Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold291
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: 742724
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 2 of 5
Found at i:109682 original size:13 final size:13
Alignment explanation
Indices: 109642--109697 Score: 53
Period size: 12 Copynumber: 4.5 Consensus size: 13
109632 AGGTGTGTTC
*
109642 GGTGAGAATATTA
1 GGTGAGAGTATTA
* *
109655 GGTG-GTGTGTTA
1 GGTGAGAGTATTA
109667 GGTGAGAGTATTA
1 GGTGAGAGTATTA
* *
109680 GGTG-GTGTGTTA
1 GGTGAGAGTATTA
109692 GGTGAG
1 GGTGAG
109698 CAATTTTTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
12 19 0.56
13 15 0.44
ACGTcount: A:0.21, C:0.00, G:0.45, T:0.34
Consensus pattern (13 bp):
GGTGAGAGTATTA
Found at i:109856 original size:30 final size:30
Alignment explanation
Indices: 109811--109933 Score: 158
Period size: 30 Copynumber: 4.1 Consensus size: 30
109801 ACTAATTTAA
* *
109811 ATCCCTTAAATTAAGGACTAGTGCACCATT
1 ATCCTTTAAATTAAGGACTAGTGCACCACT
* * *
109841 ATCCTTTAGATTAAGGATTAGCGCACCACT
1 ATCCTTTAAATTAAGGACTAGTGCACCACT
* *
109871 GTCCTTTAAATTAA-GACCTAGTGCACTACT
1 ATCCTTTAAATTAAGGA-CTAGTGCACCACT
*
109901 ATCCTTTAGATTAAGGACTAGTGCACCACT
1 ATCCTTTAAATTAAGGACTAGTGCACCACT
109931 ATC
1 ATC
109934 TAATTTAAAT
Statistics
Matches: 78, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
29 2 0.03
30 74 0.95
31 2 0.03
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.31
Consensus pattern (30 bp):
ATCCTTTAAATTAAGGACTAGTGCACCACT
Found at i:109909 original size:60 final size:60
Alignment explanation
Indices: 109816--109930 Score: 178
Period size: 60 Copynumber: 1.9 Consensus size: 60
109806 TTTAAATCCC
* *
109816 TTAAATTAAGGACTAGTGCACCATTATCCTTTAGATTAAGGATTAGCGCACCACTGTCCT
1 TTAAATTAAGGACTAGTGCACCACTATCCTTTAGATTAAGGACTAGCGCACCACTGTCCT
* *
109876 TTAAATTAA-GACCTAGTGCACTACTATCCTTTAGATTAAGGACTAGTGCACCACT
1 TTAAATTAAGGA-CTAGTGCACCACTATCCTTTAGATTAAGGACTAGCGCACCACT
109931 ATCTAATTTA
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
59 2 0.04
60 48 0.96
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (60 bp):
TTAAATTAAGGACTAGTGCACCACTATCCTTTAGATTAAGGACTAGCGCACCACTGTCCT
Found at i:112783 original size:32 final size:33
Alignment explanation
Indices: 112744--112805 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 33
112734 CAATTCAATG
*
112744 TGTATCGATACCAAG-AACATGTATCGATAGAA
1 TGTATCGATACCAAGCAACATATATCGATAGAA
* *
112776 TGTATCGATACTAAGCAATATATATCGATA
1 TGTATCGATACCAAGCAACATATATCGATA
112806 CATCTGGGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 14 0.54
33 12 0.46
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.29
Consensus pattern (33 bp):
TGTATCGATACCAAGCAACATATATCGATAGAA
Found at i:114553 original size:23 final size:22
Alignment explanation
Indices: 114510--114566 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
114500 TTTAGTAGTC
* *
114510 ACAAAATATTTACAGCTATTAAA
1 ACAAAA-ATATACAGCCATTAAA
114533 ACCAAAAATATACAGCCATTAAA
1 A-CAAAAATATACAGCCATTAAA
114556 ACAGAAAATAT
1 ACA-AAAATAT
114567 CTCTTCCTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 2 0.07
23 23 0.77
24 5 0.17
ACGTcount: A:0.56, C:0.16, G:0.05, T:0.23
Consensus pattern (22 bp):
ACAAAAATATACAGCCATTAAA
Found at i:118520 original size:35 final size:35
Alignment explanation
Indices: 118474--118545 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
118464 TATAACCCTG
*
118474 CAAGTGCAATCTTTCTATAAACAATGTGAAACAAT
1 CAAGTGCAATCTTTCTACAAACAATGTGAAACAAT
* *
118509 CAAGTGCAATCTTTCTACAAGCAATTTGAAACAAT
1 CAAGTGCAATCTTTCTACAAACAATGTGAAACAAT
118544 CA
1 CA
118546 TCTCCTTGTG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.42, C:0.19, G:0.11, T:0.28
Consensus pattern (35 bp):
CAAGTGCAATCTTTCTACAAACAATGTGAAACAAT
Found at i:122955 original size:23 final size:22
Alignment explanation
Indices: 122910--122956 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
122900 TACATTTTAA
*
122910 AATTTTTATTTAAATTTAAATT
1 AATTTTTATTTAAATATAAATT
122932 AATTTATTATTTAAA-ATAATATT
1 AATTT-TTATTTAAATATAA-ATT
122955 AA
1 AA
122957 AAAATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
AATTTTTATTTAAATATAAATT
Found at i:122962 original size:13 final size:13
Alignment explanation
Indices: 122944--122968 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
122934 TTTATTATTT
122944 AAAATAATATTAA
1 AAAATAATATTAA
122957 AAAATAATATTA
1 AAAATAATATTA
122969 TATTAATATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAATAATATTAA
Found at i:123476 original size:28 final size:25
Alignment explanation
Indices: 123428--123496 Score: 93
Period size: 28 Copynumber: 2.6 Consensus size: 25
123418 TAGTTTCTTA
* *
123428 ACATAAAATTTCAATTAAATTTTTT
1 ACATAAAATTTTAATTAAATTTTGT
123453 ACATATAAAATTTGTAATTAAATTTTGT
1 AC--ATAAAATTT-TAATTAAATTTTGT
123481 ACATAAAATTTTAATT
1 ACATAAAATTTTAATT
123497 GAGTTTACAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
25 7 0.18
26 9 0.23
27 9 0.23
28 14 0.36
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.46
Consensus pattern (25 bp):
ACATAAAATTTTAATTAAATTTTGT
Found at i:123479 original size:13 final size:14
Alignment explanation
Indices: 123441--123492 Score: 61
Period size: 14 Copynumber: 3.7 Consensus size: 14
123431 TAAAATTTCA
*
123441 ATTAAATTTTTTAC
1 ATTAAATTTTGTAC
*
123455 ATATAAAATTTGTA-
1 AT-TAAATTTTGTAC
123469 ATTAAATTTTGTAC
1 ATTAAATTTTGTAC
*
123483 ATAAAATTTT
1 ATTAAATTTT
123493 AATTGAGTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 10 0.31
14 13 0.41
15 9 0.28
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (14 bp):
ATTAAATTTTGTAC
Found at i:125321 original size:17 final size:16
Alignment explanation
Indices: 125292--125349 Score: 55
Period size: 17 Copynumber: 3.6 Consensus size: 16
125282 AATTATAACT
125292 AAAATAAAATAAAATC
1 AAAATAAAATAAAATC
* *
125308 AAAACTAAATTAAATTC
1 AAAA-TAAAATAAAATC
* *
125325 AATA-AAAATCAAATC
1 AAAATAAAATAAAATC
*
125340 AAAATTAAAT
1 AAAATAAAAT
125350 CAAACACTAC
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
15 11 0.34
16 8 0.25
17 13 0.41
ACGTcount: A:0.67, C:0.09, G:0.00, T:0.24
Consensus pattern (16 bp):
AAAATAAAATAAAATC
Found at i:125350 original size:16 final size:16
Alignment explanation
Indices: 125292--125353 Score: 56
Period size: 16 Copynumber: 3.9 Consensus size: 16
125282 AATTATAACT
* *
125292 AAAATAAAATAAAATC
1 AAAATTAAATCAAATC
* *
125308 AAAACTAAATTAAATTC
1 AAAATTAAATCAAA-TC
125325 AATAA--AAATCAAATC
1 AA-AATTAAATCAAATC
125340 AAAATTAAATCAAA
1 AAAATTAAATCAAA
125354 CACTACAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
14 2 0.05
15 4 0.11
16 26 0.68
17 4 0.11
18 2 0.05
ACGTcount: A:0.68, C:0.10, G:0.00, T:0.23
Consensus pattern (16 bp):
AAAATTAAATCAAATC
Found at i:127114 original size:14 final size:13
Alignment explanation
Indices: 127092--127129 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
127082 ATAATAACAG
127092 AATTATAAATATTAA
1 AATT-TAAATATT-A
127107 AATTTAAATATTA
1 AATTTAAATATTA
127120 AATTTAAATA
1 AATTTAAATA
127130 CATCTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 11 0.48
14 8 0.35
15 4 0.17
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
AATTTAAATATTA
Found at i:128342 original size:2 final size:2
Alignment explanation
Indices: 128332--128364 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
128322 TGTGTGTGTG
*
128332 TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
128365 GGCCTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:130145 original size:47 final size:47
Alignment explanation
Indices: 130076--130169 Score: 161
Period size: 47 Copynumber: 2.0 Consensus size: 47
130066 GGATGAAACA
*
130076 AAGTGGTTTCAATTGTACCTTAGCTATTGAGATAGTAAAATTTTTAT
1 AAGTGCTTTCAATTGTACCTTAGCTATTGAGATAGTAAAATTTTTAT
* *
130123 AAGTGCTTTCACTTGTACCTTAGCTATTGAGATGGTAAAATTTTTAT
1 AAGTGCTTTCAATTGTACCTTAGCTATTGAGATAGTAAAATTTTTAT
130170 TGATACAGAC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.43
Consensus pattern (47 bp):
AAGTGCTTTCAATTGTACCTTAGCTATTGAGATAGTAAAATTTTTAT
Found at i:133889 original size:25 final size:26
Alignment explanation
Indices: 133869--133925 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
133859 AAAAATAATC
*
133869 TCAAATG-ATAATTTTTTAAATAAAA
1 TCAAATGCAAAATTTTTTAAATAAAA
*
133894 TCAAATGCAAAATTTTTTAAACAAAA
1 TCAAATGCAAAATTTTTTAAATAAAA
*
133920 TAAAAT
1 TCAAAT
133926 TTAAAATAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 7 0.25
26 21 0.75
ACGTcount: A:0.54, C:0.07, G:0.04, T:0.35
Consensus pattern (26 bp):
TCAAATGCAAAATTTTTTAAATAAAA
Found at i:134552 original size:11 final size:12
Alignment explanation
Indices: 134518--134552 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
134508 AAGAAAAAAA
134518 TTTATTGATATTT
1 TTTATTGAT-TTT
134531 TTTATTGATTTT
1 TTTATTGATTTT
134543 TTTATT-ATTT
1 TTTATTGATTT
134553 AAAAAATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 4 0.18
12 9 0.41
13 9 0.41
ACGTcount: A:0.20, C:0.00, G:0.06, T:0.74
Consensus pattern (12 bp):
TTTATTGATTTT
Found at i:135110 original size:23 final size:24
Alignment explanation
Indices: 135084--135128 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
135074 TATTTATATT
135084 ATATTCAT-ATTATTTTT-TATGTA
1 ATATT-ATAATTATTTTTCTATGTA
*
135107 ATATTTTAATTATTTTTCTATG
1 ATATTATAATTATTTTTCTATG
135129 CTTCATTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 1 0.05
23 14 0.74
24 4 0.21
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.62
Consensus pattern (24 bp):
ATATTATAATTATTTTTCTATGTA
Found at i:137429 original size:18 final size:17
Alignment explanation
Indices: 137393--137433 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
137383 AAATTTAACT
*
137393 ATAAAAATTATATATAA
1 ATAAAAATTATATAAAA
*
137410 ATAAATATTAATATAAAA
1 ATAAAAATT-ATATAAAA
137428 ATAAAA
1 ATAAAA
137434 TTTTAAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
ATAAAAATTATATAAAA
Found at i:138248 original size:24 final size:23
Alignment explanation
Indices: 138228--138276 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
138218 ATAATATTAA
138228 AAAATTAAAATTAT-TTTATATT
1 AAAATTAAAATTATATTTATATT
* *
138250 AATATTAAAATTATATTTA-AAT
1 AAAATTAAAATTATATTTATATT
138272 AAAAT
1 AAAAT
138277 AATTTTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 19 0.83
23 4 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
AAAATTAAAATTATATTTATATT
Found at i:139320 original size:10 final size:11
Alignment explanation
Indices: 139291--139348 Score: 59
Period size: 10 Copynumber: 5.5 Consensus size: 11
139281 TTTATGTAAA
*
139291 AAATAAAAAAT
1 AAATAAAATAT
139302 -AATATAAATAT
1 AAATA-AAATAT
*
139313 AAA-AAAATTT
1 AAATAAAATAT
139323 AAATAAAATA-
1 AAATAAAATAT
139333 AAATAAAATAT
1 AAATAAAATAT
*
139344 TAATA
1 AAATA
139349 TATTAAATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
10 22 0.56
11 15 0.38
12 2 0.05
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AAATAAAATAT
Found at i:139363 original size:20 final size:19
Alignment explanation
Indices: 139340--139393 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 19
139330 ATAAAATAAA
* *
139340 ATATTAATATATTAAATTTT
1 ATATAAATATAAT-AATTTT
139360 ATATAAATATAATAATTTT
1 ATATAAATATAATAATTTT
* *
139379 ACCATAATTATAATA
1 A-TATAAATATAATA
139394 TAAAATAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 7 0.24
20 22 0.76
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (19 bp):
ATATAAATATAATAATTTT
Found at i:140475 original size:11 final size:11
Alignment explanation
Indices: 140459--140520 Score: 56
Period size: 11 Copynumber: 5.8 Consensus size: 11
140449 ATATCACTAT
140459 TTAAAATAATA
1 TTAAAATAATA
140470 TTAAAA-AAT-
1 TTAAAATAATA
* *
140479 TTAAAATTATT
1 TTAAAATAATA
* *
140490 TTATATTAATA
1 TTAAAATAATA
*
140501 TTAAAATTATA
1 TTAAAATAATA
*
140512 TTTAAATAA
1 TTAAAATAA
140521 AATAAATTTT
Statistics
Matches: 39, Mismatches: 10, Indels: 4
0.74 0.19 0.08
Matches are distributed among these distances:
9 6 0.15
10 5 0.13
11 28 0.72
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (11 bp):
TTAAAATAATA
Found at i:140685 original size:2 final size:2
Alignment explanation
Indices: 140678--140702 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
140668 ATTATATTCC
140678 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
140703 CAAAATACGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:141401 original size:2 final size:2
Alignment explanation
Indices: 141394--141443 Score: 84
Period size: 2 Copynumber: 25.0 Consensus size: 2
141384 GTAGAACATC
141394 AT AT AT AT -T CAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
141436 AT AT AT AT
1 AT AT AT AT
141444 TTTGAATTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 1 0.02
2 44 0.96
3 1 0.02
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:141622 original size:23 final size:23
Alignment explanation
Indices: 141578--141625 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
141568 ATATTATATT
**
141578 TACGTTTTAATATATCTAAAAAA
1 TACGTTTTAATATAAATAAAAAA
141601 TACG-TTTAATATAAATATAAAAA
1 TACGTTTTAATATAAATA-AAAAA
141624 TA
1 TA
141626 AATATTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (23 bp):
TACGTTTTAATATAAATAAAAAA
Found at i:142487 original size:18 final size:18
Alignment explanation
Indices: 142466--142519 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 18
142456 TATATAAAAA
142466 TATAAATATATTAAAATT
1 TATAAATATATTAAAATT
*
142484 TATATA-ATA-T-AAA-T
1 TATAAATATATTAAAATT
* *
142498 TATTAATATGTTAAAATT
1 TATAAATATATTAAAATT
142516 TATA
1 TATA
142520 TAAATAAATA
Statistics
Matches: 27, Mismatches: 5, Indels: 8
0.68 0.12 0.20
Matches are distributed among these distances:
14 5 0.19
15 5 0.19
16 2 0.07
17 6 0.22
18 9 0.33
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
TATAAATATATTAAAATT
Found at i:142493 original size:17 final size:17
Alignment explanation
Indices: 142473--142522 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
142463 AAATATAAAT
142473 ATATTAAAATTTATATA
1 ATATTAAAATTTATATA
142490 ATA-T-AAA-TTAT-TA
1 ATATTAAAATTTATATA
142503 ATATGTTAAAATTTATATA
1 ATA--TTAAAATTTATATA
142522 A
1 A
142523 ATAAATAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
13 5 0.19
14 4 0.15
15 3 0.11
16 2 0.07
17 6 0.22
18 4 0.15
19 3 0.11
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (17 bp):
ATATTAAAATTTATATA
Found at i:142539 original size:27 final size:32
Alignment explanation
Indices: 142470--142534 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
142460 TAAAAATATA
* *
142470 AATATATTAAAATTTATATAATATAAATTATT
1 AATATGTTAAAATTTATATAATATAAATTAAT
142502 AATATGTTAAAATTTATATAA-ATAAA-TAAT
1 AATATGTTAAAATTTATATAATATAAATTAAT
142532 AAT
1 AAT
142535 TTAAACATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 6 0.19
31 5 0.16
32 20 0.65
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (32 bp):
AATATGTTAAAATTTATATAATATAAATTAAT
Found at i:142808 original size:21 final size:22
Alignment explanation
Indices: 142779--142825 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
142769 TTTTAAAAAA
*
142779 ATTTATATATTTAAATAATT-AT
1 ATTTATATACTTAAAT-ATTAAT
*
142801 ATTT-TATACTTATATATTAAT
1 ATTTATATACTTAAATATTAAT
142822 ATTT
1 ATTT
142826 CAAATATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 3 0.14
21 15 0.68
22 4 0.18
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
ATTTATATACTTAAATATTAAT
Found at i:150648 original size:20 final size:21
Alignment explanation
Indices: 150623--150672 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
150613 AATATGTATG
* *
150623 ATTTTAATATATAAAAAAAT-
1 ATTTTAAAAGATAAAAAAATA
*
150643 ATTTTAAAAGATAAAATAATA
1 ATTTTAAAAGATAAAAAAATA
150664 ATTTTAAAA
1 ATTTTAAAA
150673 TACAAAGTAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (21 bp):
ATTTTAAAAGATAAAAAAATA
Found at i:151224 original size:25 final size:25
Alignment explanation
Indices: 151178--151225 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
151168 TTATTAAAAT
* *
151178 TTATATATAAAATATCTTAATATTA
1 TTATATATAAAATATATAAATATTA
151203 TTATAATATAAAA-ATATAAATAT
1 TTAT-ATATAAAATATATAAATAT
151226 ATAAATTATC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 12 0.60
26 8 0.40
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (25 bp):
TTATATATAAAATATATAAATATTA
Found at i:151416 original size:20 final size:20
Alignment explanation
Indices: 151378--151417 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
151368 TATTTTGCAT
* * *
151378 ATTATTTTTTATATTTTATA
1 ATTATTTTTAAGATATTATA
151398 ATTATTTTTAAGATATTATA
1 ATTATTTTTAAGATATTATA
151418 TATTTATATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (20 bp):
ATTATTTTTAAGATATTATA
Found at i:151417 original size:27 final size:27
Alignment explanation
Indices: 151386--151457 Score: 74
Period size: 27 Copynumber: 2.6 Consensus size: 27
151376 ATATTATTTT
151386 TTATATTTTATAATTATTTTTAAGATA
1 TTATATTTTATAATTATTTTTAAGATA
* * *
151413 TTATATATTTAT-ATAAATTTTAATATA
1 TTATAT-TTTATAATTATTTTTAAGATA
* *
151440 TTAATAATTTATATTTAT
1 TT-ATATTTTATAATTAT
151458 AAAAATTGTA
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
27 25 0.71
28 10 0.29
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (27 bp):
TTATATTTTATAATTATTTTTAAGATA
Found at i:151520 original size:28 final size:30
Alignment explanation
Indices: 151466--151522 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 30
151456 ATAAAAATTG
*
151466 TATTATATTTTTATATTTTTATCATATTTA
1 TATTATATTTTTATATTTATATCATATTTA
151496 TATTAT-TTTTT-TATTGTATAT-ATATTT
1 TATTATATTTTTATATT-TATATCATATTT
151523 TCCGTATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 10 0.40
29 9 0.36
30 6 0.24
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (30 bp):
TATTATATTTTTATATTTATATCATATTTA
Found at i:152720 original size:32 final size:33
Alignment explanation
Indices: 152679--152748 Score: 97
Period size: 32 Copynumber: 2.2 Consensus size: 33
152669 TAAATATATA
* * *
152679 TATAACCCGTCAGCGAGGT-TTATGCTGACTAT
1 TATAACCCGTCAGCGAGGTGGTATGCTAACAAT
*
152711 TATAACCCGTTAGCGAGGTGGTATGCTAACAAT
1 TATAACCCGTCAGCGAGGTGGTATGCTAACAAT
152744 TATAA
1 TATAA
152749 TCTGTTAGCA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
32 18 0.55
33 15 0.45
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (33 bp):
TATAACCCGTCAGCGAGGTGGTATGCTAACAAT
Found at i:152746 original size:33 final size:32
Alignment explanation
Indices: 152679--152757 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 32
152669 TAAATATATA
* * * *
152679 TATAACCCGTCAGCGAGGTTTATGCTGACTAT
1 TATAACCCGTTAGCGAGGTGTATGCTAACAAT
152711 TATAACCCGTTAGCGAGGTGGTATGCTAACAAT
1 TATAACCCGTTAGCGAGGT-GTATGCTAACAAT
* *
152744 TATAATCTGTTAGC
1 TATAACCCGTTAGC
152758 ATAGGCCCAC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
32 18 0.45
33 22 0.55
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.32
Consensus pattern (32 bp):
TATAACCCGTTAGCGAGGTGTATGCTAACAAT
Found at i:154888 original size:33 final size:30
Alignment explanation
Indices: 154851--154931 Score: 92
Period size: 33 Copynumber: 2.5 Consensus size: 30
154841 ATATATATTA
154851 ATAAAATATAAAGATATAA-ATATTATAACTTT
1 ATAAAATATAAA-ATATAATATATTA-AA-TTT
*
154883 CATAAAATATAAATTATTAATATATTAAATTT
1 -ATAAAATATAAAATA-TAATATATTAAATTT
154915 ATATAAATATAAAATAT
1 ATA-AAATATAAAATAT
154932 GTTGAATATA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
31 4 0.09
32 16 0.37
33 17 0.40
34 6 0.14
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.40
Consensus pattern (30 bp):
ATAAAATATAAAATATAATATATTAAATTT
Found at i:157003 original size:4 final size:4
Alignment explanation
Indices: 156994--157020 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
156984 ATTCTCATAT
156994 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
157021 TACAAATTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:158294 original size:19 final size:19
Alignment explanation
Indices: 158270--158307 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
158260 TAAATATAAT
158270 TACAAATATAATAAAAATA
1 TACAAATATAATAAAAATA
* *
158289 TACAAATGTAATATAAATA
1 TACAAATATAATAAAAATA
158308 CATGAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.63, C:0.05, G:0.03, T:0.29
Consensus pattern (19 bp):
TACAAATATAATAAAAATA
Found at i:159190 original size:21 final size:21
Alignment explanation
Indices: 159165--159206 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
159155 AATTAAAATT
*
159165 TTTAT-ATTAATATTTATATAA
1 TTTATAATTAA-ATTTAAATAA
159186 TTTATAATTAAATTTAAATAA
1 TTTATAATTAAATTTAAATAA
159207 AAATATTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTTATAATTAAATTTAAATAA
Found at i:161055 original size:15 final size:15
Alignment explanation
Indices: 161035--161064 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
161025 AATTTTTTTT
*
161035 TTAATTTAGATTAAA
1 TTAATTTAAATTAAA
161050 TTAATTTAAATTAAA
1 TTAATTTAAATTAAA
161065 AAAAATTGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (15 bp):
TTAATTTAAATTAAA
Found at i:162145 original size:25 final size:27
Alignment explanation
Indices: 162100--162150 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 27
162090 ATTTAACTTT
162100 AATTATAAATATTAATATAAA-AATAA
1 AATTATAAATATTAATATAAATAATAA
* *
162126 AATT-TAAATATTATTTTAAATAATA
1 AATTATAAATATTAATATAAATAATA
162151 TATAATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
AATTATAAATATTAATATAAATAATAA
Found at i:163104 original size:15 final size:17
Alignment explanation
Indices: 163084--163116 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
163074 TAAAAAAGTG
163084 ATTTAA-ATTTAA-ATA
1 ATTTAATATTTAATATA
163099 ATTTAATATTTAATATA
1 ATTTAATATTTAATATA
163116 A
1 A
163117 AATATTCATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 6 0.38
17 4 0.25
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATTTAATATTTAATATA
Found at i:163397 original size:28 final size:28
Alignment explanation
Indices: 163363--163419 Score: 105
Period size: 28 Copynumber: 2.0 Consensus size: 28
163353 ATGTAAATGC
163363 TGCCATTGTTAAAAAATTAGAATTTTCT
1 TGCCATTGTTAAAAAATTAGAATTTTCT
*
163391 TGCCATTGTTAAAATATTAGAATTTTCT
1 TGCCATTGTTAAAAAATTAGAATTTTCT
163419 T
1 T
163420 TCTTTTATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.46
Consensus pattern (28 bp):
TGCCATTGTTAAAAAATTAGAATTTTCT
Found at i:163937 original size:21 final size:24
Alignment explanation
Indices: 163904--163963 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 24
163894 GCTATTCATA
*
163904 TAATAAAAGAAATAATTA-AAAT-T
1 TAATATAA-AAATAATTATAAATAT
*
163927 TAAT-TATAAAT-A-TATAAATAT
1 TAATATAAAAATAATTATAAATAT
163948 TAATATAAAAATAATT
1 TAATATAAAAATAATT
163964 TTTTAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 9
0.71 0.07 0.22
Matches are distributed among these distances:
19 2 0.07
20 5 0.17
21 9 0.31
22 7 0.24
23 5 0.17
24 1 0.03
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (24 bp):
TAATATAAAAATAATTATAAATAT
Found at i:164117 original size:15 final size:15
Alignment explanation
Indices: 164099--164128 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
164089 TATAATTTTT
*
164099 AATACAAAATTAAAA
1 AATAAAAAATTAAAA
164114 AATAAAAAATTAAAA
1 AATAAAAAATTAAAA
164129 TCTTATTAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.20
Consensus pattern (15 bp):
AATAAAAAATTAAAA
Found at i:164218 original size:19 final size:19
Alignment explanation
Indices: 164171--164218 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
164161 AAAATATATA
*
164171 AAATTAATTTTTTATCGATT
1 AAATTAA-TTTTTATCAATT
*
164191 AAACT-ATTTTTATCAATT
1 AAATTAATTTTTATCAATT
164209 AAATTAATTT
1 AAATTAATTT
164219 AAATTATTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 15 0.62
19 5 0.21
20 4 0.17
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (19 bp):
AAATTAATTTTTATCAATT
Found at i:170326 original size:2 final size:2
Alignment explanation
Indices: 170321--170356 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
170311 TCTGTGTGTG
*
170321 TA TA TA CA 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
170357 GAGAGAGAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:170361 original size:2 final size:2
Alignment explanation
Indices: 170356--170381 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
170346 ATATATATAT
170356 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
170382 CTGACATGAG
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:171101 original size:5 final size:5
Alignment explanation
Indices: 171070--171131 Score: 53
Period size: 5 Copynumber: 13.2 Consensus size: 5
171060 TCAAAATTAT
* * *
171070 ATATA ATATA TTA-A ATATGA TTATA ATATA ATAAA ATAT- ATA-A ATATA
1 ATATA ATATA ATATA ATAT-A ATATA ATATA ATATA ATATA ATATA ATATA
171118 ATATA A-AT- ATATA A
1 ATATA ATATA ATATA A
171132 ATTATTATAT
Statistics
Matches: 45, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
3 1 0.02
4 13 0.29
5 27 0.60
6 4 0.09
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:171123 original size:20 final size:20
Alignment explanation
Indices: 171070--171133 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 20
171060 TCAAAATTAT
171070 ATATAATATATTAAATATGATTATA
1 ATATAATATA--AAATAT-A-TA-A
171095 ATAT-A-ATAAAATATATAA
1 ATATAATATAAAATATATAA
171113 ATATAATAT-AAATATATAA
1 ATATAATATAAAATATATAA
171132 AT
1 AT
171134 TATTATATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
18 5 0.14
19 15 0.41
20 3 0.08
21 6 0.16
23 3 0.08
24 1 0.03
25 4 0.11
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (20 bp):
ATATAATATAAAATATATAA
Found at i:171926 original size:28 final size:29
Alignment explanation
Indices: 171892--171955 Score: 87
Period size: 28 Copynumber: 2.2 Consensus size: 29
171882 TTAAAATTTA
171892 ATATAATTT-ATATAAATATAATATAAAAT
1 ATATAATTTAATATAAATA-AATATAAAAT
* *
171921 A-ATAATTTAATTTAAATAAATATAATAT
1 ATATAATTTAATATAAATAAATATAAAAT
171949 ATATAAT
1 ATATAAT
171956 AAATTATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
28 17 0.55
29 14 0.45
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (29 bp):
ATATAATTTAATATAAATAAATATAAAAT
Found at i:171934 original size:33 final size:32
Alignment explanation
Indices: 171890--171957 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 32
171880 ATTTAAAATT
*
171890 TAATATAATTTATATAAATATAATATAAAATAA
1 TAATATAATTTAAATAAATATAATAT-AAATAA
* *
171923 TAATTTAATTTAAATAAATATAATATATATAA
1 TAATATAATTTAAATAAATATAATATAAATAA
171955 TAA
1 TAA
171958 ATTATAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 8 0.25
33 24 0.75
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (32 bp):
TAATATAATTTAAATAAATATAATATAAATAA
Found at i:171939 original size:27 final size:28
Alignment explanation
Indices: 171909--171977 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
171899 TTATATAAAT
*
171909 ATAATATAAAATA-ATAATTTAATT-TAA
1 ATAATATAAAATATATAA-TAAATTATAA
*
171936 ATAAATATAATATATATAATAAATTATAA
1 AT-AATATAAAATATATAATAAATTATAA
*
171965 A-AATATATAATAT
1 ATAATATAAAATAT
171978 TTTAATACAT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
27 12 0.34
28 15 0.43
29 8 0.23
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (28 bp):
ATAATATAAAATATATAATAAATTATAA
Found at i:171956 original size:18 final size:18
Alignment explanation
Indices: 171891--171976 Score: 69
Period size: 15 Copynumber: 5.0 Consensus size: 18
171881 TTTAAAATTT
171891 AATATAAT-T-TAT-ATA
1 AATATAATATATATAATA
*
171906 AATATAATATAAAATAAT-
1 AATATAATAT-ATATAATA
*
171924 AATTTAAT-T-TA-AATA
1 AATATAATATATATAATA
171939 AATATAATATATATAATA
1 AATATAATATATATAATA
*
171957 AATTATAAAAATATATAATA
1 AA-TAT-AATATATATAATA
171977 TTTTAATACA
Statistics
Matches: 56, Mismatches: 5, Indels: 15
0.74 0.07 0.20
Matches are distributed among these distances:
14 3 0.05
15 16 0.29
16 2 0.04
17 3 0.05
18 15 0.27
19 5 0.09
20 12 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AATATAATATATATAATA
Found at i:171965 original size:29 final size:29
Alignment explanation
Indices: 171902--171977 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 29
171892 ATATAATTTA
* *
171902 TATAAATATAATATAAAATAATAATTTAAT
1 TATAAATA-AATATAATATAATAATTAAAT
171932 T-TAAATAAATATAATATATATAA-TAAAT
1 TATAAATAAATATAATATA-ATAATTAAAT
171960 TATAAA-AATATATAATAT
1 TATAAATAA-ATATAATAT
171978 TTTAATACAT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
28 17 0.41
29 23 0.56
30 1 0.02
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (29 bp):
TATAAATAAATATAATATAATAATTAAAT
Found at i:172186 original size:26 final size:26
Alignment explanation
Indices: 172134--172186 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
172124 TTCATTCTTT
*
172134 TTTATAATTAAATATAATAATTTATA
1 TTTATAATTAAATATAATAATTAATA
* *
172160 TTTATAATTATATTTAA-AATATAATA
1 TTTATAATTAAATATAATAAT-TAATA
172186 T
1 T
172187 ATTTATATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 3 0.13
26 20 0.87
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (26 bp):
TTTATAATTAAATATAATAATTAATA
Found at i:172189 original size:28 final size:28
Alignment explanation
Indices: 172156--172263 Score: 92
Period size: 28 Copynumber: 3.7 Consensus size: 28
172146 TATAATAATT
*
172156 TATATTTATAATTATATTTAAAATA-TAA
1 TATATTTAT-ATTAAATTTAAAATACTAA
* *
172184 TATATTTATATAAAATTTTAATATACTAA
1 TATATTTATATTAAA-TTTAAAATACTAA
* * *
172213 TAATTTATATTATATAAAATTTAAAATATTTA
1 T-A--TAT-TTATATTAAATTTAAAATACTAA
*
172245 TATATTTATATTATATTTA
1 TATATTTATATTAAATTTA
172264 CAACATATTT
Statistics
Matches: 66, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
27 4 0.06
28 29 0.44
29 7 0.11
30 1 0.02
31 1 0.02
32 14 0.21
33 10 0.15
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (28 bp):
TATATTTATATTAAATTTAAAATACTAA
Found at i:172257 original size:33 final size:33
Alignment explanation
Indices: 172143--172260 Score: 117
Period size: 33 Copynumber: 3.7 Consensus size: 33
172133 TTTTATAATT
*
172143 AAATA-TAATAATTTATATT-TATAATTATATTTA
1 AAATACTAATAATTTATATTATATAA-AAT-TTTA
172176 AAATA-TAAT-A--TAT-TTATATAAAATTTTA
1 AAATACTAATAATTTATATTATATAAAATTTTA
*
172204 ATATACTAATAATTTATATTATATAAAA-TTTA
1 AAATACTAATAATTTATATTATATAAAATTTTA
* *
172236 AAATATTTATATATTTATATTATAT
1 AAATACTAATA-ATTTATATTATAT
172261 TTACAACATA
Statistics
Matches: 73, Mismatches: 5, Indels: 14
0.79 0.05 0.15
Matches are distributed among these distances:
28 8 0.11
29 8 0.11
30 9 0.12
32 16 0.22
33 32 0.44
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (33 bp):
AAATACTAATAATTTATATTATATAAAATTTTA
Found at i:172279 original size:31 final size:28
Alignment explanation
Indices: 172218--172284 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
172208 ACTAATAATT
172218 TATA-TTATATAAAATTTAAAATATTTA
1 TATATTTATATAAAATTTAAAATATTTA
* *
172245 TATATTTATATTATATTTACAACATATTT-
1 TATATTTATATAAAATTTA-AA-ATATTTA
*
172274 TATATATATAT
1 TATATTTATAT
172285 TTTTTCATAC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 4 0.12
28 12 0.35
29 12 0.35
30 6 0.18
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (28 bp):
TATATTTATATAAAATTTAAAATATTTA
Found at i:175771 original size:2 final size:2
Alignment explanation
Indices: 175766--175805 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
175756 TATGTGTGTG
175766 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T- TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
175805 T
1 T
175806 TTTATCATGT
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 32 0.91
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:176191 original size:3 final size:3
Alignment explanation
Indices: 176185--176218 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
176175 GCTCAATTAC
176185 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
176219 TCAAAATTTT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:177823 original size:23 final size:24
Alignment explanation
Indices: 177775--177824 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 24
177765 TTCTTTTTTG
*
177775 TTTGTCAAAAATTATGGCTTATTT
1 TTTGTCAAAAATTATGGCTTAATT
177799 TTTGTC-AAAATTAGTGG-TTAATT
1 TTTGTCAAAAATTA-TGGCTTAATT
177822 TTT
1 TTT
177825 ATTACAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.28, C:0.06, G:0.14, T:0.52
Consensus pattern (24 bp):
TTTGTCAAAAATTATGGCTTAATT
Found at i:180444 original size:2 final size:2
Alignment explanation
Indices: 180437--180468 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
180427 ACCCACCACA
180437 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
180469 TCTTTACAAC
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:181459 original size:21 final size:21
Alignment explanation
Indices: 181434--181475 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
181424 TGAAAACGAA
181434 GGATAATCATCTCATAAGAAG
1 GGATAATCATCTCATAAGAAG
181455 GGATAATCATCTCATAAGAAG
1 GGATAATCATCTCATAAGAAG
181476 CTTTTATCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24
Consensus pattern (21 bp):
GGATAATCATCTCATAAGAAG
Found at i:186683 original size:27 final size:27
Alignment explanation
Indices: 186652--186704 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
186642 GAAGAGAAAT
186652 TAAAATTTGGGGCATAGTGAAGATCAG
1 TAAAATTTGGGGCATAGTGAAGATCAG
186679 TAAAATTTGGGGCATAGTGAAGATCA
1 TAAAATTTGGGGCATAGTGAAGATCA
186705 TGTTGCAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.38, C:0.08, G:0.28, T:0.26
Consensus pattern (27 bp):
TAAAATTTGGGGCATAGTGAAGATCAG
Found at i:187405 original size:3 final size:3
Alignment explanation
Indices: 187397--187431 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
187387 GTTACTTCAC
187397 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
187432 ATTGGCAGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:189655 original size:6 final size:6
Alignment explanation
Indices: 189644--189668 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
189634 GTATTGTTCC
189644 TAGTCT TAGTCT TAGTCT TAGTCT T
1 TAGTCT TAGTCT TAGTCT TAGTCT T
189669 TGCTTTATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.52
Consensus pattern (6 bp):
TAGTCT
Found at i:191146 original size:11 final size:11
Alignment explanation
Indices: 191132--191180 Score: 50
Period size: 9 Copynumber: 4.6 Consensus size: 11
191122 TTATTTAAAA
191132 ATTATTTTTAT
1 ATTATTTTTAT
*
191143 ATTAATATTTAT
1 ATT-ATTTTTAT
191155 A-TATTTTTAT
1 ATTATTTTTAT
*
191165 A--ATTTTTTT
1 ATTATTTTTAT
191174 ATTATTT
1 ATTATTT
191181 AAATTTTAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
9 8 0.25
10 8 0.25
11 8 0.25
12 8 0.25
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
ATTATTTTTAT
Found at i:192373 original size:14 final size:15
Alignment explanation
Indices: 192342--192381 Score: 64
Period size: 14 Copynumber: 2.7 Consensus size: 15
192332 TTTCTCTAGT
*
192342 ATTAATTGAAATCCA
1 ATTAATTTAAATCCA
192357 ATTAATTTAAA-CCA
1 ATTAATTTAAATCCA
192371 ATTAATTTAAA
1 ATTAATTTAAA
192382 AAGTTGAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 14 0.58
15 10 0.42
ACGTcount: A:0.50, C:0.10, G:0.03, T:0.38
Consensus pattern (15 bp):
ATTAATTTAAATCCA
Found at i:192528 original size:34 final size:34
Alignment explanation
Indices: 192490--192559 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
192480 AGTAATTCTG
192490 AATCAACTGAAAATTGAATGTATTTACAAATTTT
1 AATCAACTGAAAATTGAATGTATTTACAAATTTT
192524 AATCAACTGAAAATTGAATGTATTTACAAATTTT
1 AATCAACTGAAAATTGAATGTATTTACAAATTTT
192558 AA
1 AA
192560 CTGCAAGTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.37
Consensus pattern (34 bp):
AATCAACTGAAAATTGAATGTATTTACAAATTTT
Found at i:192554 original size:17 final size:17
Alignment explanation
Indices: 192500--192555 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
192490 AATCAACTGA
192500 AAATTGAATGTATTTAC
1 AAATTGAATGTATTTAC
* ** * *
192517 AAATTTTAATCAACTGA-
1 AAA-TTGAATGTATTTAC
192534 AAATTGAATGTATTTAC
1 AAATTGAATGTATTTAC
192551 AAATT
1 AAATT
192556 TTAACTGCAA
Statistics
Matches: 27, Mismatches: 10, Indels: 4
0.66 0.24 0.10
Matches are distributed among these distances:
16 8 0.30
17 11 0.41
18 8 0.30
ACGTcount: A:0.45, C:0.07, G:0.09, T:0.39
Consensus pattern (17 bp):
AAATTGAATGTATTTAC
Found at i:202527 original size:2 final size:2
Alignment explanation
Indices: 202514--202546 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
202504 CGAAGGGAGA
*
202514 AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
202547 AATCTCAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:203822 original size:18 final size:18
Alignment explanation
Indices: 203799--203860 Score: 65
Period size: 18 Copynumber: 3.3 Consensus size: 18
203789 TTAGTATGAA
203799 TTTGCATAATATATTTGT
1 TTTGCATAATATATTTGT
203817 TTTGCAATGTAA-ATAGTTT-T
1 TTTGC-A--TAATATA-TTTGT
*
203837 ATTGCATAATATATTTGT
1 TTTGCATAATATATTTGT
203855 TTTGCA
1 TTTGCA
203861 CATTTAGATT
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
17 6 0.17
18 14 0.39
19 2 0.06
20 8 0.22
21 6 0.17
ACGTcount: A:0.29, C:0.06, G:0.13, T:0.52
Consensus pattern (18 bp):
TTTGCATAATATATTTGT
Found at i:204688 original size:2 final size:2
Alignment explanation
Indices: 204681--204712 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
204671 ATCTAAGAGA
204681 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
204713 CCCTAAACAC
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:205930 original size:18 final size:18
Alignment explanation
Indices: 205907--205970 Score: 60
Period size: 18 Copynumber: 3.3 Consensus size: 18
205897 TTAGTATTAA
205907 TTTGCATAATATATTTGT
1 TTTGCATAATATATTTGT
205925 TTTGCAAGGTAA-ATAGTTT-T
1 TTTGC-A--TAATATA-TTTGT
205945 ATATTGCATAATATATTTGT
1 -T-TTGCATAATATATTTGT
205965 TTTGCA
1 TTTGCA
205971 CAATTAGGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 16
0.70 0.00 0.30
Matches are distributed among these distances:
18 10 0.26
19 8 0.21
20 8 0.21
21 8 0.21
22 4 0.11
ACGTcount: A:0.30, C:0.06, G:0.14, T:0.50
Consensus pattern (18 bp):
TTTGCATAATATATTTGT
Found at i:206866 original size:309 final size:301
Alignment explanation
Indices: 206300--206911 Score: 965
Period size: 309 Copynumber: 2.0 Consensus size: 301
206290 AATTGGAGCC
* * * ** *
206300 AAATCATATTAAATAGTATCTCTTGTTTATATGAGTTAATTTTATATTGATCTTATGTAAATATA
1 AAATCATAGTAAATAGTATCTCTTATTTATAAGAGTTAATTTTATATTGATCACATATAAATATA
* *
206365 TTTCTTTTTTAAAATTCACAACATAATATATATATATATACAAGTTCTTAGCTTCGACCCAAAGA
66 TTTCCTTTTTAAAATTCACAACATAATATATATATATATACAAATTCTTAGCTTCGACCCAAAGA
206430 ATACTTCTAAATTAAATTGGAAAAAAATTGCAAGTTTGAGAATGATTGATAGACATATATAATTA
131 ATACTTCTAAATTAAATTGGAAAAAAATTGCAAGTTTGAGAATGATTGATAGACATATATAATTA
* *
206495 AGGAAGGAATCAAACATAAGAAAGTTGAAACAAAGACGTGTGGAAATTTTAGTAAAATTTTTGAC
196 AGGAAGGAATCAAACATAAGAAAGTTGAAACAAAGACGTGTGGAAACTTGAGTAAAATTTTTGAC
* *
206560 TTTTTAAAACAATTTAAGACAACATCCATCTTGAAGAAAAA
261 TTTTTAAAACAATTTAAGACAACATCAATCATGAAGAAAAA
* *
206601 AAATC-TAGTAAATATTATCTCTTATTTATAAGAGTTAATTTTATATTGATCACATATAAATATG
1 AAATCATAGTAAATAGTATCTCTTATTTATAAGAGTTAATTTTATATTGATCACATATAAATATA
* *
206665 TTTCCTTTTTAAAATTCCCAACATAATATAAATATATATATATATATATAAGTCATTAGCTTCGA
66 TTTCCTTTTTAAAATTCACAACATAATAT--ATATATATATACA-A-AT---TC-TTAGCTTCGA
*
206730 CCCAAAGAATACTTCTAAATTAAATTGGAAAAAAATTTGTAAGTTTGAGAATGATTGATAGACAT
123 CCCAAAGAATACTTCTAAATTAAATTGGAAAAAAA-TTGCAAGTTTGAGAATGATTGATAGACAT
*
206795 ATATAATTAAGGAAGGAATCAAACATAAGAAAGTTGAAACAAAGACGTGTGGAAACTTGGGTAAA
187 ATATAATTAAGGAAGGAATCAAACATAAGAAAGTTGAAACAAAGACGTGTGGAAACTTGAGTAAA
*
206860 ATTTTTGACTTTTTAACACAATTTAAGACAACATCAATCATGAAGAAAAA
252 ATTTTTGACTTTTTAAAACAATTTAAGACAACATCAATCATGAAGAAAAA
206910 AA
1 AA
206912 TCAAAAAATA
Statistics
Matches: 283, Mismatches: 19, Indels: 10
0.91 0.06 0.03
Matches are distributed among these distances:
300 78 0.28
301 5 0.02
302 12 0.04
303 1 0.00
304 1 0.00
307 2 0.01
308 45 0.16
309 139 0.49
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (301 bp):
AAATCATAGTAAATAGTATCTCTTATTTATAAGAGTTAATTTTATATTGATCACATATAAATATA
TTTCCTTTTTAAAATTCACAACATAATATATATATATATACAAATTCTTAGCTTCGACCCAAAGA
ATACTTCTAAATTAAATTGGAAAAAAATTGCAAGTTTGAGAATGATTGATAGACATATATAATTA
AGGAAGGAATCAAACATAAGAAAGTTGAAACAAAGACGTGTGGAAACTTGAGTAAAATTTTTGAC
TTTTTAAAACAATTTAAGACAACATCAATCATGAAGAAAAA
Found at i:208324 original size:25 final size:25
Alignment explanation
Indices: 208296--208356 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
208286 AAATTTTAAA
208296 AATCAAATTAT-AAGATAACAAAACG
1 AATCAAATTATCAA-ATAACAAAACG
* * *
208321 AATCAGATTATCAAATAACAGAACT
1 AATCAAATTATCAAATAACAAAACG
*
208346 AATCATATTAT
1 AATCAAATTAT
208357 TTCAAATCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 29 0.94
26 2 0.06
ACGTcount: A:0.54, C:0.13, G:0.07, T:0.26
Consensus pattern (25 bp):
AATCAAATTATCAAATAACAAAACG
Found at i:211664 original size:45 final size:45
Alignment explanation
Indices: 211600--211689 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
211590 AACTTAATTC
211600 AGATGGTTCATTCCAGTAACCCTCTTGCGCTCAGTAAATGCCTAT
1 AGATGGTTCATTCCAGTAACCCTCTTGCGCTCAGTAAATGCCTAT
211645 AGATGGTTCATTCCAGTAACCCTCTTGCGCTCAGTAAATGCCTAT
1 AGATGGTTCATTCCAGTAACCCTCTTGCGCTCAGTAAATGCCTAT
211690 CGATTTGATG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.31
Consensus pattern (45 bp):
AGATGGTTCATTCCAGTAACCCTCTTGCGCTCAGTAAATGCCTAT
Found at i:216087 original size:12 final size:12
Alignment explanation
Indices: 216070--216095 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
216060 AATTATATTG
216070 ATAAAATATTTT
1 ATAAAATATTTT
216082 ATAAAATATTTT
1 ATAAAATATTTT
216094 AT
1 AT
216096 TTTATTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
ATAAAATATTTT
Found at i:216624 original size:22 final size:20
Alignment explanation
Indices: 216582--216620 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
216572 TATATAGTAG
216582 TATAAACAATAAAAATTATT
1 TATAAACAATAAAAATTATT
216602 TATATAAC-ATAAAAATTAT
1 TATA-AACAATAAAAATTAT
216621 ATTTTTACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (20 bp):
TATAAACAATAAAAATTATT
Found at i:218017 original size:82 final size:82
Alignment explanation
Indices: 217930--218082 Score: 252
Period size: 82 Copynumber: 1.9 Consensus size: 82
217920 ATTTATTTTA
* *
217930 TTTATTCAATGTTTAAAAATTTTGGATATTAAATATTTATAAATTTAAAATTTTAATTTGCATGT
1 TTTATTCAATGTTTAAAAATTTTGGATATCAAATATTTATAAATTTAAAATTTTAATTTGCATAT
217995 ATATATATTTTTTCATG
66 ATATATATTTTTTCATG
* ** *
218012 TTTATTTAATGTTTAAAAATTTTTTATATCAAATATTTATAATTTTAAAATTTTAATTTGCATAT
1 TTTATTCAATGTTTAAAAATTTTGGATATCAAATATTTATAAATTTAAAATTTTAATTTGCATAT
218077 ATATAT
66 ATATAT
218083 TTAAGGGATG
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
82 65 1.00
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.54
Consensus pattern (82 bp):
TTTATTCAATGTTTAAAAATTTTGGATATCAAATATTTATAAATTTAAAATTTTAATTTGCATAT
ATATATATTTTTTCATG
Found at i:218158 original size:19 final size:20
Alignment explanation
Indices: 218134--218179 Score: 67
Period size: 19 Copynumber: 2.3 Consensus size: 20
218124 AAAATAAAAT
*
218134 AAATATATAAAT-ATTTTAA
1 AAATATATAAATAAATTTAA
218153 AAATATATAAATAAATTTAA
1 AAATATATAAATAAATTTAA
218173 ATAATAT
1 A-AATAT
218180 TTCAAAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 12 0.50
20 7 0.29
21 5 0.21
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AAATATATAAATAAATTTAA
Found at i:218168 original size:31 final size:31
Alignment explanation
Indices: 218125--218193 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 31
218115 AAAAACTTGA
218125 AAATAAAATAAATATATAAAT-AT-TTTAAAAAT
1 AAAT-AAATAAAT-T-TAAATAATATTTAAAAAT
* *
218157 ATATAAATAAATTTAAATAATATTTCAAAAT
1 AAATAAATAAATTTAAATAATATTTAAAAAT
218188 AAATAA
1 AAATAA
218194 TTATTAACAC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
29 5 0.16
30 3 0.09
31 21 0.66
32 3 0.09
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.35
Consensus pattern (31 bp):
AAATAAATAAATTTAAATAATATTTAAAAAT
Found at i:222081 original size:34 final size:33
Alignment explanation
Indices: 222012--222083 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 33
222002 GAAATAACTG
*
222012 GAGAAGTAAAGAACTCTTTTTTTCTCCTTACAA
1 GAGAAGTAAAGAACTCTTTTTTTCTCCTAACAA
* * * * *
222045 GAGAGGTAAAGAATTTTTTTTTTCCTTCTAATAA
1 GAGAAGTAAAGAACTCTTTTTTT-CTCCTAACAA
222079 GAGAA
1 GAGAA
222084 CTACAGGATT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
33 20 0.65
34 11 0.35
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (33 bp):
GAGAAGTAAAGAACTCTTTTTTTCTCCTAACAA
Found at i:234362 original size:42 final size:43
Alignment explanation
Indices: 234316--234412 Score: 99
Period size: 42 Copynumber: 2.3 Consensus size: 43
234306 AATCTTTCAC
* * * *
234316 CTTTTTTTCTTTGTGTACCTTTTCAAT-TATTCTCTTTCTTTA-
1 CTTTTTTTCTTTCTCTAACTTTTC-ATCTATTCTCTTTCTGTAT
* * * *
234358 CTTTTATTGTTTCTCTAACTTTTCATCTCTTTTCTTTCTGTAT
1 CTTTTTTTCTTTCTCTAACTTTTCATCTATTCTCTTTCTGTAT
234401 CTTTTTTTCTTT
1 CTTTTTTTCTTT
234413 TACTCTCTCT
Statistics
Matches: 43, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
41 2 0.05
42 31 0.72
43 10 0.23
ACGTcount: A:0.10, C:0.20, G:0.04, T:0.66
Consensus pattern (43 bp):
CTTTTTTTCTTTCTCTAACTTTTCATCTATTCTCTTTCTGTAT
Found at i:236596 original size:2 final size:2
Alignment explanation
Indices: 236585--236623 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
236575 AAATGTGTGC
*
236585 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
236624 AATGACAACA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:237914 original size:2 final size:2
Alignment explanation
Indices: 237907--237931 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
237897 ATTAAGCAGA
237907 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
237932 AACCACTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:244521 original size:29 final size:29
Alignment explanation
Indices: 244483--244549 Score: 97
Period size: 27 Copynumber: 2.4 Consensus size: 29
244473 TTTATTTTTT
244483 TATAATTATATTTAAATTATAAAATATTA
1 TATAATTATATTTAAATTATAAAATATTA
*
244512 TATAATTATA--TAAATTTTAAAATATTA
1 TATAATTATATTTAAATTATAAAATATTA
244539 -ATAATT-TATTT
1 TATAATTATATTT
244550 TAAAATAATT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
25 2 0.06
26 6 0.17
27 17 0.49
29 10 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (29 bp):
TATAATTATATTTAAATTATAAAATATTA
Found at i:247680 original size:42 final size:43
Alignment explanation
Indices: 247633--247762 Score: 142
Period size: 42 Copynumber: 3.1 Consensus size: 43
247623 CCTCCCGCGC
** * *
247633 AAGGTCAAGATCCAAA-TCGAAATCACCCGTTAGTTATCGGAG
1 AAGGTCAAGATCCAAAGTCGAAATCACCAATCAGTTATAGGAG
* * *
247675 AAGGTCAAGAT-CAAAGTCTAGATCACCAATCAGTTATAGGCG
1 AAGGTCAAGATCCAAAGTCGAAATCACCAATCAGTTATAGGAG
* *
247717 AAGGTCAAGGTCC-AAGTC-AAGATCACCAATCAGTTATAGGCG
1 AAGGTCAAGATCCAAAGTCGAA-ATCACCAATCAGTTATAGGAG
247759 AAGG
1 AAGG
247763 AGGAGGTCTC
Statistics
Matches: 76, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
41 5 0.07
42 70 0.92
43 1 0.01
ACGTcount: A:0.37, C:0.20, G:0.23, T:0.20
Consensus pattern (43 bp):
AAGGTCAAGATCCAAAGTCGAAATCACCAATCAGTTATAGGAG
Found at i:250270 original size:1 final size:1
Alignment explanation
Indices: 250264--250322 Score: 55
Period size: 1 Copynumber: 59.0 Consensus size: 1
250254 ACTTGCCTCG
* * * * * * *
250264 TTTTTTTTTCTTTCTTTCTTTTTTTTTTTCTTTTTCTTTTTTTTTTTTGTTTGTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
250323 CTCCTTTCCA
Statistics
Matches: 44, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.00, C:0.08, G:0.03, T:0.88
Consensus pattern (1 bp):
T
Found at i:250285 original size:18 final size:17
Alignment explanation
Indices: 250264--250322 Score: 73
Period size: 18 Copynumber: 3.4 Consensus size: 17
250254 ACTTGCCTCG
250264 TTTTTTTTTCTTTCTTTC
1 TTTTTTTTT-TTTCTTTC
*
250282 TTTTTTTTTTTCTTTTTC
1 TTTTTTTTTTT-TCTTTC
* *
250300 TTTTTTTTTTTTGTTTG
1 TTTTTTTTTTTTCTTTC
250317 TTTTTT
1 TTTTTT
250323 CTCCTTTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
17 12 0.32
18 25 0.68
ACGTcount: A:0.00, C:0.08, G:0.03, T:0.88
Consensus pattern (17 bp):
TTTTTTTTTTTTCTTTC
Found at i:250307 original size:16 final size:15
Alignment explanation
Indices: 250264--250324 Score: 70
Period size: 16 Copynumber: 4.0 Consensus size: 15
250254 ACTTGCCTCG
*
250264 TTTTTTTTTCTTTCT
1 TTTTTTTTTTTTTCT
250279 TTCTTTTTTTTTTTCT
1 TT-TTTTTTTTTTTCT
250295 TTTTCTTTTTTTTT-T
1 TTTT-TTTTTTTTTCT
* *
250310 TTGTTTGTTTTTTCT
1 TTTTTTTTTTTTTCT
250325 CCTTTCCAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
14 8 0.20
15 9 0.22
16 23 0.57
ACGTcount: A:0.00, C:0.10, G:0.03, T:0.87
Consensus pattern (15 bp):
TTTTTTTTTTTTTCT
Found at i:250311 original size:20 final size:20
Alignment explanation
Indices: 250264--250310 Score: 80
Period size: 18 Copynumber: 2.5 Consensus size: 20
250254 ACTTGCCTCG
250264 TTTTTTTTTCTTTCTTTCTT
1 TTTTTTTTTCTTTCTTTCTT
250284 TTTTTTTTTC-TT-TTTCTT
1 TTTTTTTTTCTTTCTTTCTT
250302 TTTTTTTTT
1 TTTTTTTTT
250311 TGTTTGTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 15 0.56
19 2 0.07
20 10 0.37
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (20 bp):
TTTTTTTTTCTTTCTTTCTT
Found at i:251397 original size:28 final size:28
Alignment explanation
Indices: 251366--251432 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 28
251356 ATCATTTTGT
* *
251366 TTTAACATTCAGGTTCAAGTCATTTAAG
1 TTTAACATTCAGATTCAAGTCAATTAAG
* *
251394 TTTAACACTTC-GATTTAAGTCAATTAGG
1 TTTAACA-TTCAGATTCAAGTCAATTAAG
251422 TTTAACATTCA
1 TTTAACATTCA
251433 AGTTAATTGG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
27 3 0.09
28 27 0.82
29 3 0.09
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (28 bp):
TTTAACATTCAGATTCAAGTCAATTAAG
Found at i:251847 original size:4 final size:4
Alignment explanation
Indices: 251838--251876 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
251828 CCTCTTGCCC
251838 TATT TATT TATT TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TATT TATT TATT TAT
251877 ATTTAAATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:252849 original size:32 final size:33
Alignment explanation
Indices: 252813--252875 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
252803 TATATAAATG
252813 TTAAAATTTATAT-AATATAA-ATTATTAATTTT
1 TTAAAATTTATATAAATATAATATT-TTAATTTT
*
252845 TTAAATTTTATATAAATATAATATTTTAATT
1 TTAAAATTTATATAAATATAATATTTTAATT
252876 ATAGTAAAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 12 0.43
33 13 0.46
34 3 0.11
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (33 bp):
TTAAAATTTATATAAATATAATATTTTAATTTT
Found at i:253023 original size:2 final size:2
Alignment explanation
Indices: 253016--253044 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
253006 TGATAATAAG
253016 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
253045 TTATGGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:253492 original size:3 final size:3
Alignment explanation
Indices: 253484--253518 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
253474 TTCCTTACTA
253484 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
253519 AGTAAATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:253910 original size:14 final size:15
Alignment explanation
Indices: 253883--253911 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
253873 CTATATTTTA
253883 AAATATTATTATTAT
1 AAATATTATTATTAT
253898 AAATATT-TTATTAT
1 AAATATTATTATTAT
253912 TTATCATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AAATATTATTATTAT
Found at i:254967 original size:18 final size:16
Alignment explanation
Indices: 254934--254969 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
254924 AATGAACTGC
254934 ATTAAAAAATTTAAAT
1 ATTAAAAAATTTAAAT
254950 ATTAAATAAATATTAAAT
1 ATTAAA-AAAT-TTAAAT
254968 AT
1 AT
254970 AATAATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 6 0.33
17 4 0.22
18 8 0.44
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTAAAAAATTTAAAT
Found at i:255013 original size:59 final size:59
Alignment explanation
Indices: 254947--255070 Score: 194
Period size: 59 Copynumber: 2.1 Consensus size: 59
254937 AAAAAATTTA
* * * *
254947 AATATTAAATAAATATTAAATATAATAATTATTTAATGAAAATATGTATTTAATTAAAT
1 AATATTAAAGAAATATTAAATATAATAATTACTTAATAAAAATATATATTTAATTAAAT
* *
255006 AATATTAAAGAAGTATTAGATATAATAATTACTTAATAAAAATATATATTTAATTAAAT
1 AATATTAAAGAAATATTAAATATAATAATTACTTAATAAAAATATATATTTAATTAAAT
255065 AATATT
1 AATATT
255071 GATCATTTGC
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (59 bp):
AATATTAAAGAAATATTAAATATAATAATTACTTAATAAAAATATATATTTAATTAAAT
Found at i:255494 original size:17 final size:17
Alignment explanation
Indices: 255472--255506 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
255462 AAAAATTTAA
255472 ATATATTAATATTAAAT
1 ATATATTAATATTAAAT
* *
255489 ATATATTTATATTCAAT
1 ATATATTAATATTAAAT
255506 A
1 A
255507 CTCGTATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (17 bp):
ATATATTAATATTAAAT
Found at i:257029 original size:3 final size:3
Alignment explanation
Indices: 257021--257056 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
257011 TTCTCTTCCA
257021 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
257057 CTTTGTCCCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:260497 original size:30 final size:28
Alignment explanation
Indices: 260463--260518 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 28
260453 GGCGGGGGCA
*
260463 GAGGGGCTATGTTGGACAAAAAAAAAAAGG
1 GAGGGGCTATG-AGG-CAAAAAAAAAAAGG
260493 GAGGGGCTATGAGGCAAAAAAAAAAA
1 GAGGGGCTATGAGGCAAAAAAAAAAA
260519 AGGATTTAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 12 0.48
29 2 0.08
30 11 0.44
ACGTcount: A:0.50, C:0.07, G:0.32, T:0.11
Consensus pattern (28 bp):
GAGGGGCTATGAGGCAAAAAAAAAAAGG
Found at i:260519 original size:30 final size:30
Alignment explanation
Indices: 260463--260521 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 30
260453 GGCGGGGGCA
* *
260463 GAGGGGCTATGTTGGACAAAAAAAAAAAGG
1 GAGGGGCTATGTAGGAAAAAAAAAAAAAGG
*
260493 GAGGGGCTATG-AGGCAAAAAAAAAAAAGG
1 GAGGGGCTATGTAGGAAAAAAAAAAAAAGG
260522 ATTTAGGGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.49, C:0.07, G:0.34, T:0.10
Consensus pattern (30 bp):
GAGGGGCTATGTAGGAAAAAAAAAAAAAGG
Found at i:263550 original size:18 final size:19
Alignment explanation
Indices: 263512--263566 Score: 55
Period size: 18 Copynumber: 3.0 Consensus size: 19
263502 TAATAAATTA
263512 TATATTTT-A-TATTTATAT
1 TATATTTTAATTATTT-TAT
263530 TATATTTTAATTATTTT-T
1 TATATTTTAATTATTTTAT
*
263548 TATCA-TATAATTATTTTAT
1 TAT-ATTTTAATTATTTTAT
263567 GTTGATCGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
18 23 0.72
19 4 0.12
20 5 0.16
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (19 bp):
TATATTTTAATTATTTTAT
Found at i:264247 original size:16 final size:17
Alignment explanation
Indices: 264223--264255 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
264213 TTGATTATTT
264223 AATTATTAC-TTTAATA
1 AATTATTACTTTTAATA
*
264239 AATTTTTACTTTTAATA
1 AATTATTACTTTTAATA
264256 CGTTATTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (17 bp):
AATTATTACTTTTAATA
Found at i:265578 original size:17 final size:16
Alignment explanation
Indices: 265546--265584 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
265536 TAATAGTTAG
265546 ATTATTTTAAATTTAA
1 ATTATTTTAAATTTAA
*
265562 ATTATTCTTAGATTTAA
1 ATTATT-TTAAATTTAA
265579 ATTATT
1 ATTATT
265585 AATATTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (16 bp):
ATTATTTTAAATTTAA
Found at i:266004 original size:20 final size:19
Alignment explanation
Indices: 265970--266007 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
265960 AACTCAATCT
*
265970 ATACTTAAAATAATTTAAC
1 ATACATAAAATAATTTAAC
265989 ATACATAAATATAATTTAA
1 ATACATAAA-ATAATTTAA
266008 ATGATTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.55, C:0.08, G:0.00, T:0.37
Consensus pattern (19 bp):
ATACATAAAATAATTTAAC
Found at i:266327 original size:27 final size:27
Alignment explanation
Indices: 266297--266383 Score: 106
Period size: 27 Copynumber: 3.1 Consensus size: 27
266287 ATGTTTGATC
266297 ATTTATATATTTAAATTATATTT-ATAT
1 ATTT-TATATTTAAATTATATTTAATAT
*
266324 ATTTTATCATATTACAATTATATTTAAAAT
1 ATTTTAT-AT-TTA-AATTATATTTAATAT
266354 ATTTTATA-TTAAATTATTATTTAATAT
1 ATTTTATATTTAAATTA-TATTTAATAT
266381 ATT
1 ATT
266384 AACAGTAAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
26 8 0.15
27 21 0.40
28 3 0.06
29 11 0.21
30 10 0.19
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (27 bp):
ATTTTATATTTAAATTATATTTAATAT
Found at i:266342 original size:29 final size:27
Alignment explanation
Indices: 266298--266383 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 27
266288 TGTTTGATCA
266298 TTTATATATTTAAATTATATTTATATAT
1 TTTATATA-TTAAATTATATTTATATAT
*
266326 TTTATCATATTACAATTATATTTA-AAAT
1 TTTAT-ATATTA-AATTATATTTATATAT
266354 ATTT-TATATTAAATTATTATTTAATATAT
1 -TTTATATATTAAATTA-TATTT-ATATAT
266383 T
1 T
266384 AACAGTAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
26 5 0.10
27 11 0.22
28 14 0.28
29 20 0.40
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (27 bp):
TTTATATATTAAATTATATTTATATAT
Found at i:266559 original size:17 final size:17
Alignment explanation
Indices: 266537--266596 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
266527 AAATAAATCT
266537 TTTTATATTTATATAAA
1 TTTTATATTTATATAAA
*
266554 TTTTATATATTA-ATAATC
1 TTTTATAT-TTATATAA-A
266572 TTATTATATTT-TA-AAA
1 TT-TTATATTTATATAAA
266588 TATTTATAT
1 T-TTTATAT
266597 AATATTTATA
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
16 7 0.19
17 15 0.42
18 8 0.22
19 6 0.17
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTTATATTTATATAAA
Found at i:266616 original size:11 final size:11
Alignment explanation
Indices: 266541--266607 Score: 53
Period size: 11 Copynumber: 6.9 Consensus size: 11
266531 AAATCTTTTT
266541 ATATTTATATA
1 ATATTTATATA
266552 A-ATTT-TAT-
1 ATATTTATATA
266560 ATA-TTA-ATA
1 ATATTTATATA
*
266569 AT-CTTAT-T-
1 ATATTTATATA
*
266577 ATATTT-TAAA
1 ATATTTATATA
266587 ATATTTATATA
1 ATATTTATATA
266598 ATATTTATAT
1 ATATTTATAT
266608 TATTTTTATT
Statistics
Matches: 44, Mismatches: 3, Indels: 18
0.68 0.05 0.28
Matches are distributed among these distances:
8 8 0.18
9 12 0.27
10 10 0.23
11 14 0.32
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.55
Consensus pattern (11 bp):
ATATTTATATA
Found at i:267019 original size:10 final size:10
Alignment explanation
Indices: 266980--267121 Score: 91
Period size: 11 Copynumber: 14.2 Consensus size: 10
266970 ATAATTAATC
266980 ATTATAAATAT
1 ATTA-AAATAT
266991 AATTAAAA-AT
1 -ATTAAAATAT
*
267001 AATATAAATAT
1 ATTA-AAATAT
*
267012 ATTAAAATTT
1 ATTAAAATAT
* *
267022 ATATAATATAA
1 AT-TAAAATAT
*
267033 ATTATTAATAT
1 ATTA-AAATAT
267044 ATTAAAATAT
1 ATTAAAATAT
267054 A-TAAAA-AT
1 ATTAAAATAT
*
267062 A-TATAATAT
1 ATTAAAATAT
*
267071 -TTTAAATAT
1 ATTAAAATAT
267080 AATTAAAATAT
1 -ATTAAAATAT
*
267091 ATAAAAATAT
1 ATTAAAATAT
267101 A-T-AAATAT
1 ATTAAAATAT
*
267109 AATATAAATAT
1 ATTA-AAATAT
267120 AT
1 AT
267122 AAATTATCTA
Statistics
Matches: 102, Mismatches: 17, Indels: 23
0.72 0.12 0.16
Matches are distributed among these distances:
8 14 0.14
9 17 0.17
10 30 0.29
11 37 0.36
12 4 0.04
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
ATTAAAATAT
Found at i:267027 original size:25 final size:25
Alignment explanation
Indices: 266999--267114 Score: 80
Period size: 25 Copynumber: 4.6 Consensus size: 25
266989 ATAATTAAAA
266999 ATAATATAAATATATTAAAATTTAT
1 ATAATATAAATATATTAAAATTTAT
*
267024 ATAATATAAAT-TATTAATATATTA-
1 ATAATATAAATATATTAAAAT-TTAT
* * *
267048 AAATATATAAAAATATATAATATTTTAAAT
1 ATA-ATATAAATATAT-TAA-AATTT--AT
* *
267078 ATAAT-TAAAATATATAAAAATATAT
1 ATAATAT-AAATATATTAAAATTTAT
267103 A-AATAT-AATATA
1 ATAATATAAATATA
267115 AATATATAAA
Statistics
Matches: 71, Mismatches: 10, Indels: 22
0.69 0.10 0.21
Matches are distributed among these distances:
23 6 0.08
24 13 0.18
25 25 0.35
26 3 0.04
27 8 0.11
28 4 0.06
29 10 0.14
30 2 0.03
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
ATAATATAAATATATTAAAATTTAT
Found at i:267068 original size:27 final size:28
Alignment explanation
Indices: 266980--267123 Score: 116
Period size: 32 Copynumber: 4.9 Consensus size: 28
266970 ATAATTAATC
266980 ATTATAAATATAATTAAAAATAATATAAATAT
1 ATTA-AAATATAA-TAAAAAT-ATAT-AATAT
*
267012 ATTAAAATTTATATAATATAA-ATTATTAATAT
1 ATTAAAATATA-ATAA-A-AATA-TA-TAATAT
267044 ATTAAAATAT-ATAAAAATATATAATAT
1 ATTAAAATATAATAAAAATATATAATAT
* * *
267071 -TTTAAATATAATTAAAATATATAA-AA
1 ATTAAAATATAATAAAAATATATAATAT
*
267097 ATATATAAATATAATATAAATATATAA
1 AT-TA-AAATATAATAAAAATATATAA
267124 ATTATCTAAT
Statistics
Matches: 94, Mismatches: 8, Indels: 23
0.75 0.06 0.18
Matches are distributed among these distances:
26 9 0.10
27 20 0.21
28 5 0.05
29 21 0.22
30 4 0.04
31 10 0.11
32 22 0.23
33 3 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (28 bp):
ATTAAAATATAATAAAAATATATAATAT
Found at i:267090 original size:37 final size:35
Alignment explanation
Indices: 267005--267104 Score: 134
Period size: 37 Copynumber: 2.9 Consensus size: 35
266995 AAAAATAATA
* *
267005 TAAATATATTAAAATTTAT-ATAATATA-AATTAT
1 TAAATATATTAAAATATATAAAAATATATAATTAT
*
267038 T-AATATATTAAAATATATAAAAATATATAATATTT
1 TAAATATATTAAAATATATAAAAATATATAAT-TAT
267073 TAAATATAATTAAAATATATAAAAATATATAA
1 TAAATAT-ATTAAAATATATAAAAATATATAA
267105 ATATAATATA
Statistics
Matches: 59, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
32 16 0.27
33 8 0.14
34 3 0.05
35 3 0.05
36 5 0.08
37 24 0.41
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (35 bp):
TAAATATATTAAAATATATAAAAATATATAATTAT
Found at i:267106 original size:8 final size:8
Alignment explanation
Indices: 266997--267125 Score: 64
Period size: 9 Copynumber: 14.5 Consensus size: 8
266987 ATATAATTAA
266997 AAATAATAT
1 AAAT-ATAT
267006 AAATATATT
1 AAATATA-T
*
267015 AAA-ATTT
1 AAATATAT
*
267022 ATATAATAT
1 AAAT-ATAT
267031 AAAT-TAT
1 AAATATAT
*
267038 TAATATATT
1 AAATATA-T
267047 AAAATATAT
1 -AAATATAT
*
267056 AAAAATAT
1 AAATATAT
*
267064 ATAATATTTT
1 A-AATA-TAT
267074 AAATATAATT
1 AAATAT-A-T
267084 AAAATATAT
1 -AAATATAT
267093 AAAAATATAT
1 --AAATATAT
267103 AAATATAATAT
1 -AA-AT-ATAT
267114 AAATATAT
1 AAATATAT
267122 AAAT
1 AAAT
267126 TATCTAATTT
Statistics
Matches: 96, Mismatches: 10, Indels: 29
0.71 0.07 0.21
Matches are distributed among these distances:
7 9 0.09
8 24 0.25
9 29 0.30
10 24 0.25
11 10 0.10
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
AAATATAT
Done.