Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 198 of 198
Found at i:61992291 original size:56 final size:54
Alignment explanation
Indices: 61992217--61992325 Score: 132
Period size: 56 Copynumber: 2.0 Consensus size: 54
61992207 AAAAGAAAAA
* *
61992217 AAATATAAAAATTGTAAAATTGTATAAAATTAGTAAGAAAT-TATAA-AAATATAG
1 AAATATAAAAATTATAAAATTGTATAAAATTA-TAAAAAATGTA-AAGAAATATAG
* *
61992271 AAATATAAAAAACTTATAAAATTTTATAAAGTTATAAAAAATGTAAAGAAATATA
1 AAATAT-AAAAA-TTATAAAATTGTATAAAATTATAAAAAATGTAAAGAAATATA
61992326 AATTTAGTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
54 6 0.13
55 14 0.30
56 27 0.57
ACGTcount: A:0.61, C:0.01, G:0.07, T:0.31
Consensus pattern (54 bp):
AAATATAAAAATTATAAAATTGTATAAAATTATAAAAAATGTAAAGAAATATAG
Found at i:61992306 original size:29 final size:27
Alignment explanation
Indices: 61992223--61992354 Score: 83
Period size: 29 Copynumber: 4.6 Consensus size: 27
61992213 AAAAAAATAT
* *
61992223 AAAAATTGTAAAATTGTATAAAATTAGTA
1 AAAAATTATAAAATTATAT-AAATTA-TA
* * *
61992252 AGAAATTATAAAAATATAGAAA-TATA
1 AAAAATTATAAAATTATATAAATTATA
*
61992278 AAAAACTTATAAAATTTTATAAAGTTATA
1 AAAAA-TTATAAAATTATATAAA-TTATA
61992307 AAAAATGTA-AAGAA--ATATAAATTTAGTAA
1 AAAAAT-TATAA-AATTATATAAA-TTA-T-A
61992336 AAAAATTTATAAAAATTAT
1 AAAAA-TTAT-AAAATTAT
61992355 CATACCAAAA
Statistics
Matches: 80, Mismatches: 11, Indels: 21
0.71 0.10 0.19
Matches are distributed among these distances:
26 6 0.08
27 25 0.31
28 7 0.09
29 35 0.44
30 3 0.04
31 2 0.03
32 2 0.03
ACGTcount: A:0.60, C:0.01, G:0.07, T:0.33
Consensus pattern (27 bp):
AAAAATTATAAAATTATATAAATTATA
Found at i:61992527 original size:36 final size:37
Alignment explanation
Indices: 61992487--61992558 Score: 101
Period size: 36 Copynumber: 2.0 Consensus size: 37
61992477 GGGGTCATTA
* *
61992487 ATTTTGTACGATTTTTAT-AAAATTTTATAATTTTTT
1 ATTTTGTACAATTTTTATAAAAATATTATAATTTTTT
* *
61992523 ATTTTTTACAATTTTTATAAAAATATTCTAATTTTT
1 ATTTTGTACAATTTTTATAAAAATATTATAATTTTT
61992559 AATAAATTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
36 16 0.52
37 15 0.48
ACGTcount: A:0.33, C:0.04, G:0.03, T:0.60
Consensus pattern (37 bp):
ATTTTGTACAATTTTTATAAAAATATTATAATTTTTT
Found at i:61992581 original size:24 final size:26
Alignment explanation
Indices: 61992553--61992602 Score: 68
Period size: 24 Copynumber: 2.0 Consensus size: 26
61992543 AAATATTCTA
61992553 ATTTTTAAT-AAATTT-AGAATTTTT
1 ATTTTTAATAAAATTTAAGAATTTTT
* *
61992577 ATTTTTATTAAAATTTAATAATTTTT
1 ATTTTTAATAAAATTTAAGAATTTTT
61992603 CTAAAATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 8 0.36
25 6 0.27
26 8 0.36
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (26 bp):
ATTTTTAATAAAATTTAAGAATTTTT
Found at i:62005724 original size:13 final size:12
Alignment explanation
Indices: 62005690--62005722 Score: 57
Period size: 12 Copynumber: 2.7 Consensus size: 12
62005680 AATACACAAA
62005690 TAACTAAAATTTC
1 TAAC-AAAATTTC
62005703 TAACAAAATTTC
1 TAACAAAATTTC
62005715 TAACAAAA
1 TAACAAAA
62005723 ATGACTAGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 16 0.80
13 4 0.20
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.30
Consensus pattern (12 bp):
TAACAAAATTTC
Found at i:62007361 original size:182 final size:182
Alignment explanation
Indices: 62007054--62007591 Score: 1049
Period size: 182 Copynumber: 3.0 Consensus size: 182
62007044 TCTTCCCCCA
* *
62007054 GATGCAATATGCTATAACATCAACAAAACCAGTTATGGTTTTCCTGATAACAGAGTAAGAATTAA
1 GATGCAATATGCTATAACATCAACAAACCCAGTTTTGGTTTTCCTGATAACAGAGTAAGAATTAA
*
62007119 AGAAACAGATAAAATTGCAAATTATACTCCTATTCATGCAACCCAAAAATCACAAAACCAGTTCC
66 AGAAACAGATAAAATTGCAAATTATACTCCTATTCATGCAACCCAAAAAGCACAAAACCAGTTCC
62007184 CTCAACAACACTCCTAGTTATACAACATCCATGATGATACTAACCAATGGGC
131 CTCAACAACACTCCTAGTTATACAACATCCATGATGATACTAACCAATGGGC
62007236 GATGCAATATGCTATAACATCAACAAACCCAGTTTTGGTTTTCCTGATAACAGAGTAAGAATTAA
1 GATGCAATATGCTATAACATCAACAAACCCAGTTTTGGTTTTCCTGATAACAGAGTAAGAATTAA
62007301 AGAAACAGATAAAATTGCAAATTATACTCCTATTCATGCAACCCAAAAAGCACAAAACCAGTTCC
66 AGAAACAGATAAAATTGCAAATTATACTCCTATTCATGCAACCCAAAAAGCACAAAACCAGTTCC
62007366 CTCAACAACACTCCTAGTTATACAACATCCATGATGATACTAACCAATGGGC
131 CTCAACAACACTCCTAGTTATACAACATCCATGATGATACTAACCAATGGGC
62007418 GATGCAATATGCTATAACATCAACAAACCCAGTTTTGGTTTTCCTGATAACAGAGTAAGAATTAA
1 GATGCAATATGCTATAACATCAACAAACCCAGTTTTGGTTTTCCTGATAACAGAGTAAGAATTAA
62007483 AGAAACAGATAAAATTGCAAATTATACTCCTATTCATGCAACCCAAAAAGCACAAAACCAGTTCC
66 AGAAACAGATAAAATTGCAAATTATACTCCTATTCATGCAACCCAAAAAGCACAAAACCAGTTCC
62007548 CTCAACAACACTCCTAGTTATACAACATCCATGATGATACTAAC
131 CTCAACAACACTCCTAGTTATACAACATCCATGATGATACTAAC
62007592 AGGTTTGCTG
Statistics
Matches: 353, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
182 353 1.00
ACGTcount: A:0.41, C:0.23, G:0.12, T:0.24
Consensus pattern (182 bp):
GATGCAATATGCTATAACATCAACAAACCCAGTTTTGGTTTTCCTGATAACAGAGTAAGAATTAA
AGAAACAGATAAAATTGCAAATTATACTCCTATTCATGCAACCCAAAAAGCACAAAACCAGTTCC
CTCAACAACACTCCTAGTTATACAACATCCATGATGATACTAACCAATGGGC
Found at i:62011003 original size:11 final size:11
Alignment explanation
Indices: 62010964--62011044 Score: 68
Period size: 11 Copynumber: 7.8 Consensus size: 11
62010954 GCCCATTTTA
62010964 ATTTT-AAAA-
1 ATTTTAAAAAT
62010973 ATTTTAAAAA-
1 ATTTTAAAAAT
**
62010983 ATTAAAAAAAGT
1 ATTTTAAAAA-T
62010995 ATTTTAAAAAT
1 ATTTTAAAAAT
62011006 ATTTT--AAA-
1 ATTTTAAAAAT
*
62011014 A-TTAAAAAAGT
1 ATTTTAAAAA-T
62011025 ATTTTAAAAAT
1 ATTTTAAAAAT
62011036 ATTTTAAAA
1 ATTTTAAAA
62011045 TTTAAAAAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
7 2 0.03
8 1 0.02
9 11 0.19
10 12 0.21
11 17 0.29
12 15 0.26
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (11 bp):
ATTTTAAAAAT
Found at i:62011023 original size:30 final size:30
Alignment explanation
Indices: 62010964--62011053 Score: 137
Period size: 30 Copynumber: 2.9 Consensus size: 30
62010954 GCCCATTTTA
*
62010964 ATTTTAAAAAT-TTTAAAAAATTAAAAAAAGT
1 ATTTTAAAAATATTT-TAAAATT-AAAAAAGT
62010995 ATTTTAAAAATATTTTAAAATTAAAAAAGT
1 ATTTTAAAAATATTTTAAAATTAAAAAAGT
62011025 ATTTTAAAAATATTTTAAAATTTAAAAAA
1 ATTTTAAAAATATTTTAAAA-TTAAAAAA
62011054 TTAAAAAAGT
Statistics
Matches: 56, Mismatches: 1, Indels: 4
0.92 0.02 0.07
Matches are distributed among these distances:
30 28 0.50
31 25 0.45
32 3 0.05
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (30 bp):
ATTTTAAAAATATTTTAAAATTAAAAAAGT
Found at i:62013916 original size:121 final size:120
Alignment explanation
Indices: 62013551--62014020 Score: 818
Period size: 120 Copynumber: 3.9 Consensus size: 120
62013541 ATTATGATTT
62013551 TAGT-TTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
1 TAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
*
62013615 ATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTA
66 ATTATATATTTTTATTAAATTATATTTAATAATAATAATTTTAAATTATATTTTA
*
62013670 TATTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
1 TAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
*
62013735 ATTATATATTTTTATTAAATTATATTTAATAATAATAACTTTAAATTATATTTTA
66 ATTATATATTTTTATTAAATTATATTTAATAATAATAATTTTAAATTATATTTTA
*
62013790 TAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
1 TAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATT-A
*
62013855 AATTATATATTTTTATCT-AATTATATTTAATAATAATAATTTTAAATTATATTTTG
65 AATTATATATTTTTAT-TAAATTATATTTAATAATAATAATTTTAAATTATATTTTA
*
62013911 TAGTATTATACATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
1 TAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
* * * *
62013976 ATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
66 ATTATATATTTTTATTAAATTATATTTAATAATAATAATTTTAAA
62014021 ATATGATTAA
Statistics
Matches: 334, Mismatches: 13, Indels: 7
0.94 0.04 0.02
Matches are distributed among these distances:
119 4 0.01
120 215 0.64
121 114 0.34
122 1 0.00
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (120 bp):
TAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAA
ATTATATATTTTTATTAAATTATATTTAATAATAATAATTTTAAATTATATTTTA
Found at i:62013979 original size:241 final size:240
Alignment explanation
Indices: 62013557--62014011 Score: 831
Period size: 241 Copynumber: 1.9 Consensus size: 240
62013547 ATTTTAGTTT
62013557 ATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATAT
1 ATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATAT
* * *
62013622 ATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTTTATATTATTATATATTATG
66 ATTTTTATTAAATTATATTTAATAATAATAATTTTAAATTATATTTTATAGTATTATACATTATG
*
62013687 ATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATATTTTTATTA
131 ATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATATTTTAATTA
*
62013752 AATTATATTTAATAATAATAACTTTAAATTATATTTTATAGTATC
196 AAATATATTTAATAATAATAACTTTAAATTATATTTTATAGTATC
62013797 ATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAAATTATA
1 ATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATT-AAATTATA
*
62013862 TATTTTTATCT-AATTATATTTAATAATAATAATTTTAAATTATATTTTGTAGTATTATACATTA
65 TATTTTTAT-TAAATTATATTTAATAATAATAATTTTAAATTATATTTTATAGTATTATACATTA
62013926 TGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATATTTTAAT
129 TGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATATTTTAAT
62013991 TAAAATATATTTAATAATAAT
194 TAAAATATATTTAATAATAAT
62014012 TATGTTAAAA
Statistics
Matches: 207, Mismatches: 6, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
240 56 0.27
241 150 0.72
242 1 0.00
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.51
Consensus pattern (240 bp):
ATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATAT
ATTTTTATTAAATTATATTTAATAATAATAATTTTAAATTATATTTTATAGTATTATACATTATG
ATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATATTTTAATTA
AAATATATTTAATAATAATAACTTTAAATTATATTTTATAGTATC
Found at i:62013992 original size:18 final size:17
Alignment explanation
Indices: 62013966--62014000 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
62013956 AATATTAAGA
*
62013966 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
62013983 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
62014001 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:62014214 original size:19 final size:19
Alignment explanation
Indices: 62014190--62014227 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
62014180 CTATTACGCC
62014190 TCTATTCCATTATATTCAA
1 TCTATTCCATTATATTCAA
62014209 TCTATTCCATTATATTCAA
1 TCTATTCCATTATATTCAA
62014228 CCAAACAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.21, G:0.00, T:0.47
Consensus pattern (19 bp):
TCTATTCCATTATATTCAA
Found at i:62026822 original size:16 final size:16
Alignment explanation
Indices: 62026801--62026832 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
62026791 GTTTCAATGT
62026801 TGATTGAAGGTAGAAC
1 TGATTGAAGGTAGAAC
*
62026817 TGATTGAAGGTGGAAC
1 TGATTGAAGGTAGAAC
62026833 ATTTTGGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.34, C:0.06, G:0.34, T:0.25
Consensus pattern (16 bp):
TGATTGAAGGTAGAAC
Found at i:62060356 original size:33 final size:33
Alignment explanation
Indices: 62060314--62060380 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
62060304 GGAGAAAAGA
*
62060314 TTAACTAACATAAGAGAAATTTCAGGCAAATAT
1 TTAACTAACATAAGACAAATTTCAGGCAAATAT
62060347 TTAACTAACATAAGACAAATTTCAGGCAAATAT
1 TTAACTAACATAAGACAAATTTCAGGCAAATAT
62060380 T
1 T
62060381 ATCTTTGTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.48, C:0.13, G:0.10, T:0.28
Consensus pattern (33 bp):
TTAACTAACATAAGACAAATTTCAGGCAAATAT
Found at i:62066762 original size:24 final size:24
Alignment explanation
Indices: 62066717--62066763 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
62066707 TTATAAAATC
*
62066717 AATTATAGAATTAAATTTATATAA
1 AATTATAGAAATAAATTTATATAA
*
62066741 AATTATA-AAATAATTTTAATATA
1 AATTATAGAAATAAATTT-ATATA
62066764 TTTTAATTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
AATTATAGAAATAAATTTATATAA
Found at i:62071360 original size:2 final size:2
Alignment explanation
Indices: 62071353--62071400 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
62071343 GAAGAGCACT
62071353 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
62071395 GA GA GA
1 GA GA GA
62071401 TCAAACTTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:62078213 original size:14 final size:14
Alignment explanation
Indices: 62078190--62078226 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
62078180 TAAACCTTAT
*
62078190 TAGGAAAAATTTTG
1 TAGGATAAATTTTG
62078204 TAGGATAAATTTTG
1 TAGGATAAATTTTG
62078218 TAGGATAAA
1 TAGGATAAA
62078227 AACCTAATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.43, C:0.00, G:0.22, T:0.35
Consensus pattern (14 bp):
TAGGATAAATTTTG
Found at i:62080111 original size:21 final size:21
Alignment explanation
Indices: 62080087--62080128 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
62080077 TCAAACTCAC
62080087 ACATAGTGGAAAAACCAAATG
1 ACATAGTGGAAAAACCAAATG
62080108 ACATAGTGGAAAAACCAAATG
1 ACATAGTGGAAAAACCAAATG
62080129 CATTTTGCTT
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:0.52, C:0.14, G:0.19, T:0.14
Consensus pattern (21 bp):
ACATAGTGGAAAAACCAAATG
Found at i:62081279 original size:18 final size:17
Alignment explanation
Indices: 62081253--62081288 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
62081243 NNNNNNTATA
62081253 TTTAATTTTCGATATGTT
1 TTTAATTTT-GATATGTT
*
62081271 TTTATTTTTGATATGTT
1 TTTAATTTTGATATGTT
62081288 T
1 T
62081289 CATTTAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.19, C:0.03, G:0.11, T:0.67
Consensus pattern (17 bp):
TTTAATTTTGATATGTT
Found at i:62081448 original size:47 final size:47
Alignment explanation
Indices: 62081379--62081474 Score: 183
Period size: 47 Copynumber: 2.0 Consensus size: 47
62081369 TTTGGTCTTC
*
62081379 AAACAATGTTTTATATTACTTATATTGTTTGATTAAAAATTATAATT
1 AAACAATATTTTATATTACTTATATTGTTTGATTAAAAATTATAATT
62081426 AAACAATATTTTATATTACTTATATTGTTTGATTAAAAATTATAATT
1 AAACAATATTTTATATTACTTATATTGTTTGATTAAAAATTATAATT
62081473 AA
1 AA
62081475 CACTAAAAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (47 bp):
AAACAATATTTTATATTACTTATATTGTTTGATTAAAAATTATAATT
Found at i:62081816 original size:8 final size:8
Alignment explanation
Indices: 62081805--62081842 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
62081795 CAAAAACACA
62081805 TTTTTTTC
1 TTTTTTTC
62081813 TTTTCTTTC
1 TTTT-TTTC
*
62081822 TTTCTTT-
1 TTTTTTTC
62081829 TTTTTTTC
1 TTTTTTTC
62081837 TTTTTT
1 TTTTTT
62081843 GGGTGATTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
7 6 0.23
8 13 0.50
9 7 0.27
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTTTTC
Found at i:62085711 original size:58 final size:58
Alignment explanation
Indices: 62085608--62085731 Score: 178
Period size: 58 Copynumber: 2.1 Consensus size: 58
62085598 TTTAATTCAT
* *
62085608 ATAATAATTATATTAAGAATTTTATTAAATTATATATTATTTTATTAAATTATATTTA
1 ATAATAATTATATTAAGAATATGATTAAATTATATATTATTTTATTAAATTATATTTA
* * * *
62085666 ATAATAATTATGTTAA-AATATGGTTAAATTATTTATTATTTTTATTAAATTATTTTTA
1 ATAATAATTATATTAAGAATATGATTAAATTATATATTA-TTTTATTAAATTATATTTA
62085724 ATAATAAT
1 ATAATAAT
62085732 CTTATTAGAA
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
57 18 0.31
58 41 0.69
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (58 bp):
ATAATAATTATATTAAGAATATGATTAAATTATATATTATTTTATTAAATTATATTTA
Found at i:62085867 original size:16 final size:16
Alignment explanation
Indices: 62085846--62085883 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
62085836 TAAATTACTG
*
62085846 ATTACAACTTTATTCC
1 ATTACAACTCTATTCC
62085862 ATTACAACTCTATTCC
1 ATTACAACTCTATTCC
62085878 ATTACA
1 ATTACA
62085884 GTGAACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.34, C:0.26, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTACAACTCTATTCC
Found at i:62086004 original size:24 final size:24
Alignment explanation
Indices: 62085951--62085996 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
62085941 TCTTTCTAGA
* *
62085951 ATATTTAGTATTTATTAGTATAAC
1 ATATTTAGAATTTATTAGCATAAC
62085975 ATATTTAGAATTTATTAGCATA
1 ATATTTAGAATTTATTAGCATA
62085997 GTTTATTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.48
Consensus pattern (24 bp):
ATATTTAGAATTTATTAGCATAAC
Found at i:62089677 original size:9 final size:9
Alignment explanation
Indices: 62089660--62089696 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
62089650 TGAGTTTTCG
62089660 AATTCGAAT
1 AATTCGAAT
*
62089669 AACTCGAAT
1 AATTCGAAT
62089678 AATTCGAAT
1 AATTCGAAT
62089687 AATTCGAAT
1 AATTCGAAT
62089696 A
1 A
62089697 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:62089773 original size:21 final size:21
Alignment explanation
Indices: 62089732--62089774 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
62089722 ACCCCAAACT
* *
62089732 CTCAAACCTTTTTACTTTTCC
1 CTCAAAACTTTTTACTCTTCC
62089753 CTCAAAAC-TTTTACTCCTTCC
1 CTCAAAACTTTTTACT-CTTCC
62089774 C
1 C
62089775 ACTTTCCCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.21, C:0.37, G:0.00, T:0.42
Consensus pattern (21 bp):
CTCAAAACTTTTTACTCTTCC
Found at i:62095254 original size:306 final size:304
Alignment explanation
Indices: 62094652--62095266 Score: 1185
Period size: 306 Copynumber: 2.0 Consensus size: 304
62094642 GGATGGTGAT
*
62094652 TGTTAGGAATGATTGGAGGAGGATGATTTGTGTGCCGAATGTAAATTTTTCTTAGTCTTATAGCC
1 TGTTAGGAATGATTGGAGGAGGAGGATTTGTGTGCCGAATGTAAATTTTTCTTAGTCTTATAGCC
62094717 AACTCCAGATATATTGGGGATTAAGGCTTGCTGTACCATCTTGAACAAAGTAAAATCTTAAATGA
66 AACTCCAGATATATTGGGGATTAAGGCTTGCTGTACCATCTTGAACAAAGTAAAATCTTAAATGA
*
62094782 ACTTGTTGATGCCATTTTTTTTCCCTCTAGTAAAGCCCTATTTGAAGCTTTTCCAAATTGTGACA
131 ACTTGTTGATGCCATTTTTTTTCACTCTAGTAAAGCCCTATTTGAAGCTTTTCCAAATTGTGACA
62094847 TCTAATCTCCAAAGCTCTGTAAAGCTGAAATGCCCCTTGTATTTACTTCATTTTGTGATGTTATT
196 TCTAATCTCCAAAGCTCTGTAAAGCTGAAATGCCCCTTGTATTTACTTCATTTTGTGATGTTATT
62094912 GGTAATTTATGATTGATTTGAATCTAATTGCTGTAATATATAAC
261 GGTAATTTATGATTGATTTGAATCTAATTGCTGTAATATATAAC
62094956 TGTTAGGAATGATTGGAGGAGGAGGATTTGTGTGCCGAATGTAAATTTTTCTTAGTCTTATAGCC
1 TGTTAGGAATGATTGGAGGAGGAGGATTTGTGTGCCGAATGTAAATTTTTCTTAGTCTTATAGCC
62095021 AACTCCAGATATATTGGGGATTAAGGCTTGCTGTACCATCTTGAACAAAGTAAAATCTTAAATGA
66 AACTCCAGATATATTGGGGATTAAGGCTTGCTGTACCATCTTGAACAAAGTAAAATCTTAAATGA
*
62095086 ACTTGTTGATGCCATTTTTTTTTTTACTCTAGTAAAGCCCTATTTGAAGCTTTTCCAAATTGTGA
131 ACTTGTTGATGCCA--TTTTTTTTCACTCTAGTAAAGCCCTATTTGAAGCTTTTCCAAATTGTGA
62095151 CATCTAATCTCCAAAGCTCTGTAAAGCTGAAATGCCCCTTGTATTTACTTCATTTTGTGATGTTA
194 CATCTAATCTCCAAAGCTCTGTAAAGCTGAAATGCCCCTTGTATTTACTTCATTTTGTGATGTTA
62095216 TTGGTAATTTATGATTGATTTGAATCTAATTGCTGTAATATATAAC
259 TTGGTAATTTATGATTGATTTGAATCTAATTGCTGTAATATATAAC
62095262 TGTTA
1 TGTTA
62095267 CTTAATTTTA
Statistics
Matches: 306, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
304 143 0.47
306 163 0.53
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (304 bp):
TGTTAGGAATGATTGGAGGAGGAGGATTTGTGTGCCGAATGTAAATTTTTCTTAGTCTTATAGCC
AACTCCAGATATATTGGGGATTAAGGCTTGCTGTACCATCTTGAACAAAGTAAAATCTTAAATGA
ACTTGTTGATGCCATTTTTTTTCACTCTAGTAAAGCCCTATTTGAAGCTTTTCCAAATTGTGACA
TCTAATCTCCAAAGCTCTGTAAAGCTGAAATGCCCCTTGTATTTACTTCATTTTGTGATGTTATT
GGTAATTTATGATTGATTTGAATCTAATTGCTGTAATATATAAC
Found at i:62103093 original size:23 final size:26
Alignment explanation
Indices: 62103064--62103114 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
62103054 ATTTTTTTGT
62103064 TACTTATTTT-T-T-AACTTTGAAAA
1 TACTTATTTTGTATGAACTTTGAAAA
*
62103087 TACTTATTTTGTATGAATTTTGAAAA
1 TACTTATTTTGTATGAACTTTGAAAA
62103113 TA
1 TA
62103115 TCAATTAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 10 0.42
24 1 0.04
25 1 0.04
26 12 0.50
ACGTcount: A:0.35, C:0.06, G:0.08, T:0.51
Consensus pattern (26 bp):
TACTTATTTTGTATGAACTTTGAAAA
Found at i:62106468 original size:26 final size:28
Alignment explanation
Indices: 62106439--62106498 Score: 79
Period size: 30 Copynumber: 2.1 Consensus size: 28
62106429 TTACACTTTA
*
62106439 ATCACATGATTTA-TT-TTATTTCACAT
1 ATCACATAATTTACTTATTATTTCACAT
62106465 ATCACATAATTTATCTTACTTATTTCACAT
1 ATCACATAATTTA-CTTA-TTATTTCACAT
62106495 ATCA
1 ATCA
62106499 AATTTCTATA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 12 0.41
28 2 0.07
30 15 0.52
ACGTcount: A:0.33, C:0.18, G:0.02, T:0.47
Consensus pattern (28 bp):
ATCACATAATTTACTTATTATTTCACAT
Found at i:62120388 original size:75 final size:75
Alignment explanation
Indices: 62120265--62120416 Score: 304
Period size: 75 Copynumber: 2.0 Consensus size: 75
62120255 TCATACTCTT
62120265 GATAGTTTGTTGATAGTGTGATGCTTCCAAGTCAACATAACTTCGCGAATCCGAGAATATACATC
1 GATAGTTTGTTGATAGTGTGATGCTTCCAAGTCAACATAACTTCGCGAATCCGAGAATATACATC
62120330 TACATGCAAG
66 TACATGCAAG
62120340 GATAGTTTGTTGATAGTGTGATGCTTCCAAGTCAACATAACTTCGCGAATCCGAGAATATACATC
1 GATAGTTTGTTGATAGTGTGATGCTTCCAAGTCAACATAACTTCGCGAATCCGAGAATATACATC
62120405 TACATGCAAG
66 TACATGCAAG
62120415 GA
1 GA
62120417 ACAATAGTGC
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 77 1.00
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.29
Consensus pattern (75 bp):
GATAGTTTGTTGATAGTGTGATGCTTCCAAGTCAACATAACTTCGCGAATCCGAGAATATACATC
TACATGCAAG
Found at i:62122392 original size:46 final size:45
Alignment explanation
Indices: 62122277--62122489 Score: 202
Period size: 46 Copynumber: 4.7 Consensus size: 45
62122267 AGGCGCAATG
* *
62122277 GTGTCTTTCAACCATGGTCTTATTTATTATTGACT-T-GATGTT--ATA
1 GTGTCTTTCAACCATGGTCTTATTCATT-TT--CTGTCG-TGTTCCATT
*
62122322 ATGTCTTTCAACCATGGTCTTATTCATTTTCTGTCGTGTTGCCATT
1 GTGTCTTTCAACCATGGTCTTATTCATTTTCTGTCGTGTT-CCATT
* * * * *
62122368 GTATCTTTCAACTATGGTCTTATTCATTTTTTGTTGTGTTTCTATT
1 GTGTCTTTCAACCATGGTCTTATTCATTTTCTGTCGTG-TTCCATT
* * *
62122414 GTGTCTTTTAACCATGGTCTTATTCATTTT-TCGTCGTGTTTCATA
1 GTGTCTTTCAACCATGGTCTTATTCATTTTCT-GTCGTGTTCCATT
* * *
62122459 GTGTCTTTCAACTATGTTCATATTCATTTTC
1 GTGTCTTTCAACCATGGTCTTATTCATTTTC
62122490 CACCGAGTTG
Statistics
Matches: 140, Mismatches: 20, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
42 2 0.01
43 5 0.04
44 3 0.02
45 57 0.41
46 71 0.51
47 2 0.01
ACGTcount: A:0.17, C:0.17, G:0.14, T:0.52
Consensus pattern (45 bp):
GTGTCTTTCAACCATGGTCTTATTCATTTTCTGTCGTGTTCCATT
Found at i:62122528 original size:137 final size:137
Alignment explanation
Indices: 62122277--62122529 Score: 312
Period size: 137 Copynumber: 1.8 Consensus size: 137
62122267 AGGCGCAATG
* * *
62122277 GTGTCTTTCAACCATGGTCTTATTTATTATTGACTTGATGTTATAATGTCTTTCAACCATGGTCT
1 GTGTCTTTCAACCATGGTCTTATTCATTATTGACGTGATGTTATAATGTCTTTCAACCATGGTCA
*** * ** *
62122342 TATTCATTTTCTGTCGTGTTGCCATTGTATCTTTCAACTATGGTCTTATTCATTTTTTGTTGTGT
66 TATTCATTTTCCACCGAGTTGCCATAATATCATTCAACTATGGTCTTATTCATTTTTTGTTGTGT
62122407 TTCTATT
131 TTCTATT
* * * * * *
62122414 GTGTCTTTTAACCATGGTCTTATTCATTTTTCGTCGTG-T-TTCATAGTGTCTTTCAACTATGTT
1 GTGTCTTTCAACCATGGTCTTATTCATTATT-GACGTGATGTT-ATAATGTCTTTCAACCATGGT
* *
62122477 CATATTCATTTTCCACCGAGTTGCCATAATATCATTCAATTATGGTTTTATTC
64 CATATTCATTTTCCACCGAGTTGCCATAATATCATTCAACTATGGTCTTATTC
62122530 GTTTGATTCG
Statistics
Matches: 96, Mismatches: 18, Indels: 4
0.81 0.15 0.03
Matches are distributed among these distances:
136 2 0.02
137 90 0.94
138 4 0.04
ACGTcount: A:0.19, C:0.17, G:0.14, T:0.50
Consensus pattern (137 bp):
GTGTCTTTCAACCATGGTCTTATTCATTATTGACGTGATGTTATAATGTCTTTCAACCATGGTCA
TATTCATTTTCCACCGAGTTGCCATAATATCATTCAACTATGGTCTTATTCATTTTTTGTTGTGT
TTCTATT
Found at i:62131969 original size:20 final size:20
Alignment explanation
Indices: 62131925--62131963 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
62131915 CACTAACTTT
62131925 AAATGGAATACAATGAGATA
1 AAATGGAATACAATGAGATA
62131945 AAATGGAAT-CAAATGAGAT
1 AAATGGAATAC-AATGAGAT
62131964 GTAATGAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.54, C:0.05, G:0.21, T:0.21
Consensus pattern (20 bp):
AAATGGAATACAATGAGATA
Found at i:62133132 original size:14 final size:14
Alignment explanation
Indices: 62133113--62133139 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
62133103 ACATATCTAA
62133113 AGTGTTCCATCCAC
1 AGTGTTCCATCCAC
62133127 AGTGTTCCATCCA
1 AGTGTTCCATCCA
62133140 TAATAATGCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.33, G:0.15, T:0.30
Consensus pattern (14 bp):
AGTGTTCCATCCAC
Found at i:62134851 original size:13 final size:13
Alignment explanation
Indices: 62134833--62134857 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
62134823 TAATTTAATA
62134833 TTATTTTGTGTGT
1 TTATTTTGTGTGT
62134846 TTATTTTGTGTG
1 TTATTTTGTGTG
62134858 CATTTGATTG
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:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:62136050 original size:2 final size:2
Alignment explanation
Indices: 62136045--62136074 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
62136035 TATGTGTGTA
62136045 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
62136075 TTAAATTCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62136497 original size:27 final size:27
Alignment explanation
Indices: 62136459--62136512 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
62136449 AACCTAGCAA
62136459 GCTAAGTGCCGGTGATCTGAATCAGGC
1 GCTAAGTGCCGGTGATCTGAATCAGGC
62136486 GCTAAGTGCCGGTGATCTGAATCAGGC
1 GCTAAGTGCCGGTGATCTGAATCAGGC
62136513 TATAAGCCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.22, C:0.22, G:0.33, T:0.22
Consensus pattern (27 bp):
GCTAAGTGCCGGTGATCTGAATCAGGC
Found at i:62136518 original size:27 final size:27
Alignment explanation
Indices: 62136461--62136518 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
62136451 CCTAGCAAGC
*
62136461 TAAGTGCCGGTGATCTGAATCAGGCGC
1 TAAGTGCCGGTGATCTGAATCAGGCGA
*
62136488 TAAGTGCCGGTGATCTGAATCAGGCTA
1 TAAGTGCCGGTGATCTGAATCAGGCGA
62136515 TAAG
1 TAAG
62136519 CCTAGCAGGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (27 bp):
TAAGTGCCGGTGATCTGAATCAGGCGA
Found at i:62136540 original size:41 final size:41
Alignment explanation
Indices: 62136486--62136671 Score: 309
Period size: 41 Copynumber: 4.5 Consensus size: 41
62136476 TGAATCAGGC
62136486 GCTAAGTGCCGGTGATCTGAATCAGGCTATAAGCCTAGCAG
1 GCTAAGTGCCGGTGATCTGAATCAGGCTATAAGCCTAGCAG
* *
62136527 GCTAAGTACCGGTGATCTGAATCTGGCTATAAGCCTAGCAG
1 GCTAAGTGCCGGTGATCTGAATCAGGCTATAAGCCTAGCAG
*
62136568 GCTAAGTGCCGGTGATCTGAATCAGGCTATAAGCCTAGTAG
1 GCTAAGTGCCGGTGATCTGAATCAGGCTATAAGCCTAGCAG
* * * *
62136609 GCTAAGTGTCGGTGATATGAATCAGGTTATAAACCTAGCAG
1 GCTAAGTGCCGGTGATCTGAATCAGGCTATAAGCCTAGCAG
62136650 GCTAAGTGCCGGTGATCTGAAT
1 GCTAAGTGCCGGTGATCTGAAT
62136672 ATGTTAAATT
Statistics
Matches: 133, Mismatches: 12, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 133 1.00
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.25
Consensus pattern (41 bp):
GCTAAGTGCCGGTGATCTGAATCAGGCTATAAGCCTAGCAG
Found at i:62137848 original size:4 final size:4
Alignment explanation
Indices: 62137839--62137864 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
62137829 ACATAATAGC
62137839 TTTA TTTA TTTA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TT
62137865 ATCACATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:62174918 original size:21 final size:18
Alignment explanation
Indices: 62174862--62174920 Score: 66
Period size: 18 Copynumber: 3.1 Consensus size: 18
62174852 TCAAATTCCG
*
62174862 TTCCGGTTCAGAATTTTT
1 TTCCGGTTCAGATTTTTT
62174880 TTCCGGTTCAG-TTGTTTT
1 TTCCGGTTCAGATT-TTTT
62174898 GGTATCCGGTTCAGATTTTTT
1 --T-TCCGGTTCAGATTTTTT
62174919 TT
1 TT
62174921 GCGTATGGAC
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
17 1 0.03
18 16 0.46
19 1 0.03
20 1 0.03
21 14 0.40
22 2 0.06
ACGTcount: A:0.12, C:0.15, G:0.20, T:0.53
Consensus pattern (18 bp):
TTCCGGTTCAGATTTTTT
Done.