Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold64
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: 7997333
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 95991 characters in sequence are not A, C, G, or T
File 13 of 45
Found at i:2486421 original size:50 final size:50
Alignment explanation
Indices: 2486332--2486426 Score: 113
Period size: 50 Copynumber: 1.9 Consensus size: 50
2486322 TTATTTAAAT
* * *
2486332 TTAATTATAAAATATATAAATATTAATATAAAAATAATTTTAATTTTTTA
1 TTAATTATAAAATAAATAAATAATAATATAAAAATAATTTAAATTTTTTA
* *
2486382 TTAATTATAAATAATAAATAAA-AATAATATTAATA-AATTTAAATT
1 TTAATTAT-AA-AATAAATAAATAATAATATAAAAATAATTTAAATT
2486427 AAAAATAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
50 17 0.45
51 12 0.32
52 9 0.24
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (50 bp):
TTAATTATAAAATAAATAAATAATAATATAAAAATAATTTAAATTTTTTA
Found at i:2486442 original size:12 final size:11
Alignment explanation
Indices: 2486389--2486444 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 11
2486379 TTATTAATTA
2486389 TAAATAATAAA-
1 TAAA-AATAAAT
2486400 TAAAAATAATAT
1 TAAAAATAA-AT
2486412 TAATAAATTTAAAT
1 TAA-AAA--TAAAT
2486426 TAAAAATAAATT
1 TAAAAATAAA-T
2486438 TAAAAAT
1 TAAAAAT
2486445 TTTTAATTGC
Statistics
Matches: 39, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
10 5 0.13
11 9 0.23
12 11 0.28
13 6 0.15
14 5 0.13
15 3 0.08
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (11 bp):
TAAAAATAAAT
Found at i:2486452 original size:26 final size:26
Alignment explanation
Indices: 2486396--2486446 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
2486386 TTATAAATAA
2486396 TAAA-TAAAAATAATATTAATAAATT
1 TAAATTAAAAATAATATTAATAAATT
2486421 TAAATTAAAAATAA-ATTTAA-AAATT
1 TAAATTAAAAATAATA-TTAATAAATT
2486446 T
1 T
2486447 TTAATTGCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 11 0.46
26 13 0.54
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (26 bp):
TAAATTAAAAATAATATTAATAAATT
Found at i:2492136 original size:35 final size:39
Alignment explanation
Indices: 2492095--2492172 Score: 101
Period size: 39 Copynumber: 2.1 Consensus size: 39
2492085 CATTGAGTTC
* *
2492095 AAATAATT-AATTATTTTAAT-TTA-T-GAATAAAAATT
1 AAATAATTCAAATATTTTAATATTATTCAAATAAAAATT
*
2492130 AAATAATTCAAATATTTTATTATTATTCAAATAAAAATT
1 AAATAATTCAAATATTTTAATATTATTCAAATAAAAATT
2492169 AAAT
1 AAAT
2492173 CAAATTTAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
35 8 0.22
36 10 0.28
37 3 0.08
38 1 0.03
39 14 0.39
ACGTcount: A:0.53, C:0.03, G:0.01, T:0.44
Consensus pattern (39 bp):
AAATAATTCAAATATTTTAATATTATTCAAATAAAAATT
Found at i:2495137 original size:2 final size:2
Alignment explanation
Indices: 2495123--2495161 Score: 62
Period size: 2 Copynumber: 19.5 Consensus size: 2
2495113 TTATAAGGGT
2495123 TA TA TA T- TCA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2495162 GTTTAAATAC
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 33 0.94
3 1 0.03
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2499671 original size:2 final size:2
Alignment explanation
Indices: 2499666--2499697 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2499656 TTTTTAAGAT
2499666 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2499698 AAGAATATGA
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):
TA
Found at i:2504609 original size:22 final size:22
Alignment explanation
Indices: 2504556--2504609 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 22
2504546 AGATTAAGAA
2504556 AATAAAAAATCAATATATTATTT
1 AATAAAAAAT-AATATATTATTT
*
2504579 -AT-AATAATAATATATT-TTT
1 AATAAAAAATAATATATTATTT
2504598 AATACAAAAATA
1 AATA-AAAAATA
2504610 TTATTAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
19 3 0.12
20 10 0.38
21 5 0.19
22 8 0.31
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (22 bp):
AATAAAAAATAATATATTATTT
Found at i:2505675 original size:2 final size:2
Alignment explanation
Indices: 2505668--2505719 Score: 88
Period size: 2 Copynumber: 26.5 Consensus size: 2
2505658 TTACTTTTCT
*
2505668 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2505710 TA TA TA -A TA T
1 TA TA TA TA TA T
2505720 TATTAATTCT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2506041 original size:30 final size:30
Alignment explanation
Indices: 2505995--2506068 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
2505985 AAATAGATGC
*
2505995 TTAATTA-AATAAAATAATA-TTTGAA-AGAT
1 TTAATTAGAAAAAAATAATAGTTT-AAGA-AT
*
2506024 TTAATTAGACAAAAATAATAGTTTAAGAAT
1 TTAATTAGAAAAAAATAATAGTTTAAGAAT
*
2506054 TTAATTGGAAAAAAA
1 TTAATTAGAAAAAAA
2506069 AAATTAAAGG
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
29 7 0.18
30 27 0.71
31 4 0.11
ACGTcount: A:0.55, C:0.01, G:0.09, T:0.34
Consensus pattern (30 bp):
TTAATTAGAAAAAAATAATAGTTTAAGAAT
Found at i:2506645 original size:11 final size:11
Alignment explanation
Indices: 2506562--2506673 Score: 59
Period size: 11 Copynumber: 10.9 Consensus size: 11
2506552 AGACTTAATT
2506562 TATT-TATTTA
1 TATTATATTTA
2506572 TATTAT-TTT-
1 TATTATATTTA
2506581 TA-TATATTT-
1 TATTATATTTA
*
2506590 TATTATA-TAA
1 TATTATATTTA
2506600 TAATTATATTT-
1 T-ATTATATTTA
2506611 TA--A-ATTTA
1 TATTATATTTA
*
2506619 TA-TAAATTT-
1 TATTATATTTA
*
2506628 TAATATATTTA
1 TATTATATTTA
2506639 TATTATATTATAA
1 TATTATATT-T-A
*
2506652 TTATTTTATTTA
1 -TATTATATTTA
*
2506664 TGTTATATTT
1 TATTATATTT
2506674 TTATAATATG
Statistics
Matches: 81, Mismatches: 7, Indels: 27
0.70 0.06 0.23
Matches are distributed among these distances:
7 4 0.05
8 6 0.07
9 11 0.14
10 23 0.28
11 24 0.30
12 3 0.04
13 2 0.02
14 8 0.10
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (11 bp):
TATTATATTTA
Found at i:2506658 original size:30 final size:27
Alignment explanation
Indices: 2506579--2506696 Score: 87
Period size: 30 Copynumber: 4.1 Consensus size: 27
2506569 TTATATTATT
* **
2506579 TTTATATATTTTATTATATAATAATTATA
1 TTTATAT-TTTTATAATATTTTAA-TATA
* *
2506608 TTTTAAATTTATATAA-ATTTTAATATA
1 -TTTATATTTTTATAATATTTTAATATA
*
2506635 TTTATATTATATTATAATTATTTT-ATTTA
1 TTTATATT-T-TTATAA-TATTTTAATATA
2506664 TGTTATATTTTTATAATATGTTTAATATTA
1 T-TTATATTTTTATAATAT-TTTAATA-TA
2506694 TTT
1 TTT
2506697 GATCTATTTG
Statistics
Matches: 71, Mismatches: 9, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
26 7 0.10
27 8 0.11
28 19 0.27
29 16 0.23
30 21 0.30
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (27 bp):
TTTATATTTTTATAATATTTTAATATA
Found at i:2510541 original size:2 final size:2
Alignment explanation
Indices: 2510536--2510562 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2510526 AAACCAAAAC
2510536 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
2510563 ATCGGCCTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2527601 original size:2 final size:2
Alignment explanation
Indices: 2527588--2527636 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
2527578 GCCTGCCTGT
*
2527588 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2527630 TA TA TA T
1 TA TA TA T
2527637 TATCCACTGA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2535231 original size:2 final size:2
Alignment explanation
Indices: 2535224--2535255 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2535214 AAAATGACCA
*
2535224 AT AT AT AT GT 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
2535256 GGTTTTTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2535780 original size:9 final size:9
Alignment explanation
Indices: 2535736--2535784 Score: 50
Period size: 9 Copynumber: 5.7 Consensus size: 9
2535726 ACTTAACTCA
*
2535736 TATATTATT
1 TATAATATT
*
2535745 TAAAATATT
1 TATAATATT
2535754 T-TAA-A-T
1 TATAATATT
2535760 TATTAATATT
1 TA-TAATATT
2535770 TATAATATT
1 TATAATATT
2535779 TATAAT
1 TATAAT
2535785 TAAATTTAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 8
0.75 0.07 0.18
Matches are distributed among these distances:
6 2 0.06
7 1 0.03
8 5 0.15
9 22 0.67
10 3 0.09
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
TATAATATT
Found at i:2536029 original size:21 final size:21
Alignment explanation
Indices: 2535987--2536055 Score: 70
Period size: 20 Copynumber: 3.3 Consensus size: 21
2535977 CTTTTTTTTC
* * *
2535987 ATTAAATAATAATTAATATTAA
1 ATTAAATCATATTTAAAATT-A
*
2536009 ATTAAATCA-ATTTAAATTTA
1 ATTAAATCATATTTAAAATTA
*
2536029 A-TATATCATATTTAAAATTA
1 ATTAAATCATATTTAAAATTA
2536049 ATTAAAT
1 ATTAAAT
2536056 AAATAATTTA
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
19 6 0.16
20 13 0.34
21 11 0.29
22 8 0.21
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (21 bp):
ATTAAATCATATTTAAAATTA
Found at i:2536634 original size:16 final size:16
Alignment explanation
Indices: 2536581--2536655 Score: 59
Period size: 16 Copynumber: 4.6 Consensus size: 16
2536571 ATGTTTAAAT
2536581 ATTTTAT-TTTATTATA
1 ATTTTATATTTA-TATA
* *
2536597 ATTTTAT-TTAAAATTA
1 ATTTTATATTTATA-TA
2536613 ATTTTTATATTTATATA
1 A-TTTTATATTTATATA
2536630 ATTTTGATATATTA-AT-
1 ATTTT-ATAT-TTATATA
2536646 ATTTTATATT
1 ATTTTATATT
2536656 ATTTAAATTT
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
14 1 0.02
15 5 0.10
16 22 0.44
17 15 0.30
18 7 0.14
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (16 bp):
ATTTTATATTTATATA
Found at i:2536658 original size:16 final size:16
Alignment explanation
Indices: 2536578--2536658 Score: 55
Period size: 17 Copynumber: 5.0 Consensus size: 16
2536568 GTTATGTTTA
*
2536578 AATATTTTATTTTATT
1 AATATTTTATATTATT
2536594 -ATAATTTTAT-TTAAAATT
1 AAT-ATTTTATATT---ATT
2536612 AAT-TTTTATATTTATAT
1 AATATTTTATA-TTAT-T
*
2536629 AAT-TTTGATA-TATT
1 AATATTTTATATTATT
2536643 AATATTTTATATTATT
1 AATATTTTATATTATT
2536659 TAAATTTAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 20
0.71 0.03 0.27
Matches are distributed among these distances:
14 4 0.08
15 13 0.25
16 13 0.25
17 16 0.30
18 3 0.06
19 4 0.08
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (16 bp):
AATATTTTATATTATT
Found at i:2536673 original size:31 final size:31
Alignment explanation
Indices: 2536578--2536678 Score: 89
Period size: 31 Copynumber: 3.2 Consensus size: 31
2536568 GTTATGTTTA
*
2536578 AATATTTTATTTTATTATAATTTTATTTAAA-ATT
1 AATATTTTATATTATT-TAATTTTA---AAATATT
* * *
2536612 AAT-TTTTATATTTATATAATTTTGATATATT
1 AATATTTTATA-TTATTTAATTTTAAAATATT
*
2536643 AATATTTTATATTATTTAAATTTAAAATATT
1 AATATTTTATATTATTTAATTTTAAAATATT
*
2536674 TATAT
1 AATAT
2536679 ATTCGTATCA
Statistics
Matches: 55, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
30 2 0.04
31 26 0.47
32 7 0.13
33 13 0.24
34 7 0.13
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (31 bp):
AATATTTTATATTATTTAATTTTAAAATATT
Found at i:2537315 original size:32 final size:30
Alignment explanation
Indices: 2537266--2537327 Score: 79
Period size: 32 Copynumber: 2.0 Consensus size: 30
2537256 ATAAAATTAA
*
2537266 AAATTTTAAACTTAAATAAAAATTAATATT
1 AAATTTAAAACTTAAATAAAAATTAATATT
**
2537296 AAATTTAATAACTTAAAATATTAATTAATATT
1 AAATTTAA-AACTT-AAATAAAAATTAATATT
2537328 TCACGTGCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 7 0.26
31 5 0.19
32 15 0.56
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (30 bp):
AAATTTAAAACTTAAATAAAAATTAATATT
Found at i:2538347 original size:21 final size:20
Alignment explanation
Indices: 2538315--2538354 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
2538305 AACATACGAC
*
2538315 AAAACCATGAAAAAAAAAAA
1 AAAACCAGGAAAAAAAAAAA
2538335 AAAAGCCAGGAAAAACAAAA
1 AAAA-CCAGGAAAAA-AAAA
2538355 CAATCTTGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 9 0.53
22 4 0.24
ACGTcount: A:0.75, C:0.12, G:0.10, T:0.03
Consensus pattern (20 bp):
AAAACCAGGAAAAAAAAAAA
Found at i:2538497 original size:14 final size:15
Alignment explanation
Indices: 2538472--2538500 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2538462 ATGATACATT
2538472 TATAATTATAATAAA
1 TATAATTATAATAAA
2538487 TATAA-TATAATAAA
1 TATAATTATAATAAA
2538501 AAATATATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TATAATTATAATAAA
Found at i:2538725 original size:3 final size:3
Alignment explanation
Indices: 2538717--2538760 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
2538707 CTTAGCAGGA
*
2538717 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT GAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2538761 AAATCAGTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2539287 original size:32 final size:35
Alignment explanation
Indices: 2539250--2539328 Score: 89
Period size: 32 Copynumber: 2.4 Consensus size: 35
2539240 GAGTGAGGTG
*
2539250 GAAAGAGGAG-GAAGGAAAGGAGAAAG-GAGA-AAA
1 GAAAGAGGAGAAAAGGAAAGGA-AAAGAGAGAGAAA
*
2539283 -AAAGA-AAGAAAAGGAAAGGAAAAGAGAGAGAAA
1 GAAAGAGGAGAAAAGGAAAGGAAAAGAGAGAGAAA
2539316 GAAAGAGG-GAAAA
1 GAAAGAGGAGAAAA
2539329 AAGAGACGAG
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
31 6 0.16
32 19 0.50
33 3 0.08
34 10 0.26
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (35 bp):
GAAAGAGGAGAAAAGGAAAGGAAAAGAGAGAGAAA
Found at i:2539305 original size:20 final size:20
Alignment explanation
Indices: 2539282--2539320 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2539272 AAAGGAGAAA
2539282 AAAAGAAAGA-AAAGGAAAGG
1 AAAAGAAAGAGAAA-GAAAGG
*
2539302 AAAAGAGAGAGAAAGAAAG
1 AAAAGAAAGAGAAAGAAAG
2539321 AGGGAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (20 bp):
AAAAGAAAGAGAAAGAAAGG
Found at i:2539339 original size:26 final size:25
Alignment explanation
Indices: 2539285--2539339 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 25
2539275 GGAGAAAAAA
2539285 AGAAAGAAAAGGAAAGGAAAAGAGAG
1 AGAAAGAAAAGGAAA-GAAAAGAGAG
*
2539311 AGAAAGAAAGAGGGAA-AAAAGAGACG
1 AGAAAGAAA-AGGAAAGAAAAGAGA-G
2539337 AGA
1 AGA
2539340 GAAAATATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
25 8 0.31
26 13 0.50
27 5 0.19
ACGTcount: A:0.64, C:0.02, G:0.35, T:0.00
Consensus pattern (25 bp):
AGAAAGAAAAGGAAAGAAAAGAGAG
Found at i:2539349 original size:2 final size:2
Alignment explanation
Indices: 2539344--2539371 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2539334 ACGAGAGAAA
2539344 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
2539372 GAAAAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2539421 original size:27 final size:27
Alignment explanation
Indices: 2539360--2539422 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
2539350 ATATATATAT
* *
2539360 ATATATATATATGAAAAAATTTATATC
1 ATATATATATATGAAAAAAATTATACC
* * *
2539387 TTAAATATATCT-AAAATAAATTATACC
1 ATATATATATATGAAAA-AAATTATACC
2539414 ATATATATA
1 ATATATATA
2539423 ATAATAACAC
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
26 4 0.14
27 24 0.86
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (27 bp):
ATATATATATATGAAAAAAATTATACC
Found at i:2539571 original size:20 final size:19
Alignment explanation
Indices: 2539548--2539589 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
2539538 TATTTTTTAT
*
2539548 ATTTTTATCTTATTATATTA
1 ATTTTTATATTA-TATATTA
*
2539568 ATTTTTATATTATATTTTA
1 ATTTTTATATTATATATTA
2539587 ATT
1 ATT
2539590 AATTTTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 9 0.45
20 11 0.55
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (19 bp):
ATTTTTATATTATATATTA
Found at i:2539596 original size:11 final size:12
Alignment explanation
Indices: 2539560--2539601 Score: 52
Period size: 12 Copynumber: 3.5 Consensus size: 12
2539550 TTTTATCTTA
2539560 TTATATTAATTT
1 TTATATTAATTT
2539572 TTATATT-ATATT
1 TTATATTAAT-TT
2539584 TTA-ATTAATTTT
1 TTATATTAA-TTT
2539596 TTATAT
1 TTATAT
2539602 CGTGTTCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
11 5 0.19
12 18 0.69
13 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TTATATTAATTT
Found at i:2539680 original size:31 final size:32
Alignment explanation
Indices: 2539642--2539705 Score: 96
Period size: 31 Copynumber: 2.0 Consensus size: 32
2539632 ATATTTAAAT
2539642 TTTATATAAATGTTT-ACACATTAAT-TATTCG
1 TTTATATAAAT-TTTAACACATTAATATATTCG
*
2539673 TTTATATATATTTTAACACATTAATATATTCG
1 TTTATATAAATTTTAACACATTAATATATTCG
2539705 T
1 T
2539706 ATCATGTTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
30 3 0.10
31 20 0.67
32 7 0.23
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.50
Consensus pattern (32 bp):
TTTATATAAATTTTAACACATTAATATATTCG
Found at i:2539890 original size:22 final size:20
Alignment explanation
Indices: 2539851--2539890 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2539841 TGTTTGTTTA
*
2539851 TAATTTATAAATGTTTTACT
1 TAATTTATAAATGATTTACT
2539871 TAATTTATCATAATGATTTA
1 TAATTTAT-A-AATGATTTA
2539891 ATTTAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 1 0.06
22 8 0.47
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.53
Consensus pattern (20 bp):
TAATTTATAAATGATTTACT
Found at i:2541647 original size:33 final size:33
Alignment explanation
Indices: 2541607--2541679 Score: 137
Period size: 33 Copynumber: 2.2 Consensus size: 33
2541597 GAATATACTT
2541607 AAATAAAAATAAAAATAAATTTTAAATCAATTA
1 AAATAAAAATAAAAATAAATTTTAAATCAATTA
2541640 AAATAAAAATAAAAATAAATTTTAAATCAATTA
1 AAATAAAAATAAAAATAAATTTTAAATCAATTA
2541673 AATATAA
1 AA-ATAA
2541680 TTTTTTTAAC
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
33 35 0.90
34 4 0.10
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (33 bp):
AAATAAAAATAAAAATAAATTTTAAATCAATTA
Found at i:2541653 original size:5 final size:6
Alignment explanation
Indices: 2541607--2541658 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
2541597 GAATATACTT
** *
2541607 AAATAA AAATAA AAATAA ATTTTAA ATCAATTA AAATAA AAATAA AAATAA
1 AAATAA AAATAA AAATAA A-AATAA A--AATAA AAATAA AAATAA AAATAA
2541658 A
1 A
2541659 TTTTAAATCA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
6 30 0.81
7 4 0.11
8 3 0.08
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (6 bp):
AAATAA
Found at i:2541674 original size:16 final size:16
Alignment explanation
Indices: 2541622--2541675 Score: 54
Period size: 16 Copynumber: 3.3 Consensus size: 16
2541612 AAAATAAAAA
2541622 TAAATTTTAAATCAAT
1 TAAATTTTAAATCAAT
* ** * *
2541638 TAAAATAAAAATAAAAA
1 TAAATTTTAAAT-CAAT
2541655 TAAATTTTAAATCAAT
1 TAAATTTTAAATCAAT
2541671 TAAAT
1 TAAAT
2541676 ATAATTTTTT
Statistics
Matches: 27, Mismatches: 10, Indels: 2
0.69 0.26 0.05
Matches are distributed among these distances:
16 16 0.59
17 11 0.41
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (16 bp):
TAAATTTTAAATCAAT
Found at i:2542103 original size:41 final size:41
Alignment explanation
Indices: 2542023--2542137 Score: 103
Period size: 41 Copynumber: 2.8 Consensus size: 41
2542013 AAAAATATTT
* * * *
2542023 TAATTTATCTTTAATTATAAATATTAATAA-AAAAATTTAAAA
1 TAATTTAACTTAAATT-TAAATAATAA-AATAAAATTTTAAAA
* * * *
2542065 TATTTTCACATT-ATTTTAAATAATAAAATAAAATTTTAAAT
1 TAATTTAAC-TTAAATTTAAATAATAAAATAAAATTTTAAAA
2542106 TAATTTAACTTAAATTTAAAT-A-AAAATAAAAT
1 TAATTTAACTTAAATTTAAATAATAAAATAAAAT
2542138 AAATATCTTA
Statistics
Matches: 60, Mismatches: 10, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
39 10 0.17
40 5 0.08
41 34 0.57
42 9 0.15
43 2 0.03
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (41 bp):
TAATTTAACTTAAATTTAAATAATAAAATAAAATTTTAAAA
Found at i:2542150 original size:30 final size:29
Alignment explanation
Indices: 2542114--2542179 Score: 107
Period size: 30 Copynumber: 2.3 Consensus size: 29
2542104 ATTAATTTAA
*
2542114 CTTAAATTTAAATAAAAATAAAATAAATAT
1 CTTAAATTTAAATAAAAATAAAACAAAT-T
2542144 CTTAAATTTAAATAAAAATAAAACAAATT
1 CTTAAATTTAAATAAAAATAAAACAAATT
2542173 -TTAAATT
1 CTTAAATT
2542180 GTAACCTCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
28 7 0.20
29 1 0.03
30 27 0.77
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.35
Consensus pattern (29 bp):
CTTAAATTTAAATAAAAATAAAACAAATT
Found at i:2543018 original size:14 final size:13
Alignment explanation
Indices: 2542984--2543036 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
2542974 AATGAATGAA
*
2542984 AAAAATAAAATAAT
1 AAAAATATAA-AAT
*
2542998 AGAAATATAAAAT
1 AAAAATATAAAAT
2543011 AAATAATATAGAAAT
1 AAA-AATATA-AAAT
*
2543026 ATAAATATAAA
1 AAAAATATAAA
2543037 TTTATAAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
13 7 0.21
14 20 0.61
15 6 0.18
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.25
Consensus pattern (13 bp):
AAAAATATAAAAT
Found at i:2543636 original size:2 final size:2
Alignment explanation
Indices: 2543629--2543679 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
2543619 CCATAGCTAG
2543629 AT AT AT AT AT 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 AT AT AT AT AT
2543671 AT AT AT AT A
1 AT AT AT AT A
2543680 CATGATATGT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2543731 original size:8 final size:8
Alignment explanation
Indices: 2543629--2543731 Score: 52
Period size: 8 Copynumber: 13.1 Consensus size: 8
2543619 CCATAGCTAG
*
2543629 ATATATAT
1 ATATATAA
*
2543637 ATATATAT
1 ATATATAA
*
2543645 ATATATAT
1 ATATATAA
*
2543653 ATATATAT
1 ATATATAA
*
2543661 ATATATAT
1 ATATATAA
*
2543669 ATATATAT
1 ATATATAA
* *
2543677 ATACAT-G
1 ATATATAA
* *
2543684 ATATGTTA
1 ATATATAA
*
2543692 A-ACATAA
1 ATATATAA
*
2543699 TTATATAA
1 ATATATAA
2543707 A-A-ATAA
1 ATATATAA
2543713 TATAATATAA
1 -AT-ATATAA
2543723 ATATATAA
1 ATATATAA
2543731 A
1 A
2543732 AATTTTAAAA
Statistics
Matches: 78, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
6 4 0.05
7 9 0.12
8 58 0.74
9 3 0.04
10 4 0.05
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (8 bp):
ATATATAA
Found at i:2543790 original size:6 final size:6
Alignment explanation
Indices: 2543779--2543849 Score: 53
Period size: 6 Copynumber: 12.5 Consensus size: 6
2543769 TAACATTTTT
* * * *
2543779 ATATAA ATATAA A-ATAT AT-TAA ATATAT TTATAA TTAT-A ATAT-A
1 ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
*
2543823 ATAAAA TATATAA ATATAA A-ATAA ATA
1 ATATAA -ATATAA ATATAA ATATAA ATA
2543850 CATGAAATAT
Statistics
Matches: 52, Mismatches: 8, Indels: 10
0.74 0.11 0.14
Matches are distributed among these distances:
5 21 0.40
6 26 0.50
7 5 0.10
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (6 bp):
ATATAA
Found at i:2543832 original size:15 final size:16
Alignment explanation
Indices: 2543781--2543849 Score: 54
Period size: 15 Copynumber: 4.2 Consensus size: 16
2543771 ACATTTTTAT
2543781 ATAAATATAAAATATA
1 ATAAATATAAAATATA
*
2543797 TTAAATATATTTATAATTATA
1 ATAAATATA---A-AA-TATA
*
2543818 ATATA-ATAAAATAT-
1 ATAAATATAAAATATA
2543832 ATAAATATAAAATA-A
1 ATAAATATAAAATATA
2543847 ATA
1 ATA
2543850 CATGAAATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 15
0.69 0.07 0.25
Matches are distributed among these distances:
14 4 0.10
15 14 0.33
16 10 0.24
17 1 0.02
19 1 0.02
20 5 0.12
21 7 0.17
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATAAATATAAAATATA
Found at i:2543834 original size:38 final size:37
Alignment explanation
Indices: 2543709--2543834 Score: 103
Period size: 32 Copynumber: 3.6 Consensus size: 37
2543699 TTATATAAAA
2543709 ATAATATAATATAAATATATA--AAAAT-TTTAAAATT
1 ATAATATAATATAAATATATATTAAAATATTT-AAATT
*
2543744 -T-ATATAATAT-AAT-T-TATTAACATA-TTAACATT
1 ATAATATAATATAAATATATATTAAAATATTTAA-ATT
* *
2543776 TTTATATAAATATAAA-ATATATTAAATATATTTATAATT
1 ATAATAT-AATATAAATATATATTAAA-ATATTTA-AATT
2543815 ATAATATAATA-AAATATATA
1 ATAATATAATATAAATATATA
2543835 AATATAAAAT
Statistics
Matches: 73, Mismatches: 4, Indels: 25
0.72 0.04 0.25
Matches are distributed among these distances:
30 2 0.03
31 3 0.04
32 12 0.16
33 10 0.14
34 5 0.07
35 5 0.07
36 3 0.04
37 9 0.12
38 12 0.16
39 11 0.15
40 1 0.01
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (37 bp):
ATAATATAATATAAATATATATTAAAATATTTAAATT
Found at i:2543840 original size:23 final size:22
Alignment explanation
Indices: 2543781--2543846 Score: 64
Period size: 23 Copynumber: 3.0 Consensus size: 22
2543771 ACATTTTTAT
*
2543781 ATAAATATA-AAATATATTA-A
1 ATAAATATATAAATATAATATA
* * *
2543801 ATATATTTATAATTATAATATA
1 ATAAATATATAAATATAATATA
*
2543823 ATAAAATATATAAATATAAAATA
1 AT-AAATATATAAATATAATATA
2543846 A
1 A
2543847 ATACATGAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
20 7 0.20
21 8 0.23
22 3 0.09
23 17 0.49
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
ATAAATATATAAATATAATATA
Found at i:2543857 original size:20 final size:18
Alignment explanation
Indices: 2543817--2543859 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
2543807 TTATAATTAT
* *
2543817 AATATAATAAAATATATA
1 AATATAAAAAAATACATA
2543835 AATATAAAATAAATACATGA
1 AATATAAAA-AAATACAT-A
2543855 AATAT
1 AATAT
2543860 TATATCAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 8 0.38
19 7 0.33
20 6 0.29
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (18 bp):
AATATAAAAAAATACATA
Found at i:2543999 original size:6 final size:6
Alignment explanation
Indices: 2543988--2544014 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2543978 TCTCTCTAAA
2543988 AAAAAG AAAAAG AAAAAG AAAAAG AAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAA
2544015 TTAATATTGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:2544206 original size:2 final size:2
Alignment explanation
Indices: 2544188--2544233 Score: 74
Period size: 2 Copynumber: 23.0 Consensus size: 2
2544178 TTAATATTAA
* *
2544188 AT AT TT AT AT AT GT 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 AT AT AT AT AT
2544230 AT AT
1 AT AT
2544234 TCAACCACAC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (2 bp):
AT
Found at i:2544652 original size:14 final size:14
Alignment explanation
Indices: 2544635--2544666 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
2544625 TATTTAGTAT
2544635 ATTTAAAATTTATA
1 ATTTAAAATTTATA
*
2544649 ATTTAATATTTATA
1 ATTTAAAATTTATA
2544663 ATTT
1 ATTT
2544667 TTTTATTAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
ATTTAAAATTTATA
Found at i:2544652 original size:23 final size:21
Alignment explanation
Indices: 2544613--2544666 Score: 56
Period size: 23 Copynumber: 2.5 Consensus size: 21
2544603 ATATAATTAT
*
2544613 TTTAAAATATAATATTTAGTATA
1 TTTAAAATTTAATATTTA--ATA
2544636 TTTAAAATTT-ATAATTTAATA
1 TTTAAAATTTAAT-ATTTAATA
*
2544657 TTTATAATTT
1 TTTAAAATTT
2544667 TTTTATTAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 12 0.43
22 2 0.07
23 14 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (21 bp):
TTTAAAATTTAATATTTAATA
Found at i:2548272 original size:2 final size:2
Alignment explanation
Indices: 2548267--2548301 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2548257 TCTTTTAAGG
2548267 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
2548302 GTGGCTTTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2548659 original size:45 final size:44
Alignment explanation
Indices: 2548599--2548696 Score: 151
Period size: 45 Copynumber: 2.2 Consensus size: 44
2548589 AAATTTATTA
*
2548599 AAAAAATATATACGACCGAGAAAGTTATTTTTGAGTTTTTAATT
1 AAAAAATATATACGACAGAGAAAGTTATTTTTGAGTTTTTAATT
* *
2548643 AAGAAAATATATACGACAGAGGAAGTTATTTTTTAGTTTTTAATTT
1 AA-AAAATATATACGACAGAGAAAGTTATTTTTGAGTTTTTAA-TT
2548689 AAAAAATA
1 AAAAAATA
2548697 AGATTTTAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
44 2 0.04
45 43 0.88
46 4 0.08
ACGTcount: A:0.44, C:0.05, G:0.13, T:0.38
Consensus pattern (44 bp):
AAAAAATATATACGACAGAGAAAGTTATTTTTGAGTTTTTAATT
Found at i:2548782 original size:26 final size:26
Alignment explanation
Indices: 2548753--2548802 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
2548743 ATGAATCAAA
2548753 TAATATTATATTA-TTTAAATAAAAAT
1 TAATATTAT-TTATTTTAAATAAAAAT
* *
2548779 TAATTTTATTTATTTTTAATAAAA
1 TAATATTATTTATTTTAAATAAAA
2548803 TAAAATAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 3 0.14
26 18 0.86
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
TAATATTATTTATTTTAAATAAAAAT
Found at i:2548906 original size:21 final size:23
Alignment explanation
Indices: 2548858--2548906 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 23
2548848 ATCTTTTATA
2548858 AATATATATTTTATTTTAATATT
1 AATATATATTTTATTTTAATATT
*
2548881 TATATA-ATTTT-TTATTAA-ATT
1 AATATATATTTTATT-TTAATATT
2548902 AATAT
1 AATAT
2548907 CACTCTACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 9 0.39
22 9 0.39
23 5 0.22
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
AATATATATTTTATTTTAATATT
Found at i:2549821 original size:2 final size:2
Alignment explanation
Indices: 2549814--2549878 Score: 63
Period size: 2 Copynumber: 35.5 Consensus size: 2
2549804 TTCATGTTTC
*
2549814 TA TA TA TA TA TA TA TA TA TA TA TA T- TA -A AA T- TA TA T- TGA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A
2549853 TA -A TA -A T- 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
2549879 TTCATCTAAG
Statistics
Matches: 54, Mismatches: 1, Indels: 16
0.76 0.01 0.23
Matches are distributed among these distances:
1 7 0.13
2 46 0.85
3 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2550315 original size:2 final size:2
Alignment explanation
Indices: 2550302--2550333 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2550292 TTTCTGTTAT
*
2550302 TC TC TA TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2550334 CATCTATTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.03, C:0.47, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2552081 original size:2 final size:2
Alignment explanation
Indices: 2552074--2552104 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2552064 GTATGTTGAC
2552074 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2552105 CACATATGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2554606 original size:13 final size:13
Alignment explanation
Indices: 2554590--2554614 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2554580 AACTTAAAAT
2554590 TTAATTTAATTAA
1 TTAATTTAATTAA
2554603 TTAATTTAATTA
1 TTAATTTAATTA
2554615 TTTTTAAATA
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAATTTAATTAA
Found at i:2555396 original size:21 final size:20
Alignment explanation
Indices: 2555362--2555401 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
2555352 ATATTTTTTT
*
2555362 TATTTTTCAAAATTATAAAC
1 TATTTATCAAAATTATAAAC
2555382 TATTTATCATAAATTATAAA
1 TATTTATCA-AAATTATAAA
2555402 AAATTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.45
Consensus pattern (20 bp):
TATTTATCAAAATTATAAAC
Found at i:2555984 original size:2 final size:2
Alignment explanation
Indices: 2555977--2556019 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
2555967 AATATGAGGC
2555977 AT AT AT AT AT 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 AT AT AT AT AT
2556019 A
1 A
2556020 AAGCAATTGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2558082 original size:3 final size:3
Alignment explanation
Indices: 2558074--2558113 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
2558064 AATTTCACTT
2558074 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2558114 GCAAAATCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2567091 original size:2 final size:2
Alignment explanation
Indices: 2567084--2567120 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2567074 TATTCCAATC
*
2567084 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2567121 TTGATTAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2569206 original size:41 final size:42
Alignment explanation
Indices: 2569156--2569247 Score: 132
Period size: 45 Copynumber: 2.1 Consensus size: 42
2569146 AAAGTAAGCC
*
2569156 ACATTTAAACTATATGATTGCT-ACAACTGCAACTTTTCACA
1 ACATATAAACTATATGATTGCTAACAACTGCAACTTTTCACA
*
2569197 ACATATAAACTATATGCTTGCTAGCAACAACTGCAACTTTTCACA
1 ACATATAAACTATATGATTGCT---AACAACTGCAACTTTTCACA
2569242 ACATAT
1 ACATAT
2569248 TCCCAGATTG
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
41 20 0.44
45 25 0.56
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.32
Consensus pattern (42 bp):
ACATATAAACTATATGATTGCTAACAACTGCAACTTTTCACA
Found at i:2569518 original size:2 final size:2
Alignment explanation
Indices: 2569511--2569560 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
2569501 TTTTCTTCAA
2569511 AT AT AT AT AT 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 AT AT AT AT AT
2569553 AT AT AT AT
1 AT AT AT AT
2569561 TCTCACTGAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2571853 original size:21 final size:20
Alignment explanation
Indices: 2571825--2571906 Score: 69
Period size: 19 Copynumber: 3.9 Consensus size: 20
2571815 TTTTAAGATT
2571825 TAAATTATAATATTATATATA
1 TAAATTAT-ATATTATATATA
*
2571846 TTAATTAT-T-TTATATAATA
1 TAAATTATATATTATAT-ATA
*
2571865 TAAATTATATAATATATAAATA
1 TAAATTATAT-AT-TATATATA
*
2571887 TCAAAATAATATATTATATA
1 T--AAATTATATATTATATA
2571907 ATTAAAAAAT
Statistics
Matches: 49, Mismatches: 5, Indels: 13
0.73 0.07 0.19
Matches are distributed among these distances:
18 6 0.12
19 11 0.22
20 1 0.02
21 7 0.14
22 10 0.20
23 6 0.12
24 8 0.16
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (20 bp):
TAAATTATATATTATATATA
Found at i:2571870 original size:19 final size:18
Alignment explanation
Indices: 2571837--2571885 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
2571827 AATTATAATA
*
2571837 TTATATATATTAATTATT
1 TTATATATATAAATTATT
2571855 TTATATAATATAAATTA-T
1 TTATAT-ATATAAATTATT
*
2571873 ATA-ATATATAAAT
1 TTATATATATAAAT
2571886 ATCAAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 8 0.29
17 2 0.07
18 9 0.32
19 9 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTATATATATAAATTATT
Found at i:2571875 original size:16 final size:17
Alignment explanation
Indices: 2571830--2571875 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
2571820 AGATTTAAAT
2571830 TATAATATTATATAT-A
1 TATAATATTATATATAA
*
2571846 T-TAATTATTTTATATAA
1 TATAA-TATTATATATAA
2571863 TATAA-ATTATATA
1 TATAATATTATATA
2571876 ATATATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
15 3 0.12
16 17 0.68
17 2 0.08
18 3 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TATAATATTATATATAA
Found at i:2571976 original size:20 final size:20
Alignment explanation
Indices: 2571951--2571989 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2571941 GTTTCTAATG
2571951 ATAAATGTAATTTTTTTAAA
1 ATAAATGTAATTTTTTTAAA
* *
2571971 ATAAATTTTATTTTTTTAA
1 ATAAATGTAATTTTTTTAA
2571990 TTTAATATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (20 bp):
ATAAATGTAATTTTTTTAAA
Found at i:2572173 original size:11 final size:10
Alignment explanation
Indices: 2572146--2572172 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
2572136 GAAAAAGTGG
2572146 AAAAAAAGAA
1 AAAAAAAGAA
2572156 AAAAAAAGAA
1 AAAAAAAGAA
2572166 AAAAAAA
1 AAAAAAA
2572173 AAAGAGGGTG
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:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (10 bp):
AAAAAAAGAA
Found at i:2586653 original size:2 final size:2
Alignment explanation
Indices: 2586646--2586691 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
2586636 ACAGTCACAG
2586646 AT AT AT AT AT 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 AT AT AT AT AT
2586688 AT AT
1 AT AT
2586692 TTAAAGGGAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2592874 original size:11 final size:10
Alignment explanation
Indices: 2592858--2592908 Score: 54
Period size: 9 Copynumber: 5.2 Consensus size: 10
2592848 AAAATTTGAT
2592858 ATAATTTTAAA
1 ATAATTTT-AA
2592869 ATAA-TTTAA
1 ATAATTTTAA
*
2592878 ATAATTTAAAA
1 ATAATTT-TAA
2592889 ATAA-TTTAA
1 ATAATTTTAA
2592898 ATAA-TTTAA
1 ATAATTTTAA
2592907 AT
1 AT
2592909 TTTATATAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
9 19 0.53
10 7 0.19
11 10 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (10 bp):
ATAATTTTAA
Found at i:2592881 original size:9 final size:9
Alignment explanation
Indices: 2592867--2592908 Score: 66
Period size: 9 Copynumber: 4.4 Consensus size: 9
2592857 TATAATTTTA
2592867 AAATAATTT
1 AAATAATTT
2592876 AAATAATTT
1 AAATAATTT
2592885 AAAAATAATTT
1 --AAATAATTT
2592896 AAATAATTT
1 AAATAATTT
2592905 AAAT
1 AAAT
2592909 TTTATATAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
9 22 0.71
11 9 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (9 bp):
AAATAATTT
Found at i:2592883 original size:20 final size:20
Alignment explanation
Indices: 2592858--2592907 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
2592848 AAAATTTGAT
*
2592858 ATAATTTTAAAATAATTTAA
1 ATAATTTAAAAATAATTTAA
2592878 ATAATTTAAAAATAATTTAA
1 ATAATTTAAAAATAATTTAA
2592898 ATAATTTAAA
1 ATAATTTAAA
2592908 TTTTATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
ATAATTTAAAAATAATTTAA
Found at i:2592923 original size:16 final size:16
Alignment explanation
Indices: 2592904--2592950 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
2592894 TTAAATAATT
2592904 TAAATTTTATATAAAA
1 TAAATTTTATATAAAA
* *
2592920 TAAATTATTA-ATATAC
1 TAAATT-TTATATAAAA
*
2592936 CAAATTTTATATAAA
1 TAAATTTTATATAAA
2592951 TATATAATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 3 0.12
16 19 0.76
17 3 0.12
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (16 bp):
TAAATTTTATATAAAA
Found at i:2597070 original size:15 final size:15
Alignment explanation
Indices: 2597050--2597085 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
2597040 GAAATTTCGA
*
2597050 AAAATAAATCATTTT
1 AAAATAAATCAATTT
*
2597065 AAAATATATCAATTT
1 AAAATAAATCAATTT
2597080 AAAATA
1 AAAATA
2597086 GAAGTATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (15 bp):
AAAATAAATCAATTT
Found at i:2598276 original size:2 final size:2
Alignment explanation
Indices: 2598269--2598303 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2598259 ACCATTCTCT
*
2598269 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2598304 TAGTGTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:2604058 original size:2 final size:2
Alignment explanation
Indices: 2604051--2604084 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2604041 CATATTTATT
2604051 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2604085 AATGAAAAGG
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2604817 original size:18 final size:16
Alignment explanation
Indices: 2604786--2604819 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
2604776 TAAATTTTTT
2604786 ATTTAAATTTAAATTA
1 ATTTAAATTTAAATTA
2604802 ATTTAAAATATTAAATTA
1 ATTT-AAAT-TTAAATTA
2604820 TTATTTATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 4 0.25
18 8 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTTAAATTTAAATTA
Found at i:2604861 original size:19 final size:21
Alignment explanation
Indices: 2604839--2604883 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
2604829 AAATAATAAA
2604839 ATATTAA-AAAATTAT-TTTT
1 ATATTAATAAAATTATATTTT
**
2604858 ATATTAATAATTTTATATTTT
1 ATATTAATAAAATTATATTTT
2604879 ATATT
1 ATATT
2604884 TAATTTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 7 0.32
20 6 0.27
21 9 0.41
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
ATATTAATAAAATTATATTTT
Found at i:2604902 original size:27 final size:29
Alignment explanation
Indices: 2604872--2604949 Score: 97
Period size: 33 Copynumber: 2.6 Consensus size: 29
2604862 TAATAATTTT
*
2604872 ATATTTTA-TATTTAAT-TTTAAATAGAA
1 ATATTTTATTATTTAATATTTAAATAAAA
2604899 ATATTTTATTATTTAATAATAATTTAAATAAAA
1 ATATTTTATTA-TT--TAAT-ATTTAAATAAAA
2604932 ATATTTTATTATTTAATA
1 ATATTTTATTATTTAATA
2604950 ATAATTTAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
27 8 0.18
28 2 0.05
29 3 0.07
30 4 0.09
31 4 0.09
32 2 0.05
33 21 0.48
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (29 bp):
ATATTTTATTATTTAATATTTAAATAAAA
Found at i:2604924 original size:18 final size:18
Alignment explanation
Indices: 2604898--2604957 Score: 63
Period size: 18 Copynumber: 3.5 Consensus size: 18
2604888 TTTAAATAGA
*
2604898 AATATTTTATTATTTAAT
1 AATAATTTATTATTTAAT
* *
2604916 AATAATTTA--A-ATAAA
1 AATAATTTATTATTTAAT
*
2604931 AATATTTTATTATTTAAT
1 AATAATTTATTATTTAAT
2604949 AATAATTTA
1 AATAATTTA
2604958 AATAAAATAG
Statistics
Matches: 32, Mismatches: 7, Indels: 6
0.71 0.16 0.13
Matches are distributed among these distances:
15 11 0.34
16 1 0.03
17 1 0.03
18 19 0.59
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
AATAATTTATTATTTAAT
Found at i:2604934 original size:33 final size:33
Alignment explanation
Indices: 2604888--2604964 Score: 145
Period size: 33 Copynumber: 2.3 Consensus size: 33
2604878 TATATTTAAT
*
2604888 TTTAAATAGAAATATTTTATTATTTAATAATAA
1 TTTAAATAAAAATATTTTATTATTTAATAATAA
2604921 TTTAAATAAAAATATTTTATTATTTAATAATAA
1 TTTAAATAAAAATATTTTATTATTTAATAATAA
2604954 TTTAAATAAAA
1 TTTAAATAAAA
2604965 TAGATAGCTA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (33 bp):
TTTAAATAAAAATATTTTATTATTTAATAATAA
Found at i:2604960 original size:27 final size:27
Alignment explanation
Indices: 2604862--2604961 Score: 78
Period size: 33 Copynumber: 3.5 Consensus size: 27
2604852 ATTTTTATAT
*
2604862 TAATAATTT-TATATTTTA-TATTTAA
1 TAATAATTTAAATATTTTATTATTTAA
** **
2604887 TTTTAAATAGAAATATTTTATTATTTAA
1 TAAT-AATTTAAATATTTTATTATTTAA
2604915 TAATAATTTAAATAAAAATATTTTATTATTTAA
1 TAATAA-TT---T--AAATATTTTATTATTTAA
2604948 TAATAATTTAAATA
1 TAATAATTTAAATA
2604962 AAATAGATAG
Statistics
Matches: 57, Mismatches: 9, Indels: 16
0.70 0.11 0.20
Matches are distributed among these distances:
25 2 0.04
26 3 0.05
27 15 0.26
28 10 0.18
29 1 0.02
32 2 0.04
33 24 0.42
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (27 bp):
TAATAATTTAAATATTTTATTATTTAA
Found at i:2605090 original size:24 final size:27
Alignment explanation
Indices: 2605055--2605105 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
2605045 TATTTGATTC
2605055 ATTCAACT-AAAAT-AA-TTATAAAAT
1 ATTCAACTAAAAATCAAGTTATAAAAT
2605079 ATTCAA-TGAAAAATCAAGTTATAAAAT
1 ATTCAACT-AAAAATCAAGTTATAAAAT
2605106 GATATTCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
23 1 0.04
24 6 0.26
25 5 0.22
26 2 0.09
27 9 0.39
ACGTcount: A:0.57, C:0.08, G:0.04, T:0.31
Consensus pattern (27 bp):
ATTCAACTAAAAATCAAGTTATAAAAT
Found at i:2605780 original size:20 final size:19
Alignment explanation
Indices: 2605750--2605794 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
2605740 TAAGTTGTTA
*
2605750 ATTTTTT-AAAATATATATT
1 ATTTTTTAAAAATAT-TAAT
2605769 ATTTTTTAAAAAATATTAAT
1 ATTTTTT-AAAAATATTAAT
2605789 ATTTTT
1 ATTTTT
2605795 ATTTTATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 7 0.30
20 9 0.39
21 7 0.30
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
ATTTTTTAAAAATATTAAT
Found at i:2605795 original size:19 final size:20
Alignment explanation
Indices: 2605747--2605795 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 20
2605737 TTTTAAGTTG
2605747 TTAATTTTTTAAAATATATA
1 TTAATTTTTTAAAATATATA
2605767 TT-ATTTTTTAAAA-A-ATA
1 TTAATTTTTTAAAATATATA
2605784 TTAATATTTTTA
1 TTAAT-TTTTTA
2605796 TTTTATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 5 0.19
18 3 0.11
19 17 0.63
20 2 0.07
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TTAATTTTTTAAAATATATA
Found at i:2606002 original size:60 final size:60
Alignment explanation
Indices: 2605929--2606060 Score: 133
Period size: 60 Copynumber: 2.2 Consensus size: 60
2605919 ATATTTTTTA
** * * * * * *
2605929 TTATACATTAATAAACCCTTAATTTTTAATTTATA-TCAAACTAAAATTTTAACT-TTTAAT
1 TTATACAAAAATAAAACCTTAATCTTAAACTTATACCCAAA-TAAAATTTTAA-TATATAAT
* *
2605989 TTATACAAAAATAAAATCTTAATCTTAAACTTATACCCAAATAAACTTTTAATATATAAT
1 TTATACAAAAATAAAACCTTAATCTTAAACTTATACCCAAATAAAATTTTAATATATAAT
2606049 TTATACTAAAAA
1 TTATAC-AAAAA
2606061 ATAACATATA
Statistics
Matches: 59, Mismatches: 10, Indels: 5
0.80 0.14 0.07
Matches are distributed among these distances:
59 1 0.02
60 49 0.83
61 9 0.15
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (60 bp):
TTATACAAAAATAAAACCTTAATCTTAAACTTATACCCAAATAAAATTTTAATATATAAT
Found at i:2606004 original size:30 final size:30
Alignment explanation
Indices: 2605947--2606060 Score: 97
Period size: 30 Copynumber: 3.8 Consensus size: 30
2605937 TAATAAACCC
* *
2605947 TTAATTTTTAATTTATATC-AAACTAAAATT
1 TTAATATTTAATTTATA-CAAAAATAAAATT
*
2605977 TTAACT-TTTAATTTATACAAAAATAAAATC
1 TTAA-TATTTAATTTATACAAAAATAAAATT
* * * ** *
2606007 TTAATCTTAAACTTATACCCAAATAAACTT
1 TTAATATTTAATTTATACAAAAATAAAATT
*
2606037 TTAATATATAATTTATACTAAAAA
1 TTAATATTTAATTTATAC-AAAAA
2606061 ATAACATATA
Statistics
Matches: 66, Mismatches: 14, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
29 2 0.03
30 60 0.91
31 4 0.06
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (30 bp):
TTAATATTTAATTTATACAAAAATAAAATT
Found at i:2606128 original size:29 final size:29
Alignment explanation
Indices: 2606085--2606171 Score: 99
Period size: 29 Copynumber: 3.1 Consensus size: 29
2606075 TCTTTCATTT
** *
2606085 AAAATAAAAAATTATTTAAATATAAATTA
1 AAAATAAAATTTTATTTAAATATAAAATA
*
2606114 AAAATAAAATTTTATTTAAATAT--AGTA
1 AAAATAAAATTTTATTTAAATATAAAATA
* *
2606141 AAAATATAATTTT-TTTAAAAATAAAATA
1 AAAATAAAATTTTATTTAAATATAAAATA
2606169 AAA
1 AAA
2606172 TAATTTAAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
26 8 0.16
27 15 0.30
28 6 0.12
29 21 0.42
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (29 bp):
AAAATAAAATTTTATTTAAATATAAAATA
Found at i:2606727 original size:2 final size:2
Alignment explanation
Indices: 2606720--2606756 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2606710 AATGTATGGG
2606720 TA TA TA TA 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 TA TA TA TA T
2606757 GAGTGAATTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2607548 original size:16 final size:16
Alignment explanation
Indices: 2607529--2607574 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
2607519 TTAAGTTCAG
2607529 ATTATTTTAATTTTAA
1 ATTATTTTAATTTTAA
** * *
2607545 ATTACATTGATTCTAA
1 ATTATTTTAATTTTAA
2607561 ATTATTTTAATTTT
1 ATTATTTTAATTTT
2607575 GATTTATTTC
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (16 bp):
ATTATTTTAATTTTAA
Found at i:2612822 original size:3 final size:3
Alignment explanation
Indices: 2612809--2612845 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
2612799 CACGTATGAG
*
2612809 TAT TA- TAT TAT TAT TAT TAT TAT TAT TGT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
2612846 ATTGGTTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:2613435 original size:25 final size:28
Alignment explanation
Indices: 2613390--2613441 Score: 74
Period size: 25 Copynumber: 2.0 Consensus size: 28
2613380 TAAATTTTTA
*
2613390 TTTTTAAATAATAATATAAAATTATAAG
1 TTTTTAAATAATAATATAAAAATATAAG
2613418 TTTTTAAAT-AT-ATA-AAAAATATAA
1 TTTTTAAATAATAATATAAAAATATAA
2613442 AAATTATGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 9 0.39
26 3 0.13
27 2 0.09
28 9 0.39
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (28 bp):
TTTTTAAATAATAATATAAAAATATAAG
Found at i:2613779 original size:20 final size:20
Alignment explanation
Indices: 2613764--2613802 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2613754 TTATTTTTAA
*
2613764 ATTAGTAAAAAAATTTAAAAT
1 ATTA-TAAAAAAATTTTAAAT
2613785 ATTATAAAAAAATTTTAA
1 ATTATAAAAAAATTTTAA
2613803 TTTAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (20 bp):
ATTATAAAAAAATTTTAAAT
Found at i:2614167 original size:21 final size:20
Alignment explanation
Indices: 2614122--2614168 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
2614112 ATATTAATAT
* *
2614122 AGAAAAATATTTTAAAAAAT
1 AGAATAATATTTTAAAAAAC
2614142 A-AATAATAATTTTAAAAAAC
1 AGAATAAT-ATTTTAAAAAAC
2614162 AGAATAA
1 AGAATAA
2614169 ATTCAAAGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 5 0.22
20 13 0.57
21 5 0.22
ACGTcount: A:0.66, C:0.02, G:0.04, T:0.28
Consensus pattern (20 bp):
AGAATAATATTTTAAAAAAC
Found at i:2615512 original size:16 final size:17
Alignment explanation
Indices: 2615493--2615532 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
2615483 TAAAAACAAA
*
2615493 TTATAAATTGTAA-TTT
1 TTATAAATTATAATTTT
*
2615509 TTATAAGTTATAATTTT
1 TTATAAATTATAATTTT
2615526 TTATAAA
1 TTATAAA
2615533 AATAAAATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (17 bp):
TTATAAATTATAATTTT
Found at i:2624880 original size:34 final size:34
Alignment explanation
Indices: 2624837--2624905 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
2624827 GGTGAAGAGA
2624837 ACTATTGAATGGTTACACTGCAAATGTCTGTTGC
1 ACTATTGAATGGTTACACTGCAAATGTCTGTTGC
2624871 ACTATTGAATGGTTACACTGCAAATGTCTGTTGC
1 ACTATTGAATGGTTACACTGCAAATGTCTGTTGC
2624905 A
1 A
2624906 GTCATCTTCT
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:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (34 bp):
ACTATTGAATGGTTACACTGCAAATGTCTGTTGC
Found at i:2628345 original size:3 final size:3
Alignment explanation
Indices: 2628337--2628368 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2628327 TATGTCATAA
2628337 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
2628369 GATTTGATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:2630281 original size:2 final size:2
Alignment explanation
Indices: 2630274--2630307 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2630264 CTAACTTATG
2630274 AT 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 AT
2630308 GAAATTGTTC
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2631465 original size:23 final size:23
Alignment explanation
Indices: 2631438--2631496 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
2631428 TGTAACGTAT
*
2631438 TAATAAAATATTATTTAATATTA
1 TAATAAAATATTATTTAAAATTA
* * *
2631461 TAATAATATTTTATTTAAAATTG
1 TAATAAAATATTATTTAAAATTA
*
2631484 TAAAAATAATATT
1 TAATAA-AATATT
2631497 TTAGTAGTAA
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
23 24 0.86
24 4 0.14
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
TAATAAAATATTATTTAAAATTA
Found at i:2631555 original size:32 final size:32
Alignment explanation
Indices: 2631487--2631555 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 32
2631477 AAAATTGTAA
* * **
2631487 AAATAATATTTTAGTAGTAATTATATTAATTG
1 AAATAATATTTTAATAATAATTATAACAATTG
* *
2631519 AAATAATATTTTAATAATAATTATAACATTTT
1 AAATAATATTTTAATAATAATTATAACAATTG
2631551 AAATA
1 AAATA
2631556 TTTTATATAA
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:0.49, C:0.01, G:0.04, T:0.45
Consensus pattern (32 bp):
AAATAATATTTTAATAATAATTATAACAATTG
Found at i:2631619 original size:18 final size:21
Alignment explanation
Indices: 2631598--2631643 Score: 71
Period size: 18 Copynumber: 2.3 Consensus size: 21
2631588 ATTATTTAAG
2631598 TATTTAA-CATT-AATATAA-
1 TATTTAAGCATTAAATATAAT
2631616 TATTTAAGCATTAAATATAAT
1 TATTTAAGCATTAAATATAAT
2631637 TATTTAA
1 TATTTAA
2631644 AATATTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.28
19 4 0.16
20 7 0.28
21 7 0.28
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (21 bp):
TATTTAAGCATTAAATATAAT
Found at i:2632622 original size:18 final size:18
Alignment explanation
Indices: 2632583--2632622 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
2632573 ATATTTATAT
*
2632583 ATAAAATTAATTTGTTAT
1 ATAAAATTAATTTGTTAA
2632601 ATAAAATTAATTT-TTCAA
1 ATAAAATTAATTTGTT-AA
2632619 ATAA
1 ATAA
2632623 TTTATTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 2 0.10
18 18 0.90
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (18 bp):
ATAAAATTAATTTGTTAA
Found at i:2632903 original size:16 final size:17
Alignment explanation
Indices: 2632875--2632906 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
2632865 TAAACTCAAT
2632875 TAAAATGAAAAAAAAAG
1 TAAAATGAAAAAAAAAG
2632892 TAAAAT-AAAAAAAAA
1 TAAAATGAAAAAAAAA
2632907 ACCTAAATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.81, C:0.00, G:0.06, T:0.12
Consensus pattern (17 bp):
TAAAATGAAAAAAAAAG
Found at i:2632907 original size:17 final size:17
Alignment explanation
Indices: 2632875--2632907 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2632865 TAAACTCAAT
*
2632875 TAAAATGAAAAAAAAAG
1 TAAAATAAAAAAAAAAG
2632892 TAAAATAAAAAAAAAA
1 TAAAATAAAAAAAAAA
2632908 CCTAAATCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (17 bp):
TAAAATAAAAAAAAAAG
Found at i:2632913 original size:18 final size:17
Alignment explanation
Indices: 2632875--2632913 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
2632865 TAAACTCAAT
* *
2632875 TAAAATGAAAAAAAAAG
1 TAAAATAAAAAAAAAAC
2632892 TAAAATAAAAAAAAAACC
1 TAAAATAAAAAAAAAA-C
2632910 TAAA
1 TAAA
2632914 TCTTCAGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.77, C:0.05, G:0.05, T:0.13
Consensus pattern (17 bp):
TAAAATAAAAAAAAAAC
Found at i:2633907 original size:16 final size:16
Alignment explanation
Indices: 2633888--2633918 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2633878 AGTTTGAGCT
*
2633888 ATTTCGAGTTCGAATA
1 ATTTCGAATTCGAATA
2633904 ATTTCGAATTCGAAT
1 ATTTCGAATTCGAAT
2633919 TTTTAATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.13, G:0.16, T:0.39
Consensus pattern (16 bp):
ATTTCGAATTCGAATA
Found at i:2634113 original size:22 final size:22
Alignment explanation
Indices: 2634094--2634146 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
2634084 ATTCAAATTT
*
2634094 AATTAAATTTAGTATTAAATCA
1 AATTAAATTTAATATTAAATCA
*
2634116 AATTGAATTTAATATTAAATCA
1 AATTAAATTTAATATTAAATCA
*
2634138 AATTGAATT
1 AATTAAATT
2634147 GAACTTAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.42
Consensus pattern (22 bp):
AATTAAATTTAATATTAAATCA
Found at i:2634124 original size:27 final size:26
Alignment explanation
Indices: 2634086--2634146 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 26
2634076 TCAAAATGAT
* *
2634086 TCAAATTTAATTAAATTTAGTATTAAA
1 TCAAATTGAATT-AATTTAATATTAAA
2634113 TCAAATTG----AATTTAATATTAAA
1 TCAAATTGAATTAATTTAATATTAAA
2634135 TCAAATTGAATT
1 TCAAATTGAATT
2634147 GAACTTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 9
0.72 0.05 0.23
Matches are distributed among these distances:
22 21 0.75
27 7 0.25
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.43
Consensus pattern (26 bp):
TCAAATTGAATTAATTTAATATTAAA
Found at i:2634157 original size:22 final size:22
Alignment explanation
Indices: 2634110--2634157 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
2634100 ATTTAGTATT
* *
2634110 AAATCAAATTGAATTTAATATT
1 AAATCAAATTGAATTGAATATA
2634132 AAATCAAATTGAATTGAACT-TA
1 AAATCAAATTGAATTGAA-TATA
2634154 AAAT
1 AAAT
2634158 TATTTAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.35
Consensus pattern (22 bp):
AAATCAAATTGAATTGAATATA
Found at i:2634236 original size:16 final size:16
Alignment explanation
Indices: 2634153--2634237 Score: 75
Period size: 16 Copynumber: 5.3 Consensus size: 16
2634143 AATTGAACTT
*
2634153 AAAATTATTTAAAATC
1 AAAATAATTTAAAATC
*
2634169 AAAATAATTCAAACA-C
1 AAAATAATTTAAA-ATC
*
2634185 AAAATAATTTAAATATA
1 AAAATAATTTAAA-ATC
* *
2634202 AAAAT-ATTTATAATT
1 AAAATAATTTAAAATC
* *
2634217 AAAATATTTTAAACTC
1 AAAATAATTTAAAATC
2634233 AAAAT
1 AAAAT
2634238 GAACTAAACT
Statistics
Matches: 55, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
15 7 0.13
16 42 0.76
17 6 0.11
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.34
Consensus pattern (16 bp):
AAAATAATTTAAAATC
Found at i:2636421 original size:16 final size:16
Alignment explanation
Indices: 2636402--2636438 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
2636392 TTTATATGAT
2636402 TATATTTATATCAAAA
1 TATATTTATATCAAAA
*
2636418 TATATTTATATTAAAA
1 TATATTTATATCAAAA
2636434 TATAT
1 TATAT
2636439 ATATTAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (16 bp):
TATATTTATATCAAAA
Found at i:2636441 original size:14 final size:14
Alignment explanation
Indices: 2636403--2636446 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
2636393 TTATATGATT
* *
2636403 ATATTTATATCAAA
1 ATATATATATTAAA
2636417 ATATATTTATATTAAA
1 ATATA--TATATTAAA
2636433 ATATATATATTAAA
1 ATATATATATTAAA
2636447 TTACTTCGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 13 0.50
16 13 0.50
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (14 bp):
ATATATATATTAAA
Found at i:2637319 original size:2 final size:2
Alignment explanation
Indices: 2637312--2637351 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2637302 TTTCATGTGC
2637312 AT AT AT AT 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 AT AT AT AT
2637352 TCTGCGTGAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2637774 original size:21 final size:21
Alignment explanation
Indices: 2637748--2637788 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2637738 TCCTTGACAT
2637748 ATATAA-ATGTGGCAAACTTTG
1 ATATAATAT-TGGCAAACTTTG
*
2637769 ATATAATATTTGCAAACTTT
1 ATATAATATTGGCAAACTTT
2637789 TGTAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
ATATAATATTGGCAAACTTTG
Found at i:2637827 original size:12 final size:12
Alignment explanation
Indices: 2637807--2637887 Score: 51
Period size: 11 Copynumber: 7.8 Consensus size: 12
2637797 TTTTAATAGC
2637807 TTTTG-TAATAA
1 TTTTGATAATAA
2637818 TTTTGATAAT-A
1 TTTTGATAATAA
*
2637829 TTTT-ATAATAG
1 TTTTGATAATAA
2637840 TTTTGAT--T--
1 TTTTGATAATAA
2637848 TTTT-AT-ATAA
1 TTTTGATAATAA
*
2637858 TTGTGATAAT-A
1 TTTTGATAATAA
2637869 -TTTG-TAATAA
1 TTTTGATAATAA
*
2637879 TTTTAATAA
1 TTTTGATAA
2637888 CATTTAAAAG
Statistics
Matches: 55, Mismatches: 4, Indels: 21
0.69 0.05 0.26
Matches are distributed among these distances:
7 2 0.04
8 5 0.09
9 4 0.07
10 13 0.24
11 20 0.36
12 11 0.20
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (12 bp):
TTTTGATAATAA
Found at i:2637878 original size:21 final size:21
Alignment explanation
Indices: 2637808--2637892 Score: 79
Period size: 21 Copynumber: 4.1 Consensus size: 21
2637798 TTTAATAGCT
2637808 TTTGTAATAATTTTGATAATA
1 TTTGTAATAATTTTGATAATA
* *
2637829 TTTTATAATAGTTTTGAT--T-
1 -TTTGTAATAATTTTGATAATA
*
2637848 TTT-TATATAATTGTGATAATA
1 TTTGTA-ATAATTTTGATAATA
* *
2637869 TTTGTAATAATTTTAATAACA
1 TTTGTAATAATTTTGATAATA
2637890 TTT
1 TTT
2637893 AAAAGTTTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
17 2 0.04
18 12 0.24
20 2 0.04
21 18 0.35
22 17 0.33
ACGTcount: A:0.35, C:0.01, G:0.08, T:0.55
Consensus pattern (21 bp):
TTTGTAATAATTTTGATAATA
Found at i:2638638 original size:23 final size:22
Alignment explanation
Indices: 2638599--2638641 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
2638589 AAGATTAATA
2638599 TATTTTTTATTAGTTATTTATT
1 TATTTTTTATTAGTTATTTATT
*
2638621 TATTTTATTATTATTTATTTA
1 TATTTT-TTATTAGTTATTTA
2638642 AAATATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (22 bp):
TATTTTTTATTAGTTATTTATT
Found at i:2638648 original size:19 final size:19
Alignment explanation
Indices: 2638606--2638678 Score: 51
Period size: 19 Copynumber: 3.7 Consensus size: 19
2638596 ATATATTTTT
***
2638606 TATTAGTTATTTATTTATTT
1 TATTA-TTATTTATTTAAAA
2638626 TATTATTATTTATTTAAAA
1 TATTATTATTTATTTAAAA
2638645 TATT-TT-TTTAATTGTAAAA
1 TATTATTATTT-ATT-TAAAA
* *
2638664 TTATTTTTAATTATT
1 -TATTATTATTTATT
2638679 ATCAAATTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
17 3 0.07
18 5 0.11
19 20 0.45
20 9 0.20
21 5 0.11
22 2 0.05
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (19 bp):
TATTATTATTTATTTAAAA
Found at i:2638672 original size:18 final size:17
Alignment explanation
Indices: 2638627--2638675 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
2638617 TATTTATTTT
2638627 ATTATTATTT-ATTTAAA
1 ATTATT-TTTAATTTAAA
*
2638644 ATATTTTTTTAATTGTAAA
1 AT-TATTTTTAATT-TAAA
2638663 ATTATTTTTAATT
1 ATTATTTTTAATT
2638676 ATTATCAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
17 5 0.19
18 16 0.59
19 6 0.22
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (17 bp):
ATTATTTTTAATTTAAA
Found at i:2639122 original size:17 final size:16
Alignment explanation
Indices: 2639096--2639129 Score: 59
Period size: 17 Copynumber: 2.1 Consensus size: 16
2639086 AAAATATTTT
2639096 AAATAAAAATAATAAA
1 AAATAAAAATAATAAA
2639112 AAATAAAAAATAATAAA
1 AAAT-AAAAATAATAAA
2639129 A
1 A
2639130 GAAATATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (16 bp):
AAATAAAAATAATAAA
Done.