Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009569.1 Corchorus capsularis cultivar CVL-1 contig09590, 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: 96429
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:2791 original size:74 final size:74
Alignment explanation
Indices: 2713--2869 Score: 235
Period size: 74 Copynumber: 2.1 Consensus size: 74
2703 TTATCTTTTC
* ** * *
2713 ACACTTTTCGGGTGACTAAAAA-ACCCATTTATGAGTTTTTCCTATTCCTTTTCTTTCTACCCTT
1 ACACTTTTCGGATGACTAAAAAGACCC-TTTATGAGTTTCCCCAATTCCTTTTCCTTCTACCCTT
2777 TTTCGTAATT
65 TTTCGTAATT
*
2787 ACACTTTTCGGATGACTAAAAAGTCCCTTTATGAGTTTCCCCAATTCCTTTTCCTTCTACCCTTT
1 ACACTTTTCGGATGACTAAAAAGACCCTTTATGAGTTTCCCCAATTCCTTTTCCTTCTACCCTTT
2852 TTCGTAATT
66 TTCGTAATT
*
2861 ACACATTTC
1 ACACTTTTC
2870 TCTTTCTTAA
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
74 72 0.96
75 3 0.04
ACGTcount: A:0.22, C:0.25, G:0.09, T:0.43
Consensus pattern (74 bp):
ACACTTTTCGGATGACTAAAAAGACCCTTTATGAGTTTCCCCAATTCCTTTTCCTTCTACCCTTT
TTCGTAATT
Found at i:6512 original size:31 final size:31
Alignment explanation
Indices: 6470--6534 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
6460 TTGGGTTATC
*
6470 AGTCTCTAGATCTTT-AGATCTTGGATCTTTG
1 AGTCTCCAGATCTTTGA-ATCTTGGATCTTTG
*
6501 AGTCTCCAGATCTTTGAATCTTGGATGTTTG
1 AGTCTCCAGATCTTTGAATCTTGGATCTTTG
6532 AGT
1 AGT
6535 TAGTTCAGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 30 0.97
32 1 0.03
ACGTcount: A:0.20, C:0.15, G:0.22, T:0.43
Consensus pattern (31 bp):
AGTCTCCAGATCTTTGAATCTTGGATCTTTG
Found at i:12191 original size:11 final size:11
Alignment explanation
Indices: 12177--12214 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
12167 ATTCATAACA
12177 AATTTATAATT
1 AATTTATAATT
12188 AATTTATAATT
1 AATTTATAATT
12199 -ATTTGATAATT
1 AATTT-ATAATT
*
12210 TATTT
1 AATTT
12215 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:13544 original size:33 final size:32
Alignment explanation
Indices: 13499--13605 Score: 117
Period size: 33 Copynumber: 3.2 Consensus size: 32
13489 AATTGCTCAT
*
13499 GCCGCCCTAGGGGGGCGGCTGAGCCATGGTAAG
1 GCCGCCCCAGGGGGGCGGCTG-GCCATGGTAAG
* *
13532 GCCGCCCCAGGGGAGCGGCCTGGCCATGGTAAT
1 GCCGCCCCAGGGGGGCGG-CTGGCCATGGTAAG
* * *
13565 GCCGCACCAGGGGGACGGCTTGCCATGGCT-AG
1 GCCGCCCCAGGGGGGCGGCTGGCCATGG-TAAG
13597 GCCGTCCCC
1 GCCG-CCCC
13606 CTCCCTGGGG
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
32 14 0.23
33 45 0.73
34 3 0.05
ACGTcount: A:0.14, C:0.34, G:0.40, T:0.12
Consensus pattern (32 bp):
GCCGCCCCAGGGGGGCGGCTGGCCATGGTAAG
Found at i:13761 original size:32 final size:32
Alignment explanation
Indices: 13711--13772 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
13701 AAAAAGTCAT
13711 GCCGCCCTAGTGGGGCGGCTAGCCGTGGCAGA
1 GCCGCCCTAGTGGGGCGGCTAGCCGTGGCAGA
* *
13743 GCCGTCCTTGTGGGGCGGCTAGCCGTGGCA
1 GCCGCCCTAGTGGGGCGGCTAGCCGTGGCA
13773 CATATATGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.10, C:0.31, G:0.44, T:0.16
Consensus pattern (32 bp):
GCCGCCCTAGTGGGGCGGCTAGCCGTGGCAGA
Found at i:15542 original size:11 final size:11
Alignment explanation
Indices: 15526--15562 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
15516 ATAATTCATC
15526 AATTTTTGTTT
1 AATTTTTGTTT
15537 AATTTTT-TTT
1 AATTTTTGTTT
15547 CAATTTTTGTTT
1 -AATTTTTGTTT
15559 AATT
1 AATT
15563 AATACTATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.22, C:0.03, G:0.05, T:0.70
Consensus pattern (11 bp):
AATTTTTGTTT
Found at i:20633 original size:100 final size:100
Alignment explanation
Indices: 20454--20642 Score: 256
Period size: 100 Copynumber: 1.9 Consensus size: 100
20444 TAAAATTTTA
*
20454 TTTTTATTTTAAGTGTAAATTTCAAAATTAATAATTTAATGTTATAGGGTTTTAGAAATAAAATA
1 TTTTTATTTTAAGGGTAAATTTCAAAATTAATAATTTAATGTTATAGGGTTTTAGAAATAAAATA
* *
20519 CAAAACTATTTTCACTAAGTTTAGCCCCAAATTAT
66 CAAAACTATATTCACCAAGTTTAGCCCCAAATTAT
* * **
20554 TTTTTATTTTAAGGGTAAA-TTCTATAGTTAATAATATTGTTGTTATAGGGTTTTAGAAATAAAA
1 TTTTTATTTTAAGGGTAAATTTC-AAAATTAATAAT-TTAATGTTATAGGGTTTTAGAAATAAAA
* * *
20618 TATATAATTA-ATTCACCAAGTTTAG
64 TACAAAACTATATTCACCAAGTTTAG
20643 TCCAGATTAA
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
99 3 0.04
100 41 0.53
101 33 0.43
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.43
Consensus pattern (100 bp):
TTTTTATTTTAAGGGTAAATTTCAAAATTAATAATTTAATGTTATAGGGTTTTAGAAATAAAATA
CAAAACTATATTCACCAAGTTTAGCCCCAAATTAT
Found at i:30495 original size:32 final size:32
Alignment explanation
Indices: 30449--30514 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
30439 AACCACATCT
* * *
30449 CATAATTAATTACAAAAGCCAATTCATTTCAA
1 CATAATCAAATACAAAACCCAATTCATTTCAA
30481 CATAATCAAATACAAAACCCAATTCATTTCAA
1 CATAATCAAATACAAAACCCAATTCATTTCAA
30513 CA
1 CA
30515 GAAACAAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.48, C:0.23, G:0.02, T:0.27
Consensus pattern (32 bp):
CATAATCAAATACAAAACCCAATTCATTTCAA
Found at i:45492 original size:17 final size:17
Alignment explanation
Indices: 45472--45525 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
45462 TTATCTTCAT
45472 TTTATTATTAGTAATTC
1 TTTATTATTAGTAATTC
* * * *
45489 TTTATAATCATTCA-T-
1 TTTATTATTAGTAATTC
45504 TTTATTATTAGTAATTC
1 TTTATTATTAGTAATTC
45521 TTTAT
1 TTTAT
45526 AATCATTCTG
Statistics
Matches: 27, Mismatches: 8, Indels: 4
0.69 0.21 0.10
Matches are distributed among these distances:
15 10 0.37
16 2 0.07
17 15 0.56
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.59
Consensus pattern (17 bp):
TTTATTATTAGTAATTC
Found at i:45507 original size:32 final size:32
Alignment explanation
Indices: 45467--45533 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
45457 AGTGATTATC
45467 TTCATTTTATTATTAGTAATTCTTTATAATCA
1 TTCATTTTATTATTAGTAATTCTTTATAATCA
45499 TTCATTTTATTATTAGTAATTCTTTATAATCA
1 TTCATTTTATTATTAGTAATTCTTTATAATCA
45531 TTC
1 TTC
45534 TGCACAATTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.30, C:0.10, G:0.03, T:0.57
Consensus pattern (32 bp):
TTCATTTTATTATTAGTAATTCTTTATAATCA
Found at i:64698 original size:3 final size:3
Alignment explanation
Indices: 64692--64725 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
64682 ATATATATAT
64692 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
64726 ACAGAGGCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:67536 original size:1 final size:1
Alignment explanation
Indices: 67530--67557 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
67520 GTTGTTGTTG
67530 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
67558 GGGTTCATAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:67735 original size:21 final size:21
Alignment explanation
Indices: 67709--67753 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
67699 AAAAAAAAGG
**
67709 TTTGCTATTTACCGTCCCCTT
1 TTTGCTAAATACCGTCCCCTT
*
67730 TTTGCTAAATATCGTCCCCTT
1 TTTGCTAAATACCGTCCCCTT
67751 TTT
1 TTT
67754 TTATAATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.13, C:0.29, G:0.09, T:0.49
Consensus pattern (21 bp):
TTTGCTAAATACCGTCCCCTT
Found at i:68103 original size:15 final size:14
Alignment explanation
Indices: 68052--68144 Score: 58
Period size: 11 Copynumber: 7.1 Consensus size: 14
68042 TTATGATTAG
*
68052 TTTTAATTAGTTAA
1 TTTTAATTAGTTTA
** *
68066 TTAAAATTA-CTTA
1 TTTTAATTAGTTTA
*
68079 GTTT-ATTAGTTTA
1 TTTTAATTAGTTTA
68092 TGTTTAATTAG--TA
1 T-TTTAATTAGTTTA
*
68105 -TCTAATTAGTTTA
1 TTTTAATTAGTTTA
68118 TTATTAATTAG--TA
1 TT-TTAATTAGTTTA
68131 -TTTAATTAGTTTA
1 TTTTAATTAGTTTA
68144 T
1 T
68145 AATTAAAATG
Statistics
Matches: 58, Mismatches: 11, Indels: 20
0.65 0.12 0.22
Matches are distributed among these distances:
11 16 0.28
12 5 0.09
13 14 0.24
14 11 0.19
15 12 0.21
ACGTcount: A:0.33, C:0.02, G:0.09, T:0.56
Consensus pattern (14 bp):
TTTTAATTAGTTTA
Found at i:68112 original size:26 final size:26
Alignment explanation
Indices: 68083--68150 Score: 102
Period size: 26 Copynumber: 2.6 Consensus size: 26
68073 TACTTAGTTT
68083 ATTAGTTTATGT-TTAATTAGTATCTA
1 ATTAGTTTAT-TATTAATTAGTATCTA
*
68109 ATTAGTTTATTATTAATTAGTATTTA
1 ATTAGTTTATTATTAATTAGTATCTA
*
68135 ATTAGTTTATAATTAA
1 ATTAGTTTATTATTAA
68151 AATGAAGGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
25 1 0.03
26 38 0.97
ACGTcount: A:0.35, C:0.01, G:0.09, T:0.54
Consensus pattern (26 bp):
ATTAGTTTATTATTAATTAGTATCTA
Found at i:68198 original size:24 final size:25
Alignment explanation
Indices: 68159--68218 Score: 79
Period size: 25 Copynumber: 2.5 Consensus size: 25
68149 AAAATGAAGG
*
68159 AAAATGAA-TTTGAAG-ATTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
68182 AAAATGAAGTTTGAAGAAGTTGTTA
1 AAAATGAAGTTTGAAGAAGTTGTTA
* *
68207 GAAATTAAGTTT
1 AAAATGAAGTTT
68219 AGGGTTTGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
23 8 0.25
24 7 0.22
25 17 0.53
ACGTcount: A:0.43, C:0.00, G:0.20, T:0.37
Consensus pattern (25 bp):
AAAATGAAGTTTGAAGAAGTTGTTA
Found at i:73153 original size:25 final size:25
Alignment explanation
Indices: 73124--73173 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
73114 ACAAATGAAT
73124 TTAATTAGTGCAA-GATTTTGTAGTA
1 TTAATTAGTG-AAGGATTTTGTAGTA
73149 TTAATTAGTGAAGGATTTTGTAGTA
1 TTAATTAGTGAAGGATTTTGTAGTA
73174 ATGACAGCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 2 0.08
25 22 0.92
ACGTcount: A:0.32, C:0.02, G:0.22, T:0.44
Consensus pattern (25 bp):
TTAATTAGTGAAGGATTTTGTAGTA
Found at i:77194 original size:31 final size:30
Alignment explanation
Indices: 77159--77248 Score: 126
Period size: 31 Copynumber: 2.9 Consensus size: 30
77149 AGCACAAATG
*
77159 AATTTGATTAGTGCAAGATTTTGTAGTATCT
1 AATTTAATTAGTG-AAGATTTTGTAGTATCT
*
77190 AATTTAATTAGTGAAGGATTTTGTAGTATTT
1 AATTTAATTAGTGAA-GATTTTGTAGTATCT
*
77221 AATTTAATTAGTGGAGGATTTTGTAGTA
1 AATTTAATTAGT-GAAGATTTTGTAGTA
77249 ATGACAGCAC
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
30 2 0.04
31 50 0.93
32 2 0.04
ACGTcount: A:0.31, C:0.02, G:0.21, T:0.46
Consensus pattern (30 bp):
AATTTAATTAGTGAAGATTTTGTAGTATCT
Found at i:80588 original size:13 final size:13
Alignment explanation
Indices: 80570--80595 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
80560 AGAAGTTTTG
80570 CAATTGTCTTATT
1 CAATTGTCTTATT
80583 CAATTGTCTTATT
1 CAATTGTCTTATT
80596 GTCGATTATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.08, T:0.54
Consensus pattern (13 bp):
CAATTGTCTTATT
Found at i:85250 original size:2 final size:2
Alignment explanation
Indices: 85243--85276 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
85233 TCGTTCTTAA
*
85243 TC TC TC TC TC TC TC TC TC TC TC TC TC TC GC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
85277 CTTTTTATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.03, T:0.47
Consensus pattern (2 bp):
TC
Found at i:93423 original size:31 final size:31
Alignment explanation
Indices: 93355--93489 Score: 132
Period size: 30 Copynumber: 4.4 Consensus size: 31
93345 TCCTTTTGTG
* **
93355 CACGTGGCATGC-ACATGTCACATTTTGAAA
1 CACGTGGCATGCTACATGTCACTTTTTGGTA
*
93385 CATGTGGCATGCTACATGTCACTTTTTGGTA
1 CACGTGGCATGCTACATGTCACTTTTTGGTA
* **
93416 CACGTGGCGTGACATATGTGTCACTTTTTGGTA
1 CACGTGGCATG-C-TACATGTCACTTTTTGGTA
**
93449 CA-GTGGTGTG-TCACATGTCACTTTTTGGTA
1 CACGTGGCATGCT-ACATGTCACTTTTTGGTA
*
93479 CACGTAGCATG
1 CACGTGGCATG
93490 TCACGTCGGA
Statistics
Matches: 86, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
29 1 0.01
30 29 0.34
31 29 0.34
32 8 0.09
33 19 0.22
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.34
Consensus pattern (31 bp):
CACGTGGCATGCTACATGTCACTTTTTGGTA
Done.