Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011952.1 Corchorus olitorius cultivar O-4 contig11985, 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: 24234
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:1487 original size:22 final size:22
Alignment explanation
Indices: 1440--1487 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
1430 TTCGTTTTTG
*
1440 AAGACTTATTGAAGATAATTTG
1 AAGACTTATTGAAGATAATTTC
*
1462 AAGACTT-TTGAAGAATTATTTC
1 AAGACTTATTGAAG-ATAATTTC
1484 AAGA
1 AAGA
1488 GCAAGAATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.35
Consensus pattern (22 bp):
AAGACTTATTGAAGATAATTTC
Found at i:6828 original size:21 final size:21
Alignment explanation
Indices: 6802--6847 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
6792 ATGAAAAATG
*
6802 AAGAAAAGAATTGAATAAG-AA
1 AAGAAAA-AATTGAAAAAGCAA
*
6823 AAGAAAAAGTTGAAAAAGCAA
1 AAGAAAAAATTGAAAAAGCAA
6844 AAGA
1 AAGA
6848 CGGAGGAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.67, C:0.02, G:0.20, T:0.11
Consensus pattern (21 bp):
AAGAAAAAATTGAAAAAGCAA
Found at i:8301 original size:54 final size:54
Alignment explanation
Indices: 8240--8752 Score: 784
Period size: 54 Copynumber: 9.6 Consensus size: 54
8230 ACGTTCATGG
* * *
8240 CCCTGTGCGGTCTTTCATAAAAGTATTCAGAGGTTTAAGTTGATCTTTAGATGA
1 CCCTGTGCGGTCTTTCATAGAAGTTTTCAGAGGTTTAAGTTGATCTTCAGATGA
*
8294 CCCTGTGCGGTCTTTCATAGAAGTTTTCAGAGGTTTATGTTGATCTTCAGATGA
1 CCCTGTGCGGTCTTTCATAGAAGTTTTCAGAGGTTTAAGTTGATCTTCAGATGA
* * *
8348 CCTTGTGCTGTCTTTCATAGAAGTTTTCAGAGGTTTAAGTTGATCTTC--ATGG
1 CCCTGTGCGGTCTTTCATAGAAGTTTTCAGAGGTTTAAGTTGATCTTCAGATGA
* * *
8400 CCCTGTGCGGTCTTTCATAGAAGTTTTCACAAGTTTACGTTGATCTTCAGATGA
1 CCCTGTGCGGTCTTTCATAGAAGTTTTCAGAGGTTTAAGTTGATCTTCAGATGA
*
8454 CCCTGTGCGGTCTTTCATAGAAGTTTTCAGAGGTTTAAGTTGATCTTGAGATGA
1 CCCTGTGCGGTCTTTCATAGAAGTTTTCAGAGGTTTAAGTTGATCTTCAGATGA
* *
8508 CCCTGTGCGGTCTTTCATAGAAGTTTTCAGAAGTTTAAGTTGATCTTCAGATGT
1 CCCTGTGCGGTCTTTCATAGAAGTTTTCAGAGGTTTAAGTTGATCTTCAGATGA
* *
8562 CCCTATGCGGTCTTTCATAGAAGTTTTCAGAGGTTTAAGTTGATCTTCAGATAA
1 CCCTGTGCGGTCTTTCATAGAAGTTTTCAGAGGTTTAAGTTGATCTTCAGATGA
*
8616 CCCTGTGCGGTCTTTCATAGAAGTTTTCAGAGATTTAAGTTGATCTTCAGATGA
1 CCCTGTGCGGTCTTTCATAGAAGTTTTCAGAGGTTTAAGTTGATCTTCAGATGA
* * * *
8670 CCCTGTGCGGTTTTTCATAGAAG-TTTCAGAGATCTAAGTTGAT-TTTATGATGA
1 CCCTGTGCGGTCTTTCATAGAAGTTTTCAGAGGTTTAAGTTGATCTTCA-GATGA
* *
8723 CCCTGTACGGTCTTTCATA-AAGCTTTCAGA
1 CCCTGTGCGGTCTTTCATAGAAGTTTTCAGA
8753 AATCTAAATT
Statistics
Matches: 422, Mismatches: 33, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
52 52 0.12
53 48 0.11
54 322 0.76
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (54 bp):
CCCTGTGCGGTCTTTCATAGAAGTTTTCAGAGGTTTAAGTTGATCTTCAGATGA
Found at i:8487 original size:160 final size:160
Alignment explanation
Indices: 8223--8752 Score: 789
Period size: 160 Copynumber: 3.3 Consensus size: 160
8213 TTTAGAGATC
* *
8223 TAAGTTGA-CGTTCATGGCCCTGTGCGGTCTTTCATAAAAGTATTCAGAGGTTTAAGTTGATCTT
1 TAAGTTGATC-TTCATGGCCCTGTGCGGTCTTTCATAGAAGTTTTCAGAGGTTTAAGTTGATCTT
* * *
8287 TAGATGACCCTGTGCGGTCTTTCATAGAAGTTTTCAGAGGTTTATGTTGATCTTCAGATGACCTT
65 CAGATGACCCTGTGCGGTCTTTCATAGAAGTTTTCAGAGGTTTAAGTTGATCTTCAGATGACCCT
*
8352 GTGCTGTCTTTCATAGAAGTTTTCAGAGGTT
130 GTGCGGTCTTTCATAGAAGTTTTCAGAGGTT
* * *
8383 TAAGTTGATCTTCATGGCCCTGTGCGGTCTTTCATAGAAGTTTTCACAAGTTTACGTTGATCTTC
1 TAAGTTGATCTTCATGGCCCTGTGCGGTCTTTCATAGAAGTTTTCAGAGGTTTAAGTTGATCTTC
*
8448 AGATGACCCTGTGCGGTCTTTCATAGAAGTTTTCAGAGGTTTAAGTTGATCTTGAGATGACCCTG
66 AGATGACCCTGTGCGGTCTTTCATAGAAGTTTTCAGAGGTTTAAGTTGATCTTCAGATGACCCTG
*
8513 TGCGGTCTTTCATAGAAGTTTTCAGAAGTT
131 TGCGGTCTTTCATAGAAGTTTTCAGAGGTT
* *
8543 TAAGTTGATCTTCAGATGTCCCTATGCGGTCTTTCATAGAAGTTTTCAGAGGTTTAAGTTGATCT
1 TAAGTTGATCTTC--ATGGCCCTGTGCGGTCTTTCATAGAAGTTTTCAGAGGTTTAAGTTGATCT
* *
8608 TCAGATAACCCTGTGCGGTCTTTCATAGAAGTTTTCAGAGATTTAAGTTGATCTTCAGATGACCC
64 TCAGATGACCCTGTGCGGTCTTTCATAGAAGTTTTCAGAGGTTTAAGTTGATCTTCAGATGACCC
* * *
8673 TGTGCGGTTTTTCATAGAAG-TTTCAGAGATC
129 TGTGCGGTCTTTCATAGAAGTTTTCAGAGGTT
* * *
8704 TAAGTTGAT-TTTATGATGACCCTGTACGGTCTTTCATA-AAGCTTTCAGA
1 TAAGTTGATCTTCATG--G-CCCTGTGCGGTCTTTCATAGAAGTTTTCAGA
8753 AATCTAAATT
Statistics
Matches: 336, Mismatches: 28, Indels: 12
0.89 0.07 0.03
Matches are distributed among these distances:
158 3 0.01
160 172 0.51
161 35 0.10
162 126 0.38
ACGTcount: A:0.23, C:0.17, G:0.22, T:0.38
Consensus pattern (160 bp):
TAAGTTGATCTTCATGGCCCTGTGCGGTCTTTCATAGAAGTTTTCAGAGGTTTAAGTTGATCTTC
AGATGACCCTGTGCGGTCTTTCATAGAAGTTTTCAGAGGTTTAAGTTGATCTTCAGATGACCCTG
TGCGGTCTTTCATAGAAGTTTTCAGAGGTT
Found at i:8609 original size:214 final size:215
Alignment explanation
Indices: 8240--8778 Score: 809
Period size: 214 Copynumber: 2.5 Consensus size: 215
8230 ACGTTCATGG
* *
8240 CCCTGTGCGGTCTTTCATAAAAGTATTCAGAGGTTTAAGTTGATCTTTAGATGACCCTGTGCGGT
1 CCCTGTGCGGTCTTTCATAGAAGTTTTCAGAGGTTTAAGTTGATCTTTAGATGACCCTGTGCGGT
* * * * *
8305 CTTTCATAGAAGTTTTCAGAGGTTTATGTTGATCTTCAGATGACCTTGTGCTGTCTTTCATAGAA
66 CTTTCATAGAAGTTTTCAGAAGTTTAAGTTGATCTTCAGATGACCCTATGCGGTCTTTCATAGAA
**
8370 GTTTTCAGAGGTTTAAGTTGATCTTC-ATGGCCCTGTGCGGTCTTTCATAGAAGTTTTCACAAG-
131 GTTTTCAGAGGTTTAAGTTGATCTTCAATAACCCTGTGCGGTCTTTCATAGAAGTTTTCA-AAGA
*
8433 TTTACGTTGATCTTCAGATGA
195 TTTAAGTTGATCTTCAGATGA
*
8454 CCCTGTGCGGTCTTTCATAGAAGTTTTCAGAGGTTTAAGTTGATCTTGAGATGACCCTGTGCGGT
1 CCCTGTGCGGTCTTTCATAGAAGTTTTCAGAGGTTTAAGTTGATCTTTAGATGACCCTGTGCGGT
*
8519 CTTTCATAGAAGTTTTCAGAAGTTTAAGTTGATCTTCAGATGTCCCTATGCGGTCTTTCATAGAA
66 CTTTCATAGAAGTTTTCAGAAGTTTAAGTTGATCTTCAGATGACCCTATGCGGTCTTTCATAGAA
*
8584 GTTTTCAGAGGTTTAAGTTGATCTTCAGATAACCCTGTGCGGTCTTTCATAGAAGTTTTCAGAGA
131 GTTTTCAGAGGTTTAAGTTGATCTTCA-ATAACCCTGTGCGGTCTTTCATAGAAGTTTTCAAAGA
8649 TTTAAGTTGATCTTCAGATGA
195 TTTAAGTTGATCTTCAGATGA
* * * *
8670 CCCTGTGCGGTTTTTCATAGAAG-TTTCAGAGATCTAAGTTGAT-TTTATGATGACCCTGTACGG
1 CCCTGTGCGGTCTTTCATAGAAGTTTTCAGAGGTTTAAGTTGATCTTTA-GATGACCCTGTGCGG
* * * * * *
8733 TCTTTCATA-AAGCTTTCAGAAATCTAAATTGGTCTTCAAATGACCC
65 TCTTTCATAGAAGTTTTCAGAAGTTTAAGTTGATCTTCAGATGACCC
8779 GGTGATATCT
Statistics
Matches: 296, Mismatches: 25, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
214 180 0.61
215 43 0.15
216 73 0.25
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.38
Consensus pattern (215 bp):
CCCTGTGCGGTCTTTCATAGAAGTTTTCAGAGGTTTAAGTTGATCTTTAGATGACCCTGTGCGGT
CTTTCATAGAAGTTTTCAGAAGTTTAAGTTGATCTTCAGATGACCCTATGCGGTCTTTCATAGAA
GTTTTCAGAGGTTTAAGTTGATCTTCAATAACCCTGTGCGGTCTTTCATAGAAGTTTTCAAAGAT
TTAAGTTGATCTTCAGATGA
Found at i:8903 original size:53 final size:53
Alignment explanation
Indices: 8796--9089 Score: 353
Period size: 53 Copynumber: 5.5 Consensus size: 53
8786 TCTTTCGTAA
* * *
8796 AAGTTTTTAGA-GATTAGAGTTGATCCATATATGATCCAGTGCGATCATTTCAAG
1 AAGTTTTTA-ATGATCAGAGTTGATCC-CAGATGATCCAGTGCGATCATTTCAAG
*
8850 AAGTTTTTAATGATCAGAGTTGATCCCAGATGATCCAGTGCGATCATTCCAAG
1 AAGTTTTTAATGATCAGAGTTGATCCCAGATGATCCAGTGCGATCATTTCAAG
* * * * *
8903 AAGTTTTGAATGATCAGAGTTGATCCCCAAACGATCTAGTACGAT-ATTTCAAG
1 AAGTTTTTAATGATCAGAGTTGAT-CCCAGATGATCCAGTGCGATCATTTCAAG
* * *
8956 AAGTTTTCAGTGATCAGAGTTGATCCCTAGATGATCCAGTACGATCATTTCAAG
1 AAGTTTTTAATGATCAGAGTTGATCCC-AGATGATCCAGTGCGATCATTTCAAG
* * * *
9010 TAGTTTTCT-TTGATCAGAGTTGATCCCAGATGACCCAGTGCGATCATTCCAAG
1 AAGTTTT-TAATGATCAGAGTTGATCCCAGATGATCCAGTGCGATCATTTCAAG
*
9063 AATTTTTTAGA-GATCAGAGTTGATCCC
1 AAGTTTTTA-ATGATCAGAGTTGATCCC
9090 CAAATTTTTA
Statistics
Matches: 209, Mismatches: 24, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
52 4 0.02
53 135 0.65
54 70 0.33
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (53 bp):
AAGTTTTTAATGATCAGAGTTGATCCCAGATGATCCAGTGCGATCATTTCAAG
Found at i:8995 original size:160 final size:160
Alignment explanation
Indices: 8796--9093 Score: 465
Period size: 160 Copynumber: 1.9 Consensus size: 160
8786 TCTTTCGTAA
* * * *
8796 AAGTTTTTAGAGATTAGAGTTGATCCATATATGATCCAGTGCGATCATTTCAAGAAGTTTT-TAA
1 AAGTTTTCAGAGATCAGAGTTGATCCATAGATGATCCAGTACGATCATTTCAAGAAGTTTTCT-A
*
8860 TGATCAGAGTTGATCCCAGATGATCCAGTGCGATCATTCCAAGAAGTTTTGA-ATGATCAGAGTT
65 TGATCAGAGTTGATCCCAGATGACCCAGTGCGATCATTCCAAGAAGTTTTGAGA-GATCAGAGTT
8924 GATCCCCAAACGATCTAGTACGATATTTCAAG
129 GATCCCCAAACGATCTAGTACGATATTTCAAG
* * * *
8956 AAGTTTTCAGTGATCAGAGTTGATCCCTAGATGATCCAGTACGATCATTTCAAGTAGTTTTCTTT
1 AAGTTTTCAGAGATCAGAGTTGATCCATAGATGATCCAGTACGATCATTTCAAGAAGTTTTCTAT
* *
9021 GATCAGAGTTGATCCCAGATGACCCAGTGCGATCATTCCAAGAATTTTTTAGAGATCAGAGTTGA
66 GATCAGAGTTGATCCCAGATGACCCAGTGCGATCATTCCAAGAAGTTTTGAGAGATCAGAGTTGA
9086 TCCCCAAA
131 TCCCCAAA
9094 TTTTTAATGA
Statistics
Matches: 125, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
160 123 0.98
161 2 0.02
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.32
Consensus pattern (160 bp):
AAGTTTTCAGAGATCAGAGTTGATCCATAGATGATCCAGTACGATCATTTCAAGAAGTTTTCTAT
GATCAGAGTTGATCCCAGATGACCCAGTGCGATCATTCCAAGAAGTTTTGAGAGATCAGAGTTGA
TCCCCAAACGATCTAGTACGATATTTCAAG
Found at i:9001 original size:107 final size:106
Alignment explanation
Indices: 8811--9089 Score: 355
Period size: 107 Copynumber: 2.6 Consensus size: 106
8801 TTTAGAGATT
* *
8811 AGAGTTGAT-CCATATATGATCCAGTGCGATCATTTCAAGAAGTTTTTAATGATCAGAGTTGATC
1 AGAGTTGATCCCA-A-ACGATCCAGTGCGATCATTTCAAGAAGTTTTTAGTGATCAGAGTTGATC
* *
8875 CCAGATGATCCAGTGCGATCATTCCAAGAAGTTTTGAATGATC
64 CCAGATGATCCAGTACGATCATTCCAAGAAGTTTTCAATGATC
* * *
8918 AGAGTTGATCCCCAAACGATCTAGTACGAT-ATTTCAAGAAGTTTTCAGTGATCAGAGTTGATCC
1 AGAGTTGAT-CCCAAACGATCCAGTGCGATCATTTCAAGAAGTTTTTAGTGATCAGAGTTGATCC
* * **
8982 CTAGATGATCCAGTACGATCATTTCAAGTAGTTTTCTTTGATC
65 C-AGATGATCCAGTACGATCATTCCAAGAAGTTTTCAATGATC
* * * * * *
9025 AGAGTTGATCCCAGATGACCCAGTGCGATCATTCCAAGAATTTTTTAGAGATCAGAGTTGATCCC
1 AGAGTTGATCCCAAACGATCCAGTGCGATCATTTCAAGAAGTTTTTAGTGATCAGAGTTGATCCC
9090 CAAATTTTTA
Statistics
Matches: 148, Mismatches: 20, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
106 48 0.32
107 96 0.65
108 1 0.01
109 3 0.02
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.32
Consensus pattern (106 bp):
AGAGTTGATCCCAAACGATCCAGTGCGATCATTTCAAGAAGTTTTTAGTGATCAGAGTTGATCCC
AGATGATCCAGTACGATCATTCCAAGAAGTTTTCAATGATC
Found at i:10661 original size:70 final size:70
Alignment explanation
Indices: 10548--10681 Score: 207
Period size: 70 Copynumber: 1.9 Consensus size: 70
10538 CCAGACTTAT
* * * *
10548 TTTTCTATTTACATTCATAATTTATAGTGAACATGTAAAGGACCTATGAATTCATGCAAATAATT
1 TTTTCTATTTACATTCAGAATTTATAATGAACATATAAAGGACCTATGAATTCATACAAATAATT
10613 CAGAG
66 CAGAG
*
10618 TTTTCTATTTACATTCAGAATTTATAAT-AGACATATAAAGGACCTATGAATTCATACATATAAT
1 TTTTCTATTTACATTCAGAATTTATAATGA-ACATATAAAGGACCTATGAATTCATACAAATAAT
10682 ACACAACTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
69 1 0.02
70 57 0.98
ACGTcount: A:0.39, C:0.13, G:0.10, T:0.38
Consensus pattern (70 bp):
TTTTCTATTTACATTCAGAATTTATAATGAACATATAAAGGACCTATGAATTCATACAAATAATT
CAGAG
Found at i:13057 original size:13 final size:13
Alignment explanation
Indices: 13025--13064 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
13015 GCCTGACTGT
13025 TTTGGTTTATTA-
1 TTTGGTTTATTAC
13037 -TT-GTTTATTAC
1 TTTGGTTTATTAC
*
13048 TTTGGTTTATGAC
1 TTTGGTTTATTAC
13061 TTTG
1 TTTG
13065 ATTATGATAC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
10 8 0.33
11 2 0.08
12 2 0.08
13 12 0.50
ACGTcount: A:0.15, C:0.05, G:0.17, T:0.62
Consensus pattern (13 bp):
TTTGGTTTATTAC
Found at i:22447 original size:35 final size:37
Alignment explanation
Indices: 22408--22482 Score: 102
Period size: 35 Copynumber: 2.1 Consensus size: 37
22398 TGGAGGGTTT
*
22408 TTATCAATTATTTTC-TTAGTTTAT-TT-ATTGCTTTC
1 TTATCAATTATTTTCTTTAATTT-TCTTGATTGCTTTC
*
22443 TTATCAATTGTTTTCTTTAATTTTCTTGATTGCTTTC
1 TTATCAATTATTTTCTTTAATTTTCTTGATTGCTTTC
22480 TTA
1 TTA
22483 GTTAATTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
35 15 0.43
36 8 0.23
37 12 0.34
ACGTcount: A:0.19, C:0.12, G:0.07, T:0.63
Consensus pattern (37 bp):
TTATCAATTATTTTCTTTAATTTTCTTGATTGCTTTC
Done.