Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008349.1 Corchorus capsularis cultivar CVL-1 contig08370, 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: 33034
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:2920 original size:60 final size:61
Alignment explanation
Indices: 2827--2987 Score: 177
Period size: 60 Copynumber: 2.6 Consensus size: 61
2817 CTAATTGCTT
* * * * *
2827 AAATAATGGCCTAACG-T-TTGCCAAAATGTTCAAATAAGGATC-CGATCTTTTAATTTGGCC
1 AAATAAGGGCCTAACGTTATTG--AAAATGCTCAAATAAGGAGCTCGATCTTTTAATATGACC
* *
2887 AAATAAGGGCCTAACGTTATTGAAAATGCTCAAATAA-GAGCTTGATCTTTTAATATGATC
1 AAATAAGGGCCTAACGTTATTGAAAATGCTCAAATAAGGAGCTCGATCTTTTAATATGACC
**
2947 AAATAAGGGCCTAACGTTATAAAAAAAATGCTCAAATAAGG
1 AAATAAGGGCCTAACGTTAT--TGAAAATGCTCAAATAAGG
2988 GCCTAACGTT
Statistics
Matches: 86, Mismatches: 9, Indels: 9
0.83 0.09 0.09
Matches are distributed among these distances:
59 3 0.03
60 63 0.73
61 1 0.01
62 18 0.21
63 1 0.01
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.29
Consensus pattern (61 bp):
AAATAAGGGCCTAACGTTATTGAAAATGCTCAAATAAGGAGCTCGATCTTTTAATATGACC
Found at i:2924 original size:31 final size:31
Alignment explanation
Indices: 2886--3022 Score: 154
Period size: 31 Copynumber: 4.4 Consensus size: 31
2876 TTAATTTGGC
2886 CAAATAAGGGCCTAACGTTATTGAAAATGCT
1 CAAATAAGGGCCTAACGTTATTGAAAATGCT
* * * * *
2917 CAAATAAGAGCTTGATC-TT-TT-AATATGAT
1 CAAATAAGGGCCT-AACGTTATTGAAAATGCT
**
2946 CAAATAAGGGCCTAACGTTATAAAAAAAATGCT
1 CAAATAAGGGCCTAACGTTAT--TGAAAATGCT
*
2979 CAAATAAGGGCCTAACGTTATCGAAAATGCT
1 CAAATAAGGGCCTAACGTTATTGAAAATGCT
3010 CAAATAAGGGCCT
1 CAAATAAGGGCCT
3023 GGTGTCAATT
Statistics
Matches: 87, Mismatches: 13, Indels: 12
0.78 0.12 0.11
Matches are distributed among these distances:
28 2 0.02
29 19 0.22
30 3 0.03
31 34 0.39
32 2 0.02
33 27 0.31
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.26
Consensus pattern (31 bp):
CAAATAAGGGCCTAACGTTATTGAAAATGCT
Found at i:3088 original size:31 final size:30
Alignment explanation
Indices: 3053--3214 Score: 100
Period size: 31 Copynumber: 5.4 Consensus size: 30
3043 GTGAGATAGA
3053 CCCTTATTTGAGCATTTTGGCAAACGTTAGG
1 CCCTTATTTGAGCATTTT-GCAAACGTTAGG
** ***
3084 CCCTTATTTG-GCCAAATT-CAAA-GACCGGG
1 CCCTTATTTGAG-CATTTTGCAAACG-TTAGG
*
3113 CCCTAATTTGAGCATTTTGGCAAACGTTAGG
1 CCCTTATTTGAGCATTTT-GCAAACGTTAGG
** * ** * *
3144 CCCTTATTTG-GCCAAATT-AAAATATCAGA
1 CCCTTATTTGAG-CATTTTGCAAACGTTAGG
* *
3173 CCCTTATTTGAGCATTTTGTCAAATGTTAGA
1 CCCTTATTTGAGCATTTTG-CAAACGTTAGG
3204 CCCTTATTTGA
1 CCCTTATTTGA
3215 ACAATTAGCC
Statistics
Matches: 97, Mismatches: 24, Indels: 20
0.69 0.17 0.14
Matches are distributed among these distances:
28 1 0.01
29 39 0.40
30 4 0.04
31 52 0.54
32 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (30 bp):
CCCTTATTTGAGCATTTTGCAAACGTTAGG
Found at i:3125 original size:60 final size:60
Alignment explanation
Indices: 3050--3213 Score: 247
Period size: 60 Copynumber: 2.7 Consensus size: 60
3040 CGCGTGAGAT
*
3050 AGACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTCAAAGACC
1 AGACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGACC
* * * * *
3110 GGGCCCTAATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAATATC
1 AGACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGACC
* * *
3170 AGACCCTTATTTGAGCATTTTGTCAAATGTTAGACCCTTATTTG
1 AGACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTG
3214 AACAATTAGC
Statistics
Matches: 92, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
60 92 1.00
ACGTcount: A:0.27, C:0.21, G:0.18, T:0.34
Consensus pattern (60 bp):
AGACCCTTATTTGAGCATTTTGGCAAACGTTAGGCCCTTATTTGGCCAAATTAAAAGACC
Found at i:4705 original size:128 final size:128
Alignment explanation
Indices: 4472--4724 Score: 350
Period size: 128 Copynumber: 2.0 Consensus size: 128
4462 ATGAATAAAG
* * *
4472 AATAGTACATGATTTTATGGTCAATAAATATGTTTACATTGAACTGGTTAAAAATCCTTGTAATT
1 AATAATACATGATTTTATGGTCAATAAATATGTTTACATTCAACTGGTTAAAAACCCTTGTAATT
*
4537 ACAAAAAGAAGGCATAGGAAAAAGGAATGGTCAGAAACTAATTGAGAATCTTCTTAGTAAATA
66 ACAAAAAGAAGGCATAGGAAAAAGGAATAGTCAGAAACTAATTGAGAATCTTCTTAGTAAATA
*
4600 AATAATACATGATTTTATGGTCAATAAATAT-TTTCACATTCAACTGTTTAAAAACCCTTGTAAT
1 AATAATACATGATTTTATGGTCAATAAATATGTTT-ACATTCAACTGGTTAAAAACCCTTGTAAT
** * * * **
4664 TAC-AAAA-AAGGGTTGGAGGAGAAGGGAATAGTGAGAAACTAATTGAGGGTCTTCTTAGTAA
65 TACAAAAAGAAGGCAT--AGGAAAAAGGAATAGTCAGAAACTAATTGAGAATCTTCTTAGTAA
4725 TTAACCAAGT
Statistics
Matches: 110, Mismatches: 12, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
126 5 0.05
127 7 0.06
128 98 0.89
ACGTcount: A:0.41, C:0.10, G:0.18, T:0.31
Consensus pattern (128 bp):
AATAATACATGATTTTATGGTCAATAAATATGTTTACATTCAACTGGTTAAAAACCCTTGTAATT
ACAAAAAGAAGGCATAGGAAAAAGGAATAGTCAGAAACTAATTGAGAATCTTCTTAGTAAATA
Found at i:19186 original size:15 final size:16
Alignment explanation
Indices: 19164--19209 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 16
19154 GCCTTTGAAG
19164 TACTCTTCTGGAGTAA
1 TACTCTTCTGGAGTAA
***
19180 T-CTCTTCAAAAGT-A
1 TACTCTTCTGGAGTAA
19194 TACTCTTCTGGAGTAA
1 TACTCTTCTGGAGTAA
19210 CTTTGTCCTC
Statistics
Matches: 22, Mismatches: 6, Indels: 4
0.69 0.19 0.12
Matches are distributed among these distances:
14 2 0.09
15 18 0.82
16 2 0.09
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.37
Consensus pattern (16 bp):
TACTCTTCTGGAGTAA
Found at i:23441 original size:12 final size:12
Alignment explanation
Indices: 23424--23481 Score: 59
Period size: 12 Copynumber: 4.9 Consensus size: 12
23414 TACAAATAAG
23424 AAAATGAAAAAA
1 AAAATGAAAAAA
23436 AAAATG-AAAAA
1 AAAATGAAAAAA
23447 AAAA-G-AAAAA
1 AAAATGAAAAAA
**
23457 AATGTGAAAAAA
1 AAAATGAAAAAA
23469 AGAAAGTGAAAAA
1 A-AAA-TGAAAAA
23482 TGGAACACTC
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
10 8 0.21
11 10 0.26
12 12 0.32
13 1 0.03
14 7 0.18
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.09
Consensus pattern (12 bp):
AAAATGAAAAAA
Found at i:23445 original size:11 final size:11
Alignment explanation
Indices: 23424--23469 Score: 58
Period size: 11 Copynumber: 4.2 Consensus size: 11
23414 TACAAATAAG
23424 AAAATGAAAAAA
1 AAAATG-AAAAA
23436 AAAATGAAAAA
1 AAAATGAAAAA
23447 AAAA-GAAAAA
1 AAAATGAAAAA
**
23457 AATGTGAAAAA
1 AAAATGAAAAA
23468 AA
1 AA
23470 GAAAGTGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
10 8 0.26
11 17 0.55
12 6 0.19
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (11 bp):
AAAATGAAAAA
Found at i:23455 original size:19 final size:19
Alignment explanation
Indices: 23433--23473 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
23423 GAAAATGAAA
23433 AAAAAAATGAAAAAAAAAG
1 AAAAAAATGAAAAAAAAAG
**
23452 AAAAAAATGTGAAAAAAAG
1 AAAAAAATGAAAAAAAAAG
23471 AAA
1 AAA
23474 GTGAAAAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.07
Consensus pattern (19 bp):
AAAAAAATGAAAAAAAAAG
Found at i:26682 original size:83 final size:83
Alignment explanation
Indices: 26563--26723 Score: 250
Period size: 83 Copynumber: 1.9 Consensus size: 83
26553 ATAATTGAAC
* * *
26563 CGGGATGGTCAAACCGGTTATGCCAAACAATAAACATAATGCAATCAATAAACTTCAGGTTTACA
1 CGGGATGGCCAAACCGGTCATGCCAAACAAAAAACATAATGCAATCAATAAACTTCAGGTTTACA
26628 AAAGCATATGTTTATTAT
66 AAAGCATATGTTTATTAT
* * * **
26646 CGGGATGGCCTAACTGGTCATGCCAAACAAAAAACATAATGCAATCAATGAACTTTTGGTTTACA
1 CGGGATGGCCAAACCGGTCATGCCAAACAAAAAACATAATGCAATCAATAAACTTCAGGTTTACA
26711 AAAGCATATGTTT
66 AAAGCATATGTTT
26724 CAATCTTACT
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
83 70 1.00
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (83 bp):
CGGGATGGCCAAACCGGTCATGCCAAACAAAAAACATAATGCAATCAATAAACTTCAGGTTTACA
AAAGCATATGTTTATTAT
Found at i:27243 original size:29 final size:29
Alignment explanation
Indices: 27186--27246 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
27176 CTATCTTTAA
*
27186 TATGACAACTTCGGGTGTCAAAATGATAC
1 TATGACAACTTCGGGTGTCAAAATAATAC
* *
27215 TATGACAACTTCGGGTGTCATAGTAATAC
1 TATGACAACTTCGGGTGTCAAAATAATAC
27244 TAT
1 TAT
27247 ATTTTTGATG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (29 bp):
TATGACAACTTCGGGTGTCAAAATAATAC
Found at i:27293 original size:33 final size:33
Alignment explanation
Indices: 27251--27343 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
27241 TACTATATTT
*
27251 TTGATGTGACAACTTCAGGTGCCACTGATATGC
1 TTGATGTGACAACTTCAGGTGCCACTAATATGC
*
27284 TTGATGTGACAACTTCAGGTACCACTAATATGC
1 TTGATGTGACAACTTCAGGTGCCACTAATATGC
* * *
27317 TTGATATGACAACTTCAAGTGTCACTA
1 TTGATGTGACAACTTCAGGTGCCACTA
27344 TAATATATAA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.31
Consensus pattern (33 bp):
TTGATGTGACAACTTCAGGTGCCACTAATATGC
Found at i:27467 original size:36 final size:33
Alignment explanation
Indices: 27391--27463 Score: 112
Period size: 33 Copynumber: 2.2 Consensus size: 33
27381 TTTATTTTTA
* *
27391 ATGATAAAGAAATGTAGAAGGAGTAGATTATGC
1 ATGATAAAGAAAGGTAGAAGAAGTAGATTATGC
27424 ATGATAAAGAAAGGTAGAAGAAG-AGATTATGC
1 ATGATAAAGAAAGGTAGAAGAAGTAGATTATGC
*
27456 ATGTTAAA
1 ATGATAAA
27464 TAAACTTTGT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
32 16 0.43
33 21 0.57
ACGTcount: A:0.48, C:0.03, G:0.26, T:0.23
Consensus pattern (33 bp):
ATGATAAAGAAAGGTAGAAGAAGTAGATTATGC
Found at i:28978 original size:6 final size:6
Alignment explanation
Indices: 28969--29014 Score: 58
Period size: 6 Copynumber: 7.5 Consensus size: 6
28959 TTTTGCTCTG
*
28969 TTTTGT TTTTGT TTTTGT TCTTGT TTTTGTT TGTTTGT TTTT-T TTT
1 TTTTGT TTTTGT TTTTGT TTTTGT TTTTG-T T-TTTGT TTTTGT TTT
29015 GGATGTGCTG
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
5 4 0.11
6 24 0.67
7 4 0.11
8 4 0.11
ACGTcount: A:0.00, C:0.02, G:0.15, T:0.83
Consensus pattern (6 bp):
TTTTGT
Found at i:28983 original size:22 final size:25
Alignment explanation
Indices: 28953--29010 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
28943 CTTTTCCTCC
28953 TTTTT-TTTTTGCTC-TG-TTTTG-
1 TTTTTGTTTTTGCTCTTGTTTTTGT
*
28974 TTTTTGTTTTTGTTCTTGTTTTTGT
1 TTTTTGTTTTTGCTCTTGTTTTTGT
28999 TTGTTTGTTTTT
1 TT-TTTGTTTTT
29011 TTTTGGATGT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
21 5 0.16
22 8 0.26
23 2 0.06
24 5 0.16
25 2 0.06
26 9 0.29
ACGTcount: A:0.00, C:0.05, G:0.16, T:0.79
Consensus pattern (25 bp):
TTTTTGTTTTTGCTCTTGTTTTTGT
Found at i:28992 original size:18 final size:17
Alignment explanation
Indices: 28967--29015 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 17
28957 TTTTTTGCTC
28967 TGTTTTGTTTTTGTTTT
1 TGTTTTGTTTTTGTTTT
28984 TGTTCTTGTTTTTGTTTGTT
1 TGTT-TTGTTTTTG-TT-TT
29004 TGTTTT-TTTTTG
1 TGTTTTGTTTTTG
29016 GATGTGCTGG
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
17 4 0.14
18 15 0.52
19 4 0.14
20 6 0.21
ACGTcount: A:0.00, C:0.02, G:0.18, T:0.80
Consensus pattern (17 bp):
TGTTTTGTTTTTGTTTT
Found at i:32996 original size:2 final size:2
Alignment explanation
Indices: 32989--33033 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
32979 CCAAAGCCAC
32989 TA TA TA TA 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 TA TA TA TA
33031 TA T
1 TA T
33034 T
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.