Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008265.1 Corchorus capsularis cultivar CVL-1 contig08286, 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: 62868
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:9721 original size:32 final size:32
Alignment explanation
Indices: 9636--9743 Score: 128
Period size: 32 Copynumber: 3.4 Consensus size: 32
9626 TCAGGCCGTT
*
9636 TTCGGGTTCGGGTTAAAGTTGGGTC-GGTTTGA
1 TTCGGGTTCGGGTTAAATTTGGGTCAGG-TTGA
* **
9668 TTCAGGTTCACGTTAAATTTGGGTCAGGTTGA
1 TTCGGGTTCGGGTTAAATTTGGGTCAGGTTGA
* * *
9700 TTCGGGTTCGGGTCAATTTTGGGTCAGGTTAA
1 TTCGGGTTCGGGTTAAATTTGGGTCAGGTTGA
*
9732 TTCGAGTTCGGG
1 TTCGGGTTCGGG
9744 CTCGGATTGG
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
32 62 0.97
33 2 0.03
ACGTcount: A:0.16, C:0.12, G:0.35, T:0.37
Consensus pattern (32 bp):
TTCGGGTTCGGGTTAAATTTGGGTCAGGTTGA
Found at i:10127 original size:19 final size:19
Alignment explanation
Indices: 10103--10139 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
10093 CTATTATTTT
10103 TTTTAATTT-AATATTTTAC
1 TTTTAATTTCAAT-TTTTAC
10122 TTTTAATTTCAATTTTTA
1 TTTTAATTTCAATTTTTA
10140 AATGTCAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTAATTTCAATTTTTAC
Found at i:10357 original size:19 final size:21
Alignment explanation
Indices: 10302--10385 Score: 82
Period size: 22 Copynumber: 4.0 Consensus size: 21
10292 TCTTGTCTCT
10302 ATGGTTATCAAAATTTCATAAG
1 ATGGTTATCAAAATTTCAT-AG
* *
10324 ATGGTTATTATAATTTCAT-G
1 ATGGTTATCAAAATTTCATAG
*
10344 A-GGTTATCAAAATTCCATAG
1 ATGGTTATCAAAATTTCATAG
* * *
10364 TGTGGTTACCAAAATTTTATAG
1 -ATGGTTATCAAAATTTCATAG
10386 GATCAGGTTA
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
19 14 0.28
20 3 0.06
22 33 0.66
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.39
Consensus pattern (21 bp):
ATGGTTATCAAAATTTCATAG
Found at i:10437 original size:22 final size:22
Alignment explanation
Indices: 10391--10439 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
10381 TATAGGATCA
*
10391 GGTTATTGAAATCTCTTAGGTT
1 GGTTATTGAAATCTCATAGGTT
*
10413 GGTTATTGAAATTTCATATGG-T
1 GGTTATTGAAATCTCATA-GGTT
10435 GGTTA
1 GGTTA
10440 ATTATCACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 22 0.92
23 2 0.08
ACGTcount: A:0.24, C:0.06, G:0.24, T:0.45
Consensus pattern (22 bp):
GGTTATTGAAATCTCATAGGTT
Found at i:10669 original size:25 final size:26
Alignment explanation
Indices: 10641--10689 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
10631 CCCATAGAGT
* *
10641 GATTATCGAAATTT-TATAAAGATCG
1 GATTATCAAAATTTATAGAAAGATCG
10666 GATTATCAAAATTTATAGAAAGAT
1 GATTATCAAAATTTATAGAAAGAT
10690 TATCAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 13 0.62
26 8 0.38
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (26 bp):
GATTATCAAAATTTATAGAAAGATCG
Found at i:10809 original size:22 final size:22
Alignment explanation
Indices: 10643--10835 Score: 101
Period size: 22 Copynumber: 8.6 Consensus size: 22
10633 CATAGAGTGA
*
10643 TTATCGAAATTTTATAAAGATCGG
1 TTATCAAAATTTTATAAAGA--GG
*
10667 ATTATCAAAA-TTTATAGAA-AGA
1 -TTATCAAAATTTTATA-AAGAGG
* *
10689 TTATCAAAATTTCAT--AGTATTG
1 TTATCAAAATTTTATAAAG-A-GG
* *
10711 TTATCAAAATTTCA-AAGCGAGG
1 TTATCAAAATTTTATAA-AGAGG
** * * *
10733 TTATCAAAATTACATAATGTGAT
1 TTATCAAAATTTTATAAAGAG-G
* * *
10756 TTATCAGAATTTCATATAGAGGGG
1 TTATCAAAATTT--TATAAAGAGG
* *
10780 TCAACAAAATTTTATAAAGAGG
1 TTATCAAAATTTTATAAAGAGG
*
10802 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTTATAAAGAGG
10824 TTATC-AAATTTT
1 TTATCAAAATTTT
10836 CAAAATGTGA
Statistics
Matches: 129, Mismatches: 27, Indels: 28
0.70 0.15 0.15
Matches are distributed among these distances:
19 1 0.01
21 16 0.12
22 67 0.52
23 13 0.10
24 17 0.13
25 15 0.12
ACGTcount: A:0.42, C:0.09, G:0.13, T:0.36
Consensus pattern (22 bp):
TTATCAAAATTTTATAAAGAGG
Found at i:10968 original size:20 final size:20
Alignment explanation
Indices: 10943--10992 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 20
10933 TTATGGAGTA
*
10943 ATCAAAATTTCAATG-AGGAT
1 ATCAAAATTTC-AGGAAGGAT
10963 ATCAAAA-TTCAGGAAGGAT
1 ATCAAAATTTCAGGAAGGAT
10982 ATCAAAATTTC
1 ATCAAAATTTC
10993 GTAGTCTAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 2 0.07
19 15 0.56
20 10 0.37
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.28
Consensus pattern (20 bp):
ATCAAAATTTCAGGAAGGAT
Found at i:11111 original size:22 final size:22
Alignment explanation
Indices: 10943--11418 Score: 142
Period size: 22 Copynumber: 22.0 Consensus size: 22
10933 TTATGGAGTA
* *
10943 ATCAAAATTTCA-A-TGAGGAT
1 ATCAAAATTTCATAGGGAGGTT
* *
10963 ATCAAAA-TTC--AGGAAGGAT
1 ATCAAAATTTCATAGGGAGGTT
* **
10982 ATCAAAATTTCGTAGTCTA-GTT
1 ATCAAAATTTCATAG-GGAGGTT
* * *
11004 TTCAAAATTTCACA-AGAGGGTT
1 ATCAAAATTTCATAGGGA-GGTT
* * *
11026 ATCAAAATTTCATA-GTATGTAG
1 ATCAAAATTTCATAGGGAGGT-T
*
11048 ATCAAAATTTCATAGGGAGATT
1 ATCAAAATTTCATAGGGAGGTT
* **
11070 AACAAAATTTCATAATGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
**
11092 ATCAAAAAATCATAGGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* *
11114 ATCAAGA-TT--T--GTA-GTT
1 ATCAAAATTTCATAGGGAGGTT
* * * **
11130 ATCAAGATTTCATAAGAAATTT
1 ATCAAAATTTCATAGGGAGGTT
11152 ATCAAAATATT-ATAGGGAGGTTT
1 ATCAAAAT-TTCATAGGGAGG-TT
* * *
11175 ATCGAAATTTTATAGTGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
** * * *
11197 ATCACGATTTCATAGTGTGATT
1 ATCAAAATTTCATAGGGAGGTT
* * ***
11219 ATCAAATTTTCATAGTGTTATT
1 ATCAAAATTTCATAGGGAGGTT
*
11241 A-CTAACAA-TTCATATGGAGGTT
1 ATC-AA-AATTTCATAGGGAGGTT
* * * ** *
11263 TTTAAATTTTCATAACGTGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * *
11285 ATCAATATATCATATGGAGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * ** *
11307 ATCAACATCTCATAGTGTTGATT
1 ATCAAAATTTCATAG-GGAGGTT
* * *
11330 ATCAAAATTTCATTGAGAAGTT
1 ATCAAAATTTCATAGGGAGGTT
** *
11352 ATCAAAATTTCATATTGTGGTT
1 ATCAAAATTTCATAGGGAGGTT
* * *
11374 TTCAAAA-TTCTTCGGGGAGGTT
1 ATCAAAATTTCAT-AGGGAGGTT
* * * *
11396 AACCAAATTTCATAAGAAGGTT
1 ATCAAAATTTCATAGGGAGGTT
11418 A
1 A
11419 AAAAAAATTA
Statistics
Matches: 328, Mismatches: 103, Indels: 48
0.68 0.22 0.10
Matches are distributed among these distances:
16 10 0.03
17 4 0.01
18 1 0.00
19 17 0.05
20 11 0.03
21 11 0.03
22 230 0.70
23 44 0.13
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.36
Consensus pattern (22 bp):
ATCAAAATTTCATAGGGAGGTT
Found at i:11182 original size:23 final size:23
Alignment explanation
Indices: 11149--11200 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
11139 TCATAAGAAA
11149 TTTATCAAAATATTATAGGGAGG
1 TTTATCAAAATATTATAGGGAGG
* * *
11172 TTTATCGAAATTTTATAGTGAGG
1 TTTATCAAAATATTATAGGGAGG
11195 -TTATCA
1 TTTATCA
11201 CGATTTCATA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 5 0.20
23 20 0.80
ACGTcount: A:0.35, C:0.06, G:0.19, T:0.40
Consensus pattern (23 bp):
TTTATCAAAATATTATAGGGAGG
Found at i:11739 original size:15 final size:16
Alignment explanation
Indices: 11711--11769 Score: 75
Period size: 16 Copynumber: 3.7 Consensus size: 16
11701 GAGTTCGGAT
11711 TTTTTCGGGTTTCAGA
1 TTTTTCGGGTTTCAGA
11727 TTTTTCGGG-TTCAGA
1 TTTTTCGGGTTTCAGA
* * *
11742 TTTTTTTGGGTTTGAGT
1 -TTTTTCGGGTTTCAGA
11759 TTTTTCGGGTT
1 TTTTTCGGGTT
11770 CGGGTTTGGG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
15 6 0.16
16 27 0.73
17 4 0.11
ACGTcount: A:0.08, C:0.08, G:0.27, T:0.56
Consensus pattern (16 bp):
TTTTTCGGGTTTCAGA
Found at i:11744 original size:32 final size:32
Alignment explanation
Indices: 11703--11770 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 32
11693 TCAGGTTTGA
*
11703 GTTCGGATTTTTTCGGGTTTCAGATTTTTCGG
1 GTTCAGATTTTTTCGGGTTTCAGATTTTTCGG
* * *
11735 GTTCAGATTTTTTTGGGTTTGAGTTTTTTCGG
1 GTTCAGATTTTTTCGGGTTTCAGATTTTTCGG
11767 GTTC
1 GTTC
11771 GGGTTTGGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.09, C:0.10, G:0.28, T:0.53
Consensus pattern (32 bp):
GTTCAGATTTTTTCGGGTTTCAGATTTTTCGG
Found at i:11776 original size:16 final size:16
Alignment explanation
Indices: 11703--11776 Score: 60
Period size: 16 Copynumber: 4.6 Consensus size: 16
11693 TCAGGTTTGA
*
11703 GTTCGGATTTTTTCGG
1 GTTCGGGTTTTTTCGG
* *
11719 GTTTC-AGATTTTTCGG
1 G-TTCGGGTTTTTTCGG
* * *
11735 GTTCAGATTTTTTTGG
1 GTTCGGGTTTTTTCGG
* *
11751 GTTTGAGTTTTTTCGG
1 GTTCGGGTTTTTTCGG
11767 GTTCGGGTTT
1 GTTCGGGTTT
11777 GGGTGGGTTC
Statistics
Matches: 42, Mismatches: 14, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
15 3 0.07
16 36 0.86
17 3 0.07
ACGTcount: A:0.08, C:0.09, G:0.30, T:0.53
Consensus pattern (16 bp):
GTTCGGGTTTTTTCGG
Found at i:16731 original size:11 final size:11
Alignment explanation
Indices: 16694--16731 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
16684 TTTCTATATA
*
16694 AAATAAATTAT
1 AAATTAATTAT
16705 CAAA-TAATTAT
1 -AAATTAATTAT
16716 AAATTAATTAT
1 AAATTAATTAT
16727 AAATT
1 AAATT
16732 TGTTTTGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:19894 original size:3 final size:3
Alignment explanation
Indices: 19886--19910 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
19876 ACGAAAGACA
19886 GAG GAG GAG GAG GAG GAG GAG GAG G
1 GAG GAG GAG GAG GAG GAG GAG GAG G
19911 GCTTACAGTT
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:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:21531 original size:17 final size:19
Alignment explanation
Indices: 21509--21546 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
21499 AGCAGATCCA
21509 TCCCTA-ATTT-TTCTTTT
1 TCCCTATATTTCTTCTTTT
*
21526 TCCCTATCTTTCTTCTTTT
1 TCCCTATATTTCTTCTTTT
21545 TC
1 TC
21547 ATTTTTCATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 3 0.17
19 9 0.50
ACGTcount: A:0.08, C:0.29, G:0.00, T:0.63
Consensus pattern (19 bp):
TCCCTATATTTCTTCTTTT
Found at i:26920 original size:30 final size:30
Alignment explanation
Indices: 26886--26952 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
26876 CAACAACCTC
* *
26886 CAATTTGAGATTGATGGTTGAAAACAGTAT
1 CAATTTGAGATTGATGATTGAAAACAATAT
*
26916 CAATTTGAGATTGATGATTGAAGACAATAT
1 CAATTTGAGATTGATGATTGAAAACAATAT
*
26946 AAATTTG
1 CAATTTG
26953 CACATCCAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.39, C:0.06, G:0.21, T:0.34
Consensus pattern (30 bp):
CAATTTGAGATTGATGATTGAAAACAATAT
Found at i:47996 original size:14 final size:14
Alignment explanation
Indices: 47977--48005 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
47967 ACAATAACTT
47977 AGAAGTAACAGCAA
1 AGAAGTAACAGCAA
47991 AGAAGTAACAGCAA
1 AGAAGTAACAGCAA
48005 A
1 A
48006 TGTTGATTTT
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:0.59, C:0.14, G:0.21, T:0.07
Consensus pattern (14 bp):
AGAAGTAACAGCAA
Found at i:48957 original size:17 final size:17
Alignment explanation
Indices: 48935--48970 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
48925 ACGTTGGACC
48935 AAAAAAAATTTGGTGCA
1 AAAAAAAATTTGGTGCA
48952 AAAAAAAATTTGGTGCA
1 AAAAAAAATTTGGTGCA
48969 AA
1 AA
48971 CATATTCCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.56, C:0.06, G:0.17, T:0.22
Consensus pattern (17 bp):
AAAAAAAATTTGGTGCA
Found at i:49263 original size:14 final size:14
Alignment explanation
Indices: 49244--49273 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
49234 TTGACAAGAT
49244 TAGAATCCCAAACA
1 TAGAATCCCAAACA
49258 TAGAATCCCAAACA
1 TAGAATCCCAAACA
49272 TA
1 TA
49274 TCAAGCAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.50, C:0.27, G:0.07, T:0.17
Consensus pattern (14 bp):
TAGAATCCCAAACA
Found at i:49364 original size:24 final size:24
Alignment explanation
Indices: 49335--49381 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
49325 CCTTGAGAAC
49335 CTATCAAGATCATTGACAAGATTT
1 CTATCAAGATCATTGACAAGATTT
49359 CTATCAAGATCATTGACAAGATT
1 CTATCAAGATCATTGACAAGATT
49382 CGAATCCTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (24 bp):
CTATCAAGATCATTGACAAGATTT
Found at i:53153 original size:1 final size:1
Alignment explanation
Indices: 53147--53171 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
53137 ATTACTTCTC
53147 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
53172 CCCTTTTACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:58387 original size:29 final size:26
Alignment explanation
Indices: 58316--58392 Score: 82
Period size: 27 Copynumber: 2.8 Consensus size: 26
58306 AGAGTCGCCT
*
58316 AGGGGCATTTTGATCATTTTCGCACCC
1 AGGGGCATTTTG-TCATTTTTGCACCC
* *
58343 AGGGGCATTTCGGTCATTTTTGCACTC
1 AGGGGCATTT-TGTCATTTTTGCACCC
58370 AGGAGGGCATTTTAGTCATTTTT
1 A-G-GGGCATTTT-GTCATTTTT
58393 TTAAGATCAC
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
27 23 0.55
28 2 0.05
29 17 0.40
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (26 bp):
AGGGGCATTTTGTCATTTTTGCACCC
Found at i:61270 original size:51 final size:50
Alignment explanation
Indices: 61145--61401 Score: 223
Period size: 51 Copynumber: 5.1 Consensus size: 50
61135 CCTTTTGCTA
* * * *
61145 AAAGATTTAACCTCTGAATAAAAGATTGAATTTTTTAAGTAAATTGGTAAAC
1 AAAGATTTAACTTTTGAATAAAAGATTGAA-TCTTTAAGT-AATTGGTAAAT
* * * **
61197 AAAAATGTCA-TGTTTGGGTAAAAGATTGAATCTTTAGAGTAATTGGTAAAT
1 AAAGATTTAACT-TTTGAATAAAAGATTGAATCTTTA-AGTAATTGGTAAAT
* *
61248 AAAGATTTAACTTTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAGT
1 AAAGATTTAACTTTTGAATAAAAGATTGAATCTTTAAGTAATTGGTAAAT
* * * * ** *
61298 AAAAATGTCA-TGTTCGGGTAAAAGATTGAATCTTTAGAGTGATTGGTAAAT
1 AAAGATTTAACT-TTTGAATAAAAGATTGAATCTTTA-AGTAATTGGTAAAT
* * * * *
61349 AAAGCTTTAACCTTGGAATGAAAGATTGAA-CTTTTAAGTAATTAGTAAAT
1 AAAGATTTAACTTTTGAATAAAAGATTGAATC-TTTAAGTAATTGGTAAAT
61399 AAA
1 AAA
61402 ATGTTACCTT
Statistics
Matches: 162, Mismatches: 36, Indels: 16
0.76 0.17 0.07
Matches are distributed among these distances:
49 1 0.01
50 56 0.35
51 79 0.49
52 26 0.16
ACGTcount: A:0.42, C:0.05, G:0.18, T:0.35
Consensus pattern (50 bp):
AAAGATTTAACTTTTGAATAAAAGATTGAATCTTTAAGTAATTGGTAAAT
Found at i:61320 original size:50 final size:51
Alignment explanation
Indices: 61163--61351 Score: 231
Period size: 51 Copynumber: 3.7 Consensus size: 51
61153 AACCTCTGAA
* *
61163 TAAAAGATTGAATTTTTTA-AGTAAATTGGTAAACAAAAATGTCATGTTTGGG
1 TAAAAGATTGAA-TCTTTAGAGT-AATTGGTAAATAAAAATGTCATGTTTGGG
* * * **
61215 TAAAAGATTGAATCTTTAGAGTAATTGGTAAATAAAGATTTAACT-TTTGAA
1 TAAAAGATTGAATCTTTAGAGTAATTGGTAAATAAAAATGTCA-TGTTTGGG
* * *
61266 TAAAAGATTGAATTTTTA-AGTAATTGGTAAGTAAAAATGTCATGTTCGGG
1 TAAAAGATTGAATCTTTAGAGTAATTGGTAAATAAAAATGTCATGTTTGGG
*
61316 TAAAAGATTGAATCTTTAGAGTGATTGGTAAATAAA
1 TAAAAGATTGAATCTTTAGAGTAATTGGTAAATAAA
61352 GCTTTAACCT
Statistics
Matches: 115, Mismatches: 18, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
49 1 0.01
50 40 0.35
51 58 0.50
52 16 0.14
ACGTcount: A:0.41, C:0.04, G:0.19, T:0.36
Consensus pattern (51 bp):
TAAAAGATTGAATCTTTAGAGTAATTGGTAAATAAAAATGTCATGTTTGGG
Found at i:61322 original size:101 final size:101
Alignment explanation
Indices: 61145--61402 Score: 399
Period size: 101 Copynumber: 2.5 Consensus size: 101
61135 CCTTTTGCTA
* *
61145 AAAGATTTAACCTCTGAATAAAAGATTGAATTTTTTAAGTAAATTGGTAAACAAAAATGTCATGT
1 AAAGATTTAACCTTTGAATAAAAGATTGAA-TTTTTAAGT-AATTGGTAAATAAAAATGTCATGT
*
61210 TTGGGTAAAAGATTGAATCTTTAGAGTAATTGGTAAAT
64 TCGGGTAAAAGATTGAATCTTTAGAGTAATTGGTAAAT
* *
61248 AAAGATTTAACTTTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAGTAAAAATGTCATGTTC
1 AAAGATTTAACCTTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAATAAAAATGTCATGTTC
*
61313 GGGTAAAAGATTGAATCTTTAGAGTGATTGGTAAAT
66 GGGTAAAAGATTGAATCTTTAGAGTAATTGGTAAAT
* * * * *
61349 AAAGCTTTAACCTTGGAATGAAAGATTGAACTTTTAAGTAATTAGTAAATAAAA
1 AAAGATTTAACCTTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAATAAAA
61403 TGTTACCTTT
Statistics
Matches: 142, Mismatches: 13, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
101 105 0.74
102 9 0.06
103 28 0.20
ACGTcount: A:0.42, C:0.05, G:0.18, T:0.35
Consensus pattern (101 bp):
AAAGATTTAACCTTTGAATAAAAGATTGAATTTTTAAGTAATTGGTAAATAAAAATGTCATGTTC
GGGTAAAAGATTGAATCTTTAGAGTAATTGGTAAAT
Found at i:62120 original size:47 final size:47
Alignment explanation
Indices: 62052--62258 Score: 301
Period size: 47 Copynumber: 4.4 Consensus size: 47
62042 AGTAAAAAGG
* *
62052 GGTAATCAGT-AATCAGTAAAAAGAGCTTAAACAGAGTCAAGGTGAT
1 GGTAATCAGTAAATCAGTAAAAAGAGATTAAACAAAGTCAAGGTGAT
* *
62098 GGTAATCAGTAAATCAGTAAAAAGAGATTAATCAAAGTCAAAGTGAT
1 GGTAATCAGTAAATCAGTAAAAAGAGATTAAACAAAGTCAAGGTGAT
* *
62145 GGTAATCAGTAAATCAGTAAGAAGAGATTAAACAGAGTCAAGGTGAT
1 GGTAATCAGTAAATCAGTAAAAAGAGATTAAACAAAGTCAAGGTGAT
* * *
62192 GGTAATCAATAAATCAGTAAAAA-AGATTAATCAAAAGTCAAGGTAAT
1 GGTAATCAGTAAATCAGTAAAAAGAGATTAAAC-AAAGTCAAGGTGAT
*
62239 AGTAATCAGTAAATCAGTAA
1 GGTAATCAGTAAATCAGTAA
62259 TCAAGTAAAA
Statistics
Matches: 144, Mismatches: 15, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
46 18 0.12
47 126 0.88
ACGTcount: A:0.48, C:0.09, G:0.20, T:0.23
Consensus pattern (47 bp):
GGTAATCAGTAAATCAGTAAAAAGAGATTAAACAAAGTCAAGGTGAT
Found at i:62198 original size:94 final size:94
Alignment explanation
Indices: 62052--62258 Score: 337
Period size: 94 Copynumber: 2.2 Consensus size: 94
62042 AGTAAAAAGG
* *
62052 GGTAATCAGT-AATCAGTAAAAAGAGCTTAAACAGAGTCAAGGTGATGGTAATCAGTAAATCAGT
1 GGTAATCAGTAAATCAGTAAAAAGAGATTAAACAGAGTCAAGGTGATGGTAATCAATAAATCAGT
*
62116 AAAAAGAGATTAATC-AAAGTCAAAGTGAT
66 AAAAA-AGATTAATCAAAAGTCAAAGTAAT
*
62145 GGTAATCAGTAAATCAGTAAGAAGAGATTAAACAGAGTCAAGGTGATGGTAATCAATAAATCAGT
1 GGTAATCAGTAAATCAGTAAAAAGAGATTAAACAGAGTCAAGGTGATGGTAATCAATAAATCAGT
*
62210 AAAAAAGATTAATCAAAAGTCAAGGTAAT
66 AAAAAAGATTAATCAAAAGTCAAAGTAAT
*
62239 AGTAATCAGTAAATCAGTAA
1 GGTAATCAGTAAATCAGTAA
62259 TCAAGTAAAA
Statistics
Matches: 106, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
93 19 0.18
94 87 0.82
ACGTcount: A:0.48, C:0.09, G:0.20, T:0.23
Consensus pattern (94 bp):
GGTAATCAGTAAATCAGTAAAAAGAGATTAAACAGAGTCAAGGTGATGGTAATCAATAAATCAGT
AAAAAAGATTAATCAAAAGTCAAAGTAAT
Found at i:62355 original size:32 final size:31
Alignment explanation
Indices: 62290--62355 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
62280 AGTAAATTGA
*
62290 TAATTAAGAGTCAAGGTAAGAAATTAATCAG
1 TAATTAAAAGTCAAGGTAAGAAATTAATCAG
62321 TAATTAAAAGTCAAGGTAA-AAATAGTAATCAG
1 TAATTAAAAGTCAAGGTAAGAAAT--TAATCAG
62353 TAA
1 TAA
62356 ATCAGTAATC
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 4 0.12
31 18 0.56
32 10 0.31
ACGTcount: A:0.52, C:0.06, G:0.17, T:0.26
Consensus pattern (31 bp):
TAATTAAAAGTCAAGGTAAGAAATTAATCAG
Found at i:62373 original size:71 final size:71
Alignment explanation
Indices: 62203--62374 Score: 174
Period size: 71 Copynumber: 2.4 Consensus size: 71
62193 GTAATCAATA
* * *
62203 AATCAGTAAAAAAGATTAATCAAAAGTCAAGGTAATAGTAATCAGTAAATCAGTAATCAAGTAAA
1 AATCAGT-AAATAGA-TAATCAAAAGTCAAGGTAAAAGTAATCAGTAAATCAGAAATCAAGTAAA
62268 AACATAGT
64 AACATAGT
* * * * *
62276 AATCAGTAAATTGATAATTAAGAGTCAAGGTAAGAAATTAATCAGT-AATTA-AAAGTCAAGGT-
1 AATCAGTAAATAGATAATCAAAAGTCAAGGT-A-AAAGTAATCAGTAAATCAGAAA-TCAA-GTA
62338 AAAA-ATAGT
62 AAAACATAGT
62347 AATCAGTAAATCAG-TAATCAAAAGTCAA
1 AATCAGTAAAT-AGATAATCAAAAGTCAA
62375 TGGATTGATC
Statistics
Matches: 83, Mismatches: 11, Indels: 12
0.78 0.10 0.11
Matches are distributed among these distances:
71 45 0.54
72 19 0.23
73 19 0.23
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (71 bp):
AATCAGTAAATAGATAATCAAAAGTCAAGGTAAAAGTAATCAGTAAATCAGAAATCAAGTAAAAA
CATAGT
Found at i:62497 original size:21 final size:22
Alignment explanation
Indices: 62473--62521 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
62463 GAGAGTAATC
*
62473 AGTAAAAGAAAAAT-GGTAAAG
1 AGTAAAAGAAAAATCAGTAAAG
*
62494 AGT-AAAGAATAATCAGTAAAG
1 AGTAAAAGAAAAATCAGTAAAG
62515 AGTAAAA
1 AGTAAAA
62522 TAGTAATCAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 12 0.50
22 3 0.12
ACGTcount: A:0.61, C:0.02, G:0.20, T:0.16
Consensus pattern (22 bp):
AGTAAAAGAAAAATCAGTAAAG
Found at i:62551 original size:35 final size:35
Alignment explanation
Indices: 62512--62597 Score: 109
Period size: 35 Copynumber: 2.5 Consensus size: 35
62502 ATAATCAGTA
62512 AAGAGTAAAATAGTAATCAGCAAAAGACAGCCATT
1 AAGAGTAAAATAGTAATCAGCAAAAGACAGCCATT
* * * ** *
62547 AAGAGTAAAATAGTGATCAGTAGAAGGTAGTCATT
1 AAGAGTAAAATAGTAATCAGCAAAAGACAGCCATT
*
62582 AAGAGTAAAACAGTAA
1 AAGAGTAAAATAGTAA
62598 CCAGTGAGAG
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.50, C:0.09, G:0.21, T:0.20
Consensus pattern (35 bp):
AAGAGTAAAATAGTAATCAGCAAAAGACAGCCATT
Found at i:62663 original size:22 final size:21
Alignment explanation
Indices: 62581--62668 Score: 79
Period size: 21 Copynumber: 4.1 Consensus size: 21
62571 AGGTAGTCAT
* *
62581 TAAGAGTAAAACAGTAACCAG
1 TAAGAGTAAAAGAGTAATCAG
* * * *
62602 TGAGAG-CAAAGTGGTAATTAG
1 TAAGAGTAAAAG-AGTAATCAG
* *
62623 TAAGAGTTAAATAGTAATCAG
1 TAAGAGTAAAAGAGTAATCAG
62644 TAAGAAGTAAAAGAGTAATCAG
1 TAAG-AGTAAAAGAGTAATCAG
62666 TAA
1 TAA
62669 AAAAGGAGCA
Statistics
Matches: 51, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
20 3 0.06
21 27 0.53
22 21 0.41
ACGTcount: A:0.49, C:0.07, G:0.23, T:0.22
Consensus pattern (21 bp):
TAAGAGTAAAAGAGTAATCAG
Found at i:62667 original size:15 final size:15
Alignment explanation
Indices: 62649--62704 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
62639 ATCAGTAAGA
62649 AGTAAAAGAGTAATC
1 AGTAAAAGAGTAATC
* * *
62664 AGTAAAAAAG-GAGC
1 AGTAAAAGAGTAATC
*
62678 AG-AAAATAGTAATC
1 AGTAAAAGAGTAATC
62692 AGTAAAAGAGTAA
1 AGTAAAAGAGTAA
62705 AATGGTAATC
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
13 6 0.19
14 8 0.25
15 18 0.56
ACGTcount: A:0.57, C:0.05, G:0.21, T:0.16
Consensus pattern (15 bp):
AGTAAAAGAGTAATC
Found at i:62748 original size:21 final size:21
Alignment explanation
Indices: 62686--62759 Score: 71
Period size: 22 Copynumber: 3.4 Consensus size: 21
62676 GCAGAAAATA
*
62686 GTAATCAGTAAAAGAGTAAAATG
1 GTAATCAG--AAAGAGTAAAAAG
*
62709 GTAATCAGTAAAAAGTAAAAAG
1 GTAATCAG-AAAGAGTAAAAAG
62731 GTAATCA-ACAAGAGTAAAATA-
1 GTAATCAGA-AAGAGTAAAA-AG
62752 GTAATCAG
1 GTAATCAG
62760 TACAAGATAA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
20 1 0.02
21 16 0.36
22 19 0.43
23 8 0.18
ACGTcount: A:0.54, C:0.07, G:0.19, T:0.20
Consensus pattern (21 bp):
GTAATCAGAAAGAGTAAAAAG
Done.