Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003057.1 Hibiscus syriacus cultivar Beakdansim tig00006374_pilon, whole genome shotgun sequence
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: 119982
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:11708 original size:18 final size:16
Alignment explanation
Indices: 11672--11710 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
11662 GAGCCAGAGC
*
11672 TGTTGCTGTGATTTGT
1 TGTTGCTGTGATATGT
11688 TGTTGCTGATGATGATGT
1 TGTTGCTG-TGAT-ATGT
11706 TGTTG
1 TGTTG
11711 AAAGTGCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 8 0.40
17 4 0.20
18 8 0.40
ACGTcount: A:0.10, C:0.05, G:0.33, T:0.51
Consensus pattern (16 bp):
TGTTGCTGTGATATGT
Found at i:12498 original size:2 final size:2
Alignment explanation
Indices: 12491--12520 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12481 CTATAATTTA
12491 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
12521 TATGTTCCGT
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:13308 original size:18 final size:18
Alignment explanation
Indices: 13285--13322 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
13275 GAAATTGGTG
13285 AATCCGTTAATGGTAGAA
1 AATCCGTTAATGGTAGAA
13303 AATCCGTTAATGGTAGAA
1 AATCCGTTAATGGTAGAA
13321 AA
1 AA
13323 CACTATGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.42, C:0.11, G:0.21, T:0.26
Consensus pattern (18 bp):
AATCCGTTAATGGTAGAA
Found at i:16926 original size:17 final size:18
Alignment explanation
Indices: 16904--16938 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
16894 GATAAATGTA
16904 ATAC-AAAAAGATATATT
1 ATACAAAAAAGATATATT
16921 ATACAAAAAAGATATATT
1 ATACAAAAAAGATATATT
16939 GTGGTTTGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.60, C:0.06, G:0.06, T:0.29
Consensus pattern (18 bp):
ATACAAAAAAGATATATT
Found at i:19270 original size:29 final size:29
Alignment explanation
Indices: 19228--19288 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
19218 TTGGTCTCCT
19228 TTTACAAACAAGGCTAAATATTGAACCAC
1 TTTACAAACAAGGCTAAATATTGAACCAC
19257 TTTACAAACAAGGCTAAATATTGAACCAC
1 TTTACAAACAAGGCTAAATATTGAACCAC
19286 TTT
1 TTT
19289 GACATTGTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.43, C:0.20, G:0.10, T:0.28
Consensus pattern (29 bp):
TTTACAAACAAGGCTAAATATTGAACCAC
Found at i:32185 original size:23 final size:22
Alignment explanation
Indices: 32159--32235 Score: 91
Period size: 23 Copynumber: 3.4 Consensus size: 22
32149 TATATAGCAT
* *
32159 TTCGGTGCATTTTTACGTGACAC
1 TTCGGTGCAATTCTACGTG-CAC
*
32182 TTCGGTGCAATTCTACGTGCAT
1 TTCGGTGCAATTCTACGTGCAC
* *
32204 TTCAGTGTAATTCTACGTGGCAC
1 TTCGGTGCAATTCTACGT-GCAC
32227 TTCGGTGCA
1 TTCGGTGCA
32236 TTTATACGAG
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
22 18 0.40
23 27 0.60
ACGTcount: A:0.18, C:0.22, G:0.23, T:0.36
Consensus pattern (22 bp):
TTCGGTGCAATTCTACGTGCAC
Found at i:32892 original size:14 final size:14
Alignment explanation
Indices: 32873--32902 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
32863 TTGTTTGAAC
*
32873 ATATATTACATTGT
1 ATATATTACATAGT
32887 ATATATTACATAGT
1 ATATATTACATAGT
32901 AT
1 AT
32903 TCACCCCATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (14 bp):
ATATATTACATAGT
Found at i:50785 original size:2 final size:2
Alignment explanation
Indices: 50778--50802 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
50768 CTTTAATTAT
50778 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
50803 CATTTTTTAA
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:52632 original size:3 final size:3
Alignment explanation
Indices: 52624--52648 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
52614 TTGATTAGTT
52624 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
52649 AACCCAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:53228 original size:31 final size:31
Alignment explanation
Indices: 53193--53255 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
53183 TTGACATGTG
*
53193 ACATATGTT-ATATCATAACTTTATATACGTA
1 ACATAT-TTCATATCATAACTTTATACACGTA
* *
53224 ACATATTTCATATTATTACTTTATACACGTA
1 ACATATTTCATATCATAACTTTATACACGTA
53255 A
1 A
53256 AATTTATCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 2 0.07
31 26 0.93
ACGTcount: A:0.38, C:0.14, G:0.05, T:0.43
Consensus pattern (31 bp):
ACATATTTCATATCATAACTTTATACACGTA
Found at i:53637 original size:41 final size:41
Alignment explanation
Indices: 53604--53686 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 41
53594 GCATTGCTAT
* *
53604 TTTCCTAATTCGCAATGCGAATACGTAAATCGCAACGCGAA
1 TTTCCAAAATCGCAATGCGAATACGTAAATCGCAACGCGAA
** * *
53645 TTTGGAAAATCGCAATGCGATTACGTAAATCGCAATGCGAA
1 TTTCCAAAATCGCAATGCGAATACGTAAATCGCAACGCGAA
53686 T
1 T
53687 CTGACTATCG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.25
Consensus pattern (41 bp):
TTTCCAAAATCGCAATGCGAATACGTAAATCGCAACGCGAA
Found at i:53638 original size:20 final size:20
Alignment explanation
Indices: 53613--53686 Score: 94
Period size: 20 Copynumber: 3.6 Consensus size: 20
53603 TTTTCCTAAT
53613 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
53633 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
*
53654 TCGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
53674 TCGCAATGCGAAT
1 TCGCAATGCGAAT
53687 CTGACTATCG
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 28 0.65
21 15 0.35
ACGTcount: A:0.36, C:0.20, G:0.22, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:54323 original size:20 final size:20
Alignment explanation
Indices: 54298--54370 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
54288 CGATTTTCAT
*
54298 TTCGCGTTGCAATAGTCAAA
1 TTCGCGTTGCGATAGTCAAA
54318 TTCGCGTTGCGATAGTCAAA
1 TTCGCGTTGCGATAGTCAAA
**
54338 TTCGCGTTGCGATAGTCATT
1 TTCGCGTTGCGATAGTCAAA
*
54358 TTCGTGTTGCGAT
1 TTCGCGTTGCGAT
54371 TTTCATTTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.36
Consensus pattern (20 bp):
TTCGCGTTGCGATAGTCAAA
Found at i:54376 original size:20 final size:20
Alignment explanation
Indices: 54338--54392 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
54328 GATAGTCAAA
* **
54338 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
54358 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
*
54378 TTTGTGTTGCGATTT
1 TTCGTGTTGCGATTT
54393 AAAGTTTCAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.11, C:0.15, G:0.24, T:0.51
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:56539 original size:6 final size:6
Alignment explanation
Indices: 56528--56554 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
56518 GTAAGTTTAC
56528 GGGATT GGGATT GGGATT GGGATT GGG
1 GGGATT GGGATT GGGATT GGGATT GGG
56555 GCACGATGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.56, T:0.30
Consensus pattern (6 bp):
GGGATT
Found at i:57374 original size:16 final size:16
Alignment explanation
Indices: 57353--57386 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
57343 GATTTCATTG
57353 TTTGGGAAGGTTATGA
1 TTTGGGAAGGTTATGA
57369 TTTGGGAAGGTTATGA
1 TTTGGGAAGGTTATGA
57385 TT
1 TT
57387 AGAAATTAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.00, G:0.35, T:0.41
Consensus pattern (16 bp):
TTTGGGAAGGTTATGA
Found at i:60509 original size:12 final size:12
Alignment explanation
Indices: 60492--60516 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
60482 TAGATTTGCG
60492 AAAATGACCAAC
1 AAAATGACCAAC
60504 AAAATGACCAAC
1 AAAATGACCAAC
60516 A
1 A
60517 GTTGTCGTTG
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:0.60, C:0.24, G:0.08, T:0.08
Consensus pattern (12 bp):
AAAATGACCAAC
Found at i:60545 original size:19 final size:19
Alignment explanation
Indices: 60521--60574 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
60511 CCAACAGTTG
60521 TCGTTGCGATTTTTCAAAT
1 TCGTTGCGATTTTTCAAAT
* *
60540 TCGTTGCGA-TTTTCCATT
1 TCGTTGCGATTTTTCAAAT
60558 TCGCGTTGCGATTTTTC
1 T--CGTTGCGATTTTTC
60575 CAGTTCGCGT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 8 0.27
19 9 0.30
20 8 0.27
21 5 0.17
ACGTcount: A:0.13, C:0.20, G:0.19, T:0.48
Consensus pattern (19 bp):
TCGTTGCGATTTTTCAAAT
Found at i:60566 original size:20 final size:20
Alignment explanation
Indices: 60541--60651 Score: 132
Period size: 20 Copynumber: 5.5 Consensus size: 20
60531 TTTTCAAATT
*
60541 CGTTGCGATTTTCCATTTCG
1 CGTTGCGATTTTCCAGTTCG
60561 CGTTGCGATTTTTCCAGTTCG
1 CGTTGCGA-TTTTCCAGTTCG
* ** ** *
60582 CGTTGCGATAGTTGAAAATCA
1 CGTTGCGAT-TTTCCAGTTCG
*
60603 CGTTGCGATTTTCCATTTCG
1 CGTTGCGATTTTCCAGTTCG
60623 CGTTGCGATTTTCCAGTTCG
1 CGTTGCGATTTTCCAGTTCG
60643 CGTTGCGAT
1 CGTTGCGAT
60652 AGTTGAAAAT
Statistics
Matches: 75, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
20 42 0.56
21 33 0.44
ACGTcount: A:0.14, C:0.23, G:0.23, T:0.40
Consensus pattern (20 bp):
CGTTGCGATTTTCCAGTTCG
Found at i:60662 original size:61 final size:62
Alignment explanation
Indices: 60541--60672 Score: 248
Period size: 61 Copynumber: 2.1 Consensus size: 62
60531 TTTTCAAATT
60541 CGTTGCGATTTTCCATTTCGCGTTGCGATTTTTCCAGTTCGCGTTGCGATAGTTGAAAATCA
1 CGTTGCGATTTTCCATTTCGCGTTGCGATTTTTCCAGTTCGCGTTGCGATAGTTGAAAATCA
*
60603 CGTTGCGATTTTCCATTTCGCGTTGCGA-TTTTCCAGTTCGCGTTGCGATAGTTGAAAATCG
1 CGTTGCGATTTTCCATTTCGCGTTGCGATTTTTCCAGTTCGCGTTGCGATAGTTGAAAATCA
60664 CGTTGCGAT
1 CGTTGCGAT
60673 AGTCTACAGT
Statistics
Matches: 69, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
61 41 0.59
62 28 0.41
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.38
Consensus pattern (62 bp):
CGTTGCGATTTTCCATTTCGCGTTGCGATTTTTCCAGTTCGCGTTGCGATAGTTGAAAATCA
Found at i:60666 original size:21 final size:21
Alignment explanation
Indices: 60579--60675 Score: 81
Period size: 20 Copynumber: 4.7 Consensus size: 21
60569 TTTTTCCAGT
*
60579 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTCAAAA
* * * **
60600 TCACGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTCAAAA
* * **
60620 TCGCGTTGCGAT-TTTCCAGT
1 TCGCGTTGCGATAGTTCAAAA
*
60640 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTCAAAA
60661 TCGCGTTGCGATAGT
1 TCGCGTTGCGATAGT
60676 CTACAGTTGT
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
20 33 0.53
21 29 0.47
ACGTcount: A:0.20, C:0.20, G:0.26, T:0.35
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTCAAAA
Found at i:60692 original size:22 final size:21
Alignment explanation
Indices: 60664--60735 Score: 76
Period size: 22 Copynumber: 3.4 Consensus size: 21
60654 TTGAAAATCG
60664 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTT-T
* * **
60686 CGTTGCGAT--TTTGCAAATT
1 CGTTGCGATAGTCTACAGTTT
60705 CGTTGCGATAGTCTACAGTTAT
1 CGTTGCGATAGTCTACAGTT-T
60727 CGTTGCGAT
1 CGTTGCGAT
60736 TTTCCAATTG
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
19 10 0.26
20 5 0.13
21 5 0.13
22 19 0.49
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (21 bp):
CGTTGCGATAGTCTACAGTTT
Found at i:60709 original size:82 final size:81
Alignment explanation
Indices: 60514--60713 Score: 224
Period size: 82 Copynumber: 2.4 Consensus size: 81
60504 AAAATGACCA
* ** * **
60514 ACAGTTGTCGTTGCGATTTTTCAAATTCGTTGCGATTTTCCATTTCGCGTTGCGATTTTTCCAGT
1 ACAGTTGTCGTTGCGA-TTTTCAAATTCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTCAAAA
60579 TCGCGTTGCGATAGTTG
65 TCGCGTTGCGATAGTTG
** ** * * *
60596 A-AAATCACGTTGCGATTTTCCATTTCGCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTGAAA
1 ACAGTTGTCGTTGCGATTTTCAAATT--CGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTCAAA
60660 ATCGCGTTGCGATAGTCT-
64 ATCGCGTTGCGATAGT-TG
60678 ACAGTTGTCGTTGCGATTTTGCAAATTCGTTGCGAT
1 ACAGTTGTCGTTGCGATTTT-CAAATTCGTTGCGAT
60714 AGTCTACAGT
Statistics
Matches: 94, Mismatches: 19, Indels: 10
0.76 0.15 0.08
Matches are distributed among these distances:
80 8 0.09
81 10 0.11
82 57 0.61
83 15 0.16
84 4 0.04
ACGTcount: A:0.18, C:0.20, G:0.23, T:0.39
Consensus pattern (81 bp):
ACAGTTGTCGTTGCGATTTTCAAATTCGTTGCGATTTTCCAGTTCGCGTTGCGATAGTTCAAAAT
CGCGTTGCGATAGTTG
Found at i:60853 original size:6 final size:6
Alignment explanation
Indices: 60842--60885 Score: 81
Period size: 6 Copynumber: 7.5 Consensus size: 6
60832 GACACGTATT
60842 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
60886 CGAGACGGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.13
6 33 0.87
ACGTcount: A:0.32, C:0.52, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:61398 original size:6 final size:6
Alignment explanation
Indices: 61377--61431 Score: 96
Period size: 6 Copynumber: 9.5 Consensus size: 6
61367 GTCCGTCTCG
61377 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
61423 GGTCGT GGT
1 GGTCGT GGT
61432 AATACGTGTC
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 10 0.20
6 39 0.80
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:61528 original size:22 final size:22
Alignment explanation
Indices: 61502--61544 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
61492 CAAAATCTCG
*
61502 ACAACTGTAGACTTTCGCAACA
1 ACAACTGTAGACTATCGCAACA
61524 ACAACTGTAGACTATCGCAAC
1 ACAACTGTAGACTATCGCAAC
61545 GCGAATTTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.28, G:0.14, T:0.21
Consensus pattern (22 bp):
ACAACTGTAGACTATCGCAACA
Found at i:75346 original size:34 final size:36
Alignment explanation
Indices: 75264--75342 Score: 149
Period size: 36 Copynumber: 2.2 Consensus size: 36
75254 CTAACTAATG
*
75264 GCATGAACAAGCTAAAAAAAATTCTATCCTTAAATA
1 GCATGAACAAGCTAAAAAAAATTATATCCTTAAATA
75300 GCATGAACAAGCTAAAAAAAATTATATCCTTAAATA
1 GCATGAACAAGCTAAAAAAAATTATATCCTTAAATA
75336 GCATGAA
1 GCATGAA
75343 AGCTCTAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 42 1.00
ACGTcount: A:0.51, C:0.15, G:0.10, T:0.24
Consensus pattern (36 bp):
GCATGAACAAGCTAAAAAAAATTATATCCTTAAATA
Found at i:87032 original size:34 final size:31
Alignment explanation
Indices: 86952--87040 Score: 88
Period size: 34 Copynumber: 2.7 Consensus size: 31
86942 TTAGTATCTT
* * *
86952 TTTAAATAGTTATTATATTTTATATTAATATA
1 TTTATATAATTATTAT-TTTTTTATTAATATA
* *
86984 TTTATGTAAATATTATTTTTTTATTAAAATAATA
1 TTTATATAATTATTATTTTTTTATT--AAT-ATA
*
87018 TTTATATAATTATTATTTATTTA
1 TTTATATAATTATTATTTTTTTA
87041 AAATTATTAA
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
31 8 0.17
32 12 0.26
33 3 0.07
34 23 0.50
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.58
Consensus pattern (31 bp):
TTTATATAATTATTATTTTTTTATTAATATA
Found at i:87047 original size:17 final size:17
Alignment explanation
Indices: 86982--87049 Score: 54
Period size: 17 Copynumber: 4.1 Consensus size: 17
86972 TATATTAATA
*
86982 TATTTATGTAAATATTAT
1 TATTTATTTAAA-ATTAT
* *
87000 T-TTTTTATTAAAA-TAA
1 TATTTAT-TTAAAATTAT
*
87016 TATTTA--TATAATTAT
1 TATTTATTTAAAATTAT
87031 TATTTATTTAAAATTAT
1 TATTTATTTAAAATTAT
87048 TA
1 TA
87050 ATTTTGTGTG
Statistics
Matches: 38, Mismatches: 7, Indels: 11
0.68 0.12 0.20
Matches are distributed among these distances:
14 4 0.11
15 8 0.21
16 3 0.08
17 18 0.47
18 5 0.13
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.57
Consensus pattern (17 bp):
TATTTATTTAAAATTAT
Found at i:89546 original size:15 final size:15
Alignment explanation
Indices: 89504--89548 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
89494 ACGACGGATG
89504 TTTTT-TTTGTTGTT
1 TTTTTATTTGTTGTT
*
89518 TTTTTACCTT-TTGTT
1 TTTTTA-TTTGTTGTT
89533 TTTTTATTTGTTGTT
1 TTTTTATTTGTTGTT
89548 T
1 T
89549 AGGGGCTGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 7 0.27
15 17 0.65
16 2 0.08
ACGTcount: A:0.04, C:0.04, G:0.11, T:0.80
Consensus pattern (15 bp):
TTTTTATTTGTTGTT
Found at i:99329 original size:25 final size:26
Alignment explanation
Indices: 99283--99335 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
99273 TAAATATTTT
* *
99283 TTCATTATTTTTAAAAACTTTATAAA
1 TTCATCATTTTTAAAAACTTTACAAA
99309 TTCATCATTTTTAAAAA-TTTACAAA
1 TTCATCATTTTTAAAAACTTTACAAA
99334 TT
1 TT
99336 TAAGCCCATA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 9 0.36
26 16 0.64
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (26 bp):
TTCATCATTTTTAAAAACTTTACAAA
Found at i:100414 original size:2 final size:2
Alignment explanation
Indices: 100409--100442 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
100399 TATGATATCC
100409 AT 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 AT
100443 TCATATTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:101212 original size:18 final size:18
Alignment explanation
Indices: 101189--101245 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
101179 GCCACCGCTG
101189 CCATCATCGTCGTCGCCA
1 CCATCATCGTCGTCGCCA
** **
101207 CCATCA-C--CACCGCTG
1 CCATCATCGTCGTCGCCA
101222 CCATCATCGTCGTCGCCA
1 CCATCATCGTCGTCGCCA
101240 CCATCA
1 CCATCA
101246 CCACCGATAT
Statistics
Matches: 28, Mismatches: 8, Indels: 6
0.67 0.19 0.14
Matches are distributed among these distances:
15 10 0.36
16 1 0.04
17 1 0.04
18 16 0.57
ACGTcount: A:0.19, C:0.47, G:0.14, T:0.19
Consensus pattern (18 bp):
CCATCATCGTCGTCGCCA
Found at i:101222 original size:33 final size:33
Alignment explanation
Indices: 101180--101251 Score: 144
Period size: 33 Copynumber: 2.2 Consensus size: 33
101170 GTTGTCGCCG
101180 CCACCGCTGCCATCATCGTCGTCGCCACCATCA
1 CCACCGCTGCCATCATCGTCGTCGCCACCATCA
101213 CCACCGCTGCCATCATCGTCGTCGCCACCATCA
1 CCACCGCTGCCATCATCGTCGTCGCCACCATCA
101246 CCACCG
1 CCACCG
101252 ATATCATCTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.18, C:0.50, G:0.15, T:0.17
Consensus pattern (33 bp):
CCACCGCTGCCATCATCGTCGTCGCCACCATCA
Found at i:108603 original size:209 final size:212
Alignment explanation
Indices: 108208--108605 Score: 518
Period size: 209 Copynumber: 1.9 Consensus size: 212
108198 AACACATCCA
**
108208 ATACAAGAAATATCAGATGAAGCCATGAACAAATAGTGCTAACCAAATGCTCTTATTAATTTCTA
1 ATACAAGAAATATCAGACAAAGCCATGAACAAATAGTGCTAACCAAATGCTC-T-TTAATTTCTA
* *
108273 GTTTTCGAAAGGAAAACTTAGTTATTTTGTATGTCATCCTCTGCATCTTTCTGTCTACAATGGCA
64 GTTTTCGAAAGGAAAACTTAGTTATTTTGTATGTCATCCTCTGCATCCTTCTGTCTACAATGACA
* * * *
108338 TACGTCTTAGCACACGGACTAGATACATCGATAATCTGACTGATATATTTAACCAGAAACTTTGC
129 AACGACTTAGCACACGGACTAGATACATCAATAATCTGACTGATATATTCAACCAGAAACTTTGC
108403 TACATTGATAATCTGATTG
194 TACATTGATAATCTGATTG
*
108422 ATACAAGAAATATCAGACAAAG-CATGAACAAATAG-GACTAACCAAATGCTC-TTACTTT-TAG
1 ATACAAGAAATATCAGACAAAGCCATGAACAAATAGTG-CTAACCAAATGCTCTTTAATTTCTAG
** * * ** *
108483 TTTTTTAAATGAAAACTTGGTTATTTTGTATGTTGTCCTCTGCCTCCTTCTGTGCTACAATGACA
65 TTTTCGAAAGGAAAACTTAGTTATTTTGTATGTCATCCTCTGCATCCTTCTGT-CTACAATGACA
* * * * * **
108548 AATGACTTAGCACATGGTCTTGATACATTAATAATCTGGTTGATAT-TTCAACCAGAAA
129 AACGACTTAGCACACGGACTAGATACATCAATAATCTGACTGATATATTCAACCAGAAA
108606 GTTAGGTTCT
Statistics
Matches: 159, Mismatches: 23, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
209 59 0.37
210 52 0.33
212 1 0.01
213 27 0.17
214 20 0.13
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (212 bp):
ATACAAGAAATATCAGACAAAGCCATGAACAAATAGTGCTAACCAAATGCTCTTTAATTTCTAGT
TTTCGAAAGGAAAACTTAGTTATTTTGTATGTCATCCTCTGCATCCTTCTGTCTACAATGACAAA
CGACTTAGCACACGGACTAGATACATCAATAATCTGACTGATATATTCAACCAGAAACTTTGCTA
CATTGATAATCTGATTG
Found at i:112479 original size:183 final size:183
Alignment explanation
Indices: 112163--112492 Score: 545
Period size: 183 Copynumber: 1.8 Consensus size: 183
112153 CTGATGCGCA
* *
112163 CCAGACAAATGCATATTACTCAATTGATGGTCCAAACGTGGATAAGCAACAGGTAGGGCACTACC
1 CCAGACAAATGCATATTACTCAATTGATGGTCCAAACGAGGATAAGCAACAGGTACGGCACTACC
* * *
112228 TGTACTTGCTCCCACGGAACTCAAACCATCCTGCCTGTTATGTCCAGAGAAGCTATTTTGTATGG
66 TGTACTTGCTCCCAAGGAACTCAAACCATCCTGCCTGTAATGTCCAGAGAAGCTATTCTGTATGG
112293 AGTGGAGCTCAGAATTAGGAGGATATTGAGCAGGTTGTTGATAAGAGTTGGAT
131 AGTGGAGCTCAGAATTAGGAGGATATTGAGCAGGTTGTTGATAAGAGTTGGAT
112346 CCAGACAAATGCATATTACTCAATTGATGGTCCAAA-GAAGGATAAGCAACAGGTACGGCACTAC
1 CCAGACAAATGCATATTACTCAATTGATGGTCCAAACG-AGGATAAGCAACAGGTACGGCACTAC
* * ** * *
112410 CTGTACTTGCTCCTAAGGAATTCATGCTATCCTGCCTGTAATGTCCAGAGAAGCTATTCTGTCTG
65 CTGTACTTGCTCCCAAGGAACTCAAACCATCCTGCCTGTAATGTCCAGAGAAGCTATTCTGTATG
112475 GAGTGGAGCTCAGAATTA
130 GAGTGGAGCTCAGAATTA
112493 CTTTCAGGAG
Statistics
Matches: 135, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
182 1 0.01
183 134 0.99
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (183 bp):
CCAGACAAATGCATATTACTCAATTGATGGTCCAAACGAGGATAAGCAACAGGTACGGCACTACC
TGTACTTGCTCCCAAGGAACTCAAACCATCCTGCCTGTAATGTCCAGAGAAGCTATTCTGTATGG
AGTGGAGCTCAGAATTAGGAGGATATTGAGCAGGTTGTTGATAAGAGTTGGAT
Found at i:115436 original size:29 final size:29
Alignment explanation
Indices: 115379--115440 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
115369 ATAGTTTTTA
*
115379 TATTTTTTATTATATAATTATATAAATAT
1 TATTTTTTATTAAATAATTATATAAATAT
* *
115408 TATTTTTTATTAAAATAA-TATTTATATAT
1 TATTTTTTATT-AAATAATTATATAAATAT
115437 TATT
1 TATT
115441 ATATTTAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 24 0.83
30 5 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (29 bp):
TATTTTTTATTAAATAATTATATAAATAT
Found at i:115454 original size:37 final size:38
Alignment explanation
Indices: 115413--115484 Score: 94
Period size: 37 Copynumber: 1.9 Consensus size: 38
115403 AATATTATTT
115413 TTTATTAAAATAA-TATTTATATATT-ATTATATTTAAA
1 TTTATT-AAATAATTATTTATATATTAATTATATTTAAA
* * *
115450 TTTATTAATTAATTATTTTTATGTTAATTATATTT
1 TTTATTAAATAATTATTTATATATTAATTATATTT
115485 TTTTGTCTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
36 5 0.17
37 16 0.53
38 9 0.30
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (38 bp):
TTTATTAAATAATTATTTATATATTAATTATATTTAAA
Found at i:115460 original size:22 final size:23
Alignment explanation
Indices: 115427--115470 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
115417 TTAAAATAAT
115427 ATTTATATATT-ATTATATTTAA
1 ATTTATATATTAATTATATTTAA
*
115449 ATTTAT-TAATTAATTATTTTTA
1 ATTTATAT-ATTAATTATATTTA
115471 TGTTAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
21 1 0.05
22 9 0.47
23 9 0.47
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
ATTTATATATTAATTATATTTAA
Found at i:115622 original size:28 final size:29
Alignment explanation
Indices: 115568--115627 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
115558 AATATGGTAA
115568 TATTTTTTATAATTAATGTTAATATTTAT
1 TATTTTTTATAATTAATGTTAATATTTAT
115597 TATTTTTT-TAATTTAAAT-TTAA-ATTTAT
1 TATTTTTTATAA-TT-AATGTTAATATTTAT
115625 TAT
1 TAT
115628 GAATTTATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
28 12 0.41
29 14 0.48
30 3 0.10
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (29 bp):
TATTTTTTATAATTAATGTTAATATTTAT
Found at i:115632 original size:17 final size:17
Alignment explanation
Indices: 115604--115650 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
115594 TATTATTTTT
115604 TTAATT-TAAATTTAAA
1 TTAATTATAAATTTAAA
* * *
115620 TTTATTATGAATTTATA
1 TTAATTATAAATTTAAA
115637 TTAATTATAAATTT
1 TTAATTATAAATTT
115651 TTATAATGTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
16 5 0.20
17 20 0.80
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
TTAATTATAAATTTAAA
Found at i:117281 original size:21 final size:21
Alignment explanation
Indices: 117255--117315 Score: 88
Period size: 21 Copynumber: 2.9 Consensus size: 21
117245 ATCTTCGCAG
*
117255 GGTTACATTCCTAGCCC-TCA
1 GGTTACATTCCTAGCCCGCCA
117275 TGGTTACATTCCTAGCCCGCCA
1 -GGTTACATTCCTAGCCCGCCA
*
117297 GGTTACATGCCTAGCCCGC
1 GGTTACATTCCTAGCCCGC
117316 AGAGTGTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 35 0.95
22 2 0.05
ACGTcount: A:0.18, C:0.36, G:0.20, T:0.26
Consensus pattern (21 bp):
GGTTACATTCCTAGCCCGCCA
Found at i:117799 original size:56 final size:58
Alignment explanation
Indices: 117728--117866 Score: 157
Period size: 56 Copynumber: 2.5 Consensus size: 58
117718 TTTATCCATA
*
117728 CGTAAAAA-ATGTCGATGCTCATTCCATTAAACC-A-ACTTATCACTTCATATTTATT
1 CGTAAAAACATGTCGATGCTCATTCCATTAAACCGAGACTTATCACTTCACATTTATT
**
117783 CGTAAAAACATGTCGATGCTCA-T---TTAGTCCTGAGTACTTATCACTTCACATTTATT
1 CGTAAAAACATGTCGATGCTCATTCCATTAAACC-GAG-ACTTATCACTTCACATTTATT
* * *
117839 CGTAAAAACATATCGATGTTTATTCCAT
1 CGTAAAAACATGTCGATGCTCATTCCAT
117867 ACAATTTCAA
Statistics
Matches: 69, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
52 5 0.07
54 1 0.01
55 9 0.13
56 52 0.75
57 1 0.01
60 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.37
Consensus pattern (58 bp):
CGTAAAAACATGTCGATGCTCATTCCATTAAACCGAGACTTATCACTTCACATTTATT
Found at i:117852 original size:28 final size:28
Alignment explanation
Indices: 117765--117852 Score: 70
Period size: 28 Copynumber: 3.1 Consensus size: 28
117755 TAAACCAACT
*
117765 TATCACTTCATATTTATTCGTAAAAACA
1 TATCACTTCACATTTATTCGTAAAAACA
* * * * * * ** *
117793 TGTCGA-TGCTCATTTAGTCCTGAGTACT
1 TATC-ACTTCACATTTATTCGTAAAAACA
117821 TATCACTTCACATTTATTCGTAAAAACA
1 TATCACTTCACATTTATTCGTAAAAACA
117849 TATC
1 TATC
117853 GATGTTTATT
Statistics
Matches: 39, Mismatches: 19, Indels: 4
0.63 0.31 0.06
Matches are distributed among these distances:
27 1 0.03
28 37 0.95
29 1 0.03
ACGTcount: A:0.32, C:0.20, G:0.09, T:0.39
Consensus pattern (28 bp):
TATCACTTCACATTTATTCGTAAAAACA
Found at i:118434 original size:125 final size:125
Alignment explanation
Indices: 118134--118719 Score: 724
Period size: 125 Copynumber: 4.8 Consensus size: 125
118124 CCATCCATCT
*
118134 ATAGTTCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCT-GACAAAATAA
1 ATAGTTCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT-TACACAAAATAA
* *
118198 TGGAAGGCGCACCCCCAGGAACGAGCCTTCA-AGTCCCCTCAGAAATAATAGGTACTGACATGA
65 TGGAAGGCGC-GCCCCAGGAACGCGCCTTCACA-T-CCCTCAGAAATAATAGGTACTGACATGA
* * *
118261 ATAATTTCCCAGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTTACACAAAATAAT
1 ATAGTTCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTTACACAAAATAAT
**
118326 GGAAGGCGCGCCCTGGGAACGCGCCTTCACTATCCC-CAGAAATAATAGGTACTGACATGA
66 GGAAGGCGCGCCCCAGGAACGCGCCTTCAC-ATCCCTCAGAAATAATAGGTACTGACATGA
118386 ATAGTTCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTTACACAAAATAAT
1 ATAGTTCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTTACACAAAATAAT
* * * * *
118451 GGAAGGCGCGTCCCTGAGAACGCGCCTTCA-ATCCCTAAGAAATATTAAGTACTGACATGA
66 GGAAGGCGCGCCCCAG-GAACGCGCCTTCACATCCCTCAGAAATAATAGGTACTGACATGA
*
118511 ATAGTTCCCC-GGGGACATGAGTGACATAATAGGGCAATGATAAC-TATTTTTACACAAAATAAT
1 ATAGTTCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTTACACAAAATAAT
* * *
118574 TGAAGGCGCG-CCCACGAAACGCGCCTTCACCAT---T------T--TGGGTACTGACATGA
66 GGAAGGCGCGCCCCA-GGAACGCGCCTTCA-CATCCCTCAGAAATAATAGGTACTGACATGA
* * * *
118624 ATAGTGCCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTATCT-GACAAAATA
1 ATAGT-TCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT-TACACAAAATA
* * * *
118688 ATGAAAGGTGCCCCCCAGGAACGCGCTTTCAC
64 ATGGAAGGCGCGCCCCAGGAACGCGCCTTCAC
118720 GTGAATAGTG
Statistics
Matches: 413, Mismatches: 33, Indels: 38
0.85 0.07 0.08
Matches are distributed among these distances:
113 18 0.04
114 4 0.01
115 35 0.08
116 33 0.08
117 5 0.01
121 1 0.00
122 15 0.04
123 28 0.07
124 41 0.10
125 130 0.31
126 33 0.08
127 69 0.17
128 1 0.00
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (125 bp):
ATAGTTCCCCGGGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTTACACAAAATAAT
GGAAGGCGCGCCCCAGGAACGCGCCTTCACATCCCTCAGAAATAATAGGTACTGACATGA
Found at i:119478 original size:23 final size:23
Alignment explanation
Indices: 119449--119496 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
119439 CACCGAATGT
119449 CACGTAGAATTGCACCGTAGTGC
1 CACGTAGAATTGCACCGTAGTGC
*
119472 CACGTAGAATTGCACTGTAGTGC
1 CACGTAGAATTGCACCGTAGTGC
119495 CA
1 CA
119497 TATAATATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.23
Consensus pattern (23 bp):
CACGTAGAATTGCACCGTAGTGC
Done.