Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023571.1 Corchorus olitorius cultivar O-4 contig23604, 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: 9913
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.35
Found at i:1458 original size:15 final size:15
Alignment explanation
Indices: 1435--1479 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 15
1425 ATATTGTTTT
1435 AAAAA-GATTTTTCA
1 AAAAATGATTTTTCA
*
1449 AAAAATGATTTCTC-
1 AAAAATGATTTTTCA
1463 AAAAATG--TTTTCA
1 AAAAATGATTTTTCA
1476 AAAA
1 AAAA
1480 TTTGTTTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 4 0.15
13 4 0.15
14 12 0.44
15 7 0.26
ACGTcount: A:0.51, C:0.09, G:0.07, T:0.33
Consensus pattern (15 bp):
AAAAATGATTTTTCA
Found at i:1489 original size:14 final size:12
Alignment explanation
Indices: 1429--1480 Score: 52
Period size: 12 Copynumber: 4.1 Consensus size: 12
1419 AGAGTCATAT
*
1429 TGTTTTAAAAAGA
1 TGTTTTCAAAA-A
1442 T-TTTTCAAAAAA
1 TGTTTTC-AAAAA
1454 TGATTTCTCAAAAA
1 TG-TTT-TCAAAAA
1468 TGTTTTCAAAAA
1 TGTTTTCAAAAA
1480 T
1 T
1481 TTGTTTTCAC
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
12 14 0.41
13 8 0.24
14 10 0.29
15 2 0.06
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
TGTTTTCAAAAA
Found at i:1798 original size:6 final size:7
Alignment explanation
Indices: 1779--1810 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
1769 CAATAAAGAT
1779 GAAAAAA
1 GAAAAAA
1786 GGAAAAAA
1 -GAAAAAA
1794 GAAAAAA
1 GAAAAAA
1801 GAAAAAA
1 GAAAAAA
1808 GAA
1 GAA
1811 GGAAAAAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:1801 original size:25 final size:26
Alignment explanation
Indices: 1773--1832 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 26
1763 AAAAGTCAAT
1773 AAAGATGAAAA-AAGGAAAAAAGAAA
1 AAAGATGAAAAGAAGGAAAAAAGAAA
* **
1798 AAAGA-AAAAAGAAGGAAAAAAGTTA
1 AAAGATGAAAAGAAGGAAAAAAGAAA
1823 AAAG-TGAAAA
1 AAAGATGAAAA
1833 TTGAAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
24 4 0.14
25 25 0.86
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (26 bp):
AAAGATGAAAAGAAGGAAAAAAGAAA
Found at i:3142 original size:8 final size:8
Alignment explanation
Indices: 3129--3667 Score: 157
Period size: 8 Copynumber: 69.6 Consensus size: 8
3119 GTTCGATTAG
3129 CTTCAATT
1 CTTCAATT
3137 CTTCAATT
1 CTTCAATT
*
3145 CTTCAATC
1 CTTCAATT
*
3153 CTTCAATG
1 CTTCAATT
3161 CTTCAATTT
1 CTTCAA-TT
* *
3170 ATTTCAAAATG
1 -CTTC--AATT
* *
3181 ATATC-TTT
1 CT-TCAATT
3189 CTTCAATT
1 CTTCAATT
*
3197 CTTCAAAT
1 CTTCAATT
*
3205 CTTCAATA
1 CTTCAATT
3213 CTTCAA-T
1 CTTCAATT
*
3220 -TT-ATTT
1 CTTCAATT
3226 CTTCAATT
1 CTTCAATT
3234 CTTCAATT
1 CTTCAATT
* *
3242 ATT-TATT
1 CTTCAATT
*
3249 GCTTTAATT
1 -CTTCAATT
3258 CTTCAATT
1 CTTCAATT
*
3266 AC-TCAATG
1 -CTTCAATT
3274 CTTCAATT
1 CTTCAATT
3282 CTTCAATGT
1 CTTCAAT-T
* *
3291 ACTTAAATG
1 -CTTCAATT
* * **
3300 ATCCAGGGT
1 CTTCA-ATT
** *
3309 GGTC-TTT
1 CTTCAATT
*
3316 CTTCCATT
1 CTTCAATT
3324 CTTCAATT
1 CTTCAATT
* *
3332 ATTCAATG
1 CTTCAATT
*
3340 CCTCAA-T
1 CTTCAATT
*
3347 -TTCAAAT
1 CTTCAATT
*
3354 CTTCAATG
1 CTTCAATT
3362 CTTCAATT
1 CTTCAATT
3370 -TT-AATT
1 CTTCAATT
3376 CTTCAATT
1 CTTCAATT
3384 CTTCAA--
1 CTTCAATT
*
3390 ATTCAATT
1 CTTCAATT
* *
3398 TTTCAGTGT
1 CTTCAAT-T
3407 -TTCAA-T
1 CTTCAATT
3413 -TTCAATAT
1 CTTCAAT-T
***
3421 -TTCAGCG
1 CTTCAATT
3428 CTTCAA-T
1 CTTCAATT
3435 -TTCAATT
1 CTTCAATT
*
3442 CTTCAGTGT
1 CTTCAAT-T
3451 -TTCAA-T
1 CTTCAATT
3457 -TTCAAATT
1 CTTC-AATT
3465 CTTCAATGT
1 CTTCAAT-T
*
3474 -TTC-AGT
1 CTTCAATT
*
3480 -TGCAATAT
1 CTTCAAT-T
*
3488 -TTCAATG
1 CTTCAATT
3495 CTTCAA-T
1 CTTCAATT
*
3502 -TTCGATT
1 CTTCAATT
3509 CTTCAA--
1 CTTCAATT
* *
3515 ATTCAATC
1 CTTCAATT
3523 CTTCAATGT
1 CTTCAAT-T
3532 -TTCAA-T
1 CTTCAATT
3538 -TTCAATT
1 CTTCAATT
*
3545 CTTCAAATG
1 CTTC-AATT
*
3554 CTTC-AGT
1 CTTCAATT
3561 -TTCAATT
1 CTTCAATT
**
3568 CTTCAACG
1 CTTCAATT
*
3576 CTTC-ACT
1 CTTCAATT
3583 -TTCAATT
1 CTTCAATT
*
3590 CTTCAATA
1 CTTCAATT
3598 CTTCAA-T
1 CTTCAATT
*
3605 -TTCAATA
1 CTTCAATT
3612 CTTCAATT
1 CTTCAATT
3620 CTTCAATTATT
1 CTTC-A--ATT
3631 CTTCAATT
1 CTTCAATT
**
3639 CTTCAACC
1 CTTCAATT
3647 CTTCAATT
1 CTTCAATT
*
3655 CTTCAATG
1 CTTCAATT
3663 CTTCA
1 CTTCA
3668 GTTTATTTTA
Statistics
Matches: 389, Mismatches: 88, Indels: 108
0.66 0.15 0.18
Matches are distributed among these distances:
5 1 0.00
6 60 0.15
7 30 0.08
8 254 0.65
9 21 0.05
10 11 0.03
11 10 0.03
12 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.05, T:0.45
Consensus pattern (8 bp):
CTTCAATT
Found at i:3230 original size:21 final size:20
Alignment explanation
Indices: 3204--3245 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
3194 ATTCTTCAAA
3204 TCTTCAATACTTCAATTTATT
1 TCTTCAATACTTCAA-TTATT
*
3225 TCTTCAATTCTTCAATTATT
1 TCTTCAATACTTCAATTATT
3245 T
1 T
3246 ATTGCTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.26, C:0.19, G:0.00, T:0.55
Consensus pattern (20 bp):
TCTTCAATACTTCAATTATT
Found at i:3358 original size:22 final size:22
Alignment explanation
Indices: 3333--3514 Score: 152
Period size: 22 Copynumber: 8.2 Consensus size: 22
3323 TCTTCAATTA
*
3333 TTCAATGCCTCAATTTCAAATC
1 TTCAATGCTTCAATTTCAAATC
* *
3355 TTCAATGCTTCAATTTTAATTC
1 TTCAATGCTTCAATTTCAAATC
* * * *
3377 TTCAATTCTTCAAATTCAATTT
1 TTCAATGCTTCAATTTCAAATC
* *
3399 TTCAGTGTTTCAATTTCAATAT-
1 TTCAATGCTTCAATTTCAA-ATC
** *
3421 TTCAGCGCTTCAATTTCAATTC
1 TTCAATGCTTCAATTTCAAATC
* *
3443 TTCAGTGTTTCAATTTCAAATTC
1 TTCAATGCTTCAATTTCAAA-TC
* * *
3466 TTCAATGTTTCAGTTGCAATAT-
1 TTCAATGCTTCAATTTCAA-ATC
* *
3488 TTCAATGCTTCAATTTCGATTC
1 TTCAATGCTTCAATTTCAAATC
3510 TTCAA
1 TTCAA
3515 ATTCAATCCT
Statistics
Matches: 129, Mismatches: 26, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
21 2 0.02
22 106 0.82
23 20 0.16
24 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.07, T:0.46
Consensus pattern (22 bp):
TTCAATGCTTCAATTTCAAATC
Found at i:3503 original size:14 final size:13
Alignment explanation
Indices: 3486--3619 Score: 65
Period size: 14 Copynumber: 9.2 Consensus size: 13
3476 CAGTTGCAAT
3486 ATTTCAATGCTTCA
1 ATTTCAAT-CTTCA
*
3500 ATTTCGATTCTTCA
1 ATTTC-AATCTTCA
*
3514 AATTCAATCCTTCA
1 ATTTCAAT-CTTCA
3528 ATGTTTCAAT-TTCA
1 A--TTTCAATCTTCA
3542 ATTCTTCAAATGCTTCA
1 A-T-TTC-AAT-CTTCA
*
3559 GTTTCAATTCTTCA
1 ATTTCAA-TCTTCA
* *
3573 ACGCTTCACT-TTCA
1 A--TTTCAATCTTCA
3587 ATTCTTCAATACTTCA
1 A-T-TTCAAT-CTTCA
3603 ATTTCAATACTTCA
1 ATTTCAAT-CTTCA
3617 ATT
1 ATT
3620 CTTCAATTAT
Statistics
Matches: 94, Mismatches: 12, Indels: 28
0.70 0.09 0.21
Matches are distributed among these distances:
13 3 0.03
14 60 0.64
15 11 0.12
16 16 0.17
17 4 0.04
ACGTcount: A:0.28, C:0.23, G:0.04, T:0.44
Consensus pattern (13 bp):
ATTTCAATCTTCA
Found at i:3535 original size:22 final size:22
Alignment explanation
Indices: 3509--3667 Score: 171
Period size: 22 Copynumber: 7.2 Consensus size: 22
3499 AATTTCGATT
* *
3509 CTTCAAATTCAATCCTTCAATG
1 CTTCAATTTCAATTCTTCAATG
*
3531 TTTCAATTTCAATTCTTCAAATG
1 CTTCAATTTCAATTCTTC-AATG
* *
3554 CTTCAGTTTCAATTCTTCAACG
1 CTTCAATTTCAATTCTTCAATG
* *
3576 CTTCACTTTCAATTCTTCAATA
1 CTTCAATTTCAATTCTTCAATG
* *
3598 CTTCAATTTCAATACTTCAATT
1 CTTCAATTTCAATTCTTCAATG
*
3620 CTTCAA-TT--ATTCTTCAATT
1 CTTCAATTTCAATTCTTCAATG
*
3639 CTTCAACCCTTCAATTCTTCAATG
1 CTTCAA--TTTCAATTCTTCAATG
3663 CTTCA
1 CTTCA
3668 GTTTATTTTA
Statistics
Matches: 117, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
19 16 0.14
21 2 0.02
22 64 0.55
23 20 0.17
24 15 0.13
ACGTcount: A:0.28, C:0.26, G:0.03, T:0.43
Consensus pattern (22 bp):
CTTCAATTTCAATTCTTCAATG
Found at i:3591 original size:81 final size:81
Alignment explanation
Indices: 3428--3643 Score: 233
Period size: 81 Copynumber: 2.6 Consensus size: 81
3418 TATTTCAGCG
* * * *
3428 CTTCAATTTCAATTCTTCAGTGTTTCAATTTCAAATTCTTCAATGTTTCAGTTGCAATATTTCAA
1 CTTCAAATTCAATCCTTCAATGTTTCAATTTCAAATTCTTCAATGCTTCAGTTGCAATATTTCAA
* *
3493 TGCTTCAATTTCGATT
66 CGCTTCAATTTCAATT
*
3509 CTTCAAATTCAATCCTTCAATGTTTCAATTTC-AATTCTTCAAATGCTTCAGTTTCAAT-TCTTC
1 CTTCAAATTCAATCCTTCAATGTTTCAATTTCAAATTCTTC-AATGCTTCAGTTGCAATAT-TTC
*
3572 AACGCTTCACTTTCAATT
64 AACGCTTCAATTTCAATT
** *
3590 CTTCAATACTTCAAT--TTCAATACTTCAATTCTTCAATTATTCTTCAATTCTTCA
1 CTTCAA-A-TTCAATCCTTCAATGTTTCAA-T-TTCAA--ATTCTTCAATGCTTCA
3644 ACCCTTCAAT
Statistics
Matches: 115, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
80 9 0.08
81 79 0.69
82 2 0.02
83 9 0.08
84 1 0.01
85 8 0.07
86 7 0.06
ACGTcount: A:0.27, C:0.22, G:0.05, T:0.45
Consensus pattern (81 bp):
CTTCAAATTCAATCCTTCAATGTTTCAATTTCAAATTCTTCAATGCTTCAGTTGCAATATTTCAA
CGCTTCAATTTCAATT
Found at i:6948 original size:18 final size:17
Alignment explanation
Indices: 6890--6950 Score: 50
Period size: 18 Copynumber: 3.4 Consensus size: 17
6880 TTTTTCTATT
*
6890 TTGGACTTTAGATTTATG
1 TTGGGCTTTA-ATTTATG
* * *
6908 TTGGGCCCTTAATGTATTT
1 TTGGG-CTTTAATTTA-TG
6927 TTGGGCTTTAATTTATG
1 TTGGGCTTTAATTTATG
6944 CTTGGGC
1 -TTGGGC
6951 CATTGTTGCT
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
17 1 0.03
18 22 0.67
19 10 0.30
ACGTcount: A:0.16, C:0.11, G:0.25, T:0.48
Consensus pattern (17 bp):
TTGGGCTTTAATTTATG
Found at i:7470 original size:68 final size:67
Alignment explanation
Indices: 7379--7506 Score: 238
Period size: 68 Copynumber: 1.9 Consensus size: 67
7369 TACGAAGGGT
7379 CATTTTCGTCTTTTGCATTTAAGTTTAGTGTTTTCTATTTCCAAAAATACCCTTTCGGTCAAAAG
1 CATTTTCGTCTTTTGCATTTAAGTTTAGTGTTTTCTATTTCCAAAAATACCCTTTCGGTCAAAAG
7444 GC
66 GC
*
7446 CATTTTCGTCTTTTTGCATTTAAGTTTAGTGTTTTCTATTTCCAAAAATACCCTTTTGGTC
1 CATTTTCGTC-TTTTGCATTTAAGTTTAGTGTTTTCTATTTCCAAAAATACCCTTTCGGTC
7507 GTATTTATGG
Statistics
Matches: 59, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
67 10 0.17
68 49 0.83
ACGTcount: A:0.22, C:0.19, G:0.12, T:0.47
Consensus pattern (67 bp):
CATTTTCGTCTTTTGCATTTAAGTTTAGTGTTTTCTATTTCCAAAAATACCCTTTCGGTCAAAAG
GC
Done.