG
* *
21616750 AATCATTTTAAATTGGAAAATTCAA
1 AATCATTTTAAATTGCAAAATTAAA
*
21616775 AATCATTTTAAATT-CAAATCTTAAA
1 AATCATTTTAAATTGCAAA-ATTAAA
21616800 AA
1 AA
21616802 CTAAATCATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
24 3 0.13
25 20 0.87
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (25 bp):
AATCATTTTAAATTGCAAAATTAAA
Found at i:21618946 original size:12 final size:13
Alignment explanation
Indices: 21618928--21618957 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
21618918 GAAAACGAAG
21618928 CACAATTGAACAT
1 CACAATTGAACAT
21618941 -ACAATTGAACAT
1 CACAATTGAACAT
21618953 CACAA
1 CACAA
21618958 ACCTGTAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.50, C:0.23, G:0.07, T:0.20
Consensus pattern (13 bp):
CACAATTGAACAT
Found at i:21621386 original size:27 final size:27
Alignment explanation
Indices: 21621348--21621401 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
21621338 TAACTAAACT
21621348 CTAAATCTTAGTTATGATTGAGCCACA
1 CTAAATCTTAGTTATGATTGAGCCACA
21621375 CTAAATCTTAGTTATGATTGAGCCACA
1 CTAAATCTTAGTTATGATTGAGCCACA
21621402 TACCTATTAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (27 bp):
CTAAATCTTAGTTATGATTGAGCCACA
Found at i:21627135 original size:33 final size:35
Alignment explanation
Indices: 21627074--21627142 Score: 88
Period size: 35 Copynumber: 2.0 Consensus size: 35
21627064 AAATATACTT
* *
21627074 AAAAATTGAAGATAATATAATGATTATTTATAAAA
1 AAAAATTAAAGATAATATAATGAATATTTATAAAA
* *
21627109 AAAAATTAAAGATATTA-AAT-AATATTTTTAAAA
1 AAAAATTAAAGATAATATAATGAATATTTATAAAA
21627142 A
1 A
21627143 TTATAATAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 12 0.40
34 3 0.10
35 15 0.50
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (35 bp):
AAAAATTAAAGATAATATAATGAATATTTATAAAA
Found at i:21627323 original size:13 final size:13
Alignment explanation
Indices: 21627301--21627334 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
21627291 TAGATAATTT
21627301 AATAATTTTTA-A
1 AATAATTTTTATA
21627313 AATATATTTTTATA
1 AATA-ATTTTTATA
21627327 AATAATTT
1 AATAATTT
21627335 AAAATTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 4 0.20
13 11 0.55
14 5 0.25
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
AATAATTTTTATA
Found at i:21627607 original size:6 final size:6
Alignment explanation
Indices: 21627596--21627661 Score: 71
Period size: 6 Copynumber: 11.0 Consensus size: 6
21627586 GTGCTTTTAC
* *
21627596 AAATAT AAATAT AAATAT AAATAT AAATAT AAATA- AATAAAT AACTAT
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT AA-ATAT AAATAT
* * *
21627644 ATATAT ATATAT ATATAT
1 AAATAT AAATAT AAATAT
21627662 TACATACATA
Statistics
Matches: 53, Mismatches: 5, Indels: 4
0.85 0.08 0.06
Matches are distributed among these distances:
5 2 0.04
6 49 0.92
7 2 0.04
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (6 bp):
AAATAT
Found at i:21628208 original size:18 final size:18
Alignment explanation
Indices: 21628185--21628220 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
21628175 TTAAATCTAT
21628185 TAATAT-TAAATATTAAAA
1 TAATATGTAAA-ATTAAAA
21628203 TAATATGTAAAATTAAAA
1 TAATATGTAAAATTAAAA
21628221 AAGTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (18 bp):
TAATATGTAAAATTAAAA
Found at i:21630283 original size:32 final size:32
Alignment explanation
Indices: 21630247--21630310 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
21630237 CTTTGTTTGA
*
21630247 TTTTCATGTTTTGATGTATTTGTGATGATTGG
1 TTTTCATGTTTTGATATATTTGTGATGATTGG
21630279 TTTTCATGTTTTGATATATTTGTGATGATTGG
1 TTTTCATGTTTTGATATATTTGTGATGATTGG
21630311 GATCTTGTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.17, C:0.03, G:0.23, T:0.56
Consensus pattern (32 bp):
TTTTCATGTTTTGATATATTTGTGATGATTGG
Found at i:21631083 original size:27 final size:27
Alignment explanation
Indices: 21631053--21631104 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
21631043 TCAGGTTTCA
*
21631053 TTCAACCTTTGACTTATTCAATTCTCT
1 TTCAACCTATGACTTATTCAATTCTCT
* *
21631080 TTCAACCTATGCCTTTTTCAATTCT
1 TTCAACCTATGACTTATTCAATTCT
21631105 AAAGTCTTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.21, C:0.27, G:0.04, T:0.48
Consensus pattern (27 bp):
TTCAACCTATGACTTATTCAATTCTCT
Found at i:21633429 original size:20 final size:20
Alignment explanation
Indices: 21633361--21633429 Score: 67
Period size: 17 Copynumber: 3.7 Consensus size: 20
21633351 TGCAAGAATG
** *
21633361 TCATGCAAATATATTCATTA
1 TCATGCAAATATATAAAATA
*
21633381 TCATGC-AATA-ATAACA-A
1 TCATGCAAATATATAAAATA
21633398 TCATG-AAA-ATATAAAATA
1 TCATGCAAATATATAAAATA
21633416 TCATGCAAATATAT
1 TCATGCAAATATAT
21633430 TAATAATTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
16 1 0.03
17 13 0.33
18 8 0.21
19 7 0.18
20 10 0.26
ACGTcount: A:0.49, C:0.13, G:0.06, T:0.32
Consensus pattern (20 bp):
TCATGCAAATATATAAAATA
Found at i:21633525 original size:19 final size:19
Alignment explanation
Indices: 21633472--21633531 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
21633462 TTATGCACGT
*
21633472 AATAAATATAAAAACATGC
1 AATAAATATAAAATCATGC
*
21633491 AATAACATAT---ATCATGT
1 AATAA-ATATAAAATCATGC
21633508 AATAAATATAAAATCATGC
1 AATAAATATAAAATCATGC
21633527 AATAA
1 AATAA
21633532 TAAATAAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
16 4 0.12
17 10 0.29
19 16 0.47
20 4 0.12
ACGTcount: A:0.58, C:0.10, G:0.05, T:0.27
Consensus pattern (19 bp):
AATAAATATAAAATCATGC
Found at i:21633639 original size:20 final size:20
Alignment explanation
Indices: 21633625--21633694 Score: 61
Period size: 22 Copynumber: 3.4 Consensus size: 20
21633615 ACATGTAATG
21633625 AAATATATAATCATGAAAATA
1 AAATATATAATCATG-AAATA
* * * *
21633646 ACAATCTAAAAT-ATGCAATT
1 A-AATATATAATCATGAAATA
21633666 AAATATATAATCATGCAAATA
1 AAATATATAATCATG-AAATA
21633687 ATAATATA
1 A-AATATA
21633695 AATTGTGCAA
Statistics
Matches: 37, Mismatches: 8, Indels: 7
0.71 0.15 0.13
Matches are distributed among these distances:
19 8 0.22
20 7 0.19
21 8 0.22
22 14 0.38
ACGTcount: A:0.57, C:0.09, G:0.04, T:0.30
Consensus pattern (20 bp):
AAATATATAATCATGAAATA
Found at i:21633670 original size:41 final size:41
Alignment explanation
Indices: 21633625--21633710 Score: 118
Period size: 41 Copynumber: 2.1 Consensus size: 41
21633615 ACATGTAATG
* *
21633625 AAATATATAATCATGAAAATAACAATCTAAAATATGCAATT
1 AAATATATAATCATGAAAATAACAATATAAAATATGCAAAT
* * * *
21633666 AAATATATAATCATGCAAATAATAATATAAATTGTGCAAAT
1 AAATATATAATCATGAAAATAACAATATAAAATATGCAAAT
21633707 AAAT
1 AAAT
21633711 GCAATTAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.56, C:0.08, G:0.06, T:0.30
Consensus pattern (41 bp):
AAATATATAATCATGAAAATAACAATATAAAATATGCAAAT
Found at i:21633695 original size:20 final size:19
Alignment explanation
Indices: 21633629--21633709 Score: 56
Period size: 21 Copynumber: 4.0 Consensus size: 19
21633619 GTAATGAAAT
*
21633629 ATATAATCATGAAAATAACA
1 ATATAATCATGCAAATAA-A
* *
21633649 ATCTAAAAT-ATGCAATTAAA
1 A--TATAATCATGCAAATAAA
21633669 TATATAATCATGCAAATAATA
1 -ATATAATCATGCAAATAA-A
**
21633690 ATATAAATTGTGCAAATAAA
1 ATAT-AATCATGCAAATAAA
21633710 TGCAATTAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
19 5 0.10
20 16 0.33
21 22 0.46
22 5 0.10
ACGTcount: A:0.56, C:0.09, G:0.06, T:0.30
Consensus pattern (19 bp):
ATATAATCATGCAAATAAA
Found at i:21633785 original size:20 final size:20
Alignment explanation
Indices: 21633751--21633812 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
21633741 TCATATAAAT
* *
21633751 AAATAAA-TGATAATCATAC
1 AAATAAATTAATAATCATGC
*
21633770 AAATAAATTAATAATCATGT
1 AAATAAATTAATAATCATGC
* *
21633790 AGATAAATTTATAATCATGC
1 AAATAAATTAATAATCATGC
21633810 AAA
1 AAA
21633813 CATATAAATA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
19 7 0.20
20 28 0.80
ACGTcount: A:0.55, C:0.08, G:0.06, T:0.31
Consensus pattern (20 bp):
AAATAAATTAATAATCATGC
Found at i:21634753 original size:43 final size:43
Alignment explanation
Indices: 21634701--21634890 Score: 195
Period size: 43 Copynumber: 4.4 Consensus size: 43
21634691 CTTACATTTG
* * *
21634701 GGCTATTGAAACTTTTGAAAAATAAATTTTTCCCCCAAAATTGA
1 GGCT-TTGAAACTTTTGAAAAATAAATTGTTCCCCCACAATTAA
* * *
21634745 GGCTTTGAAACTTTGGAAAACTAAAATGTTCCCCCACAATTAA
1 GGCTTTGAAACTTTTGAAAAATAAATTGTTCCCCCACAATTAA
* * ** *
21634788 GGCTTTGAAACTTTTGGAAAATAAATTGTTCCTCTGCAATCAA
1 GGCTTTGAAACTTTTGAAAAATAAATTGTTCCCCCACAATTAA
* * * * *
21634831 GGCTTTGAAACTTTGGAATAATAAAATG--CCCCCTACAACTGA
1 GGCTTTGAAACTTTTGAAAAATAAATTGTTCCCCC-ACAATTAA
*
21634873 GGCATTGAAACTTTTGAA
1 GGCTTTGAAACTTTTGAA
21634891 TGCTCCCCCA
Statistics
Matches: 119, Mismatches: 26, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
41 3 0.03
42 20 0.17
43 92 0.77
44 4 0.03
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (43 bp):
GGCTTTGAAACTTTTGAAAAATAAATTGTTCCCCCACAATTAA
Found at i:21634856 original size:86 final size:85
Alignment explanation
Indices: 21634701--21634890 Score: 231
Period size: 86 Copynumber: 2.2 Consensus size: 85
21634691 CTTACATTTG
* **
21634701 GGCTATTGAAACTTTTGAAAAATAAATTTTTCCCCCAAAATTGAGGCTTTGAAACTTTGGAAAAC
1 GGCT-TTGAAACTTTTGAAAAATAAATTGTTCCCCCAAAATCAAGGCTTTGAAACTTTGGAAAAC
*
21634766 TAAAATGTTCCCCC-ACAATTAA
65 TAAAATG--CCCCCTACAACTAA
* * ***
21634788 GGCTTTGAAACTTTTGGAAAATAAATTGTTCCTCTGCAATCAAGGCTTTGAAACTTTGGAATAA-
1 GGCTTTGAAACTTTTGAAAAATAAATTGTTCCCCCAAAATCAAGGCTTTGAAACTTTGGAA-AAC
*
21634852 TAAAATGCCCCCTACAACTGA
65 TAAAATGCCCCCTACAACTAA
*
21634873 GGCATTGAAACTTTTGAA
1 GGCTTTGAAACTTTTGAA
21634891 TGCTCCCCCA
Statistics
Matches: 89, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
84 5 0.06
85 22 0.25
86 56 0.63
87 6 0.07
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (85 bp):
GGCTTTGAAACTTTTGAAAAATAAATTGTTCCCCCAAAATCAAGGCTTTGAAACTTTGGAAAACT
AAAATGCCCCCTACAACTAA
Found at i:21634991 original size:35 final size:35
Alignment explanation
Indices: 21634925--21634991 Score: 93
Period size: 35 Copynumber: 1.9 Consensus size: 35
21634915 GAACTTTCGA
*
21634925 AAAATAAAATGCTCTCCCACAACTGAAGCTTTTAG
1 AAAATAAAATGCTCTCCCACAACTCAAGCTTTTAG
21634960 AAAATAAAATGCTC-CCCTACAAC-CAATGCTTT
1 AAAATAAAATGCTCTCCC-ACAACTCAA-GCTTT
21634992 GAAACTTTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
34 5 0.17
35 24 0.83
ACGTcount: A:0.40, C:0.25, G:0.09, T:0.25
Consensus pattern (35 bp):
AAAATAAAATGCTCTCCCACAACTCAAGCTTTTAG
Found at i:21636317 original size:22 final size:23
Alignment explanation
Indices: 21636292--21636336 Score: 65
Period size: 24 Copynumber: 2.0 Consensus size: 23
21636282 TTTATTTTAA
21636292 TTTTTTT-AGCAAAATATTTCTC
1 TTTTTTTAAGCAAAATATTTCTC
*
21636314 TTTTTTTAAAGTAAAATATTTCT
1 TTTTTTT-AAGCAAAATATTTCT
21636337 TCACAACATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 7 0.35
24 13 0.65
ACGTcount: A:0.31, C:0.09, G:0.04, T:0.56
Consensus pattern (23 bp):
TTTTTTTAAGCAAAATATTTCTC
Found at i:21638786 original size:37 final size:37
Alignment explanation
Indices: 21638730--21638805 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
21638720 GAGGAGAGAG
*
21638730 ATTCCAAATAGCTCGTACTTTATCTGGATCCACCTTT
1 ATTCCAAATAGCTCATACTTTATCTGGATCCACCTTT
*
21638767 ATTCCAAATAGCTTATACTTTATCTGGATCCACCTTT
1 ATTCCAAATAGCTCATACTTTATCTGGATCCACCTTT
21638804 AT
1 AT
21638806 CCCCATTTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.26, C:0.25, G:0.09, T:0.39
Consensus pattern (37 bp):
ATTCCAAATAGCTCATACTTTATCTGGATCCACCTTT
Found at i:21644189 original size:21 final size:24
Alignment explanation
Indices: 21644163--21644213 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
21644153 GTTTATGATT
21644163 ATATTTG-TGATTATA-TG-ATGC
1 ATATTTGATGATTATATTGCATGC
*
21644184 ATATTTGAATGGTTATATTGCATGC
1 ATATTTG-ATGATTATATTGCATGC
21644209 ATATT
1 ATATT
21644214 AATTAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
21 7 0.28
23 7 0.28
24 2 0.08
25 9 0.36
ACGTcount: A:0.29, C:0.06, G:0.18, T:0.47
Consensus pattern (24 bp):
ATATTTGATGATTATATTGCATGC
Found at i:21645046 original size:247 final size:247
Alignment explanation
Indices: 21644610--21645103 Score: 916
Period size: 247 Copynumber: 2.0 Consensus size: 247
21644600 ATTTCTTGCA
* *
21644610 AATTATTTCATATTTACTTGATTTCTTGCAAAATCTTTTTAAAAAATTCTTCAAATCACCCAAAA
1 AATTATTTCATATTTACTTGATTTCTTGCAAAATCCTTTTAAAAAATTCTTCAAACCACCCAAAA
* *
21644675 TCCTTCACCTACACTTTTCCCTTTAGAAATTTGATCTCTTTCTATGCCTTCATTGAAACTAAAAC
66 TCCTTCACCCACACTTTTCCCTTTAGAAATTTGATCTCTTTCTATGCCTCCATTGAAACTAAAAC
21644740 ATTCACTCAATTTCATACATCTCTCAAACATATATTACTATTTGTCACCTATATTCACAAATTCT
131 ATTCACTCAATTTCATACATCTCTCAAACATATATTACTATTTGTCACCTATATTCACAAATTCT
21644805 TTCATCAATTTAACTTAAGCCTACTTATTTTCACTATTCCATTTTTTCCATG
196 TTCATCAATTTAACTTAAGCCTACTTATTTTCACTATTCCATTTTTTCCATG
*
21644857 AATTATTTCATATTTACTTGATTTCTTGCAAAATCCTTTTCAAAAATTCTTCAAACCACCCAAAA
1 AATTATTTCATATTTACTTGATTTCTTGCAAAATCCTTTTAAAAAATTCTTCAAACCACCCAAAA
* **
21644922 TCCTTTACCCATGCTTTTCCCTTTAGAAATTTGATCTCTTTCTATGCCTCCATTGAAACTAAAAC
66 TCCTTCACCCACACTTTTCCCTTTAGAAATTTGATCTCTTTCTATGCCTCCATTGAAACTAAAAC
21644987 ATTCACTCAATTTCATACATCTCTCAAACATATATTACTATTTGTCACCTATATTCACAAATTCT
131 ATTCACTCAATTTCATACATCTCTCAAACATATATTACTATTTGTCACCTATATTCACAAATTCT
21645052 TTCATCAATTTAACTTAAGCCTACTTATTTTCACTATTCCATTTTTTCCATG
196 TTCATCAATTTAACTTAAGCCTACTTATTTTCACTATTCCATTTTTTCCATG
21645104 GCACCTAAAA
Statistics
Matches: 239, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
247 239 1.00
ACGTcount: A:0.31, C:0.24, G:0.04, T:0.42
Consensus pattern (247 bp):
AATTATTTCATATTTACTTGATTTCTTGCAAAATCCTTTTAAAAAATTCTTCAAACCACCCAAAA
TCCTTCACCCACACTTTTCCCTTTAGAAATTTGATCTCTTTCTATGCCTCCATTGAAACTAAAAC
ATTCACTCAATTTCATACATCTCTCAAACATATATTACTATTTGTCACCTATATTCACAAATTCT
TTCATCAATTTAACTTAAGCCTACTTATTTTCACTATTCCATTTTTTCCATG
Found at i:21647050 original size:24 final size:24
Alignment explanation
Indices: 21647001--21647050 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
21646991 AAATCAGATC
* **
21647001 AAATTTGTTTGAATTAGTTATTTT
1 AAATTTGTTTGAATTAATTAAATT
21647025 AAATTT-TATTGAATTAATTAAATT
1 AAATTTGT-TTGAATTAATTAAATT
21647049 AA
1 AA
21647051 TTGAAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 1 0.05
24 21 0.95
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (24 bp):
AAATTTGTTTGAATTAATTAAATT
Found at i:21648944 original size:36 final size:36
Alignment explanation
Indices: 21648901--21648971 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
21648891 TAGTTACTTG
21648901 TTTATTTAATTT-TTTTTCTTTCTTGCATGCATTTTA
1 TTTATTT-ATTTGTTTTTCTTTCTTGCATGCATTTTA
*
21648937 TTTATTTATTTGTTTTTTTTTCTTGCATGCATTTT
1 TTTATTTATTTGTTTTTCTTTCTTGCATGCATTTT
21648972 TTAAGATATA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
35 4 0.12
36 29 0.88
ACGTcount: A:0.14, C:0.10, G:0.07, T:0.69
Consensus pattern (36 bp):
TTTATTTATTTGTTTTTCTTTCTTGCATGCATTTTA
Found at i:21651935 original size:30 final size:29
Alignment explanation
Indices: 21651901--21651971 Score: 74
Period size: 30 Copynumber: 2.4 Consensus size: 29
21651891 ATACATGCAT
21651901 TGCATCCCATTCATATCAATAA-ATAGTACA
1 TGCATCCCATTCA-A-CAATAAGATAGTACA
*
21651931 TGCATCCTA-TCAACAATAATGGATAGTACA
1 TGCATCCCATTCAACAATAA--GATAGTACA
*
21651961 TGTATCCCATT
1 TGCATCCCATT
21651972 TTAGGCACAT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
27 6 0.18
28 1 0.03
29 3 0.09
30 23 0.68
31 1 0.03
ACGTcount: A:0.37, C:0.23, G:0.10, T:0.31
Consensus pattern (29 bp):
TGCATCCCATTCAACAATAAGATAGTACA
Found at i:21653664 original size:16 final size:16
Alignment explanation
Indices: 21653645--21653700 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
21653635 AGGTACTTTG
21653645 AAAAAAGTAAAAAAAA
1 AAAAAAGTAAAAAAAA
*
21653661 AAAAAAG-ACAAAAAAC
1 AAAAAAGTA-AAAAAAA
21653677 AAAAAA-TGAAAAATGAAA
1 AAAAAAGT-AAAAA--AAA
21653695 AAAAAA
1 AAAAAA
21653701 ATTTTAGTCC
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
15 1 0.03
16 23 0.70
17 1 0.03
18 8 0.24
ACGTcount: A:0.84, C:0.04, G:0.07, T:0.05
Consensus pattern (16 bp):
AAAAAAGTAAAAAAAA
Found at i:21654579 original size:17 final size:16
Alignment explanation
Indices: 21654537--21654581 Score: 54
Period size: 17 Copynumber: 2.7 Consensus size: 16
21654527 GGGTATGTTA
*
21654537 AAAAAATAAAATTAAT
1 AAAAAATAAAAATAAT
*
21654553 AATAACATAAAAATAAT
1 AA-AAAATAAAAATAAT
21654570 AAAATAATAAAA
1 AAAA-AATAAAA
21654582 GAAGAGAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
16 4 0.17
17 20 0.83
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (16 bp):
AAAAAATAAAAATAAT
Found at i:21655452 original size:19 final size:19
Alignment explanation
Indices: 21655428--21655472 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
21655418 ATGGTGTGTT
21655428 AAAAAAACAAAAAAAAGAA
1 AAAAAAACAAAAAAAAGAA
** *
21655447 AAAAAATTAAAAAATAGAA
1 AAAAAAACAAAAAAAAGAA
*
21655466 ATAAAAA
1 AAAAAAA
21655473 TGGCTCTAAG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.84, C:0.02, G:0.04, T:0.09
Consensus pattern (19 bp):
AAAAAAACAAAAAAAAGAA
Found at i:21656045 original size:47 final size:47
Alignment explanation
Indices: 21655988--21656080 Score: 125
Period size: 47 Copynumber: 2.0 Consensus size: 47
21655978 AAAGAAATTT
* *
21655988 ACAATGGCATCACTTGCATGTACAT-TATGAGAAAGACAATTGCATTC
1 ACAATGGCATCACTTACATGTACATCT-TGAAAAAGACAATTGCATTC
* * *
21656035 ACAATTGCATCACTTACATGTGCATCTTGAAAAAGACATTTGCATT
1 ACAATGGCATCACTTACATGTACATCTTGAAAAAGACAATTGCATT
21656081 GGTATCACTT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
47 39 0.98
48 1 0.03
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.30
Consensus pattern (47 bp):
ACAATGGCATCACTTACATGTACATCTTGAAAAAGACAATTGCATTC
Found at i:21656144 original size:44 final size:43
Alignment explanation
Indices: 21656042--21656160 Score: 136
Period size: 44 Copynumber: 2.8 Consensus size: 43
21656032 TTCACAATTG
*
21656042 CATCACTTACATGTGCATCTTGAAAAAGACA-TTTGCATTGGT
1 CATCACTTACATGTGCATCATGAAAAAGACATTTTGCATTGGT
* * *
21656084 -ATCACTTGCATATGCATTACATGAAAAAGACATTTTGCATT-TT
1 CATCACTTACATGTGCA-T-CATGAAAAAGACATTTTGCATTGGT
* * *
21656127 CATCACTCACATGTGCATCATGAGAAAGATATTT
1 CATCACTTACATGTGCATCATGAAAAAGACATTT
21656161 CCATGCACAT
Statistics
Matches: 64, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
41 14 0.22
42 15 0.23
43 14 0.22
44 21 0.33
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (43 bp):
CATCACTTACATGTGCATCATGAAAAAGACATTTTGCATTGGT
Found at i:21656503 original size:110 final size:113
Alignment explanation
Indices: 21656280--21656528 Score: 290
Period size: 119 Copynumber: 2.2 Consensus size: 113
21656270 GAAAACAGGC
* * * * * *
21656280 ACATTTGCATCACTTGCATCTACATACAAAAAAGATATTCGCATTTGCATCAGTTGCCTTTGCAC
1 ACATTTGCATCA-TGGCATCTACATACAAAAAAGACATTCACATTTGCATCACTTGCATTTGAAC
21656345 TTATATCTACATCTTAACCAAGGCATTTGCATTTACACCATAAGAAAAAAGTTT
65 TTATATCTACATCTTAACCAAGG----TGCATTTA-ACCATAAGAAAAAAGTTT
* ** *
21656399 GCATTTGCATCATGGCATCTATTTCACAAGAAAGACATTCACATTTGCATCACTTGCATTTGAAC
1 ACATTTGCATCATGGCATCTACAT-ACAAAAAAGACATTCACATTTGCATCACTTGCATTTGAAC
* * *
21656464 TTGTATCTATATCTTAACCAA-G-GCA-TT-ACCATAAGAAAAAATTTT
65 TTATATCTACATCTTAACCAAGGTGCATTTAACCATAAGAAAAAAGTTT
21656509 ACATTTGCATCATGGCATCT
1 ACATTTGCATCATGGCATCT
21656529 GCATTCTAAG
Statistics
Matches: 115, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
110 36 0.31
112 2 0.02
113 3 0.03
118 10 0.09
119 64 0.56
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.33
Consensus pattern (113 bp):
ACATTTGCATCATGGCATCTACATACAAAAAAGACATTCACATTTGCATCACTTGCATTTGAACT
TATATCTACATCTTAACCAAGGTGCATTTAACCATAAGAAAAAAGTTT
Found at i:21656740 original size:19 final size:18
Alignment explanation
Indices: 21656698--21656743 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 18
21656688 TGTAAATATT
21656698 AAAAA-AAA-AAGAGAGA
1 AAAAAGAAAGAAGAGAGA
*
21656714 AAAGAGAAAGAAGAGATGA
1 AAAAAGAAAGAAGAGA-GA
21656733 AAAAAGAAAGA
1 AAAAAGAAAGA
21656744 TTTGGAATGG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 4 0.16
17 3 0.12
18 6 0.24
19 12 0.48
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.02
Consensus pattern (18 bp):
AAAAAGAAAGAAGAGAGA
Found at i:21657402 original size:74 final size:74
Alignment explanation
Indices: 21657322--21657460 Score: 201
Period size: 74 Copynumber: 1.9 Consensus size: 74
21657312 CTAATATCTC
* *
21657322 TGGGCAATACATTTTAAATTTTTAGAGTTTCAACGCCTTTGATACAGG-G-AGCATTCAAAGATT
1 TGGGCAAAACATTTTAAATTTTTAAAGTTTCAACGCCTTTGAT--AGGAGAAGCATTCAAAGATT
21657385 TTTAAAACCTT
64 TTTAAAACCTT
* * *
21657396 TGGGCAAAATATTTTAAATTTTTAAAGTTTCAATGCCTTTGATTGGAGAAGCATTCAAAGATTTT
1 TGGGCAAAACATTTTAAATTTTTAAAGTTTCAACGCCTTTGATAGGAGAAGCATTCAAAGATTTT
21657461 GACATTTGTA
Statistics
Matches: 58, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
72 2 0.03
73 1 0.02
74 55 0.95
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (74 bp):
TGGGCAAAACATTTTAAATTTTTAAAGTTTCAACGCCTTTGATAGGAGAAGCATTCAAAGATTTT
TAAAACCTT
Found at i:21657640 original size:104 final size:103
Alignment explanation
Indices: 21657497--21657725 Score: 305
Period size: 104 Copynumber: 2.2 Consensus size: 103
21657487 CTCTAAAACT
* * * * *
21657497 TTCAGGCACAATTTTCAAGACCCTGAACAAAACAATTTAAATTTTTAAAGTTTTAATGCCTTTGA
1 TTCAAGCATAATTTTCAAGACCATGAACAAAACAATTTAAAATTTTAAAGTTTCAATGCCTTTGA
* * * *
21657562 TTTGAGGAGCATTCATAGATTTTGAGATTTGTAAGACT
66 TTGGAGAAGCATTCAAAGATTTTGAGATTTGTAAGACC
* * *
21657600 TTCAAGCATTATTTTCAAGACCATCGAACAAAACATTTTAAAATTTTAAAGTTTCAATGCTTTTG
1 TTCAAGCATAATTTTCAAGACCAT-GAACAAAACAATTTAAAATTTTAAAGTTTCAATGCCTTTG
*
21657665 ATTGGAGAAGCATTCAAAGATTTTGAGATTTTTAAGACC
65 ATTGGAGAAGCATTCAAAGATTTTGAGATTTGTAAGACC
** *
21657704 TTCGGGCATAATTTTTAAGACC
1 TTCAAGCATAATTTTCAAGACC
21657726 TCTAGGCATA
Statistics
Matches: 108, Mismatches: 17, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
103 20 0.19
104 88 0.81
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (103 bp):
TTCAAGCATAATTTTCAAGACCATGAACAAAACAATTTAAAATTTTAAAGTTTCAATGCCTTTGA
TTGGAGAAGCATTCAAAGATTTTGAGATTTGTAAGACC
Found at i:21657720 original size:22 final size:22
Alignment explanation
Indices: 21657692--21657751 Score: 86
Period size: 22 Copynumber: 2.7 Consensus size: 22
21657682 AGATTTTGAG
21657692 ATTTTTAAGACCTTCGGGCATA
1 ATTTTTAAGACCTTCGGGCATA
*
21657714 ATTTTTAAGACC-TCTAGGCATA
1 ATTTTTAAGACCTTC-GGGCATA
*
21657736 ATTTTCAAGACCTTCG
1 ATTTTTAAGACCTTCG
21657752 AGTAAAACAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
21 2 0.06
22 29 0.88
23 2 0.06
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (22 bp):
ATTTTTAAGACCTTCGGGCATA
Found at i:21657840 original size:126 final size:125
Alignment explanation
Indices: 21657605--21657999 Score: 431
Period size: 126 Copynumber: 3.1 Consensus size: 125
21657595 AGACTTTCAA
* * ** *
21657605 GCATTATTTTCAAGACCATCGAACAAAACATTTTAAAATTTTAAAGTTTCAATGCTTTTGATTGG
1 GCATAATTTTCAAGACCTTCGAGTAAAACATTTTAAATTTTTAAAGTTTCAATGCTTTTGATTGG
* * *
21657670 AGAAGCATTCAAAGATTTTGAGATTTTTAAGACCT-TCGGGCATAATTTTTAAGACCTCTAG
66 AG-AGCATTCAAAGATTTTGAGATTTATAAGACCTCT-AGGCATAATTTTTAAGACCTATAG
* * * *
21657731 GCATAATTTTCAAGACCTTCGAGTAAAACATTTTCAATTTTTATAGTTTCAATGATTTTAATTGG
1 GCATAATTTTCAAGACCTTCGAGTAAAACATTTTAAATTTTTAAAGTTTCAATGCTTTTGATTGG
* * * * *
21657796 ATGAGCATTCAAAGATTTTAACATTTATAACG-CCTCTAGACATAATCTTTAAGACCTATAT
66 A-GAGCATTCAAAGATTTTGAGATTTATAA-GACCTCTAGGCATAATTTTTAAGACCTATAG
* * * * *
21657857 GCAT-ACTTTCAAGAGCTTC-AGGTAAAACATTTTAAATTTTTAAAGTTTCAATGCCTCTGATTT
1 GCATAATTTTCAAGACCTTCGA-GTAAAACATTTTAAATTTTTAAAGTTTCAATGCTTTTGATTG
* * * * * *
21657920 GAGGAACATTAAAAAATTTTGAGATTTGTAAGACCTCTAGGCATAATTTTTAAGA-CTTTTG
65 GA-GAGCATTCAAAGATTTTGAGATTTATAAGACCTCTAGGCATAATTTTTAAGACCTATAG
*
21657981 AGCATAATTTTTAAGACCT
1 -GCATAATTTTCAAGACCT
21658000 CTGGGCAAAA
Statistics
Matches: 221, Mismatches: 41, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
124 5 0.02
125 96 0.43
126 117 0.53
127 3 0.01
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Consensus pattern (125 bp):
GCATAATTTTCAAGACCTTCGAGTAAAACATTTTAAATTTTTAAAGTTTCAATGCTTTTGATTGG
AGAGCATTCAAAGATTTTGAGATTTATAAGACCTCTAGGCATAATTTTTAAGACCTATAG
Found at i:21657973 original size:22 final size:22
Alignment explanation
Indices: 21657943--21658006 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
21657933 AAATTTTGAG
*
21657943 ATTTGTAAGACCTCTAGGCATA
1 ATTTTTAAGACCTCTAGGCATA
* *
21657965 ATTTTTAAGA-CTTTTGAGCATA
1 ATTTTTAAGACCTCTAG-GCATA
*
21657987 ATTTTTAAGACCTCTGGGCA
1 ATTTTTAAGACCTCTAGGCA
21658007 AAAGGATTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 4 0.11
22 27 0.77
23 4 0.11
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.38
Consensus pattern (22 bp):
ATTTTTAAGACCTCTAGGCATA
Found at i:21662874 original size:19 final size:21
Alignment explanation
Indices: 21662830--21662877 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
21662820 GTAGTTTTTG
21662830 TTTTTTTTTTTTTACAGAAAGC
1 TTTTTTTTTTTTTACAGAAA-C
21662852 TTTTTTTTTATTTTA-A-AAA-
1 TTTTTTTTT-TTTTACAGAAAC
21662871 TTTTTTT
1 TTTTTTT
21662878 GACAATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
19 7 0.28
21 3 0.12
22 10 0.40
23 5 0.20
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.69
Consensus pattern (21 bp):
TTTTTTTTTTTTTACAGAAAC
Found at i:21663027 original size:21 final size:22
Alignment explanation
Indices: 21662976--21663018 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
21662966 ACTTTCTGAA
* *
21662976 ATTCAAATATCAGATTTTTAAT
1 ATTCAAATCTTAGATTTTTAAT
21662998 ATTCAAATCTTAGATTTTTAA
1 ATTCAAATCTTAGATTTTTAA
21663019 GTTGAAATCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.47
Consensus pattern (22 bp):
ATTCAAATCTTAGATTTTTAAT
Found at i:21663417 original size:2 final size:2
Alignment explanation
Indices: 21663410--21663438 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
21663400 CAAATCATGC
21663410 TA 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 TA T
21663439 GCAACCACCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21664884 original size:6 final size:6
Alignment explanation
Indices: 21664873--21664898 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
21664863 TGTCATTACT
21664873 CAACCA CAACCA CAACCA CAACCA CA
1 CAACCA CAACCA CAACCA CAACCA CA
21664899 GCCAACTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (6 bp):
CAACCA
Found at i:21665794 original size:25 final size:25
Alignment explanation
Indices: 21665760--21665814 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 25
21665750 TAATAGCTTG
*
21665760 GTTTGCTTCAATGTTGCACGAAGAT
1 GTTTGCTTCAATGCTGCACGAAGAT
*
21665785 GTTTGCTTCAATGCTGCATGAAGAT
1 GTTTGCTTCAATGCTGCACGAAGAT
21665810 GTTTG
1 GTTTG
21665815 TATATAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.22, C:0.15, G:0.25, T:0.38
Consensus pattern (25 bp):
GTTTGCTTCAATGCTGCACGAAGAT
Found at i:21666237 original size:21 final size:22
Alignment explanation
Indices: 21666213--21666263 Score: 54
Period size: 21 Copynumber: 2.4 Consensus size: 22
21666203 ATATTGATAT
21666213 ATAAGATTATGA-TA-GAATAAA
1 ATAAGATTAT-ATTATGAATAAA
*
21666234 ATAA-ATGATATTATGAATAAA
1 ATAAGATTATATTATGAATAAA
*
21666255 ATTAGATTA
1 ATAAGATTA
21666264 AATAATGTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 5
0.75 0.09 0.16
Matches are distributed among these distances:
19 1 0.04
20 6 0.25
21 14 0.58
22 3 0.12
ACGTcount: A:0.55, C:0.00, G:0.12, T:0.33
Consensus pattern (22 bp):
ATAAGATTATATTATGAATAAA
Found at i:21668719 original size:20 final size:20
Alignment explanation
Indices: 21668682--21668719 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
21668672 AAATAATTGT
*
21668682 TTAAAATTAAATATTATTAC
1 TTAAAATTAAATACTATTAC
21668702 TTAAAATTTAAA-ACTATT
1 TTAAAA-TTAAATACTATT
21668720 TTATTTCAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (20 bp):
TTAAAATTAAATACTATTAC
Found at i:21670209 original size:3 final size:3
Alignment explanation
Indices: 21670201--21670243 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
21670191 CTTTTAATTT
21670201 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
21670244 AATAATAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:21670248 original size:3 final size:3
Alignment explanation
Indices: 21670242--21670276 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
21670232 CATCATCATC
21670242 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
21670277 CTTTTGGACG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:21673311 original size:31 final size:32
Alignment explanation
Indices: 21673276--21673348 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 32
21673266 CTTCATAACG
* * *
21673276 AATTCACCTTG-CACAAATTCACTTCAATATA
1 AATTCACCTTGTAACAAATTCACATCAACATA
* *
21673307 AATTC-CTTTGTAATAAATTCACATCAACATA
1 AATTCACCTTGTAACAAATTCACATCAACATA
*
21673338 AATTTACCTTG
1 AATTCACCTTG
21673349 ACATGATTTC
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
30 4 0.12
31 25 0.76
32 4 0.12
ACGTcount: A:0.38, C:0.22, G:0.04, T:0.36
Consensus pattern (32 bp):
AATTCACCTTGTAACAAATTCACATCAACATA
Found at i:21674512 original size:17 final size:17
Alignment explanation
Indices: 21674490--21674524 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
21674480 ACCTAGATAG
21674490 TATCCCTTGCCAAGATC
1 TATCCCTTGCCAAGATC
21674507 TATCCCTTGCCAAGATC
1 TATCCCTTGCCAAGATC
21674524 T
1 T
21674525 TCAAAGAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.34, G:0.11, T:0.31
Consensus pattern (17 bp):
TATCCCTTGCCAAGATC
Found at i:21688487 original size:2 final size:2
Alignment explanation
Indices: 21688480--21688527 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
21688470 CTAGTATTTA
21688480 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
21688522 CT CT CT
1 CT CT CT
21688528 GCAACAATAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:21692558 original size:23 final size:24
Alignment explanation
Indices: 21692516--21692560 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
21692506 TGGTTTGAGG
21692516 GAGAAAATAAAGAAGCAAAAGAAA
1 GAGAAAATAAAGAAGCAAAAGAAA
21692540 GAGAAAA-AAAGAAAG-AAAAGA
1 GAGAAAATAAAG-AAGCAAAAGA
21692561 GAAAAATTGC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.73, C:0.02, G:0.22, T:0.02
Consensus pattern (24 bp):
GAGAAAATAAAGAAGCAAAAGAAA
Found at i:21710033 original size:2 final size:2
Alignment explanation
Indices: 21710026--21710059 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
21710016 TTGTGACAGT
21710026 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
21710060 CAGTTAATAT
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:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:21710759 original size:15 final size:15
Alignment explanation
Indices: 21710739--21710768 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
21710729 TCGATTGGGT
21710739 GGTTCAGAGTAGAGA
1 GGTTCAGAGTAGAGA
21710754 GGTTCAGAGTAGAGA
1 GGTTCAGAGTAGAGA
21710769 AACATACTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.07, G:0.40, T:0.20
Consensus pattern (15 bp):
GGTTCAGAGTAGAGA
Found at i:21710979 original size:29 final size:29
Alignment explanation
Indices: 21710901--21710973 Score: 101
Period size: 29 Copynumber: 2.4 Consensus size: 29
21710891 TGTTTTTGTT
*
21710901 TTTTAATTATAATAAAATATTTAATGTTATA
1 TTTTAATTAT-A-AAAATATTTAATGTGATA
* *
21710932 TTTAAATTTTAAAAATATTTAATGTGATA
1 TTTTAATTATAAAAATATTTAATGTGATA
21710961 TTTTAATTATAAA
1 TTTTAATTATAAA
21710974 TTTATTAATT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 28 0.76
30 1 0.03
31 8 0.22
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (29 bp):
TTTTAATTATAAAAATATTTAATGTGATA
Found at i:21711116 original size:26 final size:26
Alignment explanation
Indices: 21711067--21711116 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
21711057 ATATTAATAA
* *
21711067 ATAAATTTATATTTTAGATGTTATTT
1 ATAAAATTATATTTTAGATCTTATTT
* *
21711093 ATAAAATTATTTTTTATATCTTAT
1 ATAAAATTATATTTTAGATCTTAT
21711117 AAAATAACAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.36, C:0.02, G:0.04, T:0.58
Consensus pattern (26 bp):
ATAAAATTATATTTTAGATCTTATTT
Found at i:21723366 original size:16 final size:15
Alignment explanation
Indices: 21723346--21723385 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
21723336 TTATTAAAGT
21723346 ATATTAAAATTATTTA
1 ATATTAAAATTA-TTA
*
21723362 GTATTAAAATTATTA
1 ATATTAAAATTATTA
21723377 ATATTAAAA
1 ATATTAAAA
21723386 AATAATTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 11 0.50
16 11 0.50
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (15 bp):
ATATTAAAATTATTA
Found at i:21723382 original size:25 final size:25
Alignment explanation
Indices: 21723312--21723382 Score: 90
Period size: 26 Copynumber: 2.8 Consensus size: 25
21723302 TTAATATAAC
*
21723312 TATTAAAA-TATTAAAAATTATTTAT
1 TATTAAAATTATT-AAAATTATTTAG
*
21723337 TATTAAAGTATATTAAAATTATTTAG
1 TATTAAAAT-TATTAAAATTATTTAG
*
21723363 TATTAAAATTATTAATATTA
1 TATTAAAATTATTAAAATTA
21723383 AAAAATAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
25 17 0.43
26 19 0.47
27 4 0.10
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (25 bp):
TATTAAAATTATTAAAATTATTTAG
Found at i:21723383 original size:15 final size:16
Alignment explanation
Indices: 21723346--21723432 Score: 70
Period size: 16 Copynumber: 5.2 Consensus size: 16
21723336 TTATTAAAGT
21723346 ATATTAAAATTATTTA
1 ATATTAAAATTATTTA
*
21723362 GTATTAAAATTA-TTA
1 ATATTAAAATTATTTA
* *
21723377 ATATTAAAAAATAATTA
1 ATATT-AAAATTATTTA
*
21723394 TATTTTAATAATATTATTTA
1 -ATATT-A-AA-ATTATTTA
21723414 ATATTAAAA-TATTATA
1 ATATTAAAATTATT-TA
21723430 ATA
1 ATA
21723433 ATATAAAAAT
Statistics
Matches: 58, Mismatches: 7, Indels: 12
0.75 0.09 0.16
Matches are distributed among these distances:
15 11 0.19
16 23 0.40
17 5 0.09
18 7 0.12
19 6 0.10
20 6 0.10
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (16 bp):
ATATTAAAATTATTTA
Found at i:21723386 original size:16 final size:16
Alignment explanation
Indices: 21723346--21723442 Score: 65
Period size: 18 Copynumber: 5.7 Consensus size: 16
21723336 TTATTAAAGT
21723346 ATATT-AAAATTATTTA
1 ATATTAAAAATTA-TTA
*
21723362 GTATT-AAAATTATTA
1 ATATTAAAAATTATTA
*
21723377 ATATTAAAAAATAATTA
1 ATATT-AAAAATTATTA
*
21723394 TATTTTAATAATATTATTTA
1 -ATATTAA-AA-ATTA-TTA
21723414 ATATTAAAATATTA-TA
1 ATATTAAAA-ATTATTA
21723430 ATAATATAAAAAT
1 AT-AT-TAAAAAT
21723443 ACTTAAAATA
Statistics
Matches: 67, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
15 7 0.10
16 15 0.22
17 15 0.22
18 18 0.27
19 9 0.13
20 3 0.04
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (16 bp):
ATATTAAAAATTATTA
Found at i:21723491 original size:15 final size:15
Alignment explanation
Indices: 21723471--21723561 Score: 80
Period size: 15 Copynumber: 5.9 Consensus size: 15
21723461 TTTTATTCTT
21723471 TATATTATTTATTAA
1 TATATTATTTATTAA
21723486 TATATTA-TTA-TAA
1 TATATTATTTATTAA
*
21723499 TAT-TTATTAATTAAAA
1 TATATTATTTATT--AA
* *
21723515 TAATAATAGTTATTAA
1 T-ATATTATTTATTAA
21723531 TATATTATTTATTAGTA
1 TATATTATTTATTA--A
21723548 TAATATTATTTATT
1 T-ATATTATTTATT
21723562 TATTAACATA
Statistics
Matches: 61, Mismatches: 6, Indels: 15
0.74 0.07 0.18
Matches are distributed among these distances:
12 3 0.05
13 8 0.13
14 4 0.07
15 18 0.30
16 6 0.10
17 4 0.07
18 18 0.30
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (15 bp):
TATATTATTTATTAA
Found at i:21723546 original size:22 final size:22
Alignment explanation
Indices: 21723473--21723566 Score: 68
Period size: 22 Copynumber: 4.2 Consensus size: 22
21723463 TTATTCTTTA
*
21723473 TATTATTTATTAATATATTATT
1 TATTAGTTATTAATATATTATT
* * ** *
21723495 ATAATATTTATTAAT-TAAAATAA
1 -TATTAGTTATTAATATATTAT-T
*
21723518 TAATAGTTATTAATATATTATT
1 TATTAGTTATTAATATATTATT
21723540 TATTAG-TA-TAATATTATTTATT
1 TATTAGTTATTAATA-TA-TTATT
21723562 TATTA
1 TATTA
21723567 ACATAATAAT
Statistics
Matches: 58, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
20 5 0.09
21 4 0.07
22 32 0.55
23 17 0.29
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
TATTAGTTATTAATATATTATT
Found at i:21723572 original size:22 final size:21
Alignment explanation
Indices: 21723528--21723579 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
21723518 TAATAGTTAT
**
21723528 TAATATA-TTATTTATTAGTA
1 TAATATATTTATTTATTAACA
21723548 TAATATTATTTATTTATTAACA
1 TAATA-TATTTATTTATTAACA
21723570 TAATAATATT
1 TAAT-ATATT
21723580 ATTAATCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 5 0.19
21 2 0.07
22 19 0.70
23 1 0.04
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (21 bp):
TAATATATTTATTTATTAACA
Found at i:21723590 original size:17 final size:18
Alignment explanation
Indices: 21723561--21723611 Score: 52
Period size: 19 Copynumber: 2.8 Consensus size: 18
21723551 TATTATTTAT
21723561 TTATTAA-CATAATA-ATA
1 TTATTAATC-TAATATATA
*
21723578 TTATTAATCTAATATTATT
1 TTATTAATCTAATA-TATA
*
21723597 TTATTAATATAATAT
1 TTATTAATCTAATAT
21723612 TAATTATAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
17 12 0.41
18 2 0.07
19 15 0.52
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (18 bp):
TTATTAATCTAATATATA
Found at i:21723755 original size:42 final size:42
Alignment explanation
Indices: 21723675--21723758 Score: 100
Period size: 43 Copynumber: 2.0 Consensus size: 42
21723665 TCAATTTTTT
*
21723675 AAAAATATCTTTATCTTTTCAAATTCATAAAATAATTTTCAA
1 AAAAATATCTTTATCTTTTCAAATTAATAAAATAATTTTCAA
* *
21723717 AAAAATAAT-TTTAT-TTTTCATTAATTAATAAATTATTTTTCA
1 AAAAAT-ATCTTTATCTTTTCA--AATTAATAAAATAATTTTCA
21723759 TTGACTAATC
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
41 6 0.17
42 11 0.31
43 19 0.53
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (42 bp):
AAAAATATCTTTATCTTTTCAAATTAATAAAATAATTTTCAA
Found at i:21723767 original size:22 final size:22
Alignment explanation
Indices: 21723727--21723776 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
21723717 AAAAATAATT
*
21723727 TTATTTTTCATTAATTAATAAA
1 TTATTTTTCATTAACTAATAAA
* *
21723749 TTATTTTTCATTGACTAATCAA
1 TTATTTTTCATTAACTAATAAA
21723771 TT-TTTT
1 TTATTTT
21723777 ACTAAATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.32, C:0.08, G:0.02, T:0.58
Consensus pattern (22 bp):
TTATTTTTCATTAACTAATAAA
Found at i:21724726 original size:16 final size:18
Alignment explanation
Indices: 21724702--21724734 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
21724692 ATATTTGATA
21724702 ATTTAAATA-AAAAATTT
1 ATTTAAATATAAAAATTT
21724719 ATTT-AATATAAAAATT
1 ATTTAAATATAAAAATT
21724735 GTTTTTCCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTTAAATATAAAAATTT
Found at i:21724868 original size:153 final size:153
Alignment explanation
Indices: 21724590--21724886 Score: 504
Period size: 153 Copynumber: 1.9 Consensus size: 153
21724580 AAATCCATGT
*
21724590 CCACCATAAATATGAGGATCAAAATTCTTGAGATTGAAGCATTTAATTTTATGTCATTTGATGAT
1 CCACCATAAATATGAGGATCAAAATTCTTGAGATTGAAGCATTCAATTTTATGTCATTTGATGAT
* *
21724655 TAAACGTTGAATTTTTAATTTAAATGATTAAAATTTAATATTTGATAATTTAAATAAAAAATTTA
66 TAAACGTTGAATTTTGAATTTAAATGATTAAAATTAAATATTTGATAATTTAAATAAAAAATTTA
21724720 TTTAATATAAAAATTGTTTTTCC
131 TTTAATATAAAAATTGTTTTTCC
* * *
21724743 CCACCGTAAATATGAGGATCAAAATTCTTGAGATTGAAGCGTTCAATTTTATGTCATTTGTTGAT
1 CCACCATAAATATGAGGATCAAAATTCTTGAGATTGAAGCATTCAATTTTATGTCATTTGATGAT
* * *
21724808 TGAACGTTGAATTTTGAATTTAAATTATTAAAATTAAATATTTTATAATTTTAAATAAAAAATTT
66 TAAACGTTGAATTTTGAATTTAAATGATTAAAATTAAATATTTGATAA-TTTAAATAAAAAATTT
21724873 ATTTAATATAAAAA
130 ATTTAATATAAAAA
21724887 AGATTTTCCC
Statistics
Matches: 134, Mismatches: 9, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
153 104 0.78
154 30 0.22
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (153 bp):
CCACCATAAATATGAGGATCAAAATTCTTGAGATTGAAGCATTCAATTTTATGTCATTTGATGAT
TAAACGTTGAATTTTGAATTTAAATGATTAAAATTAAATATTTGATAATTTAAATAAAAAATTTA
TTTAATATAAAAATTGTTTTTCC
Found at i:21725431 original size:7 final size:7
Alignment explanation
Indices: 21725419--21725444 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
21725409 CCTGCGGGAG
21725419 GAGGACT
1 GAGGACT
21725426 GAGGACT
1 GAGGACT
21725433 GAGGACT
1 GAGGACT
21725440 GAGGA
1 GAGGA
21725445 GAATGCTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.12, G:0.46, T:0.12
Consensus pattern (7 bp):
GAGGACT
Found at i:21726609 original size:15 final size:15
Alignment explanation
Indices: 21726591--21726643 Score: 63
Period size: 15 Copynumber: 3.5 Consensus size: 15
21726581 AAATATCTTA
21726591 AAAAATAATAATAAT
1 AAAAATAATAATAAT
*
21726606 AAAAATAATAATACTT
1 AAAAATAATAATA-AT
*
21726622 AAAAATTAAAAAT-AT
1 AAAAA-TAATAATAAT
21726637 AAAAATA
1 AAAAATA
21726644 TTTATCAATC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
14 2 0.06
15 19 0.58
16 6 0.18
17 6 0.18
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAAATAATAATAAT
Found at i:21727131 original size:27 final size:24
Alignment explanation
Indices: 21727074--21727137 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 24
21727064 TTTAAATTAA
*
21727074 TATATATAAAAATAAAATAATAAAT
1 TATA-ATAAAAATAAAAAAATAAAT
*
21727099 TTTAATAAAAATAATAAAAATATATAT
1 TATAATAAAAATAA-AAAAATA-A-AT
21727126 TATAATATAAAA
1 TATAATA-AAAA
21727138 ACTTAAATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
24 10 0.31
25 9 0.28
26 1 0.03
27 8 0.25
28 4 0.12
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (24 bp):
TATAATAAAAATAAAAAAATAAAT
Found at i:21728288 original size:2 final size:2
Alignment explanation
Indices: 21728281--21728310 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
21728271 TCAGAGATAA
21728281 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
21728311 TTAAAAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:21729128 original size:7 final size:7
Alignment explanation
Indices: 21729116--21729148 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
21729106 AAAGGAATAA
21729116 AAAAAAG
1 AAAAAAG
21729123 AAAAAAG
1 AAAAAAG
21729130 AAAAAA-
1 AAAAAAG
*
21729136 AAAAGAG
1 AAAAAAG
21729143 AAAAAA
1 AAAAAA
21729149 AAAGAAATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 5 0.22
7 18 0.78
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:21729164 original size:30 final size:31
Alignment explanation
Indices: 21729114--21729175 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
21729104 GAAAAGGAAT
21729114 AAAAAAAAGAAAAAAGAAAAAA-AAAAGAGA
1 AAAAAAAAGAAAAAAGAAAAAACAAAAGAGA
** *
21729144 AAAAAAAAGAAATGATAAAAAACTAAAAGAGA
1 AAAAAAAAGAAAAAAGAAAAAAC-AAAAGAGA
21729176 GTAGTTAGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 19 0.70
32 8 0.30
ACGTcount: A:0.81, C:0.02, G:0.13, T:0.05
Consensus pattern (31 bp):
AAAAAAAAGAAAAAAGAAAAAACAAAAGAGA
Found at i:21737045 original size:18 final size:19
Alignment explanation
Indices: 21737009--21737045 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
21736999 AATAAATTTT
21737009 AATTTTAATATATTAAAAA
1 AATTTTAATATATTAAAAA
21737028 AATTTT-ATATAATTAAAA
1 AATTTTAATAT-ATTAAAA
21737046 TTTTATAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
AATTTTAATATATTAAAAA
Found at i:21738985 original size:25 final size:24
Alignment explanation
Indices: 21738957--21739012 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
21738947 TTTATTTTTT
*
21738957 ATTTTATTAATTTATTTTTTAAA-AA
1 ATTTTATTAA-TT-TTTATTAAATAA
*
21738982 ATTTTATTTATTTTTATTAAATAA
1 ATTTTATTAATTTTTATTAAATAA
21739006 ATTTTAT
1 ATTTTAT
21739013 AAAAAAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 8 0.29
24 11 0.39
25 9 0.32
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
ATTTTATTAATTTTTATTAAATAA
Found at i:21741150 original size:10 final size:10
Alignment explanation
Indices: 21741131--21741160 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
21741121 CTTCACCATC
21741131 CTTT-TCTCT
1 CTTTCTCTCT
21741140 CTTTCTCTCT
1 CTTTCTCTCT
21741150 CTTTCTCTCT
1 CTTTCTCTCT
21741160 C
1 C
21741161 AAAACCAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.20
10 16 0.80
ACGTcount: A:0.00, C:0.40, G:0.00, T:0.60
Consensus pattern (10 bp):
CTTTCTCTCT
Found at i:21741423 original size:26 final size:26
Alignment explanation
Indices: 21741394--21741449 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
21741384 TACCTCTATG
* *
21741394 TATTTTTCTCTGCTGATTTCTATGTT
1 TATTTTTCTCTACTCATTTCTATGTT
* *
21741420 TATTTTTCTCTATTCATTTTTATGTT
1 TATTTTTCTCTACTCATTTCTATGTT
21741446 TATT
1 TATT
21741450 ATAACCAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.14, C:0.12, G:0.07, T:0.66
Consensus pattern (26 bp):
TATTTTTCTCTACTCATTTCTATGTT
Found at i:21741926 original size:15 final size:15
Alignment explanation
Indices: 21741906--21741954 Score: 62
Period size: 15 Copynumber: 3.1 Consensus size: 15
21741896 ACCATTTCAA
*
21741906 AATTCAAAGGTTTGC
1 AATTCAAAGGTTCGC
*
21741921 AATTCAAAGATTCGC
1 AATTCAAAGGTTCGC
21741936 AAAGTTCAAAGGTTCGC
1 -AA-TTCAAAGGTTCGC
21741953 AA
1 AA
21741955 AGCTTTCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.45
16 4 0.14
17 12 0.41
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (15 bp):
AATTCAAAGGTTCGC
Found at i:21741945 original size:17 final size:17
Alignment explanation
Indices: 21741923--21741956 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
21741913 AGGTTTGCAA
21741923 TTCAAAGATTCGCAAAG
1 TTCAAAGATTCGCAAAG
*
21741940 TTCAAAGGTTCGCAAAG
1 TTCAAAGATTCGCAAAG
21741957 CTTTCAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.24
Consensus pattern (17 bp):
TTCAAAGATTCGCAAAG
Found at i:21742415 original size:21 final size:20
Alignment explanation
Indices: 21742365--21742417 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 20
21742355 CATCTAACAT
* **
21742365 TTAATGATTTACATTAAAAA
1 TTAAAGATTTACACCAAAAA
21742385 TTATAGAGATTTACACCAAAAA
1 TTA-A-AGATTTACACCAAAAA
21742407 GTTAAAGATTT
1 -TTAAAGATTT
21742418 TTATTTGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
20 3 0.11
21 7 0.26
22 14 0.52
23 3 0.11
ACGTcount: A:0.47, C:0.08, G:0.09, T:0.36
Consensus pattern (20 bp):
TTAAAGATTTACACCAAAAA
Found at i:21742639 original size:22 final size:23
Alignment explanation
Indices: 21742593--21742639 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
21742583 TTTCAGATTT
*
21742593 AAATTCAAAGGTTCACATTTGAA
1 AAATTCAAAGGTTCACATTTCAA
* *
21742616 AAATTCAAGGGTTCATA-TTCAA
1 AAATTCAAAGGTTCACATTTCAA
21742638 AA
1 AA
21742640 TTTTAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.45, C:0.13, G:0.13, T:0.30
Consensus pattern (23 bp):
AAATTCAAAGGTTCACATTTCAA
Found at i:21742845 original size:21 final size:21
Alignment explanation
Indices: 21742819--21742903 Score: 66
Period size: 23 Copynumber: 3.9 Consensus size: 21
21742809 TAAATTCTTG
21742819 AGATTCACATAAAATATTCAA
1 AGATTCACATAAAATATTCAA
* *
21742840 AGATTCACATTTAAAA-ATTTTAG
1 AGATTCACA--TAAAATA-TTCAA
* *
21742863 AGATTCACATCCAAAATTTTTAA
1 AGATTCACAT--AAAATATTCAA
*
21742886 AGATTCAC-TCAAATATTC
1 AGATTCACATAAAATATTC
21742904 TTATTTGAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
20 6 0.12
21 10 0.20
22 2 0.04
23 33 0.65
ACGTcount: A:0.45, C:0.15, G:0.06, T:0.34
Consensus pattern (21 bp):
AGATTCACATAAAATATTCAA
Found at i:21742866 original size:23 final size:23
Alignment explanation
Indices: 21742793--21742893 Score: 84
Period size: 23 Copynumber: 4.4 Consensus size: 23
21742783 ATTCGAGTTC
*
21742793 AAAGATTCACATTTGATAAATTCTT
1 AAAGATTCACATTT-AAAAATT-TT
* *
21742818 -GAGATTCACA--T-AAAATATTC
1 AAAGATTCACATTTAAAAAT-TTT
21742838 AAAGATTCACATTTAAAAATTTT
1 AAAGATTCACATTTAAAAATTTT
* ** *
21742861 AGAGATTCACATCCAAAATTTTT
1 AAAGATTCACATTTAAAAATTTT
21742884 AAAGATTCAC
1 AAAGATTCAC
21742894 TCAAATATTC
Statistics
Matches: 61, Mismatches: 10, Indels: 12
0.73 0.12 0.14
Matches are distributed among these distances:
20 5 0.08
21 10 0.16
22 1 0.02
23 31 0.51
24 14 0.23
ACGTcount: A:0.44, C:0.14, G:0.08, T:0.35
Consensus pattern (23 bp):
AAAGATTCACATTTAAAAATTTT
Found at i:21742866 original size:44 final size:46
Alignment explanation
Indices: 21742790--21742893 Score: 142
Period size: 44 Copynumber: 2.3 Consensus size: 46
21742780 CTTATTCGAG
*
21742790 TTCAAAGATTCACATTTGATAAATTCTTGAGATTCACAT-AAAATA
1 TTCAAAGATTCACATTTGAAAAATTCTTGAGATTCACATCAAAATA
*
21742835 TTCAAAGATTCACATTT-AAAAATT-TTAGAGATTCACATCCAAAATT
1 TTCAAAGATTCACATTTGAAAAATTCTT-GAGATTCACAT-CAAAATA
*
21742881 TTTAAAGATTCAC
1 TTCAAAGATTCAC
21742894 TCAAATATTC
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
43 2 0.04
44 17 0.32
45 17 0.32
46 17 0.32
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.36
Consensus pattern (46 bp):
TTCAAAGATTCACATTTGAAAAATTCTTGAGATTCACATCAAAATA
Done.