Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016008.1 Corchorus olitorius cultivar O-4 contig16041, 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: 2901
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Found at i:605 original size:40 final size:39
Alignment explanation
Indices: 561--1572 Score: 719
Period size: 40 Copynumber: 25.3 Consensus size: 39
551 AGCCACTGGC
* * * * *
561 CCTGAATAGGATTTTTGAAATTGACTGATAAAGCAAGGAT
1 CCTGAACAGGA-TTCTGAAATTAATTGATAAAGCAATGAT
* * * *
601 CCTGAATAGGATTCTGAAATTGACTGATAAAAG-GATGAT
1 CCTGAACAGGATTCTGAAATTAATTGAT-AAAGCAATGAT
* * *
640 CCTGAATAGGATTCTGAAATTAGTTTGATAAAGCAATGGT
1 CCTGAACAGGATTCTGAAATTA-ATTGATAAAGCAATGAT
* *
680 CCT-AAGCAGGATTCTGGAATTAAGTAGATAAAGCAATGAT
1 CCTGAA-CAGGATTCTGAAATTAA-TTGATAAAGCAATGAT
* * * *
720 CATGAGCAGGATTCTGAAATTAACTAGATAAAACAATGAT
1 CCTGAACAGGATTCTGAAATTAA-TTGATAAAGCAATGAT
** * * *
760 CCTGAGTAGGGTTTTGAAATTAATTTGATAAA-AAGATGAT
1 CCTGAACAGGATTCTGAAATTAA-TTGATAAAGCA-ATGAT
* * *
800 CCTGAGCAGGATTCTGAAATTGATTTGACAAAGCAATGAT
1 CCTGAACAGGATTCTGAAATT-AATTGATAAAGCAATGAT
* * * *
840 CCTGAGCAGGGTTTTGAAATTAATTTGATAAAACAATGAT
1 CCTGAACAGGATTCTGAAATTAA-TTGATAAAGCAATGAT
* * * *
880 CCTGAGCAGGGTTTTGAAATTAATTTGATAAA-AAGATGAT
1 CCTGAACAGGATTCTGAAATTAA-TTGATAAAGCA-ATGAT
* * *
920 CCT-AAGCAGGGTTTTGAAATTAATTTGATAAAACAATGAT
1 CCTGAA-CAGGATTCTGAAATTAA-TTGATAAAGCAATGAT
* * * * *
960 CCTGAGCAGGGTTATGAAATTAATTTGACAAA-AAGATGAT
1 CCTGAACAGGATTCTGAAATTAA-TTGATAAAGCA-ATGAT
* *
1000 CCTGAATAGGATTCTGAAA-TAGATTTGACAAAGCAATGAT
1 CCTGAACAGGATTCTGAAATTA-A-TTGATAAAGCAATGAT
* * * *
1040 CCTGAGCAGGGTTTTGAAATTAATTTGATAAAACAATGAT
1 CCTGAACAGGATTCTGAAATTAA-TTGATAAAGCAATGAT
* * * *
1080 CCTGAGCAGGGTTTTGAAATTAATTTGATAAA-AAGATGAT
1 CCTGAACAGGATTCTGAAATTAA-TTGATAAAGCA-ATGAT
* *
1120 CCTGAGCAGGATTCTGAAATTGATTTGATAACA-CAATGAT
1 CCTGAACAGGATTCTGAAATT-AATTGATAA-AGCAATGAT
* * * * *
1160 CCTGAGCAGGGTTTTGAAGTTAATTTGATAAAACAATGAT
1 CCTGAACAGGATTCTGAAATTAA-TTGATAAAGCAATGAT
* * * *
1200 CCTGAGCAGGGTTTTGAAATTAATTTGATAAA-AAGATGAT
1 CCTGAACAGGATTCTGAAATTAA-TTGATAAAGCA-ATGAT
* * *
1240 CCTGAGCAGGATTCTGAAATTGATTTGACAAAGCAATGAT
1 CCTGAACAGGATTCTGAAATT-AATTGATAAAGCAATGAT
* * * * **
1280 CTTGAGCAGGGTTTTGAAATTAATTTGATAAAAAAATGAT
1 CCTGAACAGGATTCTGAAATTAA-TTGATAAAGCAATGAT
* * *
1320 CCTGAGCAGGATTCTGAAATTGATTTGACAAAGCAATGAT
1 CCTGAACAGGATTCTGAAATT-AATTGATAAAGCAATGAT
* * *
1360 CCTGAGCAGGATTTTGAAATTAATTTGATAAA-AAGATGAT
1 CCTGAACAGGATTCTGAAATTAA-TTGATAAAGCA-ATGAT
* *
1400 CCTGAGCAGGATTTTGAAATTAATTTGATAAAG-AGATGAT
1 CCTGAACAGGATTCTGAAATTAA-TTGATAAAGCA-ATGAT
* *
1440 CCT-AAGCAGGATTTTGAAATTAATTTGATAAA-AAGATGAT
1 CCTGAA-CAGGATTCTGAAATTAA-TTGATAAAGCA-ATGAT
** * *
1480 CCTGAGTAGG-GTCGTGAAATTAATTTGATAAA-AAGATGAT
1 CCTGAACAGGATTC-TGAAATTAA-TTGATAAAGCA-ATGAT
* *
1520 CCTGAGCAGG-GTCATGAAATTAATTCGATAAAG-AGATGAT
1 CCTGAACAGGATTC-TGAAATTAATT-GATAAAGCA-ATGAT
*
1560 CCTGAGCAGGATT
1 CCTGAACAGGATT
1573 AAAATTGACT
Statistics
Matches: 838, Mismatches: 96, Indels: 75
0.83 0.10 0.07
Matches are distributed among these distances:
39 65 0.08
40 757 0.90
41 16 0.02
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.30
Consensus pattern (39 bp):
CCTGAACAGGATTCTGAAATTAATTGATAAAGCAATGAT
Found at i:734 original size:80 final size:79
Alignment explanation
Indices: 635--1572 Score: 1112
Period size: 80 Copynumber: 11.7 Consensus size: 79
625 TGATAAAAGG
** * * * * * * *
635 ATGATCCTGAATAGGATTCTGAAATTAGTTTGATAAAGCAATGGTCCTAAGCAGGATTCTGGAAT
1 ATGATCCTGAGCAGGATTTTGAAATTAATTTGATAAA-AAATGATCCTGAGCAGGATTTTGAAAT
* *
700 TAAGTAGATAAAGCA
65 TAATTTGATAAAGCA
* * * * * *
715 ATGATCATGAGCAGGATTCTGAAATTAACTAGATAAAACAATGATCCTGAGTAGGGTTTTGAAAT
1 ATGATCCTGAGCAGGATTTTGAAATTAATTTGATAAAA-AATGATCCTGAGCAGGATTTTGAAAT
*
780 TAATTTGATAAA-AA
65 TAATTTGATAAAGCA
* * * * *
794 GATGATCCTGAGCAGGATTCTGAAATTGATTTGACAAAGCAATGATCCTGAGCAGGGTTTTGAAA
1 -ATGATCCTGAGCAGGATTTTGAAATTAATTTGATAAA-AAATGATCCTGAGCAGGATTTTGAAA
*
859 TTAATTTGATAAAACA
64 TTAATTTGATAAAGCA
* * *
875 ATGATCCTGAGCAGGGTTTTGAAATTAATTTGATAAAAAGATGATCCTAAGCAGGGTTTTGAAAT
1 ATGATCCTGAGCAGGATTTTGAAATTAATTTGATAAAAA-ATGATCCTGAGCAGGATTTTGAAAT
*
940 TAATTTGATAAAACA
65 TAATTTGATAAAGCA
* * * ** *
955 ATGATCCTGAGCAGGGTTATGAAATTAATTTGACAAAAAGATGATCCTGAATAGGATTCTGAAA-
1 ATGATCCTGAGCAGGATTTTGAAATTAATTTGATAAAAA-ATGATCCTGAGCAGGATTTTGAAAT
*
1019 TAGATTTGACAAAGCA
65 TA-ATTTGATAAAGCA
* *
1035 ATGATCCTGAGCAGGGTTTTGAAATTAATTTGATAAAACAATGATCCTGAGCAGGGTTTTGAAAT
1 ATGATCCTGAGCAGGATTTTGAAATTAATTTGATAAAA-AATGATCCTGAGCAGGATTTTGAAAT
*
1100 TAATTTGATAAA-AA
65 TAATTTGATAAAGCA
* * * * *
1114 GATGATCCTGAGCAGGATTCTGAAATTGATTTGATAACACAATGATCCTGAGCAGGGTTTTGAAG
1 -ATGATCCTGAGCAGGATTTTGAAATTAATTTGATAA-AAAATGATCCTGAGCAGGATTTTGAAA
*
1179 TTAATTTGATAAAACA
64 TTAATTTGATAAAGCA
* *
1195 ATGATCCTGAGCAGGGTTTTGAAATTAATTTGATAAAAAGATGATCCTGAGCAGGATTCTGAAAT
1 ATGATCCTGAGCAGGATTTTGAAATTAATTTGATAAAAA-ATGATCCTGAGCAGGATTTTGAAAT
* *
1260 TGATTTGACAAAGCA
65 TAATTTGATAAAGCA
* * *
1275 ATGATCTTGAGCAGGGTTTTGAAATTAATTTGATAAAAAAATGATCCTGAGCAGGATTCTGAAAT
1 ATGATCCTGAGCAGGATTTTGAAATTAATTTGAT-AAAAAATGATCCTGAGCAGGATTTTGAAAT
* *
1340 TGATTTGACAAAGCA
65 TAATTTGATAAAGCA
1355 ATGATCCTGAGCAGGATTTTGAAATTAATTTGATAAAAAGATGATCCTGAGCAGGATTTTGAAAT
1 ATGATCCTGAGCAGGATTTTGAAATTAATTTGATAAAAA-ATGATCCTGAGCAGGATTTTGAAAT
1420 TAATTTGATAAAG-A
65 TAATTTGATAAAGCA
* * * **
1434 GATGATCCTAAGCAGGATTTTGAAATTAATTTGATAAAAAGATGATCCTGAGTAGGGTCGTGAAA
1 -ATGATCCTGAGCAGGATTTTGAAATTAATTTGATAAAAA-ATGATCCTGAGCAGGATTTTGAAA
*
1499 TTAATTTGATAAA-AA
64 TTAATTTGATAAAGCA
* ** * *
1514 GATGATCCTGAGCAGGGTCATGAAATTAATTCGATAAAGAGATGATCCTGAGCAGGATT
1 -ATGATCCTGAGCAGGATTTTGAAATTAATTTGATAAA-AAATGATCCTGAGCAGGATT
1573 AAAATTGACT
Statistics
Matches: 758, Mismatches: 83, Indels: 34
0.87 0.09 0.04
Matches are distributed among these distances:
79 13 0.02
80 733 0.97
81 12 0.02
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.30
Consensus pattern (79 bp):
ATGATCCTGAGCAGGATTTTGAAATTAATTTGATAAAAAATGATCCTGAGCAGGATTTTGAAATT
AATTTGATAAAGCA
Found at i:789 original size:120 final size:120
Alignment explanation
Indices: 573--1572 Score: 1198
Period size: 120 Copynumber: 8.3 Consensus size: 120
563 TGAATAGGAT
* * * ** * * * *
573 TTTTGAAATTGA-CTGATAAAGCAAGGATCCTGAATAGGATTCTGAAATTGA-CTGATAAAAGGA
1 TTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATTTGATAAAAAGA
** * * * * *
636 TGATCCTGAATAGGATTCTGAAATTAGTTTGATAAAGCA-ATGGTCCTAAGCAGGA
66 TGATCCTGAGCAGGATTCTGAAATTAATTTGATAAA-AAGATGATCCTGAGCAGGG
* * * * * * * *
691 TTCTGGAATTAAGTAGATAAAGCAATGATCATGAGCAGGATTCTGAAATTAACTAGATAAAACA-
1 TTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATTTGATAAAA-AG
* * * *
755 ATGATCCTGAGTAGGGTTTTGAAATTAATTTGATAAAAAGATGATCCTGAGCAGGA
65 ATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAAAGATGATCCTGAGCAGGG
* * * *
811 TTCTGAAATTGATTTGACAAAGCAATGATCCTGAGCAGGGTTTTGAAATTAATTTGATAAAACA-
1 TTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATTTGATAAAA-AG
* * *
875 ATGATCCTGAGCAGGGTTTTGAAATTAATTTGATAAAAAGATGATCCTAAGCAGGG
65 ATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAAAGATGATCCTGAGCAGGG
* * * *
931 TTTTGAAATTAATTTGATAAAACAATGATCCTGAGCAGGGTTATGAAATTAATTTGACAAAAAGA
1 TTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATTTGATAAAAAGA
** * *
996 TGATCCTGAATAGGATTCTGAAA-TAGATTTGACAAAGCA-ATGATCCTGAGCAGGG
66 TGATCCTGAGCAGGATTCTGAAATTA-ATTTGATAAA-AAGATGATCCTGAGCAGGG
* *
1051 TTTTGAAATTAATTTGATAAAACAATGATCCTGAGCAGGGTTTTGAAATTAATTTGATAAAAAGA
1 TTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATTTGATAAAAAGA
* *
1116 TGATCCTGAGCAGGATTCTGAAATTGATTTGATAACACA-ATGATCCTGAGCAGGG
66 TGATCCTGAGCAGGATTCTGAAATTAATTTGATAA-AAAGATGATCCTGAGCAGGG
* * *
1171 TTTTGAAGTTAATTTGATAAAACAATGATCCTGAGCAGGGTTTTGAAATTAATTTGATAAAAAGA
1 TTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATTTGATAAAAAGA
* * * *
1236 TGATCCTGAGCAGGATTCTGAAATTGATTTGACAAAGCA-ATGATCTTGAGCAGGG
66 TGATCCTGAGCAGGATTCTGAAATTAATTTGATAAA-AAGATGATCCTGAGCAGGG
** * * * *
1291 TTTTGAAATTAATTTGATAAAAAAATGATCCTGAGCAGGATTCTGAAATTGATTTGACAAAGCA-
1 TTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATTTGATAAA-AAG
* *
1355 ATGATCCTGAGCAGGATTTTGAAATTAATTTGATAAAAAGATGATCCTGAGCAGGA
65 ATGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAAAGATGATCCTGAGCAGGG
*
1411 TTTTGAAATTAATTTGATAAAG-AGATGATCCTAAGCAGGATTTTGAAATTAATTTGATAAAAAG
1 TTTTGAAATTAATTTGATAAAGCA-ATGATCCTGAGCAGGATTTTGAAATTAATTTGATAAAAAG
* *
1475 ATGATCCTGAGTAGG-GTCGTGAAATTAATTTGATAAAAAGATGATCCTGAGCAGGG
65 ATGATCCTGAGCAGGATTC-TGAAATTAATTTGATAAAAAGATGATCCTGAGCAGGG
** *
1531 TCATGAAATTAATTCGATAAAG-AGATGATCCTGAGCAGGATT
1 TTTTGAAATTAATTTGATAAAGCA-ATGATCCTGAGCAGGATT
1573 AAAATTGACT
Statistics
Matches: 785, Mismatches: 82, Indels: 28
0.88 0.09 0.03
Matches are distributed among these distances:
118 9 0.01
119 41 0.05
120 731 0.93
121 4 0.01
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.30
Consensus pattern (120 bp):
TTTTGAAATTAATTTGATAAAGCAATGATCCTGAGCAGGATTTTGAAATTAATTTGATAAAAAGA
TGATCCTGAGCAGGATTCTGAAATTAATTTGATAAAAAGATGATCCTGAGCAGGG
Found at i:1595 original size:4 final size:4
Alignment explanation
Indices: 1586--1615 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
1576 ATTGACTGGT
1586 AATA AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AATA AA
1616 CGATCCTGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:1950 original size:47 final size:47
Alignment explanation
Indices: 1870--1988 Score: 175
Period size: 47 Copynumber: 2.5 Consensus size: 47
1860 CTGAAATTGA
* * *
1870 AGACTCGCATGGAAGCGAGAAAAGACCAACTTTGGTCACCCAATCGT
1 AGACTCGCGTGGAAGCGAGAAAAGACCAACTTTGGTCACCAAATCGC
* * * *
1917 AGACCCGCGTGGAAGCGAGAAAAGACCATCTTTGGTCACTAAATTGC
1 AGACTCGCGTGGAAGCGAGAAAAGACCAACTTTGGTCACCAAATCGC
1964 AGACTCGCGTGGAAGCGAGAAAAGA
1 AGACTCGCGTGGAAGCGAGAAAAGA
1989 TTACCTGGAT
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 64 1.00
ACGTcount: A:0.34, C:0.23, G:0.27, T:0.16
Consensus pattern (47 bp):
AGACTCGCGTGGAAGCGAGAAAAGACCAACTTTGGTCACCAAATCGC
Found at i:2232 original size:105 final size:105
Alignment explanation
Indices: 2097--2379 Score: 478
Period size: 105 Copynumber: 2.7 Consensus size: 105
2087 ACCTCATGGG
* * *
2097 ACTTGGCTTATGGAAAAGCCCT-TGTTGCTTGGATGGAACCAATGCTTGAACTGACTCGTATGGA
1 ACTTGGCTCATGGAAAAG-CCTATGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGA
2161 AATGAGTTTAGTCTTGGAAGACTGAATTTAGATGGAAATGA
65 AATGAGTTTAGTCTTGGAAGACTGAATTTAGATGGAAATGA
* * * *
2202 ACTTGGCTCATGGAAAAGCCTATGCTGCTTGGATGGAACCAAGGCTTAAATTGATTCGTATGGGA
1 ACTTGGCTCATGGAAAAGCCTATGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAA
2267 ATGAGTTTAGTCTTGGAAGACTGAATTTAGATGGAAATGA
66 ATGAGTTTAGTCTTGGAAGACTGAATTTAGATGGAAATGA
2307 ACTTGGCTCATGGAAAAGCCTATGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAA
1 ACTTGGCTCATGGAAAAGCCTATGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAA
*
2372 ACGAGTTT
66 ATGAGTTT
2380 GGCTTGTGAA
Statistics
Matches: 165, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
104 3 0.02
105 162 0.98
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (105 bp):
ACTTGGCTCATGGAAAAGCCTATGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAA
ATGAGTTTAGTCTTGGAAGACTGAATTTAGATGGAAATGA
Found at i:2408 original size:69 final size:69
Alignment explanation
Indices: 2317--2464 Score: 253
Period size: 69 Copynumber: 2.1 Consensus size: 69
2307 ACTTGGCTCA
* * *
2317 TGGAAAAGCCTATGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGG
1 TGGAAAAGCCCATGCTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGC
2382 CTTG
66 CTTG
2386 T-GAAAATGCCCATGCTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTG
1 TGGAAAA-GCCCATGCTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTG
2450 CCTTG
65 CCTTG
2455 TGGAAAAGCC
1 TGGAAAAGCC
2465 AAAGCATTCG
Statistics
Matches: 74, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
68 5 0.07
69 64 0.86
70 5 0.07
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (69 bp):
TGGAAAAGCCCATGCTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGC
CTTG
Done.