Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009094.1 Corchorus capsularis cultivar CVL-1 contig09115, 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: 62021
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Found at i:404 original size:192 final size:194
Alignment explanation
Indices: 1--657 Score: 715
Period size: 192 Copynumber: 3.3 Consensus size: 194
* *
1 AATTAATTATGAAATGGGGTATGTGTCAATTTC-TTATCCCGCTTATGGAGTCCAAAATTTACAT
1 AATTAATTATGAAATGGGGTATGTGTCAACTTCTTTA-CCCGCTTATGGAGTCCAAAATTTACAC
* ** *
65 TAACAAT-T-TATTGTATAATAAGTTCTATTAGAACAATTATACAATGCGTCGTCAGTGGAGTTT
65 T--CAATGTGTATTGTATAATAA-TCCTA-TAGAAGTATTATAC-A--C--CGTCAGTCGAGTTT
* ** * * *
128 AGCATACTGCACGTGCAGGA-TTTAAGGGTT-ATCATGTGTCATCTTAGGGAATATGTCTTAAAA
121 AGCACACTGCACGTGCAGGAGTTTAAGGGTTGA-CATGTGTCCCCTTAAGGAATATGTATTAATA
191 TTAAATATTT
185 TTAAATATTT
* * *
201 TATTAATTATGAAATGGGGTATGTGTCAACTTCTTTACCCTCTTATGAAGTCCAAAATTTACACT
1 AATTAATTATGAAATGGGGTATGTGTCAACTTCTTTACCCGCTTATGGAGTCCAAAATTTACACT
* *
266 GAATGTGTATTGTATAATAATCCTATA-AAGTATTATACACCGTCAGTCGAGTTTAGCACACTGT
66 CAATGTGTATTGTATAATAATCCTATAGAAGTATTATACACCGTCAGTCGAGTTTAGCACACTGC
* * *
330 ACGTG-TGGAGTTTAAGGGTTGACATGTGTCCCCATAAGGAATATGTATTAATATGAAATATTT
131 ACGTGCAGGAGTTTAAGGGTTGACATGTGTCCCCTTAAGGAATATGTATTAATATTAAATATTT
* * *
393 AATTTATTATGAAATGAGGTATGTGTCAACTT-TTTAACCCGCTTATGGAGTCCAAAATTTACAT
1 AATTAATTATGAAATGGGGTATGTGTCAACTTCTTT-ACCCGCTTATGGAGTCCAAAATTTACAC
* * * * * *
457 TC-ATAGTGGATTGTATAATAATCTTATATAAGAAAAATTAAACTATACACCGTCACTCGAATTT
65 TCAAT-GTGTATTGTATAATAATC--CTAT-AG---AAGT--ATTATACACCGTCAGTCGAGTTT
** * *
521 AGCAGTCTGCATGTGCAGG-GTATAAGGGTTGACATGTGTCCCCTTAAGGAATATGTATTAATAT
121 AGCACACTGCACGTGCAGGAGTTTAAGGGTTGACATGTGTCCCCTTAAGGAATATGTATTAATAT
*
585 TAACTATTT
186 TAAATATTT
* * *
594 AATTGATTATG-AATGGGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCTAAAATTTACACT
1 AATTAATTATGAAATGGGGTATGTGTCAACTTCTTTACCCGCTTATGGAGTCCAAAATTTACACT
658 AAAAAGTGTA
Statistics
Matches: 392, Mismatches: 47, Indels: 36
0.83 0.10 0.08
Matches are distributed among these distances:
191 8 0.02
192 142 0.36
193 1 0.00
194 4 0.01
195 1 0.00
196 1 0.00
197 9 0.02
198 5 0.01
199 8 0.02
200 115 0.29
201 96 0.24
202 2 0.01
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (194 bp):
AATTAATTATGAAATGGGGTATGTGTCAACTTCTTTACCCGCTTATGGAGTCCAAAATTTACACT
CAATGTGTATTGTATAATAATCCTATAGAAGTATTATACACCGTCAGTCGAGTTTAGCACACTGC
ACGTGCAGGAGTTTAAGGGTTGACATGTGTCCCCTTAAGGAATATGTATTAATATTAAATATTT
Found at i:6420 original size:63 final size:62
Alignment explanation
Indices: 6321--6449 Score: 231
Period size: 63 Copynumber: 2.1 Consensus size: 62
6311 TCCGCATCTG
*
6321 TGAAACTCTGAATGTGAAAAGTTGAATCATGTCTCGAAATCCCTCAAAACCATCCAGACTTGA
1 TGAAACTCCGAATGTGAAAAGTTGAATCATGTCTCGAAATCCCTCAAAACCATCCAGAC-TGA
*
6384 TGAAACTCCGAATTTGAAAAGTTGAATCATGTCTCGAAATCCCTCAAAACCATCCAGACTGA
1 TGAAACTCCGAATGTGAAAAGTTGAATCATGTCTCGAAATCCCTCAAAACCATCCAGACTGA
6446 TGAA
1 TGAA
6450 CACCCCAAGA
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
62 7 0.11
63 57 0.89
ACGTcount: A:0.37, C:0.22, G:0.16, T:0.25
Consensus pattern (62 bp):
TGAAACTCCGAATGTGAAAAGTTGAATCATGTCTCGAAATCCCTCAAAACCATCCAGACTGA
Found at i:7739 original size:21 final size:21
Alignment explanation
Indices: 7713--7753 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
7703 AGTAGTTAAA
*
7713 AATAATATATAGTATATATAT
1 AATAATATATACTATATATAT
*
7734 AATAATCTATACTATATATA
1 AATAATATATACTATATATA
7754 AAAGTACGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.41
Consensus pattern (21 bp):
AATAATATATACTATATATAT
Found at i:9308 original size:3 final size:3
Alignment explanation
Indices: 9300--9327 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
9290 TTTAGTATAT
9300 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
9328 ATTTAGATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:10956 original size:2 final size:2
Alignment explanation
Indices: 10945--10978 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
10935 ACTCATTATT
10945 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
10979 TTTTCAAACT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11692 original size:3 final size:3
Alignment explanation
Indices: 11648--11735 Score: 106
Period size: 3 Copynumber: 28.3 Consensus size: 3
11638 TCCATAGGGG
* * *
11648 ATA AAA ATA ATA TATA GTA TATA TATA TATA ATT AT- ATA ATA ATA ATA
1 ATA ATA ATA ATA -ATA ATA -ATA -ATA -ATA ATA ATA ATA ATA ATA ATA
11696 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
11736 GGGTGATTAT
Statistics
Matches: 77, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
2 2 0.03
3 62 0.81
4 13 0.17
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:11937 original size:3 final size:3
Alignment explanation
Indices: 11929--11965 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
11919 ATAATTTACC
*
11929 TAA TAA TAA TAA AAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
11966 GTCAAATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:13270 original size:209 final size:213
Alignment explanation
Indices: 12904--13321 Score: 691
Period size: 209 Copynumber: 2.0 Consensus size: 213
12894 AAAAATATTG
12904 AATTTAATTAAATGAAAATAGAGTTTTTAGTAAAATAAAACTGTATATTAAAATTTTTGAATATA
1 AATTTAATTAAATGAAAATAGAGTTTTTAGTAAAATAAAACTGTATATTAAAATTTTTGAATATA
*
12969 TATCTAAATTTTTTAATGAAAAATAGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAA
66 TATCTAAAGTTTTTAATGAAAAATAGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAA
* * * * *
13034 ATAAAAATAGAGTTTTTAGTTGAATAAAATTATAATAATTTAAACAATGGCATTTAAGAAATATG
131 ATAAAAATAGAGTTTTTAGTAGAATAAAACTATAATAATTTAAACAATGACATTTAAAAAATATA
13099 TTT-AAAAATAAGGGTAT
196 TTTGAAAAATAAGGGTAT
* *
13116 AATTTAATTCAATGAAGATAGAGTTTTTAGTAAAATAAAACTGTATATTAAAATTTTTG-A-ATA
1 AATTTAATTAAATGAAAATAGAGTTTTTAGTAAAATAAAACTGTATATTAAAATTTTTGAATATA
* *
13179 TATC-CAAGTTTTTATTGAAAAATAGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAA
66 TATCTAAAGTTTTTAATGAAAAATAGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAA
* *
13243 ATAAAAATATAGTTTTTAGTAGAATAAAACTATAATAATTTAAGCAATGACATTTAAAAAATATA
131 ATAAAAATAGAGTTTTTAGTAGAATAAAACTATAATAATTTAAACAATGACATTTAAAAAATATA
*
13308 TTTGAAAAGTAAGG
196 TTTGAAAAATAAGG
13322 ATAGAATAGG
Statistics
Matches: 192, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
209 118 0.61
210 16 0.08
211 1 0.01
212 57 0.30
ACGTcount: A:0.50, C:0.03, G:0.11, T:0.37
Consensus pattern (213 bp):
AATTTAATTAAATGAAAATAGAGTTTTTAGTAAAATAAAACTGTATATTAAAATTTTTGAATATA
TATCTAAAGTTTTTAATGAAAAATAGTAAAAATAAAGTAATTATAAAGATATTAGATTTAATTAA
ATAAAAATAGAGTTTTTAGTAGAATAAAACTATAATAATTTAAACAATGACATTTAAAAAATATA
TTTGAAAAATAAGGGTAT
Found at i:14863 original size:32 final size:32
Alignment explanation
Indices: 14819--14879 Score: 113
Period size: 32 Copynumber: 1.9 Consensus size: 32
14809 TCCCTAAAGG
*
14819 GACACATGTCACCCTTGTAGACCCGCATGAGT
1 GACACATATCACCCTTGTAGACCCGCATGAGT
14851 GACACATATCACCCTTGTAGACCCGCATG
1 GACACATATCACCCTTGTAGACCCGCATG
14880 TGCAGTCTGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.26, C:0.33, G:0.20, T:0.21
Consensus pattern (32 bp):
GACACATATCACCCTTGTAGACCCGCATGAGT
Found at i:15068 original size:37 final size:37
Alignment explanation
Indices: 15027--15100 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
15017 TCAAATATAA
**
15027 GTACTTTTAAAATATATCATCATGATTAAAAAAAGTT
1 GTACTTTTAAAATATATCATCAACATTAAAAAAAGTT
15064 GTACTTTTAAAATATATCATCAACATTAAAAAAAGTT
1 GTACTTTTAAAATATATCATCAACATTAAAAAAAGTT
15101 TGTTATGACT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.47, C:0.09, G:0.07, T:0.36
Consensus pattern (37 bp):
GTACTTTTAAAATATATCATCAACATTAAAAAAAGTT
Found at i:15286 original size:12 final size:12
Alignment explanation
Indices: 15269--15296 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
15259 ATTGGGTTTG
15269 ATAATAAAACTT
1 ATAATAAAACTT
15281 ATAATAAAACTT
1 ATAATAAAACTT
15293 ATAA
1 ATAA
15297 GTTAGAACAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAATAAAACTT
Found at i:28453 original size:21 final size:19
Alignment explanation
Indices: 28429--28474 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
28419 TAAAAACTCT
*
28429 TTTTTATATAATTAAATTTAA
1 TTTTTATATAACT--ATTTAA
*
28450 TTTTTTTATAACTATTTAA
1 TTTTTATATAACTATTTAA
28469 TTTTTA
1 TTTTTA
28475 CTTACTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 11 0.50
21 11 0.50
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (19 bp):
TTTTTATATAACTATTTAA
Found at i:28474 original size:17 final size:19
Alignment explanation
Indices: 28452--28490 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
28442 AAATTTAATT
28452 TTTTTA-TAACTA-TTTAA
1 TTTTTACTAACTATTTTAA
*
28469 TTTTTACTTACTATTTTAA
1 TTTTTACTAACTATTTTAA
28488 TTT
1 TTT
28491 AAAAAACTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 5 0.26
19 8 0.42
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (19 bp):
TTTTTACTAACTATTTTAA
Found at i:29710 original size:417 final size:416
Alignment explanation
Indices: 28911--29739 Score: 1455
Period size: 417 Copynumber: 2.0 Consensus size: 416
28901 TTCTTTCATT
28911 ATAGAAAAAATGATATTTTTTTTAGCAAAAATTGCTTTTTTGCAAATCTTTATTGGAGAAAAGAT
1 ATAGAAAAAATGATATTTTTTTTAGCAAAAATTGCTTTTTTGCAAATCTTTATTGGAGAAAAGAT
*
28976 TTTTTTTTTGTAATTTATTAATCGAGAAAAGATGTTTCTTAATGTACATTAATACATTATTATTC
66 TTTTTTTTTGTAATTTATTAATCGAGAAAAGATGTTTCTTAATGGACATTAATACATTATTATTC
29041 AAGATAAAATTCTTCTCATTACAACATGTAATTTTTGTTTTTAATTTTTAGATTTTATATGCATT
131 AAGATAAAATTCTTCTCATTACAACATGTAATTTTTGTTTTTAATTTTTAGATTTTATATGC---
29106 TTATATGATTTTTCAATCCGGTTTCATTTTTAGTTAAATGTTTGGTGGGCCCATTAACAAATTGA
193 ---T-T-ATTTTTCAATCCGGTTTCATTTTTAGTTAAATGTTTGGTGGGCCCATTAACAAATTGA
* * *
29171 CAAAAGCTAACATAAAAGGTACATGAGAAAAAATAACATATGACAATCAGGAAATGCTCCTCTTC
253 CAAAAGCTAACATAAAAGGTACATCAGAAAAAATAACAGATGACAATCAAGAAATGCTCCTCTTC
*
29236 TCAAGTGGGGTCCACACAAACTAAGAATAAAATAACATATAGTTGACTAACAACCAAGAGGGGCA
318 TCAAGTGGGGTCCACACAAACTAAGAATAAAATAACATATAGTTGACTAACAACCAAGAAGGGCA
29301 ACTGTAGACACCGATTTTTGCCCTATATCCTTCGA
383 ACTG-AGACACCGATTTTTGCCCTATATCCTTCGA
*
29336 ATAGAAAAAATGATATCTTTTTTTAGCAAAAATTGCTTTTTTGCAAATCTTTATTGGAGAAAAGT
1 ATAGAAAAAATGATAT-TTTTTTTAGCAAAAATTGCTTTTTTGCAAATCTTTATTGGAGAAAAGA
29401 TTTTTTTTTCTGTAATTTATTAATCGAGAAAAGATGTTTCTTAATGGACATTAATACATTATTAT
65 TTTTTTTTT-TGTAATTTATTAATCGAGAAAAGATGTTTCTTAATGGACATTAATACATTATTAT
29466 TCAAGATAAAATTCTTCTCATTACAACATGTAATTTTTGTTTTTAATTTTTAGATTTTATATGC-
129 TCAAGATAAAATTCTTCTCATTACAACATGTAATTTTTGTTTTTAATTTTTAGATTTTATATGCT
*
29530 T-TTTTTCAATCCGGTTTCATTTTTAGTTAAATGTTTGGTGGGCCCATTAACAAATTGACAAAAT
194 TATTTTTCAATCCGGTTTCATTTTTAGTTAAATGTTTGGTGGGCCCATTAACAAATTGACAAAAG
*
29594 CTAACATAAAAGGTACTTCAGAAAAAATAACAGATGACAATCAAGAAATGCTCCTCTTCTCAAGT
259 CTAACATAAAAGGTACATCAGAAAAAATAACAGATGACAATCAAGAAATGCTCCTCTTCTCAAGT
* *
29659 GGGGTCCACACAAACTAAGGATAAAATAACATATAGTTGACTAACAACCAAGAAGGGCAGCTGAG
324 GGGGTCCACACAAACTAAGAATAAAATAACATATAGTTGACTAACAACCAAGAAGGGCAACTGAG
29724 ACACCGATTTTTGCCC
389 ACACCGATTTTTGCCC
29740 GGGGCAGCTG
Statistics
Matches: 392, Mismatches: 10, Indels: 13
0.94 0.02 0.03
Matches are distributed among these distances:
416 18 0.05
417 183 0.47
419 1 0.00
425 16 0.04
426 56 0.14
427 118 0.30
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.37
Consensus pattern (416 bp):
ATAGAAAAAATGATATTTTTTTTAGCAAAAATTGCTTTTTTGCAAATCTTTATTGGAGAAAAGAT
TTTTTTTTTGTAATTTATTAATCGAGAAAAGATGTTTCTTAATGGACATTAATACATTATTATTC
AAGATAAAATTCTTCTCATTACAACATGTAATTTTTGTTTTTAATTTTTAGATTTTATATGCTTA
TTTTTCAATCCGGTTTCATTTTTAGTTAAATGTTTGGTGGGCCCATTAACAAATTGACAAAAGCT
AACATAAAAGGTACATCAGAAAAAATAACAGATGACAATCAAGAAATGCTCCTCTTCTCAAGTGG
GGTCCACACAAACTAAGAATAAAATAACATATAGTTGACTAACAACCAAGAAGGGCAACTGAGAC
ACCGATTTTTGCCCTATATCCTTCGA
Found at i:29763 original size:28 final size:28
Alignment explanation
Indices: 29713--29768 Score: 103
Period size: 29 Copynumber: 2.0 Consensus size: 28
29703 CAACCAAGAA
29713 GGGCAGCTGAGACACCGATTTTTGCCCG
1 GGGCAGCTGAGACACCGATTTTTGCCCG
29741 GGGCAGCTGTAGACACCGATTTTTGCCC
1 GGGCAGCTG-AGACACCGATTTTTGCCC
29769 TATATCCTTC
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
28 9 0.33
29 18 0.67
ACGTcount: A:0.18, C:0.29, G:0.30, T:0.23
Consensus pattern (28 bp):
GGGCAGCTGAGACACCGATTTTTGCCCG
Found at i:32765 original size:44 final size:45
Alignment explanation
Indices: 32715--32800 Score: 165
Period size: 44 Copynumber: 1.9 Consensus size: 45
32705 AAACCTAAAC
32715 TTTTATGTTAAAATCAACTTTAAAATTGAAAC-TTTTTGTTTTTT
1 TTTTATGTTAAAATCAACTTTAAAATTGAAACTTTTTTGTTTTTT
32759 TTTTATGTTAAAATCAACTTTAAAATTGAAACTTTTTTGTTT
1 TTTTATGTTAAAATCAACTTTAAAATTGAAACTTTTTTGTTT
32801 AATGGTTTGA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 32 0.78
45 9 0.22
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (45 bp):
TTTTATGTTAAAATCAACTTTAAAATTGAAACTTTTTTGTTTTTT
Found at i:35006 original size:21 final size:21
Alignment explanation
Indices: 34980--35023 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
34970 AGTTACTGGA
* *
34980 TTGCTAAACATCGCCCCTCTT
1 TTGCTAAACACCGCCCCCCTT
*
35001 TTGCTAAATACCGCCCCCCTT
1 TTGCTAAACACCGCCCCCCTT
35022 TT
1 TT
35024 TACACTTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.18, C:0.39, G:0.09, T:0.34
Consensus pattern (21 bp):
TTGCTAAACACCGCCCCCCTT
Found at i:35115 original size:15 final size:15
Alignment explanation
Indices: 35095--35140 Score: 57
Period size: 15 Copynumber: 3.4 Consensus size: 15
35085 TCAAACGCTA
35095 AACTTCATTTCTAAC
1 AACTTCATTTCTAAC
35110 AACTTC--TTC--A-
1 AACTTCATTTCTAAC
35120 AACTTCATTTCTAAC
1 AACTTCATTTCTAAC
35135 AACTTC
1 AACTTC
35141 TTCAAACTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
10 6 0.23
11 1 0.04
12 3 0.12
13 3 0.12
14 1 0.04
15 12 0.46
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.39
Consensus pattern (15 bp):
AACTTCATTTCTAAC
Found at i:35155 original size:25 final size:25
Alignment explanation
Indices: 35094--35153 Score: 113
Period size: 25 Copynumber: 2.4 Consensus size: 25
35084 TTCAAACGCT
35094 AAACTTCATTTCTAACAACTTCTTC
1 AAACTTCATTTCTAACAACTTCTTC
35119 AAACTTCATTTCTAACAACTTCTTC
1 AAACTTCATTTCTAACAACTTCTTC
35144 AAAC-TCATTT
1 AAACTTCATTT
35154 TCCTTCATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 6 0.17
25 29 0.83
ACGTcount: A:0.33, C:0.27, G:0.00, T:0.40
Consensus pattern (25 bp):
AAACTTCATTTCTAACAACTTCTTC
Found at i:40096 original size:8 final size:8
Alignment explanation
Indices: 40083--40107 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
40073 ATGAGATGAG
40083 TAAGAAAA
1 TAAGAAAA
40091 TAAGAAAA
1 TAAGAAAA
40099 TAAGAAAA
1 TAAGAAAA
40107 T
1 T
40108 CAAATTCCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.72, C:0.00, G:0.12, T:0.16
Consensus pattern (8 bp):
TAAGAAAA
Found at i:40806 original size:110 final size:111
Alignment explanation
Indices: 40661--40862 Score: 325
Period size: 110 Copynumber: 1.8 Consensus size: 111
40651 AATGAATCAA
* * **
40661 AATTTATAACCCAAACTCACCCTTAAATATAAATAAGCATAATTTATAAGTAAAATTAAGGTCCT
1 AATTTATAACCCAAACTCACCCTTAAATATAAATAAGCACAATTTATAAGCAAAATTAAGACCCT
*
40726 AACACCAATATTCCT-AATCAAATGACCCATCTTTGTAAGCATTAT
66 AACACCAACATTCCTAAATCAAATGACCCATCTTTGTAAGCATTAT
* * *
40771 AATTTATAATCGAAACTCACCCTTAAATATAAATAAGCACACTTTATAAGCAAAATTAAGACCCT
1 AATTTATAACCCAAACTCACCCTTAAATATAAATAAGCACAATTTATAAGCAAAATTAAGACCCT
40836 AACACCAACATTCCTAAATCAAATGAC
66 AACACCAACATTCCTAAATCAAATGAC
40863 AAATGACCCA
Statistics
Matches: 83, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
110 72 0.87
111 11 0.13
ACGTcount: A:0.45, C:0.21, G:0.06, T:0.28
Consensus pattern (111 bp):
AATTTATAACCCAAACTCACCCTTAAATATAAATAAGCACAATTTATAAGCAAAATTAAGACCCT
AACACCAACATTCCTAAATCAAATGACCCATCTTTGTAAGCATTAT
Found at i:44102 original size:19 final size:19
Alignment explanation
Indices: 44078--44118 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
44068 ATAATATATT
44078 AAATCCTTTTCAAGAAGAA
1 AAATCCTTTTCAAGAAGAA
44097 AAATCCTTTTCAAGAAGAA
1 AAATCCTTTTCAAGAAGAA
44116 AAA
1 AAA
44119 CTACAAGCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.51, C:0.15, G:0.10, T:0.24
Consensus pattern (19 bp):
AAATCCTTTTCAAGAAGAA
Found at i:53756 original size:10 final size:10
Alignment explanation
Indices: 53738--53767 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
53728 GCTTTTTCTC
53738 TCTCTCACAA
1 TCTCTCACAA
*
53748 TCTCACACAA
1 TCTCTCACAA
53758 TCTCTCACAA
1 TCTCTCACAA
53768 ATTCTGTGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.33, C:0.40, G:0.00, T:0.27
Consensus pattern (10 bp):
TCTCTCACAA
Found at i:54264 original size:18 final size:17
Alignment explanation
Indices: 54237--54270 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
54227 GCTTTGATGA
*
54237 TATTCCATAAATCACAT
1 TATTCCATAAAACACAT
54254 TATTACCATAAAACACA
1 TATT-CCATAAAACACA
54271 CTTCTTGTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.47, C:0.24, G:0.00, T:0.29
Consensus pattern (17 bp):
TATTCCATAAAACACAT
Found at i:58710 original size:2 final size:2
Alignment explanation
Indices: 58703--58729 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
58693 AGATAAATCG
58703 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
58730 GAGAGAGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:61198 original size:21 final size:21
Alignment explanation
Indices: 61174--61214 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
61164 ACTGGCGGGC
*
61174 TTTACTTGCTGAGGAAGGCGT
1 TTTACTTGCTGAAGAAGGCGT
*
61195 TTTACTTGTTGAAGAAGGCG
1 TTTACTTGCTGAAGAAGGCG
61215 AACTCTTCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.12, G:0.32, T:0.34
Consensus pattern (21 bp):
TTTACTTGCTGAAGAAGGCGT
Found at i:61389 original size:17 final size:18
Alignment explanation
Indices: 61355--61392 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
61345 TCCCTCTCAT
* *
61355 GGTACCTAGGTAGTATGA
1 GGTACCTAGGCAGCATGA
61373 GGTA-CTAGGCAGCATGA
1 GGTACCTAGGCAGCATGA
61390 GGT
1 GGT
61393 GATAGGATGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.26, C:0.13, G:0.37, T:0.24
Consensus pattern (18 bp):
GGTACCTAGGCAGCATGA
Done.