Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015771.1 Corchorus olitorius cultivar O-4 contig15804, 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: 52123
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:767 original size:150 final size:151
Alignment explanation
Indices: 494--765 Score: 406
Period size: 149 Copynumber: 1.8 Consensus size: 151
484 TAAAAATTCT
* * *
494 ATTAAATACTTGGATATATTAAAATTTTTTAATACACAATTTTATTCTACTAAAAACTCTATTTT
1 ATTAAAAACTTGGATATATTAAAATTTTTTAATACACAAGTTTATTCCACTAAAAACTCTATTTT
* * * * *
559 TATTTAATTAAATTCAATATTTTTATAATTATTTTATTTTTAAAATTTTAATTTAAAAGTTTACT
66 CATTGAATTAAAGTCAAAATATTTATAATTATTTTATTTTTAAAATTTTAATTTAAAAGTTTACT
624 TTTACGATTTTACTATTTTTC
131 TTTACGATTTTACTATTTTTC
* *
645 ATTAAAAACTTGTATATATT-AAATTTTTTCAATATAC-AGTTTATTCCACTAAAAACTCTATTT
1 ATTAAAAACTTGGATATATTAAAATTTTTT-AATACACAAGTTTATTCCACTAAAAACTCTATTT
**
708 TCATTGAATT-AAGTCAAAATATTTATAATTATTTTATTTTTACCATTTTAATTTAAAA
65 TCATTGAATTAAAGTCAAAATATTTATAATTATTTTATTTTTAAAATTTTAATTTAAAA
766 AGGTTTTTGT
Statistics
Matches: 108, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
149 43 0.40
150 41 0.38
151 24 0.22
ACGTcount: A:0.38, C:0.09, G:0.03, T:0.50
Consensus pattern (151 bp):
ATTAAAAACTTGGATATATTAAAATTTTTTAATACACAAGTTTATTCCACTAAAAACTCTATTTT
CATTGAATTAAAGTCAAAATATTTATAATTATTTTATTTTTAAAATTTTAATTTAAAAGTTTACT
TTTACGATTTTACTATTTTTC
Found at i:797 original size:150 final size:149
Alignment explanation
Indices: 494--801 Score: 365
Period size: 150 Copynumber: 2.0 Consensus size: 149
484 TAAAAATTCT
* * *
494 ATTAAATACTTGGATATATTAAAATTTTTTAATACACAATTTTATTCTACTAAAAACTCTATTTT
1 ATTAAAAACTTGGATATATTAAAATTTTTTAATACACAAGTTTATTCCACTAAAAACTCTATTTT
* * * * *
559 TATTTAATTAAATTCAATATTTTTATAATTATTTTATTTTTAAAATTTTAATTTAAAAGTTTACT
66 CATTGAATTAAAGTCAAAATATTTATAATTATTTTATTTTTAAAATTTTAATTTAAAAGTTTA-T
* * * *
624 TTTACGATTTTACTATTTTTC
130 TTGAC-ATGTTAATATTTGTC
* *
645 ATTAAAAACTTGTATATATT-AAATTTTTTCAATATAC-AGTTTATTCCACTAAAAACTCTATTT
1 ATTAAAAACTTGGATATATTAAAATTTTTT-AATACACAAGTTTATTCCACTAAAAACTCTATTT
**
708 TCATTGAATT-AAGTCAAAATATTTATAATTATTTTATTTTTACCATTTTAATTTAAAAAGGTTT
65 TCATTGAATTAAAGTCAAAATATTTATAATTATTTTATTTTTAAAATTTTAATTT-AAAA-GTTT
772 -TTGTGA-ATAGTTAATATATTGTC
128 ATT-TGACAT-GTTAATAT-TTGTC
795 ATTAAAA
1 ATTAAAA
802 TTTATTATTT
Statistics
Matches: 135, Mismatches: 16, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
148 2 0.01
149 47 0.35
150 58 0.43
151 28 0.21
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.50
Consensus pattern (149 bp):
ATTAAAAACTTGGATATATTAAAATTTTTTAATACACAAGTTTATTCCACTAAAAACTCTATTTT
CATTGAATTAAAGTCAAAATATTTATAATTATTTTATTTTTAAAATTTTAATTTAAAAGTTTATT
TGACATGTTAATATTTGTC
Found at i:1067 original size:15 final size:15
Alignment explanation
Indices: 1047--1100 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
1037 CGCTCAAATG
1047 TCGGGTCATTTGGGT
1 TCGGGTCATTTGGGT
** ** *
1062 TCGGGTCGCTCAGAT
1 TCGGGTCATTTGGGT
1077 GTCGGGTCATTTGGGT
1 -TCGGGTCATTTGGGT
1093 TCGGGTCA
1 TCGGGTCA
1101 ATTCTGGTTT
Statistics
Matches: 28, Mismatches: 10, Indels: 2
0.70 0.25 0.05
Matches are distributed among these distances:
15 18 0.64
16 10 0.36
ACGTcount: A:0.09, C:0.19, G:0.39, T:0.33
Consensus pattern (15 bp):
TCGGGTCATTTGGGT
Found at i:1095 original size:31 final size:31
Alignment explanation
Indices: 1025--1099 Score: 123
Period size: 31 Copynumber: 2.4 Consensus size: 31
1015 TTCAGTTTGG
* *
1025 TTGGGTTCAGATCGCTCAAATGTCGGGTCAT
1 TTGGGTTCGGGTCGCTCAAATGTCGGGTCAT
*
1056 TTGGGTTCGGGTCGCTCAGATGTCGGGTCAT
1 TTGGGTTCGGGTCGCTCAAATGTCGGGTCAT
1087 TTGGGTTCGGGTC
1 TTGGGTTCGGGTC
1100 AATTCTGGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.12, C:0.19, G:0.36, T:0.33
Consensus pattern (31 bp):
TTGGGTTCGGGTCGCTCAAATGTCGGGTCAT
Found at i:2755 original size:439 final size:432
Alignment explanation
Indices: 1705--2779 Score: 1242
Period size: 439 Copynumber: 2.5 Consensus size: 432
1695 CGGGTCTTTC
* * * * *
1705 ATGAAAGTTGTATATCATAAAATTACCTTTTAATAAACACCTGAATTACCTTAATTGGACAAATA
1 ATGAAAGTTGTATATCATGAAATTACCTTTTAATAGACACATGAATCAACTTAATTGGACAAATA
* *
1770 GAACCAAAAAAAATAAAAATAAAATGAA-GTGTTAAATGGAGTAAGATAGAATTTGTAAAGGACT
66 GAA--AAAAATAA-AAAAATAAAAGGAACGTGTTAAAT---GTAAGATAGAATTTGTAAAGGACT
* * * * *
1834 AAGTAGCATAAAATAGAAAAGTATGAGGGTGATTTGATAACTAATTCAAATAAGAAAATATTTGT
125 AAGTAGCATAAAGTAAAAAAGTATGAGGGTCA-TTGATAAATAATCCAAATAAGAAAATATTTGT
1899 TAATGGAGATCTTGAAACATAAAAATTCCCTTTTGAACCCTTCATGAAACTCGTAGATCAAATTA
189 TAATGGAGATCTTGAAACATAAAAATTCCCTTTTGAACCCTTCATGAAACTCGTAGATCAAATTA
* * * * * *
1964 ACTTTCGGGTTCTTCATGAAAGTCGTAGATTATACATTAACCTTTTAAACACTTGAATAACTTTA
254 ACTTTCCGGTTCTTCATGAAAGTCGTAAATCATACAATAACCTTTTAAACACTTCAATAACTTCA
* * * *
2029 ATTGGACATGTGGATCGAAAATTATATAGTATTAAATAGACCAACAATCGAAAAGAACAAATTTC
319 ATCGGACATGTGGATCAAAAATTATAGAGTATTAAATAGACCAACAATCGAAAACAACAAATTTC
* * *
2094 GGAAACATTTTTTTGAATTAAAACATAAAAATTTGCTTTTCAGTCCTTT
384 GGAAACATTTTTTAGAATCAAAACATAAAAATTTGCTTTTCAGTCCTTA
* * * * *
2143 ATGAAAGCTGTAGATCATGAAATTACCTTTTAATAGACACATAAATCAACTTAATCGGATAAATA
1 ATGAAAGTTGTATATCATGAAATTACCTTTTAATAGACACATGAATCAACTTAATTGGACAAATA
* *
2208 GAACAAAGAATAAAAAAAT-AAAGTTTAAAC--GTTAGAT-TAAGATAGAATTTGTAAAGGACTA
66 GAA-AAA-AATAAAAAAATAAAAG---GAACGTGTTAAATGTAAGATAGAATTTGTAAAGGACTA
* * * *
2269 AGTAGTATAAAGTAAAAAAATATGAGGGTCATTTGATATATAATCCAAATAAGAAAATGTTTGTT
126 AGTAGCATAAAGTAAAAAAGTATGAGGGTCA-TTGATAAATAATCCAAATAAGAAAATATTTGTT
2334 AATGGAGATCTTGAAACATAAAAATTCCCTTTTGAACCCTTCATGAAACTCGTAGATCAAATTTA
190 AATGGAGATCTTGAAACATAAAAATTCCCTTTTGAACCCTTCATGAAACTCGTAGATCAAA-TTA
* *
2399 GCTTTCCGGTTCTTCATGAAAGTCGTAAATCATGCAATAACCTTTTAACCGACACTTCAATAACT
254 ACTTTCCGGTTCTTCATGAAAGTCGTAAATCATACAATAACCTTTTAA---ACACTTCAATAACT
** *
2464 TCAATCGGACATGTGGA-CAAAAAAATTATACGA-TATTAAATTA-ACCGGCAATC-AAAACCAC
316 TCAATCGGACATGTGGATC--AAAAATTATA-GAGTATTAAA-TAGACCAACAATCGAAAACAAC
** * * *
2525 AAAATTTCGGAAGTATTTTTTAGAATCAAAACATTAAAA-TTGACTTTTGAGTTCTTA
377 -AAATTTCGGAAACATTTTTTAGAATCAAAACATAAAAATTTG-CTTTTCAGTCCTTA
* * * * *
2582 ATGAAAATTGTATATCATGAAACTATCTTTTAATAGACACTTGAATCATCTTAATTGGACAAATA
1 ATGAAAGTTGTATATCATGAAATTACCTTTTAATAGACACATGAATCAACTTAATTGGACAAATA
* ** *
2647 GAAAAAAATACAAAAATAAAAGGCAACGTGTTAAATCGTCCAACCTATAA-TTGTAAAGGACTAA
66 GAAAAAAATAAAAAAATAAAAGG-AACGTGTTAAAT-GT--AAGATAGAATTTGTAAAGGACTAA
* * * * * * *
2711 ATAGCATAAAGCATAAAAGTATGAGGATCA-AGATAAATAATCCAACA-AA-AAAATATTAGTTT
127 GTAGCATAAAGTAAAAAAGTATGAGGGTCATTGATAAATAATCCAA-ATAAGAAAATATTTGTTA
2773 ATGGAGA
191 ATGGAGA
2780 ATGGGACACA
Statistics
Matches: 540, Mismatches: 73, Indels: 48
0.82 0.11 0.07
Matches are distributed among these distances:
434 141 0.26
435 45 0.08
436 6 0.01
437 21 0.04
438 135 0.25
439 143 0.26
440 5 0.01
441 38 0.07
442 6 0.01
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.30
Consensus pattern (432 bp):
ATGAAAGTTGTATATCATGAAATTACCTTTTAATAGACACATGAATCAACTTAATTGGACAAATA
GAAAAAAATAAAAAAATAAAAGGAACGTGTTAAATGTAAGATAGAATTTGTAAAGGACTAAGTAG
CATAAAGTAAAAAAGTATGAGGGTCATTGATAAATAATCCAAATAAGAAAATATTTGTTAATGGA
GATCTTGAAACATAAAAATTCCCTTTTGAACCCTTCATGAAACTCGTAGATCAAATTAACTTTCC
GGTTCTTCATGAAAGTCGTAAATCATACAATAACCTTTTAAACACTTCAATAACTTCAATCGGAC
ATGTGGATCAAAAATTATAGAGTATTAAATAGACCAACAATCGAAAACAACAAATTTCGGAAACA
TTTTTTAGAATCAAAACATAAAAATTTGCTTTTCAGTCCTTA
Found at i:3267 original size:2 final size:2
Alignment explanation
Indices: 3205--3253 Score: 82
Period size: 2 Copynumber: 25.0 Consensus size: 2
3195 TTGTTAGGCA
*
3205 AT AT AT AT AT AT AT AT AT AT AT AT AT AC 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 AT AT AT AT
3247 AT -T AT AT
1 AT AT AT AT
3254 GTTAAGTAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4902 original size:10 final size:10
Alignment explanation
Indices: 4887--4936 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 10
4877 CCGTTTAATA
4887 ATTATATATT
1 ATTATATATT
4897 ATTATATATGT
1 ATTATATAT-T
4908 AATTATAT-TT
1 -ATTATATATT
4918 ATCTA-ATATT
1 AT-TATATATT
*
4928 ATTTTATAT
1 ATTATATAT
4937 ATAAAAAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
9 5 0.15
10 20 0.59
11 2 0.06
12 7 0.21
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (10 bp):
ATTATATATT
Found at i:4946 original size:21 final size:21
Alignment explanation
Indices: 4922--4962 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
4912 ATATTTATCT
*
4922 AATAT-TATTTTATATATAAAA
1 AATATATATTTAAT-TATAAAA
4943 AATATATATTTAATTATAAA
1 AATATATATTTAATTATAAA
4963 TATTACTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AATATATATTTAATTATAAAA
Found at i:9095 original size:22 final size:21
Alignment explanation
Indices: 9043--9096 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
9033 TACTTCTTGA
9043 AATAATTCTTC-AATGATCTTC
1 AATAA-TCTTCAAATGATCTTC
*
9064 -A-AATCTTCAAATTATCTTC
1 AATAATCTTCAAATGATCTTC
9083 AATAAGTCTTCAAA
1 AATAA-TCTTCAAA
9097 CATGAACTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (21 bp):
AATAATCTTCAAATGATCTTC
Found at i:10610 original size:19 final size:20
Alignment explanation
Indices: 10572--10612 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
10562 TCAAGGAAAA
*
10572 TTCTGCTCCTCTTTGTTAAT
1 TTCTGCTCCTATTTGTTAAT
*
10592 TTCTGCTCTTATTTG-TAAT
1 TTCTGCTCCTATTTGTTAAT
10611 TT
1 TT
10613 GTTTTATTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.12, C:0.20, G:0.10, T:0.59
Consensus pattern (20 bp):
TTCTGCTCCTATTTGTTAAT
Found at i:11283 original size:51 final size:50
Alignment explanation
Indices: 11199--11372 Score: 192
Period size: 50 Copynumber: 3.5 Consensus size: 50
11189 TTTGAGGAAG
* *
11199 TTTTTCCTCTTCGTATTTTGTTTGACGCTACAAATATCTGTTGTATTTTGT
1 TTTTTCCTCTTTGTATTTTGTTTGA-GCTACAAATATATGTTGTATTTTGT
* * * *
11250 TTTTTTCTCTTTGTATTTTGTTTAGAGCAACAAATATGTGTTGTATTTT-A
1 TTTTTCCTCTTTGTATTTTGTTT-GAGCTACAAATATATGTTGTATTTTGT
* * * *
11300 TTTTTCCTCTTTGCATTTTGTTTGAAGCTGCAAATATATGTTATATATTG-
1 TTTTTCCTCTTTGTATTTTGTTTG-AGCTACAAATATATGTTGTATTTTGT
*
11350 TTTTT-CTCCTTTATATTTTGTTT
1 TTTTTCCT-CTTTGTATTTTGTTT
11373 ATTTTGCTCA
Statistics
Matches: 105, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
49 3 0.03
50 58 0.55
51 42 0.40
52 2 0.02
ACGTcount: A:0.18, C:0.12, G:0.13, T:0.57
Consensus pattern (50 bp):
TTTTTCCTCTTTGTATTTTGTTTGAGCTACAAATATATGTTGTATTTTGT
Found at i:20057 original size:28 final size:28
Alignment explanation
Indices: 20019--20095 Score: 82
Period size: 36 Copynumber: 2.5 Consensus size: 28
20009 TTGATGCGAC
20019 ATATATTTTGGGAGTAATATTATATGAT
1 ATATATTTTGGGAGTAATATTATATGAT
20047 ATATATTTTGGGACAGAGGGAGTAATATTATATGAT
1 ATATATTTT--------GGGAGTAATATTATATGAT
20083 ATATATTTTGGGA
1 ATATATTTTGGGA
20096 TAGAGGGAGT
Statistics
Matches: 41, Mismatches: 0, Indels: 16
0.72 0.00 0.28
Matches are distributed among these distances:
28 13 0.32
36 28 0.68
ACGTcount: A:0.35, C:0.01, G:0.22, T:0.42
Consensus pattern (28 bp):
ATATATTTTGGGAGTAATATTATATGAT
Found at i:20075 original size:36 final size:36
Alignment explanation
Indices: 20028--20115 Score: 167
Period size: 36 Copynumber: 2.4 Consensus size: 36
20018 CATATATTTT
20028 GGGAGTAATATTATATGATATATATTTTGGGACAGA
1 GGGAGTAATATTATATGATATATATTTTGGGACAGA
*
20064 GGGAGTAATATTATATGATATATATTTTGGGATAGA
1 GGGAGTAATATTATATGATATATATTTTGGGACAGA
20100 GGGAGTAATATTATAT
1 GGGAGTAATATTATAT
20116 TATGTATTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.36, C:0.01, G:0.25, T:0.38
Consensus pattern (36 bp):
GGGAGTAATATTATATGATATATATTTTGGGACAGA
Found at i:20125 original size:12 final size:12
Alignment explanation
Indices: 20108--20134 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
20098 GAGGGAGTAA
20108 TATTATATTATG
1 TATTATATTATG
20120 TATTATATTATG
1 TATTATATTATG
20132 TAT
1 TAT
20135 GTAAGTACTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.59
Consensus pattern (12 bp):
TATTATATTATG
Found at i:21053 original size:22 final size:23
Alignment explanation
Indices: 21019--21096 Score: 85
Period size: 22 Copynumber: 3.5 Consensus size: 23
21009 CGTTTAGTAA
21019 TTAAATATATATTATTTATTTATT
1 TTAAA-ATATATTATTTATTTATT
*
21043 TTAAACT-TATTATTTA-TTA-T
1 TTAAAATATATTATTTATTTATT
21063 TTAAAATATATT-TATTATTTA-T
1 TTAAAATATATTAT-TTATTTATT
21085 TTAATAATATAT
1 TTAA-AATATAT
21097 ATTATATCTA
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
20 8 0.17
21 10 0.21
22 17 0.35
23 8 0.17
24 5 0.10
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (23 bp):
TTAAAATATATTATTTATTTATT
Found at i:21096 original size:25 final size:25
Alignment explanation
Indices: 21049--21099 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
21039 TATTTTAAAC
*
21049 TTATTATTTATTATTTAAAATATAT
1 TTATTATTTATTATATAAAATATAT
*
21074 TTATTATTTATT-TAATAATATATAT
1 TTATTATTTATTAT-ATAAAATATAT
21099 T
1 T
21100 ATATCTAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 1 0.04
25 22 0.96
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (25 bp):
TTATTATTTATTATATAAAATATAT
Found at i:21572 original size:29 final size:28
Alignment explanation
Indices: 21528--21583 Score: 94
Period size: 29 Copynumber: 2.0 Consensus size: 28
21518 TTCTTCAAAC
*
21528 TTTCTAATTTCAAGAACGCTCAAGAACA
1 TTTCTAATTTCAAGAACGCTAAAGAACA
21556 TTTCTAATCTTCAAGAACGCTAAAGAAC
1 TTTCTAAT-TTCAAGAACGCTAAAGAAC
21584 GTGGAATAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 8 0.31
29 18 0.69
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (28 bp):
TTTCTAATTTCAAGAACGCTAAAGAACA
Found at i:23230 original size:15 final size:15
Alignment explanation
Indices: 23198--23256 Score: 52
Period size: 15 Copynumber: 4.0 Consensus size: 15
23188 GTTTGTTAAA
**
23198 TTAAGTACTGAAAAT
1 TTAAGTACTGAATTT
23213 TTAAGTACTGAATTT
1 TTAAGTACTGAATTT
*
23228 TTATGGCTACTGAA--T
1 TTA-AG-TACTGAATTT
23243 TTAA-TACTGAATTT
1 TTAAGTACTGAATTT
23257 GTGGTGAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 9
0.73 0.08 0.18
Matches are distributed among these distances:
12 7 0.19
14 1 0.03
15 20 0.56
16 1 0.03
17 7 0.19
ACGTcount: A:0.36, C:0.08, G:0.14, T:0.42
Consensus pattern (15 bp):
TTAAGTACTGAATTT
Found at i:24260 original size:5 final size:5
Alignment explanation
Indices: 24246--24279 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
24236 TTTTTGGCCT
24246 TTTTC TTTTTC TTTTC TTTTC TTTTC TTTT- TTTT
1 TTTTC -TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
24280 AATGTTTTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.14
5 19 0.68
6 5 0.18
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (5 bp):
TTTTC
Found at i:29384 original size:16 final size:15
Alignment explanation
Indices: 29334--29407 Score: 58
Period size: 16 Copynumber: 4.7 Consensus size: 15
29324 TACGAACCTT
* *
29334 AACCCCAAAAAACCTG
1 AACCCGAAAAAACC-A
**
29350 AACCCGAAAAAGTTCA
1 AACCCGAAAAA-ACCA
29366 AACCCGAAAAAACCAA
1 AACCCGAAAAAACC-A
* *
29382 AACTCGAAAAAACTGA
1 AACCCGAAAAAAC-CA
29398 AACCCGAAAA
1 AACCCGAAAA
29408 GCCCCGAACC
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
15 1 0.02
16 44 0.96
17 1 0.02
ACGTcount: A:0.55, C:0.28, G:0.09, T:0.07
Consensus pattern (15 bp):
AACCCGAAAAAACCA
Found at i:29390 original size:32 final size:32
Alignment explanation
Indices: 29334--29407 Score: 85
Period size: 32 Copynumber: 2.3 Consensus size: 32
29324 TACGAACCTT
* ** **
29334 AACCCCAAAAAACCTGAACCCGAAAAAGTTCA
1 AACCCGAAAAAACCAAAACCCGAAAAAACTCA
* *
29366 AACCCGAAAAAACCAAAACTCGAAAAAACTGA
1 AACCCGAAAAAACCAAAACCCGAAAAAACTCA
29398 AACCCGAAAA
1 AACCCGAAAA
29408 GCCCCGAACC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.55, C:0.28, G:0.09, T:0.07
Consensus pattern (32 bp):
AACCCGAAAAAACCAAAACCCGAAAAAACTCA
Found at i:29678 original size:15 final size:15
Alignment explanation
Indices: 29636--29712 Score: 55
Period size: 16 Copynumber: 4.9 Consensus size: 15
29626 AATCCGAATT
*
29636 AACCTGACCCAAATT
1 AACCTGACCCAAATC
* *
29651 GACCCGAACCCAAATC
1 AACCTG-ACCCAAATC
*
29667 AACCTGACCCAAATTT
1 AACCTGACCCAAA-TC
* *
29683 AACATGAACCCGAATC
1 AACCTG-ACCCAAATC
* *
29699 AATCTAACCCAAAT
1 AACCTGACCCAAAT
29713 TTAACTCGAC
Statistics
Matches: 46, Mismatches: 13, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
15 18 0.39
16 22 0.48
17 6 0.13
ACGTcount: A:0.42, C:0.34, G:0.08, T:0.17
Consensus pattern (15 bp):
AACCTGACCCAAATC
Found at i:29699 original size:32 final size:32
Alignment explanation
Indices: 29624--29717 Score: 109
Period size: 32 Copynumber: 3.0 Consensus size: 32
29614 AGCTCGAACC
* * * *
29624 TGAATCCGAATTAACCTGACCCAAA-TTGACC
1 TGAACCCGAATCAACCTGACCCAAATTTAACA
* *
29655 CGAACCCAAATCAACCTGACCCAAATTTAACA
1 TGAACCCGAATCAACCTGACCCAAATTTAACA
* *
29687 TGAACCCGAATCAATCTAACCCAAATTTAAC
1 TGAACCCGAATCAACCTGACCCAAATTTAAC
29718 TCGACCTGAC
Statistics
Matches: 52, Mismatches: 10, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
31 21 0.40
32 31 0.60
ACGTcount: A:0.40, C:0.31, G:0.09, T:0.20
Consensus pattern (32 bp):
TGAACCCGAATCAACCTGACCCAAATTTAACA
Found at i:30268 original size:15 final size:16
Alignment explanation
Indices: 30232--30270 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
30222 TCTGAATCTG
30232 AACCCGAAAAACTCGA
1 AACCCGAAAAACTCGA
*
30248 ATCCCGAAAAACTC-A
1 AACCCGAAAAACTCGA
30263 AACCCGAA
1 AACCCGAA
30271 TCTGAATCCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.49, C:0.33, G:0.10, T:0.08
Consensus pattern (16 bp):
AACCCGAAAAACTCGA
Found at i:30481 original size:32 final size:32
Alignment explanation
Indices: 30431--30520 Score: 126
Period size: 32 Copynumber: 2.8 Consensus size: 32
30421 ACCTAGATCA
* * *
30431 AACCTGAATTAACATGACCCAAATTCAACCCG
1 AACCCGAATTAACCTGACCCAAATTCAACACG
* *
30463 AACCCGAATTAACCTGACCCAAATTTAATACG
1 AACCCGAATTAACCTGACCCAAATTCAACACG
*
30495 AACCCGAATTAACCTAACCCAAATTC
1 AACCCGAATTAACCTGACCCAAATTC
30521 CTGACTCAAG
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 51 1.00
ACGTcount: A:0.41, C:0.31, G:0.08, T:0.20
Consensus pattern (32 bp):
AACCCGAATTAACCTGACCCAAATTCAACACG
Found at i:30490 original size:16 final size:16
Alignment explanation
Indices: 30439--30490 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
30429 CAAACCTGAA
*
30439 TTAACATGACCCAAAT
1 TTAACCTGACCCAAAT
* * *
30455 TCAACCCGAACCCGAA-
1 TTAACCTG-ACCCAAAT
30471 TTAACCTGACCCAAAT
1 TTAACCTGACCCAAAT
30487 TTAA
1 TTAA
30491 TACGAACCCG
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
15 6 0.22
16 15 0.56
17 6 0.22
ACGTcount: A:0.40, C:0.31, G:0.08, T:0.21
Consensus pattern (16 bp):
TTAACCTGACCCAAAT
Found at i:33435 original size:3 final size:3
Alignment explanation
Indices: 33427--33494 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
33417 TGTTTCGGAA
33427 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
33475 AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AA
33495 TGTGTTTCTA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:35391 original size:31 final size:31
Alignment explanation
Indices: 35353--35419 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
35343 TCCCTTTAAC
35353 ACTAGTTATATAAATTCTTTTTATTTAACGT
1 ACTAGTTATATAAATTCTTTTTATTTAACGT
*
35384 ACTAGTTATATCAATTCTTTTTATTTAACGT
1 ACTAGTTATATAAATTCTTTTTATTTAACGT
35415 ACTAG
1 ACTAG
35420 CATCATTCAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.31, C:0.12, G:0.07, T:0.49
Consensus pattern (31 bp):
ACTAGTTATATAAATTCTTTTTATTTAACGT
Found at i:36615 original size:11 final size:10
Alignment explanation
Indices: 36586--36629 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
36576 AGGAAGATGG
*
36586 AAGAAAAAGA
1 AAGAAAAAAA
*
36596 AAGAGAAAAA
1 AAGAAAAAAA
36606 AAGTAAAAAAA
1 AAG-AAAAAAA
36617 AAGAAAATAAA
1 AAGAAAA-AAA
36628 AA
1 AA
36630 AAGACACGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
10 15 0.52
11 14 0.48
ACGTcount: A:0.82, C:0.00, G:0.14, T:0.05
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:36628 original size:21 final size:21
Alignment explanation
Indices: 36589--36629 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
36579 AAGATGGAAG
*
36589 AAAAAGAAAGAGAAAAAAAGT
1 AAAAAAAAAGAGAAAAAAAGT
*
36610 AAAAAAAAAGAAAATAAAAA
1 AAAAAAAAAGAGAA-AAAAA
36630 AAGACACGTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.83, C:0.00, G:0.12, T:0.05
Consensus pattern (21 bp):
AAAAAAAAAGAGAAAAAAAGT
Found at i:42875 original size:5 final size:5
Alignment explanation
Indices: 42864--42904 Score: 64
Period size: 5 Copynumber: 8.2 Consensus size: 5
42854 ATAATAGAAT
* *
42864 ATACC ATGCC ATACC ATACC ATACC ATACC ATACC AAACC A
1 ATACC ATACC ATACC ATACC ATACC ATACC ATACC ATACC A
42905 GACCCGACCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.41, C:0.39, G:0.02, T:0.17
Consensus pattern (5 bp):
ATACC
Found at i:43942 original size:18 final size:18
Alignment explanation
Indices: 43916--43958 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
43906 CCGCTAACCG
* * *
43916 CCTCTTCTTCTTCCTCCT
1 CCTCCTCTTCATCATCCT
43934 CCTCCTCTTCATCATCCT
1 CCTCCTCTTCATCATCCT
*
43952 CGTCCTC
1 CCTCCTC
43959 GTCGTAGTAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.05, C:0.51, G:0.02, T:0.42
Consensus pattern (18 bp):
CCTCCTCTTCATCATCCT
Found at i:45904 original size:46 final size:50
Alignment explanation
Indices: 45856--45958 Score: 154
Period size: 52 Copynumber: 2.0 Consensus size: 50
45846 CATTAGTCAC
*
45856 ATAA-TATTTAAATTTTAATTAGCAGCAAACTTGATAAAGAATGAACATA
1 ATAATTATGTAAATTTTAATTAGCAGCAAACTTGATAAAGAATGAACATA
* *
45905 ATTTAATTATGTGAATTTTAATTAGTAGCAAACTTGATAAAGAATGAACATA
1 A--TAATTATGTAAATTTTAATTAGCAGCAAACTTGATAAAGAATGAACATA
45957 AT
1 AT
45959 TTTGTAATGA
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
49 1 0.02
50 1 0.02
51 3 0.06
52 43 0.90
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.35
Consensus pattern (50 bp):
ATAATTATGTAAATTTTAATTAGCAGCAAACTTGATAAAGAATGAACATA
Found at i:46088 original size:16 final size:16
Alignment explanation
Indices: 46067--46097 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
46057 TAGAAAAATA
46067 TTACTAAATCTTTATT
1 TTACTAAATCTTTATT
46083 TTACTAAATCTTTAT
1 TTACTAAATCTTTAT
46098 AATTTGTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.13, G:0.00, T:0.55
Consensus pattern (16 bp):
TTACTAAATCTTTATT
Found at i:46993 original size:20 final size:22
Alignment explanation
Indices: 46954--46995 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
46944 AATTTGAAAA
*
46954 CTTTTAGATAATCTTATTTAAC
1 CTTTTAGATAAACTTATTTAAC
46976 CTTTTA-ATAAAC-TATTTAAC
1 CTTTTAGATAAACTTATTTAAC
46996 GTAACTGGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 5 0.26
22 6 0.32
ACGTcount: A:0.36, C:0.14, G:0.02, T:0.48
Consensus pattern (22 bp):
CTTTTAGATAAACTTATTTAAC
Found at i:49561 original size:199 final size:192
Alignment explanation
Indices: 49188--49575 Score: 555
Period size: 199 Copynumber: 2.0 Consensus size: 192
49178 AATATTCAAA
* * * *
49188 ACTCTATAAGCGGGTTAAGAAGTTAGCACATACCTCATTTCATCATTATTTAAATATTTAATATT
1 ACTCCATAAGCGGGTTAAGAAGTTAGCACATACCTCATTTCATAATAAATTAAATATTTAATATT
** * *
49253 AATACATATTCTCAAAGGGGACACATGTCAAACCCTGTACGTGTAGTCTGTTAAACTCTACTGAC
66 AATACATATTCTCAAAGGGGACACATGTCAAACCCTACACGTGTAGTCTGCTAAACTCGACTGAC
* *
49318 GGTGTATAGTATAATTTTTCTTATATGATTATTATACAATACACTGTTAGTGTAAATTTTGG
131 AGTGTATAGTATAATTTTTCTTATAAGATTATTATACAATACACTGTTAGTGTAAATTTTGG
*
49380 ACTCCATAGGCGGGTTAAGAAGTT-GACACATACCTCATTTCATAATAAATTAAATATTTAATAT
1 ACTCCATAAGCGGGTTAAGAAGTTAG-CACATACCTCATTTCATAATAAATTAAATATTTAATAT
* *
49444 TAATATATATTC-CTTAAGGGGACACATGTCAACCATTAAACCCTACACGTGTAGTCTGCTAAAC
65 TAATACATATTCTC-AAAGGGGACACATGT----C---AAACCCTACACGTGTAGTCTGCTAAAC
*
49508 TCGACTGACAGTGTATAGTATAATTTTTCTTATAAGATTATTATACAATACACTTTTAGTGTAAA
122 TCGACTGACAGTGTATAGTATAATTTTTCTTATAAGATTATTATACAATACACTGTTAGTGTAAA
49573 TTT
187 TTT
49576 GTTTGTGTAT
Statistics
Matches: 173, Mismatches: 14, Indels: 11
0.87 0.07 0.06
Matches are distributed among these distances:
191 2 0.01
192 82 0.47
196 1 0.01
199 88 0.51
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (192 bp):
ACTCCATAAGCGGGTTAAGAAGTTAGCACATACCTCATTTCATAATAAATTAAATATTTAATATT
AATACATATTCTCAAAGGGGACACATGTCAAACCCTACACGTGTAGTCTGCTAAACTCGACTGAC
AGTGTATAGTATAATTTTTCTTATAAGATTATTATACAATACACTGTTAGTGTAAATTTTGG
Done.