Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015862.1 Corchorus capsularis cultivar CVL-1 contig15883, 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: 31409
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:330 original size:188 final size:189
Alignment explanation
Indices: 1--360 Score: 704
Period size: 188 Copynumber: 1.9 Consensus size: 189
1 TTTTCTTTTTCTTTTAACATGAATAAAAAAATTTACTATTATTCATGATGTGGGAAGGGAGAGAA
1 TTTTCTTTTTCTTTTAACATGAATAAAAAAATTTACTATTATTCATGATGTGGGAAGGGAGAGAA
*
66 AATGATGTGGCAAAATCTGATTGGCCCAAAATATTAGTAGAAAGACATTTTCAGGCAATGAAAAC
66 AATGATGTGGCAAAATCTGATTGGCCCAAAATATTAGTAGAAAGACATTTTCAGACAATGAAAAC
131 AGTGGAAAACAGGGAGTATTTTTTTAAAGGGCTCTGTTAACCTCTCGTGGCCCAGAAAG
131 AGTGGAAAACAGGGAGTATTTTTTTAAAGGGCTCTGTTAACCTCTCGTGGCCCAGAAAG
190 TTTTCTTTTTC-TTTAACATGAATAAAAAAATTTACTATTATTCATGATGTGGGAAGGGAGAGAA
1 TTTTCTTTTTCTTTTAACATGAATAAAAAAATTTACTATTATTCATGATGTGGGAAGGGAGAGAA
254 AATGATGTGGCAAAATCTGATTGGCCCAAAATATTAGTAGAAAGACATTTTCAGACAATGAAAAC
66 AATGATGTGGCAAAATCTGATTGGCCCAAAATATTAGTAGAAAGACATTTTCAGACAATGAAAAC
319 AGTGGAAAACAGGGAGTATTTTTTTAAAGGGCTCTGTTAACC
131 AGTGGAAAACAGGGAGTATTTTTTTAAAGGGCTCTGTTAACC
361 CCGGTTTTTT
Statistics
Matches: 170, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
188 159 0.94
189 11 0.06
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (189 bp):
TTTTCTTTTTCTTTTAACATGAATAAAAAAATTTACTATTATTCATGATGTGGGAAGGGAGAGAA
AATGATGTGGCAAAATCTGATTGGCCCAAAATATTAGTAGAAAGACATTTTCAGACAATGAAAAC
AGTGGAAAACAGGGAGTATTTTTTTAAAGGGCTCTGTTAACCTCTCGTGGCCCAGAAAG
Found at i:1768 original size:24 final size:25
Alignment explanation
Indices: 1708--1766 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
1698 TTCAAACCCT
* *
1708 AAACTTCATTTCTAACAACTTTTTC
1 AAACTTCATTTCTAACAACATCTTC
1733 AAACTTCATTTCTAACAA-ATCTTC
1 AAACTTCATTTCTAACAACATCTTC
1757 AAA-TTCATTT
1 AAACTTCATTT
1767 TCCTTCATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 7 0.22
24 7 0.22
25 18 0.56
ACGTcount: A:0.36, C:0.22, G:0.00, T:0.42
Consensus pattern (25 bp):
AAACTTCATTTCTAACAACATCTTC
Found at i:1800 original size:11 final size:11
Alignment explanation
Indices: 1786--1834 Score: 53
Period size: 11 Copynumber: 4.1 Consensus size: 11
1776 TTAATCATAA
1786 ACTAATTAAAT
1 ACTAATTAAAT
1797 ACTAATTAATCAT
1 ACTAATTAA--AT
*
1810 AAACTAATTAGAT
1 --ACTAATTAAAT
1823 ACTAATTAAAT
1 ACTAATTAAAT
1834 A
1 A
1835 TAAACTAATA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
11 20 0.62
13 4 0.12
15 8 0.25
ACGTcount: A:0.53, C:0.10, G:0.02, T:0.35
Consensus pattern (11 bp):
ACTAATTAAAT
Found at i:1805 original size:26 final size:26
Alignment explanation
Indices: 1776--1843 Score: 111
Period size: 26 Copynumber: 2.6 Consensus size: 26
1766 TTCCTTCATT
1776 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
1802 TTAATCATAAACTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
1828 TTAAAT-ATAAACTAAT
1 TT-AATCATAAACTAAT
1844 AAACTAAGTA
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
26 37 0.93
27 3 0.08
ACGTcount: A:0.53, C:0.10, G:0.01, T:0.35
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:1806 original size:15 final size:15
Alignment explanation
Indices: 1776--1819 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
1766 TTCCTTCATT
1776 TTAATCATAAACTAA
1 TTAATCATAAACTAA
1791 TTAA--AT--ACTAA
1 TTAATCATAAACTAA
1802 TTAATCATAAACTAA
1 TTAATCATAAACTAA
1817 TTA
1 TTA
1820 GATACTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
11 9 0.36
13 4 0.16
15 12 0.48
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.36
Consensus pattern (15 bp):
TTAATCATAAACTAA
Found at i:1843 original size:15 final size:14
Alignment explanation
Indices: 1776--1843 Score: 58
Period size: 15 Copynumber: 5.1 Consensus size: 14
1766 TTCCTTCATT
1776 TTAATCATAAACTAA
1 TTAAT-ATAAACTAA
1791 TTAA-AT--ACTAA
1 TTAATATAAACTAA
1802 TTAATCATAAACTAA
1 TTAAT-ATAAACTAA
*
1817 TT-AGAT--ACTAA
1 TTAATATAAACTAA
1828 TTAAATATAAACTAA
1 TT-AATATAAACTAA
1843 T
1 T
1844 AAACTAAGTA
Statistics
Matches: 43, Mismatches: 2, Indels: 16
0.70 0.03 0.26
Matches are distributed among these distances:
11 16 0.37
13 9 0.21
14 1 0.02
15 17 0.40
ACGTcount: A:0.53, C:0.10, G:0.01, T:0.35
Consensus pattern (14 bp):
TTAATATAAACTAA
Found at i:2232 original size:17 final size:17
Alignment explanation
Indices: 2210--2242 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
2200 AATTAGCTTG
2210 GAGATTTAAGAGGATTT
1 GAGATTTAAGAGGATTT
*
2227 GAGATTTCAGAGGATT
1 GAGATTTAAGAGGATT
2243 CATATGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.33
Consensus pattern (17 bp):
GAGATTTAAGAGGATTT
Found at i:2638 original size:23 final size:23
Alignment explanation
Indices: 2571--2688 Score: 86
Period size: 23 Copynumber: 5.3 Consensus size: 23
2561 AATCGCACTC
*
2571 TGAAATTTTGAT-AATC-ACACTA
1 TGAAATTTTGATAAATCTTC-CTA
*
2593 TG-AATTTGTGAT-AA-CCTCGCTA
1 TGAAATTT-TGATAAATCTTC-CTA
2615 TGAAATTTTGATAAATCTTCCTA
1 TGAAATTTTGATAAATCTTCCTA
* * * *
2638 TAAAATTTTAATAAACCTCCCTA
1 TGAAATTTTGATAAATCTTCCTA
* * *
2661 TAAAATTTTGATAACT-TTCTTA
1 TGAAATTTTGATAAATCTTCCTA
2683 TGAAAT
1 TGAAAT
2689 CTTGTTAACT
Statistics
Matches: 78, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
21 6 0.08
22 27 0.35
23 42 0.54
24 3 0.04
ACGTcount: A:0.37, C:0.14, G:0.08, T:0.40
Consensus pattern (23 bp):
TGAAATTTTGATAAATCTTCCTA
Found at i:2718 original size:60 final size:62
Alignment explanation
Indices: 2640--2757 Score: 152
Period size: 60 Copynumber: 1.9 Consensus size: 62
2630 TCTTCCTATA
*
2640 AAATTTTAATAAACCTCCCTATAAAATTTTGATAACTTTC-TTAT-GAAATCTTGTTAACTAC
1 AAATTTTAATAAACCTCCCTATAAAATTTTGATAAC-CTCATTATGGAAATCTTGTTAACTAC
* * ** *
2701 AAATTTTGAT-AACCTCCCTATGATTTTTTGATAACCTCATTATGGAAATTTTGTTAA
1 AAATTTTAATAAACCTCCCTATAAAATTTTGATAACCTCATTATGGAAATCTTGTTAA
2758 TCTCCCTATG
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
59 2 0.04
60 26 0.53
61 21 0.43
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.42
Consensus pattern (62 bp):
AAATTTTAATAAACCTCCCTATAAAATTTTGATAACCTCATTATGGAAATCTTGTTAACTAC
Found at i:2733 original size:128 final size:127
Alignment explanation
Indices: 2573--2803 Score: 302
Period size: 128 Copynumber: 1.8 Consensus size: 127
2563 TCGCACTCTG
* * *
2573 AAATTTTGATAATCACACTATGAATTTGTGATAACCTCGCTAT-GAAATTTTGATAAATCTTCCT
1 AAATTTTGATAACCACACTATGAATTTGTGATAACCTCACTATGGAAATTTTG-TAAATCTCCCT
*
2637 ATAAAATTTTAATAAACCTCCCTATAAAATTTTGATAACTTTCTTATGAAATCTTGTTAACTAC
65 ATAAAATTTTAATAAACCT-CCTATAAAATTTTGAAAACTTTCTTATGAAATCTTGTTAACTAC
* * * * * *
2701 AAATTTTGATAACCTCCCTATGATTTTTTGATAACCTCATTATGGAAATTTTGTTAATCTCCCTA
1 AAATTTTGATAACCACACTATGAATTTGTGATAACCTCACTATGGAAATTTTGTAAATCTCCCTA
* * * * *
2766 TGAAATTTTGATAACCCTCTTATGAAATTTTGAAAACT
66 TAAAATTTTAATAAACCTCCTATAAAATTTTGAAAACT
2804 AAACTATTAA
Statistics
Matches: 87, Mismatches: 15, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
127 17 0.20
128 61 0.70
129 9 0.10
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.41
Consensus pattern (127 bp):
AAATTTTGATAACCACACTATGAATTTGTGATAACCTCACTATGGAAATTTTGTAAATCTCCCTA
TAAAATTTTAATAAACCTCCTATAAAATTTTGAAAACTTTCTTATGAAATCTTGTTAACTAC
Found at i:2767 original size:23 final size:22
Alignment explanation
Indices: 2303--2861 Score: 193
Period size: 22 Copynumber: 25.6 Consensus size: 22
2293 ATGATCTCAT
* *
2303 TATGAAATTTCGATAACCTTCC
1 TATGAAATTTTGATAACCTCCC
* * ** *
2325 TATAAAATTTTAATAATGAT-AC
1 TATGAAATTTTGATAA-CCTCCC
* * ***
2347 TATGAAATTTCGAGAACCTTTT
1 TATGAAATTTTGATAACCTCCC
** * *
2369 TAT-AAATTTTTTTAACCTTCT
1 TATGAAATTTTGATAACCTCCC
*
2390 TATGAAATTTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTCCC
* * **
2412 TAAGCAATTTTGA-AGACCTCAA
1 TATGAAATTTTGATA-ACCTCCC
* *
2434 TATGAAATTTTGATAACTTTCC
1 TATGAAATTTTGATAACCTCCC
* * * *
2456 AATTAAATTTTGATAACCAACAC
1 TATGAAATTTTGATAACC-TCCC
* * * *
2479 TATGAGATGTTGATAATTCCTTCA
1 TATGAAATTTTGATAA--CCTCCC
* * **
2503 TATGATATATTGATAACCAT-GT
1 TATGAAATTTTGATAACC-TCCC
* * * * *
2525 TATGAAAATTTAAAAATCTCCA
1 TATGAAATTTTGATAACCTCCC
* * *
2547 TATG-AATTGTT-AGTAATCGCAC
1 TATGAAATT-TTGA-TAACCTCCC
* * * *
2569 TCTGAAATTTTGATAATCACAC
1 TATGAAATTTTGATAACCTCCC
*
2591 TATG-AATTTGTGATAACCTCGC
1 TATGAAATTT-TGATAACCTCCC
* *
2613 TATGAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AACCTCCC
* *
2636 TATAAAATTTTAATAAACCTCCC
1 TATGAAATTTTGAT-AACCTCCC
* * * *
2659 TATAAAATTTTGATAACTTTCT
1 TATGAAATTTTGATAACCTCCC
* *
2681 TATGAAATCTTGTTAA-----C
1 TATGAAATTTTGATAACCTCCC
*
2698 TA-CAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCTCCC
** **
2719 TATGATTTTTTGATAACCTCAT
1 TATGAAATTTTGATAACCTCCC
* *
2741 TATGGAAATTTTGTTAATCTCCC
1 TAT-GAAATTTTGATAACCTCCC
*
2764 TATGAAATTTTGATAACC-CTCT
1 TATGAAATTTTGATAACCTC-CC
* **
2786 TATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-CCC
* * *
2808 TATTAAATTTTAATATCCTCCC
1 TATGAAATTTTGATAACCTCCC
**
2830 --TGAAATTTTGATATGCTCCC
1 TATGAAATTTTGATAACCTCCC
2850 --TGAAATTTTGAT
1 TATGAAATTTTGAT
2862 CACTTCATAA
Statistics
Matches: 394, Mismatches: 115, Indels: 58
0.69 0.20 0.10
Matches are distributed among these distances:
16 10 0.03
17 2 0.01
20 29 0.07
21 35 0.09
22 220 0.56
23 82 0.21
24 14 0.04
25 2 0.01
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCC
Found at i:2859 original size:20 final size:20
Alignment explanation
Indices: 2812--2861 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
2802 CTAAACTATT
*
2812 AAATTTTAATATCCTCCCTG
1 AAATTTTGATATCCTCCCTG
*
2832 AAATTTTGATATGCTCCCTG
1 AAATTTTGATATCCTCCCTG
2852 AAATTTTGAT
1 AAATTTTGAT
2862 CACTTCATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.30, C:0.18, G:0.10, T:0.42
Consensus pattern (20 bp):
AAATTTTGATATCCTCCCTG
Found at i:3614 original size:26 final size:27
Alignment explanation
Indices: 3564--3614 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
3554 TGGACTTTCT
* * *
3564 TATAATTTAATTAATATACATATTATA
1 TATAATCTAATTAATATAAAAATTATA
3591 TATAATCTAA-TAATATAAAAATTA
1 TATAATCTAATTAATATAAAAATTA
3615 ATGACGAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 12 0.57
27 9 0.43
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (27 bp):
TATAATCTAATTAATATAAAAATTATA
Found at i:4124 original size:30 final size:31
Alignment explanation
Indices: 4089--4153 Score: 105
Period size: 30 Copynumber: 2.1 Consensus size: 31
4079 TGACAATTTA
* *
4089 GAAATATGTTTTAAAAA-AAGGGTACAATTG
1 GAAATATATTTTAAAAATAAGGGTACAATCG
4119 GAAATATATTTTAAAAATAAGGGTACAATCG
1 GAAATATATTTTAAAAATAAGGGTACAATCG
4150 GAAA
1 GAAA
4154 ACATAAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 16 0.50
31 16 0.50
ACGTcount: A:0.49, C:0.05, G:0.18, T:0.28
Consensus pattern (31 bp):
GAAATATATTTTAAAAATAAGGGTACAATCG
Found at i:4604 original size:35 final size:35
Alignment explanation
Indices: 4558--4629 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
4548 TGTAAACTCG
4558 GAGACACACACTAACAGAGTGTGACTAACTGAACT
1 GAGACACACACTAACAGAGTGTGACTAACTGAACT
4593 GAGACACACACTAACAGAGTGTGACTAACTGAACT
1 GAGACACACACTAACAGAGTGTGACTAACTGAACT
4628 GA
1 GA
4630 CTGACTCAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.40, C:0.22, G:0.21, T:0.17
Consensus pattern (35 bp):
GAGACACACACTAACAGAGTGTGACTAACTGAACT
Found at i:18059 original size:41 final size:41
Alignment explanation
Indices: 17997--18102 Score: 158
Period size: 41 Copynumber: 2.6 Consensus size: 41
17987 CTGGAGTAAC
*
17997 ACTTCTGGTGTTAAAGGTAATTTTAATTTACCAAAATGACA
1 ACTTCTGGTGTCAAAGGTAATTTTAATTTACCAAAATGACA
** *
18038 ACTTCTGGTGTCAAAAATAATTTTAATTTACCAAAGTGACA
1 ACTTCTGGTGTCAAAGGTAATTTTAATTTACCAAAATGACA
* *
18079 ACTTCTAGTATCAAAGGTAATTTT
1 ACTTCTGGTGTCAAAGGTAATTTT
18103 CAATATTATT
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (41 bp):
ACTTCTGGTGTCAAAGGTAATTTTAATTTACCAAAATGACA
Found at i:18164 original size:15 final size:16
Alignment explanation
Indices: 18138--18167 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
18128 AGATAACAAT
18138 ATAAACAACTTAAGAA
1 ATAAACAACTTAAGAA
18154 ATAAA-AACTTAAGA
1 ATAAACAACTTAAGA
18168 TTGGAAGATC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.63, C:0.10, G:0.07, T:0.20
Consensus pattern (16 bp):
ATAAACAACTTAAGAA
Found at i:19550 original size:78 final size:78
Alignment explanation
Indices: 19462--19708 Score: 406
Period size: 78 Copynumber: 3.2 Consensus size: 78
19452 GTTTTTGAAT
*
19462 TAAAATAGTAAAATGGTAAAATATAATAGTAATAAGGATATTATATTTAATTATATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTATATTTAATTATATAAAAATAGA
*
19527 GTTTTTAATTGAG
66 GTTTTTAGTTGAG
*
19540 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTAAATTTAATTATATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTATATTTAATTATATAAAAATAGA
19605 GTTTTTAGTTGAG
66 GTTTTTAGTTGAG
* * * *
19618 TGAAATAGTAAAATGGTAAAATAAAATAGTTATAAAGATATTATATTTAATTAAATAAAAATAGA
1 TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTATATTTAATTATATAAAAATAGA
*
19683 GTTTTTAGTTGAA
66 GTTTTTAGTTGAG
19696 TAAAACTA-TAAAA
1 TAAAA-TAGTAAAA
19709 AGTTAAATAA
Statistics
Matches: 158, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
78 156 0.99
79 2 0.01
ACGTcount: A:0.51, C:0.00, G:0.13, T:0.36
Consensus pattern (78 bp):
TAAAATAGTAAAATGGTAAAATATAATAGTTATAAGGATATTATATTTAATTATATAAAAATAGA
GTTTTTAGTTGAG
Found at i:20112 original size:7 final size:7
Alignment explanation
Indices: 20100--20132 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
20090 TGAATTTATT
20100 TGGCATG
1 TGGCATG
20107 TGGCATG
1 TGGCATG
20114 TGGCATG
1 TGGCATG
20121 TGGCATG
1 TGGCATG
20128 TGGCA
1 TGGCA
20133 CATCACACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.15, C:0.15, G:0.42, T:0.27
Consensus pattern (7 bp):
TGGCATG
Found at i:20276 original size:32 final size:32
Alignment explanation
Indices: 20234--20321 Score: 144
Period size: 32 Copynumber: 2.8 Consensus size: 32
20224 ATTTATGAAT
20234 TGAATT-GAACATGTTAAGGCTATATGTAACA
1 TGAATTGGAACATGTTAAGGCTATATGTAACA
20265 TGACA-TGGAACATGTTAAGGCTATATGTAACA
1 TGA-ATTGGAACATGTTAAGGCTATATGTAACA
*
20297 TGAATTGGAAAATGTTAAGGCTATA
1 TGAATTGGAACATGTTAAGGCTATA
20322 CCAATAAGGG
Statistics
Matches: 53, Mismatches: 1, Indels: 5
0.90 0.02 0.08
Matches are distributed among these distances:
31 5 0.09
32 48 0.91
ACGTcount: A:0.39, C:0.09, G:0.22, T:0.31
Consensus pattern (32 bp):
TGAATTGGAACATGTTAAGGCTATATGTAACA
Found at i:20546 original size:32 final size:32
Alignment explanation
Indices: 20505--20566 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
20495 TACCAAAAAA
20505 AAAATGTTAAGGCTATATGTAACATGAATTGG
1 AAAATGTTAAGGCTATATGTAACATGAATTGG
20537 AAAATGTTAAGGCTATATGTAACATGAATT
1 AAAATGTTAAGGCTATATGTAACATGAATT
20567 TATGTAGTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.32
Consensus pattern (32 bp):
AAAATGTTAAGGCTATATGTAACATGAATTGG
Found at i:26839 original size:22 final size:21
Alignment explanation
Indices: 26799--26843 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
26789 TTCAATATTC
*
26799 AATAAAAATAAATATTTTAAT
1 AATAAAAATAAATAATTTAAT
*
26820 AATAAAATATCAATAATTTAAT
1 AATAAAA-ATAAATAATTTAAT
26842 AA
1 AA
26844 GGTATTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (21 bp):
AATAAAAATAAATAATTTAAT
Found at i:26883 original size:17 final size:15
Alignment explanation
Indices: 26863--26905 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 15
26853 ATAATTTAAA
26863 TATTAACATATATATAT
1 TATTAA-ATATAT-TAT
26880 TATTAAATATATTAT
1 TATTAAATATATTAT
*
26895 TA-AAAATATAT
1 TATTAAATATAT
26906 AGGTGCTCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 8 0.32
15 5 0.20
16 6 0.24
17 6 0.24
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (15 bp):
TATTAAATATATTAT
Found at i:26905 original size:14 final size:12
Alignment explanation
Indices: 26874--26903 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
26864 ATTAACATAT
26874 ATATATTATTAA
1 ATATATTATTAA
26886 ATATATTATTAA
1 ATATATTATTAA
*
26898 AAATAT
1 ATATAT
26904 ATAGGTGCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (12 bp):
ATATATTATTAA
Found at i:28181 original size:3 final size:3
Alignment explanation
Indices: 28169--28198 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
28159 GCTCACGGAA
28169 GAT G-T GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT G
28199 GGGGAAATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:29292 original size:13 final size:12
Alignment explanation
Indices: 29262--29305 Score: 79
Period size: 12 Copynumber: 3.6 Consensus size: 12
29252 CATCGATACC
29262 TCGATATATCCG
1 TCGATATATCCG
29274 TCGATATATCCG
1 TCGATATATCCG
29286 TTCGATATATCCG
1 -TCGATATATCCG
29299 TCGATAT
1 TCGATAT
29306 CTGTATTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
12 19 0.61
13 12 0.39
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (12 bp):
TCGATATATCCG
Found at i:30949 original size:12 final size:12
Alignment explanation
Indices: 30932--30986 Score: 92
Period size: 12 Copynumber: 4.5 Consensus size: 12
30922 CATCGATACC
*
30932 TCGATATATTCG
1 TCGATATATCCG
30944 TCGATATATCCG
1 TCGATATATCCG
30956 TCGATATATCCG
1 TCGATATATCCG
30968 TTCGATATATCCG
1 -TCGATATATCCG
30981 TCGATA
1 TCGATA
30987 CCTGTATTAA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
12 29 0.71
13 12 0.29
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.36
Consensus pattern (12 bp):
TCGATATATCCG
Found at i:30977 original size:25 final size:24
Alignment explanation
Indices: 30932--30986 Score: 92
Period size: 25 Copynumber: 2.2 Consensus size: 24
30922 CATCGATACC
*
30932 TCGATATATTCGTCGATATATCCG
1 TCGATATATCCGTCGATATATCCG
30956 TCGATATATCCGTTCGATATATCCG
1 TCGATATATCCG-TCGATATATCCG
30981 TCGATA
1 TCGATA
30987 CCTGTATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 11 0.38
25 18 0.62
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.36
Consensus pattern (24 bp):
TCGATATATCCGTCGATATATCCG
Found at i:31119 original size:21 final size:21
Alignment explanation
Indices: 31076--31118 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
31066 CTTGAATGGA
31076 TTGCTAAACACCGTCCCCCTT
1 TTGCTAAACACCGTCCCCCTT
*
31097 TTGCTAAATACCG-CCCCCTT
1 TTGCTAAACACCGTCCCCCTT
31117 TT
1 TT
31119 TACACTTTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.19, C:0.40, G:0.09, T:0.33
Consensus pattern (21 bp):
TTGCTAAACACCGTCCCCCTT
Found at i:31219 original size:26 final size:25
Alignment explanation
Indices: 31189--31250 Score: 83
Period size: 24 Copynumber: 2.5 Consensus size: 25
31179 TTCAAACCCT
*
31189 AAACTTCATTTTCTAACAACTTCTTC
1 AAACTTCATTTTCTAACAA-ATCTTC
*
31215 AAACTTCA-TTACTAACAAATCTTC
1 AAACTTCATTTTCTAACAAATCTTC
31239 AAA-TTCATTTTC
1 AAACTTCATTTTC
31251 CTTCATTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
23 4 0.12
24 11 0.34
25 9 0.28
26 8 0.25
ACGTcount: A:0.35, C:0.24, G:0.00, T:0.40
Consensus pattern (25 bp):
AAACTTCATTTTCTAACAAATCTTC
Found at i:31287 original size:26 final size:26
Alignment explanation
Indices: 31258--31325 Score: 118
Period size: 26 Copynumber: 2.6 Consensus size: 26
31248 TTCCTTCATT
31258 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
31284 TTAATCATAAACTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
31310 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
31326 AAACTAAGTA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:31288 original size:15 final size:15
Alignment explanation
Indices: 31258--31325 Score: 62
Period size: 15 Copynumber: 5.1 Consensus size: 15
31248 TTCCTTCATT
31258 TTAATCATAAACTAA
1 TTAATCATAAACTAA
31273 TTAA--AT--ACTAA
1 TTAATCATAAACTAA
31284 TTAATCATAAACTAA
1 TTAATCATAAACTAA
*
31299 TT-A-GAT--ACTAA
1 TTAATCATAAACTAA
*
31310 TTAAACATAAACTAA
1 TTAATCATAAACTAA
31325 T
1 T
31326 AAACTAAGTA
Statistics
Matches: 43, Mismatches: 2, Indels: 16
0.70 0.03 0.26
Matches are distributed among these distances:
11 16 0.37
12 1 0.02
13 8 0.19
14 1 0.02
15 17 0.40
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34
Consensus pattern (15 bp):
TTAATCATAAACTAA
Done.