Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003528.1 Hibiscus syriacus cultivar Beakdansim tig00007450_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: 83097
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1433 original size:30 final size:30
Alignment explanation
Indices: 1393--1481 Score: 169
Period size: 30 Copynumber: 3.0 Consensus size: 30
1383 TATGGACAGT
1393 TTACCGAGGATCTTTATGACCTCTGGATAG
1 TTACCGAGGATCTTTATGACCTCTGGATAG
*
1423 TTATCGAGGATCTTTATGACCTCTGGATAG
1 TTACCGAGGATCTTTATGACCTCTGGATAG
1453 TTACCGAGGATCTTTATGACCTCTGGATA
1 TTACCGAGGATCTTTATGACCTCTGGATA
1482 TTCTTCGGGA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 57 1.00
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (30 bp):
TTACCGAGGATCTTTATGACCTCTGGATAG
Found at i:1946 original size:20 final size:22
Alignment explanation
Indices: 1908--1949 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1898 ATATGAAAGA
*
1908 TATATATATATATAGTATTTGT
1 TATATATATACATAGTATTTGT
1930 TATATATA-ACATA-TATTTGT
1 TATATATATACATAGTATTTGT
1950 AAGAAATGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 4 0.21
22 8 0.42
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.52
Consensus pattern (22 bp):
TATATATATACATAGTATTTGT
Found at i:5566 original size:18 final size:18
Alignment explanation
Indices: 5543--5578 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
5533 GTACCTTAGC
5543 CATATGAAGAGTGAGGTT
1 CATATGAAGAGTGAGGTT
5561 CATATGAAGAGTGAGGTT
1 CATATGAAGAGTGAGGTT
5579 GTATTTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.33, T:0.28
Consensus pattern (18 bp):
CATATGAAGAGTGAGGTT
Found at i:9193 original size:16 final size:16
Alignment explanation
Indices: 9168--9200 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
9158 TAATAAATAA
9168 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
9184 ACGAATATAAACGAAC
1 ACGAACATAAACGAAC
9200 A
1 A
9201 AAATTTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.21, G:0.12, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:9291 original size:16 final size:16
Alignment explanation
Indices: 9270--9329 Score: 102
Period size: 16 Copynumber: 3.8 Consensus size: 16
9260 TAATAAATAA
9270 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
9286 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
* *
9302 ATGAACATAAATGAAC
1 ACGAACATAAACGAAC
9318 ACGAACATAAAC
1 ACGAACATAAAC
9330 ATTGGAGACC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.57, C:0.22, G:0.12, T:0.10
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:9711 original size:14 final size:14
Alignment explanation
Indices: 9694--9787 Score: 96
Period size: 14 Copynumber: 7.3 Consensus size: 14
9684 AACGAACATA
9694 AACGAACATAACCG
1 AACGAACATAACCG
9708 AACGAACAT-A---
1 AACGAACATAACCG
* *
9718 AACAAACATAACCA
1 AACGAACATAACCG
9732 AACGAACATAACCG
1 AACGAACATAACCG
9746 AACGAACAT-A---
1 AACGAACATAACCG
*
9756 AACAAACATAACCG
1 AACGAACATAACCG
*
9770 AACAAACATAACCG
1 AACGAACATAACCG
9784 AACG
1 AACG
9788 TTCACGAACG
Statistics
Matches: 67, Mismatches: 5, Indels: 16
0.76 0.06 0.18
Matches are distributed among these distances:
10 16 0.24
11 2 0.03
13 2 0.03
14 47 0.70
ACGTcount: A:0.56, C:0.27, G:0.10, T:0.07
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:9711 original size:24 final size:24
Alignment explanation
Indices: 9674--9748 Score: 105
Period size: 24 Copynumber: 3.1 Consensus size: 24
9664 GATTGGGTTA
**
9674 AACATAAATAAACGAACATAAACG
1 AACATAACCAAACGAACATAAACG
* *
9698 AACATAACCGAACGAACATAAACA
1 AACATAACCAAACGAACATAAACG
*
9722 AACATAACCAAACGAACATAACCG
1 AACATAACCAAACGAACATAAACG
9746 AAC
1 AAC
9749 GAACATAAAC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.59, C:0.24, G:0.08, T:0.09
Consensus pattern (24 bp):
AACATAACCAAACGAACATAAACG
Found at i:9735 original size:38 final size:38
Alignment explanation
Indices: 9693--9787 Score: 172
Period size: 38 Copynumber: 2.5 Consensus size: 38
9683 AAACGAACAT
9693 AAACGAACATAACCGAACGAACATAAACAAACATAACC
1 AAACGAACATAACCGAACGAACATAAACAAACATAACC
9731 AAACGAACATAACCGAACGAACATAAACAAACATAACC
1 AAACGAACATAACCGAACGAACATAAACAAACATAACC
* *
9769 GAACAAACATAACCGAACG
1 AAACGAACATAACCGAACG
9788 TTCACGAACG
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 55 1.00
ACGTcount: A:0.57, C:0.26, G:0.09, T:0.07
Consensus pattern (38 bp):
AAACGAACATAACCGAACGAACATAAACAAACATAACC
Found at i:9758 original size:24 final size:24
Alignment explanation
Indices: 9681--9786 Score: 99
Period size: 24 Copynumber: 4.4 Consensus size: 24
9671 TTAAACATAA
*
9681 ATAAACGAACATAAACGAACATAAC
1 ATAAACGAACATAACCGAACA-AAC
** * *
9706 -CGAACGAACATAAACAAACATAAC
1 ATAAACGAACATAACCGAACA-AAC
* *
9730 -CAAACGAACATAACCGAACGAAC
1 ATAAACGAACATAACCGAACAAAC
*
9753 ATAAACAAACATAACCGAACAAAC
1 ATAAACGAACATAACCGAACAAAC
*
9777 ATAACCGAAC
1 ATAAACGAAC
9787 GTTCACGAAC
Statistics
Matches: 68, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
23 3 0.04
24 65 0.96
ACGTcount: A:0.58, C:0.25, G:0.08, T:0.08
Consensus pattern (24 bp):
ATAAACGAACATAACCGAACAAAC
Found at i:9773 original size:10 final size:10
Alignment explanation
Indices: 9681--9710 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
9671 TTAAACATAA
9681 ATAAACGAAC
1 ATAAACGAAC
9691 ATAAACGAAC
1 ATAAACGAAC
*
9701 ATAACCGAAC
1 ATAAACGAAC
9711 GAACATAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.57, C:0.23, G:0.10, T:0.10
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:12667 original size:31 final size:31
Alignment explanation
Indices: 12625--12747 Score: 117
Period size: 31 Copynumber: 4.0 Consensus size: 31
12615 TAACTAAACA
* *
12625 ACAATAAAATCTAAAGTGAGTGACTAAAATG
1 ACAAGAAAATCTAAAGTGAGTGATTAAAATG
* * *
12656 ACAACAAAATCTAAGGTGACTGATTAAAAT-
1 ACAAGAAAATCTAAAGTGAGTGATTAAAATG
* * * *
12686 ATAAAGAAAATTTAATGCGAGTGATTAAAATG
1 A-CAAGAAAATCTAAAGTGAGTGATTAAAATG
*
12718 -GAAGAAAATCTAACA-TGAGTGATTAAAATG
1 ACAAGAAAATCTAA-AGTGAGTGATTAAAATG
12748 CAAACAATGT
Statistics
Matches: 75, Mismatches: 14, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
30 26 0.35
31 49 0.65
ACGTcount: A:0.50, C:0.08, G:0.17, T:0.24
Consensus pattern (31 bp):
ACAAGAAAATCTAAAGTGAGTGATTAAAATG
Found at i:12725 original size:30 final size:30
Alignment explanation
Indices: 12689--12747 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
12679 TTAAAATATA
* **
12689 AAGAAAATTTAATGCGAGTGATTAAAATGG
1 AAGAAAATCTAACACGAGTGATTAAAATGG
*
12719 AAGAAAATCTAACATGAGTGATTAAAATG
1 AAGAAAATCTAACACGAGTGATTAAAATG
12748 CAAACAATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.49, C:0.05, G:0.20, T:0.25
Consensus pattern (30 bp):
AAGAAAATCTAACACGAGTGATTAAAATGG
Found at i:21774 original size:62 final size:62
Alignment explanation
Indices: 21677--21801 Score: 207
Period size: 62 Copynumber: 2.0 Consensus size: 62
21667 GTACGAGGCA
21677 TGGGAATGGTTGTGGAGAGTGAAGCCAAAGTTTTATGTCATTATCTTTGGAGAACTGCCATG
1 TGGGAATGGTTGTGGAGAGTGAAGCCAAAGTTTTATGTCATTATCTTTGGAGAACTGCCATG
** *
21739 TGGGAATGGTTGTGGAGAGTGAATTCATAA-TTTTATGTCATTATCTTTGGAGAACTGTCATG
1 TGGGAATGGTTGTGGAGAGTGAAGCCA-AAGTTTTATGTCATTATCTTTGGAGAACTGCCATG
21801 T
1 T
21802 AATACACTTA
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
62 57 0.97
63 2 0.03
ACGTcount: A:0.26, C:0.10, G:0.29, T:0.36
Consensus pattern (62 bp):
TGGGAATGGTTGTGGAGAGTGAAGCCAAAGTTTTATGTCATTATCTTTGGAGAACTGCCATG
Found at i:37265 original size:13 final size:13
Alignment explanation
Indices: 37247--37288 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
37237 GATTCGTGCT
37247 TTATGATTAATTA
1 TTATGATTAATTA
*
37260 TTATGATTAGTT-
1 TTATGATTAATTA
* *
37272 TGATCATTAATTA
1 TTATGATTAATTA
37285 TTAT
1 TTAT
37289 AAATTTTAAA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
12 9 0.39
13 14 0.61
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (13 bp):
TTATGATTAATTA
Found at i:42703 original size:20 final size:20
Alignment explanation
Indices: 42680--42852 Score: 224
Period size: 20 Copynumber: 8.6 Consensus size: 20
42670 CAGTTTCCAG
* ** *
42680 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
42700 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
42720 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
42740 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
42760 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
42780 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
42800 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGTATCCGT-A
*
42821 AATCGCAACGCTTATCCGTA
1 AATCGCAACGCGTATCCGTA
42841 AATCGCAACGCG
1 AATCGCAACGCG
42853 ATTTTTAAAG
Statistics
Matches: 136, Mismatches: 12, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
19 1 0.01
20 116 0.85
21 19 0.14
ACGTcount: A:0.36, C:0.28, G:0.18, T:0.17
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:42744 original size:60 final size:59
Alignment explanation
Indices: 42620--42852 Score: 215
Period size: 60 Copynumber: 3.9 Consensus size: 59
42610 ATGACCAACA
* ** ** *
42620 AAATCGCAACGCGAAATA--AAAATCGCAACGCGATCCCCAGAATCGCAAATCAGTTTCC--
1 AAATCGCAACGCG-AATACGAAAATCGCAACGCGAACCATA-AATCGCAACGC-GTATCCGT
*
42678 AGAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 A-AATCGCAACGCGAATACGAAAATCGCAACGCGAAC-CATAAATCGCAACGCGTATCCGT
* * * * *
42739 AAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGTAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATACGAAAATCGCAACGCG-AACCATAAATCGCAACGCGTATCCGT
* * *
42799 AAATCGCAACGAC-AATACGTAAAATCGCAACGCTTATCCGTAAATCGCAACGCG
1 AAATCGCAACG-CGAATACG-AAAATCGCAACGC-GAACCATAAATCGCAACGCG
42853 ATTTTTAAAG
Statistics
Matches: 149, Mismatches: 16, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
58 5 0.03
59 17 0.11
60 90 0.60
61 37 0.25
ACGTcount: A:0.37, C:0.28, G:0.18, T:0.17
Consensus pattern (59 bp):
AAATCGCAACGCGAATACGAAAATCGCAACGCGAACCATAAATCGCAACGCGTATCCGT
Found at i:43260 original size:33 final size:33
Alignment explanation
Indices: 43221--43291 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
43211 TTCACTTAGA
43221 TTTCATTTCGCGTTGCAATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTGCAATTCTCTCGTTGCGAT
**
43254 TTTCATTTCGCGTTGTTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTGCAATTCTCTCGTTGCGAT
43287 TTTCA
1 TTTCA
43292 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.23, G:0.17, T:0.49
Consensus pattern (33 bp):
TTTCATTTCGCGTTGCAATTCTCTCGTTGCGAT
Found at i:43397 original size:21 final size:21
Alignment explanation
Indices: 43371--43447 Score: 102
Period size: 21 Copynumber: 3.7 Consensus size: 21
43361 TGCAGAAGAG
43371 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
* **
43392 TCGCAACGCGA-AAATGACTA
1 TCGCAACGAGAGAAATGAAAA
43412 TCTGCAACGAGAGAAATGAAAA
1 TC-GCAACGAGAGAAATGAAAA
*
43434 TCACAACGAGAGAA
1 TCGCAACGAGAGAA
43448 TCGCAACGCG
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 9 0.19
21 29 0.62
22 9 0.19
ACGTcount: A:0.48, C:0.18, G:0.22, T:0.12
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:43454 original size:14 final size:14
Alignment explanation
Indices: 43432--43488 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
43422 GAGAAATGAA
*
43432 AATCACAACGAGAG
1 AATCGCAACGAGAG
*
43446 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
43465 AATCGCAACGAGAG
1 AATCGCAACGAGAG
43479 AATCGCAACG
1 AATCGCAACG
43489 CGAAACCAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.46, C:0.23, G:0.23, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:43462 original size:33 final size:33
Alignment explanation
Indices: 43424--43493 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
43414 TGCAACGAGA
43424 GAAATGAAAATCACAACGAGAGAATCGCAACGC
1 GAAATGAAAATCACAACGAGAGAATCGCAACGC
*
43457 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCACAACGAGAGAATCGCAACGC
43490 GAAA
1 GAAA
43494 CCAAAATCGC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.49, C:0.20, G:0.23, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCACAACGAGAGAATCGCAACGC
Found at i:43500 original size:33 final size:33
Alignment explanation
Indices: 43430--43504 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
43420 GAGAGAAATG
* **
43430 AAAATCACAACGAGAGAATCGCAACGCGAAATG
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
43463 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
43496 AAAATCGCA
1 AAAATCGCA
43505 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.48, C:0.24, G:0.20, T:0.08
Consensus pattern (33 bp):
AAAATCGCAACGAGAGAATCGCAACGCGAAACC
Found at i:43556 original size:20 final size:19
Alignment explanation
Indices: 43500--43559 Score: 75
Period size: 19 Copynumber: 3.1 Consensus size: 19
43490 GAAACCAAAA
*
43500 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
43519 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
43538 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
43558 TC
1 TC
43560 AACCAAAAGA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:45605 original size:19 final size:19
Alignment explanation
Indices: 45485--45599 Score: 141
Period size: 19 Copynumber: 6.3 Consensus size: 19
45475 TAGTTTACTT
* *
45485 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
45505 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
45524 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
45543 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
45557 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
45576 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
45595 TCGCA
1 TCGCA
45600 TTGCGATTTT
Statistics
Matches: 83, Mismatches: 7, Indels: 11
0.82 0.07 0.11
Matches are distributed among these distances:
14 9 0.11
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 55 0.66
20 13 0.16
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:45617 original size:19 final size:19
Alignment explanation
Indices: 45595--45753 Score: 175
Period size: 19 Copynumber: 8.6 Consensus size: 19
45585 GAAACCAAAA
*
45595 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
45614 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
45633 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
45649 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
45666 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
**
45685 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
* *
45704 TCTCGTTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
*
45723 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
45743 TCGTGTTGCGA
1 TCGCGTTGCGA
45754 AAGTAAACTA
Statistics
Matches: 119, Mismatches: 15, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
14 7 0.06
16 5 0.04
17 5 0.04
19 90 0.76
20 12 0.10
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:45662 original size:52 final size:54
Alignment explanation
Indices: 45600--45737 Score: 190
Period size: 52 Copynumber: 2.5 Consensus size: 54
45590 CAAAATCGCA
45600 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCATTGCGATTCT-G-TCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCATTGCGATTCTGGTTCG
** * *
45652 TTGCGATTTTCATTTCGCGTTGCGATTTTGGTTTCGCGTTGCGATTTTGGTTTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCATTGCGATTCTGG--T-TCG
*
45709 TTGCGATTCTCATTTCGCGTTGCGATTTT
1 TTGCGATTTTCATTTCGCGTTGCGATTTT
45738 AAGTTTCGTG
Statistics
Matches: 76, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
52 44 0.58
53 1 0.01
57 31 0.41
ACGTcount: A:0.09, C:0.20, G:0.23, T:0.48
Consensus pattern (54 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTCATTTCGCATTGCGATTCTGGTTCG
Found at i:47700 original size:14 final size:14
Alignment explanation
Indices: 47681--47716 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
47671 ATTGTTTAAT
47681 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
47695 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
47709 TGATTTGT
1 TGATTTGT
47717 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:47858 original size:19 final size:19
Alignment explanation
Indices: 47823--47920 Score: 127
Period size: 19 Copynumber: 5.4 Consensus size: 19
47813 AAAAATGACT
47823 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
47843 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
47862 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
47876 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
47895 ATCGCAATGCGGAAATG-AA
1 ATCGCAATGC-GAAATGAAA
47914 ATCGCAA
1 ATCGCAA
47921 CGAGAGAATC
Statistics
Matches: 70, Mismatches: 2, Indels: 13
0.82 0.02 0.15
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 38 0.54
20 16 0.23
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:47952 original size:52 final size:53
Alignment explanation
Indices: 47823--47939 Score: 211
Period size: 52 Copynumber: 2.2 Consensus size: 53
47813 AAAAATGACT
47823 ATCGCAATGCGGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
47876 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATG-AAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
47928 ATCGCAATGCGA
1 ATCGCAATGCGA
47940 TTTTCATTTC
Statistics
Matches: 63, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
52 47 0.75
53 16 0.25
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:47998 original size:53 final size:52
Alignment explanation
Indices: 47935--48152 Score: 311
Period size: 53 Copynumber: 4.1 Consensus size: 52
47925 AGAATCGCAA
47935 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
47988 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTCTCTCGT
*
48041 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCAT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG--T
*
48099 TGCGATTTTCA--T-G--TTGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
48146 TGCGATT
1 TGCGATT
48153 GTAATTTCCG
Statistics
Matches: 156, Mismatches: 3, Indels: 18
0.88 0.02 0.10
Matches are distributed among these distances:
47 8 0.05
49 2 0.01
50 2 0.01
51 3 0.02
52 10 0.06
53 110 0.71
54 3 0.02
55 3 0.02
56 3 0.02
58 12 0.08
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (52 bp):
TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:48016 original size:72 final size:71
Alignment explanation
Indices: 47929--48138 Score: 264
Period size: 72 Copynumber: 2.9 Consensus size: 71
47919 AACGAGAGAA
* * *
47929 TCGCAATGCGATTTTCATTT-CGCATTGCGATTTTCATTTCCGCA-TTGCGATTCTCTCGTTGCG
1 TCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCCG-ATTTGC-ATT-TCGCATTGCG
47992 ATTTTCATT
63 ATTTTCATT
* * *
48001 TCGCATTGCGATTTTCATTTCCGCATTGCGATTCTCTC-GTTGCGATTTTCATTTCGCATTGCGA
1 TCGCATTGCGATTTTCATTTCCGCATTGCGATT-T-TCATTTCCGATTTGCATTTCGCATTGCGA
48065 TTTTCATT
64 TTTTCATT
** *
48073 TCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATGTTGGGATTTTCATTTCGCATTGCGAT
1 TCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCAT-TTCCGATTTGCATTTCGCATTGCGAT
48138 T
65 T
48139 CTCTCGTTGC
Statistics
Matches: 124, Mismatches: 8, Indels: 12
0.86 0.06 0.08
Matches are distributed among these distances:
70 2 0.02
71 1 0.01
72 95 0.77
73 16 0.13
74 8 0.06
75 2 0.02
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (71 bp):
TCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCCGATTTGCATTTCGCATTGCGATT
TTCATT
Found at i:48160 original size:33 final size:33
Alignment explanation
Indices: 48006--48152 Score: 188
Period size: 33 Copynumber: 4.2 Consensus size: 33
47996 TCATTTCGCA
48006 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTT-CGCATTGCGATTCTCTCG
*
48040 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
*
48076 CATTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 --TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
48112 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
48145 TTGCGATT
1 TTGCGATT
48153 GTAATTTCCG
Statistics
Matches: 99, Mismatches: 6, Indels: 17
0.81 0.05 0.14
Matches are distributed among these distances:
32 1 0.01
33 32 0.32
34 29 0.29
35 3 0.03
36 6 0.06
37 3 0.03
38 15 0.15
39 10 0.10
ACGTcount: A:0.14, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:50441 original size:12 final size:12
Alignment explanation
Indices: 50424--50448 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
50414 TTCTTCGGGA
50424 CTTTTTCTTCTT
1 CTTTTTCTTCTT
50436 CTTTTTCTTCTT
1 CTTTTTCTTCTT
50448 C
1 C
50449 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:50662 original size:24 final size:23
Alignment explanation
Indices: 50623--50668 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
50613 CTGAAACATC
50623 ATCAAATCCGTGTATTGACCAAT
1 ATCAAATCCGTGTATTGACCAAT
50646 ATCAAAGTCCG-GATATTGACCAA
1 ATCAAA-TCCGTG-TATTGACCAA
50669 GACCAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (23 bp):
ATCAAATCCGTGTATTGACCAAT
Found at i:51387 original size:20 final size:20
Alignment explanation
Indices: 51359--51587 Score: 237
Period size: 20 Copynumber: 11.4 Consensus size: 20
51349 AAATTTCAGT
* * *
51359 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
51379 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
51399 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
51419 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
51439 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
51459 GTTGCGATTTACGGATAT-GC
1 GTTGCGATTTACGGAT-TCGC
* *
51479 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
51499 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* * *
51519 GTTGCGGTTTACGGATACGT
1 GTTGCGATTTACGGATTCGC
*
51539 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
51559 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
51579 GTTGCGATT
1 GTTGCGATT
51588 CTGGAAAATC
Statistics
Matches: 179, Mismatches: 26, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
20 178 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:60254 original size:182 final size:181
Alignment explanation
Indices: 59947--60311 Score: 583
Period size: 182 Copynumber: 2.0 Consensus size: 181
59937 AAATTAAATG
*
59947 TTTTTAATTGAAAAAAAGTTTATAATTAATTTAAATAATATATTATAAAATAAAAAATTTCAGAT
1 TTTTTAATTGAAAAAAAGTTTACAATTAATTTAAATAATATATTATAAAAT-AAAAATTTCAGAT
** *
60012 AATTTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTATTAGATCTTAAATTATTAATTGG
65 AAAATTTTTAATTAATTAATATTGACTTAGGTTTAAAAGTTATTAGATCTTAAATTATTAATTGG
*
60077 GTTTTAAATGGTTTGGGTTGAGCCCATATGTTATATATAATATATATAATAT
130 GTTTTAAATAGTTTGGGTTGAGCCCATATGTTATATATAATATATATAATAT
*
60129 TTTTTAATT-AAAAAACATTTTACAATTAATTTAAATAATATATAATTATAAAAT-AAAATTT-A
1 TTTTTAATTGAAAAAA-AGTTTACAATTAATTTAAAT-A-ATAT-ATTATAAAATAAAAATTTCA
* *
60191 TATAAAATTTTTAATTAATTAATATTGACTTAGGTTTAAAAGTTATTGGATCTTAAATTATTAAT
62 GATAAAATTTTTAATTAATTAATATTGACTTAGGTTTAAAAGTTATTAGATCTTAAATTATTAAT
*
60256 TGGGTTTTAAATAGTTTGGGTTGAGCCCATATGTTATATATAATATATTTAATAT
127 TGGGTTTTAAATAGTTTGGGTTGAGCCCATATGTTATATATAATATATATAATAT
60311 T
1 T
60312 GAAATTTAAT
Statistics
Matches: 170, Mismatches: 9, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
181 6 0.04
182 142 0.84
183 8 0.05
184 4 0.02
185 10 0.06
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.46
Consensus pattern (181 bp):
TTTTTAATTGAAAAAAAGTTTACAATTAATTTAAATAATATATTATAAAATAAAAATTTCAGATA
AAATTTTTAATTAATTAATATTGACTTAGGTTTAAAAGTTATTAGATCTTAAATTATTAATTGGG
TTTTAAATAGTTTGGGTTGAGCCCATATGTTATATATAATATATATAATAT
Found at i:64232 original size:2 final size:2
Alignment explanation
Indices: 64225--64280 Score: 112
Period size: 2 Copynumber: 28.0 Consensus size: 2
64215 AAACAAAGTA
64225 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
64267 AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG
64281 GTATAGATAA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 54 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:66842 original size:17 final size:16
Alignment explanation
Indices: 66816--66851 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
66806 TACAAATATA
66816 ATTACAAATAACTATC
1 ATTACAAATAACTATC
*
66832 ATTATCAAATAACTTTC
1 ATTA-CAAATAACTATC
66849 ATT
1 ATT
66852 CTTTCCAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.44, C:0.17, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTACAAATAACTATC
Found at i:75878 original size:20 final size:21
Alignment explanation
Indices: 75855--75897 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
75845 TTAATTGTTT
* *
75855 AATTTTAATTTTTTAT-TTAA
1 AATTTTAAATTTTAATCTTAA
75875 AATTTTAAATTTTAATCTTAA
1 AATTTTAAATTTTAATCTTAA
75896 AA
1 AA
75898 GTCTAATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (21 bp):
AATTTTAAATTTTAATCTTAA
Found at i:78397 original size:2 final size:2
Alignment explanation
Indices: 78390--78427 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
78380 ATAATCTTTA
78390 AT AT AT AT AT AT AT AT AT AT -T 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
78428 CACACACTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:78413 original size:17 final size:17
Alignment explanation
Indices: 78393--78426 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
78383 ATCTTTAATA
78393 TATATATATATATATAT
1 TATATATATATATATAT
78410 TATATATATATATATAT
1 TATATATATATATATAT
78427 ACACACACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATATATATATATAT
Found at i:78487 original size:2 final size:2
Alignment explanation
Indices: 78482--78513 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
78472 ATGTTTTTTA
78482 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
78514 TAAGTTTCTA
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:78645 original size:27 final size:27
Alignment explanation
Indices: 78596--78649 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
78586 ATTAAAATTA
*
78596 TTTAAAAGAATTATAAATTATTTCATAT
1 TTTAAAAGAATTATAAATAATTT-ATAT
78624 TTTAAAAGAA-TA-AACATAATTTATAT
1 TTTAAAAGAATTATAA-ATAATTTATAT
78650 ATAAAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 6 0.25
27 8 0.33
28 10 0.42
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.43
Consensus pattern (27 bp):
TTTAAAAGAATTATAAATAATTTATAT
Done.