Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014243.1 Corchorus olitorius cultivar O-4 contig14276, 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: 21895
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:2078 original size:411 final size:401
Alignment explanation
Indices: 1010--1984 Score: 1267
Period size: 408 Copynumber: 2.4 Consensus size: 401
1000 AGCCACCCTC
* * * *
1010 AGATTTGGTTAGATCAATATATATATTTCTAGAAGTTTTTCTGCCAAAAATCATGCAAAACTGAG
1 AGATTTGATTAGATCAATATAGATATTTCGAGAAGTCTTTCTGCCAAAAATCATGCAAAACTGAG
** * * *
1075 TTAGGGCCCCGAAACTCATTTTTAGCCAAAAATCGTGACGGTTATTACACGATTTTAGCTAAAAT
66 CCAGGGCCCCGAAACGCATTTTTAGCCAAAAATCGTGACGGTTAGTACACGATTTCAGCTAAAAT
* ** * * ** *
1140 TTTGCAAAAAACTGATCCGAAAAGTTATATATTTCGAAAAGTTAAATAGTGCTAGTACACTATTT
131 TTTGCAAAAAACTGACCCGAAAAGTTATATATCACCAAAAGTTAAATACTGCTAAAAAACTATTT
* *
1205 CGGCTAAAATTTTGCAAAAAAACTGATCCGAAAAGTTTCTTTCCAA-TTTTTTCCCACAATACTC
196 CGCCTAAAATTTT----AAAAACTGATCC--AAAG--TCTTCCCAATTTTTTTCCCACAATACTC
*
1269 AGAAAAATCATATAATTCAATGCCAAAACTATTTTATGGTTTTTCACGCTTCTAATATCGTTTTC
253 AGAAAAATCATATAATTCAATGCCAAAACTAATTTATGGTTTTTCACGCTTCTAATATCGTTTTC
* *
1334 CATTTTTTTCTGAATTTATTTCTAATTAAATCATAACAAGATTCAGATGCTCGTAAAAACAAATC
318 CATTTTTTTCTGAATTTATTTCTAAATAAATCATAACAAGATTCAGATACTCGTAAAAACAAATC
1399 CGTAAAGCCAATGTTGGTG
383 CGTAAAGCCAATGTTGGTG
* * * * *
1418 AGATTTGGTTAGATCAGTATATATATTTCTAGAAGTTTTTCTGCCAAAAATCATGCAAAACTGAG
1 AGATTTGATTAGATCAATATAGATATTTCGAGAAGTCTTTCTGCCAAAAATCATGCAAAACTGAG
** * *
1483 TTAGGGCCCCGAAACTCATTTTTAGCCAAAAATCGTGACGGTTATTACACGATTTCAGCTAAAAT
66 CCAGGGCCCCGAAACGCATTTTTAGCCAAAAATCGTGACGGTTAGTACACGATTTCAGCTAAAAT
* ** * * ** *
1548 TTTGCAAAAAACTGATCCGAAAAGTTATATATTTCGAAAAGTTAAATAGTGCTAGTACACTATTT
131 TTTGCAAAAAACTGACCCGAAAAGTTATATATCACCAAAAGTTAAATACTGCTAAAAAACTATTT
*
1613 CGGCTAAAATTTTGCAAAAAAACTGATCCGAAAAGTTTCTTCCCAATTTTTTTCCCACAATACTC
196 CGCCTAAAATTTT----AAAAACTGATCC--AAAG--TCTTCCCAATTTTTTTCCCACAATACTC
* *
1678 AGAAAAATCATATAATTCAATGCCAAAACTAATTTATGGTTTTTCATGCTTTTAATATCGTTTTT
253 AGAAAAATCATATAATTCAATGCCAAAACTAATTTATGGTTTTTCACGCTTCTAATATCG-TTTT
* * *
1743 CCA-TTTTTTCTGAATTTATTTCTAAATAAATCGA-AACAAGATTGAGATACTTGTAAAAATAAA
317 CCATTTTTTTCTGAATTTATTTCTAAATAAATC-ATAACAAGATTCAGATACTCGTAAAAACAAA
* *
1806 TCTGTAAATG-CATTG-TGGCTGAG
381 TCCGTAAA-GCCAATGTTGG-T--G
*
1829 AGATTTGATTAGATGAATATAGATATTTCGAGAAGTCTTTCTGCCAAAAATCATGCAAAACTGAG
1 AGATTTGATTAGATCAATATAGATATTTCGAGAAGTCTTTCTGCCAAAAATCATGCAAAACTGAG
* *
1894 CCAGGGCCCCGAAACGCATTTTTAGCCAAAAATCGTGATGGTTAGTACACGATTTCGGCTAAAAT
66 CCAGGGCCCCGAAACGCATTTTTAGCCAAAAATCGTGACGGTTAGTACACGATTTCAGCTAAAAT
1959 TTTGCAAAAAACTGACCCGAAAAGTT
131 TTTGCAAAAAACTGACCCGAAAAGTT
1985 TTTCACCAAT
Statistics
Matches: 534, Mismatches: 26, Indels: 11
0.94 0.05 0.02
Matches are distributed among these distances:
408 241 0.45
409 140 0.26
410 9 0.02
411 144 0.27
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (401 bp):
AGATTTGATTAGATCAATATAGATATTTCGAGAAGTCTTTCTGCCAAAAATCATGCAAAACTGAG
CCAGGGCCCCGAAACGCATTTTTAGCCAAAAATCGTGACGGTTAGTACACGATTTCAGCTAAAAT
TTTGCAAAAAACTGACCCGAAAAGTTATATATCACCAAAAGTTAAATACTGCTAAAAAACTATTT
CGCCTAAAATTTTAAAAACTGATCCAAAGTCTTCCCAATTTTTTTCCCACAATACTCAGAAAAAT
CATATAATTCAATGCCAAAACTAATTTATGGTTTTTCACGCTTCTAATATCGTTTTCCATTTTTT
TCTGAATTTATTTCTAAATAAATCATAACAAGATTCAGATACTCGTAAAAACAAATCCGTAAAGC
CAATGTTGGTG
Found at i:2340 original size:330 final size:329
Alignment explanation
Indices: 1602--3301 Score: 2088
Period size: 330 Copynumber: 5.2 Consensus size: 329
1592 AATAGTGCTA
* * * *
1602 GTACACTATTTCGGCTAAAATTTTGCAAAAAAACTGATCCGAAAAGTTTCTTCCCAATTTTTTTC
1 GTACACGATTTCGGCTAAAATTTTGC-AAAAAACTGACCCGAAAAGTTT-TCCCCAA-TTTTTTG
* * * * * *
1667 CCACAATACTCAGAAAAATCATATAATTCAATGCCAAAACTAATTTATGGTTTTTCATGCTTTTA
63 CCACAATACTCTGAAAAATCATATAATTCAACGCCAAAA-TATTTTAGGGTTTTTCACGCTTCTA
* * *
1732 ATATCGTTTTTCCA-TTTTTTCTGAATTTATTTCTAAATAAATCGAAACAAGATTGAGATACTTG
127 ATATCGTTTTTCCATTTTTTTCTGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATACTCG
* *
1796 TAAAAATAAATCTGTAAATGCATTGTGGCTGAGAGATTTGATTAGATGAATATAGATATTTCGAG
192 TAAAAATAAATCCGTAAATGCATTGTGGGT-A-AGATTTGATTAGATGAATATAGATATTTCGAG
*
1861 AAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCAGGGCCCCGAAACGCATTTTTAGCCAAAAA
255 AAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCAGGGCCCCGAAACGCATTTTTAGCCAAAAA
*
1926 TCGTGATGGTT
320 CCGTGATGG-T
*
1937 AGTACACGATTTCGGCTAAAATTTTGCAAAAAACTGACCCGAAAAGTTTTTCACCAATTTTTTGC
1 -GTACACGATTTCGGCTAAAATTTTGCAAAAAACTGACCCGAAAAG-TTTTCCCCAATTTTTTGC
*
2002 CACAATACTCTGAAAAAACATATAATTCAACGCCTAAAATATTTTAGGGTTTTTCACGCTTCTAA
64 CACAATACTCTGAAAAATCATATAATTCAACGCC-AAAATATTTTAGGGTTTTTCACGCTTCTAA
* * * * *
2067 TATCGTTTTTCCATTTTTTTCTGAACTGATTTCTAATTAAATC-ATAAGAATATTCAGATGCTCG
128 TATCGTTTTTCCATTTTTTTCTGAATTTATTTCTAATTAAATCGA-AACAAGATTCAGATACTCG
* * * * *
2131 TAAAAACAAATCCGTAGA-GCCAATGTGGGTAAGATTTGGTTAGATGAATATAGATATTTTGAGA
192 TAAAAATAAATCCGTAAATG-CATTGTGGGTAAGATTTGATTAGATGAATATAGATATTTCGAGA
* * *** *
2195 AATCTTTCTGCCAAAAATCATGGAAAACTGAGTCAGGGTTTCGAAACACATTTTTAGCCGAAAAA
256 AGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCAGGGCCCCGAAACGCATTTTTAGCC-AAAAA
2260 CCGTGAT-G-
320 CCGTGATGGT
*
2268 GTACACGATTTCGGCTAAAATTTTGCAAAAAACTGGCCCGAAAAGTTATTCCCCAATTTTTTGCC
1 GTACACGATTTCGGCTAAAATTTTGCAAAAAACTGACCCGAAAAGTT-TTCCCCAATTTTTTGCC
* ** *
2333 ACAATACTCAGAAAAATCATATAATTCAACGCCAAAAATATTTTCTGATTTTTCACGCTTCTAAT
65 ACAATACTCTGAAAAATCATATAATTCAACGCC-AAAATATTTTAGGGTTTTTCACGCTTCTAAT
* ** *
2398 ATCATTTTTCCATTTTTTTCTGAATTTATTTCTCTTTAAATC-ATAACAAGATTCAGATGCTCGT
129 ATCGTTTTTCCATTTTTTTCTGAATTTATTTCTAATTAAATCGA-AACAAGATTCAGATACTCGT
* * * * * * *
2462 AAAAACAAATTCGTAAA-GCCAATGTAGGTGAGATTTGGTTAGATGAATATAGATATTTCAAGAA
193 AAAAATAAATCCGTAAATG-CATTGTGGGTAAGATTTGATTAGATGAATATAGATATTTCGAGAA
* * *
2526 GTCTTTTTGCCAAAAATCATGCAAAACTGAGTCAGGGCCCCGAAACACATTTTTAGCCAAAAAAC
257 GTCTTTCTGCCAAAAATCATGCAAAACTGAGTCAGGGCCCCGAAACGCATTTTTAGCCAAAAACC
2591 -T-A---T
322 GTGATGGT
* * *
2594 G-A-A-GGTTCCGGCTAAAATTTTGCAAAAAAACTGATCCGAAAAGTTTTCCCCAATTTTTTG-C
1 GTACACGATTTCGGCTAAAATTTTGC-AAAAAACTGACCCGAAAAGTTTTCCCCAATTTTTTGCC
* * * **
2655 AGAATACT-TAGAAAAATCATATAATTCAACACCAAAAATATTTCAGAATTTTTCACGCTTCTAA
65 ACAATACTCT-GAAAAATCATATAATTCAACGCC-AAAATATTTTAGGGTTTTTCACGCTTCTAA
*
2719 TATCGTTTTTCTATTTTTTTCTGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATACTCGT
128 TATCGTTTTTCCATTTTTTTCTGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATACTCGT
*
2784 AAAAATAAATCCGTAAATGCATTGTGGCTTAGAGATTTGATTAGATGAATATAGATATTTCGAGA
193 AAAAATAAATCCGTAAATGCATTGTGG-GTA-AGATTTGATTAGATGAATATAGATATTTCGAGA
* *
2849 AGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCAAGCCCCCGAAACGCATTTTTAGCCAAAAAC
256 AGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCAGGGCCCCGAAACGCATTTTTAGCCAAAAAC
2914 CGTGATGGTT
321 CGTGATGG-T
* *
2924 AGTACACGATTTCGACTAAAATTTTGCACAAAACTGACCCG-AAA---------AA-TTTTTGCC
1 -GTACACGATTTCGGCTAAAATTTTGCAAAAAACTGACCCGAAAAGTTTTCCCCAATTTTTTGCC
* *
2978 AC-A-A---T---AAATCATATAATTCAACGCCATAAATATTTTAGGGTTTTTCAGGATTCTAAT
65 ACAATACTCTGAAAAATCATATAATTCAACGCCA-AAATATTTTAGGGTTTTTCACGCTTCTAAT
* * *
3035 ATCGTTTTTCCATTTTTTTTCTGAATTTATTTCTATTTAAATCGAAACAAGATTCAAATACTTGT
129 ATCGTTTTTCCA-TTTTTTTCTGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATACTCGT
* * *
3100 AAAAATAAATCTGTAAATGCATTGTGGCTGAAAGATTTGATTAGATGAATATAAATATTTCGAGA
193 AAAAATAAATCCGTAAATGCATTGTGG--GTAAGATTTGATTAGATGAATATAGATATTTCGAGA
** * * * *
3165 AGTCTTTCTG-TGAAAATCATGCAAAACTGAGCCATGGCCCCGAAACGCGTTTTTAGTCAAAAAG
256 AGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCAGGGCCCCGAAACGCATTTTTAGCCAAAAA-
*
3229 CCGTGATAGTT
320 CCGTGAT-GGT
* *
3240 AGTACACGATTTCAGCTAAAATTTTGTAAAAAACTGACCCGAAAAGTTTTTCCCCAATTTTT
1 -GTACACGATTTCGGCTAAAATTTTGCAAAAAACTGACCCGAAAAG-TTTTCCCCAATTTTT
3302 GGCATGCCAC
Statistics
Matches: 1197, Mismatches: 125, Indels: 92
0.85 0.09 0.07
Matches are distributed among these distances:
314 1 0.00
315 101 0.08
316 162 0.14
317 5 0.00
319 1 0.00
321 1 0.00
322 143 0.12
323 40 0.03
324 112 0.09
325 2 0.00
326 2 0.00
327 3 0.00
328 5 0.00
329 8 0.01
330 287 0.24
331 1 0.00
332 4 0.00
333 97 0.08
334 104 0.09
335 90 0.08
336 28 0.02
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (329 bp):
GTACACGATTTCGGCTAAAATTTTGCAAAAAACTGACCCGAAAAGTTTTCCCCAATTTTTTGCCA
CAATACTCTGAAAAATCATATAATTCAACGCCAAAATATTTTAGGGTTTTTCACGCTTCTAATAT
CGTTTTTCCATTTTTTTCTGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAA
AATAAATCCGTAAATGCATTGTGGGTAAGATTTGATTAGATGAATATAGATATTTCGAGAAGTCT
TTCTGCCAAAAATCATGCAAAACTGAGTCAGGGCCCCGAAACGCATTTTTAGCCAAAAACCGTGA
TGGT
Found at i:3489 original size:23 final size:25
Alignment explanation
Indices: 3443--3498 Score: 89
Period size: 25 Copynumber: 2.3 Consensus size: 25
3433 ATGTCCTCCA
3443 ATATTTTAGGCGTTAAAATCTATAT
1 ATATTTTAGGCGTTAAAATCTATAT
*
3468 ATATTTTTGGCGTT-AAAT-TATAT
1 ATATTTTAGGCGTTAAAATCTATAT
3491 ATATTTTA
1 ATATTTTA
3499 TGAGTATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 12 0.41
24 4 0.14
25 13 0.45
ACGTcount: A:0.34, C:0.05, G:0.11, T:0.50
Consensus pattern (25 bp):
ATATTTTAGGCGTTAAAATCTATAT
Found at i:10910 original size:22 final size:22
Alignment explanation
Indices: 10885--11117 Score: 113
Period size: 22 Copynumber: 10.5 Consensus size: 22
10875 TGTCTCTGTG
10885 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
10907 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
* *
10930 -GGTTATCAAAATTCCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
*
10951 TGGTTACCAAAATTTCATATAGA
1 TGGTTATCAAAATTTCATA-AGA
* **
10974 -AGTTATCAAAATTTCATGGGA
1 TGGTTATCAAAATTTCATAAGA
* * * *
10995 AGGTTACCAAAATTTCA-CAGTG
1 TGGTTATCAAAATTTCATAAG-A
* *
11017 TGGTTACCAAAATTTCATAGGA
1 TGGTTATCAAAATTTCATAAGA
* *
11039 TCATGTTATTAAAATTTCTTATAA-A
1 T--GGTTATCAAAATTTC--ATAAGA
**
11064 -GGTTATTGAAATTTCATAATG-
1 TGGTTATCAAAATTTCATAA-GA
* * *
11085 TGATTATCACAATTTTAT-AGAA
1 TGGTTATCAAAATTTCATAAG-A
*
11107 AGGTTATCAAA
1 TGGTTATCAAA
11118 GAGATTATCA
Statistics
Matches: 156, Mismatches: 38, Indels: 34
0.68 0.17 0.15
Matches are distributed among these distances:
20 6 0.04
21 4 0.03
22 124 0.79
23 4 0.03
24 14 0.09
25 1 0.01
26 3 0.02
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.37
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:10965 original size:44 final size:43
Alignment explanation
Indices: 10886--11037 Score: 137
Period size: 44 Copynumber: 3.5 Consensus size: 43
10876 GTCTCTGTGT
* ** * *
10886 GGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGA-GGA
1 GGTTATCAAAATTTCAT-AGGTGGTTACCAAAATTTCAT-ATAGA
*
10930 GGTTATCAAAATTCCATAGTGTGGTTACCAAAATTTCATATAGA
1 GGTTATCAAAATTTCATAG-GTGGTTACCAAAATTTCATATAGA
* * * * *
10974 AGTTATCAAAATTTCATGGGAAGGTTACCAAAATTTCACAGT-GT
1 GGTTATCAAAATTTCATAGG-TGGTTACCAAAATTTCATA-TAGA
*
11018 GGTTACCAAAATTTCATAGG
1 GGTTATCAAAATTTCATAGG
11038 ATCATGTTAT
Statistics
Matches: 89, Mismatches: 15, Indels: 8
0.79 0.13 0.07
Matches are distributed among these distances:
43 4 0.04
44 84 0.94
45 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (43 bp):
GGTTATCAAAATTTCATAGGTGGTTACCAAAATTTCATATAGA
Found at i:10988 original size:66 final size:66
Alignment explanation
Indices: 10882--11056 Score: 219
Period size: 66 Copynumber: 2.6 Consensus size: 66
10872 TTTTGTCTCT
* * * * *
10882 GTGTGGTTATCAAAATTTCATAAGATGGTTATTATAATTTCATGAGG-AGGTTATCAAAATTCCA
1 GTGTGGTTACCAAAATTTCATAAGATAGTTATCAAAATTTCATG-GGAAGGTTACCAAAATTCCA
*
10946 TA
65 CA
*
10948 GTGTGGTTACCAAAATTTCATATAGA-AGTTATCAAAATTTCATGGGAAGGTTACCAAAATTTCA
1 GTGTGGTTACCAAAATTTCATA-AGATAGTTATCAAAATTTCATGGGAAGGTTACCAAAATTCCA
11012 CA
65 CA
* *
11014 GTGTGGTTACCAAAATTTCATAGGATCATGTTATTAAAATTTC
1 GTGTGGTTACCAAAATTTCATAAGAT-A-GTTATCAAAATTTC
11057 TTATAAAGGT
Statistics
Matches: 95, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
65 4 0.04
66 74 0.78
67 4 0.04
68 13 0.14
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.36
Consensus pattern (66 bp):
GTGTGGTTACCAAAATTTCATAAGATAGTTATCAAAATTTCATGGGAAGGTTACCAAAATTCCAC
A
Found at i:11320 original size:22 final size:22
Alignment explanation
Indices: 11292--11728 Score: 110
Period size: 22 Copynumber: 20.0 Consensus size: 22
11282 TCAGGGAGGA
11292 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
* **
11314 TATCAAAATCTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * *
11336 TTTCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* * **
11357 AGATCAAAATTTCATAGGAAAAT
1 -TATCAAAATTTCATATGAAGGT
*
11380 TAACAAAATTTCATAATG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
** * *
11402 TATCAAAAAATCATAGGGAGGT
1 TATCAAAATTTCATATGAAGGT
* * *
11424 TAT-AAAA----ATTTGTA-GC
1 TATCAAAATTTCATATGAAGGT
* * *
11440 TATCAAGATTTCATAAGGAGGT
1 TATCAAAATTTCATATGAAGGT
* * * *
11462 TATCAAAATTTTATAGGGATGTT
1 TATCAAAATTTCATA-TGAAGGT
* *
11485 TATCAAAATTTTATA-GCGAGGT
1 TATCAAAATTTCATATG-AAGGT
* * *
11507 TATCACAATTTCATAGTG-TGAT
1 TATCAAAATTTCATA-TGAAGGT
*
11529 TATCAAAATTTCAAAGTGTAA--T
1 TATCAAAATTTCATA-TG-AAGGT
*
11551 TA-CTAACAA-TTCATATGGAGGT
1 TATC-AA-AATTTCATATGAAGGT
* * * *
11573 TCTTAAATTTTCATA--ACGTGAT
1 TATCAAAATTTCATATGAAG-G-T
* **
11595 TATCAATACATCATAT-AGAGGT
1 TATCAAAATTTCATATGA-AGGT
* * **
11617 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATA-TGAAGGT
11640 TATCAAAATTTCAT-TCGGAA-GT
1 TATCAAAATTTCATAT--GAAGGT
11662 TATCAAAATTTCATAGTG-AGGT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
11684 CT-TCAAAATTCCTTATGGATGT
1 -TATCAAAATTTCATATGAAGGT
*
11706 TGA-CAAAATTTCATAAGAAGGT
1 T-ATCAAAATTTCATATGAAGGT
11728 T
1 T
11729 TAAAAAAATT
Statistics
Matches: 300, Mismatches: 76, Indels: 78
0.66 0.17 0.17
Matches are distributed among these distances:
16 4 0.01
17 7 0.02
20 4 0.01
21 23 0.08
22 212 0.71
23 47 0.16
24 3 0.01
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:11416 original size:66 final size:66
Alignment explanation
Indices: 11293--11417 Score: 144
Period size: 66 Copynumber: 1.9 Consensus size: 66
11283 CAGGGAGGAT
* ** * * * * **
11293 ATCAAAATTTCATATGAAGGTTATCAAAATCTCATAGTTTAGTTTTCAAAATTTCATAGTATGTA
1 ATCAAAATTTCATAGGAAAATTAACAAAATCTCATAGATGAGTTATCAAAAAATCATAGTATGTA
11358 G
66 G
*
11359 ATCAAAATTTCATAGGAAAATTAACAAAATTTCATA-ATGAGGTTATCAAAAAATCATAG
1 ATCAAAATTTCATAGGAAAATTAACAAAATCTCATAGATGA-GTTATCAAAAAATCATAG
11418 GGAGGTTATA
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
65 2 0.04
66 46 0.96
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.34
Consensus pattern (66 bp):
ATCAAAATTTCATAGGAAAATTAACAAAATCTCATAGATGAGTTATCAAAAAATCATAGTATGTA
G
Found at i:11506 original size:45 final size:44
Alignment explanation
Indices: 11440--11541 Score: 125
Period size: 45 Copynumber: 2.3 Consensus size: 44
11430 AATTTGTAGC
* * *
11440 TATCAAGATTTCATAAGGAGGTTATCAAAATTTTATAGGGATGTT
1 TATCAAAATTTCATAAGGAGGTTATCAAAATTTCATAGGG-TGAT
* * *
11485 TATCAAAATTTTAT-AGCGAGGTTATCACAATTTCATAGTGTGAT
1 TATCAAAATTTCATAAG-GAGGTTATCAAAATTTCATAGGGTGAT
11529 TATCAAAATTTCA
1 TATCAAAATTTCA
11542 AAGTGTAATT
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
44 17 0.35
45 32 0.65
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (44 bp):
TATCAAAATTTCATAAGGAGGTTATCAAAATTTCATAGGGTGAT
Found at i:11653 original size:23 final size:23
Alignment explanation
Indices: 11440--11720 Score: 123
Period size: 22 Copynumber: 12.7 Consensus size: 23
11430 AATTTGTAGC
* *
11440 TATCAAGATTTCATA-AGGAGGT
1 TATCAAAATTTCATAGTGGAGGT
* *
11462 TATCAAAATTTTATAG-GGATGTT
1 TATCAAAATTTCATAGTGGA-GGT
* *
11485 TATCAAAATTTTATAG-CGAGGT
1 TATCAAAATTTCATAGTGGAGGT
*
11507 TATCACAATTTCATAGTGTGA--T
1 TATCAAAATTTCATAGTG-GAGGT
* * *
11529 TATCAAAATTTCAAAGTGTA-AT
1 TATCAAAATTTCATAGTGGAGGT
11551 TA-CTAACAA-TTCATA-TGGAGGT
1 TATC-AA-AATTTCATAGTGGAGGT
* * *
11573 TCTTAAATTTTCATAACGT-GA--T
1 TATCAAAATTTCAT-A-GTGGAGGT
* ** *
11595 TATCAATACATCATA-TAGAGGT
1 TATCAAAATTTCATAGTGGAGGT
* * **
11617 TATCAACATCTCATAGTGTTGGT
1 TATCAAAATTTCATAGTGGAGGT
*
11640 TATCAAAATTTCAT--TCGGAAGT
1 TATCAAAATTTCATAGT-GGAGGT
11662 TATCAAAATTTCATAGT-GAGGT
1 TATCAAAATTTCATAGTGGAGGT
* * *
11684 CT-TCAAAATTCCTTA-TGGATGT
1 -TATCAAAATTTCATAGTGGAGGT
11706 TGA-CAAAATTTCATA
1 T-ATCAAAATTTCATA
11721 AGAAGGTTTA
Statistics
Matches: 195, Mismatches: 40, Indels: 48
0.69 0.14 0.17
Matches are distributed among these distances:
19 1 0.01
20 2 0.01
21 10 0.05
22 136 0.70
23 40 0.21
24 5 0.03
25 1 0.01
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (23 bp):
TATCAAAATTTCATAGTGGAGGT
Found at i:16592 original size:54 final size:54
Alignment explanation
Indices: 16510--16617 Score: 198
Period size: 54 Copynumber: 2.0 Consensus size: 54
16500 GGAACCCAAT
*
16510 CTTTGTAATAATGGACCACATCTTGATTTTTTTTTTTTATATGTGAATATGAAA
1 CTTTGTAATAATGGACCACATCTTGATTTTTTTTTTCTATATGTGAATATGAAA
*
16564 CTTTGTAATAATGGACCACATTTTGATTTTTTTTTTCTATATGTGAATATGAAA
1 CTTTGTAATAATGGACCACATCTTGATTTTTTTTTTCTATATGTGAATATGAAA
16618 TTAAATGATA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.30, C:0.09, G:0.13, T:0.48
Consensus pattern (54 bp):
CTTTGTAATAATGGACCACATCTTGATTTTTTTTTTCTATATGTGAATATGAAA
Done.