Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013362.1 Corchorus olitorius cultivar O-4 contig13395, 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: 18885
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Found at i:6765 original size:26 final size:23
Alignment explanation
Indices: 6735--6781 Score: 67
Period size: 26 Copynumber: 1.9 Consensus size: 23
6725 CTTGAAAATT
6735 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAAC-TTGAT-GAT-AGATGGA
6761 TGAAAAACTTGATGATAGATG
1 TGAAAAACTTGATGATAGATG
6782 AATAGAAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 3 0.14
25 5 0.24
26 8 0.38
ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28
Consensus pattern (23 bp):
TGAAAAACTTGATGATAGATGGA
Found at i:8035 original size:24 final size:25
Alignment explanation
Indices: 8003--8050 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
7993 GTAGCTCATC
*
8003 GAAAACTCCTTA-AAAGAAAGAAGT
1 GAAAACTCCATACAAAGAAAGAAGT
*
8027 GAAAACTCCATACAAAGAGAGAAG
1 GAAAACTCCATACAAAGAAAGAAG
8051 GTAGCGCAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.54, C:0.15, G:0.19, T:0.12
Consensus pattern (25 bp):
GAAAACTCCATACAAAGAAAGAAGT
Found at i:10132 original size:54 final size:53
Alignment explanation
Indices: 10074--10299 Score: 226
Period size: 54 Copynumber: 4.2 Consensus size: 53
10064 TATTACTACT
*
10074 TTTTACTTTTTAGCCTAATTACTCTGAATTAAACTAATTACTGCTTAGTCTTTC
1 TTTTACTTTTTAGCTTAATTACTCTGAATTAAACTAATTACTG-TTAGTCTTTC
* * * *
10128 TTTTACTATTCAGCTTAATTAC-CTAGAATTAAGCT--TTACTGTTTACG-CCTTC
1 TTTTACTTTTTAGCTTAATTACTCT-GAATTAAACTAATTACTG-TTA-GTCTTTC
** * * * *
10180 TTTTACTTCCTAGTTTAATTACCCTGAATTAAACTAATTACTGTTTGCTCTTTA
1 TTTTACTTTTTAGCTTAATTACTCTGAATTAAACTAATTACTGTTAG-TCTTTC
** *
10234 TTTTACTTTTTAGCTTAATTACTCTTGAATTAAACTAATCTTTTGATTACTCTTTC
1 TTTTACTTTTTAGCTTAATTACTC-TGAATTAAACTAAT-TACTG-TTAGTCTTTC
10290 TTTTACTTTT
1 TTTTACTTTT
10300 GATTAGTGTT
Statistics
Matches: 138, Mismatches: 24, Indels: 18
0.77 0.13 0.10
Matches are distributed among these distances:
52 40 0.29
53 7 0.05
54 57 0.41
55 14 0.10
56 18 0.13
57 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.07, T:0.50
Consensus pattern (53 bp):
TTTTACTTTTTAGCTTAATTACTCTGAATTAAACTAATTACTGTTAGTCTTTC
Found at i:10301 original size:22 final size:22
Alignment explanation
Indices: 10277--10495 Score: 228
Period size: 22 Copynumber: 10.0 Consensus size: 22
10267 ACTAATCTTT
*
10277 TGATTACTCTTTCTTTTACTTT
1 TGATTACTCTTTCTTTTACTTC
* *
10299 TGATTAGTGTTTCTTTTACTTC
1 TGATTACTCTTTCTTTTACTTC
* *
10321 TGATTACTCTTTCTTCTATTTC
1 TGATTACTCTTTCTTTTACTTC
10343 TGATTACTCTTTCTTTTACTTC
1 TGATTACTCTTTCTTTTACTTC
* **
10365 TGATTATTCTTTCTTCAACTTC
1 TGATTACTCTTTCTTTTACTTC
*
10387 TAATTACTCTTTCTTTTAC-TC
1 TGATTACTCTTTCTTTTACTTC
** * **
10408 TTTTTACGCTCCCTTTTACTTC
1 TGATTACTCTTTCTTTTACTTC
* * *
10430 TGATTACTCTTCCTTCTACTCC
1 TGATTACTCTTTCTTTTACTTC
* *
10452 TGATTACT-TTTCCTTCTACTCC
1 TGATTACTCTTT-CTTTTACTTC
*
10474 TGATTACTTTTTCTTTTA-TTC
1 TGATTACTCTTTCTTTTACTTC
10495 T
1 T
10496 CTTTTAGTTT
Statistics
Matches: 164, Mismatches: 30, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
21 21 0.13
22 140 0.85
23 3 0.02
ACGTcount: A:0.14, C:0.24, G:0.05, T:0.57
Consensus pattern (22 bp):
TGATTACTCTTTCTTTTACTTC
Found at i:10480 original size:87 final size:88
Alignment explanation
Indices: 10340--10501 Score: 220
Period size: 87 Copynumber: 1.9 Consensus size: 88
10330 TTTCTTCTAT
* * * * *
10340 TTCTGATTACTCTTTCTTTTACTTCTGATTATTCTTTCTTCAACTTCTAATTACTCTTTCTTTTA
1 TTCTGATTACTCTTCCTTCTACTCCTGATTATTCTTCCTTCAACTCCTAATTACTCTTTCTTTTA
10405 CTCT-TTTTACGCTCCCTTTTAC
66 CTCTCTTTTACGCTCCCTTTTAC
* * *
10427 TTCTGATTACTCTTCCTTCTACTCCTGATTACTT-TTCCTTCTACTCCTGATTACTTTTTCTTTT
1 TTCTGATTACTCTTCCTTCTACTCCTGATTA-TTCTTCCTTCAACTCCTAATTACTCTTTCTTTT
*
10491 ATTCTCTTTTA
65 ACTCTCTTTTA
10502 GTTTAATTAC
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
87 57 0.89
88 7 0.11
ACGTcount: A:0.14, C:0.26, G:0.04, T:0.56
Consensus pattern (88 bp):
TTCTGATTACTCTTCCTTCTACTCCTGATTATTCTTCCTTCAACTCCTAATTACTCTTTCTTTTA
CTCTCTTTTACGCTCCCTTTTAC
Found at i:10540 original size:28 final size:28
Alignment explanation
Indices: 10507--10601 Score: 84
Period size: 28 Copynumber: 3.3 Consensus size: 28
10497 TTTTAGTTTA
10507 ATTACTCTTGAATTAAACTAATCTTCTG
1 ATTACTCTTGAATTAAACTAATCTTCTG
** ** ** * *
10535 ATTACTCTT-TCTTTTACTCTTTTTAGCTTA
1 ATTACTCTTGAATTAAACTAATCTT--C-TG
10565 ATTACTCTTGAATTAAACTAATCTTCTG
1 ATTACTCTTGAATTAAACTAATCTTCTG
10593 ATTACTCTT
1 ATTACTCTT
10602 TCTTTTTCTT
Statistics
Matches: 47, Mismatches: 16, Indels: 8
0.66 0.23 0.11
Matches are distributed among these distances:
27 8 0.17
28 19 0.40
29 2 0.04
30 10 0.21
31 8 0.17
ACGTcount: A:0.26, C:0.19, G:0.05, T:0.49
Consensus pattern (28 bp):
ATTACTCTTGAATTAAACTAATCTTCTG
Found at i:10573 original size:58 final size:59
Alignment explanation
Indices: 10473--10607 Score: 236
Period size: 58 Copynumber: 2.3 Consensus size: 59
10463 CCTTCTACTC
* * *
10473 CTGATTACTTTTTCTTTTATTCTCTTTTAGTTTAATTACTCTTGAATTAAACTAATCTT
1 CTGATTACTCTTTCTTTTACTCTCTTTTAGCTTAATTACTCTTGAATTAAACTAATCTT
10532 CTGATTACTCTTTCTTTTACTCT-TTTTAGCTTAATTACTCTTGAATTAAACTAATCTT
1 CTGATTACTCTTTCTTTTACTCTCTTTTAGCTTAATTACTCTTGAATTAAACTAATCTT
10590 CTGATTACTCTTTCTTTT
1 CTGATTACTCTTTCTTTT
10608 TCTTATGATT
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
58 52 0.71
59 21 0.29
ACGTcount: A:0.22, C:0.18, G:0.05, T:0.55
Consensus pattern (59 bp):
CTGATTACTCTTTCTTTTACTCTCTTTTAGCTTAATTACTCTTGAATTAAACTAATCTT
Found at i:10616 original size:22 final size:22
Alignment explanation
Indices: 10586--10651 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
10576 ATTAAACTAA
*
10586 TCTTCTGATTACTCTTTCTTTT
1 TCTTATGATTACTCTTTCTTTT
* **
10608 TCTTATGATTACTTTTTCTCCT
1 TCTTATGATTACTCTTTCTTTT
* *
10630 ACGTATGATTACTCTTTCTTTT
1 TCTTATGATTACTCTTTCTTTT
10652 ACCTTTTTTA
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.14, C:0.21, G:0.06, T:0.59
Consensus pattern (22 bp):
TCTTATGATTACTCTTTCTTTT
Found at i:10651 original size:102 final size:103
Alignment explanation
Indices: 10533--10756 Score: 362
Period size: 102 Copynumber: 2.2 Consensus size: 103
10523 ACTAATCTTC
*
10533 TGATTACTCTTTCTTTTACTC-TTTTTAGCTTAATTACTCTTGAATTAAACTAATCTTCTGATTA
1 TGATTACTCTTTCTTTTACTCTTTTTTAGCTTAATTACTCTTGAATTAAACTAATCTTCCGATTA
* * *
10597 CTCTTTCTTTTTCTTATGATTACTTTTTCTCCTACGTA
66 CTCTTCCTTTTACTTATGATTACTCTTTCTCCTACGTA
10635 TGATTACTCTTTCTTTTAC-CTTTTTTAGCTTAATTACTCTTGAATTAAACTAATCTTCCGATTA
1 TGATTACTCTTTCTTTTACTCTTTTTTAGCTTAATTACTCTTGAATTAAACTAATCTTCCGATTA
* * * *
10699 CTCTTCCTTTTACTTTTGATTACTCTTTCTTCTACTTC
66 CTCTTCCTTTTACTTATGATTACTCTTTCTCCTACGTA
10737 TGATTACTCTTTCTTTTACT
1 TGATTACTCTTTCTTTTACT
10757 TTTGATTACT
Statistics
Matches: 112, Mismatches: 8, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
101 1 0.01
102 111 0.99
ACGTcount: A:0.20, C:0.21, G:0.05, T:0.54
Consensus pattern (103 bp):
TGATTACTCTTTCTTTTACTCTTTTTTAGCTTAATTACTCTTGAATTAAACTAATCTTCCGATTA
CTCTTCCTTTTACTTATGATTACTCTTTCTCCTACGTA
Found at i:10722 original size:22 final size:22
Alignment explanation
Indices: 10694--10778 Score: 143
Period size: 22 Copynumber: 3.9 Consensus size: 22
10684 CTAATCTTCC
*
10694 GATTACTCTTCCTTTTACTTTT
1 GATTACTCTTTCTTTTACTTTT
* *
10716 GATTACTCTTTCTTCTACTTCT
1 GATTACTCTTTCTTTTACTTTT
10738 GATTACTCTTTCTTTTACTTTT
1 GATTACTCTTTCTTTTACTTTT
10760 GATTACTCTTTCTTTTACT
1 GATTACTCTTTCTTTTACT
10779 CTTTTTACTC
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 58 1.00
ACGTcount: A:0.14, C:0.22, G:0.05, T:0.59
Consensus pattern (22 bp):
GATTACTCTTTCTTTTACTTTT
Found at i:10726 original size:12 final size:12
Alignment explanation
Indices: 10711--10804 Score: 51
Period size: 12 Copynumber: 8.2 Consensus size: 12
10701 CTTCCTTTTA
10711 CTTTTGATTACT
1 CTTTTGATTACT
*
10723 C-TTT-CTT-CT
1 CTTTTGATTACT
*
10732 ACTTCTGATTACT
1 -CTTTTGATTACT
*
10745 CTTTCT-TTTA--
1 CTTT-TGATTACT
10755 CTTTTGATTACT
1 CTTTTGATTACT
*
10767 CTTTCT-TTTACT
1 CTTT-TGATTACT
* *
10779 CTTTTTACT-CT
1 CTTTTGATTACT
10790 CTTTTGATTACT
1 CTTTTGATTACT
10802 CTT
1 CTT
10805 CCTTTCTACT
Statistics
Matches: 60, Mismatches: 11, Indels: 22
0.65 0.12 0.24
Matches are distributed among these distances:
9 3 0.05
10 10 0.17
11 15 0.25
12 28 0.47
13 4 0.07
ACGTcount: A:0.13, C:0.22, G:0.04, T:0.61
Consensus pattern (12 bp):
CTTTTGATTACT
Done.