Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167871.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_14, 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: 22631831
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 114000 characters in sequence are not A, C, G, or T
File 89 of 125
Found at i:17470855 original size:18 final size:20
Alignment explanation
Indices: 17470809--17470854 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
17470799 ATAATTATAT
17470809 TTTTATATTTAAAAAAAATA
1 TTTTATATTTAAAAAAAATA
**
17470829 TTTTATATTTAAAAAATTTA
1 TTTTATATTTAAAAAAAATA
17470849 TTTTAT
1 TTTTAT
17470855 TAATTTCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTTATATTTAAAAAAAATA
Found at i:17471138 original size:3 final size:3
Alignment explanation
Indices: 17471132--17471165 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
17471122 TCCAGAAAAT
17471132 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
17471166 GGGTTGTGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:17474378 original size:19 final size:20
Alignment explanation
Indices: 17474341--17474378 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
17474331 TTCAATTATT
17474341 TTTTATATATGAATGTAATA
1 TTTTATATATGAATGTAATA
17474361 TTTTAT-TAT-AATTGTAAT
1 TTTTATATATGAA-TGTAAT
17474379 TTCTTTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 2 0.12
19 9 0.53
20 6 0.35
ACGTcount: A:0.37, C:0.00, G:0.08, T:0.55
Consensus pattern (20 bp):
TTTTATATATGAATGTAATA
Found at i:17475622 original size:15 final size:15
Alignment explanation
Indices: 17475601--17475631 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
17475591 TAAAAAATAA
17475601 ATTTTTTT-AAATTT
1 ATTTTTTTAAAATTT
17475615 ATTTTTTTAAAATTT
1 ATTTTTTTAAAATTT
17475630 AT
1 AT
17475632 AAAATTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
ATTTTTTTAAAATTT
Found at i:17475913 original size:12 final size:12
Alignment explanation
Indices: 17475885--17475926 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
17475875 TATTTTTTTT
17475885 ATTTTTATATAA
1 ATTTTTATATAA
17475897 A--TTTATATAA
1 ATTTTTATATAA
*
17475907 ATTTTTATTTAA
1 ATTTTTATATAA
*
17475919 CTTTTTAT
1 ATTTTTAT
17475927 TTTGGAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
10 10 0.38
12 16 0.62
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (12 bp):
ATTTTTATATAA
Found at i:17476836 original size:3 final size:3
Alignment explanation
Indices: 17476828--17476886 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
17476818 CTTTCATGCG
17476828 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
17476876 TAA TAA TAA TA
1 TAA TAA TAA TA
17476887 GATTTAACGA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:17476997 original size:12 final size:12
Alignment explanation
Indices: 17476980--17477022 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
17476970 TATTAATAAA
*
17476980 AAATTTATCGAT
1 AAATTTATCAAT
17476992 AAATTTTATCAAT
1 AAA-TTTATCAAT
17477005 -AA-TTATCAAT
1 AAATTTATCAAT
17477015 AAATTTAT
1 AAATTTAT
17477023 TACCAATGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
10 8 0.30
11 2 0.07
12 9 0.33
13 8 0.30
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (12 bp):
AAATTTATCAAT
Found at i:17477394 original size:10 final size:11
Alignment explanation
Indices: 17477353--17477402 Score: 68
Period size: 11 Copynumber: 4.7 Consensus size: 11
17477343 TTAATCAAAT
17477353 ACAT-CATAAA
1 ACATCCATAAA
*
17477363 ACATCCATCAA
1 ACATCCATAAA
17477374 ACATCCATAAA
1 ACATCCATAAA
17477385 ACAT-CATAAA
1 ACATCCATAAA
*
17477395 ATATCCAT
1 ACATCCAT
17477403 CCATAAAACA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
10 13 0.37
11 22 0.63
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.22
Consensus pattern (11 bp):
ACATCCATAAA
Found at i:17480004 original size:3 final size:3
Alignment explanation
Indices: 17479996--17480042 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
17479986 CTCATGTGTT
**
17479996 TCA TCA TCA TCA TCA TTG TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
17480043 TTCTTCTTCT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.30, C:0.32, G:0.02, T:0.36
Consensus pattern (3 bp):
TCA
Found at i:17481953 original size:21 final size:20
Alignment explanation
Indices: 17481929--17481970 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 20
17481919 TTTACCTTTA
17481929 ACATCCATTATTGTGTTAAAT
1 ACAT-CATTATTGTGTTAAAT
17481950 --A-CATTATTGTGTTAAAT
1 ACATCATTATTGTGTTAAAT
17481967 ACAT
1 ACAT
17481971 TATCAAAGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 7
0.72 0.00 0.28
Matches are distributed among these distances:
17 16 0.89
19 2 0.11
ACGTcount: A:0.36, C:0.12, G:0.10, T:0.43
Consensus pattern (20 bp):
ACATCATTATTGTGTTAAAT
Found at i:17481956 original size:17 final size:17
Alignment explanation
Indices: 17481934--17481973 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
17481924 CTTTAACATC
17481934 CATTATTGTGTTAAATA
1 CATTATTGTGTTAAATA
17481951 CATTATTGTGTTAAATA
1 CATTATTGTGTTAAATA
17481968 CATTAT
1 CATTAT
17481974 CAAAGACATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.35, C:0.07, G:0.10, T:0.47
Consensus pattern (17 bp):
CATTATTGTGTTAAATA
Found at i:17483269 original size:20 final size:21
Alignment explanation
Indices: 17483192--17483269 Score: 115
Period size: 20 Copynumber: 3.8 Consensus size: 21
17483182 TTCAAAATTA
17483192 ATAAAATATTATTTTTTAAAT
1 ATAAAATATTATTTTTTAAAT
*
17483213 ATAAAATACTA-TTTTTAAAT
1 ATAAAATATTATTTTTTAAAT
*
17483233 ATAAAATATTATTTTTTTAA-
1 ATAAAATATTATTTTTTAAAT
*
17483253 ACAAAATATTATTTTTT
1 ATAAAATATTATTTTTT
17483270 GATAAAAATA
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
20 35 0.67
21 17 0.33
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (21 bp):
ATAAAATATTATTTTTTAAAT
Found at i:17483269 original size:41 final size:41
Alignment explanation
Indices: 17483192--17483268 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
17483182 TTCAAAATTA
*
17483192 ATAAAATATTATTTTTTAAATATAAAATACTATTTTTAAAT
1 ATAAAATATTATTTTTTAAATACAAAATACTATTTTTAAAT
* *
17483233 ATAAAATATTATTTTTTTAA-ACAAAATATTATTTTT
1 ATAAAATATTATTTTTTAAATACAAAATACTATTTTT
17483269 TGATAAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
40 14 0.42
41 19 0.58
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.51
Consensus pattern (41 bp):
ATAAAATATTATTTTTTAAATACAAAATACTATTTTTAAAT
Found at i:17485281 original size:59 final size:59
Alignment explanation
Indices: 17485107--17485261 Score: 238
Period size: 59 Copynumber: 2.6 Consensus size: 59
17485097 AACAAATATA
* * *
17485107 TAACTAAAACCCAAACAAATTTTAACAAATATAAAATCAACAAAAACTCAACAAATTGG
1 TAACCAAAACCCAAACAAATTTCAACAAATATATAATCAACAAAAACTCAACAAATTGG
* * *
17485166 TAACCAAAACCCAAACAAATTTCAATAAATAAATAACCAACAAAAACTCAACAAATTGG
1 TAACCAAAACCCAAACAAATTTCAACAAATATATAATCAACAAAAACTCAACAAATTGG
* *
17485225 TAACCAAAACCTAAACAAATTTCAACAAATTTATAAT
1 TAACCAAAACCCAAACAAATTTCAACAAATATATAAT
17485262 AAAAAATTAA
Statistics
Matches: 85, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 85 1.00
ACGTcount: A:0.57, C:0.20, G:0.03, T:0.21
Consensus pattern (59 bp):
TAACCAAAACCCAAACAAATTTCAACAAATATATAATCAACAAAAACTCAACAAATTGG
Found at i:17485581 original size:64 final size:66
Alignment explanation
Indices: 17485489--17485635 Score: 151
Period size: 64 Copynumber: 2.2 Consensus size: 66
17485479 TTTTTTTTTG
* * * * *
17485489 TTTTATCAATGGATTTAGTGAAAGAATTT-TCATCAGTAATGT-ATAAA-ATTTTCTTTTTCAAA
1 TTTTACCAATGGATTTAGTCAAAGAATTTCT-ATCAATAATGTGAAAAATATTTTC-TTTGCAAA
17485551 -TT
64 TTT
* *
17485553 TTTTACCAATGGATTTAG-CAATGAAATTTCTGTCAATAATGTGAAAAATATTTTCTTTGCAAAT
1 TTTTACCAATGGATTTAGTCAAAG-AATTTCTATCAATAATGTGAAAAATATTTTCTTTGCAAA-
17485617 TTT
64 TTT
*
17485620 TTTTACCGATGGATTT
1 TTTTACCAATGGATTT
17485636 TTTCATCACT
Statistics
Matches: 69, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
63 3 0.04
64 31 0.45
65 12 0.17
66 6 0.09
67 17 0.25
ACGTcount: A:0.33, C:0.10, G:0.12, T:0.46
Consensus pattern (66 bp):
TTTTACCAATGGATTTAGTCAAAGAATTTCTATCAATAATGTGAAAAATATTTTCTTTGCAAATT
T
Found at i:17493522 original size:20 final size:20
Alignment explanation
Indices: 17493493--17493537 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
17493483 GGATGGTGCA
* *
17493493 TTTAAAATTTTGATTTGATTT
1 TTTAAATTTTTAATTT-ATTT
17493514 TTTAAATTTTTAATTTATTT
1 TTTAAATTTTTAATTTATTT
17493534 TTTA
1 TTTA
17493538 TTTTCAATCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (20 bp):
TTTAAATTTTTAATTTATTT
Found at i:17494882 original size:16 final size:15
Alignment explanation
Indices: 17494861--17494904 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
17494851 AATTTTTGTT
17494861 TTTAATTTAATTCAAG
1 TTTAATTTAATTC-AG
* *
17494877 TTTAATTTAGTTCTG
1 TTTAATTTAATTCAG
17494892 TTTGAATTTAATT
1 TTT-AATTTAATT
17494905 TAAGGTTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
15 4 0.17
16 20 0.83
ACGTcount: A:0.30, C:0.05, G:0.09, T:0.57
Consensus pattern (15 bp):
TTTAATTTAATTCAG
Found at i:17497349 original size:10 final size:10
Alignment explanation
Indices: 17497336--17497362 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
17497326 AATTTGTGAA
17497336 AAAATTTTTC
1 AAAATTTTTC
17497346 AAAATTTTTC
1 AAAATTTTTC
17497356 AAAATTT
1 AAAATTT
17497363 CAATTTTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.48
Consensus pattern (10 bp):
AAAATTTTTC
Found at i:17498487 original size:6 final size:6
Alignment explanation
Indices: 17498461--17498614 Score: 81
Period size: 7 Copynumber: 24.8 Consensus size: 6
17498451 GTTAAGAGTT
*
17498461 GGTTTG GGTTT- GGTTTAA GGTTTA GGTTTTAA GGTTTA GGTTTTAA GGTTT-
1 GGTTTA GGTTTA GGTTT-A GGTTTA GG-TTT-A GGTTTA GG-TTT-A GGTTTA
* * *
17498512 GGGTT- GGTTTG GAGTCTA GG-TTA GGATTTA GGGTTT- GGTTTA GGTTTA
1 GGTTTA GGTTTA G-GTTTA GGTTTA GG-TTTA -GGTTTA GGTTTA GGTTTA
* *
17498560 GAGTTTG GGTTTA GGGTTGA GGTTT- GGTTTA GGGTTT- GAG-TTA GGTTTAA
1 G-GTTTA GGTTTA -GGTTTA GGTTTA GGTTTA -GGTTTA G-GTTTA GGTTT-A
17498610 GGTTT
1 GGTTT
17498615 CATGAATGGT
Statistics
Matches: 119, Mismatches: 9, Indels: 39
0.71 0.05 0.23
Matches are distributed among these distances:
5 31 0.26
6 32 0.27
7 48 0.40
8 8 0.07
ACGTcount: A:0.15, C:0.01, G:0.38, T:0.47
Consensus pattern (6 bp):
GGTTTA
Found at i:17498488 original size:18 final size:17
Alignment explanation
Indices: 17498461--17498614 Score: 89
Period size: 18 Copynumber: 8.3 Consensus size: 17
17498451 GTTAAGAGTT
*
17498461 GGTTTGGGTTTGGTTTAA
1 GGTTTAGGTTTGGTTT-A
17498479 GGTTTAGGTTTTAAGGTTTA
1 GGTTTAGG-TTT--GGTTTA
*
17498499 GGTTTTAAGGTTTGGGTT-
1 GG-TTT-AGGTTTGGTTTA
* *
17498517 GGTTTGGAGTCTAGG-TTA
1 GGTTTAG-GT-TTGGTTTA
17498535 GGATTTAGGGTTTGGTTTA
1 GG-TTTA-GGTTTGGTTTA
17498554 GGTTTAGAGTTTGGGTTTA
1 GGTTTAG-GTTT-GGTTTA
*
17498573 GGGTTGAGGTTTGGTTTA
1 -GGTTTAGGTTTGGTTTA
*
17498591 GGGTTT-GAGTTAGGTTTAA
1 -GGTTTAG-GTTTGGTTT-A
17498610 GGTTT
1 GGTTT
17498615 CATGAATGGT
Statistics
Matches: 111, Mismatches: 9, Indels: 32
0.73 0.06 0.21
Matches are distributed among these distances:
16 1 0.01
17 9 0.08
18 49 0.44
19 28 0.25
20 10 0.09
21 11 0.10
22 3 0.03
ACGTcount: A:0.15, C:0.01, G:0.38, T:0.47
Consensus pattern (17 bp):
GGTTTAGGTTTGGTTTA
Found at i:17498558 original size:37 final size:34
Alignment explanation
Indices: 17498496--17498606 Score: 98
Period size: 37 Copynumber: 3.1 Consensus size: 34
17498486 GTTTTAAGGT
* *
17498496 TTAGGTTTTAAGGTTTGGGTT-GGTTTGGAGTCTAGG
1 TTAGGATTT-AGGTTTGGTTTAGGTTT-GAGT-TAGG
*
17498532 TTAGGATTTAGGGTTTGGTTTAGGTTTAGAGTTTGGG
1 TTAGGATTTA-GGTTTGGTTTAGGTTT-GAG-TTAGG
* *
17498569 TTTAGGGTTGAGGTTTGGTTTAGGGTTTGAGTTAGG
1 -TTAGGATTTAGGTTTGGTTTA-GGTTTGAGTTAGG
17498605 TT
1 TT
17498607 TAAGGTTTCA
Statistics
Matches: 63, Mismatches: 7, Indels: 11
0.78 0.09 0.14
Matches are distributed among these distances:
35 3 0.05
36 21 0.33
37 25 0.40
38 14 0.22
ACGTcount: A:0.14, C:0.01, G:0.39, T:0.46
Consensus pattern (34 bp):
TTAGGATTTAGGTTTGGTTTAGGTTTGAGTTAGG
Found at i:17498573 original size:31 final size:31
Alignment explanation
Indices: 17498538--17498614 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
17498528 TAGGTTAGGA
*
17498538 TTTAGGGTT-TGGTTTAGGTTTAGAGTTTGGG
1 TTTAGGGTTGAGGTTT-GGTTTAGAGTTTGGG
* *
17498569 TTTAGGGTTGAGGTTTGGTTTAGGGTTTGAG
1 TTTAGGGTTGAGGTTTGGTTTAGAGTTTGGG
* *
17498600 -TTAGGTTTAAGGTTT
1 TTTAGGGTTGAGGTTT
17498615 CATGAATGGT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
30 13 0.32
31 22 0.55
32 5 0.12
ACGTcount: A:0.14, C:0.00, G:0.38, T:0.48
Consensus pattern (31 bp):
TTTAGGGTTGAGGTTTGGTTTAGAGTTTGGG
Found at i:17501415 original size:12 final size:12
Alignment explanation
Indices: 17501398--17501429 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
17501388 ATTGTTGTTT
17501398 AAAAAGAAAAAA
1 AAAAAGAAAAAA
17501410 AAAAAGAAAAAA
1 AAAAAGAAAAAA
*
17501422 AGAAAGAA
1 AAAAAGAA
17501430 GAATCTAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAAA
Found at i:17501664 original size:34 final size:34
Alignment explanation
Indices: 17501621--17501689 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
17501611 AGAGAGAGTA
17501621 TGTGAAAAGAAAAACTTATGAAATTTTTGCATAC
1 TGTGAAAAGAAAAACTTATGAAATTTTTGCATAC
17501655 TGTGAAAAGAAAAACTTATGAAATTTTTGCATAC
1 TGTGAAAAGAAAAACTTATGAAATTTTTGCATAC
17501689 T
1 T
17501690 TTTAAGATTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.33
Consensus pattern (34 bp):
TGTGAAAAGAAAAACTTATGAAATTTTTGCATAC
Found at i:17503170 original size:21 final size:19
Alignment explanation
Indices: 17503126--17503174 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
17503116 TCAATTTAGT
17503126 GTTTTTCAAGTTAATCTAA
1 GTTTTTCAAGTTAATCTAA
* *
17503145 ATTTTTGCAAGTTTAATTTAA
1 GTTTTT-CAAG-TTAATCTAA
17503166 G-TTTTCAAG
1 GTTTTTCAAG
17503175 CAATTTAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
19 9 0.36
20 8 0.32
21 8 0.32
ACGTcount: A:0.31, C:0.08, G:0.12, T:0.49
Consensus pattern (19 bp):
GTTTTTCAAGTTAATCTAA
Found at i:17503542 original size:6 final size:6
Alignment explanation
Indices: 17503533--17503563 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
17503523 GTTTGTTAAG
*
17503533 TTTAAT TTTAGT TTTAGT TTTAGT TTTAGT T
1 TTTAGT TTTAGT TTTAGT TTTAGT TTTAGT T
17503564 AATTCAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.19, C:0.00, G:0.13, T:0.68
Consensus pattern (6 bp):
TTTAGT
Found at i:17512524 original size:32 final size:32
Alignment explanation
Indices: 17512459--17512527 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 32
17512449 CATTAATTCT
** *
17512459 TAAAAATTAAAGATTATTATATTTGGTATTAC
1 TAAAAATTAAAGATTATTATATTTGAAAGTAC
* * *
17512491 TAAAAATTAAATATTATTCTGTTTGAAAGTAC
1 TAAAAATTAAAGATTATTATATTTGAAAGTAC
17512523 TAAAA
1 TAAAA
17512528 TAATATTGTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.46, C:0.04, G:0.09, T:0.41
Consensus pattern (32 bp):
TAAAAATTAAAGATTATTATATTTGAAAGTAC
Found at i:17520473 original size:17 final size:17
Alignment explanation
Indices: 17520443--17520499 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
17520433 AGGCCAGTCA
* *
17520443 AGAAGGAAAGAAGAGATG
1 AGAA-GAAAAAAGAGAGG
17520461 AGAAGAAAAAAGAGAGG
1 AGAAGAAAAAAGAGAGG
*
17520478 A-AA-AAAAAAAAGAGG
1 AGAAGAAAAAAGAGAGG
*
17520493 AAAAGAA
1 AGAAGAA
17520500 CAGAAACTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
15 12 0.35
16 4 0.12
17 14 0.41
18 4 0.12
ACGTcount: A:0.68, C:0.00, G:0.30, T:0.02
Consensus pattern (17 bp):
AGAAGAAAAAAGAGAGG
Found at i:17520486 original size:15 final size:15
Alignment explanation
Indices: 17520466--17520496 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
17520456 AGATGAGAAG
*
17520466 AAAAAAGAGAGGAAA
1 AAAAAAAAGAGGAAA
17520481 AAAAAAAAGAGGAAA
1 AAAAAAAAGAGGAAA
17520496 A
1 A
17520497 GAACAGAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (15 bp):
AAAAAAAAGAGGAAA
Found at i:17521015 original size:43 final size:43
Alignment explanation
Indices: 17520934--17521017 Score: 107
Period size: 43 Copynumber: 2.0 Consensus size: 43
17520924 TATTTACTTA
* *
17520934 ATTTTTAAATGTAATAATCTATTAAATATTTATTATTTTTATG
1 ATTTTGAAATGTAATAATCTATTAAATATTTATAATTTTTATG
* * *
17520977 ATTTTGAAATGTAGTAATTTATTAAGTATTT-TAAATTTTTA
1 ATTTTGAAATGTAATAATCTATTAAATATTTAT-AATTTTTA
17521018 CACATTAATT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 1 0.03
43 34 0.97
ACGTcount: A:0.37, C:0.01, G:0.07, T:0.55
Consensus pattern (43 bp):
ATTTTGAAATGTAATAATCTATTAAATATTTATAATTTTTATG
Found at i:17521144 original size:21 final size:20
Alignment explanation
Indices: 17521110--17521148 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
17521100 TTCACAAAAA
17521110 TAATAATAATAAAAATTAATC
1 TAATAATAA-AAAAATTAATC
*
17521131 TAATAGTAAAAAAATTAA
1 TAATAATAAAAAAATTAA
17521149 CAATACAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (20 bp):
TAATAATAAAAAAATTAATC
Found at i:17526244 original size:2 final size:2
Alignment explanation
Indices: 17526237--17526266 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
17526227 GTCCATTTTC
17526237 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17526267 GTCCATTTAA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17528343 original size:109 final size:110
Alignment explanation
Indices: 17528152--17528350 Score: 314
Period size: 109 Copynumber: 1.8 Consensus size: 110
17528142 ACTATAAATA
*
17528152 GCATACCTGTAAAAGTGCAGCAATAGTACCAAAAGAATTCCACAACAATGGAGCCAAATCTTGAA
1 GCATACCTGTAAAAGTGCAGCAATAGTACCAAAAGAATTCCACAACAAAGGAGCCAAATCTTGAA
17528217 ATAATTCTCTCTTCT-AAAAATAAAAACAAAAACAAGTTTATTAG
66 ATAATTCTCTCTTCTAAAAAATAAAAACAAAAACAAGTTTATTAG
** *
17528261 GCATACCTGTATGAGTGCAGCTATAGTACCAAAAGAATTCCAC-ACGAAAGGAGCCAAATCTTGA
1 GCATACCTGTAAAAGTGCAGCAATAGTACCAAAAGAATTCCACAAC-AAAGGAGCCAAATCTTGA
*
17528325 AATAATTC-CTTGTTCTAAAAAATAAA
65 AATAATTCTC-TCTTCTAAAAAATAAA
17528351 CCAAAGGTAG
Statistics
Matches: 82, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
108 3 0.04
109 70 0.85
110 9 0.11
ACGTcount: A:0.44, C:0.19, G:0.14, T:0.24
Consensus pattern (110 bp):
GCATACCTGTAAAAGTGCAGCAATAGTACCAAAAGAATTCCACAACAAAGGAGCCAAATCTTGAA
ATAATTCTCTCTTCTAAAAAATAAAAACAAAAACAAGTTTATTAG
Found at i:17531020 original size:18 final size:17
Alignment explanation
Indices: 17530997--17531030 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
17530987 ATTGACATAT
17530997 AAACAAAATAAAAAATAC
1 AAACAAAA-AAAAAATAC
*
17531015 AAACAACAAAAAAATA
1 AAACAAAAAAAAAATA
17531031 AGGCAAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.79, C:0.12, G:0.00, T:0.09
Consensus pattern (17 bp):
AAACAAAAAAAAAATAC
Found at i:17534777 original size:17 final size:16
Alignment explanation
Indices: 17534747--17534789 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 16
17534737 TCAAATAGAT
17534747 ATAAC-AAA-AATAAA
1 ATAACAAAATAATAAA
17534761 ATAACATAAATAATAAA
1 ATAACA-AAATAATAAA
*
17534778 TTAACAAAATAA
1 ATAACAAAATAA
17534790 CATATTTCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 5 0.20
16 9 0.36
17 11 0.44
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (16 bp):
ATAACAAAATAATAAA
Found at i:17537366 original size:26 final size:27
Alignment explanation
Indices: 17537337--17537393 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
17537327 CATAGTGAAA
17537337 AATTCTTAAGAATTT-AGATTCGCAAG
1 AATTCTTAAGAATTTCAGATTCGCAAG
*
17537363 AATTCTTAAGAGTTTCAGATTCGCAAG
1 AATTCTTAAGAATTTCAGATTCGCAAG
17537390 AATT
1 AATT
17537394 AAGATTTGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 14 0.48
27 15 0.52
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (27 bp):
AATTCTTAAGAATTTCAGATTCGCAAG
Found at i:17537410 original size:43 final size:42
Alignment explanation
Indices: 17537344--17537445 Score: 141
Period size: 43 Copynumber: 2.4 Consensus size: 42
17537334 AAAAATTCTT
* * *
17537344 AAGAATTTAGATTCGCAAGAATTCTTAAGAGTTTCAGATTCGC
1 AAGAATTAAGATTTGCAAGAATTCATAAGAGTTTCAGATT-GC
*
17537387 AAGAATTAAGATTTGCAATAATTCATAAGAGTTTCAGATTGC
1 AAGAATTAAGATTTGCAAGAATTCATAAGAGTTTCAGATTGC
17537429 AAGAATTGAAAGATTTG
1 AAGAATT--AAGATTTG
17537446 TAAAACTTTA
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
42 9 0.17
43 36 0.68
44 8 0.15
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.32
Consensus pattern (42 bp):
AAGAATTAAGATTTGCAAGAATTCATAAGAGTTTCAGATTGC
Found at i:17537525 original size:16 final size:16
Alignment explanation
Indices: 17537504--17537558 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
17537494 AGAACTTCAA
*
17537504 AGATTCACAAGAATTC
1 AGATTCATAAGAATTC
*
17537520 AGATTCGTAAGAATTTTC
1 AGATTCATAAGAA--TTC
* *
17537538 ATATTCATAAGAATTT
1 AGATTCATAAGAATTC
17537554 AGATT
1 AGATT
17537559 TGTAAGACCT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
16 17 0.55
18 14 0.45
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (16 bp):
AGATTCATAAGAATTC
Found at i:17537538 original size:18 final size:17
Alignment explanation
Indices: 17537512--17537565 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
17537502 AAAGATTCAC
17537512 AAGAA-TTCAGATTCGT
1 AAGAATTTCAGATTCGT
* *
17537528 AAGAATTTTCATATTCAT
1 AAGAA-TTTCAGATTCGT
*
17537546 AAGAATTT-AGATTTGT
1 AAGAATTTCAGATTCGT
17537562 AAGA
1 AAGA
17537566 CCTCAAAGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
16 14 0.45
17 3 0.10
18 14 0.45
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (17 bp):
AAGAATTTCAGATTCGT
Found at i:17537594 original size:17 final size:18
Alignment explanation
Indices: 17537551--17537599 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 18
17537541 TTCATAAGAA
17537551 TTTAGATTTGTAAGACCT
1 TTTAGATTTGTAAGACCT
***
17537569 CAAAGATTTGTAAGA-CT
1 TTTAGATTTGTAAGACCT
17537586 TTTAGATTTGTAAG
1 TTTAGATTTGTAAG
17537600 GATCTAAGTT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.33, C:0.08, G:0.18, T:0.41
Consensus pattern (18 bp):
TTTAGATTTGTAAGACCT
Found at i:17537616 original size:34 final size:34
Alignment explanation
Indices: 17537545--17537627 Score: 93
Period size: 34 Copynumber: 2.4 Consensus size: 34
17537535 TTCATATTCA
17537545 TAAGAA-TTTAGATTTGTAAGACCTCAAAGATTTG
1 TAAGAACTTTAGATTTGTAAGA-CTCAAAGATTTG
*
17537579 TAAG-ACTTTTAGATTTGTAAGGA-TCTAAG-TTTGG
1 TAAGAAC-TTTAGATTTGTAA-GACTCAAAGATTT-G
17537613 TAAGAACTTTAGATT
1 TAAGAACTTTAGATT
17537628 CACGGGTTCA
Statistics
Matches: 43, Mismatches: 1, Indels: 10
0.80 0.02 0.19
Matches are distributed among these distances:
33 4 0.09
34 22 0.51
35 15 0.35
36 2 0.05
ACGTcount: A:0.35, C:0.07, G:0.19, T:0.39
Consensus pattern (34 bp):
TAAGAACTTTAGATTTGTAAGACTCAAAGATTTG
Found at i:17539023 original size:32 final size:31
Alignment explanation
Indices: 17538982--17539052 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 31
17538972 TTGCTTAAAC
*
17538982 CAAAAACCCATCTT-TCTTTGCATTATAAAAT
1 CAAAAACCCA-CTTCTCTTTGCATTACAAAAT
*
17539013 CAAAAGACCCACTTCTCTTTGTATTACAAAAT
1 CAAAA-ACCCACTTCTCTTTGCATTACAAAAT
17539045 CAAGAAAC
1 CAA-AAAC
17539053 TCATAAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
31 8 0.23
32 25 0.71
33 2 0.06
ACGTcount: A:0.41, C:0.24, G:0.06, T:0.30
Consensus pattern (31 bp):
CAAAAACCCACTTCTCTTTGCATTACAAAAT
Found at i:17539195 original size:21 final size:21
Alignment explanation
Indices: 17539149--17539188 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
17539139 TAATTAAAAA
17539149 CAAAACCAAAAAACCCAAACT
1 CAAAACCAAAAAACCCAAACT
* *
17539170 AAAAACCAAAAAACTCAAA
1 CAAAACCAAAAAACCCAAA
17539189 TCCAAAATAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.68, C:0.28, G:0.00, T:0.05
Consensus pattern (21 bp):
CAAAACCAAAAAACCCAAACT
Found at i:17540086 original size:19 final size:19
Alignment explanation
Indices: 17540064--17540118 Score: 74
Period size: 19 Copynumber: 2.9 Consensus size: 19
17540054 AAAAATCTAA
*
17540064 AAATCCAAAATTTTAAAAG
1 AAATCAAAAATTTTAAAAG
*
17540083 AAATTAAAAATTTTAAAAG
1 AAATCAAAAATTTTAAAAG
* *
17540102 AAATTAAAAACTTTAAA
1 AAATCAAAAATTTTAAA
17540119 TGACAATGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.62, C:0.05, G:0.04, T:0.29
Consensus pattern (19 bp):
AAATCAAAAATTTTAAAAG
Found at i:17552785 original size:16 final size:16
Alignment explanation
Indices: 17552754--17552783 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
17552744 CCTTTCACAT
17552754 TTTCCTAAAATGCCCA
1 TTTCCTAAAATGCCCA
17552770 TTTCCT-AAATGCCC
1 TTTCCTAAAATGCCC
17552784 CACAAATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.27, C:0.33, G:0.07, T:0.33
Consensus pattern (16 bp):
TTTCCTAAAATGCCCA
Found at i:17554039 original size:7 final size:7
Alignment explanation
Indices: 17554027--17554158 Score: 66
Period size: 7 Copynumber: 19.4 Consensus size: 7
17554017 TTTTTTAGCA
17554027 TTAGGGT
1 TTAGGGT
17554034 TTAGGGTT
1 TTAGGG-T
*
17554042 TTAGGAT
1 TTAGGGT
17554049 TTAGGGT
1 TTAGGGT
*
17554056 TT-GAG-
1 TTAGGGT
17554061 TTAGGGT
1 TTAGGGT
*
17554068 TTATGGT
1 TTAGGGT
17554075 TT-GGAGT
1 TTAGG-GT
17554082 TTA--GT
1 TTAGGGT
17554087 TTAGGGT
1 TTAGGGT
*
17554094 TTA-AGT
1 TTAGGGT
*
17554100 TTAGAGT
1 TTAGGGT
*
17554107 TT-GTAGTT
1 TTAG--GGT
17554115 TTA-GGT
1 TTAGGGT
*
17554121 TTAAGGT
1 TTAGGGT
17554128 TTAGGGT
1 TTAGGGT
17554135 TT-GAGGT
1 TTAG-GGT
* *
17554142 TTAAGAT
1 TTAGGGT
*
17554149 TTAGGTT
1 TTAGGGT
17554156 TTA
1 TTA
17554159 AGATTAAGGT
Statistics
Matches: 96, Mismatches: 15, Indels: 28
0.69 0.11 0.20
Matches are distributed among these distances:
5 7 0.07
6 17 0.18
7 63 0.66
8 9 0.09
ACGTcount: A:0.20, C:0.00, G:0.33, T:0.48
Consensus pattern (7 bp):
TTAGGGT
Found at i:17554051 original size:15 final size:15
Alignment explanation
Indices: 17554027--17554057 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
17554017 TTTTTTAGCA
*
17554027 TTAGGGTTTAGGGTT
1 TTAGGATTTAGGGTT
17554042 TTAGGATTTAGGGTT
1 TTAGGATTTAGGGTT
17554057 T
1 T
17554058 GAGTTAGGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.00, G:0.35, T:0.48
Consensus pattern (15 bp):
TTAGGATTTAGGGTT
Found at i:17554067 original size:27 final size:26
Alignment explanation
Indices: 17554032--17554156 Score: 114
Period size: 27 Copynumber: 4.7 Consensus size: 26
17554022 TAGCATTAGG
17554032 GTTTAGGGTTTTAGGATTTAGGGTTTGA
1 GTTTAGGG-TTTAGG-TTTAGGGTTTGA
17554060 G-TTAGGGTTTATGGTTT-GGAGTTT-A
1 GTTTAGGGTTTA-GGTTTAGG-GTTTGA
* *
17554085 GTTTAGGGTTTAAGTTTAGAGTTTGTA
1 GTTTAGGGTTTAGGTTTAGGGTTTG-A
17554112 GTTTTA-GGTTTAAGGTTTAGGGTTTGA
1 G-TTTAGGGTTT-AGGTTTAGGGTTTGA
* *
17554139 GGTTTAAGATTTAGGTTT
1 -GTTTAGGGTTTAGGTTT
17554157 TAAGATTAAG
Statistics
Matches: 82, Mismatches: 5, Indels: 21
0.76 0.05 0.19
Matches are distributed among these distances:
25 12 0.15
26 22 0.27
27 26 0.32
28 22 0.27
ACGTcount: A:0.19, C:0.00, G:0.33, T:0.48
Consensus pattern (26 bp):
GTTTAGGGTTTAGGTTTAGGGTTTGA
Found at i:17554070 original size:19 final size:19
Alignment explanation
Indices: 17554027--17554100 Score: 61
Period size: 19 Copynumber: 4.1 Consensus size: 19
17554017 TTTTTTAGCA
17554027 TTAGGGTTTAGGG-TT---
1 TTAGGGTTTAGGGTTTGAG
*
17554042 TTAGGATTTAGGGTTTGAG
1 TTAGGGTTTAGGGTTTGAG
*
17554061 TTAGGGTTTATGGTTTGGAG
1 TTAGGGTTTAGGGTTT-GAG
*
17554081 TTTA--GTTTAGGGTTTAAG
1 -TTAGGGTTTAGGGTTTGAG
17554099 TT
1 TT
17554101 TAGAGTTTGT
Statistics
Matches: 48, Mismatches: 5, Indels: 10
0.76 0.08 0.16
Matches are distributed among these distances:
15 12 0.25
16 2 0.04
17 2 0.04
18 2 0.04
19 24 0.50
20 3 0.06
21 3 0.06
ACGTcount: A:0.18, C:0.00, G:0.35, T:0.47
Consensus pattern (19 bp):
TTAGGGTTTAGGGTTTGAG
Found at i:17554102 original size:13 final size:13
Alignment explanation
Indices: 17554032--17554136 Score: 74
Period size: 14 Copynumber: 7.8 Consensus size: 13
17554022 TAGCATTAGG
*
17554032 GTTTAGGGTTTTAG
1 GTTTAGGG-TTTAA
*
17554046 GATTTAGGGTTTGA
1 G-TTTAGGGTTTAA
*
17554060 G-TTAGGGTTTATG
1 GTTTAGGGTTTA-A
17554073 GTTT-GGAGTTT-A
1 GTTTAGG-GTTTAA
17554085 GTTTAGGGTTTAA
1 GTTTAGGGTTTAA
* *
17554098 GTTTAGAGTTTGTA
1 GTTTAGGGTTT-AA
17554112 GTTTTA-GGTTTAA
1 G-TTTAGGGTTTAA
17554125 GGTTTAGGGTTT
1 -GTTTAGGGTTT
17554137 GAGGTTTAAG
Statistics
Matches: 72, Mismatches: 9, Indels: 20
0.71 0.09 0.20
Matches are distributed among these distances:
12 17 0.24
13 21 0.29
14 23 0.32
15 11 0.15
ACGTcount: A:0.18, C:0.00, G:0.33, T:0.49
Consensus pattern (13 bp):
GTTTAGGGTTTAA
Found at i:17554172 original size:7 final size:7
Alignment explanation
Indices: 17554112--17554184 Score: 78
Period size: 7 Copynumber: 10.6 Consensus size: 7
17554102 AGAGTTTGTA
*
17554112 GTTTTAG
1 GTTTAAG
17554119 GTTTAAG
1 GTTTAAG
*
17554126 GTTTAGG
1 GTTTAAG
*
17554133 GTTTGAG
1 GTTTAAG
17554140 GTTTAAG
1 GTTTAAG
*
17554147 ATTT-AG
1 GTTTAAG
17554153 GTTTTAA-
1 G-TTTAAG
*
17554160 GATTAAG
1 GTTTAAG
17554167 GTTTAAG
1 GTTTAAG
17554174 GTTTAAG
1 GTTTAAG
17554181 GTTT
1 GTTT
17554185 TCATGGAATT
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
6 6 0.11
7 47 0.87
8 1 0.02
ACGTcount: A:0.25, C:0.00, G:0.29, T:0.47
Consensus pattern (7 bp):
GTTTAAG
Found at i:17554183 original size:41 final size:42
Alignment explanation
Indices: 17554085--17554184 Score: 125
Period size: 41 Copynumber: 2.4 Consensus size: 42
17554075 TTGGAGTTTA
* * *
17554085 GTTTAGGGTTTAA-GTTTAGAGTTTGTAGTTTTAGGTTTAAG
1 GTTTAGGGTTTAAGGTTTAGAGATTGTAGTTTTAAGATTAAG
*
17554126 GTTTAGGGTTTGAGGTTTA-AGATT-TAGGTTTTAAGATTAAG
1 GTTTAGGGTTTAAGGTTTAGAGATTGTA-GTTTTAAGATTAAG
*
17554167 GTTTAAGGTTTAAGGTTT
1 GTTTAGGGTTTAAGGTTT
17554185 TCATGGAATT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
40 2 0.04
41 44 0.86
42 5 0.10
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.47
Consensus pattern (42 bp):
GTTTAGGGTTTAAGGTTTAGAGATTGTAGTTTTAAGATTAAG
Found at i:17569100 original size:2 final size:2
Alignment explanation
Indices: 17569093--17569117 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17569083 TGATTTTTCT
17569093 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 T
17569118 TCAAGGTCAA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17571865 original size:16 final size:16
Alignment explanation
Indices: 17571844--17571876 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
17571834 TAAATAGATG
*
17571844 TTTAAAAGAAAATTAA
1 TTTAAAAGAAAACTAA
17571860 TTTAAAAGAAAACTAA
1 TTTAAAAGAAAACTAA
17571876 T
1 T
17571877 GTAATTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.30
Consensus pattern (16 bp):
TTTAAAAGAAAACTAA
Found at i:17574685 original size:59 final size:58
Alignment explanation
Indices: 17574508--17574838 Score: 386
Period size: 59 Copynumber: 5.7 Consensus size: 58
17574498 TTTTATGCAG
* * *
17574508 GGAAAATTGATACTTTCAAC-TTTTCCGCAAAAATATTTTTTAGAAATTTTAATTTTAA
1 GGAAAATTGATACTTTCAACTTTTTCC-CAAAAATATTTTTTGGAAACTTTAATTTTGA
* * * * *
17574566 GAAAAATTAATACTTTCAACTTCTGCCC-AATATA-TTTTTGGAAACTTTAATTTTGA
1 GGAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTGGAAACTTTAATTTTGA
* * * ** * *
17574622 GAAAAATTGATACTTTTAAC-TTTTCCTTAAAAACCTTTCTTTGGAAAC-TTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTTCC-CAAAAATATTT-TTTGGAAACTTTAATTTTGA
*
17574680 GGAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTGGAAAACTTTAATTTCGA
1 GGAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTGG-AAACTTTAATTTTGA
* * *
17574739 GGAAAATTGATACTTTCTACTTTTTCCCAAAAATATTTTTTGGAAACTTTTCATTTCGA
1 GGAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTGGAAAC-TTTAATTTTGA
*
17574798 GAAAAATTGATACTTTCAAC-TTTTCCTCAAAAATATTTTTT
1 GGAAAATTGATACTTTCAACTTTTTCC-CAAAAATATTTTTT
17574839 TTGAATTTTA
Statistics
Matches: 233, Mismatches: 30, Indels: 19
0.83 0.11 0.07
Matches are distributed among these distances:
55 4 0.02
56 37 0.16
57 13 0.06
58 69 0.30
59 110 0.47
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.43
Consensus pattern (58 bp):
GGAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTGGAAACTTTAATTTTGA
Found at i:17575918 original size:24 final size:25
Alignment explanation
Indices: 17575875--17575927 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
17575865 TAATGGTACC
* * *
17575875 AAAGGCAGGGATGCTTGTGG-ACCT
1 AAAGGCAGGGATACTCGTGGCACCA
17575899 AAAGGCAGGGATACTCGTGGCACCA
1 AAAGGCAGGGATACTCGTGGCACCA
17575924 AAAG
1 AAAG
17575928 TAAGAGTACT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.32, C:0.19, G:0.34, T:0.15
Consensus pattern (25 bp):
AAAGGCAGGGATACTCGTGGCACCA
Found at i:17576995 original size:97 final size:98
Alignment explanation
Indices: 17576864--17577519 Score: 744
Period size: 97 Copynumber: 6.7 Consensus size: 98
17576854 TTTTTTTACT
* *
17576864 TTTTTTTGTTTTTTTATTTTTTAAATTTTGATCAAAGCTCCTCTAAGTAGAGGCTCAATGACTTT
1 TTTTTTTG--TTTTT-TTTTTTAAATTTTGATCAAAGCTCCTCTAAGCAGAGGCTCAACGACTTT
*
17576929 GAGAAACATAAACAAAGCTCCTCTAAATAGAGGTAA
63 GAGAAACATAAACAAAGCTCCTCTAAACAGAGGTAA
* * **
17576965 -TTTTTTGTTTTTTTTTTTAAATTTTGATCAAAGCTCTTCTAAGCAAAGGCTCAATAACTTTGAG
1 TTTTTTTGTTTTTTTTTTTAAATTTTGATCAAAGCTCCTCTAAGCAGAGGCTCAACGACTTTGAG
17577029 AAACATAAACAAAGCTCCTCTAAACAGAGGTAATA
66 AAACATAAACAAAGCTCCTCTAAACAGAGGT-A-A
* * * *
17577064 TTTTGTTTTTTTATTTTTTTTTAAATTTTGATCAAAACTCCTCTAAGCAGAGGCTTAATGACTTT
1 -TTT-TTTTGTT-TTTTTTTTTAAATTTTGATCAAAGCTCCTCTAAGCAGAGGCTCAACGACTTT
*
17577129 GAGAAACATAAACAAAGCTCCTTTAAACAGAGGTAA
63 GAGAAACATAAACAAAGCTCCTCTAAACAGAGGTAA
* *
17577165 TTTTTTTGTTTTTTTTTTTAAA-TTTGATCAAAACTCCTATAAGCAGAGGCTCAACGACTTTGAG
1 TTTTTTTGTTTTTTTTTTTAAATTTTGATCAAAGCTCCTCTAAGCAGAGGCTCAACGACTTTGAG
* *
17577229 AAACATAAACAAAGCTGCTATAAACAGAGGTAA
66 AAACATAAACAAAGCTCCTCTAAACAGAGGTAA
*
17577262 TTTTTTTATTTTTTTTATTTTTTTATTTTTTTTAATTTTGATCAAAGCTCCTCTAAGCAGAGGCT
1 ---TTTT-TTTGTTTT-TTTTTTTA--------AATTTTGATCAAAGCTCCTCTAAGCAGAGGCT
* * *
17577327 CAACGACTTTGAGAAAAATAAACAAAGCTCATCTAAATAGAGGTAA
53 CAACGACTTTGAGAAACATAAACAAAGCTCCTCTAAACAGAGGTAA
17577373 TTTTTTTGTTTTTTTTTTTTAAA-TTTGATCAAAG------T----AGAGGCTCAACGACTTTGA
1 TTTTTTTG-TTTTTTTTTTTAAATTTTGATCAAAGCTCCTCTAAGCAGAGGCTCAACGACTTTGA
* *
17577427 GAAATATAAACAAAGCTCCTCTAAATAGAGGTAA
65 GAAACATAAACAAAGCTCCTCTAAACAGAGGTAA
* *
17577461 ---------TTTTTTTTTAAAATTTTGATCAAAGCTCCTCTAGGCAGAGGCTCAACGACTTTGAG
1 TTTTTTTGTTTTTTTTTTTAAATTTTGATCAAAGCTCCTCTAAGCAGAGGCTCAACGACTTTGAG
17577517 AAA
66 AAA
17577520 TAAATGGCTC
Statistics
Matches: 493, Mismatches: 30, Indels: 76
0.82 0.05 0.13
Matches are distributed among these distances:
78 12 0.02
79 11 0.02
85 1 0.00
88 51 0.10
89 23 0.05
92 1 0.00
97 148 0.30
98 29 0.06
99 9 0.02
100 14 0.03
101 10 0.02
102 15 0.03
103 80 0.16
107 11 0.02
108 8 0.02
110 2 0.00
111 68 0.14
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.39
Consensus pattern (98 bp):
TTTTTTTGTTTTTTTTTTTAAATTTTGATCAAAGCTCCTCTAAGCAGAGGCTCAACGACTTTGAG
AAACATAAACAAAGCTCCTCTAAACAGAGGTAA
Found at i:17577217 original size:200 final size:201
Alignment explanation
Indices: 17576867--17577467 Score: 791
Period size: 200 Copynumber: 3.0 Consensus size: 201
17576857 TTTTACTTTT
*
17576867 TTTTGTTTTTTTA---TTTTTTAAATTTTGATCAAAGCTCCTCTAAGTAGAGGCTCAATGACTTT
1 TTTTGTTTTTTTATTTTTTTTTAAATTTTGATCAAAGCTCCTCTAAGCAGAGGCTCAATGACTTT
17576929 GAGAAACATAAACAAAGCTCCTCTAAATAGAGGTAA-TTTTTTGTTTTTTTTTTTAAATTTTGAT
66 GAGAAACATAAACAAAGCTCCTCTAAATAGAGGTAATTTTTTTGTTTTTTTTTTTAAA-TTTGAT
* * * * *
17576993 CAAAGCTCTTCTAAGCAAAGGCTCAATAACTTTGAGAAACATAAACAAAGCTCCTCTAAACAGAG
130 CAAAACTCCTATAAGCAAAGGCTCAACAACTTTGAGAAACATAAACAAAGCTCCTATAAACAGAG
17577058 GTAA-TA
195 GTAATTA
* *
17577064 TTTTGTTTTTTTATTTTTTTTTAAATTTTGATCAAAACTCCTCTAAGCAGAGGCTTAATGACTTT
1 TTTTGTTTTTTTATTTTTTTTTAAATTTTGATCAAAGCTCCTCTAAGCAGAGGCTCAATGACTTT
* *
17577129 GAGAAACATAAACAAAGCTCCTTTAAACAGAGGTAATTTTTTTGTTTTTTTTTTTAAATTTGATC
66 GAGAAACATAAACAAAGCTCCTCTAAATAGAGGTAATTTTTTTGTTTTTTTTTTTAAATTTGATC
* * *
17577194 AAAACTCCTATAAGCAGAGGCTCAACGACTTTGAGAAACATAAACAAAGCTGCTATAAACAGAGG
131 AAAACTCCTATAAGCAAAGGCTCAACAACTTTGAGAAACATAAACAAAGCTCCTATAAACAGAGG
17577259 TAATTTTTTTA
196 TAA-----TTA
* * * *
17577270 TTTTTTTTATTTTTTTATTTTTTTTAATTTTGATCAAAGCTCCTCTAAGCAGAGGCTCAACGACT
1 TTTTGTTT-TTTTATT-TTTTTTTAAATTTTGATCAAAGCTCCTCTAAGCAGAGGCTCAATGACT
* *
17577335 TTGAGAAAAATAAACAAAGCTCATCTAAATAGAGGTAATTTTTTTGTTTTTTTTTTTTAAATTTG
64 TTGAGAAACATAAACAAAGCTCCTCTAAATAGAGGTAATTTTTTTG-TTTTTTTTTTTAAATTTG
* * * * *
17577400 ATC-AAA-----GT-AG---AGGCTCAACGACTTTGAGAAATATAAACAAAGCTCCTCTAAATAG
128 ATCAAAACTCCTATAAGCAAAGGCTCAACAACTTTGAGAAACATAAACAAAGCTCCTATAAACAG
*
17577455 AGGTAATTT
193 AGGTAATTA
17577464 TTTT
1 TTTT
17577468 TTAAAATTTT
Statistics
Matches: 362, Mismatches: 29, Indels: 29
0.86 0.07 0.07
Matches are distributed among these distances:
194 6 0.02
197 13 0.04
199 47 0.13
200 147 0.41
201 21 0.06
202 2 0.01
203 1 0.00
206 9 0.02
207 6 0.02
208 89 0.25
209 21 0.06
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.40
Consensus pattern (201 bp):
TTTTGTTTTTTTATTTTTTTTTAAATTTTGATCAAAGCTCCTCTAAGCAGAGGCTCAATGACTTT
GAGAAACATAAACAAAGCTCCTCTAAATAGAGGTAATTTTTTTGTTTTTTTTTTTAAATTTGATC
AAAACTCCTATAAGCAAAGGCTCAACAACTTTGAGAAACATAAACAAAGCTCCTATAAACAGAGG
TAATTA
Found at i:17577276 original size:9 final size:9
Alignment explanation
Indices: 17577262--17577300 Score: 62
Period size: 9 Copynumber: 4.3 Consensus size: 9
17577252 ACAGAGGTAA
17577262 TTTTTTTAT
1 TTTTTTTAT
17577271 TTTTTTTA-
1 TTTTTTTAT
17577279 TTTTTTTAT
1 TTTTTTTAT
17577288 TTTTTTTAAT
1 TTTTTTT-AT
17577298 TTT
1 TTT
17577301 GATCAAAGCT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.29
9 15 0.54
10 5 0.18
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:17577283 original size:17 final size:18
Alignment explanation
Indices: 17577259--17577300 Score: 77
Period size: 17 Copynumber: 2.4 Consensus size: 18
17577249 TAAACAGAGG
17577259 TAATTTTTTTATTTTTTT
1 TAATTTTTTTATTTTTTT
17577277 T-ATTTTTTTATTTTTTT
1 TAATTTTTTTATTTTTTT
17577294 TAATTTT
1 TAATTTT
17577301 GATCAAAGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 17 0.74
18 6 0.26
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (18 bp):
TAATTTTTTTATTTTTTT
Found at i:17577300 original size:8 final size:8
Alignment explanation
Indices: 17577261--17577293 Score: 57
Period size: 8 Copynumber: 4.0 Consensus size: 8
17577251 AACAGAGGTA
17577261 ATTTTTTT
1 ATTTTTTT
17577269 ATTTTTTTT
1 A-TTTTTTT
17577278 ATTTTTTT
1 ATTTTTTT
17577286 ATTTTTTT
1 ATTTTTTT
17577294 TAATTTTGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 16 0.67
9 8 0.33
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (8 bp):
ATTTTTTT
Found at i:17577331 original size:111 final size:111
Alignment explanation
Indices: 17577165--17577392 Score: 352
Period size: 111 Copynumber: 2.1 Consensus size: 111
17577155 ACAGAGGTAA
*
17577165 TTTTTTTGTTTTTTTTTTTAAATTTGATCAAAACTCCTATAAGCAGAGGCTCAACGACTTTGAGA
1 TTTTTTTGTTATTTTTTTTAAATTTGATCAAAACTCCTATAAGCAGAGGCTCAACGACTTTGAGA
*
17577230 AACATAAACAAAGCTGC-TATAAACAGAGGTAATTTTTTTATTTTTT
66 AAAATAAACAAAGCT-CATATAAACAGAGGTAATTTTTTTATTTTTT
* * *
17577276 TTATTTTT-TTATTTTTTTTAATTTTGATCAAAGCTCCTCTAAGCAGAGGCTCAACGACTTTGAG
1 TT-TTTTTGTTATTTTTTTTAAATTTGATCAAAACTCCTATAAGCAGAGGCTCAACGACTTTGAG
* * *
17577340 AAAAATAAACAAAGCTCATCTAAATAGAGGTAATTTTTTTGTTTTTT
65 AAAAATAAACAAAGCTCATATAAACAGAGGTAATTTTTTTATTTTTT
17577387 TTTTTT
1 TTTTTT
17577393 AAATTTGATC
Statistics
Matches: 107, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
110 5 0.05
111 97 0.91
112 5 0.05
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.44
Consensus pattern (111 bp):
TTTTTTTGTTATTTTTTTTAAATTTGATCAAAACTCCTATAAGCAGAGGCTCAACGACTTTGAGA
AAAATAAACAAAGCTCATATAAACAGAGGTAATTTTTTTATTTTTT
Found at i:17577541 original size:41 final size:41
Alignment explanation
Indices: 17577485--17577734 Score: 306
Period size: 41 Copynumber: 6.1 Consensus size: 41
17577475 TTTGATCAAA
** * *
17577485 GCTCCTCTAGGCAGAGGCTCAACGACTTTGAGAAATAAATG
1 GCTCCTCTAATCAGAGGCTCAATGACTTTGAAAAATAAATG
*
17577526 GCTCCTCTAATCAGAGGCTTAATGACTTTGAAAAATAAATG
1 GCTCCTCTAATCAGAGGCTCAATGACTTTGAAAAATAAATG
* * * *
17577567 GCTCCTTTAATCAGAAGCTCAACGACTTTAAAAAATAAATG
1 GCTCCTCTAATCAGAGGCTCAATGACTTTGAAAAATAAATG
* * *
17577608 GCTCATCTAATCAAAGGCTCAATGACTTTGAAAAATAAACG
1 GCTCCTCTAATCAGAGGCTCAATGACTTTGAAAAATAAATG
* *
17577649 GCTCCTCTAATCAGAGGCTCAATGACTTTGAGAAATAAATT
1 GCTCCTCTAATCAGAGGCTCAATGACTTTGAAAAATAAATG
* * * *
17577690 TCTCCTCTAAACAAAGG--CAATGAAACTTTGAAAAATAAATT
1 GCTCCTCTAATCAGAGGCTCAATG--ACTTTGAAAAATAAATG
17577731 GCTC
1 GCTC
17577735 ATTGACAATC
Statistics
Matches: 180, Mismatches: 27, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
39 5 0.03
41 175 0.97
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (41 bp):
GCTCCTCTAATCAGAGGCTCAATGACTTTGAAAAATAAATG
Found at i:17578095 original size:42 final size:42
Alignment explanation
Indices: 17578026--17578106 Score: 119
Period size: 42 Copynumber: 1.9 Consensus size: 42
17578016 ATTTGGCAAA
* *
17578026 TTGGAATTCATATCCAAAAATCTAAAGCTTTTCATTTGAATT
1 TTGGAATTCACATCCAAAAATCTAAAGCTTCTCATTTGAATT
*
17578068 TTGGAGATTCACATCCAAAATTC-AAAGCTTCTCATTTGA
1 TTGGA-ATTCACATCCAAAAATCTAAAGCTTCTCATTTGA
17578107 GTTCAAAGAC
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
42 20 0.57
43 15 0.43
ACGTcount: A:0.35, C:0.17, G:0.11, T:0.37
Consensus pattern (42 bp):
TTGGAATTCACATCCAAAAATCTAAAGCTTCTCATTTGAATT
Found at i:17578340 original size:22 final size:21
Alignment explanation
Indices: 17578291--17578331 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
17578281 GGTTTCACTC
17578291 CTCAAAGATTCTCATTTTGAAA
1 CTCAAAGATTCTCA-TTTGAAA
17578313 CTCAAAGATTCTCATTTGA
1 CTCAAAGATTCTCATTTGA
17578332 GTTTTCAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.34, C:0.20, G:0.10, T:0.37
Consensus pattern (21 bp):
CTCAAAGATTCTCATTTGAAA
Found at i:17578854 original size:63 final size:63
Alignment explanation
Indices: 17578750--17578878 Score: 204
Period size: 63 Copynumber: 2.0 Consensus size: 63
17578740 ACATGCCAGG
* * * *
17578750 CTTATCAGCACTAACCATTTCAAAATAAATTTCATCTTCTGTCACTTGGTCATCGTTCATAAA
1 CTTATCAACACTAACCATTTCAAAACAAATTTCATCATCTGTCACTTGGTCATCATTCATAAA
* *
17578813 CTTATCAATACTAGCCATTTCAAAACAAATTTCATCATCTGTCACTTGGTCATCATTCATAAA
1 CTTATCAACACTAACCATTTCAAAACAAATTTCATCATCTGTCACTTGGTCATCATTCATAAA
17578876 CTT
1 CTT
17578879 CTCAGCACCA
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
63 60 1.00
ACGTcount: A:0.33, C:0.24, G:0.07, T:0.36
Consensus pattern (63 bp):
CTTATCAACACTAACCATTTCAAAACAAATTTCATCATCTGTCACTTGGTCATCATTCATAAA
Found at i:17579624 original size:10 final size:8
Alignment explanation
Indices: 17579568--17579597 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
17579558 AAATTAAATC
17579568 TTTTTTAT
1 TTTTTTAT
17579576 TTTTTTAT
1 TTTTTTAT
17579584 TTTTTTAT
1 TTTTTTAT
17579592 TTTTTT
1 TTTTTT
17579598 TCATTTTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTAT
Found at i:17579631 original size:14 final size:13
Alignment explanation
Indices: 17579598--17579642 Score: 76
Period size: 13 Copynumber: 3.6 Consensus size: 13
17579588 TTATTTTTTT
17579598 TCATTTTTTGTCA
1 TCATTTTTTGTCA
17579611 TCATTTTTTGTCA
1 TCATTTTTTGTCA
17579624 TCATTTTTT-TC-
1 TCATTTTTTGTCA
17579635 TCATTTTT
1 TCATTTTT
17579643 CATCCATTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
11 8 0.25
12 2 0.06
13 22 0.69
ACGTcount: A:0.13, C:0.16, G:0.04, T:0.67
Consensus pattern (13 bp):
TCATTTTTTGTCA
Found at i:17584545 original size:56 final size:56
Alignment explanation
Indices: 17584405--17584545 Score: 223
Period size: 56 Copynumber: 2.5 Consensus size: 56
17584395 TTGTACAGGA
17584405 AAAATTGATACTTTCAAC-TTTTCCCAAAATATTTTTGAAAACTTTAATTTCAAGG
1 AAAATTGATACTTTCAACTTTTTCCCAAAATATTTTTGAAAACTTTAATTTCAAGG
* *
17584460 AAAATTGATACTTTCAACTTCTCCCCAAAATATTTTTGAAAACTTTAATTTCGAA-G
1 AAAATTGATACTTTCAACTTTTTCCCAAAATATTTTTGAAAACTTTAATTTC-AAGG
* *
17584516 AAAATTGATAATTTCAACTTTTTCTCAAAA
1 AAAATTGATACTTTCAACTTTTTCCCAAAA
17584546 AAACCTTTTT
Statistics
Matches: 78, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
55 18 0.23
56 58 0.74
57 2 0.03
ACGTcount: A:0.39, C:0.16, G:0.06, T:0.39
Consensus pattern (56 bp):
AAAATTGATACTTTCAACTTTTTCCCAAAATATTTTTGAAAACTTTAATTTCAAGG
Found at i:17584588 original size:98 final size:97
Alignment explanation
Indices: 17584481--17584670 Score: 287
Period size: 100 Copynumber: 1.9 Consensus size: 97
17584471 TTTCAACTTC
*
17584481 TCCCCAAAATA-TTTTT-GAAAACTTTAATTTCGAAGAAAATTGATAATTTCAACTTTTTCTCAA
1 TCCCCAAAATATTTTTTGGAAAACTTTAATTTCGAAGAAAATTGATAATTTCAACTTTTCCTC--
17584544 AAAAACC-TTTTTTGAAAATTTATTTTTAAGCTTT
64 -AAAACCATTTTTTGAAAATTTATTTTTAAGCTTT
** *
17584578 TCCCCAAAAATATTTTTTGGAAATTTTTAATTTCGAAGAAAATTGATACTTTCAACTTTTCCTCA
1 TCCCC-AAAATATTTTTTGGAAAACTTTAATTTCGAAGAAAATTGATAATTTCAACTTTTCCTCA
17584643 AAACCATTTTTTGAAAATTTATTTTTAA
65 AAACCATTTTTTGAAAATTTATTTTTAA
17584671 AAAAAATTGA
Statistics
Matches: 85, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
97 11 0.13
98 28 0.33
99 5 0.06
100 41 0.48
ACGTcount: A:0.36, C:0.14, G:0.06, T:0.44
Consensus pattern (97 bp):
TCCCCAAAATATTTTTTGGAAAACTTTAATTTCGAAGAAAATTGATAATTTCAACTTTTCCTCAA
AACCATTTTTTGAAAATTTATTTTTAAGCTTT
Found at i:17584621 original size:156 final size:151
Alignment explanation
Indices: 17584422--17584716 Score: 389
Period size: 156 Copynumber: 1.9 Consensus size: 151
17584412 ATACTTTCAA
17584422 CTTTTCCCAAAATATTTTTGAAAACTTTAATTTCAAGGAAAATTGATACTTTCAACTTCTCCCCA
1 CTTTTCCCAAAATATTTTTGAAAACTTTAATTTCAAGGAAAATTGATACTTTCAACTTCTCCCCA
* * * *
17584487 AAA-TA-TTTTTGAAAACTTTAATTTCGAAGAAAATTGATAATTTCAACTTTTTCTCAAAAAAAC
66 AAACCATTTTTTGAAAA-TTTAATTTCAAAAAAAATTGATAATTTCAACTTTTTCCCAAAAAAA-
17584550 CTTTTTTGAAAATTTATTTTTAAG
129 -TTTTTTGAAAATTTATTTTTAAG
** *
17584574 CTTTTCCCCAAAAATATTTTTTGGAAATTTTTAATTTCGAA-GAAAATTGATACTTTCAACTTTT
1 CTTTT-CCC-AAAATA-TTTTT-GAAAACTTTAATTTC-AAGGAAAATTGATACTTTCAACTTCT
* * * *
17584638 CCTCAAAACCATTTTTTGAAAATTTATTTTTAAAAAAAATTGATATTTTCAACTTTTTCCCAAAA
61 CCCCAAAACCATTTTTTGAAAATTTAATTTCAAAAAAAATTGATAATTTCAACTTTTTCCCAAAA
*
17584703 ATATTTTTTGAAAA
126 AAATTTTTTGAAAA
17584717 CTTTTAATTT
Statistics
Matches: 124, Mismatches: 12, Indels: 11
0.84 0.08 0.07
Matches are distributed among these distances:
152 5 0.04
153 3 0.02
154 6 0.05
155 16 0.13
156 42 0.34
157 42 0.34
158 10 0.08
ACGTcount: A:0.37, C:0.14, G:0.06, T:0.43
Consensus pattern (151 bp):
CTTTTCCCAAAATATTTTTGAAAACTTTAATTTCAAGGAAAATTGATACTTTCAACTTCTCCCCA
AAACCATTTTTTGAAAATTTAATTTCAAAAAAAATTGATAATTTCAACTTTTTCCCAAAAAAATT
TTTTGAAAATTTATTTTTAAG
Found at i:17584639 original size:59 final size:57
Alignment explanation
Indices: 17584574--17584827 Score: 302
Period size: 57 Copynumber: 4.4 Consensus size: 57
17584564 TATTTTTAAG
* *
17584574 CTTTTCCCCAAAAATATTTTTTGGAAATTT-TTAATTTCGAAGAAAATTGATACTTTCAA
1 CTTTTCCTCAAAAATATTTTTTGAAAATTTATT--TTT-GAAGAAAATTGATACTTTCAA
** * * *
17584633 CTTTTCCTCAAAACCATTTTTTGAAAATTTATTTTTAAAAAAAATTGATATTTTCAA
1 CTTTTCCTCAAAAATATTTTTTGAAAATTTATTTTTGAAGAAAATTGATACTTTCAA
* *
17584690 CTTTTTCC-CAAAAATATTTTTTGAAAACTTTTAATTTCG-AGAAAAATTGATACTTTCAA
1 C-TTTTCCTCAAAAATATTTTTTGAAAA--TTTATTTTTGAAG-AAAATTGATACTTTCAA
*
17584749 CTTTTCCTCAAAACCT-TTTTTTGAAAATTTATTTTT-AAGGAAAATTGATACTTTCAA
1 CTTTTCCTCAAAA-ATATTTTTTGAAAATTTATTTTTGAA-GAAAATTGATACTTTCAA
17584806 CTTTTCCTCAAAAATATTTTTT
1 CTTTTCCTCAAAAATATTTTTT
17584828 TTGAATTTTA
Statistics
Matches: 167, Mismatches: 18, Indels: 22
0.81 0.09 0.11
Matches are distributed among these distances:
56 1 0.01
57 80 0.48
58 17 0.10
59 66 0.40
60 3 0.02
ACGTcount: A:0.35, C:0.14, G:0.06, T:0.45
Consensus pattern (57 bp):
CTTTTCCTCAAAAATATTTTTTGAAAATTTATTTTTGAAGAAAATTGATACTTTCAA
Found at i:17584737 original size:116 final size:116
Alignment explanation
Indices: 17584564--17584827 Score: 415
Period size: 116 Copynumber: 2.3 Consensus size: 116
17584554 TTTGAAAATT
* * * *
17584564 TATTTTTAAGCTTTTCCCCAAAAATATTTTTTGGAAATTTTTAATTTCGAAGAAAATTGATACTT
1 TATTTTCAA-CTTTTTCCCAAAAATATTTTTTGAAAACTTTTAATTTCGAAGAAAATTGATACTT
17584629 TCAACTTTTCCTCAAAACCATTTTTTGAAAATTTATTTTTAAAAAAAATTGA
65 TCAACTTTTCCTCAAAACCATTTTTTGAAAATTTATTTTTAAAAAAAATTGA
17584681 TATTTTCAACTTTTTCCCAAAAATATTTTTTGAAAACTTTTAATTTCG-AGAAAAATTGATACTT
1 TATTTTCAACTTTTTCCCAAAAATATTTTTTGAAAACTTTTAATTTCGAAG-AAAATTGATACTT
* **
17584745 TCAACTTTTCCTCAAAACCTTTTTTTGAAAATTTATTTTTAAGGAAAATTGA
65 TCAACTTTTCCTCAAAACCATTTTTTGAAAATTTATTTTTAAAAAAAATTGA
*
17584797 TACTTTCAAC-TTTTCCTCAAAAATATTTTTT
1 TATTTTCAACTTTTTCC-CAAAAATATTTTTT
17584828 TTGAATTTTA
Statistics
Matches: 137, Mismatches: 8, Indels: 5
0.91 0.05 0.03
Matches are distributed among these distances:
115 8 0.06
116 121 0.88
117 8 0.06
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.45
Consensus pattern (116 bp):
TATTTTCAACTTTTTCCCAAAAATATTTTTTGAAAACTTTTAATTTCGAAGAAAATTGATACTTT
CAACTTTTCCTCAAAACCATTTTTTGAAAATTTATTTTTAAAAAAAATTGA
Found at i:17584878 original size:6 final size:6
Alignment explanation
Indices: 17584845--17584903 Score: 77
Period size: 6 Copynumber: 9.8 Consensus size: 6
17584835 TTATTTAAAG
*
17584845 AAAAT- AAAATA ATAAA-A TAAAATG AAAATA AAAATA AAAATA AAAATA
1 AAAATA AAAATA A-AAATA -AAAATA AAAATA AAAATA AAAATA AAAATA
17584893 AAAATA AAAAT
1 AAAATA AAAAT
17584904 GAAATTTAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
5 5 0.10
6 39 0.81
7 4 0.08
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.19
Consensus pattern (6 bp):
AAAATA
Found at i:17584884 original size:18 final size:18
Alignment explanation
Indices: 17584845--17584907 Score: 85
Period size: 18 Copynumber: 3.5 Consensus size: 18
17584835 TTATTTAAAG
17584845 AAAAT-AAAATAATAAA-A
1 AAAATGAAAATAA-AAATA
17584862 TAAAATGAAAATAAAAATA
1 -AAAATGAAAATAAAAATA
*
17584881 AAAATAAAAATAAAAATA
1 AAAATGAAAATAAAAATA
17584899 AAAATGAAA
1 AAAATGAAA
17584908 TTTAAACCAG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
18 33 0.80
19 8 0.20
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.17
Consensus pattern (18 bp):
AAAATGAAAATAAAAATA
Found at i:17587911 original size:22 final size:22
Alignment explanation
Indices: 17587886--17587943 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
17587876 ATTTAAATAC
*
17587886 ATTTATATATAAAAT-AATTTTT
1 ATTTA-ATAAAAAATAAATTTTT
17587908 ATTTAATAAAAAATAAATTTTT
1 ATTTAATAAAAAATAAATTTTT
*
17587930 ATTTAA-AAATAATA
1 ATTTAATAAAAAATA
17587944 CAAATATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 15 0.45
22 18 0.55
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATTTAATAAAAAATAAATTTTT
Found at i:17589197 original size:16 final size:18
Alignment explanation
Indices: 17589159--17589201 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
17589149 ACTTTTTCCC
*
17589159 TTTTTTATATATTTAATA
1 TTTTTTAAATATTTAATA
*
17589177 ATTTTTAAAT-TTTAAT-
1 TTTTTTAAATATTTAATA
17589193 TTTTTTAAA
1 TTTTTTAAA
17589202 AAACCACTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 8 0.36
17 6 0.27
18 8 0.36
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTTTAAATATTTAATA
Found at i:17593319 original size:17 final size:17
Alignment explanation
Indices: 17593297--17593335 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
17593287 AAAAAATATT
17593297 TTTAACTTAATTTTTGG
1 TTTAACTTAATTTTTGG
* *
17593314 TTTAACTTATTTTTTTG
1 TTTAACTTAATTTTTGG
17593331 TTTAA
1 TTTAA
17593336 TTTTACTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.23, C:0.05, G:0.08, T:0.64
Consensus pattern (17 bp):
TTTAACTTAATTTTTGG
Found at i:17594406 original size:25 final size:26
Alignment explanation
Indices: 17594378--17594435 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
17594368 TTTTTCACTC
17594378 TATTTTTTG-T-TTTGACTTTTTATTT
1 TATTTTTTGCTATTTGA-TTTTTATTT
*
17594403 TA-TTTTTGCTATTTTATTTTTATTT
1 TATTTTTTGCTATTTGATTTTTATTT
*
17594428 TATGTTTT
1 TATTTTTT
17594436 ATTTATTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 6 0.21
25 14 0.50
26 8 0.29
ACGTcount: A:0.14, C:0.03, G:0.07, T:0.76
Consensus pattern (26 bp):
TATTTTTTGCTATTTGATTTTTATTT
Found at i:17594424 original size:20 final size:20
Alignment explanation
Indices: 17594378--17594428 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
17594368 TTTTTCACTC
17594378 TATTTTT-TGTTTTGACTTTT
1 TATTTTTAT-TTTTGACTTTT
17594398 TA-TTTTATTTTTG-CTATTT
1 TATTTTTATTTTTGACT-TTT
17594417 TATTTTTATTTT
1 TATTTTTATTTT
17594429 ATGTTTTATT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 2 0.07
19 14 0.50
20 12 0.43
ACGTcount: A:0.14, C:0.04, G:0.06, T:0.76
Consensus pattern (20 bp):
TATTTTTATTTTTGACTTTT
Found at i:17594441 original size:11 final size:11
Alignment explanation
Indices: 17594394--17594439 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 11
17594384 TTGTTTTGAC
17594394 TTTTTATTTTA
1 TTTTTATTTTA
17594405 TTTTTGCTATTTTA
1 -TTTT--TATTTTA
17594419 TTTTTATTTTA
1 TTTTTATTTTA
17594430 TGTTTTATTT
1 T-TTTTATTT
17594440 ATTCATTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
11 8 0.26
12 12 0.39
13 4 0.13
14 7 0.23
ACGTcount: A:0.15, C:0.02, G:0.04, T:0.78
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:17594457 original size:31 final size:32
Alignment explanation
Indices: 17594400--17594461 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
17594390 TGACTTTTTA
17594400 TTTTATTTTTGCTATTTTATTTTTATTTTATG
1 TTTTATTTTTGCTATTTTATTTTTATTTTATG
17594432 TTTTATTTATT-C-ATTTT-TTTCTTATTTTAT
1 TTTTATTT-TTGCTATTTTATTT-TTATTTTAT
17594462 TCAATATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
30 3 0.11
31 14 0.50
32 9 0.32
33 2 0.07
ACGTcount: A:0.16, C:0.05, G:0.03, T:0.76
Consensus pattern (32 bp):
TTTTATTTTTGCTATTTTATTTTTATTTTATG
Found at i:17600156 original size:35 final size:35
Alignment explanation
Indices: 17600117--17600184 Score: 109
Period size: 35 Copynumber: 1.9 Consensus size: 35
17600107 TGCGAATTTG
*
17600117 AAATTCTTGAGAAATTGAATTTCTTACGAATCTAA
1 AAATTCTTGAGAAACTGAATTTCTTACGAATCTAA
* *
17600152 AAATTCTTGTGAAACTGAATTTCTTTCGAATCT
1 AAATTCTTGAGAAACTGAATTTCTTACGAATCT
17600185 TCCACTCTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (35 bp):
AAATTCTTGAGAAACTGAATTTCTTACGAATCTAA
Found at i:17600160 original size:52 final size:53
Alignment explanation
Indices: 17600051--17600160 Score: 125
Period size: 52 Copynumber: 2.1 Consensus size: 53
17600041 AATCTTTGAG
* ** * * *
17600051 TTCTTGCAAACTTAAAATTCTTGTGAAATTGAATTTCTTGTGAGTCTTTACAA
1 TTCTTGCAAACTTAAAATTCTTGAGAAATTGAATTTCTTACGAATCTTAAAAA
* * *
17600104 -TCTTGCGAATTTGAAATTCTTGAGAAATTGAATTTCTTACGAATC-TAAAAA
1 TTCTTGCAAACTTAAAATTCTTGAGAAATTGAATTTCTTACGAATCTTAAAAA
17600155 TTCTTG
1 TTCTTG
17600161 TGAAACTGAA
Statistics
Matches: 47, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
51 4 0.09
52 43 0.91
ACGTcount: A:0.32, C:0.13, G:0.14, T:0.42
Consensus pattern (53 bp):
TTCTTGCAAACTTAAAATTCTTGAGAAATTGAATTTCTTACGAATCTTAAAAA
Found at i:17600959 original size:86 final size:86
Alignment explanation
Indices: 17600795--17601000 Score: 236
Period size: 86 Copynumber: 2.4 Consensus size: 86
17600785 ATCCCAATAA
* * * * * *
17600795 CTCATTTTAAAGTTGTTTAGCCTTTATTCAAAGGAGCCCATTTCTCATTTTAAAGTTGTTTAGGC
1 CTCAATTTAAAGTTGTTTAGCCTTTGTTTAAAAGAGCCCATTTCTCATTTTAAAGTTATTTAGCC
* * *
17600860 TCTGTTTAGAGAAGTCCATTT
66 TCTATTTAAAGAAGCCCATTT
* * * *
17600881 CTCAGTTTAAAGTTGTTTAGTCTTTGTTTAAAAGAGCCTATTTTTC-TGTTTAAAGTTATTTAGC
1 CTCAATTTAAAGTTGTTTAGCCTTTGTTTAAAAGAGCCCATTTCTCAT-TTTAAAGTTATTTAGC
17600945 CTCTATTTAAAGAAGCCCATTT
65 CTCTATTTAAAGAAGCCCATTT
* * * *
17600967 TTTAATTTAAATTTGTTT-GCCTCTGTTTAAAAGA
1 CTCAATTTAAAGTTGTTTAGCCTTTGTTTAAAAGA
17601001 TCCTTAAGTT
Statistics
Matches: 101, Mismatches: 18, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
85 15 0.15
86 86 0.85
ACGTcount: A:0.26, C:0.14, G:0.15, T:0.45
Consensus pattern (86 bp):
CTCAATTTAAAGTTGTTTAGCCTTTGTTTAAAAGAGCCCATTTCTCATTTTAAAGTTATTTAGCC
TCTATTTAAAGAAGCCCATTT
Found at i:17601000 original size:43 final size:43
Alignment explanation
Indices: 17600795--17600997 Score: 203
Period size: 43 Copynumber: 4.7 Consensus size: 43
17600785 ATCCCAATAA
* * * * *
17600795 CTCATTTTAAAGTTGTTTAGCCTTTATTCAAAGGAGCCCATTT
1 CTCAGTTTAAAGTTGTTTAGCCTCTGTTTAAAGAAGCCCATTT
* * * *
17600838 CTCATTTTAAAGTTGTTTAGGCTCTGTTTAGAGAAGTCCATTT
1 CTCAGTTTAAAGTTGTTTAGCCTCTGTTTAAAGAAGCCCATTT
* * *
17600881 CTCAGTTTAAAGTTGTTTAGTCTTTGTTTAAA-AGAGCCTATTT
1 CTCAGTTTAAAGTTGTTTAGCCTCTGTTTAAAGA-AGCCCATTT
* * * *
17600924 TTCTGTTTAAAGTTATTTAGCCTCTATTTAAAGAAGCCCATTT
1 CTCAGTTTAAAGTTGTTTAGCCTCTGTTTAAAGAAGCCCATTT
* * * *
17600967 TTTAATTTAAATTTGTTT-GCCTCTGTTTAAA
1 CTCAGTTTAAAGTTGTTTAGCCTCTGTTTAAA
17600998 AGATCCTTAA
Statistics
Matches: 132, Mismatches: 26, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
42 13 0.10
43 118 0.89
44 1 0.01
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.46
Consensus pattern (43 bp):
CTCAGTTTAAAGTTGTTTAGCCTCTGTTTAAAGAAGCCCATTT
Found at i:17602288 original size:20 final size:20
Alignment explanation
Indices: 17602260--17602299 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
17602250 CTATTTTCTG
17602260 TTTTGATTTTATTTTTATTT
1 TTTTGATTTTATTTTTATTT
*
17602280 TTTTTATTTTATTTTTATTT
1 TTTTGATTTTATTTTTATTT
17602300 AATGTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (20 bp):
TTTTGATTTTATTTTTATTT
Found at i:17602307 original size:12 final size:11
Alignment explanation
Indices: 17602260--17602312 Score: 56
Period size: 11 Copynumber: 4.9 Consensus size: 11
17602250 CTATTTTCTG
* *
17602260 TTTTGATTTTA
1 TTTTTATTTAA
17602271 TTTTTATTT--
1 TTTTTATTTAA
*
17602280 TTTTTATTTTA
1 TTTTTATTTAA
17602291 TTTTTATTTAA
1 TTTTTATTTAA
17602302 TGTTTTATTTA
1 T-TTTTATTTA
17602313 TTCCTTTCTT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
9 9 0.24
11 19 0.51
12 9 0.24
ACGTcount: A:0.19, C:0.00, G:0.04, T:0.77
Consensus pattern (11 bp):
TTTTTATTTAA
Found at i:17604101 original size:16 final size:16
Alignment explanation
Indices: 17604062--17604103 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
17604052 TTATTTAATT
*
17604062 TTATATTTA-AATATA
1 TTATATTAATAATATA
17604077 TTATATTAATAATATTA
1 TTATATTAATAATA-TA
17604094 TTAT-TTAATA
1 TTATATTAATA
17604104 TTTTAATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 8 0.33
16 10 0.42
17 6 0.25
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTATATTAATAATATA
Found at i:17604103 original size:29 final size:25
Alignment explanation
Indices: 17604036--17604113 Score: 70
Period size: 29 Copynumber: 2.9 Consensus size: 25
17604026 TATATATATA
17604036 ATTATATTTTAAT-TATTTATTTAAT
1 ATTATA-TTTAATATATTTATTTAAT
*
17604061 TTTATATTTAAATATATTATATTAATAAT
1 ATTATATTT-AATATATT-TATT--TAAT
17604090 ATTATTATTTAATAT-TTTAATTTA
1 ATTA-TATTTAATATATTT-ATTTA
17604114 GTAAAAATAT
Statistics
Matches: 44, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
24 3 0.07
25 8 0.18
26 6 0.14
27 5 0.11
28 5 0.11
29 12 0.27
30 5 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
ATTATATTTAATATATTTATTTAAT
Found at i:17604742 original size:18 final size:18
Alignment explanation
Indices: 17604721--17604764 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
17604711 TAGATAAAAG
17604721 TTTTTAATATTTTGTTTA
1 TTTTTAATATTTTGTTTA
17604739 TTTTTAATATTTTGTTTA
1 TTTTTAATATTTTGTTTA
17604757 TTTTTAAT
1 TTTTTAAT
17604765 TAATAAAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.73
Consensus pattern (18 bp):
TTTTTAATATTTTGTTTA
Found at i:17604899 original size:27 final size:27
Alignment explanation
Indices: 17604846--17604904 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
17604836 TGCCCAATGA
* * *
17604846 TTTTTCAATTTTTTTTGTTTTTGTTTT
1 TTTTTCAATTTTTCTTGTTTCTCTTTT
17604873 TTTTTCAATTTTTCCTT-TTTCTCTTTT
1 TTTTTCAATTTTT-CTTGTTTCTCTTTT
17604900 TTTTT
1 TTTTT
17604905 TGTTTTTTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 26 0.93
28 2 0.07
ACGTcount: A:0.07, C:0.10, G:0.03, T:0.80
Consensus pattern (27 bp):
TTTTTCAATTTTTCTTGTTTCTCTTTT
Found at i:17605040 original size:16 final size:17
Alignment explanation
Indices: 17605019--17605052 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
17605009 TATTTTTGAA
*
17605019 AAATTTT-TAATTAAAT
1 AAATTTTGTAATAAAAT
17605035 AAATTTTGTAATAAAAT
1 AAATTTTGTAATAAAAT
17605052 A
1 A
17605053 TTTCAATTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
AAATTTTGTAATAAAAT
Found at i:17606494 original size:41 final size:41
Alignment explanation
Indices: 17606437--17606519 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
17606427 TCCTTTCATA
17606437 CAATCTCCTATTCTCTCCTTCAGATAAAGTCAAATAAAATT
1 CAATCTCCTATTCTCTCCTTCAGATAAAGTCAAATAAAATT
17606478 CAATCTCCTATTCTCTCCTTCAGATAAAGTCAAATAAAATT
1 CAATCTCCTATTCTCTCCTTCAGATAAAGTCAAATAAAATT
17606519 C
1 C
17606520 CCAATCATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.36, C:0.25, G:0.05, T:0.34
Consensus pattern (41 bp):
CAATCTCCTATTCTCTCCTTCAGATAAAGTCAAATAAAATT
Found at i:17608433 original size:27 final size:27
Alignment explanation
Indices: 17608395--17608447 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
17608385 TCGTTTAAAA
*
17608395 CCAAGCCATGGTGAT-GAACAACCTGGG
1 CCAAGCCATGGTCATCG-ACAACCTGGG
17608422 CCAAGCCATGGTCATCGACAACCTGG
1 CCAAGCCATGGTCATCGACAACCTGG
17608448 ACCATCTAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 23 0.96
28 1 0.04
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.15
Consensus pattern (27 bp):
CCAAGCCATGGTCATCGACAACCTGGG
Found at i:17611547 original size:47 final size:47
Alignment explanation
Indices: 17611494--17611588 Score: 127
Period size: 47 Copynumber: 2.0 Consensus size: 47
17611484 CATATCTGGC
* * * *
17611494 GTGGTGCAGTGAAATCTAGTTTCCTTTTGAGTGCTAATTGTACCATG
1 GTGGTGCAGTGAAATCCAGTTTACTTTTGAGTACTAATTGCACCATG
* * *
17611541 GTGGTGCATTGAAATCCAGTTTATTTTTTAGTACTAATTGCACCATG
1 GTGGTGCAGTGAAATCCAGTTTACTTTTGAGTACTAATTGCACCATG
17611588 G
1 G
17611589 GATGCCCTTG
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
47 41 1.00
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.39
Consensus pattern (47 bp):
GTGGTGCAGTGAAATCCAGTTTACTTTTGAGTACTAATTGCACCATG
Found at i:17611930 original size:33 final size:33
Alignment explanation
Indices: 17611884--17611949 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
17611874 ATCTTCATCT
* *
17611884 AAACTTTTAGTTTTGTGGTTTTGTTTGAGGATG
1 AAACTTTTAGTTTTATGGTTTTATTTGAGGATG
*
17611917 AAACTTTTGGTTTTATGGTTTTATTTGAGGATG
1 AAACTTTTAGTTTTATGGTTTTATTTGAGGATG
17611950 GTTTCAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.20, C:0.03, G:0.26, T:0.52
Consensus pattern (33 bp):
AAACTTTTAGTTTTATGGTTTTATTTGAGGATG
Found at i:17613075 original size:17 final size:17
Alignment explanation
Indices: 17613053--17613085 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
17613043 ATTAGTATTA
17613053 TAAATACAAAATAATTC
1 TAAATACAAAATAATTC
17613070 TAAATACAAAATAATT
1 TAAATACAAAATAATT
17613086 GTTAACATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (17 bp):
TAAATACAAAATAATTC
Found at i:17617865 original size:22 final size:25
Alignment explanation
Indices: 17617837--17617889 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 25
17617827 TCATTTTCTT
*
17617837 TATTTATCTTTTTTTAACATTTAAA
1 TATTCATCTTTTTTTAACATTTAAA
17617862 TTATCTCATCTTTTTTTAACATTTAAA
1 -TAT-TCATCTTTTTTTAACATTTAAA
17617889 T
1 T
17617890 TCTTGCTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 4 0.16
27 21 0.84
ACGTcount: A:0.30, C:0.11, G:0.00, T:0.58
Consensus pattern (25 bp):
TATTCATCTTTTTTTAACATTTAAA
Found at i:17618610 original size:11 final size:11
Alignment explanation
Indices: 17618596--17618622 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
17618586 GAAAAAAAAT
17618596 AAAAAAATTTG
1 AAAAAAATTTG
17618607 AAAAAAATTTG
1 AAAAAAATTTG
17618618 AAAAA
1 AAAAA
17618623 GGTACTCTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.22
Consensus pattern (11 bp):
AAAAAAATTTG
Found at i:17619120 original size:16 final size:16
Alignment explanation
Indices: 17619099--17619130 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
17619089 TTATCCCGAT
17619099 TTAATTCTATATTTAG
1 TTAATTCTATATTTAG
17619115 TTAATTCTATATTTAG
1 TTAATTCTATATTTAG
17619131 ACCCATAATG
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:0.06, G:0.06, T:0.56
Consensus pattern (16 bp):
TTAATTCTATATTTAG
Found at i:17621740 original size:56 final size:56
Alignment explanation
Indices: 17621680--17621877 Score: 165
Period size: 56 Copynumber: 3.5 Consensus size: 56
17621670 TATATATAAC
17621680 ATTTAAAATTAATAA-TGATAAATATAAAATTAAAAAATTACTTTTATAACAAGTAT
1 ATTTAAAATTAA-AATTGATAAATATAAAATTAAAAAATTACTTTTATAACAAGTAT
* * ** * * * *
17621736 ATTTATAATTAAAATTGATAAATAT--TATT-ACTAA-TAATGTGTAAAATAAGTATATAT
1 ATTTAAAATTAAAATTGATAAATATAAAATTAAAAAATTACT-TTTATAACAAG----TAT
17621793 AACATTTAAAATTAATAA-TGATAAATATAAAATTAAAAAATTACTTTTATAACAAGTAT
1 ---ATTTAAAATTAA-AATTGATAAATATAAAATTAAAAAATTACTTTTATAACAAGTAT
* * *
17621852 CTTTATAATTAAAATTGATAATTATA
1 ATTTAAAATTAAAATTGATAAATATA
17621878 TTTATTTACT
Statistics
Matches: 108, Mismatches: 19, Indels: 30
0.69 0.12 0.19
Matches are distributed among these distances:
52 3 0.03
53 11 0.10
54 3 0.03
55 4 0.04
56 41 0.38
57 3 0.03
59 3 0.03
60 21 0.19
61 2 0.02
62 3 0.03
63 11 0.10
64 3 0.03
ACGTcount: A:0.53, C:0.04, G:0.05, T:0.39
Consensus pattern (56 bp):
ATTTAAAATTAAAATTGATAAATATAAAATTAAAAAATTACTTTTATAACAAGTAT
Found at i:17621770 original size:116 final size:116
Alignment explanation
Indices: 17621640--17621872 Score: 457
Period size: 116 Copynumber: 2.0 Consensus size: 116
17621630 TATATATAAT
17621640 AATATTATTACTAATAATGTGTAAAATAAGTATATATAACATTTAAAATTAATAATGATAAATAT
1 AATATTATTACTAATAATGTGTAAAATAAGTATATATAACATTTAAAATTAATAATGATAAATAT
17621705 AAAATTAAAAAATTACTTTTATAACAAGTATATTTATAATTAAAATTGATA
66 AAAATTAAAAAATTACTTTTATAACAAGTATATTTATAATTAAAATTGATA
17621756 AATATTATTACTAATAATGTGTAAAATAAGTATATATAACATTTAAAATTAATAATGATAAATAT
1 AATATTATTACTAATAATGTGTAAAATAAGTATATATAACATTTAAAATTAATAATGATAAATAT
*
17621821 AAAATTAAAAAATTACTTTTATAACAAGTATCTTTATAATTAAAATTGATA
66 AAAATTAAAAAATTACTTTTATAACAAGTATATTTATAATTAAAATTGATA
17621872 A
1 A
17621873 TTATATTTAT
Statistics
Matches: 116, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
116 116 1.00
ACGTcount: A:0.52, C:0.04, G:0.05, T:0.39
Consensus pattern (116 bp):
AATATTATTACTAATAATGTGTAAAATAAGTATATATAACATTTAAAATTAATAATGATAAATAT
AAAATTAAAAAATTACTTTTATAACAAGTATATTTATAATTAAAATTGATA
Found at i:17621913 original size:16 final size:16
Alignment explanation
Indices: 17621876--17621914 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
17621866 TTGATAATTA
*
17621876 TATTTATTTACTTAAT
1 TATTTATTTAATTAAT
*
17621892 TATTTATTTAATTTAT
1 TATTTATTTAATTAAT
*
17621908 TGTTTAT
1 TATTTAT
17621915 ATATTATCTC
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:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (16 bp):
TATTTATTTAATTAAT
Found at i:17622163 original size:20 final size:20
Alignment explanation
Indices: 17622138--17622182 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
17622128 TTTTTACTTT
*
17622138 TAATTTTAATTATC-TTTTAA
1 TAATTTT-ATTATCATTTCAA
*
17622158 TAATTTTTTTATCATTTCAA
1 TAATTTTATTATCATTTCAA
17622178 TAATT
1 TAATT
17622183 AATTATTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 5 0.23
20 17 0.77
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (20 bp):
TAATTTTATTATCATTTCAA
Found at i:17622188 original size:19 final size:19
Alignment explanation
Indices: 17622142--17622188 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
17622132 TACTTTTAAT
*
17622142 TTTAATTATCTTTTAATAA
1 TTTAATTATCTTTCAATAA
**
17622161 TTTTTTTATCATTTCAATAA
1 TTTAATTATC-TTTCAATAA
17622181 -TTAATTAT
1 TTTAATTAT
17622189 TAAAAAATTG
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTAATTATCTTTCAATAA
Found at i:17624000 original size:43 final size:43
Alignment explanation
Indices: 17623910--17624061 Score: 139
Period size: 43 Copynumber: 3.5 Consensus size: 43
17623900 TGAGTGTTAT
*
17623910 AGAGCTTTATTTA-TTTTCAAAGTCATTGAGCCTCTACTTAGA
1 AGAGCTTTATTTATTTTTCAAAGTCATTAAGCCTCTACTTAGA
**
17623952 AGAGC-TTATTTATTTTTTCAAAGTCATTAAGCCTCTGTTTA-A
1 AGAGCTTTATTTA-TTTTTCAAAGTCATTAAGCCTCTACTTAGA
* * ** * * *
17623994 AGGAGCTTTGTTTATTTTTCAAAAACTTGTTCAGCCTTTATTTAGA
1 A-GAGCTTTATTTATTTTTC--AAAGTCATTAAGCCTCTACTTAGA
* *
17624040 AGAGCCTTGTTTATTTTTCAAA
1 AGAGCTTTATTTATTTTTCAAA
17624062 AATTGTTGAA
Statistics
Matches: 92, Mismatches: 11, Indels: 13
0.79 0.09 0.11
Matches are distributed among these distances:
41 7 0.08
42 7 0.08
43 37 0.40
44 6 0.07
45 33 0.36
46 2 0.02
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (43 bp):
AGAGCTTTATTTATTTTTCAAAGTCATTAAGCCTCTACTTAGA
Found at i:17624057 original size:88 final size:88
Alignment explanation
Indices: 17623938--17624142 Score: 229
Period size: 88 Copynumber: 2.3 Consensus size: 88
17623928 AAAGTCATTG
* *
17623938 AGCCTCTACTTAGAAGAGCTTATTTATTTTTTC-AAAGTCATT-AAGCCTCTGTTTAAAGGAG-C
1 AGCCTCTATTTAGAAGAGCTTATTTATTTTTTCAAAAATCATTGAA-CCTCTGTTTAAAGGAGAC
17624000 TTTGTTTATTTTTCAAAAACTTGTTC
65 -TTGTTTATTTTTC-AAAACTTGTTC
* * ** * *
17624026 AGCCTTTATTTAGAAGAGCCTTGTTTA-TTTTTCAAAAATTGTTGAACCTTTGTTTAGAGGAGAC
1 AGCCTCTATTTAGAAGAG-CTTATTTATTTTTTCAAAAATCATTGAACCTCTGTTTAAAGGAGAC
* *
17624090 TTGTTTATTTTTCAAAAGTTGTTG
65 TTGTTTATTTTTCAAAACTTGTTC
* *
17624114 AGCCTCTATTTAGAGGAGTTTATATTATT
1 AGCCTCTATTTAGAAGAGCTTAT-TTATT
17624143 CAACAAGTTT
Statistics
Matches: 97, Mismatches: 14, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
87 3 0.03
88 50 0.52
89 41 0.42
90 3 0.03
ACGTcount: A:0.27, C:0.13, G:0.16, T:0.44
Consensus pattern (88 bp):
AGCCTCTATTTAGAAGAGCTTATTTATTTTTTCAAAAATCATTGAACCTCTGTTTAAAGGAGACT
TGTTTATTTTTCAAAACTTGTTC
Found at i:17624126 original size:44 final size:43
Alignment explanation
Indices: 17623919--17624131 Score: 198
Period size: 44 Copynumber: 4.9 Consensus size: 43
17623909 TAGAGCTTTA
** * * *
17623919 TTTA-TTTTC-AAAGTCATTGAGCCTCTACTTAGAAGAGCTTA
1 TTTATTTTTCAAAAGTTGTTGAGCCTCTATTTAGAGGAGCTTG
** * * *
17623960 TTTATTTTTTC-AAAGTCATTAAGCCTCTGTTTAAAGGAGCTTTG
1 TTTA-TTTTTCAAAAGTTGTTGAGCCTCTATTTAGAGGAGC-TTG
* * * *
17624004 TTTATTTTTCAAAAACTTGTTCAGCCTTTATTTAGAAGAGCCTTG
1 TTTATTTTTC-AAAAGTTGTTGAGCCTCTATTTAGAGGAG-CTTG
* * * *
17624049 TTTATTTTTCAAAAATTGTTGAACCTTTGTTTAGAGGAGACTTG
1 TTTATTTTTCAAAAGTTGTTGAGCCTCTATTTAGAGGAG-CTTG
17624093 TTTATTTTTCAAAAGTTGTTGAGCCTCTATTTAGAGGAG
1 TTTATTTTTCAAAAGTTGTTGAGCCTCTATTTAGAGGAG
17624132 TTTATATTAT
Statistics
Matches: 142, Mismatches: 24, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.03
43 35 0.25
44 69 0.49
45 33 0.23
46 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.16, T:0.44
Consensus pattern (43 bp):
TTTATTTTTCAAAAGTTGTTGAGCCTCTATTTAGAGGAGCTTG
Found at i:17627180 original size:19 final size:19
Alignment explanation
Indices: 17627156--17627193 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
17627146 GATGTCTAAT
17627156 GGGTAGGTTCCCAACCTAG
1 GGGTAGGTTCCCAACCTAG
17627175 GGGTAGGTTCCCAACCTAG
1 GGGTAGGTTCCCAACCTAG
17627194 ACATTATGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.26, G:0.32, T:0.21
Consensus pattern (19 bp):
GGGTAGGTTCCCAACCTAG
Found at i:17628507 original size:15 final size:16
Alignment explanation
Indices: 17628489--17628518 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
17628479 ATTCTTTTAA
17628489 TGTTTCTTTT-TTTTT
1 TGTTTCTTTTATTTTT
17628504 TGTTTCTTTTATTTT
1 TGTTTCTTTTATTTT
17628519 ATCTTTTGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.03, C:0.07, G:0.07, T:0.83
Consensus pattern (16 bp):
TGTTTCTTTTATTTTT
Found at i:17630464 original size:20 final size:19
Alignment explanation
Indices: 17630424--17630460 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
17630414 AAAACAAGAT
17630424 CAATTAAGGCATTTGTTTA
1 CAATTAAGGCATTTGTTTA
*
17630443 CAATTAAGGCGTTTGTTT
1 CAATTAAGGCATTTGTTT
17630461 TACACAAACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.27, C:0.11, G:0.19, T:0.43
Consensus pattern (19 bp):
CAATTAAGGCATTTGTTTA
Found at i:17630820 original size:125 final size:121
Alignment explanation
Indices: 17630443--17630859 Score: 374
Period size: 125 Copynumber: 3.3 Consensus size: 121
17630433 CATTTGTTTA
* *
17630443 CAATTAAGGCGTTTGTTTTACACAAACGCCTTAATTGATCTTGTTTTTAATTTATAACAAAGGAT
1 CAATTAAGGTGTTTG-GTTACACAAACGCCTTAATTGATCTTGTTTTTAATTTAT---AAAGGAT
* * * *
17630508 CAATTAAGGTGTTTGTATAACCAAATGCTTTAATTGATCT-TTGTATAAATTTATAAACAAGAT
62 CAATTAAGGTGTTTGTCT-ACCAGACGCCTTAATTGATCTCTT-TATAAATTTATAAA-AA-AT
* * ** * **** *
17630571 TAATTAAGGCGTTTCATTACAAAAACTAAGTAATTGATCTT-TTTATAAATTTATAAAGGATCAA
1 CAATTAAGGTGTTTGGTTACACAAACGCCTTAATTGATCTTGTTT-TTAATTTATAAAGGATCAA
** * ** **
17630635 TTAAGGCATTTGGC-ACTTTGAACGCCTTAATTGATC-CTTTATTTATTTAAATAAAAAAAAT
65 TTAAGGTGTTTGTCTAC-CAG-ACGCCTTAATTGATCTCTTTATAAATTT--AT--AAAAAAT
* *
17630696 CAATTAAGGTATTTGGTTACACAAACGCCTTAATTGGTCTTGTTTTTAATTTATAAATTGGATCA
1 CAATTAAGGTGTTTGGTTACACAAACGCCTTAATTGATCTTGTTTTTAATTTATAAA--GGATCA
* *
17630761 ATTAAGGTGTTTGTCTAGCCAGACACCTTAATTGATCTCATTATAAATTTATAATAAAAT
64 ATTAAGGTGTTTGTCTA-CCAGACGCCTTAATTGATCTCTTTATAAATTTATAA-AAAAT
* *
17630821 CAATTAAAGTGTTTGGTTACACAATCGCCTTAATTGATC
1 CAATTAAGGTGTTTGGTTACACAAACGCCTTAATTGATC
17630860 CTTTATATAT
Statistics
Matches: 229, Mismatches: 45, Indels: 33
0.75 0.15 0.11
Matches are distributed among these distances:
122 2 0.01
123 7 0.03
124 37 0.16
125 85 0.37
126 10 0.04
127 63 0.28
128 24 0.10
129 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.39
Consensus pattern (121 bp):
CAATTAAGGTGTTTGGTTACACAAACGCCTTAATTGATCTTGTTTTTAATTTATAAAGGATCAAT
TAAGGTGTTTGTCTACCAGACGCCTTAATTGATCTCTTTATAAATTTATAAAAAAT
Found at i:17630852 original size:62 final size:62
Alignment explanation
Indices: 17630443--17630859 Score: 190
Period size: 63 Copynumber: 6.6 Consensus size: 62
17630433 CATTTGTTTA
* * ** * * *
17630443 CAATTAAGGCGTTTGTTTTACACAAACGCCTTAATTGATCTTGTTTTTAATTTATAACA-AAGGA
1 CAATTAAGGTGTTTG-GTTACAC-AACGCCTTAATTGATCTCATTATAAATTTATAA-ATAA-AA
17630507 T
62 T
* * * * *
17630508 CAATTAAGGTGTTT-GTATA-ACCAAATGCTTTAATTGATCT-TTGTATAAATTTATAAACAAGA
1 CAATTAAGGTGTTTGGT-TACA-C-AACGCCTTAATTGATCTCAT-TATAAATTTATAAATAAAA
17630570 T
62 T
* * ** * **** ** **
17630571 TAATTAAGGCGTTTCATTACAAAAACTAAGTAATTGATCTTTTTATAAATTTAT-AA-AGGAT
1 CAATTAAGGTGTTTGGTTAC-ACAACGCCTTAATTGATCTCATTATAAATTTATAAATAAAAT
** * ** * ** *
17630632 CAATTAAGGCATTTGG-CACTTTGAACGCCTTAATTGATC-CTTTATTTATTTAAATAAAAAAAA
1 CAATTAAGGTGTTTGGTTAC--ACAACGCCTTAATTGATCTCATTATAAATTT--ATAAATAAAA
17630695 T
62 T
* * ** * * ***
17630696 CAATTAAGGTATTTGGTTACACAAACGCCTTAATTGGTCTTGTTTTTAATTTATAAATTGGAT
1 CAATTAAGGTGTTTGGTTACAC-AACGCCTTAATTGATCTCATTATAAATTTATAAATAAAAT
*
17630759 CAATTAAGGTGTTT-GTCTAGC-CAGACACCTTAATTGATCTCATTATAAATTTAT-AATAAAAT
1 CAATTAAGGTGTTTGGT-TA-CACA-ACGCCTTAATTGATCTCATTATAAATTTATAAATAAAAT
*
17630821 CAATTAAAGTGTTTGGTTACACAATCGCCTTAATTGATC
1 CAATTAAGGTGTTTGGTTACACAA-CGCCTTAATTGATC
17630860 CTTTATATAT
Statistics
Matches: 271, Mismatches: 59, Indels: 47
0.72 0.16 0.12
Matches are distributed among these distances:
60 11 0.04
61 30 0.11
62 42 0.15
63 95 0.35
64 69 0.25
65 24 0.09
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.39
Consensus pattern (62 bp):
CAATTAAGGTGTTTGGTTACACAACGCCTTAATTGATCTCATTATAAATTTATAAATAAAAT
Found at i:17631025 original size:61 final size:61
Alignment explanation
Indices: 17630896--17631187 Score: 224
Period size: 61 Copynumber: 4.7 Consensus size: 61
17630886 CAACGCAAAT
* * * * *
17630896 GCCTTAATTAATCTCTTTTTAAATTTATAA-AAGATCAATTAAGGCATTTGTGTAGCCAAAC
1 GCCTTAATTGATCTATTTATAAATTTATAATAAGATCAATTAAGGCGTTTGT-TAGCAAAAC
* * *
17630957 GCCTTAATTGATCT-TTTATAAATTTATAATAAAATCAATTAAGGTGTTTGGTTA-CAAAAGT
1 GCCTTAATTGATCTATTTATAAATTTATAATAAGATCAATTAAGGCGTTT-GTTAGCAAAA-C
* * * ** * * *
17631018 GCTTTAATCGATCTAATTTAT-AATTTA-AGTTGGATCAGTTAAGGCGATCATG-TAGCCAAAC
1 GCCTTAATTGATCT-ATTTATAAATTTATAATAAGATCAATTAAGGCG-T-TTGTTAGCAAAAC
** * *
17631079 GCCTTAATTGATCTCCTTATAAATTTATAACAAGATCAATTAAGGCGTTTGGTTA-CACAAGC
1 GCCTTAATTGATCTATTTATAAATTTATAATAAGATCAATTAAGGCGTTT-GTTAGCA-AAAC
*
17631141 GCCTTAATTGATCATTAATTTA-AAA-TTATAATGTAGATCAATTAAGG
1 GCCTTAATTGATC--T-ATTTATAAATTTATAAT-AAGATCAATTAAGG
17631188 TATTTATGTA
Statistics
Matches: 180, Mismatches: 34, Indels: 31
0.73 0.14 0.13
Matches are distributed among these distances:
60 23 0.13
61 79 0.44
62 46 0.26
63 12 0.07
64 17 0.09
65 3 0.02
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (61 bp):
GCCTTAATTGATCTATTTATAAATTTATAATAAGATCAATTAAGGCGTTTGTTAGCAAAAC
Found at i:17631150 original size:294 final size:297
Alignment explanation
Indices: 17630601--17631153 Score: 715
Period size: 294 Copynumber: 1.9 Consensus size: 297
17630591 AAAAACTAAG
* * **
17630601 TAATTGATCTTTTTATAAATTTATAAAGGATCAATTAAGGCATTTGGCACTTTGAACGCCTTAAT
1 TAATTAATCTTTTTATAAATTTATAAAAGATCAATTAAGGCATTTGGCAC-TCAAACGCCTTAAT
** *
17630666 TGATCCTTTATTTATTTAAATAAAAAAAATCAATTAAGGTATTTGGTTACACAAACGCCTTAATT
65 TGATCCTTTATAAATTT-AATAAAAAAAATCAATTAAGGTATTTGGTTACACAAACGCCTTAATC
* ** * * * ** *
17630731 GGTCTTGTTTTTAATTTATAAATTGGATCAATTAAGGTGTTTGTCTAGCCAGACACCTTAATTGA
129 GATCTAATTTATAATTTATAAATTGGATCAATTAAGGCGATCATCTAGCCAAACACCTTAATTGA
* * *
17630796 TCTCATTATAAATTTATAATAAAATCAATTAAAGTGTTTGGTTACACAATCGCCTTAATTGATCC
194 TCTCATTATAAATTTATAACAAAATCAATTAAAGCGTTTGGTTACACAAGCGCCTTAATTGATCC
17630861 TTTATATATAATTTATACATGGAATCAACGCAAATGCCT
259 TTTATATATAATTTATACATGGAATCAACGCAAATGCCT
*
17630900 TAATTAATCTCTTTT-TAAATTTATAAAAGATCAATTAAGGCATTTGTGTAGC-CAAACGCCTTA
1 TAATTAATCT-TTTTATAAATTTATAAAAGATCAATTAAGGCATTTG-GCA-CTCAAACGCCTTA
* * * * *
17630963 ATTGATCTTTTATAAATTT-AT-AATAAAATCAATTAAGGTGTTTGGTTACA-AAAGTGCTTTAA
63 ATTGATCCTTTATAAATTTAATAAAAAAAATCAATTAAGGTATTTGGTTACACAAA-CGCCTTAA
* * * *
17631025 TCGATCTAATTTATAA-TT-TAAGTTGGATCAGTTAAGGCGATCATGTAGCCAAACGCCTTAATT
127 TCGATCTAATTTATAATTTATAAATTGGATCAATTAAGGCGATCATCTAGCCAAACACCTTAATT
* * *
17631088 GATCTCCTTATAAATTTATAACAAGATCAATTAAGGCGTTTGGTTACACAAGCGCCTTAATTGAT
192 GATCTCATTATAAATTTATAACAAAATCAATTAAAGCGTTTGGTTACACAAGCGCCTTAATTGAT
17631153 C
257 C
17631154 ATTAATTTAA
Statistics
Matches: 218, Mismatches: 32, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
294 96 0.44
295 5 0.02
296 44 0.20
297 2 0.01
299 64 0.29
300 6 0.03
301 1 0.00
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (297 bp):
TAATTAATCTTTTTATAAATTTATAAAAGATCAATTAAGGCATTTGGCACTCAAACGCCTTAATT
GATCCTTTATAAATTTAATAAAAAAAATCAATTAAGGTATTTGGTTACACAAACGCCTTAATCGA
TCTAATTTATAATTTATAAATTGGATCAATTAAGGCGATCATCTAGCCAAACACCTTAATTGATC
TCATTATAAATTTATAACAAAATCAATTAAAGCGTTTGGTTACACAAGCGCCTTAATTGATCCTT
TATATATAATTTATACATGGAATCAACGCAAATGCCT
Found at i:17633969 original size:20 final size:19
Alignment explanation
Indices: 17633936--17633974 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
17633926 ATTACATCTA
17633936 ATATCATGTCTATTACTTTT
1 ATATCATGTCTATTA-TTTT
17633956 ATATCATG-CTTATTATTTT
1 ATATCATGTC-TATTATTTT
17633975 GTAGATGTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.26, C:0.13, G:0.05, T:0.56
Consensus pattern (19 bp):
ATATCATGTCTATTATTTT
Found at i:17638070 original size:21 final size:21
Alignment explanation
Indices: 17638024--17638070 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
17638014 TGATGGATGT
*
17638024 TAAAACTGAAATTGGTTTAAA
1 TAAAACTGAAATTGGTTGAAA
* *
17638045 GAAAACTGAGATAT-GTTGAAA
1 TAAAACTGAAAT-TGGTTGAAA
17638066 TAAAA
1 TAAAA
17638071 ATAAGAAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 20 0.95
22 1 0.05
ACGTcount: A:0.51, C:0.04, G:0.17, T:0.28
Consensus pattern (21 bp):
TAAAACTGAAATTGGTTGAAA
Found at i:17639096 original size:15 final size:16
Alignment explanation
Indices: 17639069--17639102 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
17639059 ATTACCACGT
17639069 TTTGGATTCCTTAAAG
1 TTTGGATTCCTTAAAG
*
17639085 TTTGGA-TCCTTACAG
1 TTTGGATTCCTTAAAG
17639100 TTT
1 TTT
17639103 TACCTTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.21, C:0.15, G:0.18, T:0.47
Consensus pattern (16 bp):
TTTGGATTCCTTAAAG
Found at i:17640202 original size:2 final size:2
Alignment explanation
Indices: 17640195--17640226 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
17640185 TGCACAGATA
17640195 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17640227 TAAATGGTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.