Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold693
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: 92958
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:2027 original size:49 final size:49
Alignment explanation
Indices: 1972--2166 Score: 309
Period size: 49 Copynumber: 4.0 Consensus size: 49
1962 TTCGTTTTCT
* * *
1972 CGATGCCATAGTCCAACTATGGTCTTACACGTAATCACAAATCACATAC
1 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACAAATCACATAC
* * *
2021 CGATGCCATAGCCCAGCTATGGTCTTACACGAAATCACATATCACTTAC
1 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACAAATCACATAC
* *
2070 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATATCACTTAC
1 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACAAATCACATAC
2119 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATAATCACAT
1 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACA-AATCACAT
2167 GTTCACATGT
Statistics
Matches: 137, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
49 131 0.96
50 6 0.04
ACGTcount: A:0.31, C:0.30, G:0.15, T:0.24
Consensus pattern (49 bp):
CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACAAATCACATAC
Found at i:3520 original size:37 final size:37
Alignment explanation
Indices: 3420--3527 Score: 177
Period size: 36 Copynumber: 3.0 Consensus size: 37
3410 TACGTATGAT
*
3420 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
*
3455 CACCTATCACTTTGT-TCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
3491 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
3528 TAAAGCTATC
Statistics
Matches: 67, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
35 9 0.13
36 37 0.55
37 21 0.31
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (37 bp):
CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
Found at i:3570 original size:52 final size:52
Alignment explanation
Indices: 3491--3759 Score: 370
Period size: 52 Copynumber: 5.2 Consensus size: 52
3481 TAAGTGTAGC
* * **
3491 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTAT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
* *
3544 CACTTTTCACTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
3596 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
* *
3648 CAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
* ** *
3694 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
3746 CACTTTGTCACTTG
1 CACTTT-TCACTTG
3760 ATCAGAAGTA
Statistics
Matches: 194, Mismatches: 15, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
46 43 0.22
49 1 0.01
52 135 0.70
53 15 0.08
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.36
Consensus pattern (52 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
Found at i:3665 original size:46 final size:46
Alignment explanation
Indices: 3593--3765 Score: 231
Period size: 46 Copynumber: 3.7 Consensus size: 46
3583 AGCTATCACT
*
3593 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCCGAAGC
1 TATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGC
*
3638 TATCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGC
1 TATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGC
* **
3684 TATTACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGC
1 TATCACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGC
*
3736 TACCACTTATCACTTTGTCACTTGATCAGA
1 TATCACTTATCACTTTGTCACTTGATCAGA
3766 AGTACTCAAA
Statistics
Matches: 113, Mismatches: 8, Indels: 13
0.84 0.06 0.10
Matches are distributed among these distances:
45 12 0.11
46 59 0.52
48 1 0.01
50 1 0.01
52 40 0.35
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (46 bp):
TATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGC
Found at i:3677 original size:98 final size:98
Alignment explanation
Indices: 3491--3765 Score: 415
Period size: 98 Copynumber: 2.7 Consensus size: 98
3481 TAAGTGTAGC
* *
3491 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTTCACTT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCAC---T---TT
*
3556 GTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
59 GTCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
**
3596 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
*
3661 GATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
3694 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
3759 GATCAGA
66 GATCAGA
3766 AGTACTCAAA
Statistics
Matches: 160, Mismatches: 10, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
98 108 0.68
101 1 0.01
104 42 0.26
105 9 0.06
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:7034 original size:37 final size:37
Alignment explanation
Indices: 6970--7041 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 37
6960 TTTTCATAAT
* * *
6970 TTCACTTTTTCACTTTTAATCACTATTCAATTCAAAA
1 TTCACTTTTCCACTTTCAATCAATATTCAATTCAAAA
7007 TTCACTTTTCCA-TTTCAAGTCAATATTCAATTCAA
1 TTCACTTTTCCACTTTCAA-TCAATATTCAATTCAA
7042 TTCCACATAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
36 5 0.16
37 26 0.84
ACGTcount: A:0.32, C:0.22, G:0.01, T:0.44
Consensus pattern (37 bp):
TTCACTTTTCCACTTTCAATCAATATTCAATTCAAAA
Found at i:7195 original size:23 final size:23
Alignment explanation
Indices: 7169--7221 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
7159 ATAAGTGCCA
*
7169 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCAAAGCTAC
*
7192 CACTGAAATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCAAAGCTAC
7215 CACTGAT
1 CACTGAT
7222 CAATAACACT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.21
Consensus pattern (23 bp):
CACTGATATGTAGCCAAAGCTAC
Found at i:15590 original size:42 final size:42
Alignment explanation
Indices: 15543--15626 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
15533 TGCTTGCATT
15543 AGGCTGATACTTGCCATATATGATAATCATGCCAAGGAACTC
1 AGGCTGATACTTGCCATATATGATAATCATGCCAAGGAACTC
15585 AGGCTGATACTTGCCATATATGATAATCATGCCAAGGAACTC
1 AGGCTGATACTTGCCATATATGATAATCATGCCAAGGAACTC
15627 TATTTCTTCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.26
Consensus pattern (42 bp):
AGGCTGATACTTGCCATATATGATAATCATGCCAAGGAACTC
Found at i:16378 original size:51 final size:51
Alignment explanation
Indices: 16265--16378 Score: 122
Period size: 52 Copynumber: 2.2 Consensus size: 51
16255 ACTTATACAG
** * * *
16265 ACAATAATGCACAAGAGGACTATGACTCATTAAACTTTATCAAAATTAAAGT
1 ACAATAATTTACAAGAGGACGATGACTCATTAAACTTTA-CAAAAGTAAAGC
* * * *
16317 TCAATAATTTACAAGAGTACGATGACTCACTTATACTTTA-ATAAGTAAAGC
1 ACAATAATTTACAAGAGGACGATGACTCA-TTAAACTTTACAAAAGTAAAGC
16368 ACAATAATTTA
1 ACAATAATTTA
16379 TAAAAGGAAG
Statistics
Matches: 51, Mismatches: 10, Indels: 3
0.80 0.16 0.05
Matches are distributed among these distances:
51 18 0.35
52 24 0.47
53 9 0.18
ACGTcount: A:0.45, C:0.15, G:0.11, T:0.30
Consensus pattern (51 bp):
ACAATAATTTACAAGAGGACGATGACTCATTAAACTTTACAAAAGTAAAGC
Found at i:29466 original size:31 final size:31
Alignment explanation
Indices: 29425--29492 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
29415 TTACAATTTG
* *
29425 GTCACTGAACTATTCGAAAGTTTTCATTTAA
1 GTCACTGAACTATTCAAAAATTTTCATTTAA
* * *
29456 GTCATTGAACTATTTAAAAATTTTTATTTAA
1 GTCACTGAACTATTCAAAAATTTTCATTTAA
29487 GTCACT
1 GTCACT
29493 AGGTTGTTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.34, C:0.13, G:0.10, T:0.43
Consensus pattern (31 bp):
GTCACTGAACTATTCAAAAATTTTCATTTAA
Found at i:31473 original size:19 final size:18
Alignment explanation
Indices: 31418--31469 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
31408 TCTTAAATAT
31418 TTATATAATTATATATAAA
1 TTATATAATTATATAT-AA
*
31437 TTAT-TCAATTTTGATATAA
1 TTATAT-AATTAT-ATATAA
31456 TTATATAATTATAT
1 TTATATAATTATAT
31470 TATATTTTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
18 3 0.11
19 20 0.71
20 5 0.18
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (18 bp):
TTATATAATTATATATAA
Found at i:32408 original size:34 final size:34
Alignment explanation
Indices: 32365--32433 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
32355 ATATCCAAAA
32365 TCTTGCTACCCTATTACCACCTACTGCCATCTTT
1 TCTTGCTACCCTATTACCACCTACTGCCATCTTT
32399 TCTTGCTACCCTATTACCACCTACTGCCATCTTT
1 TCTTGCTACCCTATTACCACCTACTGCCATCTTT
32433 T
1 T
32434 TTGATCTTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.17, C:0.38, G:0.06, T:0.39
Consensus pattern (34 bp):
TCTTGCTACCCTATTACCACCTACTGCCATCTTT
Found at i:34712 original size:14 final size:14
Alignment explanation
Indices: 34693--34721 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
34683 TGTCTTATTG
34693 TCTTTTCAAAGCTA
1 TCTTTTCAAAGCTA
34707 TCTTTTCAAAGCTA
1 TCTTTTCAAAGCTA
34721 T
1 T
34722 TTACTAAGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.21, G:0.07, T:0.45
Consensus pattern (14 bp):
TCTTTTCAAAGCTA
Found at i:35285 original size:12 final size:12
Alignment explanation
Indices: 35268--35292 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35258 GTACAGTATC
35268 TTTCTCATTGAA
1 TTTCTCATTGAA
35280 TTTCTCATTGAA
1 TTTCTCATTGAA
35292 T
1 T
35293 GAATGCAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.08, T:0.52
Consensus pattern (12 bp):
TTTCTCATTGAA
Found at i:47868 original size:21 final size:21
Alignment explanation
Indices: 47844--47886 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
47834 TTAATAATTT
47844 TTTATATGAAATTTTAA-TTAA
1 TTTAT-TGAAATTTTAACTTAA
* *
47865 TTTATTTAATTTTTAACTTAA
1 TTTATTGAAATTTTAACTTAA
47886 T
1 T
47887 AAATTGCCTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTATTGAAATTTTAACTTAA
Found at i:55054 original size:66 final size:66
Alignment explanation
Indices: 54948--55076 Score: 249
Period size: 66 Copynumber: 2.0 Consensus size: 66
54938 CATTTCAGAG
54948 AGCACACTCCCGCGAACCTCATCCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTGCAAGA
1 AGCACACTCCCGCGAACCTCATCCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTGCAAGA
55013 T
66 T
*
55014 AGCACACTCCTGCGAACCTCATCCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTGCAA
1 AGCACACTCCCGCGAACCTCATCCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTGCAA
55077 TATAAACTCA
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.27, C:0.36, G:0.18, T:0.19
Consensus pattern (66 bp):
AGCACACTCCCGCGAACCTCATCCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTGCAAGA
T
Found at i:55288 original size:57 final size:60
Alignment explanation
Indices: 55195--55342 Score: 214
Period size: 57 Copynumber: 2.5 Consensus size: 60
55185 ACCCTAATTC
* * *
55195 GGATTACCCGTCCGGGCTAAATCCATTTTCCACATATTCTTCGGGAGGGCTATATC-A-A
1 GGATCACCCGTCCGGGCTAGATCCTTTTTCCACATATTCTTCGGGAGGGCTATATCGATA
55253 -GATCACCCGTCCGGGCTAGAT-CTTTTTCACACATATTCTTCGGGAGGGCTATATCAGGATA
1 GGATCACCCGTCCGGGCTAGATCCTTTTTC-CACATATTCTTCGGGAGGGCTATATC--GATA
55314 GGATCACCCGTCCGGGCTAGATCCTTTTT
1 GGATCACCCGTCCGGGCTAGATCCTTTTT
55343 ACCGTCAATT
Statistics
Matches: 80, Mismatches: 3, Indels: 9
0.87 0.03 0.10
Matches are distributed among these distances:
56 6 0.08
57 45 0.56
60 1 0.01
61 1 0.01
62 21 0.26
63 6 0.08
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (60 bp):
GGATCACCCGTCCGGGCTAGATCCTTTTTCCACATATTCTTCGGGAGGGCTATATCGATA
Found at i:58475 original size:41 final size:41
Alignment explanation
Indices: 58430--58622 Score: 305
Period size: 41 Copynumber: 4.7 Consensus size: 41
58420 GGTTTTAAAA
58430 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
*
58471 CCTAGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
* *
58512 CCTAGCAGGCTAAGTGCCGGTGATCTAAATCAGGTTATAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
* *
58553 CCTAGCAGGCTAAGTGTCGGTGATCTGAATCAGGCTTTAAG
1 CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
* *
58594 CCTAACAGGGCTAAGTGCCAGTGAATCTG
1 CCTAGCA-GGCTAAGTGCCGGTG-ATCTG
58623 TTTAAATTAA
Statistics
Matches: 139, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
41 121 0.87
42 13 0.09
43 5 0.04
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.23
Consensus pattern (41 bp):
CCTAGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAG
Found at i:62705 original size:6 final size:6
Alignment explanation
Indices: 62694--62731 Score: 69
Period size: 6 Copynumber: 6.5 Consensus size: 6
62684 AGCGCATGAA
62694 AGAGAT AGAGAT AGAGAT AGAGAT AGAGAT -GAGAT AGA
1 AGAGAT AGAGAT AGAGAT AGAGAT AGAGAT AGAGAT AGA
62732 AGTGTCAGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.50, C:0.00, G:0.34, T:0.16
Consensus pattern (6 bp):
AGAGAT
Found at i:72326 original size:36 final size:36
Alignment explanation
Indices: 72279--72350 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
72269 TGAGGGAAAG
72279 AAAACTAGTCTGTGAGCATGGAAGCAGTAAACTACA
1 AAAACTAGTCTGTGAGCATGGAAGCAGTAAACTACA
*
72315 AAAACTAGTCTGTGAGCATGGAAGTAGTAAACTACA
1 AAAACTAGTCTGTGAGCATGGAAGCAGTAAACTACA
72351 TAAGCTCATC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.42, C:0.15, G:0.22, T:0.21
Consensus pattern (36 bp):
AAAACTAGTCTGTGAGCATGGAAGCAGTAAACTACA
Found at i:73841 original size:2 final size:2
Alignment explanation
Indices: 73834--73887 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
73824 TTGGGAGAAT
73834 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
73876 AG AG AG AG AG AG
1 AG AG AG AG AG AG
73888 CGCAAAAGCA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:78325 original size:19 final size:19
Alignment explanation
Indices: 78301--78338 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
78291 TATCAAATAA
* *
78301 AAAATTCATGTGTAAAATT
1 AAAATTCATATATAAAATT
78320 AAAATTCATATATAAAATT
1 AAAATTCATATATAAAATT
78339 GCATAAAATT
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:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (19 bp):
AAAATTCATATATAAAATT
Found at i:78382 original size:31 final size:29
Alignment explanation
Indices: 78313--78395 Score: 112
Period size: 29 Copynumber: 2.8 Consensus size: 29
78303 AATTCATGTG
* *
78313 TAAAATTAAAATTCATATATAAAATTGCA
1 TAAAATTAAAATTTATATATAATATTGCA
*
78342 TAAAATTAAAATTTATGTATAATATTGTACA
1 TAAAATTAAAATTTATATATAATATTG--CA
*
78373 TTAAATTAAAATTTATATATAAT
1 TAAAATTAAAATTTATATATAAT
78396 TTTCAGAATT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 24 0.51
31 23 0.49
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.41
Consensus pattern (29 bp):
TAAAATTAAAATTTATATATAATATTGCA
Found at i:85005 original size:18 final size:18
Alignment explanation
Indices: 84979--85013 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
84969 TAAATTATGC
*
84979 ATAACAAAATAAAAATAT
1 ATAAAAAAATAAAAATAT
*
84997 ATAAAAAAATGAAAATA
1 ATAAAAAAATAAAAATA
85014 GAGCATTTGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.74, C:0.03, G:0.03, T:0.20
Consensus pattern (18 bp):
ATAAAAAAATAAAAATAT
Found at i:85676 original size:7 final size:7
Alignment explanation
Indices: 85664--85694 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
85654 ATTGAACCTA
85664 AAATTTG
1 AAATTTG
85671 AAATTTG
1 AAATTTG
85678 AAATTTG
1 AAATTTG
85685 AAATTTG
1 AAATTTG
85692 AAA
1 AAA
85695 AGTAAAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.48, C:0.00, G:0.13, T:0.39
Consensus pattern (7 bp):
AAATTTG
Found at i:86264 original size:5 final size:5
Alignment explanation
Indices: 86232--86261 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
86222 ATAGAATTTA
*
86232 GTTCG GTTCG GTTCG GTTCG GTTCG ATTCG
1 GTTCG GTTCG GTTCG GTTCG GTTCG GTTCG
86262 ATTTTGAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.03, C:0.20, G:0.37, T:0.40
Consensus pattern (5 bp):
GTTCG
Found at i:86980 original size:29 final size:29
Alignment explanation
Indices: 86938--86999 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
86928 TTTTATTAAA
* *
86938 ATGAAGAGACTAAAAAAACTTAAAATAGT
1 ATGAAAAGACTAAAAAAACTTAAAATAAT
* * *
86967 ATGAAAAGACTAAAATATCTTAGAATAAT
1 ATGAAAAGACTAAAAAAACTTAAAATAAT
86996 ATGA
1 ATGA
87000 CTAATTATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.56, C:0.06, G:0.13, T:0.24
Consensus pattern (29 bp):
ATGAAAAGACTAAAAAAACTTAAAATAAT
Done.