Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold112
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: 1714866
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.32
Warning! 134939 characters in sequence are not A, C, G, or T
File 5 of 11
Found at i:513832 original size:16 final size:16
Alignment explanation
Indices: 513791--513832 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
513781 TGAGATTTAT
*
513791 TTTAAATTAATTTAAA
1 TTTAAATTATTTTAAA
513807 TTTAAATTATTTTAAA
1 TTTAAATTATTTTAAA
513823 TTTAAATTAT
1 TTTAAATTAT
513833 ATAACATCAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
TTTAAATTATTTTAAA
Found at i:515569 original size:23 final size:23
Alignment explanation
Indices: 515539--515589 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
515529 TTTTAAAAAA
*
515539 ATATTTTTATCATTTATTTGAAT
1 ATATTTTTATCAATTATTTGAAT
*
515562 ATATTTTTATCAATTATTTGGAT
1 ATATTTTTATCAATTATTTGAAT
515585 ATATT
1 ATATT
515590 CAAACCATTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.31, C:0.04, G:0.06, T:0.59
Consensus pattern (23 bp):
ATATTTTTATCAATTATTTGAAT
Found at i:516725 original size:18 final size:19
Alignment explanation
Indices: 516682--516725 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
516672 TAATATTTTA
*
516682 ATATATATAAAATTAATTT
1 ATATATATAAAATAAATTT
*
516701 TTA-ATATATAAATAAATTT
1 ATATATATA-AAATAAATTT
516720 ATATAT
1 ATATAT
516726 TAATCGTGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
18 5 0.25
19 13 0.65
20 2 0.10
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATATATATAAAATAAATTT
Found at i:516728 original size:24 final size:23
Alignment explanation
Indices: 516671--516729 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
516661 TGATGCATAG
*
516671 TTAATATTTTAATATATATAAAA
1 TTAATATTTTAATATATAAAAAA
516694 TTAAT-TTTTAATATATAAATAAA
1 TTAATATTTTAATATATAAA-AAA
* *
516717 TTTATATATTAAT
1 TTAATATTTTAAT
516730 CGTGATAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 13 0.42
23 12 0.39
24 6 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
TTAATATTTTAATATATAAAAAA
Found at i:516951 original size:32 final size:32
Alignment explanation
Indices: 516901--516964 Score: 78
Period size: 32 Copynumber: 2.0 Consensus size: 32
516891 AGAAAGAAAC
516901 AATTTTATAAAATTAATTT-TTAATTTATAAAA
1 AATTTTATAAAATTAATTTGTTAA-TTATAAAA
* *
516933 AATTTTAT-ATATTAAATTTGTTTATTATAAAA
1 AATTTTATAAAATT-AATTTGTTAATTATAAAA
516965 TAATAAAGCC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 4 0.14
32 21 0.75
33 3 0.11
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (32 bp):
AATTTTATAAAATTAATTTGTTAATTATAAAA
Found at i:517624 original size:19 final size:20
Alignment explanation
Indices: 517590--517629 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
517580 ATGAAATTTG
517590 AGAAAAAAACAAGAGA-AAT
1 AGAAAAAAACAAGAGATAAT
517609 AGAAAAAAA-AAGGAGATAAT
1 AGAAAAAAACAA-GAGATAAT
517629 A
1 A
517630 ATGATGATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 2 0.11
19 13 0.68
20 4 0.21
ACGTcount: A:0.72, C:0.03, G:0.17, T:0.07
Consensus pattern (20 bp):
AGAAAAAAACAAGAGATAAT
Found at i:518655 original size:2 final size:2
Alignment explanation
Indices: 518650--518676 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
518640 ATTAAGAATC
518650 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 T
518677 TTATTAATTA
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:519993 original size:45 final size:45
Alignment explanation
Indices: 519925--520016 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 45
519915 AAACAGCAAT
* *
519925 CAGGTTCCGGAACATTTGATCCAGTAATACCGCCAGATTATGGAG
1 CAGGTTCCAGAACATTTGATCCAGTAATACCGCCAGACTATGGAG
* *
519970 CAGGTTCCAGAACATTTGTTCCAGTAGTACCGCCAGACTATGGAG
1 CAGGTTCCAGAACATTTGATCCAGTAATACCGCCAGACTATGGAG
520015 CA
1 CA
520017 CAGGCACTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (45 bp):
CAGGTTCCAGAACATTTGATCCAGTAATACCGCCAGACTATGGAG
Found at i:520051 original size:45 final size:45
Alignment explanation
Indices: 520002--520089 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
519992 AGTAGTACCG
*
520002 CCAGACTATGGAGCACAGGCACTTCTCGAACACCAAGTAATGCTA
1 CCAGACTATGGAGCACAGGCACTTCTCGAACAACAAGTAATGCTA
* *
520047 CCAGATTATGGAGCACAGGCTCTTCTCGAACAACAAGTAATGC
1 CCAGACTATGGAGCACAGGCACTTCTCGAACAACAAGTAATGC
520090 AGCCTCATAT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.33, C:0.27, G:0.20, T:0.19
Consensus pattern (45 bp):
CCAGACTATGGAGCACAGGCACTTCTCGAACAACAAGTAATGCTA
Found at i:520216 original size:24 final size:24
Alignment explanation
Indices: 520175--520232 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
520165 AGCAACTAGG
*
520175 TTCGTCAATTTTTTTCTTCAATTTT
1 TTCGTCAA-TTTTATCTTCAATTTT
520200 TTCGTCAATTTTATCTTCAATTTT
1 TTCGTCAATTTTATCTTCAATTTT
*
520224 TTCATCAAT
1 TTCGTCAAT
520233 GTTTTTTTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 23 0.74
25 8 0.26
ACGTcount: A:0.21, C:0.17, G:0.03, T:0.59
Consensus pattern (24 bp):
TTCGTCAATTTTATCTTCAATTTT
Found at i:520245 original size:12 final size:12
Alignment explanation
Indices: 520179--520244 Score: 80
Period size: 12 Copynumber: 5.4 Consensus size: 12
520169 ACTAGGTTCG
520179 TCAATTTTTTTCT
1 TCAA-TTTTTTCT
*
520192 TCAATTTTTTCG
1 TCAATTTTTTCT
*
520204 TCAATTTTATCT
1 TCAATTTTTTCT
*
520216 TCAATTTTTTCA
1 TCAATTTTTTCT
520228 TCAATGTTTTT-T
1 TCAAT-TTTTTCT
520240 TCAAT
1 TCAAT
520245 GCAGCCTCGT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
12 37 0.80
13 9 0.20
ACGTcount: A:0.21, C:0.15, G:0.03, T:0.61
Consensus pattern (12 bp):
TCAATTTTTTCT
Found at i:520573 original size:15 final size:15
Alignment explanation
Indices: 520538--520576 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 15
520528 TTTGTTTAAG
520538 TTAATTAAATATTTTT
1 TTAATT-AATATTTTT
520554 TTAATTAAT-TTTTT
1 TTAATTAATATTTTT
520568 TATAATTAA
1 T-TAATTAA
520577 GCATTTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.27
15 10 0.45
16 6 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTAATTAATATTTTT
Found at i:521014 original size:33 final size:33
Alignment explanation
Indices: 520976--521040 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
520966 ATTTGATACA
520976 TGTAAAATAAGAAAACTTGAAACCATTAGAGAC
1 TGTAAAATAAGAAAACTTGAAACCATTAGAGAC
** *
521009 TGTAAAATAAGGGAACTTGACACCATTAGAGA
1 TGTAAAATAAGAAAACTTGAAACCATTAGAGA
521041 GGAATTGGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.48, C:0.12, G:0.18, T:0.22
Consensus pattern (33 bp):
TGTAAAATAAGAAAACTTGAAACCATTAGAGAC
Found at i:522173 original size:14 final size:15
Alignment explanation
Indices: 522154--522182 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
522144 ATGGTAGTAC
522154 ACTTGATTTA-ATTA
1 ACTTGATTTATATTA
522168 ACTTGATTTATATTA
1 ACTTGATTTATATTA
522183 GATCAAGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.34, C:0.07, G:0.07, T:0.52
Consensus pattern (15 bp):
ACTTGATTTATATTA
Found at i:522209 original size:16 final size:16
Alignment explanation
Indices: 522190--522248 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 16
522180 TTAGATCAAG
522190 TTTAATTTTTTTTAAA
1 TTTAATTTTTTTTAAA
522206 TTTAATTTGTTTGATTAAA
1 TTTAATTT-TTT--TTAAA
** *
522225 TAAAAATTTTATTTAAA
1 T-TTAATTTTTTTTAAA
522242 TTTAATT
1 TTTAATT
522249 ATAAATATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
16 12 0.35
17 9 0.26
19 8 0.24
20 5 0.15
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.59
Consensus pattern (16 bp):
TTTAATTTTTTTTAAA
Found at i:522259 original size:36 final size:35
Alignment explanation
Indices: 522193--522264 Score: 83
Period size: 36 Copynumber: 2.0 Consensus size: 35
522183 GATCAAGTTT
* ***
522193 AATTTTTTTTAAATTTAATTTGTTTGATTAAATAAA
1 AATTTTATTTAAATTTAATTTAAATGATT-AATAAA
522229 AATTTTATTTAAATTTAATTATAAAT-ATTAATAAA
1 AATTTTATTTAAATTTAATT-TAAATGATTAATAAA
522264 A
1 A
522265 TTAAATTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
35 7 0.23
36 22 0.71
37 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (35 bp):
AATTTTATTTAAATTTAATTTAAATGATTAATAAA
Found at i:522545 original size:3 final size:3
Alignment explanation
Indices: 522537--522564 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
522527 CTAAGTCATA
522537 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT T
522565 TTGCTCTTCC
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:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:525390 original size:16 final size:16
Alignment explanation
Indices: 525371--525416 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
525361 TTTGAATCTA
525371 ATTTAATTAAATTATT
1 ATTTAATTAAATTATT
525387 ATTTAATT-AATTAATT
1 ATTTAATTAAATT-ATT
525403 -TTT-ATTAAA-TATT
1 ATTTAATTAAATTATT
525416 A
1 A
525417 ATATAAAAGT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
13 3 0.11
14 4 0.15
15 9 0.33
16 11 0.41
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTTAATTAAATTATT
Found at i:525938 original size:23 final size:23
Alignment explanation
Indices: 525908--525954 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
525898 GGGAAGATAG
*
525908 GTAAATGAATTGCCCATCTAATC
1 GTAAATGAATCGCCCATCTAATC
525931 GTAAATGAATCGCCCATCTAATC
1 GTAAATGAATCGCCCATCTAATC
525954 G
1 G
525955 ATTTTCGATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (23 bp):
GTAAATGAATCGCCCATCTAATC
Found at i:531096 original size:22 final size:22
Alignment explanation
Indices: 531069--531110 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
531059 TATTAAATAT
531069 TATTTTTAT-ATTAATATTTATA
1 TATTTTTATAATTAA-ATTTATA
531091 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
531111 AATAAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTATA
Found at i:531589 original size:19 final size:18
Alignment explanation
Indices: 531528--531620 Score: 57
Period size: 18 Copynumber: 4.9 Consensus size: 18
531518 ATTTACATTA
* *
531528 ATATAAAATTAATTAATTT
1 ATATATAATTAA-TATTTT
* *
531547 ATATAT-TTTTATAATTTT
1 ATATATAATTAAT-ATTTT
531565 ATATATAATTAATATTTTAAT
1 ATATATAATTAATA-TTT--T
531586 ATATTGATAATTAA-ATTTT
1 ATA-T-ATAATTAATATTTT
531605 ATAATATAATT-ATATT
1 AT-ATATAATTAATATT
531621 CATTTTGTAT
Statistics
Matches: 59, Mismatches: 6, Indels: 19
0.70 0.07 0.23
Matches are distributed among these distances:
17 2 0.03
18 23 0.39
19 16 0.27
20 1 0.02
21 7 0.12
22 2 0.03
23 8 0.14
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (18 bp):
ATATATAATTAATATTTT
Found at i:536673 original size:10 final size:10
Alignment explanation
Indices: 536658--536732 Score: 61
Period size: 10 Copynumber: 7.5 Consensus size: 10
536648 CGTTATATTA
536658 ATTAATTTTT
1 ATTAATTTTT
536668 ATTAATTTTT
1 ATTAATTTTT
*
536678 A-T-A-TTAT
1 ATTAATTTTT
536685 ATTATATTTTAT
1 ATTA-ATTTT-T
536697 ATT-ATATTTT
1 ATTAAT-TTTT
536707 ATT-ATTTTT
1 ATTAATTTTT
536716 ATTATATTTTT
1 ATTA-ATTTTT
536727 CATTAA
1 -ATTAA
536733 AATAATATTA
Statistics
Matches: 54, Mismatches: 2, Indels: 17
0.74 0.03 0.23
Matches are distributed among these distances:
7 4 0.07
8 2 0.04
9 8 0.15
10 20 0.37
11 12 0.22
12 8 0.15
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.67
Consensus pattern (10 bp):
ATTAATTTTT
Found at i:536686 original size:5 final size:5
Alignment explanation
Indices: 536676--536723 Score: 53
Period size: 5 Copynumber: 9.4 Consensus size: 5
536666 TTATTAATTT
* *
536676 TTATA TTATA TTATA TTTTATA TTATA TTTTA TTAT- TTTTA TTATA TT
1 TTATA TTATA TTATA --TTATA TTATA TTATA TTATA TTATA TTATA TT
536724 TTTCATTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
4 3 0.08
5 28 0.78
7 5 0.14
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (5 bp):
TTATA
Found at i:536694 original size:17 final size:18
Alignment explanation
Indices: 536674--536723 Score: 68
Period size: 17 Copynumber: 2.8 Consensus size: 18
536664 TTTTATTAAT
536674 TTTTATATTATATTA-TA
1 TTTTATATTATATTATTA
536691 TTTTATATTATATTTTATTA
1 TTTTATATTATA--TTATTA
536711 TTTT-TATTATATT
1 TTTTATATTATATT
536724 TTTCATTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
17 14 0.47
19 10 0.33
20 6 0.20
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTTATATTATATTATTA
Found at i:536696 original size:12 final size:12
Alignment explanation
Indices: 536681--536708 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
536671 AATTTTTATA
536681 TTATATTATATT
1 TTATATTATATT
536693 TTATATTATATT
1 TTATATTATATT
536705 TTAT
1 TTAT
536709 TATTTTTATT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTATATTATATT
Found at i:536731 original size:21 final size:20
Alignment explanation
Indices: 536664--536725 Score: 78
Period size: 19 Copynumber: 3.2 Consensus size: 20
536654 ATTAATTAAT
536664 TTTTATTAATTTTTATATTATA
1 TTTTATT-A-TTTTATATTATA
536686 --TTA-TATTTTATATTATA
1 TTTTATTATTTTATATTATA
536703 TTTTATTATTTT-TATTATA
1 TTTTATTATTTTATATTATA
536722 TTTT
1 TTTT
536726 TCATTAAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
17 12 0.32
18 1 0.03
19 15 0.41
20 9 0.24
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTTATTATTTTATATTATA
Found at i:537280 original size:25 final size:26
Alignment explanation
Indices: 537208--537280 Score: 73
Period size: 25 Copynumber: 2.9 Consensus size: 26
537198 TTAGTTTGTA
537208 ATAATATTAATTAAAATAATAT-TTTT
1 ATAAT-TTAATTAAAATAATATATTTT
* * *
537234 AAAAATTAATTAATA-AAT-TATTTT
1 ATAATTTAATTAAAATAATATATTTT
*
537258 -TAATTTAATAAAAATAATATATT
1 ATAATTTAATTAAAATAATATATT
537281 AAATATAAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
23 11 0.30
24 10 0.27
25 13 0.35
26 3 0.08
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
ATAATTTAATTAAAATAATATATTTT
Found at i:537654 original size:16 final size:16
Alignment explanation
Indices: 537612--537645 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
537602 AATTTATTTA
*
537612 TATTACATT-TAATAT
1 TATTAGATTATAATAT
537627 TATTAGATTATAATAT
1 TATTAGATTATAATAT
537643 TAT
1 TAT
537646 ATATGTATAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.53
Consensus pattern (16 bp):
TATTAGATTATAATAT
Found at i:548251 original size:50 final size:50
Alignment explanation
Indices: 548197--548352 Score: 170
Period size: 50 Copynumber: 3.1 Consensus size: 50
548187 TTTTTCATTG
* * * *
548197 TCAAAGGTTGGTGAAGAATTGTAAATAATTATGACCACTTCTTTCTATTA
1 TCAAAGGTTGGTGAAGAATCGTAAACAATTATGACCACCTCTCTCTATTA
* * * **
548247 TCAAAGTTTGGTGAAAAATCGTCAACAATTATGGTCACCTCTCTCTATTA
1 TCAAAGGTTGGTGAAGAATCGTAAACAATTATGACCACCTCTCTCTATTA
* * * * *
548297 TTAAAAGTTGATGAAGAATCGTTAACAATTAT-AGCCACCTCTCTCTATTG
1 TCAAAGGTTGGTGAAGAATCGTAAACAATTATGA-CCACCTCTCTCTATTA
548347 TCAAAG
1 TCAAAG
548353 TTACTTTCCA
Statistics
Matches: 85, Mismatches: 20, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
50 85 1.00
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.35
Consensus pattern (50 bp):
TCAAAGGTTGGTGAAGAATCGTAAACAATTATGACCACCTCTCTCTATTA
Found at i:548456 original size:34 final size:33
Alignment explanation
Indices: 548418--548484 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 33
548408 ACGATAAAAA
*
548418 TAATAAATAATATT-ATTATTTTATTAAAGATAAT
1 TAATAAA-AATATTAATTATTATATTAAA-ATAAT
* *
548452 TAATAAAATTATTAATTATTATATTTAAATAAT
1 TAATAAAAATATTAATTATTATATTAAAATAAT
548485 ATTATTTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
33 10 0.34
34 19 0.66
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (33 bp):
TAATAAAAATATTAATTATTATATTAAAATAAT
Found at i:548487 original size:16 final size:16
Alignment explanation
Indices: 548468--548502 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
548458 AATTATTAAT
548468 TATTATATT-TAAATAA
1 TATTAT-TTATAAATAA
548484 TATTATTTATAAATAA
1 TATTATTTATAAATAA
548500 TAT
1 TAT
548503 ATTAATTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 2 0.11
16 16 0.89
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TATTATTTATAAATAA
Found at i:548897 original size:25 final size:23
Alignment explanation
Indices: 548851--548897 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
548841 ATATTTTATC
* *
548851 CTTTATATGATAAAAATTATATA
1 CTTTATATAATAAAAATAATATA
548874 CTTTATATAATACAAAATCAATAT
1 CTTTATATAATA-AAAAT-AATAT
548898 CTATTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 11 0.55
24 5 0.25
25 4 0.20
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (23 bp):
CTTTATATAATAAAAATAATATA
Found at i:559237 original size:20 final size:20
Alignment explanation
Indices: 559212--559261 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
559202 ATTCGCCTGC
* *
559212 CTCTTGTTGCCCATCTCATG
1 CTCTTGTTCCCCATCTCATA
559232 CTCTTGTTCCCCATCTCATA
1 CTCTTGTTCCCCATCTCATA
559252 CTCTTGTTCC
1 CTCTTGTTCC
559262 ATTTCTATCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.10, C:0.38, G:0.10, T:0.42
Consensus pattern (20 bp):
CTCTTGTTCCCCATCTCATA
Found at i:560677 original size:20 final size:21
Alignment explanation
Indices: 560652--560699 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
560642 TTTTTAAAAA
560652 TTTAATTAT-A-AAATAATATT
1 TTTAATTATGATAAA-AATATT
560672 TTTAA-TATGATAAAAATATT
1 TTTAATTATGATAAAAATATT
*
560692 TTTTATTA
1 TTTAATTA
560700 AATTTATAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 3 0.12
20 16 0.67
21 5 0.21
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
TTTAATTATGATAAAAATATT
Found at i:560985 original size:11 final size:11
Alignment explanation
Indices: 560971--561114 Score: 55
Period size: 11 Copynumber: 13.5 Consensus size: 11
560961 ATTTATTTTT
560971 TATTTTAATTA
1 TATTTTAATTA
*
560982 TATTTAAAATACTA
1 TATTT-TAAT--TA
560996 TATATTT-ATATA
1 TAT-TTTAAT-TA
*
561008 AATTTTAA-TA
1 TATTTTAATTA
*
561018 TATTAATAATT-
1 TATT-TTAATTA
561029 T-TTTT-ATATA
1 TATTTTAAT-TA
*
561039 AATTTTAA-TA
1 TATTTTAATTA
561049 TA-TTT-A-TA
1 TATTTTAATTA
561057 TA-TTTATATTA
1 TATTTTA-ATTA
*
561068 T-GTTTATATTA
1 TATTTTA-ATTA
561079 T-TTTT-ATTA
1 TATTTTAATTA
561088 TATTTTAATTA
1 TATTTTAATTA
561099 T-TTTTATATTA
1 TATTTTA-ATTA
561110 TATTT
1 TATTT
561115 ATAAAATATC
Statistics
Matches: 104, Mismatches: 10, Indels: 37
0.69 0.07 0.25
Matches are distributed among these distances:
8 10 0.10
9 10 0.10
10 20 0.19
11 42 0.40
12 13 0.12
13 2 0.02
14 5 0.05
15 2 0.02
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.61
Consensus pattern (11 bp):
TATTTTAATTA
Found at i:561018 original size:20 final size:20
Alignment explanation
Indices: 560995--561058 Score: 65
Period size: 20 Copynumber: 3.6 Consensus size: 20
560985 TTAAAATACT
560995 ATATATTTATATAAATTTTA
1 ATATATTTATATAAATTTTA
561015 ATATA-TTA-AT-AA--TT-
1 ATATATTTATATAAATTTTA
561029 -T-T-TTTATATAAATTTTA
1 ATATATTTATATAAATTTTA
561046 ATATATTTATATA
1 ATATATTTATATA
561059 TTTATATTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 18
0.66 0.00 0.34
Matches are distributed among these distances:
12 4 0.11
13 3 0.09
14 2 0.06
15 2 0.06
16 2 0.06
17 2 0.06
18 3 0.09
19 4 0.11
20 13 0.37
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
ATATATTTATATAAATTTTA
Found at i:561038 original size:31 final size:32
Alignment explanation
Indices: 561000--561061 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 32
560990 ATACTATATA
561000 TTTATATAAATTTTAATATATTAATA-ATTTT
1 TTTATATAAATTTTAATATATTAATATATTTT
*
561031 TTTATATAAATTTTAATATATTTATATATTT
1 TTTATATAAATTTTAATATATTAATATATTT
561062 ATATTATGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 25 0.86
32 4 0.14
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (32 bp):
TTTATATAAATTTTAATATATTAATATATTTT
Found at i:561050 original size:14 final size:14
Alignment explanation
Indices: 561002--561051 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
560992 ACTATATATT
561002 TATATAAATTTTAA
1 TATATAAATTTTAA
**
561016 TATATTAATAATTTTTT
1 TATA-T-A-AATTTTAA
561033 TATATAAATTTTAA
1 TATATAAATTTTAA
561047 TATAT
1 TATAT
561052 TTATATATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
14 15 0.52
15 2 0.07
16 2 0.07
17 10 0.34
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TATATAAATTTTAA
Found at i:561058 original size:39 final size:39
Alignment explanation
Indices: 561015--561092 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 39
561005 ATAAATTTTA
*
561015 ATATATTAATAATT-TTTTTATATAAATTTTAATATATTT
1 ATATATTAAT-ATTATGTTTATATAAATTTTAATATATTT
* * * *
561054 ATATATTTATATTATGTTTATATTATTTTTATTATATTT
1 ATATATTAATATTATGTTTATATAAATTTTAATATATTT
561093 TAATTATTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
38 3 0.09
39 30 0.91
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (39 bp):
ATATATTAATATTATGTTTATATAAATTTTAATATATTT
Found at i:561086 original size:20 final size:20
Alignment explanation
Indices: 561031--561117 Score: 88
Period size: 20 Copynumber: 4.3 Consensus size: 20
561021 TAATAATTTT
* * *
561031 TTTATATAAATTTTAATATA
1 TTTATATTATTTTTATTATA
* *
561051 TTTATA-TATTTATATTATG
1 TTTATATTATTTTTATTATA
561070 TTTATATTATTTTTATTATA
1 TTTATATTATTTTTATTATA
561090 TTT-TAATTATTTTTATATTATA
1 TTTAT-ATTA-TTTT-TATTATA
561112 TTTATA
1 TTTATA
561118 AAATATCTAA
Statistics
Matches: 55, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
19 15 0.27
20 24 0.44
21 4 0.07
22 11 0.20
23 1 0.02
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (20 bp):
TTTATATTATTTTTATTATA
Found at i:561088 original size:9 final size:9
Alignment explanation
Indices: 561041--561105 Score: 58
Period size: 10 Copynumber: 6.7 Consensus size: 9
561031 TTTATATAAA
*
561041 TTTTAATAT
1 TTTTATTAT
*
561050 ATTTATATAT
1 TTTTAT-TAT
*
561060 TTATATTAT
1 TTTTATTAT
561069 GTTTATATTAT
1 -TTT-TATTAT
561080 TTTTATTAT
1 TTTTATTAT
561089 ATTTTAATTAT
1 -TTTT-ATTAT
561100 TTTTAT
1 TTTTAT
561106 ATTATATTTA
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
9 15 0.33
10 20 0.43
11 11 0.24
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.68
Consensus pattern (9 bp):
TTTTATTAT
Found at i:561099 original size:31 final size:33
Alignment explanation
Indices: 561052--561116 Score: 98
Period size: 31 Copynumber: 2.0 Consensus size: 33
561042 TTTAATATAT
*
561052 TTATATATTTATATTATGTTTATATTATTTTTA
1 TTATATATTTATATTATGTTTATATTATATTTA
*
561085 TTATAT-TTTA-ATTATTTTTATATTATATTTA
1 TTATATATTTATATTATGTTTATATTATATTTA
561116 T
1 T
561117 AAAATATCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 20 0.67
32 4 0.13
33 6 0.20
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.68
Consensus pattern (33 bp):
TTATATATTTATATTATGTTTATATTATATTTA
Found at i:561115 original size:11 final size:11
Alignment explanation
Indices: 561055--561117 Score: 78
Period size: 11 Copynumber: 5.9 Consensus size: 11
561045 AATATATTTA
561055 TATATTTATAT
1 TATATTTATAT
*
561066 TATGTTTATAT
1 TATATTTATAT
561077 TAT-TTT-TAT
1 TATATTTATAT
561086 TATATTT-TAAT
1 TATATTTAT-AT
*
561097 TATTTTTATAT
1 TATATTTATAT
561108 TATATTTATA
1 TATATTTATA
561118 AAATATCTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
9 6 0.13
10 7 0.15
11 32 0.70
12 1 0.02
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (11 bp):
TATATTTATAT
Found at i:563090 original size:60 final size:61
Alignment explanation
Indices: 562979--563097 Score: 204
Period size: 60 Copynumber: 2.0 Consensus size: 61
562969 GGGTAGAGTG
* *
562979 ACAACCTCCTGTCAATGGCAGAGAAAATTGCAGGAAAATGAAAATAGAAAATTGTTTGCCC
1 ACAACCTCCTGTCAATGGCAGAGAAAATAGCAGGAAAATGAAAATAAAAAATTGTTTGCCC
*
563040 ACAACCTCCTGTCAATGG-AGAGGAAATAGCAGGAAAATGAAAATAAAAAATTGTTTGC
1 ACAACCTCCTGTCAATGGCAGAGAAAATAGCAGGAAAATGAAAATAAAAAATTGTTTGC
563098 TCACCTTCTT
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
60 37 0.67
61 18 0.33
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.21
Consensus pattern (61 bp):
ACAACCTCCTGTCAATGGCAGAGAAAATAGCAGGAAAATGAAAATAAAAAATTGTTTGCCC
Found at i:565863 original size:28 final size:28
Alignment explanation
Indices: 565807--565861 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 28
565797 TCATTATTTA
* *
565807 TTAATTAAAATAATATTTTAATTTAAAT
1 TTAATTAAAATAATATATAAATTTAAAT
565835 TTAATTATAAA-AATATATAAATATTAA
1 TTAATTA-AAATAATATATAAAT-TTAA
565862 TTAAAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 16 0.70
29 7 0.30
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (28 bp):
TTAATTAAAATAATATATAAATTTAAAT
Found at i:565875 original size:23 final size:22
Alignment explanation
Indices: 565830--565875 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
565820 TATTTTAATT
*
565830 TAAATTTAATTATAAAAATATA
1 TAAATTTAATTATAAAAAAATA
565852 TAAATATTAATTA-AAAATAAATA
1 TAAAT-TTAATTATAAAA-AAATA
565875 T
1 T
565876 TTTATTATAG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 9 0.43
23 12 0.57
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
TAAATTTAATTATAAAAAAATA
Found at i:567057 original size:20 final size:19
Alignment explanation
Indices: 567029--567079 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
567019 TTATATATAA
567029 TATTAATTTAATATTAAAAT
1 TATT-ATTTAATATTAAAAT
*
567049 TAATTATTTAATATTTAAAT
1 T-ATTATTTAATATTAAAAT
*
567069 TATTTTTTAAT
1 TATTATTTAAT
567080 TATATATCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 9 0.32
20 16 0.57
21 3 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATTATTTAATATTAAAAT
Found at i:568737 original size:29 final size:32
Alignment explanation
Indices: 568677--568738 Score: 85
Period size: 30 Copynumber: 2.0 Consensus size: 32
568667 CTTTTTAAAA
*
568677 AATATTTTTAATTTAATTTTTAATAACATAAT
1 AATATTTTTAATTTAAGTTTTAATAACATAAT
*
568709 AATATTTTT-A-TTAAGTTTTAA-AATATAAT
1 AATATTTTTAATTTAAGTTTTAATAACATAAT
568738 A
1 A
568739 GCTCACTACT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 8 0.29
30 10 0.36
31 1 0.04
32 9 0.32
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (32 bp):
AATATTTTTAATTTAAGTTTTAATAACATAAT
Found at i:568807 original size:25 final size:26
Alignment explanation
Indices: 568772--568843 Score: 69
Period size: 25 Copynumber: 2.8 Consensus size: 26
568762 ATATATATTT
*
568772 TATTTTTTATATAATAAAAATT-ATA
1 TATTTTATATATAATAAAAATTAATA
*
568797 TATTTTATATATGAACATAAAATTAATA
1 TATTTTATATAT-AATA-AAAATTAATA
*
568825 TATATTA-A-ATAATTAAAAA
1 TATTTTATATATAA-TAAAAA
568844 ATGAATCGAG
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
25 17 0.44
26 6 0.15
27 7 0.18
28 9 0.23
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (26 bp):
TATTTTATATATAATAAAAATTAATA
Found at i:569976 original size:16 final size:16
Alignment explanation
Indices: 569924--569979 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
569914 CTAATTTGAG
569924 AAAGTTTTTCTATTTTT
1 AAAGTTTTTCTA-TTTT
* * * *
569941 AAAGTTTAATGT-TGTC
1 AAAGTTT-TTCTATTTT
569957 AAAGTTTTTCTATTTT
1 AAAGTTTTTCTATTTT
569973 AAAGTTT
1 AAAGTTT
569980 AATGCTGCCA
Statistics
Matches: 29, Mismatches: 8, Indels: 5
0.69 0.19 0.12
Matches are distributed among these distances:
15 2 0.07
16 18 0.62
17 7 0.24
18 2 0.07
ACGTcount: A:0.29, C:0.05, G:0.11, T:0.55
Consensus pattern (16 bp):
AAAGTTTTTCTATTTT
Found at i:570182 original size:104 final size:103
Alignment explanation
Indices: 569989--570183 Score: 239
Period size: 104 Copynumber: 1.9 Consensus size: 103
569979 TAATGCTGCC
* * * * * * *
569989 ATATATATATATATATATGATAGAATAAATTTATTACAAAGTATATTTTAATTTGTCTCTTTAAA
1 ATATATATATATACACACGATAGAATAAATTAATTACAAAATATATCTTAATTCGTCTCTTTAAA
* * * *
570054 ATTAAATTTTAAAAATCATTATTAAATCATACATACAT
66 ATTAAATCTCAAAAACCATCATTAAATCATACATACAT
*
570092 ATATATATATATACACACGATAGAA-AAACGTTAATTATAAAATATATCTTAATTCGTCTCTTTA
1 ATATATATATATACACACGATAGAATAAA--TTAATTACAAAATATATCTTAATTCGTCTCTTTA
* *
570156 AAATTAAATCTCAAGACCCATCATTAAA
64 AAATTAAATCTCAAAAACCATCATTAAA
570184 AAAGTGCCAT
Statistics
Matches: 76, Mismatches: 14, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
102 3 0.04
103 22 0.29
104 51 0.67
ACGTcount: A:0.46, C:0.11, G:0.05, T:0.39
Consensus pattern (103 bp):
ATATATATATATACACACGATAGAATAAATTAATTACAAAATATATCTTAATTCGTCTCTTTAAA
ATTAAATCTCAAAAACCATCATTAAATCATACATACAT
Found at i:572593 original size:21 final size:21
Alignment explanation
Indices: 572569--572626 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
572559 TTAATTCTTG
* *
572569 TATAATTTAAATTATATAATA
1 TATAATTAAAATAATATAATA
* *
572590 TATAAATAAAATAATATATTA
1 TATAATTAAAATAATATAATA
*
572611 TATAATAAAAAATAAT
1 TATAAT-TAAAATAAT
572627 TGGGCTAGGC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 22 0.73
22 8 0.27
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TATAATTAAAATAATATAATA
Found at i:574864 original size:2 final size:2
Alignment explanation
Indices: 574857--574939 Score: 166
Period size: 2 Copynumber: 41.5 Consensus size: 2
574847 CCAAACAAAG
574857 TC TC TC TC TC TC TC TC 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 TC TC TC TC TC
574899 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
574940 ATATATATAT
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 81 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:574944 original size:2 final size:2
Alignment explanation
Indices: 574939--574980 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
574929 TCTCTCTCTC
574939 TA 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 TA
574981 GGACAAGAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:576206 original size:13 final size:13
Alignment explanation
Indices: 576173--576200 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
576163 AAAGAGAATT
576173 AAAAAAATTGAAA
1 AAAAAAATTGAAA
576186 AAAAAAATTGAAA
1 AAAAAAATTGAAA
576199 AA
1 AA
576201 TGAAATGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (13 bp):
AAAAAAATTGAAA
Found at i:577575 original size:28 final size:29
Alignment explanation
Indices: 577530--577592 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
577520 TTAAAAAAAT
* *
577530 TATTTTAAATAATAATATTTAAATTTTTAA
1 TATTTTAAAT-ATAATATTAAAAATTTTAA
* *
577560 TATTTTAAAT-TTATATTAAAAATTTTAT
1 TATTTTAAATATAATATTAAAAATTTTAA
577588 TATTT
1 TATTT
577593 AATTAAATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 19 0.66
30 10 0.34
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (29 bp):
TATTTTAAATATAATATTAAAAATTTTAA
Found at i:577586 original size:20 final size:20
Alignment explanation
Indices: 577561--577599 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
577551 AATTTTTAAT
577561 ATTTTA-AATTTATATTAAAA
1 ATTTTATAATTTA-ATTAAAA
*
577581 ATTTTATTATTTAATTAAA
1 ATTTTATAATTTAATTAAA
577600 TATATATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
ATTTTATAATTTAATTAAAA
Found at i:581726 original size:10 final size:10
Alignment explanation
Indices: 581698--581736 Score: 53
Period size: 9 Copynumber: 3.9 Consensus size: 10
581688 ATATCTAACA
581698 TAAATATTTT
1 TAAATATTTT
581708 T-AATATTTT
1 TAAATATTTT
*
581717 TAAATTTTTT
1 TAAATATTTT
581727 TCAAATATTT
1 T-AAATATTT
581737 AAATAATCAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
9 9 0.36
10 9 0.36
11 7 0.28
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (10 bp):
TAAATATTTT
Found at i:581726 original size:19 final size:19
Alignment explanation
Indices: 581698--581741 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
581688 ATATCTAACA
*
581698 TAAATATTTTT-AATATTTT
1 TAAATATTTTTCAA-ATATT
*
581717 TAAATTTTTTTCAAATATT
1 TAAATATTTTTCAAATATT
581736 TAAATA
1 TAAATA
581742 ATCATAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
TAAATATTTTTCAAATATT
Found at i:582292 original size:27 final size:25
Alignment explanation
Indices: 582252--582301 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
582242 TTTTTATATT
582252 AATATTTATAATTAAATTTAAATAAAA
1 AATATTTATAATT--ATTTAAATAAAA
* *
582279 AATATTTTTTATTATTTAAATAA
1 AATATTTATAATTATTTAAATAA
582302 TAATTTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 10 0.48
27 11 0.52
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (25 bp):
AATATTTATAATTATTTAAATAAAA
Found at i:582989 original size:22 final size:24
Alignment explanation
Indices: 582962--583008 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
582952 GCTCATTTAA
582962 TATTTTA-A-AAATATTAAAATAT
1 TATTTTATATAAATATTAAAATAT
* *
582984 TATTTTATATTAATATTAATATAT
1 TATTTTATATAAATATTAAAATAT
583008 T
1 T
583009 TTATAATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 7 0.33
23 1 0.05
24 13 0.62
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
TATTTTATATAAATATTAAAATAT
Found at i:583001 original size:24 final size:24
Alignment explanation
Indices: 582971--583024 Score: 71
Period size: 21 Copynumber: 2.4 Consensus size: 24
582961 ATATTTTAAA
582971 AATATTAAAATATTATTTTAT-ATT
1 AATATTAAAATA-TATTTTATAATT
582995 AATATT--AATATATTTTATAATT
1 AATATTAAAATATATTTTATAATT
583017 AAT-TTAAA
1 AATATTAAA
583025 TAAAATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
21 10 0.37
22 10 0.37
23 1 0.04
24 6 0.22
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
AATATTAAAATATATTTTATAATT
Found at i:583026 original size:22 final size:22
Alignment explanation
Indices: 582961--583026 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 22
582951 GGCTCATTTA
* * *
582961 ATATTTTAAAAAT-ATTAAAAT
1 ATATTTTATAATTAATTTAAAT
582982 ATTATTTTAT-ATTAATATT-AAT
1 A-TATTTTATAATTAAT-TTAAAT
583004 ATATTTTATAATTAATTTAAAT
1 ATATTTTATAATTAATTTAAAT
583026 A
1 A
583027 AAATTTTTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
21 13 0.35
22 23 0.62
23 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
ATATTTTATAATTAATTTAAAT
Found at i:584335 original size:28 final size:27
Alignment explanation
Indices: 584276--584335 Score: 68
Period size: 29 Copynumber: 2.2 Consensus size: 27
584266 ATTAATTGGG
**
584276 TAAAAAATATTATTTTTTAAATTTTTA
1 TAAAAAATATTATTTTTTAAACGTTTA
*
584303 TAAAAATATATTTATTTTTTTAACGTTTA
1 TAAAAA-ATA-TTATTTTTTAAACGTTTA
584332 -AAAA
1 TAAAA
584336 TGCACACTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 6 0.21
28 7 0.25
29 15 0.54
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (27 bp):
TAAAAAATATTATTTTTTAAACGTTTA
Found at i:584656 original size:23 final size:23
Alignment explanation
Indices: 584630--584677 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
584620 TTTTGAAATG
* *
584630 AATTTATTAAATATTTTTATTTA
1 AATTAATTAAATATTATTATTTA
*
584653 AATTAATTAATTATTATTATTTA
1 AATTAATTAAATATTATTATTTA
584676 AA
1 AA
584678 ATTTTAATGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
AATTAATTAAATATTATTATTTA
Found at i:584912 original size:25 final size:27
Alignment explanation
Indices: 584870--584923 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
584860 ATCTATGAAC
** *
584870 TTTTTAAAATAATGATAA-TTAATATA
1 TTTTTAAAATAAAAATAACATAATATA
584896 TTTTT-AAATAAAAATAACATAATATA
1 TTTTTAAAATAAAAATAACATAATATA
584922 TT
1 TT
584924 AATATCAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (27 bp):
TTTTTAAAATAAAAATAACATAATATA
Found at i:585146 original size:17 final size:18
Alignment explanation
Indices: 585126--585163 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
585116 AGTTTGTAAT
* *
585126 TAAAAATATTTAAA-AAA
1 TAAAAAAATTAAAATAAA
585143 TAAAAAAATTAAAATAAA
1 TAAAAAAATTAAAATAAA
585161 TAA
1 TAA
585164 TTGATAAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
TAAAAAAATTAAAATAAA
Found at i:586628 original size:17 final size:18
Alignment explanation
Indices: 586595--586630 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
586585 ATTAAAGATA
*
586595 ATTTTATAGTTAAAAAAT
1 ATTTTATAGTAAAAAAAT
586613 ATTTTA-AGTAAAAAAAT
1 ATTTTATAGTAAAAAAAT
586630 A
1 A
586631 AAAAACAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.39
Consensus pattern (18 bp):
ATTTTATAGTAAAAAAAT
Found at i:587854 original size:18 final size:18
Alignment explanation
Indices: 587833--587885 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 18
587823 GATAATTTAT
587833 TTTATTATTAAAATATTA
1 TTTATTATTAAAATATTA
*
587851 TTTATATATAAAAAATATTA
1 TTTAT-TAT-TAAAATATTA
587871 TTTA-TATTATAAATA
1 TTTATTATTA-AAATA
587886 AATTTTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
17 1 0.03
18 13 0.43
19 3 0.10
20 13 0.43
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTATTATTAAAATATTA
Found at i:587867 original size:20 final size:21
Alignment explanation
Indices: 587829--587888 Score: 81
Period size: 20 Copynumber: 3.0 Consensus size: 21
587819 ACTTGATAAT
*
587829 TTATTT-TATTAT-TAAAATA
1 TTATTTATATTATAAAAAATA
587848 TTATTTATA-TATAAAAAATA
1 TTATTTATATTATAAAAAATA
587868 TTATTTATATTATAAATAAAT
1 TTATTTATATTATAAA-AAAT
587889 TTTAAATATT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
19 9 0.25
20 17 0.47
21 6 0.17
22 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTATTTATATTATAAAAAATA
Found at i:591316 original size:20 final size:21
Alignment explanation
Indices: 591271--591316 Score: 51
Period size: 19 Copynumber: 2.3 Consensus size: 21
591261 AATAAATTTT
*
591271 TGATATATTAAAATTTATATA
1 TGATATATTAAAATTTAAATA
* *
591292 -AATATA-TAAATTTTAAATA
1 TGATATATTAAAATTTAAATA
591311 TGATAT
1 TGATAT
591317 GAATAAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (21 bp):
TGATATATTAAAATTTAAATA
Found at i:591788 original size:16 final size:17
Alignment explanation
Indices: 591763--591800 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
591753 TTTGATATGT
*
591763 TTATATTTTTTATTATA
1 TTATATTTTTAATTATA
*
591780 TTATA-TTTTAATTATT
1 TTATATTTTTAATTATA
591796 TTATA
1 TTATA
591801 ATATATTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTATATTTTTAATTATA
Found at i:591795 original size:26 final size:27
Alignment explanation
Indices: 591766--591816 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
591756 GATATGTTTA
* *
591766 TATTTTTTATTATA-TTATATTTTAAT
1 TATTTTATAATATATTTATATTTTAAT
591792 TATTTTATAATATATTTATATTTTA
1 TATTTTATAATATATTTATATTTTA
591817 TAATCATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (27 bp):
TATTTTATAATATATTTATATTTTAAT
Found at i:591805 original size:21 final size:19
Alignment explanation
Indices: 591775--591833 Score: 68
Period size: 18 Copynumber: 3.1 Consensus size: 19
591765 ATATTTTTTA
*
591775 TTATATTATATTTTAATTATT
1 TTATAATATATTTT-A-TATT
591796 TTATAATATA-TTTATATT
1 TTATAATATATTTTATATT
591814 TTATAATCATATTTT-TATT
1 TTATAAT-ATATTTTATATT
591833 T
1 T
591834 AAAATCATCA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
18 11 0.31
19 9 0.26
20 6 0.17
21 9 0.26
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (19 bp):
TTATAATATATTTTATATT
Found at i:591839 original size:18 final size:19
Alignment explanation
Indices: 591792--591841 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
591782 ATATTTTAAT
*
591792 TATTTTATAAT-ATATTTA
1 TATTTTAAAATCATATTTA
* *
591810 TATTTTATAATCATATTTT
1 TATTTTAAAATCATATTTA
591829 TA-TTTAAAATCAT
1 TATTTTAAAATCAT
591842 CAAATCTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 21 0.72
19 8 0.28
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (19 bp):
TATTTTAAAATCATATTTA
Found at i:592320 original size:10 final size:9
Alignment explanation
Indices: 592305--592483 Score: 50
Period size: 8 Copynumber: 20.6 Consensus size: 9
592295 GTCGAAATAT
592305 ATATTTATA
1 ATATTTATA
592314 ATCATTTAT-
1 AT-ATTTATA
592323 ATATTTATA
1 ATATTTATA
592332 TTATATTTAT-
1 --ATATTTATA
* *
592342 AT-TTTTTT
1 ATATTTATA
*
592350 TTA-TTATAA
1 ATATTTAT-A
*
592359 CATATTTAAA
1 -ATATTTATA
592369 ATATTT-T-
1 ATATTTATA
592376 ATATTTATTTA
1 ATATTTA--TA
592387 A-ATTT-TA
1 ATATTTATA
*
592394 ATATATATTA
1 ATATTTA-TA
592404 ATAATTTATA
1 AT-ATTTATA
592414 ATA--TATA
1 ATATTTATA
592421 A-ATTT-TA
1 ATATTTATA
* *
592428 AAATATA-A
1 ATATTTATA
* *
592436 ATTTTTATT
1 ATATTTATA
592445 ATA-TTATA
1 ATATTTATA
*
592453 TTATATTAT-
1 ATAT-TTATA
592462 ATATTTAT-
1 ATATTTATA
592470 AT-TTTATA
1 ATATTTATA
592478 TATATT
1 -ATATT
592484 ATATTTATTT
Statistics
Matches: 125, Mismatches: 18, Indels: 53
0.64 0.09 0.27
Matches are distributed among these distances:
6 1 0.01
7 26 0.21
8 36 0.29
9 18 0.14
10 28 0.22
11 16 0.13
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (9 bp):
ATATTTATA
Found at i:592448 original size:15 final size:14
Alignment explanation
Indices: 592406--592440 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
592396 ATATATTAAT
592406 AATTTATAATATATA
1 AATTT-TAATATATA
*
592421 AATTTTAAAATATA
1 AATTTTAATATATA
592435 AATTTT
1 AATTTT
592441 TATTATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.74
15 5 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
AATTTTAATATATA
Found at i:592451 original size:5 final size:5
Alignment explanation
Indices: 592441--592502 Score: 69
Period size: 5 Copynumber: 12.8 Consensus size: 5
592431 TATAAATTTT
*
592441 TATTA TATTA TATTA TATTA TA-TA T-TTA TATTT TATATA TATTA TATT-
1 TATTA TATTA TATTA TATTA TATTA TATTA TATTA TAT-TA TATTA TATTA
592489 TATT- TAATTA TATT
1 TATTA T-ATTA TATT
592503 TTAAATTATT
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
4 11 0.22
5 34 0.68
6 5 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (5 bp):
TATTA
Found at i:592477 original size:30 final size:31
Alignment explanation
Indices: 592443--592511 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 31
592433 TAAATTTTTA
*
592443 TTATATTATATTATA-TTATATATTTATATT
1 TTATATTATATTATATTTATATAATTATATT
*
592473 TTATA-TATATTATATTTATTTAATTATATT
1 TTATATTATATTATATTTATATAATTATATT
*
592503 TTAAATTAT
1 TTATATTAT
592512 TAAGTTTAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 9 0.26
30 22 0.65
31 3 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (31 bp):
TTATATTATATTATATTTATATAATTATATT
Found at i:592504 original size:64 final size:64
Alignment explanation
Indices: 592319--592511 Score: 143
Period size: 64 Copynumber: 3.1 Consensus size: 64
592309 TTATAATCAT
* * ** *
592319 TTATA-TAT-TTATAT-TATATTTATATTTT-TTTTTATTATAACATATTTAA-AATATTTTATA
1 TTATATTATATTATATATATATTTATATTTTATATATATTAT-ATTTATTTAATTATATTTTATA
* * * * * ** *
592379 TT-TATTTAAATTTTAATATATATTAATAATTTATA-ATATATAAATTT-TAAAATATAAATTTT
1 TTATA-TTATATTAT-ATATATATTTATATTTTATATATAT-TATATTTATTTAAT-TATATTTT
592441 -TA
62 ATA
*
592443 TTATATTATATTATATTATATATTTATATTTTATATATATTATATTTATTTAATTATATTTTAAA
1 TTATATTATATTATA-TATATATTTATATTTTATATATATTATATTTATTTAATTATATTTTATA
592508 TTAT
1 TTAT
592512 TAAGTTTAAT
Statistics
Matches: 97, Mismatches: 22, Indels: 23
0.68 0.15 0.16
Matches are distributed among these distances:
59 2 0.02
60 2 0.02
61 2 0.02
62 3 0.03
63 6 0.06
64 58 0.60
65 24 0.25
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (64 bp):
TTATATTATATTATATATATATTTATATTTTATATATATTATATTTATTTAATTATATTTTATA
Found at i:592505 original size:15 final size:16
Alignment explanation
Indices: 592438--592505 Score: 79
Period size: 15 Copynumber: 4.3 Consensus size: 16
592428 AAATATAAAT
592438 TTTTA-TTATATTATA
1 TTTTATTTATATTATA
*
592453 TTATATTATATATTTATA
1 TTTTATT-TATA-TTATA
*
592471 TTTTATATATATTATA
1 TTTTATTTATATTATA
592487 -TTTATTTA-ATTATA
1 TTTTATTTATATTATA
592501 TTTTA
1 TTTTA
592506 AATTATTAAG
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
14 6 0.13
15 15 0.33
16 6 0.13
17 8 0.18
18 10 0.22
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTATTTATATTATA
Found at i:592769 original size:18 final size:18
Alignment explanation
Indices: 592748--592803 Score: 60
Period size: 18 Copynumber: 3.1 Consensus size: 18
592738 TTTATAAATT
592748 TTATTATTTTAATTTAAA
1 TTATTATTTTAATTTAAA
*
592766 TTATTA-TTTAATAATAAA
1 TTATTATTTTAAT-TTAAA
* * *
592784 ATAATATTTTTATTTAAA
1 TTATTATTTTAATTTAAA
592802 TT
1 TT
592804 TAATTATAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
17 6 0.20
18 19 0.63
19 5 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTATTATTTTAATTTAAA
Found at i:593906 original size:17 final size:17
Alignment explanation
Indices: 593886--593939 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 17
593876 TTTACTTTTA
593886 AAATCATAAAATCTAAT
1 AAATCATAAAATCTAAT
*
593903 AAATC--AAAAT-AAAT
1 AAATCATAAAATCTAAT
*
593917 -AATACCTAAAATCTAAT
1 AAAT-CATAAAATCTAAT
593934 AAATCA
1 AAATCA
593940 AAATAAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 10
0.69 0.07 0.24
Matches are distributed among these distances:
13 3 0.10
14 4 0.14
15 5 0.17
16 5 0.17
17 9 0.31
18 3 0.10
ACGTcount: A:0.61, C:0.13, G:0.00, T:0.26
Consensus pattern (17 bp):
AAATCATAAAATCTAAT
Found at i:593927 original size:31 final size:31
Alignment explanation
Indices: 593892--593952 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
593882 TTTAAAATCA
593892 TAAAATCTAATAAATCAAAATAAATAATACC
1 TAAAATCTAATAAATCAAAATAAATAATACC
593923 TAAAATCTAATAAATCAAAATAAATAATAC
1 TAAAATCTAATAAATCAAAATAAATAATAC
593953 ATTACATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.62, C:0.11, G:0.00, T:0.26
Consensus pattern (31 bp):
TAAAATCTAATAAATCAAAATAAATAATACC
Found at i:593950 original size:17 final size:17
Alignment explanation
Indices: 593899--593951 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
593889 TCATAAAATC
593899 TAATAAATCAAAATAAA
1 TAATAAATCAAAATAAA
** *
593916 TAATACCT-AAAAT--C
1 TAATAAATCAAAATAAA
593930 TAATAAATCAAAATAAA
1 TAATAAATCAAAATAAA
593947 TAATA
1 TAATA
593952 CATTACATAT
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
14 6 0.22
15 5 0.19
16 5 0.19
17 11 0.41
ACGTcount: A:0.64, C:0.09, G:0.00, T:0.26
Consensus pattern (17 bp):
TAATAAATCAAAATAAA
Found at i:594295 original size:23 final size:23
Alignment explanation
Indices: 594266--594329 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
594256 AATCTACCCA
594266 AAAAAATATTTTTAAAATAAAAT
1 AAAAAATATTTTTAAAATAAAAT
** * *
594289 ATTAAATA-TATTAAAATTAAATT
1 AAAAAATATTTTTAAAA-TAAAAT
594312 AAAAAATATTTTTAAAAT
1 AAAAAATATTTTTAAAAT
594330 CATTCAAAAA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
22 7 0.22
23 18 0.56
24 7 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
AAAAAATATTTTTAAAATAAAAT
Found at i:596257 original size:22 final size:21
Alignment explanation
Indices: 596226--596268 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
596216 AATTTATTAA
596226 AAAATATTATATATTTTTAATT
1 AAAATATTAT-TATTTTTAATT
* *
596248 AAAATTTTATTTTTTTTAATT
1 AAAATATTATTATTTTTAATT
596269 TTTAAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
AAAATATTATTATTTTTAATT
Found at i:596692 original size:33 final size:32
Alignment explanation
Indices: 596632--596693 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 32
596622 TTATTAAAAA
**
596632 TTTTTAAATTTATTAATTTTATTTAAATTTGT
1 TTTTTAAATTTATTAATTTTAAATAAATTTGT
596664 TTTTATAAATTTATT-ATTTTCAAATAAATT
1 TTTT-TAAATTTATTAATTTT-AAATAAATT
596694 ATCATATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 9 0.35
33 17 0.65
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (32 bp):
TTTTTAAATTTATTAATTTTAAATAAATTTGT
Found at i:600629 original size:11 final size:11
Alignment explanation
Indices: 600613--600778 Score: 64
Period size: 11 Copynumber: 15.2 Consensus size: 11
600603 TTCATAATTT
600613 TTATATTTATA
1 TTATATTTATA
600624 TTATATTTTATAA
1 TTATA-TTTAT-A
*
600637 TTATATATTTTTA
1 -T-TATATTTATA
* *
600650 TT-TATTAAAA
1 TTATATTTATA
*
600660 ATATATTTAAAATA
1 TTATATTT---ATA
600674 TTATATATT-TA
1 TTATAT-TTATA
* * *
600685 ATATAATAATA
1 TTATATTTATA
*
600696 TTTTATTT-TA
1 TTATATTTATA
*
600706 TATAAATTT-TA
1 T-TATATTTATA
*
600717 ATATATTTATA
1 TTATATTTATA
600728 -TATA---A-A
1 TTATATTTATA
* *
600734 TTATATTTTTG
1 TTATATTTATA
*
600745 TTATATTTTTA
1 TTATATTTATA
600756 TTAT-TTTATA
1 TTATATTTATA
600766 TTATATTTATA
1 TTATATTTATA
600777 TT
1 TT
600779 TTATAATTAT
Statistics
Matches: 114, Mismatches: 23, Indels: 36
0.66 0.13 0.21
Matches are distributed among these distances:
6 1 0.01
7 5 0.04
10 29 0.25
11 53 0.46
12 6 0.05
13 2 0.02
14 12 0.11
15 6 0.05
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (11 bp):
TTATATTTATA
Found at i:600681 original size:16 final size:16
Alignment explanation
Indices: 600660--600698 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
600650 TTTATTAAAA
*
600660 ATATATTTAAAATATT
1 ATATATTTAAAATAAT
*
600676 ATATATTTAATATAAT
1 ATATATTTAAAATAAT
600692 A-ATATTT
1 ATATATTT
600699 TATTTTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 6 0.29
16 15 0.71
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATATATTTAAAATAAT
Found at i:600756 original size:19 final size:21
Alignment explanation
Indices: 600737--600790 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 21
600727 ATATAAATTA
*
600737 TATTTT-TGTTATATTTTTAT
1 TATTTTATATTATATTTTTAT
600757 TATTTTATATTATA--TTTA-
1 TATTTTATATTATATTTTTAT
600775 TATTTTATAATTATAT
1 TATTTTAT-ATTATAT
600791 CAAGTGTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
18 8 0.27
19 10 0.33
20 6 0.20
21 6 0.20
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (21 bp):
TATTTTATATTATATTTTTAT
Found at i:600771 original size:21 final size:19
Alignment explanation
Indices: 600671--600790 Score: 79
Period size: 20 Copynumber: 6.2 Consensus size: 19
600661 TATATTTAAA
* * *
600671 ATATTATATATTTAATATA
1 ATATTTTATATTTTATATT
600690 ATAATATTT-TATTTTATA-T
1 AT-AT-TTTATATTTTATATT
*
600709 AAATTTTAATATATTTATA-T
1 ATATTTT-ATAT-TTTATATT
** *
600729 ATAAATTATATTTT-TGTT
1 ATATTTTATATTTTATATT
600747 ATATTTTTATTATTTTATATT
1 ATA-TTTTA-TATTTTATATT
600768 ATA-TTTATATTTTATAATT
1 ATATTTTATATTTTAT-ATT
600787 ATAT
1 ATAT
600791 CAAGTGTAAA
Statistics
Matches: 79, Mismatches: 11, Indels: 21
0.71 0.10 0.19
Matches are distributed among these distances:
17 4 0.05
18 17 0.22
19 23 0.29
20 27 0.34
21 8 0.10
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (19 bp):
ATATTTTATATTTTATATT
Found at i:600775 original size:6 final size:6
Alignment explanation
Indices: 600718--600790 Score: 50
Period size: 6 Copynumber: 12.8 Consensus size: 6
600708 TAAATTTTAA
* * *
600718 TATATT TATATA TA-AAT TATATT T-T-TGT TATATT TTTA-T TAT-TT
1 TATATT TATATT TATATT TATATT TATAT-T TATATT TATATT TATATT
*
600762 TATA-T TATATT TATATTT TATAAT TATAT
1 TATATT TATATT TATA-TT TATATT TATAT
600791 CAAGTGTAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 16
0.68 0.11 0.21
Matches are distributed among these distances:
4 1 0.02
5 18 0.35
6 25 0.49
7 7 0.14
ACGTcount: A:0.34, C:0.00, G:0.01, T:0.64
Consensus pattern (6 bp):
TATATT
Found at i:601418 original size:3 final size:3
Alignment explanation
Indices: 601410--601443 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
601400 TGCTTGTTCG
601410 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT G
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT G
601444 TGGCTGTTGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.35, T:0.32
Consensus pattern (3 bp):
GCT
Found at i:606264 original size:17 final size:19
Alignment explanation
Indices: 606212--606283 Score: 60
Period size: 17 Copynumber: 3.7 Consensus size: 19
606202 AACCAATACT
*
606212 ATAAATTTAAAATATAATTTA
1 ATAAATTTATAAT-T-ATTTA
*
606233 ATTAATTTATATAATTATTT-
1 A-TAAATT-TATAATTATTTA
*
606253 TTAAA-TTATAA-TATTTA
1 ATAAATTTATAATTATTTA
606270 ATAAATTTATAATT
1 ATAAATTTATAATT
606284 TAAATATCGA
Statistics
Matches: 41, Mismatches: 5, Indels: 12
0.71 0.09 0.21
Matches are distributed among these distances:
16 5 0.12
17 9 0.22
18 7 0.17
19 4 0.10
21 5 0.12
22 6 0.15
23 5 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATAAATTTATAATTATTTA
Found at i:606760 original size:18 final size:19
Alignment explanation
Indices: 606737--606777 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
606727 AATTTACGAT
* *
606737 ATTTATTTAA-ATTTAAAG
1 ATTTATTAAATATTTAAAA
606755 ATTTATTAAATATTTAAAA
1 ATTTATTAAATATTTAAAA
606774 ATTT
1 ATTT
606778 TACACAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 9 0.45
19 11 0.55
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (19 bp):
ATTTATTAAATATTTAAAA
Found at i:607119 original size:41 final size:43
Alignment explanation
Indices: 607042--607121 Score: 105
Period size: 41 Copynumber: 1.9 Consensus size: 43
607032 AAATGAGTTT
*
607042 AATTATATATTTATAAATATAAATAAATTGTGATAAAATTTAA
1 AATTATATATTTATAAATATAAATAAATTGTAATAAAATTTAA
607085 AATT-TATATTT-TAAA-ATAAATTAAATT-TAAATAAAAT
1 AATTATATATTTATAAATATAAA-TAAATTGT-AATAAAAT
607122 AAATATTATA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
40 6 0.18
41 17 0.50
42 7 0.21
43 4 0.12
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (43 bp):
AATTATATATTTATAAATATAAATAAATTGTAATAAAATTTAA
Found at i:608172 original size:18 final size:19
Alignment explanation
Indices: 608141--608178 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
608131 TTATTTAATT
608141 TTTTTAAATATTAAATAAA
1 TTTTTAAATATTAAATAAA
*
608160 TTTTT-AATTTTAAATAAA
1 TTTTTAAATATTAAATAAA
608178 T
1 T
608179 AATTCAATCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTTAAATATTAAATAAA
Found at i:609109 original size:9 final size:8
Alignment explanation
Indices: 609091--609165 Score: 70
Period size: 9 Copynumber: 9.4 Consensus size: 8
609081 CAATTTGAAT
609091 TTTTAATA
1 TTTTAATA
609099 TTTTAATTA
1 TTTTAA-TA
609108 TTTTGAATCA
1 TTTT-AAT-A
609118 -TTTAA-A
1 TTTTAATA
609124 TTTTAAATA
1 TTTT-AATA
609133 TTTTAA-A
1 TTTTAATA
609140 TTTTAATTA
1 TTTTAA-TA
609149 TTTTAA-A
1 TTTTAATA
609156 -TTTAATA
1 TTTTAATA
609163 TTT
1 TTT
609166 AAATTAATCA
Statistics
Matches: 57, Mismatches: 0, Indels: 20
0.74 0.00 0.26
Matches are distributed among these distances:
6 6 0.11
7 12 0.21
8 14 0.25
9 22 0.39
10 3 0.05
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (8 bp):
TTTTAATA
Found at i:609112 original size:25 final size:25
Alignment explanation
Indices: 609084--609156 Score: 87
Period size: 25 Copynumber: 2.9 Consensus size: 25
609074 TTTAGATCAA
*
609084 TTTGAATTTTTAATATTTTAATTAT
1 TTTGAATTTTTAATATTTTAAATAT
*
609109 TTTGAATCATTTAA-ATTTTAAATAT
1 TTTGAAT-TTTTAATATTTTAAATAT
*
609134 TTT-AAATTTTAATTATTTTAAAT
1 TTTGAATTTTTAA-TATTTTAAAT
609157 TTAATATTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
23 5 0.12
24 2 0.05
25 29 0.71
26 5 0.12
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (25 bp):
TTTGAATTTTTAATATTTTAAATAT
Found at i:609137 original size:16 final size:16
Alignment explanation
Indices: 609088--609170 Score: 84
Period size: 16 Copynumber: 5.2 Consensus size: 16
609078 GATCAATTTG
*
609088 AATTTTTAATATTTTA
1 AATTTTAAATATTTTA
*
609104 ATTATTTTGAATCA-TTTA
1 A--ATTTTAAAT-ATTTTA
609122 AATTTTAAATATTTTA
1 AATTTTAAATATTTTA
*
609138 AATTTTAATTATTTTA
1 AATTTTAAATATTTTA
609154 AA-TTT-AATA-TTTA
1 AATTTTAAATATTTTA
609167 AATT
1 AATT
609171 AATCAAGTTT
Statistics
Matches: 58, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
13 6 0.10
14 4 0.07
15 4 0.07
16 30 0.52
18 13 0.22
19 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (16 bp):
AATTTTAAATATTTTA
Found at i:609196 original size:15 final size:15
Alignment explanation
Indices: 609157--609197 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
609147 TATTTTAAAT
609157 TTAATATTTAAATTAA
1 TTAA-ATTTAAATTAA
* *
609173 TCAAGTTTAAATTAA
1 TTAAATTTAAATTAA
609188 TTAAATTTAA
1 TTAAATTTAA
609198 CACTTTAATT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 18 0.86
16 3 0.14
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (15 bp):
TTAAATTTAAATTAA
Found at i:609343 original size:16 final size:16
Alignment explanation
Indices: 609324--609366 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
609314 AAAATGATTT
*
609324 ATTTTGAATTGAAATA
1 ATTTTAAATTGAAATA
*
609340 ATTTTAAATTTAAATTA
1 ATTTTAAATTGAAA-TA
*
609357 TTTTTAAATT
1 ATTTTAAATT
609367 AAAAGTCAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 12 0.52
17 11 0.48
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (16 bp):
ATTTTAAATTGAAATA
Found at i:609825 original size:15 final size:16
Alignment explanation
Indices: 609801--609837 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
609791 TATTATATAG
*
609801 TTAATAAAAAAATTA-
1 TTAATTAAAAAATTAT
609816 TTAATT-AAAAATTAT
1 TTAATTAAAAAATTAT
609831 TTAATTA
1 TTAATTA
609838 TCATATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TTAATTAAAAAATTAT
Found at i:609827 original size:14 final size:15
Alignment explanation
Indices: 609808--609837 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
609798 TAGTTAATAA
609808 AAAAATTA-TTAATT
1 AAAAATTATTTAATT
609822 AAAAATTATTTAATT
1 AAAAATTATTTAATT
609837 A
1 A
609838 TCATATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
AAAAATTATTTAATT
Found at i:610791 original size:20 final size:19
Alignment explanation
Indices: 610768--610809 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
610758 AGTATATTAA
610768 TTTTAAATTATATTTTAATT
1 TTTTAAATTAT-TTTTAATT
*
610788 TTTTAAATTATTTTTACTT
1 TTTTAAATTATTTTTAATT
610807 TTT
1 TTT
610810 CGAATCATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTTAAATTATTTTTAATT
Found at i:611137 original size:18 final size:18
Alignment explanation
Indices: 611116--611156 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
611106 ATTTGAAATA
611116 TAAATTT-TAAATTTTATT
1 TAAATTTATAAATTTT-TT
*
611134 TAAATTTATATATTTTTT
1 TAAATTTATAAATTTTTT
611152 TAAAT
1 TAAAT
611157 GAATAGTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TAAATTTATAAATTTTTT
Found at i:611402 original size:22 final size:21
Alignment explanation
Indices: 611377--611418 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
611367 TATAATTAAA
*
611377 AAATAAATAAAATTAATGTTTT
1 AAAT-AATAAAATTAAAGTTTT
*
611399 AAATATTAAAATTAAAGTTT
1 AAATAATAAAATTAAAGTTT
611419 AATCCGTGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (21 bp):
AAATAATAAAATTAAAGTTTT
Found at i:611620 original size:25 final size:25
Alignment explanation
Indices: 611564--611641 Score: 72
Period size: 24 Copynumber: 3.1 Consensus size: 25
611554 TATGGTAAAA
611564 ATAAATTTAATAAATTATTTTTTAT
1 ATAAATTTAATAAATTATTTTTTAT
*
611589 -TACATTTAA-AAATT-TTATATTTAT
1 ATAAATTTAATAAATTATT-T-TTTAT
* *
611613 ATAAATTTTAATACATTAATTATTTAT
1 ATAAA-TTTAATAAATT-ATTTTTTAT
611640 AT
1 AT
611642 TATAAAATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
22 2 0.05
23 6 0.14
24 13 0.31
25 3 0.07
26 5 0.12
27 11 0.26
29 2 0.05
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (25 bp):
ATAAATTTAATAAATTATTTTTTAT
Found at i:611628 original size:35 final size:31
Alignment explanation
Indices: 611583--611657 Score: 78
Period size: 32 Copynumber: 2.3 Consensus size: 31
611573 ATAAATTATT
*
611583 TTTTATTACATTTAAAAATTTTATATTTATATAAA
1 TTTTAATACA-TTAAAAA-TTTATA-TTATA-AAA
**
611618 TTTTAATACATTAATTATTTATATTATAAAA
1 TTTTAATACATTAAAAATTTATATTATAAAA
611649 TATTTAATA
1 T-TTTAATA
611658 TATATATATA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
31 4 0.11
32 12 0.33
33 6 0.17
34 5 0.14
35 9 0.25
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (31 bp):
TTTTAATACATTAAAAATTTATATTATAAAA
Found at i:611662 original size:2 final size:2
Alignment explanation
Indices: 611655--611680 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
611645 AAAATATTTA
611655 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
611681 GAGTTATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:612078 original size:2 final size:2
Alignment explanation
Indices: 612071--612101 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
612061 GTAATTCTGA
612071 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
612102 GTGTAGTGAA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:623107 original size:56 final size:56
Alignment explanation
Indices: 623047--623161 Score: 203
Period size: 56 Copynumber: 2.1 Consensus size: 56
623037 TGATTATTTA
* * *
623047 TTAAAATTTTACAATACAAAATGAGACACTACGACGCTACAAATGAAAGTACAAGC
1 TTAAAAATTTACAATACAAAATGAGACACTACGACACTACAAATGAAAGCACAAGC
623103 TTAAAAATTTACAATACAAAATGAGACACTACGACACTACAAATGAAAGCACAAGC
1 TTAAAAATTTACAATACAAAATGAGACACTACGACACTACAAATGAAAGCACAAGC
623159 TTA
1 TTA
623162 GATACTAACT
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.50, C:0.18, G:0.11, T:0.21
Consensus pattern (56 bp):
TTAAAAATTTACAATACAAAATGAGACACTACGACACTACAAATGAAAGCACAAGC
Found at i:623878 original size:23 final size:25
Alignment explanation
Indices: 623824--623878 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
623814 ATATGTATAC
* *
623824 ATATATTTATATATAAATATAAAAT
1 ATATATTTATAAATAAATATAAAAA
*
623849 ATAATATTT-TAAATATATA-AAAAA
1 AT-ATATTTATAAATAAATATAAAAA
623873 ATATAT
1 ATATAT
623879 ATTCATATCC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 4 0.15
24 6 0.23
25 10 0.38
26 6 0.23
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
ATATATTTATAAATAAATATAAAAA
Found at i:626522 original size:15 final size:16
Alignment explanation
Indices: 626496--626537 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 16
626486 GATAAATAAG
626496 ATTAATATTTAAATTA
1 ATTAATATTTAAATTA
*
626512 ATTAA-ATTTAAGTTA
1 ATTAATATTTAAATTA
*
626527 A-TCATATTTAA
1 ATTAATATTTAA
626538 TATTTAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 2 0.09
15 16 0.70
16 5 0.22
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (16 bp):
ATTAATATTTAAATTA
Found at i:626607 original size:17 final size:16
Alignment explanation
Indices: 626557--626609 Score: 63
Period size: 17 Copynumber: 3.2 Consensus size: 16
626547 ATTACGTTCG
626557 ATTA-TTTAAAGTTTAA
1 ATTATTTTAAA-TTTAA
*
626573 ATTATTTTAGATTATAA
1 ATTATTTTAAATT-TAA
626590 ATTATTTTTAAATTTAA
1 ATTA-TTTTAAATTTAA
626607 ATT
1 ATT
626610 GTTCGACTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 6 0.19
17 18 0.56
18 8 0.25
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (16 bp):
ATTATTTTAAATTTAA
Found at i:626829 original size:23 final size:21
Alignment explanation
Indices: 626802--626851 Score: 55
Period size: 23 Copynumber: 2.3 Consensus size: 21
626792 AAAAAATATT
* *
626802 TATATTCAATACATAATTTAATA
1 TATATTAAATACA-AATATAA-A
*
626825 TATATTAAATATAAATATAAA
1 TATATTAAATACAAATATAAA
626846 TATATT
1 TATATT
626852 TATATTAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 7 0.29
22 6 0.25
23 11 0.46
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (21 bp):
TATATTAAATACAAATATAAA
Found at i:626860 original size:21 final size:23
Alignment explanation
Indices: 626821--626867 Score: 71
Period size: 21 Copynumber: 2.1 Consensus size: 23
626811 TACATAATTT
626821 AATATATATTAAATATAAATATA
1 AATATATATTAAATATAAATATA
*
626844 AATATAT-TTATAT-TAAATATA
1 AATATATATTAAATATAAATATA
626865 AAT
1 AAT
626868 CTCAATAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 11 0.48
22 5 0.22
23 7 0.30
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
AATATATATTAAATATAAATATA
Found at i:626874 original size:27 final size:26
Alignment explanation
Indices: 626820--626879 Score: 84
Period size: 27 Copynumber: 2.3 Consensus size: 26
626810 ATACATAATT
*
626820 TAATATATATTAAATATAAATATAAA
1 TAATTTATATTAAATATAAATATAAA
* *
626846 TATATTTATATTAAATATAAATCTCAA
1 TA-ATTTATATTAAATATAAATATAAA
626873 TAATTTA
1 TAATTTA
626880 CTTAATATAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 7 0.23
27 23 0.77
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (26 bp):
TAATTTATATTAAATATAAATATAAA
Found at i:627707 original size:19 final size:20
Alignment explanation
Indices: 627679--627720 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
627669 TGAAAATTTA
*
627679 AAAAATAAAT-TTACTTTTTT
1 AAAAATAAATGATA-TTTTTT
627699 AAAAA-AAATGATATTTTTT
1 AAAAATAAATGATATTTTTT
627718 AAA
1 AAA
627721 GTCTAAAAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (20 bp):
AAAAATAAATGATATTTTTT
Done.