Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014675.1 Corchorus capsularis cultivar CVL-1 contig14696, 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: 8638
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:5333 original size:34 final size:33
Alignment explanation
Indices: 5285--5350 Score: 105
Period size: 34 Copynumber: 2.0 Consensus size: 33
5275 TTGGAATAGT
* *
5285 AGAGTCATGGTTTTCAAAAATATTTTTTCAAAAG
1 AGAGTCATGATTTTCAAAAAT-GTTTTTCAAAAG
5319 AGAGTCATGATTTTCAAAAATGTTTTTCAAAA
1 AGAGTCATGATTTTCAAAAATGTTTTTCAAAA
5351 ATGATTTTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 10 0.33
34 20 0.67
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (33 bp):
AGAGTCATGATTTTCAAAAATGTTTTTCAAAAG
Found at i:5350 original size:12 final size:13
Alignment explanation
Indices: 5325--5362 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
5315 AAAGAGAGTC
5325 ATGATTTTCAAAA
1 ATGATTTTCAAAA
*
5338 ATGTTTTTCAAAA
1 ATGATTTTCAAAA
5351 ATGATTTTCAAA
1 ATGATTTTCAAA
5363 TAATAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (13 bp):
ATGATTTTCAAAA
Found at i:5369 original size:3 final size:3
Alignment explanation
Indices: 5361--5420 Score: 97
Period size: 3 Copynumber: 20.7 Consensus size: 3
5351 ATGATTTTCA
5361 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
5408 AA- AAT AAA AAT AA
1 AAT AAT AAT AAT AA
5421 ATTTTGAAAC
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
2 4 0.08
3 49 0.92
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:6110 original size:8 final size:8
Alignment explanation
Indices: 6083--6112 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
6073 TTCCAAGTAC
6083 AATGAAAA
1 AATGAAAA
*
6091 AATAAAAA
1 AATGAAAA
6099 AATGAAAA
1 AATGAAAA
6107 AATGAA
1 AATGAA
6113 TGGAAAAGAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (8 bp):
AATGAAAA
Found at i:7158 original size:24 final size:23
Alignment explanation
Indices: 7126--7227 Score: 111
Period size: 24 Copynumber: 4.4 Consensus size: 23
7116 TCTCTTCGAC
*
7126 TCTTTAATTATTCAATGCTTCAAT
1 TCTTCAATTATT-AATGCTTCAAT
* *
7150 ACTTCAATTTATT--T-CTTCCAT
1 TCTTCAA-TTATTAATGCTTCAAT
*
7171 TCTTCAATTACTTATTGCTTCAAT
1 TCTTCAATTA-TTAATGCTTCAAT
7195 TCTTCAATTATTCAATGCTTCAAT
1 TCTTCAATTATT-AATGCTTCAAT
7219 TCTTCAATT
1 TCTTCAATT
7228 CACTTTCAAT
Statistics
Matches: 66, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
20 3 0.05
21 14 0.21
22 1 0.02
23 3 0.05
24 40 0.61
25 5 0.08
ACGTcount: A:0.26, C:0.21, G:0.03, T:0.50
Consensus pattern (23 bp):
TCTTCAATTATTAATGCTTCAAT
Found at i:7180 original size:45 final size:45
Alignment explanation
Indices: 7102--7203 Score: 125
Period size: 45 Copynumber: 2.3 Consensus size: 45
7092 TTAGTTCTTT
* * *
7102 AATACTTCAAATTATCTCTTCGACTCTTTAATTA-TTCAATGCTTC
1 AATACTTCAATTTATCTCTTCCACTCTTCAATTACTT-AATGCTTC
* * *
7147 AATACTTCAATTTATTTCTTCCATTCTTCAATTACTTATTGCTTC
1 AATACTTCAATTTATCTCTTCCACTCTTCAATTACTTAATGCTTC
*
7192 AATTCTTCAATT
1 AATACTTCAATT
7204 ATTCAATGCT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
45 47 0.96
46 2 0.04
ACGTcount: A:0.27, C:0.22, G:0.03, T:0.48
Consensus pattern (45 bp):
AATACTTCAATTTATCTCTTCCACTCTTCAATTACTTAATGCTTC
Found at i:7227 original size:8 final size:8
Alignment explanation
Indices: 7126--7228 Score: 81
Period size: 8 Copynumber: 13.2 Consensus size: 8
7116 TCTCTTCGAC
*
7126 TCTTTAAT
1 TCTTCAAT
*
7134 TATTCAAT
1 TCTTCAAT
*
7142 GCTTCAAT
1 TCTTCAAT
*
7150 ACTTCAA-
1 TCTTCAAT
*
7157 T-TT-ATT
1 TCTTCAAT
*
7163 TCTTCCAT
1 TCTTCAAT
7171 TCTTCAAT
1 TCTTCAAT
7179 TACTT--AT
1 T-CTTCAAT
7186 TGCTTCAAT
1 T-CTTCAAT
7195 TCTTCAAT
1 TCTTCAAT
*
7203 TATTCAAT
1 TCTTCAAT
*
7211 GCTTCAAT
1 TCTTCAAT
7219 TCTTCAAT
1 TCTTCAAT
7227 TC
1 TC
7229 ACTTTCAATG
Statistics
Matches: 74, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
5 1 0.01
6 3 0.04
7 8 0.11
8 56 0.76
9 6 0.08
ACGTcount: A:0.26, C:0.21, G:0.03, T:0.50
Consensus pattern (8 bp):
TCTTCAAT
Found at i:7368 original size:14 final size:14
Alignment explanation
Indices: 7344--7392 Score: 55
Period size: 14 Copynumber: 3.4 Consensus size: 14
7334 AATGTCTCAA
7344 TTTCAATTTTCAATG
1 TTTCAA-TTTCAATG
7359 CTTT-AATTTCAATG
1 -TTTCAATTTCAATG
* *
7373 TTTCAATTCCAATT
1 TTTCAATTTCAATG
7387 TTTCAA
1 TTTCAA
7393 ATGCAATTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 3 0.10
14 22 0.73
15 2 0.07
16 3 0.10
ACGTcount: A:0.29, C:0.16, G:0.04, T:0.51
Consensus pattern (14 bp):
TTTCAATTTCAATG
Found at i:7407 original size:22 final size:22
Alignment explanation
Indices: 7382--7436 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
7372 GTTTCAATTC
* *
7382 CAATTTTTCAAATGCAATTCTT
1 CAATTATTCAAATGCAATCCTT
** *
7404 CAATCCTTCAAATTCAATCCTT
1 CAATTATTCAAATGCAATCCTT
7426 CAATTATTCAA
1 CAATTATTCAA
7437 TGCTTCAATT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.40
Consensus pattern (22 bp):
CAATTATTCAAATGCAATCCTT
Found at i:7419 original size:14 final size:15
Alignment explanation
Indices: 7402--7445 Score: 63
Period size: 14 Copynumber: 2.9 Consensus size: 15
7392 AATGCAATTC
7402 TTCAATCCTTCAA-A
1 TTCAATCCTTCAATA
7416 TTCAATCCTTCAATTA
1 TTCAATCCTTCAA-TA
*
7432 TTCAATGCTTCAAT
1 TTCAATCCTTCAAT
7446 TTACTTGAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 13 0.48
15 1 0.04
16 13 0.48
ACGTcount: A:0.32, C:0.25, G:0.02, T:0.41
Consensus pattern (15 bp):
TTCAATCCTTCAATA
Found at i:7436 original size:16 final size:16
Alignment explanation
Indices: 7396--7446 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
7386 TTTTCAAATG
*
7396 CAATTCTTCAATCCTT
1 CAATTATTCAATCCTT
7412 CAA--ATTCAATCCTT
1 CAATTATTCAATCCTT
*
7426 CAATTATTCAATGCTT
1 CAATTATTCAATCCTT
7442 CAATT
1 CAATT
7447 TACTTGAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 13 0.42
16 18 0.58
ACGTcount: A:0.31, C:0.25, G:0.02, T:0.41
Consensus pattern (16 bp):
CAATTATTCAATCCTT
Found at i:7509 original size:14 final size:13
Alignment explanation
Indices: 7474--7688 Score: 55
Period size: 14 Copynumber: 15.1 Consensus size: 13
7464 ATGGTCTTTC
7474 TTCAACTCTTCAATT
1 TTCAA-TCTTCAA-T
7489 ATTCAATGCTTCAAT
1 -TTCAAT-CTTCAAT
*
7504 TTCAATTCTACAAT
1 TTCAA-TCTTCAAT
7518 GCTTCAAT-TTCAAT
1 --TTCAATCTTCAAT
*
7532 TCTCCAA-ATTCAAT
1 T-T-CAATCTTCAAT
*
7546 CCTTCAATGCTCCAAT
1 --TTCAAT-CTTCAAT
* *
7562 TCCAATTCTTCAAA
1 TTCAA-TCTTCAAT
*
7576 TTCAATCCTTCGATGT
1 TTCAAT-CTTC-A-AT
*
7592 TTCAAT-TGCAATT
1 TTCAATCTTCAA-T
* *
7605 CTTCAATGTTTCAGT
1 -TTCAAT-CTTCAAT
*
7620 TCCAAT-TTC-AT
1 TTCAATCTTCAAT
7631 TTCCAATGCTTCAAT
1 TT-CAAT-CTTCAAT
*
7646 TTCAATTCTTCAAA
1 TTCAA-TCTTCAAT
*
7660 TTCAGTACTTCAAAGT
1 TTCAAT-CTTC-AA-T
7676 TTCAAT-TTCAAT
1 TTCAATCTTCAAT
7688 T
1 T
7689 CTTCAGCGCT
Statistics
Matches: 151, Mismatches: 21, Indels: 58
0.66 0.09 0.25
Matches are distributed among these distances:
11 2 0.01
12 10 0.07
13 7 0.05
14 81 0.54
15 15 0.10
16 36 0.24
ACGTcount: A:0.29, C:0.24, G:0.05, T:0.42
Consensus pattern (13 bp):
TTCAATCTTCAAT
Found at i:7533 original size:22 final size:22
Alignment explanation
Indices: 7473--7534 Score: 88
Period size: 22 Copynumber: 2.7 Consensus size: 22
7463 GATGGTCTTT
* *
7473 CTTCAACTCTTCAATTATTCAATG
1 CTTCAA-T-TTCAATTCTACAATG
7497 CTTCAATTTCAATTCTACAATG
1 CTTCAATTTCAATTCTACAATG
7519 CTTCAATTTCAATTCT
1 CTTCAATTTCAATTCT
7535 CCAAATTCAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
22 29 0.81
23 1 0.03
24 6 0.17
ACGTcount: A:0.29, C:0.24, G:0.03, T:0.44
Consensus pattern (22 bp):
CTTCAATTTCAATTCTACAATG
Found at i:7551 original size:22 final size:22
Alignment explanation
Indices: 7526--7574 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
7516 ATGCTTCAAT
*
7526 TTCAATTCTCCAAATT-CAATCC
1 TTCAATGCTCC-AATTCCAATCC
*
7548 TTCAATGCTCCAATTCCAATTC
1 TTCAATGCTCCAATTCCAATCC
7570 TTCAA
1 TTCAA
7575 ATTCAATCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 4 0.17
22 20 0.83
ACGTcount: A:0.31, C:0.31, G:0.02, T:0.37
Consensus pattern (22 bp):
TTCAATGCTCCAATTCCAATCC
Found at i:7555 original size:159 final size:158
Alignment explanation
Indices: 7264--7586 Score: 386
Period size: 159 Copynumber: 2.0 Consensus size: 158
7254 TTTTTCGTTT
* * * * * *
7264 CTTCAATTATTCAATGCTTCAATTGGCTTCAATAATACATGGTGGTCTTTCTTCCATTCCTCAAT
1 CTTCAATTATTCAATGCTTCAATTGACTTCAATAACACAAGATGGTCTTTCTTCAACTCCTCAAT
* * * **
7329 TATTCAATGTCTCAATTTCAATTTTCAATGCTTTAATTTCAATGTTTCAATTCCAATTTTTCAAA
66 TATTCAATGTCTCAATTTCAATTTACAATGCTTCAATTTCAATGTTCCAATTCCAATCCTTCAAA
7394 TG-CAATTCTTCAATCCTTCAAATTCAATC
131 TGCCAATTC--CAATCCTTCAAATTCAATC
* * * * *
7423 CTTCAATTATTCAATGCTTCAATTTACTTGAATGACCCAAGATGGTCTTTCTTCAACTCTTCAAT
1 CTTCAATTATTCAATGCTTCAATTGACTTCAATAACACAAGATGGTCTTTCTTCAACTCCTCAAT
7488 TATTCAATG-CTTCAATTTCAATTCTACAATGCTTCAATTTCAAT-TCTCCAAATT-CAATCCTT
66 TATTCAATGTC-TCAATTTCAATT-TACAATGCTTCAATTTCAATGT-TCC-AATTCCAATCCTT
*
7550 C-AATGCTCCAATTCCAATTCTTCAAATTCAATC
127 CAAATG--CCAATTCCAATCCTTCAAATTCAATC
7583 CTTC
1 CTTC
7587 GATGTTTCAA
Statistics
Matches: 140, Mismatches: 17, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
158 1 0.01
159 80 0.57
160 49 0.35
161 4 0.03
162 6 0.04
ACGTcount: A:0.29, C:0.24, G:0.06, T:0.41
Consensus pattern (158 bp):
CTTCAATTATTCAATGCTTCAATTGACTTCAATAACACAAGATGGTCTTTCTTCAACTCCTCAAT
TATTCAATGTCTCAATTTCAATTTACAATGCTTCAATTTCAATGTTCCAATTCCAATCCTTCAAA
TGCCAATTCCAATCCTTCAAATTCAATC
Found at i:7607 original size:36 final size:36
Alignment explanation
Indices: 7492--7610 Score: 148
Period size: 36 Copynumber: 3.3 Consensus size: 36
7482 TTCAATTATT
* * * * *
7492 CAATGCTTCAATTTCAATTCTACAATGCTTCAATTT
1 CAATTCTTCAAATTCAATCCTTCAATGCTTCAATTC
* *
7528 CAATTCTCCAAATTCAATCCTTCAATGCTCCAATTC
1 CAATTCTTCAAATTCAATCCTTCAATGCTTCAATTC
* * *
7564 CAATTCTTCAAATTCAATCCTTCGATGTTTCAATTG
1 CAATTCTTCAAATTCAATCCTTCAATGCTTCAATTC
7600 CAATTCTTCAA
1 CAATTCTTCAA
7611 TGTTTCAGTT
Statistics
Matches: 71, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 71 1.00
ACGTcount: A:0.30, C:0.26, G:0.05, T:0.39
Consensus pattern (36 bp):
CAATTCTTCAAATTCAATCCTTCAATGCTTCAATTC
Found at i:7625 original size:22 final size:22
Alignment explanation
Indices: 7574--7658 Score: 73
Period size: 22 Copynumber: 3.7 Consensus size: 22
7564 CAATTCTTCA
* *
7574 AATT-CAATCCTTCGATGTTTC
1 AATTCCAATTCTTCAATGTTTC
*
7595 AATTGCAATTCTTCAATGTTTC
1 AATTCCAATTCTTCAATGTTTC
* *
7617 AGTTCCAATTTCATTTCCAATGCTTC
1 AATTCCAA-TTC--TT-CAATGTTTC
*
7643 AATTTCAATTCTTCAA
1 AATTCCAATTCTTCAA
7659 ATTCAGTACT
Statistics
Matches: 52, Mismatches: 7, Indels: 9
0.76 0.10 0.13
Matches are distributed among these distances:
21 4 0.08
22 24 0.46
23 5 0.10
25 5 0.10
26 14 0.27
ACGTcount: A:0.27, C:0.22, G:0.07, T:0.44
Consensus pattern (22 bp):
AATTCCAATTCTTCAATGTTTC
Found at i:7893 original size:6 final size:6
Alignment explanation
Indices: 7882--7942 Score: 50
Period size: 6 Copynumber: 9.2 Consensus size: 6
7872 CTTCAAATGC
* *
7882 TTCAAT TTCAAT TCTCCAAT GCTTCAAT TCCAAT TTCATT TTCAATGT
1 TTCAAT TTCAAT T-T-CAAT --TTCAAT TTCAAT TTCAAT TTCAA--T
7930 TTCAAT TTCAAT T
1 TTCAAT TTCAAT T
7943 CTTCAATGCT
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
6 28 0.62
7 1 0.02
8 14 0.31
9 1 0.02
10 1 0.02
ACGTcount: A:0.28, C:0.21, G:0.03, T:0.48
Consensus pattern (6 bp):
TTCAAT
Found at i:7933 original size:26 final size:28
Alignment explanation
Indices: 7851--7942 Score: 80
Period size: 26 Copynumber: 3.2 Consensus size: 28
7841 GGTCCTTCTA
* *
7851 CAATTTCAATTCTCCAATTTTCTTCAAATGCTT
1 CAATTTCAATTCTCCAA--TGCTTC-AAT--TC
7884 CAATTTCAATTCTCCAATGCTTCAATTC
1 CAATTTCAATTCTCCAATGCTTCAATTC
* * *
7912 CAATTTC-ATT-TTCAATGTTTCAATTT
1 CAATTTCAATTCTCCAATGCTTCAATTC
7938 CAATT
1 CAATT
7943 CTTCAATGCT
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
26 18 0.33
27 3 0.06
28 8 0.15
30 3 0.06
31 5 0.09
33 17 0.31
ACGTcount: A:0.28, C:0.23, G:0.03, T:0.46
Consensus pattern (28 bp):
CAATTTCAATTCTCCAATGCTTCAATTC
Found at i:7947 original size:14 final size:14
Alignment explanation
Indices: 7881--7972 Score: 52
Period size: 14 Copynumber: 6.6 Consensus size: 14
7871 TCTTCAAATG
7881 CTTCAATTTCAATT
1 CTTCAATTTCAATT
*
7895 CTCCAATGCTTCAATT
1 CTTCAAT--TTCAATT
7911 C--CAATTTC-ATT
1 CTTCAATTTCAATT
7922 -TTCAATGTTTCAA-T
1 CTTCAA--TTTCAATT
*
7936 -TTCAATTCTTCAATG
1 CTTCAA-T-TTCAATT
*
7951 CTTCACTTTCAATT
1 CTTCAATTTCAATT
*
7965 CTTTAATT
1 CTTCAATT
7973 CCCCAATTTA
Statistics
Matches: 61, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
11 3 0.05
12 6 0.10
13 1 0.02
14 37 0.61
15 2 0.03
16 12 0.20
ACGTcount: A:0.26, C:0.23, G:0.03, T:0.48
Consensus pattern (14 bp):
CTTCAATTTCAATT
Found at i:7950 original size:22 final size:21
Alignment explanation
Indices: 7851--7972 Score: 87
Period size: 22 Copynumber: 5.9 Consensus size: 21
7841 GGTCCTTCTA
*
7851 CAATTTCAATTCTCCAATTTT
1 CAATTTCAATTCTTCAATTTT
*
7872 C---TTCAAATGCTTCAA-TTT
1 CAATTTC-AATTCTTCAATTTT
* *
7890 CAATTCTCCAATGCTTCAA-TTC
1 CAATT-T-CAATTCTTCAATTTT
7912 CAATTTC-ATT-TTCAATGTTT
1 CAATTTCAATTCTTCAAT-TTT
*
7932 CAATTTCAATTCTTCAATGCTT
1 CAATTTCAATTCTTCAAT-TTT
* *
7954 CACTTTCAATTCTTTAATT
1 CAATTTCAATTCTTCAATT
7973 CCCCAATTTA
Statistics
Matches: 82, Mismatches: 9, Indels: 20
0.74 0.08 0.18
Matches are distributed among these distances:
18 12 0.15
19 10 0.12
20 10 0.12
21 6 0.07
22 43 0.52
23 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.03, T:0.47
Consensus pattern (21 bp):
CAATTTCAATTCTTCAATTTT
Done.