Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018387.1 Corchorus olitorius cultivar O-4 contig18420, 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: 19848
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--44 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
1 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
43 AT
1 AT
45 GGTAATAATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1437 original size:13 final size:13
Alignment explanation
Indices: 1419--1453 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
1409 CCACATCAGT
1419 GTTGACTTTGACC
1 GTTGACTTTGACC
*
1432 GTTGACTTTGACT
1 GTTGACTTTGACC
*
1445 ATTGACTTT
1 GTTGACTTT
1454 TGAGAGTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.17, C:0.17, G:0.20, T:0.46
Consensus pattern (13 bp):
GTTGACTTTGACC
Found at i:1673 original size:47 final size:47
Alignment explanation
Indices: 1590--1707 Score: 184
Period size: 47 Copynumber: 2.5 Consensus size: 47
1580 TTTCGCTCTG
* *
1590 TTTGACCTTTCGGTCCTGTTTTCTGCATGTTTGACCTCTTGGTCCTA
1 TTTGACCTTTCGGTCCTGTTTTTTGCATGTTCGACCTCTTGGTCCTA
* *
1637 TTTGACCCTTT-GGTCCTGTTTTTTGCCTGTTCGACCTCTTGGTCCTG
1 TTTGA-CCTTTCGGTCCTGTTTTTTGCATGTTCGACCTCTTGGTCCTA
1684 TTTGACCTTTCGGTCCTGTTTTTT
1 TTTGACCTTTCGGTCCTGTTTTTT
1708 AGCCCTTGAT
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
46 5 0.08
47 55 0.85
48 5 0.08
ACGTcount: A:0.06, C:0.25, G:0.19, T:0.49
Consensus pattern (47 bp):
TTTGACCTTTCGGTCCTGTTTTTTGCATGTTCGACCTCTTGGTCCTA
Found at i:1704 original size:18 final size:18
Alignment explanation
Indices: 1617--1704 Score: 77
Period size: 18 Copynumber: 5.3 Consensus size: 18
1607 GTTTTCTGCA
1617 TGTTTGACCTCTTGGTCC
1 TGTTTGACCTCTTGGTCC
*
1635 TATTTGACC-CTTTGGTCC
1 TGTTTGACCTC-TTGGTCC
1653 TGTTT----T-TT-G-CC
1 TGTTTGACCTCTTGGTCC
*
1664 TGTTCGACCTCTTGGTCC
1 TGTTTGACCTCTTGGTCC
1682 TGTTTGACCT-TTCGGTCC
1 TGTTTGACCTCTT-GGTCC
1700 TGTTT
1 TGTTT
1705 TTTAGCCCTT
Statistics
Matches: 56, Mismatches: 4, Indels: 20
0.70 0.05 0.25
Matches are distributed among these distances:
11 6 0.11
12 1 0.02
13 2 0.04
15 1 0.02
16 2 0.04
17 4 0.07
18 40 0.71
ACGTcount: A:0.06, C:0.26, G:0.20, T:0.48
Consensus pattern (18 bp):
TGTTTGACCTCTTGGTCC
Found at i:2018 original size:22 final size:21
Alignment explanation
Indices: 1971--2018 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 21
1961 TTGCCCTTCT
*
1971 TCTCT-CTCCCCCACTAACTC
1 TCTCTCCTCCCCCACTAACTA
* *
1991 TTTCTCCTCCTCCCACTCACTA
1 TCTCTCCTCC-CCCACTAACTA
2013 TCTCTC
1 TCTCTC
2019 TTCATAAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 4 0.18
21 4 0.18
22 14 0.64
ACGTcount: A:0.12, C:0.52, G:0.00, T:0.35
Consensus pattern (21 bp):
TCTCTCCTCCCCCACTAACTA
Found at i:4390 original size:3 final size:3
Alignment explanation
Indices: 4382--4423 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
4372 CAATATATCA
*
4382 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT TAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
4424 GCTCAATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:4445 original size:12 final size:12
Alignment explanation
Indices: 4383--4445 Score: 65
Period size: 12 Copynumber: 5.2 Consensus size: 12
4373 AATATATCAA
*
4383 ATAATAATAATA
1 ATAATAATAATT
*
4395 ATAATAATAATA
1 ATAATAATAATT
4407 ATAATAATAATT
1 ATAATAATAATT
**
4419 ATAATGCTCAA-T
1 ATAATAAT-AATT
*
4431 ATAATAATTATT
1 ATAATAATAATT
4443 ATA
1 ATA
4446 TGCTTAGATA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
11 1 0.02
12 40 0.93
13 2 0.05
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (12 bp):
ATAATAATAATT
Found at i:5649 original size:13 final size:13
Alignment explanation
Indices: 5617--5643 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
5607 ATGAAATTTT
5617 CAACAAAGATTAA
1 CAACAAAGATTAA
5630 CAACAAAGATTAA
1 CAACAAAGATTAA
5643 C
1 C
5644 TCCAAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.59, C:0.19, G:0.07, T:0.15
Consensus pattern (13 bp):
CAACAAAGATTAA
Found at i:5793 original size:3 final size:3
Alignment explanation
Indices: 5781--5859 Score: 99
Period size: 3 Copynumber: 27.0 Consensus size: 3
5771 AAATATTTTG
* * *
5781 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA CAA CAA CAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
5828 CAA TAA TAA TAA TAA TAA TAA T-T TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5860 AGATGATGAT
Statistics
Matches: 70, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
2 3 0.04
3 67 0.96
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:5867 original size:3 final size:3
Alignment explanation
Indices: 5861--5885 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5851 TAATAATAAA
5861 GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT G
5886 CTCGATTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:7279 original size:3 final size:3
Alignment explanation
Indices: 7271--7333 Score: 126
Period size: 3 Copynumber: 21.0 Consensus size: 3
7261 CATATACCAA
7271 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
7319 AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT
7334 GAAACACATT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:7328 original size:84 final size:84
Alignment explanation
Indices: 7238--7399 Score: 254
Period size: 84 Copynumber: 1.9 Consensus size: 84
7228 TTTATTTTTA
7238 AATAATAATAATGAAACACATTTCATATACCAAAATAATAATA-ATAATAATAATAATAATAATA
1 AATAATAATAATGAAACACATTTCATATACCAAAATAAT-ATAGATAATAATAATAATAATAATA
7302 ATAATAATAATAATAATAAT
65 ATAATAATAATAATAATAAT
* * ** **
7322 AATAATAATAATGAAACACATTTCATATATCAAAATAATATAGTTTGTTGTAATAATAATAATAA
1 AATAATAATAATGAAACACATTTCATATACCAAAATAATATAGATAATAATAATAATAATAATAA
7387 TAATAATAATAAT
66 TAATAATAATAAT
7400 TACACTTAGA
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
83 3 0.04
84 68 0.96
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.33
Consensus pattern (84 bp):
AATAATAATAATGAAACACATTTCATATACCAAAATAATATAGATAATAATAATAATAATAATAA
TAATAATAATAATAATAAT
Found at i:7378 original size:3 final size:3
Alignment explanation
Indices: 7372--7399 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
7362 TAGTTTGTTG
7372 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
7400 TACACTTAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:7927 original size:18 final size:20
Alignment explanation
Indices: 7904--7940 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
7894 ACGATTATGG
7904 TAACACG-TT-AGACACGAT
1 TAACACGTTTAAGACACGAT
7922 TAACACGTTTAAGACACGA
1 TAACACGTTTAAGACACGA
7941 GAGACACGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 2 0.12
20 8 0.47
ACGTcount: A:0.41, C:0.22, G:0.16, T:0.22
Consensus pattern (20 bp):
TAACACGTTTAAGACACGAT
Found at i:8979 original size:152 final size:152
Alignment explanation
Indices: 8703--9007 Score: 592
Period size: 152 Copynumber: 2.0 Consensus size: 152
8693 CGGGGGGGGG
8703 GGGAGCCCCGCGTTAGCACTTCGATGATTAAGTAAGTAGTGGAAAGTGGGCGTATGGTAGGTTTT
1 GGGAGCCCCGCGTTAGCACTTCGATGATTAAGTAAGTAGTGGAAAGTGGGCGTATGGTAGGTTTT
8768 AGAGAGATAGGTAGAGAGAGAGAGTTCTTATCTGAATACTGAGATAATACATTGGTGTATATATA
66 AGAGAGATAGGTAGAGAGAGAGAGTTCTTATCTGAATACTGAGATAATACATTGGTGTATATATA
8833 GGGGGGTTCGTACAGTTTACCA
131 GGGGGGTTCGTACAGTTTACCA
*
8855 GGGAGCCCCGCGTTAGCACTTCGATGATTAAGTAAGTAGTGGGAAGTGGGCGTATGGTAGGTTTT
1 GGGAGCCCCGCGTTAGCACTTCGATGATTAAGTAAGTAGTGGAAAGTGGGCGTATGGTAGGTTTT
8920 AGAGAGATAGGTAGAGAGAGAGAGTTCTTATCTGAATACTGAGATAATACATTGGTGTATATATA
66 AGAGAGATAGGTAGAGAGAGAGAGTTCTTATCTGAATACTGAGATAATACATTGGTGTATATATA
*
8985 GTGGGGTTCGTACAGTTTACCA
131 GGGGGGTTCGTACAGTTTACCA
9007 G
1 G
9008 TCTCTTCGTA
Statistics
Matches: 151, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
152 151 1.00
ACGTcount: A:0.29, C:0.11, G:0.32, T:0.29
Consensus pattern (152 bp):
GGGAGCCCCGCGTTAGCACTTCGATGATTAAGTAAGTAGTGGAAAGTGGGCGTATGGTAGGTTTT
AGAGAGATAGGTAGAGAGAGAGAGTTCTTATCTGAATACTGAGATAATACATTGGTGTATATATA
GGGGGGTTCGTACAGTTTACCA
Found at i:13326 original size:22 final size:22
Alignment explanation
Indices: 13298--13343 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
13288 TCTCACCTAC
13298 CCTCATTCTCTGGATACACAGA
1 CCTCATTCTCTGGATACACAGA
13320 CCTCATTCTCTGGATACACAGA
1 CCTCATTCTCTGGATACACAGA
13342 CC
1 CC
13344 CCATCTCCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.26, C:0.35, G:0.13, T:0.26
Consensus pattern (22 bp):
CCTCATTCTCTGGATACACAGA
Done.