Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016133.1 Corchorus olitorius cultivar O-4 contig16166, 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: 33760
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Found at i:359 original size:3 final size:3
Alignment explanation
Indices: 351--382 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
341 ATATATATAT
351 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
383 GTAGACAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:881 original size:34 final size:34
Alignment explanation
Indices: 836--906 Score: 115
Period size: 34 Copynumber: 2.1 Consensus size: 34
826 TTAACTGTTA
*
836 GTTATGCTTAGTTAAGTAAATCTATTAGTTAGTT
1 GTTATGCTTAGTTAAGTAAATATATTAGTTAGTT
* *
870 GTTATGTTTAGTTAAGTAAATATGTTAGTTAGTT
1 GTTATGCTTAGTTAAGTAAATATATTAGTTAGTT
904 GTT
1 GTT
907 GCTAGTTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.28, C:0.03, G:0.20, T:0.49
Consensus pattern (34 bp):
GTTATGCTTAGTTAAGTAAATATATTAGTTAGTT
Found at i:2246 original size:33 final size:33
Alignment explanation
Indices: 2185--2247 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
2175 ACCACAGATT
* *
2185 CATCAAGTCAATGCAGTTGTTACTCTTCCTCAA
1 CATCAAGTCAATGCAGTTGCTACACTTCCTCAA
* *
2218 CATCATGTCAATGCAGTTGCTGCACTTCCT
1 CATCAAGTCAATGCAGTTGCTACACTTCCT
2248 TATAATTCTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.24, C:0.29, G:0.14, T:0.33
Consensus pattern (33 bp):
CATCAAGTCAATGCAGTTGCTACACTTCCTCAA
Found at i:3394 original size:65 final size:65
Alignment explanation
Indices: 3284--3413 Score: 197
Period size: 65 Copynumber: 2.0 Consensus size: 65
3274 GAAAAAACTG
* ** * * *
3284 GTCCTACCCATGCATGGGGTACCCTTGGCCTACCCACGCCTGGGCTAGTGTAGAAAGTTTGAATC
1 GTCCAACCCATGCATGGGGTACCCTTGGCCTACCCACGCAAGGGCTAGTGCAGAAAATTGGAATC
*
3349 GTCCAACCCATGCATGGGGTACCCTTGGCCTACCCATGCAAGGGCTAGTGCAGAAAATTGGAATC
1 GTCCAACCCATGCATGGGGTACCCTTGGCCTACCCACGCAAGGGCTAGTGCAGAAAATTGGAATC
3414 AATAGCAAGC
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
65 58 1.00
ACGTcount: A:0.23, C:0.28, G:0.26, T:0.22
Consensus pattern (65 bp):
GTCCAACCCATGCATGGGGTACCCTTGGCCTACCCACGCAAGGGCTAGTGCAGAAAATTGGAATC
Found at i:8605 original size:21 final size:21
Alignment explanation
Indices: 8579--8619 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
8569 TAAAAAACCC
8579 TAGTACCACTTATATCCAATT
1 TAGTACCACTTATATCCAATT
* *
8600 TAGTACCACTTGTCTCCAAT
1 TAGTACCACTTATATCCAAT
8620 AGGGTTTAAA
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:0.29, C:0.27, G:0.07, T:0.37
Consensus pattern (21 bp):
TAGTACCACTTATATCCAATT
Found at i:9817 original size:65 final size:65
Alignment explanation
Indices: 9707--9836 Score: 197
Period size: 65 Copynumber: 2.0 Consensus size: 65
9697 GAAAAAACTG
* ** * * *
9707 GTCCTACCCATGCATGGGGTACCCTTGGCCTACCCACGCCTGGGCTAGTGTAGAAAGTTTGAATC
1 GTCCAACCCATGCATGGGGTACCCTTGGCCTACCCACGCAAGGGCTAGTGCAGAAAATTGGAATC
*
9772 GTCCAACCCATGCATGGGGTACCCTTGGCCTACCCATGCAAGGGCTAGTGCAGAAAATTGGAATC
1 GTCCAACCCATGCATGGGGTACCCTTGGCCTACCCACGCAAGGGCTAGTGCAGAAAATTGGAATC
9837 AATAGCAAGC
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
65 58 1.00
ACGTcount: A:0.23, C:0.28, G:0.26, T:0.22
Consensus pattern (65 bp):
GTCCAACCCATGCATGGGGTACCCTTGGCCTACCCACGCAAGGGCTAGTGCAGAAAATTGGAATC
Found at i:16906 original size:184 final size:178
Alignment explanation
Indices: 16588--17059 Score: 678
Period size: 184 Copynumber: 2.6 Consensus size: 178
16578 TTACCCTAAC
* * *
16588 ATATATAACATAAAATATTGAGTTTTATAATCATATATAAT-AAAAAAATCCAAATTCAAATAGA
1 ATATATAACAT-GAATATTGAGTTTTATAATCATATATAATAAAAAAAATCCAAATCCAAATGGA
*
16652 ATAAGTATATATAATAAATAATATATACTTAAAGCTACGTGCGTTGCACGTGGTTTAATAATTTA
65 ATAAG--TATATAATAAATAATATATACTTAAAGCTACGTGCGTTGCACGTGGTTTAATAACTTA
16717 TAAAACATAAAAATTGAAATAACAAATATAACAAATGATATATTAATTTGTA
128 TAAAACATAAAAATT-AAATAACAAATATAACAAATGATATATTAATTTGTA
16769 ATATATAACATGAATATTGAGTTTTATAATCATATATAATAAGAAAATCTAAATCCAAATCCAAA
1 ATATATAACATGAATATTGAGTTTTATAATCATATATAAT-A-AAAA---AAATCCAAATCCAAA
** * *
16834 TGGAATAAGTATATAATACGTAATATATGCTTAAAGCTGCGTGCGTTGCACGTGCG-TTAATAAC
61 TGGAATAAGTATATAATAAATAATATATACTTAAAGCTACGTGCGTTGCACGTG-GTTTAATAAC
* * *
16898 TTATAAAACATAAAAATTAAATAATAAATATAATAAATGGTATATTAATTTGTA
125 TTATAAAACATAAAAATTAAATAACAAATATAACAAATGATATATTAATTTGTA
** * * *
16952 ACGTATAACATGAAATATCGAGTTTTATAACCATATATAATAAAAAAAATCCAAATCCAAATGAA
1 ATATATAACATG-AATATTGAGTTTTATAATCATATATAATAAAAAAAATCCAAATCCAAATGGA
*
17017 ATAAGTATATAATAAATGATATATACTTAAAGCTACGTGCGTT
65 ATAAGTATATAATAAATAATATATACTTAAAGCTACGTGCGTT
17060 AATAACTTAT
Statistics
Matches: 262, Mismatches: 21, Indels: 18
0.87 0.07 0.06
Matches are distributed among these distances:
179 56 0.21
180 28 0.11
181 11 0.04
182 4 0.02
183 48 0.18
184 92 0.35
185 1 0.00
186 22 0.08
ACGTcount: A:0.48, C:0.09, G:0.10, T:0.33
Consensus pattern (178 bp):
ATATATAACATGAATATTGAGTTTTATAATCATATATAATAAAAAAAATCCAAATCCAAATGGAA
TAAGTATATAATAAATAATATATACTTAAAGCTACGTGCGTTGCACGTGGTTTAATAACTTATAA
AACATAAAAATTAAATAACAAATATAACAAATGATATATTAATTTGTA
Found at i:20144 original size:11 final size:11
Alignment explanation
Indices: 20128--20175 Score: 50
Period size: 11 Copynumber: 4.7 Consensus size: 11
20118 GAAGTTCGTG
20128 TTTGAAGACCA
1 TTTGAAGACCA
**
20139 TTTGAAGATAA
1 TTTGAAGACCA
20150 TTTGAAGA-C-
1 TTTGAAGACCA
20159 -TTGAAGACCA
1 TTTGAAGACCA
20169 -TTGAAGA
1 TTTGAAGA
20176 TTTTGATGCC
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
8 7 0.22
9 1 0.03
10 7 0.22
11 17 0.53
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (11 bp):
TTTGAAGACCA
Found at i:21588 original size:15 final size:15
Alignment explanation
Indices: 21555--21596 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
21545 TTACTTTGCT
*
21555 TTGTTTTCTAGTTTCA
1 TTGTTTTCT-GTTTAA
21571 TTGTTTTCTGTTTAA
1 TTGTTTTCTGTTTAA
*
21586 TTGCTTTCTGT
1 TTGTTTTCTGT
21597 CAACCTCTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.10, C:0.12, G:0.14, T:0.64
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:22336 original size:21 final size:22
Alignment explanation
Indices: 22295--22338 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
22285 AGCTACTCGG
22295 GTTCGACTCGAGAAAAATTCGA
1 GTTCGACTCGAGAAAAATTCGA
* *
22317 GTTCGGCTCG-GAAAATTTCGA
1 GTTCGACTCGAGAAAAATTCGA
22338 G
1 G
22339 CCGAGCTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (22 bp):
GTTCGACTCGAGAAAAATTCGA
Found at i:28240 original size:19 final size:18
Alignment explanation
Indices: 28205--28243 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
28195 ATTTAAGCTC
28205 AATCTTCAATGATCTTCA
1 AATCTTCAATGATCTTCA
*
28223 AATCTTCAAATTATCTTCA
1 AATCTTC-AATGATCTTCA
28242 AA
1 AA
28244 AAATCTTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.38, C:0.21, G:0.03, T:0.38
Consensus pattern (18 bp):
AATCTTCAATGATCTTCA
Found at i:31475 original size:129 final size:129
Alignment explanation
Indices: 31245--31505 Score: 486
Period size: 129 Copynumber: 2.0 Consensus size: 129
31235 TTTTAAAAAG
*
31245 AATTTTTTTTAACTACCCTTTTTATAAGTAGTCCCCCACACTTGTTCTTGACATATCCATAACAT
1 AATTTTTCTTAACTACCCTTTTTATAAGTAGTCCCCCACACTTGTTCTTGACATATCCATAACAT
* *
31310 ACTTTCATAATTGTAATTTCAACAAGATTAAACACAAGTTCTAGAAATAGATAATTATATAAGC
66 ACTTTCATAATTGTAATTTCAACAAGATTAAACACAAGTTCTAGAAATAGACAATTATAGAAGC
31374 AATTTTTCTTAACTACCCTTTTTATAAGTAGTCCCCCACACTTGTTCTTGACATATCCATAACAT
1 AATTTTTCTTAACTACCCTTTTTATAAGTAGTCCCCCACACTTGTTCTTGACATATCCATAACAT
*
31439 ACTTTCATAATTGTAATTTCAACAAGATTAACCACAAGTTCTAGAAATAGACAATTATAGAAGC
66 ACTTTCATAATTGTAATTTCAACAAGATTAAACACAAGTTCTAGAAATAGACAATTATAGAAGC
31503 AAT
1 AAT
31506 AAATAAATAA
Statistics
Matches: 128, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
129 128 1.00
ACGTcount: A:0.36, C:0.20, G:0.08, T:0.36
Consensus pattern (129 bp):
AATTTTTCTTAACTACCCTTTTTATAAGTAGTCCCCCACACTTGTTCTTGACATATCCATAACAT
ACTTTCATAATTGTAATTTCAACAAGATTAAACACAAGTTCTAGAAATAGACAATTATAGAAGC
Done.