Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold229
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: 643502
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 5 of 5
Found at i:580045 original size:24 final size:24
Alignment explanation
Indices: 580013--580060 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
580003 GTCCTTCATT
*
580013 ATTTTCAATAATATTAACATGCAA
1 ATTTTCAATAATATTAAAATGCAA
580037 ATTTTCAATAATATTAAAATGCAA
1 ATTTTCAATAATATTAAAATGCAA
580061 TTAATTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.48, C:0.10, G:0.04, T:0.38
Consensus pattern (24 bp):
ATTTTCAATAATATTAAAATGCAA
Found at i:582747 original size:17 final size:17
Alignment explanation
Indices: 582727--582762 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
582717 ATGATTGTAT
*
582727 TTTTATTATATTTATAA
1 TTTTATTATATTTAAAA
582744 TTTTATTATATTTAAAA
1 TTTTATTATATTTAAAA
582761 TT
1 TT
582763 AATATTTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTATTATATTTAAAA
Found at i:583159 original size:23 final size:25
Alignment explanation
Indices: 583112--583159 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
583102 ATGTGAAAAA
583112 TTTTAAAATATTATAAAAATATAAT
1 TTTTAAAATATTATAAAAATATAAT
*
583137 TTTTAAAATTTTA-AAAAAT-TAAT
1 TTTTAAAATATTATAAAAATATAAT
583160 GAGTTAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 4 0.18
24 6 0.27
25 12 0.55
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
TTTTAAAATATTATAAAAATATAAT
Found at i:587452 original size:24 final size:24
Alignment explanation
Indices: 587409--587465 Score: 66
Period size: 23 Copynumber: 2.4 Consensus size: 24
587399 AGGAAGGAAA
587409 TAAAA-AA-ATTTTAATTTAATAATT
1 TAAAATAATATTTTAA-TTAAT-ATT
587433 TAAAATAATATTTTAA-TAATATT
1 TAAAATAATATTTTAATTAATATT
*
587456 TTAAATAATA
1 TAAAATAATA
587466 AAATAAATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
23 12 0.40
24 9 0.30
25 2 0.07
26 7 0.23
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
TAAAATAATATTTTAATTAATATT
Found at i:587462 original size:12 final size:12
Alignment explanation
Indices: 587425--587465 Score: 57
Period size: 11 Copynumber: 3.4 Consensus size: 12
587415 AATTTTAATT
*
587425 TAATAATTTAAAA
1 TAAT-ATTTTAAA
587438 TAATATTTT-AA
1 TAATATTTTAAA
587449 TAATATTTTAAA
1 TAATATTTTAAA
587461 TAATA
1 TAATA
587466 AAATAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 11 0.42
12 11 0.42
13 4 0.15
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
TAATATTTTAAA
Found at i:587466 original size:26 final size:27
Alignment explanation
Indices: 587406--587469 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 27
587396 TTAAGGAAGG
*
587406 AAATAAAAAAATTTTAATTTAATAATTT
1 AAATAATAAAATTTTAA-TTAATAATTT
* *
587434 -AA-AATAATATTTTAA-TAATATTTT
1 AAATAATAAAATTTTAATTAATAATTT
587458 AAATAATAAAAT
1 AAATAATAAAAT
587470 AAATTTTTAG
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
24 8 0.27
25 2 0.07
26 18 0.60
27 2 0.07
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
AAATAATAAAATTTTAATTAATAATTT
Found at i:588127 original size:17 final size:18
Alignment explanation
Indices: 588089--588134 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
588079 TGAAATAGAT
*
588089 ATAAATAAAAAAACTTTTA
1 ATAAAT-AAAAAACTTTGA
588108 ATAAATAAAAAA-TTTGA
1 ATAAATAAAAAACTTTGA
588125 ATAATATAAA
1 ATAA-ATAAA
588135 TGCTCTTGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 8 0.32
18 11 0.44
19 6 0.24
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.30
Consensus pattern (18 bp):
ATAAATAAAAAACTTTGA
Found at i:588395 original size:14 final size:14
Alignment explanation
Indices: 588376--588406 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
588366 ACACTTTCTG
*
588376 AATAATAAATTAAA
1 AATAATAAATGAAA
588390 AATAATAAATGAAA
1 AATAATAAATGAAA
588404 AAT
1 AAT
588407 TAATTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (14 bp):
AATAATAAATGAAA
Found at i:589027 original size:17 final size:17
Alignment explanation
Indices: 589001--589036 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
588991 TGCTAAATTC
*
589001 ATCCACTTATACCAAAG
1 ATCCAATTATACCAAAG
*
589018 ATCCAATTATACCTAAG
1 ATCCAATTATACCAAAG
589035 AT
1 AT
589037 GTGACGTTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.42, C:0.25, G:0.06, T:0.28
Consensus pattern (17 bp):
ATCCAATTATACCAAAG
Found at i:597793 original size:19 final size:19
Alignment explanation
Indices: 597753--597795 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
597743 AAATTAAAAA
* *
597753 TTAAATTAATAAAATATTT
1 TTAAAATAATAAAATATAT
597772 TTAAAATAATTAAAA-ATAT
1 TTAAAATAA-TAAAATATAT
597791 TTAAA
1 TTAAA
597796 TTATTTATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TTAAAATAATAAAATATAT
Found at i:598656 original size:26 final size:26
Alignment explanation
Indices: 598627--598681 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 26
598617 TTTGTAAATA
*
598627 ATTTTAGATATACATATTAAA-ATTTT
1 ATTTTA-AAATACATATTAAATATTTT
*
598653 ATTTTAAAATATATATTAAATATTTT
1 ATTTTAAAATACATATTAAATATTTT
598679 ATT
1 ATT
598682 CAATAACATC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 12 0.46
26 14 0.54
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (26 bp):
ATTTTAAAATACATATTAAATATTTT
Found at i:599981 original size:6 final size:6
Alignment explanation
Indices: 599970--599997 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
599960 TAACCAGCAG
599970 ATATAA ATATAA ATATAA ATATAA ATAT
1 ATATAA ATATAA ATATAA ATATAA ATAT
599998 CAACCTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (6 bp):
ATATAA
Found at i:600117 original size:14 final size:14
Alignment explanation
Indices: 600087--600131 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
600077 AATATAATTT
600087 AATTA-ATTT-ATA
1 AATTATATTTAATA
*
600099 TAATTATTTTTAATA
1 -AATTATATTTAATA
600114 AATTATATTTAATA
1 AATTATATTTAATA
600128 AATT
1 AATT
600132 TGAAGTTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 5 0.18
14 20 0.71
15 3 0.11
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
AATTATATTTAATA
Found at i:600878 original size:2 final size:2
Alignment explanation
Indices: 600871--600901 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
600861 ACACCAAGCC
600871 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
600902 GCTACATTGA
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:601128 original size:21 final size:21
Alignment explanation
Indices: 601102--601169 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
601092 TAATTAAATT
*
601102 ATTTTATATAATTAT-TTTAAA
1 ATTTTA-AAAATTATATTTAAA
*
601123 ATTTTAAAAATTATATTTAAT
1 ATTTTAAAAATTATATTTAAA
** *
601144 A-TTTAAATTTTGATATTTATA
1 ATTTTAAAAATT-ATATTTAAA
601165 ATTTT
1 ATTTT
601170 TTTTTAGATT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
20 15 0.39
21 20 0.53
22 3 0.08
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (21 bp):
ATTTTAAAAATTATATTTAAA
Found at i:602903 original size:37 final size:36
Alignment explanation
Indices: 602862--602934 Score: 87
Period size: 37 Copynumber: 2.0 Consensus size: 36
602852 TACCGAGCTC
602862 AAAAAATTAA-ATTTAAT-TAATTTATATATTTATTTTT
1 AAAAAA-TAATATTTAATAT-ATTTA-ATATTTATTTTT
* *
602899 AAAAAATAATTTTTAATATATTTAATTTTTATTTTT
1 AAAAAATAATATTTAATATATTTAATATTTATTTTT
602935 TTTAATTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
36 14 0.44
37 17 0.53
38 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (36 bp):
AAAAAATAATATTTAATATATTTAATATTTATTTTT
Found at i:602926 original size:16 final size:16
Alignment explanation
Indices: 602872--602944 Score: 55
Period size: 16 Copynumber: 4.7 Consensus size: 16
602862 AAAAAATTAA
602872 ATTTAATTAATTT-ATAT
1 ATTTAATT--TTTAATAT
602889 ATTT-ATTTTTAA-A-
1 ATTTAATTTTTAATAT
**
602902 AAATAATTTTTAATAT
1 ATTTAATTTTTAATAT
* *
602918 ATTTAATTTTTATTTT
1 ATTTAATTTTTAATAT
*
602934 TTTTAATTTTT
1 ATTTAATTTTT
602945 TTAAAAAAGA
Statistics
Matches: 45, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
13 2 0.04
14 12 0.27
15 2 0.04
16 25 0.56
17 4 0.09
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTTAATTTTTAATAT
Found at i:603467 original size:20 final size:21
Alignment explanation
Indices: 603422--603501 Score: 85
Period size: 20 Copynumber: 3.9 Consensus size: 21
603412 TATATGTTTG
* *
603422 TATTATATTTATATATTTTAATA
1 TATTATATAT-TATA-TTTAAAA
*
603445 TATTATA-ATTATGTTTAAAA
1 TATTATATATTATATTTAAAA
603465 TATTATATATT-TATTT-AAA
1 TATTATATATTATATTTAAAA
*
603484 TTTTATATATTATATTTA
1 TATTATATATTATATTTA
603502 TATAATAATA
Statistics
Matches: 49, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
19 13 0.27
20 22 0.45
21 6 0.12
22 1 0.02
23 7 0.14
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (21 bp):
TATTATATATTATATTTAAAA
Found at i:603701 original size:2 final size:2
Alignment explanation
Indices: 603694--603725 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
603684 CACTTGAACA
603694 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
603726 GCATTCCACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:606268 original size:44 final size:43
Alignment explanation
Indices: 606220--606306 Score: 106
Period size: 44 Copynumber: 2.0 Consensus size: 43
606210 TATCATTTAA
*
606220 TAAT-AAAATAATTTTATTTAA-ATTTAATTATATTATATAAATAT
1 TAATAAAAATAATTTT-TTTAATATTT--TAATATTATATAAATAT
*
606264 TAATAAAAAATAATTTTTTTAATATTTTAATATTATTTAAATA
1 TAAT-AAAAATAATTTTTTTAATATTTTAATATTATATAAATA
606307 ATAAAAAGAG
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
44 18 0.47
45 5 0.13
46 15 0.39
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (43 bp):
TAATAAAAATAATTTTTTTAATATTTTAATATTATATAAATAT
Found at i:606795 original size:2 final size:2
Alignment explanation
Indices: 606788--606837 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
606778 AGGAAGTAAA
606788 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
606830 AG AG AG AG
1 AG AG AG AG
606838 GAATGGCCAC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:607739 original size:24 final size:24
Alignment explanation
Indices: 607702--607757 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
607692 AGAATACAAA
607702 AATA-ATTT-AATATACA-TAATGT
1 AATATATTTAAATATA-ATTAATGT
*
607724 AATATATTTAAATATAATTATTGT
1 AATATATTTAAATATAATTAATGT
*
607748 AAAATATTTA
1 AATATATTTA
607758 TTAATTTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 4 0.14
23 5 0.17
24 20 0.69
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.45
Consensus pattern (24 bp):
AATATATTTAAATATAATTAATGT
Found at i:608046 original size:11 final size:12
Alignment explanation
Indices: 608016--608080 Score: 53
Period size: 13 Copynumber: 5.2 Consensus size: 12
608006 TTTTTAAAAA
608016 ATAAAAATATAAT
1 ATAAAAA-ATAAT
608029 ATAAAAAAATAAT
1 AT-AAAAAATAAT
*
608042 -TAAAATATAAT
1 ATAAAAAATAAT
608053 ATAATAAAA-ATAT
1 ATAA-AAAATA-AT
*
608066 ATAAATATATAAT
1 ATAAA-AAATAAT
608079 AT
1 AT
608081 TTTTTATAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
11 9 0.21
12 6 0.14
13 22 0.51
14 6 0.14
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAAAAAATAAT
Found at i:608061 original size:24 final size:23
Alignment explanation
Indices: 608010--608080 Score: 88
Period size: 24 Copynumber: 2.9 Consensus size: 23
608000 ATAATTTTTT
*
608010 TAAAAAATAAAAATATAATATAA
1 TAAAAAATTAAAATATAATATAA
*
608033 AAAAATAATTAAAATATAATATAA
1 TAAAA-AATTAAAATATAATATAA
608057 TAAAAATATATAAATATATAATAT
1 TAAAAA-AT-TAAA-ATATAATAT
608081 TTTTTATAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
23 5 0.12
24 23 0.56
25 4 0.10
26 9 0.22
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (23 bp):
TAAAAAATTAAAATATAATATAA
Found at i:608116 original size:24 final size:24
Alignment explanation
Indices: 608042--608116 Score: 71
Period size: 26 Copynumber: 3.0 Consensus size: 24
608032 AAAAAATAAT
* * *
608042 TAAAATA-TAATATAATAAAAATA
1 TAAAATATTAATATTATTAATATA
* *
608065 TATAAATATATAATATTTTTTATAATA
1 TA-AAATAT-TAATATTATTAAT-ATA
608092 TAAAATATTAATATTATTAATATA
1 TAAAATATTAATATTATTAATATA
608116 T
1 T
608117 TATATAATTT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
23 2 0.05
24 9 0.22
25 11 0.27
26 14 0.34
27 5 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
TAAAATATTAATATTATTAATATA
Found at i:608121 original size:22 final size:22
Alignment explanation
Indices: 608063--608144 Score: 84
Period size: 22 Copynumber: 3.8 Consensus size: 22
608053 ATAATAAAAA
608063 TATATAAATATATAATATT--TT
1 TATAT-AATATATAATATTAATT
*
608084 T-TATAATATAAAATATTAATAT
1 TATATAATATATAATATTAAT-T
*
608106 TAT-TAATATATTATA-TAATT
1 TATATAATATATAATATTAATT
608126 TATATAAATATATAATATT
1 TATAT-AATATATAATATT
608145 TTAAATATAA
Statistics
Matches: 50, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
19 12 0.24
20 7 0.14
21 7 0.14
22 22 0.44
23 2 0.04
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TATATAATATATAATATTAATT
Found at i:608152 original size:22 final size:21
Alignment explanation
Indices: 608064--608163 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 21
608054 TAATAAAAAT
608064 ATATAAATATATAATATTTT-
1 ATATAAATATATAATATTTTA
* * *
608084 TTAT-AATATAAAATATTAATA
1 ATATAAATATATAATATT-TTA
* * *
608105 TTATTAATATATTATATAATTT-
1 ATATAAATATA-TA-ATATTTTA
608127 ATATAAATATATAATATTTTA
1 ATATAAATATATAATATTTTA
608148 A-ATATAAT-TATAATAT
1 ATATA-AATATATAATAT
608164 ATAAAAATAT
Statistics
Matches: 64, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
19 12 0.19
20 21 0.33
21 10 0.16
22 15 0.23
23 2 0.03
24 4 0.06
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATATAAATATATAATATTTTA
Found at i:608161 original size:6 final size:7
Alignment explanation
Indices: 608051--608167 Score: 70
Period size: 7 Copynumber: 16.9 Consensus size: 7
608041 TTAAAATATA
608051 ATATAAT
1 ATATAAT
*
608058 A-AAAAT
1 ATATAAT
608064 ATATAAAT
1 ATAT-AAT
608072 ATATAAT
1 ATATAAT
*
608079 AT-T-TT
1 ATATAAT
*
608084 TTATAAT
1 ATATAAT
*
608091 ATAAAAT
1 ATATAAT
608098 AT-TAAT
1 ATATAAT
608104 ATTATTAAT
1 A-TA-TAAT
608113 ATAT--T
1 ATATAAT
608118 ATATAATTT
1 ATATAA--T
608127 ATATAAAT
1 ATAT-AAT
608135 ATATAAT
1 ATATAAT
*
608142 ATTTTAA-
1 A-TATAAT
608149 ATATAAT
1 ATATAAT
608156 -TATAAT
1 ATATAAT
608162 ATATAA
1 ATATAA
608168 AAATATATAA
Statistics
Matches: 85, Mismatches: 10, Indels: 30
0.68 0.08 0.24
Matches are distributed among these distances:
5 7 0.08
6 21 0.25
7 27 0.32
8 18 0.21
9 10 0.12
10 2 0.02
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
ATATAAT
Found at i:608188 original size:11 final size:10
Alignment explanation
Indices: 608046--608191 Score: 62
Period size: 9 Copynumber: 14.9 Consensus size: 10
608036 AATAATTAAA
608046 ATAT-AATAT
1 ATATAAATAT
*
608055 A-ATAAAAAT
1 ATATAAATAT
608064 ATATAAATAT
1 ATATAAATAT
* *
608074 ATA-ATATTTT
1 ATATA-AATAT
* *
608084 TTATAATATAAA
1 ATATAA-AT-AT
*
608096 ATATTAATAT
1 ATATAAATAT
*
608106 -TATTAATAT
1 ATATAAATAT
*
608115 ATTATATAATTT
1 A-TATA-AATAT
608127 ATAT-AA-AT
1 ATATAAATAT
608135 ATAT-AATAT
1 ATATAAATAT
*
608144 -TTTAAATAT
1 ATATAAATAT
608153 A-ATTATAATAT
1 ATA-TA-AATAT
608164 ATA-AAA-AT
1 ATATAAATAT
608172 ATATAAATAT
1 ATATAAATAT
608182 GATATAAATA
1 -ATATAAATA
608192 CGAAGATTAT
Statistics
Matches: 103, Mismatches: 16, Indels: 34
0.67 0.10 0.22
Matches are distributed among these distances:
8 16 0.16
9 30 0.29
10 22 0.21
11 25 0.24
12 10 0.10
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (10 bp):
ATATAAATAT
Found at i:608191 original size:29 final size:27
Alignment explanation
Indices: 608127--608191 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 27
608117 TATATAATTT
* *
608127 ATATAAATATATAATATTTTAAATATA
1 ATATAAATATATAAAATTATAAATATA
*
608154 AT-TATAATATATAAAAATATATAAATATG
1 ATATA-AATATAT-AAAAT-TATAAATATA
608183 ATATAAATA
1 ATATAAATA
608192 CGAAGATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
26 2 0.06
27 9 0.29
28 4 0.13
29 14 0.45
30 2 0.06
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (27 bp):
ATATAAATATATAAAATTATAAATATA
Found at i:609330 original size:39 final size:39
Alignment explanation
Indices: 609287--609361 Score: 91
Period size: 39 Copynumber: 1.9 Consensus size: 39
609277 GATTTCTGAC
*
609287 ATAAATAATAAATAAAAT-ATTAA-TAATTTTTAAATAAAA
1 ATAAA-AAT-AATAAAATAATAAATTAATTTTTAAATAAAA
**
609326 ATAAAAATTTTAAAATAATAAATTAATTTTTAAATA
1 ATAAAAATAATAAAATAATAAATTAATTTTTAAATA
609362 TTATTTTAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
37 6 0.19
38 7 0.23
39 18 0.58
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (39 bp):
ATAAAAATAATAAAATAATAAATTAATTTTTAAATAAAA
Found at i:609336 original size:20 final size:20
Alignment explanation
Indices: 609295--609361 Score: 75
Period size: 20 Copynumber: 3.3 Consensus size: 20
609285 ACATAAATAA
609295 TAAATAAAATATTAATAATTTT
1 TAAATAAAA-A-TAATAATTTT
*
609317 TAAATAAAAATAAAAATTTT
1 TAAATAAAAATAATAATTTT
*
609337 AAAATAATAAAT--TAATTTT
1 TAAATAA-AAATAATAATTTT
609356 TAAATA
1 TAAATA
609362 TTATTTTAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
19 11 0.28
20 15 0.38
21 5 0.12
22 9 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAATAAAAATAATAATTTT
Found at i:609380 original size:14 final size:12
Alignment explanation
Indices: 609353--609382 Score: 51
Period size: 12 Copynumber: 2.4 Consensus size: 12
609343 ATAAATTAAT
609353 TTTTAAATATTA
1 TTTTAAATATTA
609365 TTTTAAATATTA
1 TTTTAAATATTA
609377 TATTTA
1 T-TTTA
609383 TTTTAATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 13 0.76
13 4 0.24
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTTAAATATTA
Found at i:611087 original size:24 final size:27
Alignment explanation
Indices: 611014--611084 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
611004 AAACAAGCCT
* *
611014 CCATATTTGACAAATACAAAGGA-AACCA
1 CCATTTTTGACAAACACAAA--ATAACCA
611042 CCATTTTTGACAAACACAAAATAACCA
1 CCATTTTTGACAAACACAAAATAACCA
611069 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
611085 AATGGGTGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.23
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAATAACCA
Found at i:613006 original size:21 final size:22
Alignment explanation
Indices: 612968--613013 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
612958 ATCTGTTGAA
* **
612968 ACTCCACCTGTTTTGGAGTA-T
1 ACTCCACCTGCTGCGGAGTACT
612989 ACTCCACCTGCTGCGGAGTACT
1 ACTCCACCTGCTGCGGAGTACT
613011 ACT
1 ACT
613014 TGTCTGAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (22 bp):
ACTCCACCTGCTGCGGAGTACT
Found at i:615994 original size:92 final size:92
Alignment explanation
Indices: 615837--616025 Score: 360
Period size: 92 Copynumber: 2.1 Consensus size: 92
615827 CGATCTTTAA
*
615837 GTTATGCAACGCCCAGCTGCAATTCCGATGGTATGGCCTTCGTTCCATCTCTAAATCGTACATTG
1 GTTATGCAACGCCCAGCTGCAATTCCGATGGTATGGCCTTCGCTCCATCTCTAAATCGTACATTG
615902 CTAAGGCTTCCAGCTTCAAGGACACAT
66 CTAAGGCTTCCAGCTTCAAGGACACAT
615929 GTTATGCAACGCCCAGCTGCAATTCCGATGGTATGGCCTTCGCTCCATCTCTAAATCGTACATTG
1 GTTATGCAACGCCCAGCTGCAATTCCGATGGTATGGCCTTCGCTCCATCTCTAAATCGTACATTG
615994 CTAAGGCTTCCAGCTTCAAGGACACAT
66 CTAAGGCTTCCAGCTTCAAGGACACAT
*
616021 ATTAT
1 GTTAT
616026 CGGAGCATCA
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
92 95 1.00
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.29
Consensus pattern (92 bp):
GTTATGCAACGCCCAGCTGCAATTCCGATGGTATGGCCTTCGCTCCATCTCTAAATCGTACATTG
CTAAGGCTTCCAGCTTCAAGGACACAT
Found at i:616134 original size:2 final size:2
Alignment explanation
Indices: 616129--616155 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
616119 AAGTGTGTGC
616129 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 A
616156 GTGCAAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:618477 original size:28 final size:30
Alignment explanation
Indices: 618446--618507 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
618436 AAATAATGAA
*
618446 AATATA-TAATA-TTTATATTTTTAAAATT
1 AATATATTAATATTTTATATTTATAAAATT
*
618474 AATATATTATTATTTTATATTTATAAAATT
1 AATATATTAATATTTTATATTTATAAAATT
618504 AATA
1 AATA
618508 AAAAGCATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
28 6 0.20
29 4 0.13
30 20 0.67
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (30 bp):
AATATATTAATATTTTATATTTATAAAATT
Found at i:618756 original size:18 final size:18
Alignment explanation
Indices: 618703--618765 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 18
618693 AAAATCTAAA
618703 TTTAATTATAAATATATATAT
1 TTTAATT-TAAA-ATA-ATAT
* *
618724 ATTAATATAAAAATAATAT
1 TTTAAT-TTAAAATAATAT
*
618743 TTTAATTTAAAATAATAA
1 TTTAATTTAAAATAATAT
618761 TTTAA
1 TTTAA
618766 AATGATGAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
18 15 0.42
19 9 0.25
20 3 0.08
21 8 0.22
22 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (18 bp):
TTTAATTTAAAATAATAT
Found at i:618759 original size:21 final size:21
Alignment explanation
Indices: 618703--618761 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 21
618693 AAAATCTAAA
618703 TTTAA-TTATAAAT-ATATATAT
1 TTTAATTTA-AAATAATA-ATAT
* *
618724 ATTAATAT-AAA-AATAATAT
1 TTTAATTTAAAATAATAATAT
618743 TTTAATTTAAAATAATAAT
1 TTTAATTTAAAATAATAAT
618762 TTAAAATGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 8
0.71 0.10 0.19
Matches are distributed among these distances:
19 10 0.33
20 9 0.30
21 10 0.33
22 1 0.03
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
TTTAATTTAAAATAATAATAT
Found at i:618887 original size:24 final size:24
Alignment explanation
Indices: 618860--618910 Score: 93
Period size: 24 Copynumber: 2.1 Consensus size: 24
618850 AACATCTCTA
*
618860 ATTTCATATAATATGCATACATTT
1 ATTTCATATAATATGCATACATCT
618884 ATTTCATATAATATGCATACATCT
1 ATTTCATATAATATGCATACATCT
618908 ATT
1 ATT
618911 ACGTAAGTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.37, C:0.14, G:0.04, T:0.45
Consensus pattern (24 bp):
ATTTCATATAATATGCATACATCT
Found at i:621911 original size:20 final size:18
Alignment explanation
Indices: 621889--621965 Score: 79
Period size: 20 Copynumber: 4.3 Consensus size: 18
621879 TTTTTAAAAA
621889 ATTTAAATATAAATTAAAT
1 ATTTAAATATAAA-TAAAT
*
621908 AATTTTAATATCAAATAAAT
1 -ATTTAAATAT-AAATAAAT
621928 A-TTAAATAT-AATAAAT
1 ATTTAAATATAAATAAAT
* *
621944 ATTT-AATAAAAATATAT
1 ATTTAAATATAAATAAAT
621961 ATTTA
1 ATTTA
621966 GTTAAATGGT
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
16 12 0.24
17 12 0.24
18 7 0.14
19 1 0.02
20 14 0.29
21 3 0.06
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTTAAATATAAATAAAT
Found at i:621923 original size:21 final size:20
Alignment explanation
Indices: 621882--621949 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
621872 TATTTAGTTT
*
621882 TTAAAAAATTTAAATATAAA
1 TTAAATAATTTAAATATAAA
*
621902 TTAAATAATTTTAATATCAAA
1 TTAAATAATTTAAATAT-AAA
621923 -TAAAT-A-TTAAATAT-AA
1 TTAAATAATTTAAATATAAA
621939 -TAAAT-ATTTAA
1 TTAAATAATTTAA
621950 TAAAAATATA
Statistics
Matches: 43, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
16 8 0.19
17 4 0.09
18 7 0.16
19 1 0.02
20 20 0.47
21 3 0.07
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (20 bp):
TTAAATAATTTAAATATAAA
Found at i:621957 original size:17 final size:16
Alignment explanation
Indices: 621897--621965 Score: 57
Period size: 16 Copynumber: 4.0 Consensus size: 16
621887 AAATTTAAAT
*
621897 ATAAATTAAATAATTTTA
1 ATAAAATAAAT-A-TTTA
*
621915 ATATCAAATAAATATTAA
1 ATA--AAATAAATATTTA
*
621933 ATATAATAAATATTTA
1 ATAAAATAAATATTTA
*
621949 ATAAAAATATATATTTA
1 AT-AAAATAAATATTTA
621966 GTTAAATGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
16 13 0.31
17 12 0.29
18 9 0.21
19 1 0.02
20 7 0.17
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (16 bp):
ATAAAATAAATATTTA
Found at i:622499 original size:3 final size:3
Alignment explanation
Indices: 622491--622527 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
622481 ATATTTTTAA
*
622491 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAA AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
622528 AAACAGGTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:625014 original size:5 final size:5
Alignment explanation
Indices: 625004--625081 Score: 58
Period size: 5 Copynumber: 16.2 Consensus size: 5
624994 CATATTTCAA
* * *
625004 AATAT AATAT AA-A- AATAT AATGT AA-AT ATTAT ATATTT AATA- AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT A-ATAT AATAT AATAT
* *
625051 AAAAAT AATAT AATA- AATAT AAAAT AATAT A
1 -AATAT AATAT AATAT AATAT AATAT AATAT A
625082 TTTAATACAC
Statistics
Matches: 56, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
3 2 0.04
4 12 0.21
5 35 0.62
6 7 0.12
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (5 bp):
AATAT
Found at i:625030 original size:24 final size:24
Alignment explanation
Indices: 625003--625082 Score: 72
Period size: 24 Copynumber: 3.2 Consensus size: 24
624993 TCATATTTCA
*
625003 AAATATAATATAAAAATATAATGT
1 AAATATAATATAAAAATATAATAT
* **
625027 AAATATTATATATTTAATA-AATAT
1 AAATATAATATA-AAAATATAATAT
* *
625051 AAAAATAATATAATAAATATAAAAT
1 AAATATAATATAA-AAATATAATAT
625076 AATATAT
1 AA-ATAT
625083 TTAATACACA
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
24 29 0.69
25 10 0.24
26 3 0.07
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (24 bp):
AAATATAATATAAAAATATAATAT
Found at i:625076 original size:19 final size:20
Alignment explanation
Indices: 625041--625081 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
625031 ATTATATATT
625041 TAATAAATATAAAAATAATA
1 TAATAAATATAAAAATAATA
625061 TAATAAATAT-AAAATAATA
1 TAATAAATATAAAAATAATA
625080 TA
1 TA
625082 TTTAATACAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
TAATAAATATAAAAATAATA
Found at i:626012 original size:2 final size:2
Alignment explanation
Indices: 626007--626048 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
625997 ACACGCACGC
* *
626007 AT AT AT -T AT A- AT AT AA AT AT AT AA AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
626047 AT
1 AT
626049 TAAAATAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:628705 original size:16 final size:16
Alignment explanation
Indices: 628650--628705 Score: 78
Period size: 16 Copynumber: 3.5 Consensus size: 16
628640 GTTGGATAAG
628650 TTAA-TTAAGATTTAAA
1 TTAATTTAA-ATTTAAA
*
628666 TTAATTAAAATTTAAA
1 TTAATTTAAATTTAAA
*
628682 TTATTTTAAATTTAAA
1 TTAATTTAAATTTAAA
628698 TTAATTTA
1 TTAATTTA
628706 TGTTCGATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
16 32 0.91
17 3 0.09
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (16 bp):
TTAATTTAAATTTAAA
Found at i:629238 original size:3 final size:3
Alignment explanation
Indices: 629230--629270 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
629220 ATTTGGGGTT
629230 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
629271 TAGTTTAGGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:631031 original size:16 final size:18
Alignment explanation
Indices: 630997--631033 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
630987 ATTTTAAGGC
630997 TTTCTATAGACATAAAAA
1 TTTCTATAGACATAAAAA
*
631015 TTTCT-TAG-CATATAAA
1 TTTCTATAGACATAAAAA
631031 TTT
1 TTT
631034 AACATCAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 10 0.56
17 3 0.17
18 5 0.28
ACGTcount: A:0.41, C:0.11, G:0.05, T:0.43
Consensus pattern (18 bp):
TTTCTATAGACATAAAAA
Found at i:633718 original size:19 final size:19
Alignment explanation
Indices: 633694--633734 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
633684 AAACAACCCA
*
633694 AATTTGATCTTGTAATAAT
1 AATTTGATCCTGTAATAAT
633713 AATTTGATCCTGTAATAAT
1 AATTTGATCCTGTAATAAT
633732 AAT
1 AAT
633735 CAGATCAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.39, C:0.07, G:0.10, T:0.44
Consensus pattern (19 bp):
AATTTGATCCTGTAATAAT
Found at i:633740 original size:19 final size:19
Alignment explanation
Indices: 633699--633740 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
633689 ACCCAAATTT
* **
633699 GATCTTGTAATAATAATTT
1 GATCCTGTAATAATAATCA
633718 GATCCTGTAATAATAATCA
1 GATCCTGTAATAATAATCA
633737 GATC
1 GATC
633741 AAGTGATAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (19 bp):
GATCCTGTAATAATAATCA
Found at i:641558 original size:25 final size:25
Alignment explanation
Indices: 641530--641579 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
641520 CTACCTCCAG
641530 TTAAGAAACTCAGCTCAAATTCTAA
1 TTAAGAAACTCAGCTCAAATTCTAA
*
641555 TTAAGAAACTCAGCTCAAGTTCTAA
1 TTAAGAAACTCAGCTCAAATTCTAA
641580 ATGTAAATAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28
Consensus pattern (25 bp):
TTAAGAAACTCAGCTCAAATTCTAA
Done.