Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011832.1 Corchorus capsularis cultivar CVL-1 contig11853, 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: 24689
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34
Found at i:117 original size:3 final size:3
Alignment explanation
Indices: 109--134 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
99 TAATGTAAAA
109 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
135 ATTTAGCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:1063 original size:21 final size:18
Alignment explanation
Indices: 1039--1101 Score: 51
Period size: 21 Copynumber: 3.4 Consensus size: 18
1029 TTTAATAATT
1039 ATATATTATTATATATACCTA
1 ATATATT-TTATATATA--TA
*
1060 ATATTATTTTTTATATATA
1 ATA-TATTTTATATATATA
1079 ATATATATTTA-AT-TATA
1 ATATAT-TTTATATATATA
1096 A-ATATT
1 ATATATT
1102 ACTAACAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
15 1 0.03
16 4 0.11
17 5 0.13
18 5 0.13
19 8 0.21
21 11 0.29
22 4 0.11
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (18 bp):
ATATATTTTATATATATA
Found at i:1074 original size:19 final size:19
Alignment explanation
Indices: 1041--1088 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
1031 TAATAATTAT
* *
1041 ATATTATTATATATACCTA
1 ATATTATTTTATATACATA
* *
1060 ATATTATTTTTTATATATA
1 ATATTATTTTATATACATA
1079 ATATATATTT
1 ATAT-TATTT
1089 AATTATAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 19 0.79
20 5 0.21
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (19 bp):
ATATTATTTTATATACATA
Found at i:1482 original size:92 final size:93
Alignment explanation
Indices: 1311--1493 Score: 264
Period size: 92 Copynumber: 2.0 Consensus size: 93
1301 TTCAGATGAC
* *
1311 AAAAGAAAAAACCTCATCCAAATAGTTGCCATATCAATGTGGTGAGTTTTGTCGATGGACAAAAG
1 AAAAGAAAAAACCCCATCCAAATAGTTGCCAAATCAATGTGGTGAGTTTTGTCGATGGACAAAAG
* * *
1376 GATAATTAATACTTCTC-TCTTTAGTGTG
66 AATAACTAACACTTCTCGT-TTTAGTGTG
* *
1404 AAAA-AAAAAACCCCATCCAAATAGTTGCCAAATCAATGTGGTGA-TCTTTGTGGTTGGACAAAA
1 AAAAGAAAAAACCCCATCCAAATAGTTGCCAAATCAATGTGGTGAGT-TTTGTCGATGGACAAAA
1467 GAATAACTAACACTTCTCGTTTTAGTG
65 GAATAACTAACACTTCTCGTTTTAGTG
1494 ATATAATATA
Statistics
Matches: 81, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
91 1 0.01
92 75 0.93
93 5 0.06
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (93 bp):
AAAAGAAAAAACCCCATCCAAATAGTTGCCAAATCAATGTGGTGAGTTTTGTCGATGGACAAAAG
AATAACTAACACTTCTCGTTTTAGTGTG
Found at i:3111 original size:29 final size:30
Alignment explanation
Indices: 3078--3135 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 30
3068 AAATAAAAAC
*
3078 TACCAATTTTAGATAAAAA-CTACCCATTG
1 TACCAATTTTAGAAAAAAACCTACCCATTG
3107 TACCAATTTTAGAAAAAAACCTACCCATT
1 TACCAATTTTAGAAAAAAACCTACCCATT
3136 ATAAGATAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 18 0.67
30 9 0.33
ACGTcount: A:0.43, C:0.22, G:0.05, T:0.29
Consensus pattern (30 bp):
TACCAATTTTAGAAAAAAACCTACCCATTG
Found at i:5393 original size:17 final size:18
Alignment explanation
Indices: 5371--5404 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5361 CAAAACCCAC
5371 AAAATTA-AAATAAAAAT
1 AAAATTACAAATAAAAAT
*
5388 AAAATTACATATAAAAA
1 AAAATTACAAATAAAAA
5405 AGCTAGAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (18 bp):
AAAATTACAAATAAAAAT
Found at i:13352 original size:2 final size:2
Alignment explanation
Indices: 13345--13378 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
13335 ATTAGTAGTG
13345 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13379 AAGTAGGGGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20616 original size:11 final size:11
Alignment explanation
Indices: 20596--20638 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
20586 TATACTATAT
*
20596 CTAATCAATAG
1 CTAATTAATAG
*
20607 CTAATTAATAT
1 CTAATTAATAG
*
20618 ATAATTAATAG
1 CTAATTAATAG
*
20629 TTAATTAATA
1 CTAATTAATA
20639 ATGAACAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.40
Consensus pattern (11 bp):
CTAATTAATAG
Found at i:20622 original size:22 final size:22
Alignment explanation
Indices: 20592--20638 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
20582 CCATTATACT
*
20592 ATATCTAATCAATAGCTAATTA
1 ATATATAATCAATAGCTAATTA
* *
20614 ATATATAATTAATAGTTAATTA
1 ATATATAATCAATAGCTAATTA
20636 ATA
1 ATA
20639 ATGAACAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.40
Consensus pattern (22 bp):
ATATATAATCAATAGCTAATTA
Found at i:21197 original size:31 final size:31
Alignment explanation
Indices: 21159--21217 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
21149 AGTTTTGAGA
*
21159 AACTTTTGAAATACCTATTGTACCCTTATTT
1 AACTTTTGAAATACCTATTATACCCTTATTT
*
21190 AACTTTTGAAATACCTATTATATCCTTA
1 AACTTTTGAAATACCTATTATACCCTTA
21218 CTTATCTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.32, C:0.19, G:0.05, T:0.44
Consensus pattern (31 bp):
AACTTTTGAAATACCTATTATACCCTTATTT
Found at i:22060 original size:105 final size:108
Alignment explanation
Indices: 21942--22156 Score: 319
Period size: 109 Copynumber: 2.0 Consensus size: 108
21932 ATAATGTAAA
* *
21942 AATTAATTAACAATATCCTT-ATCAATTTTTTTATTTT-TTTTT-CCGAATATCTCAGCCTTATA
1 AATTAATTAACAATATCCTTAATCAATTTTTTTATTTTCTTTTTCCCGAATATCCCAGCCTTAAA
** *
22004 ATTTATAATGCAAAGTCGGATTATTTTGTTCAATAATTAATAT
66 ATTTATAATGCAAAACCGGATTATTTTGTTCAAGAATTAATAT
*
22047 AATTAATTAACAATATCCTTAAATCAATTTTTTTGTTTTCTTTTTCCCGAATATCCCAGCCTTAA
1 AATTAATTAACAATATCCTT-AATCAATTTTTTTATTTTCTTTTTCCCGAATATCCCAGCCTTAA
* * *
22112 AATTTATAATGTAAAACCGGATTATTTTGTTGAAGATTTAATAT
65 AATTTATAATGCAAAACCGGATTATTTTGTTCAAGAATTAATAT
22156 A
1 A
22157 TCCGATTAAT
Statistics
Matches: 97, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
105 20 0.21
107 16 0.16
108 5 0.05
109 56 0.58
ACGTcount: A:0.34, C:0.13, G:0.07, T:0.46
Consensus pattern (108 bp):
AATTAATTAACAATATCCTTAATCAATTTTTTTATTTTCTTTTTCCCGAATATCCCAGCCTTAAA
ATTTATAATGCAAAACCGGATTATTTTGTTCAAGAATTAATAT
Found at i:23071 original size:14 final size:14
Alignment explanation
Indices: 23054--23084 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
23044 ATTATATAAC
*
23054 AATAATTGATTTTA
1 AATAATTAATTTTA
23068 AATAATTAATTTTA
1 AATAATTAATTTTA
23082 AAT
1 AAT
23085 TCAAACAACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (14 bp):
AATAATTAATTTTA
Done.