Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014758.1 Corchorus capsularis cultivar CVL-1 contig14779, 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: 52026
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:367 original size:2 final size:2
Alignment explanation
Indices: 356--392 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
346 ATTTTACTAT
356 TA TA TA -A TA TA TA TA TA TA TA TA TA TCA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA T
393 TATCATTGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 30 0.91
3 2 0.06
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:380 original size:19 final size:19
Alignment explanation
Indices: 356--392 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
346 ATTTTACTAT
356 TATATA-AT-ATATATATA
1 TATATATATCATATATATA
373 TATATATATCATATATATA
1 TATATATATCATATATATA
392 T
1 T
393 TATCATTGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
18 2 0.11
19 10 0.56
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
TATATATATCATATATATA
Found at i:2917 original size:2 final size:2
Alignment explanation
Indices: 2910--2935 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2900 TAGATCAAAG
2910 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2936 GCTGCGTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8172 original size:16 final size:16
Alignment explanation
Indices: 8153--8289 Score: 70
Period size: 16 Copynumber: 8.6 Consensus size: 16
8143 GAACCCACCC
8153 GACCCGAGACCCGAGT
1 GACCCGAGACCCGAGT
*
8169 GACCCGCA-ATCC-AGAT
1 GACCCG-AGACCCGAG-T
* *
8185 GACCCGAGACCTGAAT
1 GACCCGAGACCCGAGT
* *
8201 GGCCCGTA-A-CCTAGAT
1 GACCCG-AGACCCGAG-T
* *
8217 GACCCGAAACCCGAAT
1 GACCCGAGACCCGAGT
8233 GACCCGTA-ACCCGAGT
1 GACCCG-AGACCCGAGT
*
8249 GATCCGAGACCCGTA-T
1 GACCCGAGACCCG-AGT
* * *
8265 GACCCCAAACCCGAAT
1 GACCCGAGACCCGAGT
*
8281 AACCCGAGA
1 GACCCGAGA
8290 AGTTAACCCG
Statistics
Matches: 90, Mismatches: 19, Indels: 24
0.68 0.14 0.18
Matches are distributed among these distances:
15 8 0.09
16 74 0.82
17 8 0.09
ACGTcount: A:0.31, C:0.36, G:0.23, T:0.11
Consensus pattern (16 bp):
GACCCGAGACCCGAGT
Found at i:8190 original size:32 final size:31
Alignment explanation
Indices: 8153--8269 Score: 135
Period size: 32 Copynumber: 3.7 Consensus size: 31
8143 GAACCCACCC
* *
8153 GACCCGAGACCCGAGTGACCCGCAATCCAGAT
1 GACCCGAGACCCGAATGACCCGTAA-CCAGAT
* *
8185 GACCCGAGACCTGAATGGCCCGTAACCTAGAT
1 GACCCGAGACCCGAATGACCCGTAACC-AGAT
* *
8217 GACCCGAAACCCGAATGACCCGTAACCCGAGT
1 GACCCGAGACCCGAATGACCCGTAACCAGA-T
* *
8249 GATCCGAGACCCGTATGACCC
1 GACCCGAGACCCGAATGACCC
8270 CAAACCCGAA
Statistics
Matches: 72, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
31 4 0.06
32 68 0.94
ACGTcount: A:0.28, C:0.36, G:0.24, T:0.12
Consensus pattern (31 bp):
GACCCGAGACCCGAATGACCCGTAACCAGAT
Found at i:8288 original size:32 final size:32
Alignment explanation
Indices: 8154--8289 Score: 87
Period size: 32 Copynumber: 4.2 Consensus size: 32
8144 AACCCACCCG
* * * *
8154 ACCCGAGACCCGAGTGACCCGCAATCCAG-ATG
1 ACCCGAGACCCGAATGACCC-CAAACCCGAATA
* * ** * *
8186 ACCCGAGACCTGAATGGCCCGTAA-CCTAGATG
1 ACCCGAGACCCGAATGACCCCAAACCCGA-ATA
* ** * *
8218 ACCCGAAACCCGAATGACCCGTAACCCGAGTG
1 ACCCGAGACCCGAATGACCCCAAACCCGAATA
* *
8250 ATCCGAGACCCGTATGACCCCAAACCCGAATA
1 ACCCGAGACCCGAATGACCCCAAACCCGAATA
8282 ACCCGAGA
1 ACCCGAGA
8290 AGTTAACCCG
Statistics
Matches: 80, Mismatches: 21, Indels: 6
0.75 0.20 0.06
Matches are distributed among these distances:
30 1 0.01
31 1 0.01
32 75 0.94
33 3 0.04
ACGTcount: A:0.31, C:0.36, G:0.22, T:0.11
Consensus pattern (32 bp):
ACCCGAGACCCGAATGACCCCAAACCCGAATA
Found at i:9150 original size:16 final size:16
Alignment explanation
Indices: 9116--9266 Score: 130
Period size: 16 Copynumber: 9.5 Consensus size: 16
9106 AACCCGTCCA
*
9116 ACCCGAGACCCG-GTAG
1 ACCCGAGACCCGAAT-G
9132 ACCCGAGACCCGAATG
1 ACCCGAGACCCGAATG
9148 ACCCG-GAACCCGAATG
1 ACCCGAG-ACCCGAATG
**
9164 ACCCGAGATTCGAATG
1 ACCCGAGACCCGAATG
* *
9180 ACCCGAAACCCGTATG
1 ACCCGAGACCCGAATG
9196 ACCCGAGACCCGAATG
1 ACCCGAGACCCGAATG
* * * *
9212 ACTCGAAACTCGAATA
1 ACCCGAGACCCGAATG
* **
9228 ACCTGA-A-CTTAGATG
1 ACCCGAGACCCGA-ATG
*
9243 ACCCGAAACCCGAATG
1 ACCCGAGACCCGAATG
9259 ACCCGAGA
1 ACCCGAGA
9267 AAACTGTCTG
Statistics
Matches: 106, Mismatches: 23, Indels: 12
0.75 0.16 0.09
Matches are distributed among these distances:
14 1 0.01
15 9 0.08
16 92 0.87
17 4 0.04
ACGTcount: A:0.33, C:0.33, G:0.23, T:0.11
Consensus pattern (16 bp):
ACCCGAGACCCGAATG
Found at i:9150 original size:25 final size:25
Alignment explanation
Indices: 9122--9169 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
9112 TCCAACCCGA
9122 GACCCGGTAGACCCG-A-GACCCGAAT
1 GACCCGG-A-ACCCGAATGACCCGAAT
9147 GACCCGGAACCCGAATGACCCGA
1 GACCCGGAACCCGAATGACCCGA
9170 GATTCGAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 5 0.24
24 2 0.10
25 14 0.67
ACGTcount: A:0.29, C:0.38, G:0.27, T:0.06
Consensus pattern (25 bp):
GACCCGGAACCCGAATGACCCGAAT
Found at i:9219 original size:32 final size:32
Alignment explanation
Indices: 9116--9266 Score: 146
Period size: 32 Copynumber: 4.8 Consensus size: 32
9106 AACCCGTCCA
*
9116 ACCCGAGACCCGGTA-GACCCGAGACCCGAATG
1 ACCCGAAACCC-GTATGACCCGAGACCCGAATG
* * **
9148 ACCCGGAACCCGAATGACCCGAGATTCGAATG
1 ACCCGAAACCCGTATGACCCGAGACCCGAATG
9180 ACCCGAAACCCGTATGACCCGAGACCCGAATG
1 ACCCGAAACCCGTATGACCCGAGACCCGAATG
* * * * * **
9212 ACTCGAAACTCGAATAACCTGA-A-CTTAGATG
1 ACCCGAAACCCGTATGACCCGAGACCCGA-ATG
*
9243 ACCCGAAACCCGAATGACCCGAGA
1 ACCCGAAACCCGTATGACCCGAGA
9267 AAACTGTCTG
Statistics
Matches: 96, Mismatches: 20, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
30 2 0.02
31 24 0.25
32 70 0.73
ACGTcount: A:0.33, C:0.33, G:0.23, T:0.11
Consensus pattern (32 bp):
ACCCGAAACCCGTATGACCCGAGACCCGAATG
Found at i:9952 original size:29 final size:30
Alignment explanation
Indices: 9891--9952 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
9881 TTTATCAAGG
* *
9891 TATTATAGTTTAAAAACTTATTTCTCAAAA
1 TATTATACTTTAAAAACTTATTTCCCAAAA
* * *
9921 TATTATACTTTTAAAA-TTGTTTCCCAATA
1 TATTATACTTTAAAAACTTATTTCCCAAAA
9950 TAT
1 TAT
9953 GGTATTTTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 13 0.48
30 14 0.52
ACGTcount: A:0.39, C:0.11, G:0.03, T:0.47
Consensus pattern (30 bp):
TATTATACTTTAAAAACTTATTTCCCAAAA
Found at i:10467 original size:42 final size:43
Alignment explanation
Indices: 10402--10484 Score: 134
Period size: 42 Copynumber: 2.0 Consensus size: 43
10392 CGTGTTTGAC
*
10402 TTATCGTGTTTCGTGTCTGAATCGTGTC-GGACACGATTAAGA
1 TTATCGTGTTTCGTGTCTGAATCGTGTCAAGACACGATTAAGA
10444 TTATCGTGTTTCGTGTC-GTAATCGTGTCAAGACACGATTAA
1 TTATCGTGTTTCGTGTCTG-AATCGTGTCAAGACACGATTAA
10485 CACGTTTAAG
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
41 1 0.03
42 26 0.68
43 11 0.29
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.36
Consensus pattern (43 bp):
TTATCGTGTTTCGTGTCTGAATCGTGTCAAGACACGATTAAGA
Found at i:10497 original size:20 final size:21
Alignment explanation
Indices: 10472--10514 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
10462 TAATCGTGTC
*
10472 AAGACACGATTAACACG-TTT
1 AAGACACGAGTAACACGCTTT
*
10492 AAGACACGAGTGACACGCTTT
1 AAGACACGAGTAACACGCTTT
10513 AA
1 AA
10515 TTAACGGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (21 bp):
AAGACACGAGTAACACGCTTT
Found at i:10674 original size:14 final size:14
Alignment explanation
Indices: 10655--10682 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
10645 CAATTATCTT
10655 TAATTATATATATA
1 TAATTATATATATA
10669 TAATTATATATATA
1 TAATTATATATATA
10683 GTTTAGTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
TAATTATATATATA
Found at i:15848 original size:139 final size:139
Alignment explanation
Indices: 15615--15879 Score: 521
Period size: 139 Copynumber: 1.9 Consensus size: 139
15605 ATGAATCAGC
15615 TACATGGTTACAATCACCATGTCCACAAACCAATGACACTGTCTCCTCATCAGAAACAACTACAG
1 TACATGGTTACAATCACCATGTCCACAAACCAATGACACTGTCTCCTCATCAGAAACAACTACAG
15680 TAACATTGCTTTCTTCCTCTGAATTCTTCTTGCTTTTCCCATCTTTCCGCTCTTGCTTCAATAGT
66 TAACATTGCTTTCTTCCTCTGAATTCTTCTTGCTTTTCCCATCTTTCCGCTCTTGCTTCAATAGT
15745 AGAATTAAT
131 AGAATTAAT
*
15754 TACATGGTTACAATCACCATGTCCACAAATCAATGACACTGTCTCCTCATCAGAAACAACTACAG
1 TACATGGTTACAATCACCATGTCCACAAACCAATGACACTGTCTCCTCATCAGAAACAACTACAG
15819 TAACATTGCTTTCTTCCTCTGAATTCTTCTTGCTTTTCCCATCTTTCCGCTCTTGCTTCAA
66 TAACATTGCTTTCTTCCTCTGAATTCTTCTTGCTTTTCCCATCTTTCCGCTCTTGCTTCAA
15880 GAGCTTGCAG
Statistics
Matches: 125, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
139 125 1.00
ACGTcount: A:0.26, C:0.29, G:0.10, T:0.35
Consensus pattern (139 bp):
TACATGGTTACAATCACCATGTCCACAAACCAATGACACTGTCTCCTCATCAGAAACAACTACAG
TAACATTGCTTTCTTCCTCTGAATTCTTCTTGCTTTTCCCATCTTTCCGCTCTTGCTTCAATAGT
AGAATTAAT
Found at i:20088 original size:2 final size:2
Alignment explanation
Indices: 20083--20107 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20073 CTATAGATGA
20083 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
20108 GAGTACTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20357 original size:34 final size:35
Alignment explanation
Indices: 20298--20365 Score: 97
Period size: 34 Copynumber: 2.0 Consensus size: 35
20288 AAGCTAACAC
20298 TAATTTCTTTACTCTTTATCTTTTCTTT-TTCTTT
1 TAATTTCTTTACTCTTTATCTTTTCTTTCTTCTTT
20332 TAATTTCTTTACT-TTTATAGC-TTTCTTTCTTCTT
1 TAATTTCTTTACTCTTTAT--CTTTTCTTTCTTCTT
20366 ACTTCTTATG
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
33 5 0.16
34 20 0.65
35 6 0.19
ACGTcount: A:0.13, C:0.18, G:0.01, T:0.68
Consensus pattern (35 bp):
TAATTTCTTTACTCTTTATCTTTTCTTTCTTCTTT
Found at i:35590 original size:2 final size:2
Alignment explanation
Indices: 35583--35608 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
35573 TTAATAACCC
35583 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
35609 ATTTGAAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:42546 original size:6 final size:6
Alignment explanation
Indices: 42535--42567 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
42525 GTATGCTTAA
*
42535 TTTTCT TTTTCT TTTTGT TTTT-T TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCT TTTT
42568 AAGAGGTGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.00, C:0.09, G:0.03, T:0.88
Consensus pattern (6 bp):
TTTTCT
Found at i:42560 original size:17 final size:17
Alignment explanation
Indices: 42535--42567 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
42525 GTATGCTTAA
42535 TTTTCTTTTTCTTTTTG
1 TTTTCTTTTTCTTTTTG
*
42552 TTTTTTTTTTCTTTTT
1 TTTTCTTTTTCTTTTT
42568 AAGAGGTGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.09, G:0.03, T:0.88
Consensus pattern (17 bp):
TTTTCTTTTTCTTTTTG
Found at i:43954 original size:15 final size:15
Alignment explanation
Indices: 43934--43965 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
43924 GAGAAAATTT
43934 TATTGGTTAGGACCA
1 TATTGGTTAGGACCA
43949 TATTGGTTAGGACCA
1 TATTGGTTAGGACCA
43964 TA
1 TA
43966 ACTAACGCGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.25, T:0.34
Consensus pattern (15 bp):
TATTGGTTAGGACCA
Found at i:45168 original size:2 final size:2
Alignment explanation
Indices: 45161--45188 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
45151 CAAAACATAA
45161 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
45189 GGTAGGTACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47203 original size:59 final size:60
Alignment explanation
Indices: 47127--47243 Score: 175
Period size: 60 Copynumber: 2.0 Consensus size: 60
47117 CTGATGTTAG
*
47127 GTCCTTATTTGAACATTTTCAAT-ACATT-GGACCCTTATTTGGTCAAATTAAAAGATCGA
1 GTCCTTATTTGAACATTTTCAATAACATTAGG-CCCTTATTTGGCCAAATTAAAAGATCGA
* * *
47186 GTCCTTATTTGAGCATTTTCAATAACGTTAGGTCCTTATTTGGCCAAATTAAAAGATC
1 GTCCTTATTTGAACATTTTCAATAACATTAGGCCCTTATTTGGCCAAATTAAAAGATC
47244 ATACCCTTAT
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
59 22 0.42
60 28 0.54
61 2 0.04
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.38
Consensus pattern (60 bp):
GTCCTTATTTGAACATTTTCAATAACATTAGGCCCTTATTTGGCCAAATTAAAAGATCGA
Found at i:47285 original size:60 final size:60
Alignment explanation
Indices: 47127--47286 Score: 157
Period size: 60 Copynumber: 2.7 Consensus size: 60
47117 CTGATGTTAG
* * * * *
47127 GTCCTTATTTGAACATTTTCAAT-ACATTGGACCCTTATTTGGTCAAATTAAAAGATCGA
1 GTCCTTATATAAACATTTTCAATAACATTAGATCCTTATTTGGCCAAATTAAAAGATCGA
* * * * *
47186 GTCCTTATTTGAGCATTTTCAATAACGTTAGGTCCTTATTTGGCCAAATTAAAAGATC-A
1 GTCCTTATATAAACATTTTCAATAACATTAGATCCTTATTTGGCCAAATTAAAAGATCGA
* *
47245 -TACCCTTATATAAACATTTTGACA-AACATTAGATCTTTATTT
1 GT--CCTTATATAAACATTTTCA-ATAACATTAGATCCTTATTT
47287 AAGCAATTAG
Statistics
Matches: 84, Mismatches: 13, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
58 1 0.01
59 23 0.27
60 59 0.70
61 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.39
Consensus pattern (60 bp):
GTCCTTATATAAACATTTTCAATAACATTAGATCCTTATTTGGCCAAATTAAAAGATCGA
Found at i:52002 original size:1 final size:1
Alignment explanation
Indices: 51996--52026 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
51986 AAGTTCCTTC
51996 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.