Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012754.1 Corchorus capsularis cultivar CVL-1 contig12775, 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: 15085
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:3637 original size:48 final size:48
Alignment explanation
Indices: 3424--3852 Score: 588
Period size: 48 Copynumber: 8.9 Consensus size: 48
3414 AAAAGCGAGT
* * **
3424 AAAATTAGCGCCTTCCGTCCGGGAAGGGCGTTTTAGGAAAAGAGTGAGTA
1 AAAATTAGTGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAA-ACAG-GTA
* * * *
3474 AAAATTGGTGTCTTCCGTCCGGGAAGGGCGTTTTAGGAAAAATCAAGTA
1 AAAATTAGTGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAA-CAGGTA
* *
3523 AAAATTAGTGCCTTCCATCCGGGAAGGGCGTTTTGGGAAAATGCAGGTA
1 AAAATTAGTGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAA-ACAGGTA
* * *
3572 AAGATTAATGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAACACAGGTA
1 AAAATTAGTGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAACAGGTA
* * *
3620 AAAATCAGTGCCTTCCGTCCGGGAAGGGCGTTCTGGGAAAAACAGGTG
1 AAAATTAGTGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAACAGGTA
* *
3668 AAGATTAGTGCCTTCCGTCCGGGAAGGGCGTTTTAGGAAAAACAGGTA
1 AAAATTAGTGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAACAGGTA
* * *
3716 AAAATCAGTGCCTTCCGTGCGGGAAGGGCGTTTTGGGAAAAACATGTA
1 AAAATTAGTGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAACAGGTA
*
3764 AAAATCAGTGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAACAGGTA
1 AAAATTAGTGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAACAGGTA
* * * *
3812 AAAATAAATGCCTTCCGTCCGGGAAGGGCATTATGGGAAAA
1 AAAATTAGTGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAA
3853 GCGAGTGAAA
Statistics
Matches: 338, Mismatches: 39, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
48 217 0.64
49 83 0.25
50 38 0.11
ACGTcount: A:0.30, C:0.17, G:0.31, T:0.22
Consensus pattern (48 bp):
AAAATTAGTGCCTTCCGTCCGGGAAGGGCGTTTTGGGAAAAACAGGTA
Found at i:5003 original size:25 final size:27
Alignment explanation
Indices: 4975--5025 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
4965 TTTGCTTATT
4975 TTCATTTAG-T-AA-TATTAGTTGCATC
1 TTCATTTAGCTCAAGTATT-GTTGCATC
5000 TTCATTTAGCTCAAGTATTGTTGCAT
1 TTCATTTAGCTCAAGTATTGTTGCAT
5026 TTTAATCATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 9 0.39
26 1 0.04
27 9 0.39
28 4 0.17
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.47
Consensus pattern (27 bp):
TTCATTTAGCTCAAGTATTGTTGCATC
Found at i:8471 original size:71 final size:70
Alignment explanation
Indices: 8386--8729 Score: 332
Period size: 71 Copynumber: 4.7 Consensus size: 70
8376 ATTCATAAGA
*
8386 AGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGTAAATTGATGATTACGAGTCAAGATAATA
1 AGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGTAAATTGATAATTA-GAGTCAAGATAATA
8451 GTAATC
65 GTAATC
* * * *
8457 GGTAAATTAGTAATTAAGTAAAAGGAGATTAATCAGTAAATTGATAATTAAGAGTCAAGGTAATA
1 AGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGTAAATTGATAATT-AGAGTCAAGATAATA
8522 GTAATC
65 GTAATC
* * * *
8528 AGTAAATCGGTAATTAAGTAAAAAGATAGTAATCAGTAAATTGATAATTTAGAGTCAAGGTAAGA
1 AGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGTAAATTGATAA-TTAGAGTCAAGAT-A-A
* *
8593 AATTAATC
63 TAGTAATC
* * * *
8601 AGTAAAGTCAGTAATTAAAGAGTCAAGGTAAAAATAGTAATCAGTAAATCGATAATTAAGAGTCA
1 AGTAAA-TCAGTAATT--A-AGT-AA---AAAGAGATTAATCAGTAAATTGATAATT-AGAGTCA
* *
8666 A-AGTGATGGTAATC
57 AGA-TAATAGTAATC
* *** *
8680 AGCAAATCAGTAATTAAG-AGTTGAGTGATTAATCAGTAAATTGATAATTA
1 AGTAAATCAGTAATTAAGTA-AAAAGAGATTAATCAGTAAATTGATAATTA
8730 AGAGAGAAAG
Statistics
Matches: 228, Mismatches: 30, Indels: 31
0.79 0.10 0.11
Matches are distributed among these distances:
70 1 0.00
71 137 0.60
72 4 0.02
73 14 0.06
74 8 0.04
75 2 0.01
76 2 0.01
77 3 0.01
78 11 0.05
79 11 0.05
80 2 0.01
81 33 0.14
ACGTcount: A:0.47, C:0.06, G:0.19, T:0.28
Consensus pattern (70 bp):
AGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGTAAATTGATAATTAGAGTCAAGATAATAG
TAATC
Found at i:8496 original size:34 final size:33
Alignment explanation
Indices: 8386--8576 Score: 120
Period size: 34 Copynumber: 5.4 Consensus size: 33
8376 ATTCATAAGA
*
8386 AGTAAATCAGTAATTAAGTAAAAAGAGATTAATC
1 AGTAAAT-TGTAATTAAGTAAAAAGAGATTAATC
* *
8420 AGTAAATTGATGATTACGAGTCAAGATAATAG--TAATC
1 AGTAAATTG-TAATTA--AGT-AA-A-AAGAGATTAATC
* *
8457 GGTAAATTAGTAATTAAGTAAAAGGAGATTAATC
1 AGTAAATT-GTAATTAAGTAAAAAGAGATTAATC
**
8491 AGTAAATTGATAATTAAG-AGTCAAG-GTAATAGTAATC
1 AGTAAATTG-TAATTAAGTA-AAAAGAG--AT--TAATC
* * *
8528 AGTAAATCGGTAATTAAGTAAAAAGATAGTAATC
1 AGTAAAT-TGTAATTAAGTAAAAAGAGATTAATC
8562 AGTAAATTGATAATT
1 AGTAAATTG-TAATT
8577 TAGAGTCAAG
Statistics
Matches: 121, Mismatches: 17, Indels: 38
0.69 0.10 0.22
Matches are distributed among these distances:
32 3 0.02
33 6 0.05
34 53 0.44
35 5 0.04
36 4 0.03
37 42 0.35
38 4 0.03
39 4 0.03
ACGTcount: A:0.48, C:0.05, G:0.18, T:0.29
Consensus pattern (33 bp):
AGTAAATTGTAATTAAGTAAAAAGAGATTAATC
Found at i:8714 original size:34 final size:36
Alignment explanation
Indices: 8486--8733 Score: 170
Period size: 37 Copynumber: 6.7 Consensus size: 36
8476 AAAAGGAGAT
* * *
8486 TAATCAGTAAATTGATAATTAAGAGTCAAGGTAATAG
1 TAATCAGTAAATCGATAATTAAGAGTCAAAGTGAT-G
* **
8523 TAATCAGTAAATCGGTAATT-A-AGT-AAAAAGATAG
1 TAATCAGTAAATCGATAATTAAGAGTCAAAGTGAT-G
* * *
8557 TAATCAGTAAATTGATAATTTAGAGTCAAGGTAAGAAAT-
1 TAATCAGTAAATCGATAATTAAGAGTCAAAGT--G--ATG
* *
8596 TAATCAGTAAAGTC-AGTAATTAAAGAGTCAAGGTAAAAATAG
1 TAATCAGTAAA-TCGA-TAATT-AAGAGTCAAAGT---GAT-G
8638 TAATCAGTAAATCGATAATTAAGAGTCAAAGTGATGG
1 TAATCAGTAAATCGATAATTAAGAGTCAAAGTGAT-G
* **
8675 TAATCAGCAAATC-AGTAATTAAGAGT-TGAGTGAT-
1 TAATCAGTAAATCGA-TAATTAAGAGTCAAAGTGATG
*
8709 TAATCAGTAAATTGATAATTAAGAG
1 TAATCAGTAAATCGATAATTAAGAG
8734 AGAAAGTTGA
Statistics
Matches: 173, Mismatches: 22, Indels: 35
0.75 0.10 0.15
Matches are distributed among these distances:
34 45 0.26
35 5 0.03
36 11 0.06
37 46 0.27
39 13 0.08
40 19 0.11
41 20 0.12
42 14 0.08
ACGTcount: A:0.46, C:0.06, G:0.19, T:0.28
Consensus pattern (36 bp):
TAATCAGTAAATCGATAATTAAGAGTCAAAGTGATG
Found at i:9228 original size:40 final size:40
Alignment explanation
Indices: 9179--9297 Score: 134
Period size: 40 Copynumber: 2.9 Consensus size: 40
9169 CAATAAAGAA
*
9179 AAAATGGTAATCAGTAAAGAGTAATAGTAATCAGTAA-G-
1 AAAATGGTAATAAGTAAAGAGTAATAGTAATCAGTAAGGC
* * * *
9217 AAGTAGTGGTAATTAGAAAAGTGTAATAGTAATCAGTAAGGGC
1 AA--AATGGTAATAAGTAAAGAGTAATAGTAATCAGTAA-GGC
*
9260 AAAATGGTAATAAGTAAAGAGTAAATGGTAATCAGTAA
1 AAAATGGTAATAAGTAAAGAGT-AATAGTAATCAGTAA
9298 AGAGTAAAAT
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
38 2 0.03
40 31 0.47
41 16 0.24
42 15 0.23
43 2 0.03
ACGTcount: A:0.48, C:0.04, G:0.24, T:0.24
Consensus pattern (40 bp):
AAAATGGTAATAAGTAAAGAGTAATAGTAATCAGTAAGGC
Found at i:9413 original size:21 final size:20
Alignment explanation
Indices: 8992--9415 Score: 178
Period size: 21 Copynumber: 20.7 Consensus size: 20
8982 AGAAAGTAAA
* *
8992 AAAAGGCAACCAGTAAGAGT
1 AAAAGGTAATCAGTAAGAGT
* *
9012 AAGAAGGTAGTCAGTAAAAAGT
1 AA-AAGGTAATCAGT-AAGAGT
*
9034 AAAAGGTAGTCAGTAAGAGT
1 AAAAGGTAATCAGTAAGAGT
* *
9054 AAGAGAGTAATTAGTAAAGAAGT
1 AAAAG-GTAATCAGT-AAG-AGT
9077 AAATA-GTAATCAGTAAGAGT
1 AAA-AGGTAATCAGTAAGAGT
*
9097 AAAAGAGCAATCAGTAAAGAG-
1 AAAAG-GTAATCAGT-AAGAGT
* ** *
9118 AGATCA-GTAAAAAG-AAAATGGT
1 A-A-AAGGTAATCAGTAAGA--GT
*
9140 -AAAGAGTAA--AGTAAAAAGT
1 AAAAG-GTAATCAGT-AAGAGT
* * *
9159 AAAAAGTAATCAATAA-AGAA
1 AAAAGGTAATCAGTAAGAG-T
9179 AAAATGGTAATCAGTAAAGAGT
1 AAAA-GGTAATCAGT-AAGAGT
*
9201 AATA-GTAATCAGTAAGAAGT
1 AAAAGGTAATCAGTAAG-AGT
** * * *
9221 -AGTGGTAATTAGAAAAGTGT
1 AAAAGGTAATCAG-TAAGAGT
* * *
9241 AATA-GTAATCAGTAAGGGC
1 AAAAGGTAATCAGTAAGAGT
*
9260 AAAATGGTAATAAGTAAAGAGT
1 AAAA-GGTAATCAGT-AAGAGT
*
9282 AAATGGTAATCAGTAAAGAGT
1 AAAAGGTAATCAGT-AAGAGT
* **
9303 AAAA--TAGT--G-ATCAGT
1 AAAAGGTAATCAGTAAGAGT
9318 AAAAGGTAATCAGTAAGAGT
1 AAAAGGTAATCAGTAAGAGT
* *
9338 AAAATAGTAATCAGTAAGAGC
1 AAAA-GGTAATCAGTAAGAGT
* *
9359 AAATTGGTAATTAGTAAGAGT
1 AAA-AGGTAATCAGTAAGAGT
*
9380 AAAATAGTAATCAGTAAGGAGT
1 AAAA-GGTAATCAGTAA-GAGT
*
9402 AAAAGGTGATCAGT
1 AAAAGGTAATCAGT
9416 GATTCAAAGA
Statistics
Matches: 304, Mismatches: 59, Indels: 81
0.68 0.13 0.18
Matches are distributed among these distances:
15 8 0.03
17 4 0.01
19 30 0.10
20 63 0.21
21 146 0.48
22 44 0.14
23 8 0.03
24 1 0.00
ACGTcount: A:0.51, C:0.05, G:0.23, T:0.21
Consensus pattern (20 bp):
AAAAGGTAATCAGTAAGAGT
Found at i:9500 original size:28 final size:27
Alignment explanation
Indices: 9450--9527 Score: 81
Period size: 27 Copynumber: 2.9 Consensus size: 27
9440 AGTATAAGAA
9450 AAAAGAAGAGTAA-AAAATG-GTAATCAAT
1 AAAAG-AGAGTAAGAAAA-GAGTAAT-AAT
*
9478 AAAAGAGAGTAAGAAAAGAGTAAATAGT
1 AAAAGAGAGTAAGAAAAGAGT-AATAAT
*
9506 AAAA-ACAGTAAGAAAAGAGTAA
1 AAAAGAGAGTAAGAAAAGAGTAA
9528 AAATGATAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
26 2 0.04
27 23 0.51
28 17 0.38
29 3 0.07
ACGTcount: A:0.63, C:0.03, G:0.21, T:0.14
Consensus pattern (27 bp):
AAAAGAGAGTAAGAAAAGAGTAATAAT
Found at i:10510 original size:18 final size:18
Alignment explanation
Indices: 10485--10550 Score: 105
Period size: 18 Copynumber: 3.7 Consensus size: 18
10475 CTGCAATAAC
*
10485 ACTATGAACTCTTAAGAA
1 ACTATGAACCCTTAAGAA
*
10503 ATTATGAACCCTTAAGAA
1 ACTATGAACCCTTAAGAA
*
10521 ACTATGAACCCTAAAGAA
1 ACTATGAACCCTTAAGAA
10539 ACTATGAACCCT
1 ACTATGAACCCT
10551 CAAGTTTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.44, C:0.21, G:0.11, T:0.24
Consensus pattern (18 bp):
ACTATGAACCCTTAAGAA
Found at i:13509 original size:15 final size:15
Alignment explanation
Indices: 13489--13519 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
13479 ATTGCTCTGG
13489 CCTCATTTCAAATTC
1 CCTCATTTCAAATTC
13504 CCTCATTTCAAATTC
1 CCTCATTTCAAATTC
13519 C
1 C
13520 TATTGCTCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.35, G:0.00, T:0.39
Consensus pattern (15 bp):
CCTCATTTCAAATTC
Found at i:14643 original size:24 final size:23
Alignment explanation
Indices: 14598--14644 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
14588 GCTTTCTGTT
** *
14598 GAATCCCCCTCTAAGTATCTCTC
1 GAATCCCCCTCTAAAAACCTCTC
14621 GAATGCCCCCTCTAAAAACCTCTC
1 GAAT-CCCCCTCTAAAAACCTCTC
14645 TTTGAATCAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.26, C:0.40, G:0.09, T:0.26
Consensus pattern (23 bp):
GAATCCCCCTCTAAAAACCTCTC
Done.