Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold140
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: 3130556
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82166 characters in sequence are not A, C, G, or T
File 16 of 20
Found at i:2539972 original size:2 final size:2
Alignment explanation
Indices: 2539965--2539999 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2539955 TCATAAATAC
2539965 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2540000 GCTTGAATGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2542811 original size:18 final size:19
Alignment explanation
Indices: 2542790--2542830 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
2542780 AATTTTTAGA
2542790 TTAAATA-A-TTTTATTATT
1 TTAAATATATTTTTA-TATT
2542808 TTAAATATATTTTTATATT
1 TTAAATATATTTTTATATT
2542827 TTAA
1 TTAA
2542831 TTTTTAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.33
19 9 0.43
20 5 0.24
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTAAATATATTTTTATATT
Found at i:2546395 original size:16 final size:16
Alignment explanation
Indices: 2546374--2546408 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2546364 CTCGATCAAA
*
2546374 TAATTTATTTTAAATT
1 TAATTTAATTTAAATT
*
2546390 TAATTTAATTTAATTT
1 TAATTTAATTTAAATT
2546406 TAA
1 TAA
2546409 AATTTACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TAATTTAATTTAAATT
Found at i:2547686 original size:40 final size:40
Alignment explanation
Indices: 2547637--2547713 Score: 100
Period size: 40 Copynumber: 1.9 Consensus size: 40
2547627 AATTTTATGA
* * *
2547637 ATGAAAGATCATCTTTAATAATCATTTCTAAAATTATTGG
1 ATGAAAGATCATCCTCAACAATCATTTCTAAAATTATTGG
* * *
2547677 ATGAAAGATCGTCCTCAACAATTATTTTTAAAATTAT
1 ATGAAAGATCATCCTCAACAATCATTTCTAAAATTAT
2547714 CTTTGAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.40, C:0.12, G:0.09, T:0.39
Consensus pattern (40 bp):
ATGAAAGATCATCCTCAACAATCATTTCTAAAATTATTGG
Found at i:2553088 original size:12 final size:12
Alignment explanation
Indices: 2553067--2553097 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2553057 TAATTTCAAC
*
2553067 AAAAATATCCAA
1 AAAAAAATCCAA
2553079 AAAAAAATCCAA
1 AAAAAAATCCAA
2553091 AAAAAAA
1 AAAAAAA
2553098 AGGAAAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.77, C:0.13, G:0.00, T:0.10
Consensus pattern (12 bp):
AAAAAAATCCAA
Found at i:2556950 original size:17 final size:16
Alignment explanation
Indices: 2556916--2556954 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
2556906 TAATTCTTAC
*
2556916 TTTA-TTTTTAAAATT
1 TTTATTTTTTAAAAAT
2556931 TTTATTTTTATAAAAAT
1 TTTATTTTT-TAAAAAT
2556948 TTTATTT
1 TTTATTT
2556955 CAACTTATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 4 0.19
16 4 0.19
17 13 0.62
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTATTTTTTAAAAAT
Found at i:2557574 original size:28 final size:26
Alignment explanation
Indices: 2557542--2557629 Score: 70
Period size: 28 Copynumber: 3.2 Consensus size: 26
2557532 GGTAAAAACT
2557542 ATATTATCCTACTTATGATAAATTTATA
1 ATATTAT--TACTTATGATAAATTTATA
* * * *
2557570 ATATTATTAATTTTGAAAAAATTGATA
1 ATATTATTACTTATG-ATAAATTTATA
2557597 TATATTATATTACTTATGAT-AATCTTATA
1 -ATA-T-TATTACTTATGATAAAT-TTATA
2557626 ATAT
1 ATAT
2557630 GATTTAATTA
Statistics
Matches: 47, Mismatches: 8, Indels: 11
0.71 0.12 0.17
Matches are distributed among these distances:
26 6 0.13
27 10 0.21
28 16 0.34
29 6 0.13
30 9 0.19
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.48
Consensus pattern (26 bp):
ATATTATTACTTATGATAAATTTATA
Found at i:2558597 original size:15 final size:16
Alignment explanation
Indices: 2558564--2558601 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
2558554 TTTAAAATTT
*
2558564 AATAAATTGAATCCAA
1 AATAATTTGAATCCAA
*
2558580 AATAATTTGAATTC-A
1 AATAATTTGAATCCAA
2558595 AATAATT
1 AATAATT
2558602 CGAGTTACAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.53, C:0.08, G:0.05, T:0.34
Consensus pattern (16 bp):
AATAATTTGAATCCAA
Found at i:2558681 original size:16 final size:16
Alignment explanation
Indices: 2558662--2558708 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
2558652 GATCCAAACT
*
2558662 TAAAATAATTAAAATA
1 TAAAATAATTTAAATA
*
2558678 TAAAATATTTTAAATA
1 TAAAATAATTTAAATA
*
2558694 AAAAATAATTTAAAT
1 TAAAATAATTTAAAT
2558709 TAATCTAACT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
TAAAATAATTTAAATA
Found at i:2559686 original size:18 final size:17
Alignment explanation
Indices: 2559665--2559712 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
2559655 ATAACATGGA
2559665 TTATTAATATATCAAAAT
1 TTATTAATATAT-AAAAT
2559683 TTATATAAATATATAAAAT
1 TTAT-T-AATATATAAAAT
*
2559702 TT-TAAATATAT
1 TTATTAATATAT
2559713 TTATAACATA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 7 0.26
18 5 0.19
19 8 0.30
20 7 0.26
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (17 bp):
TTATTAATATATAAAAT
Found at i:2563364 original size:17 final size:15
Alignment explanation
Indices: 2563336--2563372 Score: 56
Period size: 17 Copynumber: 2.3 Consensus size: 15
2563326 ATTTTCTAAA
2563336 AATTTAAATTTTATT
1 AATTTAAATTTTATT
2563351 AATTTAATATTTTTATT
1 AATTTAA-A-TTTTATT
2563368 AATTT
1 AATTT
2563373 TTAAAATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 7 0.35
16 1 0.05
17 12 0.60
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
AATTTAAATTTTATT
Found at i:2563690 original size:440 final size:443
Alignment explanation
Indices: 2562855--2563734 Score: 1351
Period size: 440 Copynumber: 2.0 Consensus size: 443
2562845 AGTCAAAATC
* *
2562855 TATTTAGGTCACATATTATGTATTTTATATTTTTTAAAAATATAAACTTTATTAATTTAATATTT
1 TATTTAGGTCACATATTATATATTTTATATTTTCTAAAAATATAAACTTTATTAATTTAATATTT
2562920 TTTATTAATTTTTAAAATATAATTTTAATAATTTTTAATGTTTACACTACAACATTATTAATTTA
66 TTTATTAATTTTTAAAATATAATTTTAATAATTTTTAATGTTTACACTACAACATTATTAATTTA
* *
2562985 GTTTTACATGATATAAATTATATAATATATAAATATTTTATATATATTATATACTGAAAAGGGGT
131 ATTTTACATGATATAAATTACATAATATATAAATATTTTATATATATTATATACTGAAAAGGGGT
* * * *
2563050 TGGGCCCTATCTTAAATTTTAGAACCAAAGTTTGATCATTTTTTAAATATGTTTCATTTTTTACT
196 TGGGCCCTATCCT--ATGTTAAAACCAAAGTTTGATCATTTTTTAAATATATTTCATTTTTTACT
* *
2563115 TAAACTCATTTTTCAGGTCTAATAATTTTGTTTAAGTCCTTTCAAATATTAAATCGACCTTTAGA
259 TAAACTCATTTTTCAGGTCTAATAATTTTATTTAAATCCTTTCAAATATTAAATCGACCTTTAGA
* *
2563180 CTTGGATAGCGTAACCTAACCCTTGAACACTTCTAATTGTAAATAGATATTAAAATCAATGATAA
324 CTTAGACAGCGTAACCTAACCCTTGAACACTTCTAATTGTAAATAGATATTAAAATCAATGATAA
** *
2563245 AATATATTTAGATGTAAAAATAACAGTAATAATAAGGTAAAATATAATATTTTTA
389 AATATATTTAGATACAAAAATAACAGTAATAAGAAGGTAAAATATAATATTTTTA
* * *
2563300 TATTTAGG-C-CATATTATATGTTTTATATTTTCTAAAAATTTAAATTTTATTAATTTAATA-TT
1 TATTTAGGTCACATATTATATATTTTATATTTTCTAAAAATATAAACTTTATTAATTTAATATTT
* * * * *
2563362 TTTATTAATTTTTAAAATATATTTTTATTAATTTTTAATGTTTACATTATAACATTGTTAATTTA
66 TTTATTAATTTTTAAAATATAATTTTAATAATTTTTAATGTTTACACTACAACATTATTAATTTA
2563427 ATTTTACATGATATAAATTACATAATATATAAATATTTTATATATATTATATGACTGAAAAGGGG
131 ATTTTACATGATATAAATTACATAATATATAAATATTTTATATATATTATAT-ACTGAAAAGGGG
* * *
2563492 TTGGGCCTTA-CCT-TGTTAAAACCAAAGTTTGATCCATTTTTTAAATATATTTTATTTTTT-GT
195 TTGGGCCCTATCCTATGTTAAAACCAAAGTTTGAT-CATTTTTTAAATATATTTCATTTTTTACT
* * *
2563554 CTAAACTCATTTTTC-GGATCTAATAATTTTATTTAAATCCTTTCAAATATTAGATCGGCCTTTG
259 -TAAACTCATTTTTCAGG-TCTAATAATTTTATTTAAATCCTTTCAAATATTAAATCGACCTTTA
* * * *
2563618 GACTTAGACAGTGTAACCTAACCCTTGAACACTTTTAATTGTAAGTAGATATTAAAATTAATGAT
322 GACTTAGACAGCGTAACCTAACCCTTGAACACTTCTAATTGTAAATAGATATTAAAATCAATGAT
*
2563683 AAAATATATTTGGATACAAAAATAACAGTAATAAGAAGGTAAAATATAATAT
387 AAAATATATTTAGATACAAAAATAACAGTAATAAGAAGGTAAAATATAATAT
2563735 AAAAAATTAC
Statistics
Matches: 397, Mismatches: 34, Indels: 13
0.89 0.08 0.03
Matches are distributed among these distances:
439 21 0.05
440 186 0.47
442 114 0.29
443 67 0.17
444 1 0.00
445 8 0.02
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (443 bp):
TATTTAGGTCACATATTATATATTTTATATTTTCTAAAAATATAAACTTTATTAATTTAATATTT
TTTATTAATTTTTAAAATATAATTTTAATAATTTTTAATGTTTACACTACAACATTATTAATTTA
ATTTTACATGATATAAATTACATAATATATAAATATTTTATATATATTATATACTGAAAAGGGGT
TGGGCCCTATCCTATGTTAAAACCAAAGTTTGATCATTTTTTAAATATATTTCATTTTTTACTTA
AACTCATTTTTCAGGTCTAATAATTTTATTTAAATCCTTTCAAATATTAAATCGACCTTTAGACT
TAGACAGCGTAACCTAACCCTTGAACACTTCTAATTGTAAATAGATATTAAAATCAATGATAAAA
TATATTTAGATACAAAAATAACAGTAATAAGAAGGTAAAATATAATATTTTTA
Found at i:2563758 original size:15 final size:15
Alignment explanation
Indices: 2563734--2563781 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
2563724 AAATATAATA
*
2563734 TAAAAA-ATTACCAT
1 TAAAAATATTACAAT
2563748 TAAAAATATTA-AAT
1 TAAAAATATTACAAT
2563762 TAAAATATATTACAA-
1 TAAAA-ATATTACAAT
2563777 TAAAA
1 TAAAA
2563782 TTTATAACAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 13 0.43
15 15 0.50
16 2 0.07
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.31
Consensus pattern (15 bp):
TAAAAATATTACAAT
Found at i:2565528 original size:20 final size:21
Alignment explanation
Indices: 2565486--2565536 Score: 79
Period size: 20 Copynumber: 2.5 Consensus size: 21
2565476 TTCAACAATT
2565486 TGTATCGATACAATAAGGCAA
1 TGTATCGATACAATAAGGCAA
2565507 TGTATCGATAC-ATAAGTG-AA
1 TGTATCGATACAATAAG-GCAA
2565527 TGTATCGATA
1 TGTATCGATA
2565537 AATGTCTGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (21 bp):
TGTATCGATACAATAAGGCAA
Found at i:2566522 original size:23 final size:23
Alignment explanation
Indices: 2566495--2566544 Score: 100
Period size: 23 Copynumber: 2.2 Consensus size: 23
2566485 AGCTTTAGGA
2566495 TTGTTTTGATGTTTTCATGCCAT
1 TTGTTTTGATGTTTTCATGCCAT
2566518 TTGTTTTGATGTTTTCATGCCAT
1 TTGTTTTGATGTTTTCATGCCAT
2566541 TTGT
1 TTGT
2566545 GTGATTAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.12, C:0.12, G:0.18, T:0.58
Consensus pattern (23 bp):
TTGTTTTGATGTTTTCATGCCAT
Found at i:2570774 original size:3 final size:3
Alignment explanation
Indices: 2570759--2570799 Score: 73
Period size: 3 Copynumber: 13.3 Consensus size: 3
2570749 ACAAAACACT
2570759 ATA ATA TATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2570800 GAGGGGGCAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2571161 original size:3 final size:3
Alignment explanation
Indices: 2571155--2571204 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
2571145 AAACCTTCAT
2571155 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2571203 AT
1 AT
2571205 TTGTTTCTTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2574231 original size:2 final size:2
Alignment explanation
Indices: 2574224--2574263 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2574214 TACAGTACAT
2574224 TA TA 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
2574264 CACACACACA
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):
TA
Found at i:2574515 original size:2 final size:2
Alignment explanation
Indices: 2574508--2574538 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2574498 ATTGCACATC
*
2574508 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2574539 GCCTGGATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2576028 original size:22 final size:22
Alignment explanation
Indices: 2575969--2576028 Score: 52
Period size: 22 Copynumber: 2.7 Consensus size: 22
2575959 AAAAATATAA
*
2575969 AAAAATTTATAGATATTAATATT
1 AAAAATTTATAAAT-TTAATATT
* **
2575992 -AAAATTTTTTTATTT-ATATTT
1 AAAAATTTATAAATTTAATA-TT
2576013 AAAAATTTATAAATTT
1 AAAAATTTATAAATTT
2576029 TAAAATTTAA
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
20 3 0.10
21 4 0.14
22 22 0.76
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (22 bp):
AAAAATTTATAAATTTAATATT
Found at i:2576044 original size:16 final size:17
Alignment explanation
Indices: 2576007--2576045 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
2575997 TTTTTTATTT
*
2576007 ATATTTAAAAATTTATA
1 ATATTTTAAAATTTATA
2576024 A-ATTTTAAAATTTA-A
1 ATATTTTAAAATTTATA
2576039 ATATTTT
1 ATATTTT
2576046 TTATCTGCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 2 0.10
16 17 0.85
17 1 0.05
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATATTTTAAAATTTATA
Found at i:2577257 original size:3 final size:3
Alignment explanation
Indices: 2577249--2577292 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
2577239 AATGAGAGCA
2577249 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2577293 ATAAGATAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2578546 original size:17 final size:20
Alignment explanation
Indices: 2578507--2578546 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2578497 AAATTTAATT
2578507 ATAAAATTATATAATTATTA
1 ATAAAATTATATAATTATTA
2578527 ATAAAATTA-AT-ATT-TTA
1 ATAAAATTATATAATTATTA
2578544 ATA
1 ATA
2578547 TTATTATGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 6 0.30
18 3 0.15
19 2 0.10
20 9 0.45
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATAAAATTATATAATTATTA
Found at i:2578570 original size:29 final size:29
Alignment explanation
Indices: 2578515--2578571 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
2578505 TTATAAAATT
* *
2578515 ATATAATTATTAATAAAATTAATATTTTA
1 ATATAATTATGAATAAAAGTAATATTTTA
*
2578544 ATATTATTATGAATAATAAGTAA-ATTTT
1 ATATAATTATGAATAA-AAGTAATATTTT
2578572 TAAATAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (29 bp):
ATATAATTATGAATAAAAGTAATATTTTA
Found at i:2578594 original size:11 final size:11
Alignment explanation
Indices: 2578570--2578608 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
2578560 TAAGTAAATT
2578570 TTTAAA-TAAA
1 TTTAAATTAAA
2578580 TTTAAACTT-AA
1 TTTAAA-TTAAA
2578591 TTTAAATTAAA
1 TTTAAATTAAA
2578602 TTTAAAT
1 TTTAAAT
2578609 AAAAAATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 8 0.31
11 17 0.65
12 1 0.04
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (11 bp):
TTTAAATTAAA
Found at i:2579830 original size:2 final size:2
Alignment explanation
Indices: 2579823--2579873 Score: 57
Period size: 2 Copynumber: 25.5 Consensus size: 2
2579813 AAGGAGTATG
* * * *
2579823 TA TA TA TA CA TA CA CA TA AA 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
*
2579865 TA TC TA TA T
1 TA TA TA TA T
2579874 CTGAAAATTC
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (2 bp):
TA
Found at i:2583544 original size:14 final size:14
Alignment explanation
Indices: 2583525--2583571 Score: 76
Period size: 14 Copynumber: 3.4 Consensus size: 14
2583515 CCTCTTATGC
2583525 ATTCAAATACATTT
1 ATTCAAATACATTT
*
2583539 ATTCAAATACATTC
1 ATTCAAATACATTT
*
2583553 ATTTAAATACATTT
1 ATTCAAATACATTT
2583567 ATTCA
1 ATTCA
2583572 TTCAAATATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.43, C:0.15, G:0.00, T:0.43
Consensus pattern (14 bp):
ATTCAAATACATTT
Found at i:2583953 original size:16 final size:16
Alignment explanation
Indices: 2583920--2583954 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2583910 CAGCAAAAAG
* *
2583920 TATGTATGTATGTGTA
1 TATGTATGTATATATA
2583936 TATGTATGTATATATA
1 TATGTATGTATATATA
2583952 TAT
1 TAT
2583955 TTTTTTTTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.51
Consensus pattern (16 bp):
TATGTATGTATATATA
Found at i:2585985 original size:58 final size:58
Alignment explanation
Indices: 2585904--2586015 Score: 215
Period size: 58 Copynumber: 1.9 Consensus size: 58
2585894 AAATTGAACT
2585904 CGTACCATTGGATGGTGATGACTGAAATGATGATACGAATGCTCCTCCAGAACTCGTA
1 CGTACCATTGGATGGTGATGACTGAAATGATGATACGAATGCTCCTCCAGAACTCGTA
*
2585962 CGTACCATTGGATGGTGATGACTGAAATGATGATACGAATGCTCCTCCTGAACT
1 CGTACCATTGGATGGTGATGACTGAAATGATGATACGAATGCTCCTCCAGAACT
2586016 GCTTCCATCT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
58 53 1.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.27
Consensus pattern (58 bp):
CGTACCATTGGATGGTGATGACTGAAATGATGATACGAATGCTCCTCCAGAACTCGTA
Found at i:2587560 original size:17 final size:17
Alignment explanation
Indices: 2587505--2587567 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 17
2587495 TATAATATGA
* *
2587505 TATTATTAAACTTTATTAA
1 TATTA-TAAATTTTA-TAT
* *
2587524 TATTTTAAGTTTTATAT
1 TATTATAAATTTTATAT
2587541 TATTA-AAATTTTATACT
1 TATTATAAATTTTATA-T
2587558 TATTATAAAT
1 TATTATAAAT
2587568 ATAATTTTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
16 9 0.25
17 12 0.33
18 11 0.31
19 4 0.11
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.56
Consensus pattern (17 bp):
TATTATAAATTTTATAT
Found at i:2587696 original size:20 final size:20
Alignment explanation
Indices: 2587668--2587706 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2587658 ATTAATCAAC
* *
2587668 TAAATTAATTGATATAATTT
1 TAAAATAATTAATATAATTT
2587688 TAAAATAATTAATATAATT
1 TAAAATAATTAATATAATT
2587707 CATTTATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (20 bp):
TAAAATAATTAATATAATTT
Found at i:2593373 original size:21 final size:23
Alignment explanation
Indices: 2593338--2593384 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
2593328 CTACATAATC
2593338 TTTAAAAATATTATTTA-ATAAA
1 TTTAAAAATATTATTTATATAAA
* *
2593360 TTTAAAATTA-TATTTATATATA
1 TTTAAAAATATTATTTATATAAA
2593382 TTT
1 TTT
2593385 TTATTTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TTTAAAAATATTATTTATATAAA
Found at i:2598763 original size:14 final size:13
Alignment explanation
Indices: 2598739--2598765 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2598729 AAAAATTATA
2598739 AAAATTATTTTTT
1 AAAATTATTTTTT
2598752 AAAATTATTTTTT
1 AAAATTATTTTTT
2598765 A
1 A
2598766 CAGTGCTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
AAAATTATTTTTT
Found at i:2599068 original size:11 final size:11
Alignment explanation
Indices: 2599052--2599082 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
2599042 CTGGGAAACC
*
2599052 GAATTTTAGGT
1 GAATTTAAGGT
2599063 GAATTTAAGGT
1 GAATTTAAGGT
2599074 GAATTTAAG
1 GAATTTAAG
2599083 CGGAGTTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.26, T:0.39
Consensus pattern (11 bp):
GAATTTAAGGT
Found at i:2601618 original size:21 final size:21
Alignment explanation
Indices: 2601592--2601636 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
2601582 GTTATAATAC
2601592 AATGACTATGTCTCTACTTAA
1 AATGACTATGTCTCTACTTAA
*
2601613 AATGACTATGTTTCTACTTAA
1 AATGACTATGTCTCTACTTAA
2601634 AAT
1 AAT
2601637 TTCTTGTGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.40
Consensus pattern (21 bp):
AATGACTATGTCTCTACTTAA
Found at i:2604178 original size:19 final size:20
Alignment explanation
Indices: 2604154--2604193 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
2604144 TTTATATATC
2604154 ATTTAAAAATTAAATA-AAA
1 ATTTAAAAATTAAATATAAA
*
2604173 ATTTAAAATTTAAATATAAA
1 ATTTAAAAATTAAATATAAA
2604193 A
1 A
2604194 AATCTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
ATTTAAAAATTAAATATAAA
Found at i:2604206 original size:20 final size:21
Alignment explanation
Indices: 2604169--2604209 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
2604159 AAAATTAAAT
*
2604169 AAAAATTTAAAATTTAAATATA
1 AAAAATCTAAAA-TTAAATATA
2604191 AAAAATCTAAAA-TAAATAT
1 AAAAATCTAAAATTAAATAT
2604210 TTTTAAAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
22 11 0.61
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (21 bp):
AAAAATCTAAAATTAAATATA
Found at i:2604694 original size:27 final size:26
Alignment explanation
Indices: 2604656--2604706 Score: 84
Period size: 27 Copynumber: 1.9 Consensus size: 26
2604646 ATACATAAAA
*
2604656 TTTTTTCTTTTTCTTTCTTTCTTTTT
1 TTTTTTCCTTTTCTTTCTTTCTTTTT
2604682 TTTTTTCCCTTTTCTTTCTTTCTTT
1 TTTTTT-CCTTTTCTTTCTTTCTTT
2604707 CCCATATCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 6 0.26
27 17 0.74
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (26 bp):
TTTTTTCCTTTTCTTTCTTTCTTTTT
Found at i:2604695 original size:19 final size:19
Alignment explanation
Indices: 2604673--2604709 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2604663 TTTTTCTTTC
* *
2604673 TTTCTTTTTTTTTTTCCCT
1 TTTCTTTCTTTCTTTCCCT
2604692 TTTCTTTCTTTCTTTCCC
1 TTTCTTTCTTTCTTTCCC
2604710 ATATCTCCCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTCTTTCTTTCTTTCCCT
Found at i:2604879 original size:16 final size:16
Alignment explanation
Indices: 2604835--2604888 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
2604825 TTTATTTCAT
2604835 ATATATTTAAATATA-A
1 ATAT-TTTAAATATATA
2604851 ATA---TAAA-ATATA
1 ATATTTTAAATATATA
2604863 ATATTTTAAATATATA
1 ATATTTTAAATATATA
*
2604879 ATTTTTTAAA
1 ATATTTTAAA
2604889 AAAATTTATA
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
11 3 0.09
12 8 0.25
15 4 0.12
16 17 0.53
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATATTTTAAATATATA
Found at i:2604882 original size:14 final size:13
Alignment explanation
Indices: 2604840--2604883 Score: 52
Period size: 14 Copynumber: 3.2 Consensus size: 13
2604830 TTCATATATA
2604840 TTTAAATATAAAT
1 TTTAAATATAAAT
* *
2604853 ATAAAATATAATAT
1 TTTAAATATAA-AT
2604867 TTTAAATATATAAT
1 TTTAAATATA-AAT
2604881 TTT
1 TTT
2604884 TTAAAAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
13 9 0.36
14 15 0.60
15 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TTTAAATATAAAT
Found at i:2612808 original size:2 final size:2
Alignment explanation
Indices: 2612801--2612830 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2612791 GATTAAGCGT
2612801 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
2612831 TTGACTGAAT
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2615634 original size:4 final size:4
Alignment explanation
Indices: 2615625--2615678 Score: 54
Period size: 4 Copynumber: 13.2 Consensus size: 4
2615615 AGCAATGTTG
* * * * *
2615625 CTTT CTTT CTTT CTTT CTTC CTGTT CTCT CTTT CTTT TTTT GTTA CTTT
1 CTTT CTTT CTTT CTTT CTTT CT-TT CTTT CTTT CTTT CTTT CTTT CTTT
2615674 CTTT C
1 CTTT C
2615679 CTTCCTAATT
Statistics
Matches: 40, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
4 37 0.93
5 3 0.08
ACGTcount: A:0.02, C:0.26, G:0.04, T:0.69
Consensus pattern (4 bp):
CTTT
Found at i:2615788 original size:11 final size:11
Alignment explanation
Indices: 2615772--2615858 Score: 70
Period size: 11 Copynumber: 7.8 Consensus size: 11
2615762 TAATTTAATA
2615772 ATTTATATTAT
1 ATTTATATTAT
*
2615783 ATTTATATTTT
1 ATTTATATTAT
*
2615794 A-TTATTTTAT
1 ATTTATATTAT
*
2615804 AATTATATTAAAT
1 ATTTATATT--AT
**
2615817 ATAAATATTAT
1 ATTTATATTAT
* *
2615828 ATTTATATAAA
1 ATTTATATTAT
2615839 ATTT-TATTAT
1 ATTTATATTAT
2615849 ATTTGATATT
1 ATTT-ATATT
2615859 TTTATTATTT
Statistics
Matches: 58, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
10 16 0.28
11 30 0.52
12 4 0.07
13 8 0.14
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (11 bp):
ATTTATATTAT
Found at i:2615828 original size:18 final size:17
Alignment explanation
Indices: 2615804--2615847 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
2615794 ATTATTTTAT
2615804 AATTATATTAAATATAA
1 AATTATATTAAATATAA
*
2615821 ATATTATATT-TATATAA
1 A-ATTATATTAAATATAA
*
2615838 AATTTTATTA
1 AATTATATTA
2615848 TATTTGATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 7 0.30
17 8 0.35
18 8 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AATTATATTAAATATAA
Found at i:2615879 original size:18 final size:18
Alignment explanation
Indices: 2615764--2615878 Score: 66
Period size: 18 Copynumber: 6.7 Consensus size: 18
2615754 TTGTTGAATA
*
2615764 ATTTAATAATTTATATTAT
1 ATTTAAT-ATTTTTATTAT
2615783 ATTT-ATA-TTTTATTAT
1 ATTTAATATTTTTATTAT
* * *
2615799 -TTT-ATAATTATATTAA
1 ATTTAATATTTTTATTAT
* *
2615815 ATATAA-ATATTATATT-T
1 ATTTAATAT-TTTTATTAT
* *
2615832 ATATAA-AATTTTATTAT
1 ATTTAATATTTTTATTAT
*
2615849 ATTTGATATTTTTATTAT
1 ATTTAATATTTTTATTAT
*
2615867 TTTTAAT-TTTTT
1 ATTTAATATTTTT
2615879 TTTGTTGTCC
Statistics
Matches: 77, Mismatches: 13, Indels: 14
0.74 0.12 0.13
Matches are distributed among these distances:
15 6 0.08
16 21 0.27
17 21 0.27
18 25 0.32
19 4 0.05
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (18 bp):
ATTTAATATTTTTATTAT
Found at i:2616379 original size:14 final size:15
Alignment explanation
Indices: 2616356--2616401 Score: 53
Period size: 14 Copynumber: 3.1 Consensus size: 15
2616346 ATGGTAATAG
2616356 TAATAAAAATTATAA
1 TAATAAAAATTATAA
2616371 TAA-AAAAATT-TAGA
1 TAATAAAAATTATA-A
2616385 TAATAAAAGA-TATAA
1 TAATAAAA-ATTATAA
2616400 TA
1 TA
2616402 TTTTAAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
13 2 0.07
14 11 0.41
15 11 0.41
16 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.30
Consensus pattern (15 bp):
TAATAAAAATTATAA
Found at i:2616835 original size:15 final size:15
Alignment explanation
Indices: 2616783--2616837 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 15
2616773 ATTGAAATCA
2616783 AAATTTAT-TTTAAT
1 AAATTTATATTTAAT
*
2616797 TAATTTATA--TAAT
1 AAATTTATATTTAAT
*
2616810 TAA-TTATTATTTAAT
1 AAATTTA-TATTTAAT
2616825 AAATTTATATTTA
1 AAATTTATATTTA
2616838 TAATTGTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
12 3 0.09
13 9 0.26
14 7 0.21
15 12 0.35
16 3 0.09
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
AAATTTATATTTAAT
Found at i:2616850 original size:28 final size:28
Alignment explanation
Indices: 2616790--2616851 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
2616780 TCAAAATTTA
*
2616790 TTTTAATTAATTTATATAATTAATTATT
1 TTTTAATAAATTTATATAATTAATTATT
* * *
2616818 ATTTAATAAATTTATAT-TTATAATTGTT
1 TTTTAATAAATTTATATAAT-TAATTATT
2616846 TTTTAA
1 TTTTAA
2616852 AATTTTCATT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
27 1 0.04
28 27 0.96
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.60
Consensus pattern (28 bp):
TTTTAATAAATTTATATAATTAATTATT
Found at i:2618906 original size:34 final size:34
Alignment explanation
Indices: 2618863--2619081 Score: 255
Period size: 34 Copynumber: 6.5 Consensus size: 34
2618853 GTAAAAACCA
*
2618863 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
2618897 CCATTTAATCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* * * *
2618931 TCATTTAATCAACAATGGTAAGCTACCAAATTTT
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * * *
2618965 TCATTTAATCAACAATGGTAAGCTATCAAATCTA
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
2618999 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * *
2619033 CCATTTAATCAATAATGGTAAACTACCAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
2619066 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
2619082 TCTCCCACTT
Statistics
Matches: 158, Mismatches: 23, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
33 19 0.12
34 134 0.85
35 5 0.03
ACGTcount: A:0.41, C:0.25, G:0.07, T:0.26
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:2618973 original size:68 final size:67
Alignment explanation
Indices: 2618861--2619081 Score: 307
Period size: 68 Copynumber: 3.3 Consensus size: 67
2618851 TGGTAAAAAC
* *
2618861 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAATCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
2618926 AT
66 AT
* * * ** *
2618928 CACTCATTTAATCAACAATGGTAAGCTACCAAATTTTTCATTTAATCAACAATGGTAAGCTATCA
1 CAC-CATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
2618993 AAT
65 AAT
* * * * *
2618996 CTACCATTTAGTCAACAATGGCAAACCACCAAATCACCCATTTAATCAATAATGGTAAACTACCA
1 C-ACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCA
2619061 AAT
65 AAT
2619064 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
2619082 TCTCCCACTT
Statistics
Matches: 133, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
67 19 0.14
68 112 0.84
69 2 0.02
ACGTcount: A:0.41, C:0.25, G:0.07, T:0.26
Consensus pattern (67 bp):
CACCATTTAATCAACAATGGCAAACTACCAAATCTCCCATTTAATCAACAATGGTAAGCTACCAA
AT
Found at i:2619005 original size:102 final size:101
Alignment explanation
Indices: 2618861--2619081 Score: 316
Period size: 102 Copynumber: 2.2 Consensus size: 101
2618851 TGGTAAAAAC
* * *
2618861 CACCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAATCAACAATGGTAAGCCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAATCAACAATGGCAAACCACCAA
* *
2618926 ATCACTCATTTAATCAACAATGGTAAGCTACCAAATT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAA-T
*** * * * *
2618963 TTTCATTTAATCAACAATGGTAAGCTATCAAATCTACCATTTAGTCAACAATGGCAAACCACCAA
1 CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAATCAACAATGGCAAACCACCAA
*
2619028 ATCACCCATTTAATCAATAATGGTAAACTACCAAAT
66 ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
2619064 CACCATTTAATCAACAAT
1 CACCATTTAATCAACAAT
2619082 TCTCCCACTT
Statistics
Matches: 103, Mismatches: 16, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
101 16 0.16
102 87 0.84
ACGTcount: A:0.41, C:0.25, G:0.07, T:0.26
Consensus pattern (101 bp):
CACCATTTAATCAACAATGGCAACCTACCAAATCTACCATTTAATCAACAATGGCAAACCACCAA
ATCACCCATTTAATCAACAATGGTAAACTACCAAAT
Found at i:2623183 original size:19 final size:19
Alignment explanation
Indices: 2623133--2623184 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
2623123 CCACTATTTC
* * *
2623133 ACGTGTATAGTAACCGTAT
1 ACGTGAATAGTACCCATAT
*
2623152 ACTTGAATAGTACCCATAT
1 ACGTGAATAGTACCCATAT
2623171 ACGTGAATAGTACC
1 ACGTGAATAGTACC
2623185 TCAACAACCA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (19 bp):
ACGTGAATAGTACCCATAT
Found at i:2623537 original size:34 final size:34
Alignment explanation
Indices: 2623491--2623708 Score: 233
Period size: 34 Copynumber: 6.4 Consensus size: 34
2623481 GTAAAAACTA
*
2623491 CCATTTAATCAACAATGGCAA-CATACCAAATCTC
1 CCATTTAATCAACAATGGTAAGC-TACCAAATCTC
* * *
2623525 CCATTTAGTCAACAATGGTAAGCCACCAAATCAC
1 CCATTTAATCAACAATGGTAAGCTACCAAATCTC
* * * *
2623559 CCATTTAATCAATAATGATAAGCTACTAAATTTC
1 CCATTTAATCAACAATGGTAAGCTACCAAATCTC
*
2623593 TCATTTAATCAACAATGGTAAGCTACCAAATCTC
1 CCATTTAATCAACAATGGTAAGCTACCAAATCTC
* * * * *
2623627 CCATTTAGTGAACAATGGTAAACCACCAAATCAC
1 CCATTTAATCAACAATGGTAAGCTACCAAATCTC
** * * * *
2623661 TTATTTAATCAACAATGATAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAAGCTACCAAATCTC
2623694 CCATTTAATCAACAA
1 CCATTTAATCAACAA
2623709 AATTTAATTT
Statistics
Matches: 151, Mismatches: 32, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
33 13 0.09
34 137 0.91
35 1 0.01
ACGTcount: A:0.42, C:0.24, G:0.07, T:0.27
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAAGCTACCAAATCTC
Found at i:2623668 original size:102 final size:101
Alignment explanation
Indices: 2623490--2623708 Score: 332
Period size: 102 Copynumber: 2.2 Consensus size: 101
2623480 GGTAAAAACT
*
2623490 ACCATTTAATCAACAATGGCAACATACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAAA
1 ACCATTTAATCAACAATGGCAACATACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAA
* * *
2623555 TCACCCATTTAATCAATAATGATAAGCTACTAAATT
66 TCACCCATTTAATCAACAATGATAAACTACTAAATC
* * *
2623591 TCTCATTTAATCAACAATGGTAAGC-TACCAAATCTCCCATTTAGTGAACAATGGTAAACCACCA
1 AC-CATTTAATCAACAATGGCAA-CATACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCA
**
2623655 AATCACTTATTTAATCAACAATGATAAACTACTAAATC
64 AATCACCCATTTAATCAACAATGATAAACTACTAAATC
2623693 ACCATTTAATCAACAA
1 ACCATTTAATCAACAA
2623709 AATTTAATTT
Statistics
Matches: 106, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
101 15 0.14
102 90 0.85
103 1 0.01
ACGTcount: A:0.42, C:0.24, G:0.07, T:0.27
Consensus pattern (101 bp):
ACCATTTAATCAACAATGGCAACATACCAAATCTCCCATTTAGTCAACAATGGTAAACCACCAAA
TCACCCATTTAATCAACAATGATAAACTACTAAATC
Found at i:2623809 original size:7 final size:7
Alignment explanation
Indices: 2623789--2623818 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
2623779 TTTTTTTATT
2623789 TTTAAAA
1 TTTAAAA
2623796 TTATAAAA
1 TT-TAAAA
2623804 TTTAAAA
1 TTTAAAA
2623811 TTTAAAA
1 TTTAAAA
2623818 T
1 T
2623819 ATAAGATGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 15 0.68
8 7 0.32
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
TTTAAAA
Found at i:2623809 original size:15 final size:14
Alignment explanation
Indices: 2623789--2623818 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
2623779 TTTTTTTATT
2623789 TTTAAAATTATAAAA
1 TTTAAAATT-TAAAA
2623804 TTTAAAATTTAAAA
1 TTTAAAATTTAAAA
2623818 T
1 T
2623819 ATAAGATGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TTTAAAATTTAAAA
Found at i:2624331 original size:18 final size:20
Alignment explanation
Indices: 2624308--2624457 Score: 64
Period size: 17 Copynumber: 8.1 Consensus size: 20
2624298 TCGGATCTCA
2624308 ATATTTTAT-TTA-ATTTAT
1 ATATTTTATATTATATTTAT
*
2624326 ATATTTTTTATTATATTTAT
1 ATATTTTATATTATATTTAT
**
2624346 AT-TTAAAATAATATATATTTAT
1 ATATT-TTAT-AT-TATATTTAT
* *
2624368 ATAAATTTTATA-T-CATGTA-
1 AT--ATTTTATATTATATTTAT
**
2624387 ATAAATTATA-T-TATTTA-
1 ATATTTTATATTATATTTAT
2624404 A-ATTTTA-A-TATATTTAT
1 ATATTTTATATTATATTTAT
2624421 ATA-TTTATA-TA-ATTT-T
1 ATATTTTATATTATATTTAT
*
2624437 ATATTTTA-ATTATTTTTAT
1 ATATTTTATATTATATTTAT
2624456 AT
1 AT
2624458 CATATAATTA
Statistics
Matches: 101, Mismatches: 15, Indels: 31
0.69 0.10 0.21
Matches are distributed among these distances:
15 2 0.02
16 15 0.15
17 27 0.27
18 15 0.15
19 10 0.10
20 13 0.13
21 3 0.03
22 11 0.11
23 1 0.01
24 2 0.02
25 2 0.02
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.59
Consensus pattern (20 bp):
ATATTTTATATTATATTTAT
Found at i:2624370 original size:8 final size:8
Alignment explanation
Indices: 2624357--2624442 Score: 52
Period size: 8 Copynumber: 10.1 Consensus size: 8
2624347 TTTAAAATAA
2624357 TATATATT
1 TATATATT
2624365 TATATAAATTT
1 TATAT--A-TT
2624376 TATATCATGT
1 TATAT-AT-T
* *
2624386 AATAAAT-
1 TATATATT
2624393 TATATTATT
1 TATA-TATT
*
2624402 TAAAT-TT
1 TATATATT
2624409 TAATATATT
1 T-ATATATT
2624418 TATATATT
1 TATATATT
2624426 TATATAATT
1 TATAT-ATT
2624435 T-TATATT
1 TATATATT
2624442 T
1 T
2624443 TAATTATTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 19
0.70 0.08 0.22
Matches are distributed among these distances:
7 10 0.16
8 26 0.42
9 13 0.21
10 6 0.10
11 7 0.11
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (8 bp):
TATATATT
Found at i:2624440 original size:77 final size:76
Alignment explanation
Indices: 2624331--2624476 Score: 179
Period size: 77 Copynumber: 1.9 Consensus size: 76
2624321 TTTATATATT
* *
2624331 TTTTATTATATTTATATTTAAAATAATATATA-TTTATATAAATTTTATATCATGTAA-TAAATT
1 TTTTAATATATTTATATTTAAAATAATATATATTTTA-ATAAATTTTATATCATATAATTAAATT
2624394 ATATTATTTAAA
65 ATATTATTTAAA
* * * * *
2624406 TTTTAATATATTTATATATTTATATAATTTTATATTTTAATTATTTTTATATCATATAATTAAAT
1 TTTTAATATATTTATAT-TTAAAATAA-TATATATTTTAATAAATTTTATATCATATAATTAAAT
*
2624471 TTTATT
64 TATATT
2624477 TAAAATTATT
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
75 16 0.27
76 7 0.12
77 22 0.37
78 14 0.24
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (76 bp):
TTTTAATATATTTATATTTAAAATAATATATATTTTAATAAATTTTATATCATATAATTAAATTA
TATTATTTAAA
Found at i:2625064 original size:3 final size:3
Alignment explanation
Indices: 2625021--2625047 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2625011 GTCTCCATCT
2625021 CCA CCA CCA CCA CCA CCA CCA CCA CCA
1 CCA CCA CCA CCA CCA CCA CCA CCA CCA
2625048 GCAAAGTCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.67, G:0.00, T:0.00
Consensus pattern (3 bp):
CCA
Found at i:2625435 original size:18 final size:18
Alignment explanation
Indices: 2625400--2625455 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 18
2625390 TGTTTTAAAA
2625400 TATAATTTTAAATATTTT
1 TATAATTTTAAATATTTT
* *
2625418 TAT-ATTTTTAATTTTTT
1 TATAATTTTAAATATTTT
** *
2625435 TA-AAAATTAAATATTAT
1 TATAATTTTAAATATTTT
2625452 TATA
1 TATA
2625456 TATCCAATTG
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
17 25 0.86
18 4 0.14
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TATAATTTTAAATATTTT
Found at i:2630953 original size:2 final size:2
Alignment explanation
Indices: 2630940--2630982 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
2630930 AAAGAGACAA
* *
2630940 AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2630982 A
1 A
2630983 AAGAAATTAC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2630953 original size:8 final size:8
Alignment explanation
Indices: 2630928--2630982 Score: 69
Period size: 8 Copynumber: 7.1 Consensus size: 8
2630918 AACTGCAAAA
2630928 AGAAAGAG
1 AGAAAGAG
*
2630936 ACAAAGAG
1 AGAAAGAG
2630944 AGAAAGAG
1 AGAAAGAG
2630952 AG--AGAG
1 AGAAAGAG
*
2630958 AGAGAGAG
1 AGAAAGAG
*
2630966 AGAGAGAG
1 AGAAAGAG
2630974 AGAAAGAG
1 AGAAAGAG
2630982 A
1 A
2630983 AAGAAATTAC
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
6 6 0.14
8 36 0.86
ACGTcount: A:0.58, C:0.02, G:0.40, T:0.00
Consensus pattern (8 bp):
AGAAAGAG
Found at i:2630953 original size:10 final size:10
Alignment explanation
Indices: 2630926--2630988 Score: 74
Period size: 10 Copynumber: 6.3 Consensus size: 10
2630916 CAAACTGCAA
*
2630926 AAAGAAAGAG
1 AAAGAGAGAG
2630936 ACAA-AGAGAG
1 A-AAGAGAGAG
2630946 AAAGAGAGAG
1 AAAGAGAGAG
*
2630956 AGAGAGAGAG
1 AAAGAGAGAG
*
2630966 AGAGAGAGAG
1 AAAGAGAGAG
*
2630976 AAAGAGAAAG
1 AAAGAGAGAG
2630986 AAA
1 AAA
2630989 TTACTTTAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
9 2 0.04
10 43 0.91
11 2 0.04
ACGTcount: A:0.62, C:0.02, G:0.37, T:0.00
Consensus pattern (10 bp):
AAAGAGAGAG
Found at i:2632790 original size:16 final size:17
Alignment explanation
Indices: 2632770--2632816 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
2632760 AATAAAACTA
2632770 ATAAAATATATATTAAT
1 ATAAAATATATATTAAT
*
2632787 -TAAAATTTATATTAAT
1 ATAAAATATATATTAAT
* *
2632803 ATATAATATTTATT
1 ATAAAATATATATT
2632817 TGATGTGTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 15 0.60
17 10 0.40
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATAAAATATATATTAAT
Found at i:2634540 original size:2 final size:2
Alignment explanation
Indices: 2634522--2634556 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
2634512 CATTTTTCTG
* *
2634522 AT AT AC AT AT AT TT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2634557 AAGATAATTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2634832 original size:18 final size:19
Alignment explanation
Indices: 2634809--2634857 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
2634799 AAAATTTAAT
2634809 ATTAAATATATTAAT-TTA
1 ATTAAATATATTAATATTA
*
2634827 ATTAAA-AAATTTAATATTA
1 ATTAAATATA-TTAATATTA
2634846 ATATAAATATAT
1 AT-TAAATATAT
2634858 AAAATATTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
17 2 0.08
18 11 0.44
19 5 0.20
20 5 0.20
21 2 0.08
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTAAATATATTAATATTA
Found at i:2634839 original size:33 final size:33
Alignment explanation
Indices: 2634784--2634850 Score: 109
Period size: 33 Copynumber: 2.0 Consensus size: 33
2634774 AATTTAATTG
2634784 ATTAATTCAATTAAAAAAATTTAATATTAAATAT
1 ATTAATTCAATTAAAAAAATTTAATATT-AATAT
*
2634818 ATTAATTTAATT-AAAAAATTTAATATTAATAT
1 ATTAATTCAATTAAAAAAATTTAATATTAATAT
2634850 A
1 A
2634851 AATATATAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 6 0.19
33 15 0.47
34 11 0.34
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (33 bp):
ATTAATTCAATTAAAAAAATTTAATATTAATAT
Found at i:2636714 original size:10 final size:10
Alignment explanation
Indices: 2636699--2636741 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
2636689 TTTTATTATT
2636699 AAAATATTTA
1 AAAATATTTA
**
2636709 AAAATATCCA
1 AAAATATTTA
2636719 ATAAATATTTA
1 A-AAATATTTA
*
2636730 AAAATTTTTA
1 AAAATATTTA
2636740 AA
1 AA
2636742 GTCTAAAATT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
10 19 0.70
11 8 0.30
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (10 bp):
AAAATATTTA
Found at i:2636924 original size:175 final size:176
Alignment explanation
Indices: 2636667--2636989 Score: 422
Period size: 175 Copynumber: 1.8 Consensus size: 176
2636657 TTATTTCATA
* *
2636667 ATTTTTTAACCTAGTAAATGCATTTTATTATTAAAATATTTAAAAATATCCAATAAATATTTAAA
1 ATTTTTTAACCTAGTAAATGCATTTTATTATTAAAACATCTAAAAATATCCAATAAATATTTAAA
* *
2636732 AATTTTTAAAGTCTAAAATTATGTAAAATA-A-AGCTTAC-TTCGCTTAAGAAACTGTCATATTT
66 AATTTTAAAAATCTAAAATTATGTAAAA-ACATAGCTTACATT-GCTTAAGAAACTGTCATATTT
*
2636794 TAATGCAAAAGCATAAATTTATATTTTCATTAGAGATTTATCCATTCGT
129 TAATACAAAA-CATAAATTTATATTTTCATTAGAGATTTATCCATTCGT
* * * * * *
2636843 ATTTTTTAA-CTTGTAAATGCATTTTATTATTGAAACATCTAAAATTTTCTAATGAATATTT-AA
1 ATTTTTTAACCTAGTAAATGCATTTTATTATTAAAACATCTAAAAATATCCAATAAATATTTAAA
* ** * *
2636906 AATTTTAAAATATCTAAAATTATTTAAAAACATATTTTTCATTGCTTAAGAAACTGTCGTATTTT
66 AATTTTAAAA-ATCTAAAATTATGTAAAAACATAGCTTACATTGCTTAAGAAACTGTCATATTTT
*
2636971 AATACAAAACATCAATTTA
130 AATACAAAACATAAATTTA
2636990 CGTTTTTTTT
Statistics
Matches: 126, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
174 12 0.10
175 70 0.56
176 42 0.33
177 2 0.02
ACGTcount: A:0.41, C:0.10, G:0.07, T:0.42
Consensus pattern (176 bp):
ATTTTTTAACCTAGTAAATGCATTTTATTATTAAAACATCTAAAAATATCCAATAAATATTTAAA
AATTTTAAAAATCTAAAATTATGTAAAAACATAGCTTACATTGCTTAAGAAACTGTCATATTTTA
ATACAAAACATAAATTTATATTTTCATTAGAGATTTATCCATTCGT
Found at i:2636925 original size:9 final size:9
Alignment explanation
Indices: 2636897--2636934 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
2636887 TTTTCTAATG
2636897 AATATTTAA
1 AATATTTAA
2636906 AAT-TTTAA
1 AATATTTAA
*
2636914 AATATCTAA
1 AATATTTAA
2636923 AATTATTTAA
1 AA-TATTTAA
2636933 AA
1 AA
2636935 ACATATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 8 0.32
9 9 0.36
10 8 0.32
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (9 bp):
AATATTTAA
Found at i:2636933 original size:19 final size:18
Alignment explanation
Indices: 2636879--2636934 Score: 60
Period size: 17 Copynumber: 2.9 Consensus size: 18
2636869 TTATTGAAAC
2636879 ATCTAAAATTTTCTAATGAAT
1 ATCTAAAATTTT-TAA--AAT
*
2636900 ATTTAAAA-TTTTAAAAT
1 ATCTAAAATTTTTAAAAT
2636917 ATCTAAAATTATTTAAAA
1 ATCTAAAATT-TTTAAAA
2636935 ACATATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
17 10 0.32
18 1 0.03
19 10 0.32
20 3 0.10
21 7 0.23
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (18 bp):
ATCTAAAATTTTTAAAAT
Found at i:2637154 original size:26 final size:26
Alignment explanation
Indices: 2637114--2637163 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
2637104 TTTAACTAAA
2637114 TAAATATATTTTATTATTAA-AATATC
1 TAAATATATTTTATT-TTAATAATATC
2637140 TAAATAT-TTTATATTTTAATAATA
1 TAAATATATTT-TATTTTAATAATA
2637164 AAATATATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 7 0.32
26 15 0.68
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (26 bp):
TAAATATATTTTATTTTAATAATATC
Found at i:2637318 original size:21 final size:21
Alignment explanation
Indices: 2637257--2637319 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
2637247 TTCATGTTAC
2637257 ATAATTTTAG--ATTTTAAT-
1 ATAATTTTAGATATTTTAATA
* * *
2637275 AT-TTTTTAAATA-TTTACTAA
1 ATAATTTTAGATATTTTAAT-A
2637295 ATAATTTTAGATATTTTAATA
1 ATAATTTTAGATATTTTAATA
2637316 ATAA
1 ATAA
2637320 AATATATTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 9
0.69 0.12 0.19
Matches are distributed among these distances:
17 5 0.15
18 7 0.21
19 1 0.03
20 2 0.06
21 13 0.39
22 5 0.15
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.52
Consensus pattern (21 bp):
ATAATTTTAGATATTTTAATA
Found at i:2637512 original size:13 final size:13
Alignment explanation
Indices: 2637487--2637519 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
2637477 ATAGTTTCAA
2637487 AATAATATTATTTT
1 AATAAT-TTATTTT
2637501 AATAATTTATTTT
1 AATAATTTATTTT
2637514 AA-AATT
1 AATAATT
2637520 AAAAGCACCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 4 0.21
13 9 0.47
14 6 0.32
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
AATAATTTATTTT
Found at i:2637696 original size:19 final size:18
Alignment explanation
Indices: 2637668--2637704 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
2637658 TATAGATATA
*
2637668 TTTAATATTTTAAAATTT
1 TTTAATATTTAAAAATTT
2637686 TTTATATATTTAAAAATTT
1 TTTA-ATATTTAAAAATTT
2637705 ATATTAATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTAATATTTAAAAATTT
Found at i:2637777 original size:18 final size:20
Alignment explanation
Indices: 2637746--2637789 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
2637736 ATATAAATAT
2637746 TTTAAATAAAATAAA-AA-A
1 TTTAAATAAAATAAATAAGA
**
2637764 TTTAAATATCATAAATAAGA
1 TTTAAATAAAATAAATAAGA
2637784 TTTAAA
1 TTTAAA
2637790 GCTTTCTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 13 0.59
19 2 0.09
20 7 0.32
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (20 bp):
TTTAAATAAAATAAATAAGA
Found at i:2638089 original size:2 final size:2
Alignment explanation
Indices: 2638082--2638107 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2638072 TAATATTTCC
2638082 CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT
2638108 TTCTTCCGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2642730 original size:13 final size:13
Alignment explanation
Indices: 2642712--2642738 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2642702 ACAAAGATCA
2642712 AATGTATCGATAC
1 AATGTATCGATAC
2642725 AATGTATCGATAC
1 AATGTATCGATAC
2642738 A
1 A
2642739 TTTCCTTGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:2642780 original size:13 final size:13
Alignment explanation
Indices: 2642762--2642813 Score: 50
Period size: 13 Copynumber: 3.5 Consensus size: 13
2642752 AGCTTCGTAG
2642762 CGATACATTGTAT
1 CGATACATTGTAT
2642775 CGATACAAAACTTATGTAT
1 CGATAC---A-TT--GTAT
2642794 CGATACATTGTAT
1 CGATACATTGTAT
2642807 CGATACA
1 CGATACA
2642814 ACATTTATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 17 0.52
15 2 0.06
16 2 0.06
17 2 0.06
19 10 0.30
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (13 bp):
CGATACATTGTAT
Found at i:2642794 original size:19 final size:17
Alignment explanation
Indices: 2642770--2642831 Score: 60
Period size: 19 Copynumber: 3.6 Consensus size: 17
2642760 AGCGATACAT
2642770 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAA-TTA
2642789 TGTATCGATAC--A-T-
1 TGTATCGATACAAATTA
2642802 TGTATCGATACAACATTTA
1 TGTATCGATACAA-A-TTA
2642821 TGTATCGATAC
1 TGTATCGATAC
2642832 CTTGTATCGA
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.30
14 1 0.03
16 2 0.05
18 1 0.03
19 22 0.59
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (17 bp):
TGTATCGATACAAATTA
Found at i:2642803 original size:32 final size:32
Alignment explanation
Indices: 2642762--2642843 Score: 137
Period size: 32 Copynumber: 2.6 Consensus size: 32
2642752 AGCTTCGTAG
2642762 CGATACATTGTATCGATACAAAACTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
* *
2642794 CGATACATTGTATCGATACAACATTTATGTAT
1 CGATACATTGTATCGATACAAAACTTATGTAT
*
2642826 CGATACCTTGTATCGATA
1 CGATACATTGTATCGATA
2642844 TAAATTGTTG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.35
Consensus pattern (32 bp):
CGATACATTGTATCGATACAAAACTTATGTAT
Found at i:2648308 original size:28 final size:29
Alignment explanation
Indices: 2648277--2648334 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
2648267 AATATAAAAA
2648277 TATTAATA-TTAATATAA-AATTAATTTTT
1 TATTAATATTTAAT-TAATAATTAATTTTT
*
2648305 TATTAATATTTAATTAATAATTCATTTTT
1 TATTAATATTTAATTAATAATTAATTTTT
2648334 T
1 T
2648335 TGAATTGGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 11 0.41
29 16 0.59
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (29 bp):
TATTAATATTTAATTAATAATTAATTTTT
Found at i:2648894 original size:22 final size:22
Alignment explanation
Indices: 2648876--2648921 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 22
2648866 AATATACATA
2648876 TAAAAATTAA-ATAAAATACAAT
1 TAAAAA-TAATATAAAATACAAT
*
2648898 TAAAAATAATATAAATATATAAT
1 TAAAAATAATATAAA-ATACAAT
2648921 T
1 T
2648922 TATATAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 3 0.14
22 11 0.52
23 7 0.33
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAAATAATATAAAATACAAT
Found at i:2648988 original size:22 final size:21
Alignment explanation
Indices: 2648963--2649027 Score: 64
Period size: 20 Copynumber: 3.1 Consensus size: 21
2648953 TATAAATTAT
2648963 TAATATGTTAAATTTATATATA
1 TAATAT-TTAAATTTATATATA
*
2648985 TAATATTTTAAATATA-AT-TA
1 TAATA-TTTAAATTTATATATA
* *
2649005 TAATATATAAATTAATATA-A
1 TAATATTTAAATTTATATATA
2649025 TAA
1 TAA
2649028 AAATATATAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
19 7 0.19
20 13 0.36
21 2 0.06
22 13 0.36
23 1 0.03
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
TAATATTTAAATTTATATATA
Found at i:2649006 original size:20 final size:20
Alignment explanation
Indices: 2648951--2649026 Score: 68
Period size: 22 Copynumber: 3.8 Consensus size: 20
2648941 AAATTTATAT
*
2648951 AATATAAATTATTAATATGTTA
1 AATAT-AATTA-TAATATTTTA
*
2648973 AATTTATATATATAATATTTTA
1 AATATA-AT-TATAATATTTTA
*
2648995 AATATAATTATAATA-TATA
1 AATATAATTATAATATTTTA
2649014 AAT-TAA-TATAATA
1 AATATAATTATAATA
2649027 AAAATATATA
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
17 7 0.15
18 3 0.06
19 6 0.12
20 7 0.15
21 3 0.06
22 20 0.42
23 2 0.04
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (20 bp):
AATATAATTATAATATTTTA
Found at i:2649008 original size:6 final size:7
Alignment explanation
Indices: 2648903--2649023 Score: 50
Period size: 6 Copynumber: 18.1 Consensus size: 7
2648893 ACAATTAAAA
2648903 ATAATAT
1 ATAATAT
2648910 A-AATAT
1 ATAATAT
*
2648916 ATAATTT
1 ATAATAT
*
2648923 AT-ATAA
1 ATAATAT
2648929 ATAATTAT
1 ATAA-TAT
2648937 GATAA-A-
1 -ATAATAT
*
2648943 AT-TTAT
1 ATAATAT
2648949 ATAATAT
1 ATAATAT
2648956 A-AAT-T
1 ATAATAT
2648961 ATTAATAT
1 A-TAATAT
*
2648969 GTTAA-AT
1 -ATAATAT
*
2648976 TTATATAT
1 ATA-ATAT
2648984 ATAATATT
1 ATAATA-T
*
2648992 TTAA-AT
1 ATAATAT
2648998 ATAAT-T
1 ATAATAT
2649004 ATAATAT
1 ATAATAT
2649011 ATAA-AT
1 ATAATAT
2649017 -TAATAT
1 ATAATAT
2649023 A
1 A
2649024 ATAAAAATAT
Statistics
Matches: 86, Mismatches: 10, Indels: 36
0.65 0.08 0.27
Matches are distributed among these distances:
5 8 0.09
6 32 0.37
7 28 0.33
8 14 0.16
9 4 0.05
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (7 bp):
ATAATAT
Found at i:2649025 original size:17 final size:17
Alignment explanation
Indices: 2648866--2649026 Score: 55
Period size: 15 Copynumber: 9.5 Consensus size: 17
2648856 ATTTGAACAC
*
2648866 AATATACATATAAAAATT
1 AATATA-ATATATAAATT
2648884 AA-ATAA-A-ATACAATT
1 AATATAATATATA-AATT
2648899 AA-A-AATAATATAAA-T
1 AATATAAT-ATATAAATT
2648914 -ATATAATTTATATAAA-T
1 AATATAA--TATATAAATT
2648931 AAT-T-ATGATA-AAATT
1 AATATAAT-ATATAAATT
*
2648946 TATAT-A-ATATAAATT
1 AATATAATATATAAATT
*
2648961 -AT-TAATATGTTAAATTTAT
1 AATATAATAT-ATAAA--T-T
*
2648980 ATATATAATATTTTAAATAT
1 A-ATATAATA-TATAAAT-T
2649000 AATTATAATATATAAATT
1 AA-TATAATATATAAATT
2649018 AATATAATA
1 AATATAATA
2649027 AAAATATATA
Statistics
Matches: 115, Mismatches: 4, Indels: 49
0.68 0.02 0.29
Matches are distributed among these distances:
13 1 0.01
14 15 0.13
15 23 0.20
16 13 0.11
17 22 0.19
18 9 0.08
19 8 0.07
20 11 0.10
21 2 0.02
22 10 0.09
23 1 0.01
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (17 bp):
AATATAATATATAAATT
Found at i:2649025 original size:23 final size:23
Alignment explanation
Indices: 2648995--2649041 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
2648985 TAATATTTTA
* *
2648995 AATATAATTATAATATATAAATT
1 AATATAATAAAAATATATAAATT
2649018 AATATAATAAAAATATATAAATT
1 AATATAATAAAAATATATAAATT
2649041 A
1 A
2649042 TCCGATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
AATATAATAAAAATATATAAATT
Found at i:2649276 original size:12 final size:12
Alignment explanation
Indices: 2649256--2649287 Score: 55
Period size: 12 Copynumber: 2.6 Consensus size: 12
2649246 ACTAATGTAT
2649256 TAAAGTTATATGA
1 TAAA-TTATATGA
2649269 TAAATTATATGA
1 TAAATTATATGA
2649281 TAAATTA
1 TAAATTA
2649288 AGATTCATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 15 0.79
13 4 0.21
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (12 bp):
TAAATTATATGA
Found at i:2649370 original size:17 final size:17
Alignment explanation
Indices: 2649344--2649377 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2649334 TTATTAAATT
2649344 ATTTTAATATAATTATA
1 ATTTTAATATAATTATA
*
2649361 ATTTTTATATAATTATA
1 ATTTTAATATAATTATA
2649378 TAAAATTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTTTAATATAATTATA
Found at i:2649842 original size:31 final size:31
Alignment explanation
Indices: 2649779--2649847 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 31
2649769 GTATCGTGAC
* *
2649779 TTAATTTTTTTTTTTAATTGAATTTTGATTTA
1 TTAATTCTTTTTTTTAATTAAATTTT-ATTTA
2649811 -TAATTCTTTTTTTTAAGTTAAATATTT-TTTA
1 TTAATTCTTTTTTTTAA-TTAAAT-TTTATTTA
2649842 TTAATT
1 TTAATT
2649848 TATTATTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
31 19 0.59
32 10 0.31
33 3 0.09
ACGTcount: A:0.28, C:0.01, G:0.04, T:0.67
Consensus pattern (31 bp):
TTAATTCTTTTTTTTAATTAAATTTTATTTA
Found at i:2650120 original size:19 final size:19
Alignment explanation
Indices: 2650092--2650128 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
2650082 TGTCGAACAA
* *
2650092 AAAATTTATTTAAATATTT
1 AAAATATATTAAAATATTT
2650111 AAAATATATTAAAATATT
1 AAAATATATTAAAATATT
2650129 ATTTTTAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AAAATATATTAAAATATTT
Found at i:2650160 original size:21 final size:21
Alignment explanation
Indices: 2650124--2650166 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2650114 ATATATTAAA
*
2650124 ATATTATTTTTAATTAATATTT
1 ATATTATTTATAATTAA-ATTT
2650146 ATATT-TTTATAATTAAATTT
1 ATATTATTTATAATTAAATTT
2650166 A
1 A
2650167 AATAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 10 0.50
22 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATTATTTATAATTAAATTT
Found at i:2653796 original size:32 final size:31
Alignment explanation
Indices: 2653760--2653821 Score: 99
Period size: 33 Copynumber: 2.0 Consensus size: 31
2653750 TAATATTTAT
2653760 ATATTTTTA-TAATTAAATAATTAAATTTAAAA
1 ATATTTTTATTAATTAAATAA-T-AATTTAAAA
2653792 ATATTTTTATTAATTAAATAATAATTTAAA
1 ATATTTTTATTAATTAAATAATAATTTAAA
2653822 CATTACCGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
31 8 0.28
32 10 0.34
33 11 0.38
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (31 bp):
ATATTTTTATTAATTAAATAATAATTTAAAA
Found at i:2655054 original size:2 final size:2
Alignment explanation
Indices: 2655047--2655077 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2655037 TATAAGAAGA
2655047 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
2655078 GATTTTGAAC
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:2655447 original size:23 final size:22
Alignment explanation
Indices: 2655421--2655464 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2655411 ATATCTTTAA
2655421 TTTTAATATTTTATAA-TAATTAT
1 TTTTAAT-TTTT-TAATTAATTAT
2655444 TTTTAATTTTTTAATTAATTA
1 TTTTAATTTTTTAATTAATTA
2655465 AATTGGTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 3 0.15
22 10 0.50
23 7 0.35
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTTAATTTTTTAATTAATTAT
Found at i:2657198 original size:16 final size:15
Alignment explanation
Indices: 2657165--2657217 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 15
2657155 ATTAAATTTG
2657165 TTATAATTAAACATATT
1 TTATAA-TAAA-ATATT
2657182 TTATGAATAAAATATT
1 TTAT-AATAAAATATT
2657198 TTA-AATAAAATTATT
1 TTATAATAAAA-TATT
2657213 TTATA
1 TTATA
2657218 TTATTAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
14 7 0.21
15 7 0.21
16 9 0.27
17 8 0.24
18 2 0.06
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (15 bp):
TTATAATAAAATATT
Found at i:2658016 original size:29 final size:27
Alignment explanation
Indices: 2657968--2658038 Score: 81
Period size: 27 Copynumber: 2.6 Consensus size: 27
2657958 AAAAATTTAA
* * *
2657968 AAATATAAATAT-TTTAAATATAATTAT
1 AAATATAAAAATATATAAATACAA-TAT
2657995 AATATATAAAAATATATAAATACAATAT
1 AA-ATATAAAAATATATAAATACAATAT
*
2658023 AAATATATAAATATAT
1 AAATATAAAAATATAT
2658039 CAAAATTTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
27 15 0.39
28 14 0.37
29 9 0.24
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (27 bp):
AAATATAAAAATATATAAATACAATAT
Found at i:2658044 original size:10 final size:8
Alignment explanation
Indices: 2657965--2658038 Score: 55
Period size: 8 Copynumber: 9.1 Consensus size: 8
2657955 ATAAAAAATT
*
2657965 TAAAAATA
1 TAAATATA
*
2657973 TAAATATT
1 TAAATATA
*
2657981 TTAA-ATA
1 TAAATATA
2657988 T-AAT-TA
1 TAAATATA
2657994 TAATATATA
1 TAA-ATATA
*
2658003 AAAATATA
1 TAAATATA
2658011 TAAATACAATA
1 TAAAT---ATA
2658022 TAAATATA
1 TAAATATA
2658030 TAAATATA
1 TAAATATA
2658038 T
1 T
2658039 CAAAATTTAT
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
6 5 0.09
7 4 0.08
8 32 0.60
9 4 0.08
11 8 0.15
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (8 bp):
TAAATATA
Found at i:2658044 original size:29 final size:27
Alignment explanation
Indices: 2657960--2658044 Score: 73
Period size: 29 Copynumber: 3.0 Consensus size: 27
2657950 GACGTATAAA
* * * *
2657960 AAATTTAAAAATATAAATATTTTAAAT
1 AAATATAAATATATAAATATATAAAAT
*
2657987 ATAAT-TATAATATATAAAAATATATAAAT
1 A-AATATA-AATATATAAATATATA-AAAT
2658016 ACAATATAAATATATAAATATATCAAAAT
1 A-AATATAAATATATAAATATAT-AAAAT
2658045 TTATATAATA
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
27 3 0.06
28 15 0.32
29 26 0.55
30 3 0.06
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (27 bp):
AAATATAAATATATAAATATATAAAAT
Found at i:2658054 original size:19 final size:17
Alignment explanation
Indices: 2657855--2658055 Score: 77
Period size: 19 Copynumber: 10.9 Consensus size: 17
2657845 TATGACTAAA
*
2657855 AAAATATAT-ATTATAT
1 AAAATATATAAATATAT
*
2657871 AAAATATATTATAAGATA-
1 AAAATATA-TA-AATATAT
2657889 AAAATTATATAAATATATT
1 AAAA-TATATAAATATA-T
*
2657908 ATAAATATATAAATAAAT
1 A-AAATATATAAATATAT
* *
2657926 CAAAATTATGTAACATAAAT
1 -AAAA-TATATAA-ATATAT
* * * *
2657946 -TATTGACGTATAAAAAATTT
1 AAAAT-A--TAT-AAATATAT
*
2657966 AAAA-ATATAAATATTT
1 AAAATATATAAATATAT
*
2657982 TAAATATAATTATAATATAT
1 AAAATAT-A-TA-AATATAT
*
2658002 AAAAATATATAAATACAAT
1 -AAAATATATAAATA-TAT
2658021 ATAAATATATAAATATAT
1 A-AAATATATAAATATAT
*
2658039 CAAAATTTATATAATAT
1 -AAAATATATA-AATAT
2658056 GAATAATTAA
Statistics
Matches: 141, Mismatches: 20, Indels: 45
0.68 0.10 0.22
Matches are distributed among these distances:
16 18 0.13
17 12 0.09
18 28 0.20
19 53 0.38
20 21 0.15
21 9 0.06
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (17 bp):
AAAATATATAAATATAT
Found at i:2659421 original size:16 final size:18
Alignment explanation
Indices: 2659378--2659421 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
2659368 ATATGTAATA
*
2659378 ATTTATATAATACAAATT
1 ATTTATATATTACAAATT
*
2659396 ATTGATATATTA-AAATT
1 ATTTATATATTACAAATT
2659413 -TTTATATAT
1 ATTTATATAT
2659422 ATGTATTACC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 8 0.35
17 5 0.22
18 10 0.43
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.50
Consensus pattern (18 bp):
ATTTATATATTACAAATT
Found at i:2661539 original size:14 final size:15
Alignment explanation
Indices: 2661509--2661548 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
2661499 AATTTTTATA
2661509 TAATTTATATTAATT
1 TAATTTATATTAATT
*
2661524 TAATTTA-ATTATTT
1 TAATTTATATTAATT
*
2661538 TATTTTATATT
1 TAATTTATATT
2661549 TTACTCACGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (15 bp):
TAATTTATATTAATT
Found at i:2661783 original size:15 final size:15
Alignment explanation
Indices: 2661751--2661780 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
2661741 AATAATTTAT
2661751 TTATTAAAATATTAA
1 TTATTAAAATATTAA
2661766 TTATATAAAATATTA
1 TTAT-TAAAATATTA
2661781 TTAAAATATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TTATTAAAATATTAA
Found at i:2661857 original size:12 final size:12
Alignment explanation
Indices: 2661840--2661867 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
2661830 TCCTTGCCAC
2661840 TATAATATATAA
1 TATAATATATAA
2661852 TATAATATATAA
1 TATAATATATAA
2661864 TATA
1 TATA
2661868 GTACAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
TATAATATATAA
Found at i:2663020 original size:15 final size:15
Alignment explanation
Indices: 2663000--2663065 Score: 60
Period size: 15 Copynumber: 4.2 Consensus size: 15
2662990 TTTATAATTT
2663000 TTTATATAATTTAAA
1 TTTATATAATTTAAA
*
2663015 TTTATATAATTTAATG
1 TTTATATAATTTAA-A
* * *
2663031 TTGTATTTCATGTTCAA
1 TT-TATATAAT-TTAAA
*
2663048 TTTATATAAATTAAA
1 TTTATATAATTTAAA
2663063 TTT
1 TTT
2663066 CAAATAAAAT
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
15 21 0.54
16 7 0.18
17 8 0.21
18 3 0.08
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.55
Consensus pattern (15 bp):
TTTATATAATTTAAA
Found at i:2663475 original size:42 final size:43
Alignment explanation
Indices: 2663403--2663485 Score: 109
Period size: 42 Copynumber: 1.9 Consensus size: 43
2663393 AAAACTTGAA
2663403 TTATAATTTATAATTAATAAAAAATTTATTTTTATT-TTAATAT
1 TTATAATTTATAATTAATAAAAAA-TTATTTTTATTATTAATAT
*
2663446 TTATATTTTA-AATTAATAAATTAAA-TATTTTTATTATTAA
1 TTATAATTTATAATTAATAAA--AAATTATTTTTATTATTAA
2663486 ATACTAATTA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
42 20 0.56
43 13 0.36
44 3 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (43 bp):
TTATAATTTATAATTAATAAAAAATTATTTTTATTATTAATAT
Found at i:2663506 original size:33 final size:28
Alignment explanation
Indices: 2663441--2663506 Score: 69
Period size: 28 Copynumber: 2.2 Consensus size: 28
2663431 TTTTTATTTT
*
2663441 AATATTTATATTTTAAATTAATAAATTA
1 AATATTTATATTTTAAATTAATAAATCA
*
2663469 AATATTTTTATTATTAAATACTAATTAAAATCA
1 AATATTTATATT-TTAAAT--TAA-T-AAATCA
2663502 AATAT
1 AATAT
2663507 ATATCAATCA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 11 0.35
29 6 0.19
31 3 0.10
32 1 0.03
33 10 0.32
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (28 bp):
AATATTTATATTTTAAATTAATAAATCA
Found at i:2664010 original size:3 final size:3
Alignment explanation
Indices: 2664002--2664029 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
2663992 TTTGTAAAAG
2664002 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
2664030 GCAATTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:2667141 original size:2 final size:2
Alignment explanation
Indices: 2667134--2667165 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2667124 TATTCACTTT
2667134 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
2667166 ATTAGTTTAT
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:2667777 original size:2 final size:2
Alignment explanation
Indices: 2667770--2667806 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2667760 AAATCTATTC
2667770 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2667807 ATCAGTTTAT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2668076 original size:2 final size:2
Alignment explanation
Indices: 2668071--2668100 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2668061 TTTAATTTGC
2668071 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
2668101 TTTTTTGTAA
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:2668866 original size:21 final size:22
Alignment explanation
Indices: 2668824--2668866 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
2668814 AAAATTTTTA
*
2668824 AATTTTAAATAATGATATATTT
1 AATTTGAAATAATGATATATTT
2668846 AATTTGAAA-AAT-ATACTATTT
1 AATTTGAAATAATGATA-TATTT
2668867 CAAATATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 3 0.16
21 8 0.42
22 8 0.42
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.47
Consensus pattern (22 bp):
AATTTGAAATAATGATATATTT
Found at i:2669425 original size:27 final size:28
Alignment explanation
Indices: 2669389--2669454 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 28
2669379 GCCACCCATT
*
2669389 TGTTTATCAAAAATAGTGGTTAT-TTTG
1 TGTTTGTCAAAAATAGTGGTTATCTTTG
* *
2669416 TGTTTGTCAAAAATGGTGGTTTTCTTTG
1 TGTTTGTCAAAAATAGTGGTTATCTTTG
2669444 -GATTTGTCAAA
1 TG-TTTGTCAAA
2669455 TATGAAGGCT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 21 0.62
28 13 0.38
ACGTcount: A:0.26, C:0.06, G:0.21, T:0.47
Consensus pattern (28 bp):
TGTTTGTCAAAAATAGTGGTTATCTTTG
Found at i:2672813 original size:23 final size:21
Alignment explanation
Indices: 2672759--2672805 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
2672749 TGGACATGTT
2672759 AAAAATGCATGAAACATAATA
1 AAAAATGCATGAAACATAATA
2672780 AAAAATGCATGAAACATAATA
1 AAAAATGCATGAAACATAATA
2672801 AAAAA
1 AAAAA
2672806 AATGCATGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.66, C:0.09, G:0.09, T:0.17
Consensus pattern (21 bp):
AAAAATGCATGAAACATAATA
Found at i:2673771 original size:20 final size:20
Alignment explanation
Indices: 2673724--2673798 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
2673714 AAAAAGACAT
*
2673724 AATGTATCGATACATT-GTA
1 AATGTATCGATACATTCATA
*
2673743 GAATATATCGATACATTCATA
1 -AATGTATCGATACATTCATA
* * * *
2673764 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTCATA
*
2673784 AATGTATTGATACAT
1 AATGTATCGATACAT
2673799 CAGGGTATGA
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 42 0.95
21 2 0.05
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (20 bp):
AATGTATCGATACATTCATA
Found at i:2673796 original size:40 final size:39
Alignment explanation
Indices: 2673721--2673798 Score: 102
Period size: 40 Copynumber: 2.0 Consensus size: 39
2673711 GGTAAAAAGA
* *
2673721 CATAATGTATCGATACATTGTAGAATATATCGATACATT
1 CATAATGTATCGATACATTGAAAAATATATCGATACATT
* * *
2673760 CATACATGTATCGATATATTGAAAAATGTATTGATACAT
1 CATA-ATGTATCGATACATTGAAAAATATATCGATACAT
2673799 CAGGGTATGA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.36
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAATATATCGATACATT
Found at i:2674374 original size:32 final size:32
Alignment explanation
Indices: 2674333--2675598 Score: 2300
Period size: 32 Copynumber: 39.6 Consensus size: 32
2674323 GATTTGAAAA
* ** **
2674333 GGGTTGCCACTGACTTGCATGGGCTTTTAAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
*
2674365 GGGTTGCCACCGACTTGTGTGGGCTTTGAAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
* *
2674397 GAGTTGCCACCAACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
*
2674429 GGGTTGCCACCGACTTGTGTGGGCTTTGAAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
*
2674461 GGGTTGCCACCGACTTGTGTGGGCTTTGAAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
2674493 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
2674525 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
2674557 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
2674589 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
2674621 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
2674653 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
*
2674685 GGGTTGCCACCGACTTGTGTGGGCTTTGAAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
*
2674717 GGGTTGCCACCGACTTGTGTGGGCTTTGAAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
* *
2674749 GGGTTGCCACCAACTTGTGTGGGCTTTGAAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
2674781 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
2674813 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
*
2674845 GGGTTGCCACCGACTTGTGTGGGCTTTGAAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
*
2674877 GGGTTGCCACCGACTTGTGTGGGCTTTGAAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
2674909 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
2674941 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
*
2674973 GGGTTGCCACCGACTTGTGTGGGCTTTGAAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
2675005 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
2675037 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
*
2675069 GGGTTGCCACCGACTTGTGTGGGCTTTGAAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
*
2675101 GAGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
2675133 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
**
2675165 GGGTTGCCACCGACTTGTGTGGGCTTTCAAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
2675197 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
2675229 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
2675261 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
2675293 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
2675325 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
2675357 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
2675389 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
2675421 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
2675453 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
2675485 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
*
2675517 GGGTTGCCACCGACTTGTGTGGGCTTTGAAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
*
2675549 GGGTTGCCACCGACTTGTGTGGGCTTTGAAAT
1 GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
* *
2675581 GGG-TGCCACGGAGTTGTG
1 GGGTTGCCACCGACTTGTG
2675599 GATTTAAAAG
Statistics
Matches: 1204, Mismatches: 30, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
31 13 0.01
32 1191 0.99
ACGTcount: A:0.14, C:0.19, G:0.36, T:0.31
Consensus pattern (32 bp):
GGGTTGCCACCGACTTGTGTGGGCTTTGGAAT
Done.