Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016034.1 Corchorus olitorius cultivar O-4 contig16067, 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: 65526
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Found at i:22562 original size:21 final size:19
Alignment explanation
Indices: 22537--22585 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
22527 CTGCACCTCA
22537 CACACACATATGAATATTC
1 CACACACATATGAATATTC
* *
22556 TACACACATACGAATATTC
1 CACACACATATGAATATTC
22575 CACACACATAT
1 CACACACATAT
22586 TCACATATGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.43, C:0.29, G:0.04, T:0.24
Consensus pattern (19 bp):
CACACACATATGAATATTC
Found at i:22600 original size:26 final size:27
Alignment explanation
Indices: 22560--22610 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
22550 ATATTCTACA
22560 CACATACGAATATTCCACACACATATT
1 CACATACGAATATTCCACACACATATT
* *
22587 CACATATG-ATATTCTACACACATA
1 CACATACGAATATTCCACACACATA
22611 CGGAGTACTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.41, C:0.27, G:0.04, T:0.27
Consensus pattern (27 bp):
CACATACGAATATTCCACACACATATT
Found at i:22690 original size:16 final size:16
Alignment explanation
Indices: 22669--22701 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
22659 TACACACACG
22669 AGTATTCCACAAATAA
1 AGTATTCCACAAATAA
*
22685 AGTATTCCACACATAA
1 AGTATTCCACAAATAA
22701 A
1 A
22702 AAAGGGCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.48, C:0.21, G:0.06, T:0.24
Consensus pattern (16 bp):
AGTATTCCACAAATAA
Found at i:25588 original size:29 final size:29
Alignment explanation
Indices: 25556--25820 Score: 255
Period size: 29 Copynumber: 9.1 Consensus size: 29
25546 TTGCTCGCCC
*
25556 AGGGGCATTTTAGTCATTTTTGCACATCT
1 AGGGGCATTTTGGTCATTTTTGCACATCT
* * * * *
25585 AGGGGCATTTCGGTCATTTATACATATCC
1 AGGGGCATTTTGGTCATTTTTGCACATCT
* * * *
25614 AGGGGCACTCTAGTCATTTTTGCACATCC
1 AGGGGCATTTTGGTCATTTTTGCACATCT
* *
25643 AAGGGCATTTTGGTCATATTTGCACATCT
1 AGGGGCATTTTGGTCATTTTTGCACATCT
*
25672 AGGGGCATTTTGGTCATTTTTGCACATCC
1 AGGGGCATTTTGGTCATTTTTGCACATCT
* * * *
25701 AAGGGCATTATGGTCATTTTTGCATATTT
1 AGGGGCATTTTGGTCATTTTTGCACATCT
* * *
25730 AGGGGTATTTTGGTCATTTTTGCGCATCC
1 AGGGGCATTTTGGTCATTTTTGCACATCT
* * **
25759 AGAGGCATTATGGTCATTTTCACACATTCT
1 AGGGGCATTTTGGTCATTTTTGCACA-TCT
* *
25789 -GGGGCAGTTTT-GTCATCTTTGCATACTCT
1 AGGGGCA-TTTTGGTCATTTTTGCACA-TCT
25818 AGG
1 AGG
25821 TTCTCTTTGG
Statistics
Matches: 185, Mismatches: 48, Indels: 5
0.78 0.20 0.02
Matches are distributed among these distances:
29 178 0.96
30 7 0.04
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (29 bp):
AGGGGCATTTTGGTCATTTTTGCACATCT
Found at i:32005 original size:21 final size:21
Alignment explanation
Indices: 31961--32007 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
31951 GACCAATTTA
* *
31961 TTAAAACAAGTGACCCAAGCT
1 TTAAGACAAGTGACCAAAGCT
*
31982 TTAAGACAAGTGACCAAAGTT
1 TTAAGACAAGTGACCAAAGCT
32003 TTAAG
1 TTAAG
32008 GCTCAATTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.23
Consensus pattern (21 bp):
TTAAGACAAGTGACCAAAGCT
Found at i:37142 original size:20 final size:21
Alignment explanation
Indices: 37117--37159 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
37107 TACTTGATAG
*
37117 GTTTATTGTTTG-ATAATTGA
1 GTTTATTGCTTGAATAATTGA
37137 GTTTATTGCTTGAATAATTGA
1 GTTTATTGCTTGAATAATTGA
37158 GT
1 GT
37160 CATATGCTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.26, C:0.02, G:0.21, T:0.51
Consensus pattern (21 bp):
GTTTATTGCTTGAATAATTGA
Found at i:43947 original size:1 final size:1
Alignment explanation
Indices: 43895--43930 Score: 63
Period size: 1 Copynumber: 36.0 Consensus size: 1
43885 CTAATAGCCT
*
43895 AAAAAAAAAAAAAATAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
43931 CTAAACAGCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.97, C:0.00, G:0.00, T:0.03
Consensus pattern (1 bp):
A
Found at i:44330 original size:2 final size:2
Alignment explanation
Indices: 44323--44382 Score: 102
Period size: 2 Copynumber: 29.0 Consensus size: 2
44313 GTTGGTACTC
44323 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT CAT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T -AT AT AT
44367 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
44383 TAAATTCTTT
Statistics
Matches: 56, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 53 0.95
3 2 0.04
4 1 0.02
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:45127 original size:50 final size:50
Alignment explanation
Indices: 45068--45245 Score: 286
Period size: 50 Copynumber: 3.5 Consensus size: 50
45058 AGATATCCTG
45068 AAGAGTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT
1 AAGAGTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT
* *
45118 AAGAGTGAATTGGAAGACATTTCAAAGGATAAGCGGAAGACGATCCTTTT
1 AAGAGTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT
45168 AAGAGTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT
1 AAGAGTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT
* * *
45218 TATATTTGAATTGGAAGAC-GATTCAAAG
1 AAGA-GTGAATTGGAAGACAG-TTCAAAG
45246 AAGTTGATTC
Statistics
Matches: 119, Mismatches: 7, Indels: 3
0.92 0.05 0.02
Matches are distributed among these distances:
50 99 0.83
51 20 0.17
ACGTcount: A:0.37, C:0.11, G:0.28, T:0.24
Consensus pattern (50 bp):
AAGAGTGAATTGGAAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTT
Found at i:45259 original size:26 final size:26
Alignment explanation
Indices: 45230--45317 Score: 90
Period size: 26 Copynumber: 3.4 Consensus size: 26
45220 TATTTGAATT
45230 GGAAGACGATTCAAAGAAGTTGATTC
1 GGAAGACGATTCAAAGAAGTTGATTC
***
45256 GGAAGACGATTCCCCGAAGATTGAATT-
1 GGAAGACGATTCAAAGAAG-TTG-ATTC
* *
45283 GGAAGACAATTCGAAGAAGTTGA-TC
1 GGAAGACGATTCAAAGAAGTTGATTC
*
45308 GGGAGACGAT
1 GGAAGACGAT
45318 CCATTTCAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 7
0.76 0.14 0.11
Matches are distributed among these distances:
24 1 0.02
25 9 0.18
26 19 0.38
27 18 0.36
28 3 0.06
ACGTcount: A:0.36, C:0.14, G:0.30, T:0.20
Consensus pattern (26 bp):
GGAAGACGATTCAAAGAAGTTGATTC
Found at i:45287 original size:27 final size:26
Alignment explanation
Indices: 45223--45305 Score: 96
Period size: 26 Copynumber: 3.2 Consensus size: 26
45213 CTTTTTATAT
45223 TTGAATTGGAAGACGATTCAAAGAAG
1 TTGAATTGGAAGACGATTCAAAGAAG
***
45249 TTG-ATTCGGAAGACGATTCCCCGAAG
1 TTGAATT-GGAAGACGATTCAAAGAAG
* *
45275 ATTGAATTGGAAGACAATTCGAAGAAG
1 -TTGAATTGGAAGACGATTCAAAGAAG
45302 TTGA
1 TTGA
45306 TCGGGAGACG
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
25 3 0.06
26 23 0.49
27 18 0.38
28 3 0.06
ACGTcount: A:0.37, C:0.12, G:0.27, T:0.24
Consensus pattern (26 bp):
TTGAATTGGAAGACGATTCAAAGAAG
Found at i:45557 original size:28 final size:28
Alignment explanation
Indices: 45517--45638 Score: 185
Period size: 28 Copynumber: 4.4 Consensus size: 28
45507 ATTTACTTCT
45517 TATTTTGGTCATTTTGCATGTCCAGGGG
1 TATTTTGGTCATTTTGCATGTCCAGGGG
*
45545 TATTTTGGTCATTTTGCATGTCCAGCGG
1 TATTTTGGTCATTTTGCATGTCCAGGGG
*
45573 CATTTTGGTCATTTTGCATGTCCAGGGG
1 TATTTTGGTCATTTTGCATGTCCAGGGG
*
45601 TATTTTAGTCATTTGTGCA--TCCAGGGG
1 TATTTTGGTCATTT-TGCATGTCCAGGGG
*
45628 CATTTTGGTCA
1 TATTTTGGTCA
45639 CTTCAAGTAC
Statistics
Matches: 86, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
27 17 0.20
28 65 0.76
29 4 0.05
ACGTcount: A:0.16, C:0.16, G:0.26, T:0.42
Consensus pattern (28 bp):
TATTTTGGTCATTTTGCATGTCCAGGGG
Found at i:48240 original size:31 final size:31
Alignment explanation
Indices: 48205--48263 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
48195 GATGCTGATG
* *
48205 ATGTTTAATTG-TTGCAATTTGGGGCTTGTTT
1 ATGTTGAATTGCTT-CAATTTAGGGCTTGTTT
*
48236 ATGTTGATTTGCTTCAATTTAGGGCTTG
1 ATGTTGAATTGCTTCAATTTAGGGCTTG
48264 ATTGTTCTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 22 0.92
32 2 0.08
ACGTcount: A:0.17, C:0.08, G:0.25, T:0.49
Consensus pattern (31 bp):
ATGTTGAATTGCTTCAATTTAGGGCTTGTTT
Found at i:49498 original size:12 final size:13
Alignment explanation
Indices: 49472--49501 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
49462 AAAAAATCAA
49472 AAAAGAGATTAAT
1 AAAAGAGATTAAT
49485 AAAAGAGA-TAAT
1 AAAAGAGATTAAT
49497 AAAAG
1 AAAAG
49502 TGTTTTCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.17
Consensus pattern (13 bp):
AAAAGAGATTAAT
Found at i:50319 original size:13 final size:13
Alignment explanation
Indices: 50298--50330 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
50288 AAAAAAATAC
50298 TAAAA-AATAAAA
1 TAAAATAATAAAA
50310 TAAAATAATAAAA
1 TAAAATAATAAAA
50323 TAATAATA
1 TAA-AATA
50331 GCGAGAGGGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 5 0.26
13 10 0.53
14 4 0.21
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAAATAATAAAA
Found at i:52290 original size:7 final size:7
Alignment explanation
Indices: 52279--52310 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
52269 ATAGGTAAGA
*
52279 TATATAA
1 TATATAC
52286 TATATAC
1 TATATAC
52293 TATATAC
1 TATATAC
52300 TATATAC
1 TATATAC
52307 TATA
1 TATA
52311 CATATTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (7 bp):
TATATAC
Found at i:52612 original size:53 final size:52
Alignment explanation
Indices: 52495--52614 Score: 163
Period size: 53 Copynumber: 2.3 Consensus size: 52
52485 TTCGTTTCCT
*
52495 TTCACACAATAAATGTTATAATAAATCCTATCCCCCTATTACTTAAGTATTC
1 TTCACAAAATAAATGTTATAATAAATCCTATCCCCCTATTACTTAAGTATTC
* *
52547 TTTCACACAATAAATGTTATAATAAATCCTATCCCCCTATCTCTACTTAATTATTC
1 -TTCACAAAATAAATGTTATAATAAATCCTATCCCCCTA--T-TACTTAAGTATTC
52603 -T-ACAAAATAAAT
1 TTCACAAAATAAAT
52615 AATATTTTCT
Statistics
Matches: 62, Mismatches: 2, Indels: 6
0.89 0.03 0.09
Matches are distributed among these distances:
53 48 0.77
54 1 0.02
55 1 0.02
56 12 0.19
ACGTcount: A:0.38, C:0.23, G:0.03, T:0.37
Consensus pattern (52 bp):
TTCACAAAATAAATGTTATAATAAATCCTATCCCCCTATTACTTAAGTATTC
Found at i:52728 original size:42 final size:42
Alignment explanation
Indices: 52669--52749 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
52659 TAAGGATCAG
*
52669 GATTTGAGTTGAGTATTTCTTATTTTACAAAGAATTTTCTAT
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
* *
52711 GATTTGAGTTGAGTATTTCTTAATTTATAGAGAATTTTC
1 GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTC
52750 AAGACTTAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.28, C:0.06, G:0.16, T:0.49
Consensus pattern (42 bp):
GATTTGAGTTGAGTATTTCTTAATTTACAAAGAATTTTCTAT
Found at i:57989 original size:1 final size:1
Alignment explanation
Indices: 57945--57971 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
57935 ATAATAAATG
57945 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
57972 AAAGTTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:64471 original size:50 final size:50
Alignment explanation
Indices: 64413--64513 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
64403 CGTGCGCAAT
64413 TGATCTATTAAGTTCAGAATAAAAATTTAGCAAATTTTAGCAACGGAAAA
1 TGATCTATTAAGTTCAGAATAAAAATTTAGCAAATTTTAGCAACGGAAAA
64463 TGATCTATTAAGTTCAGAATAAAAATTTAGCAAATTTTAGCAACGGAAAA
1 TGATCTATTAAGTTCAGAATAAAAATTTAGCAAATTTTAGCAACGGAAAA
64513 T
1 T
64514 CCATAGCGTG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.46, C:0.10, G:0.14, T:0.31
Consensus pattern (50 bp):
TGATCTATTAAGTTCAGAATAAAAATTTAGCAAATTTTAGCAACGGAAAA
Found at i:64926 original size:21 final size:21
Alignment explanation
Indices: 64900--64991 Score: 150
Period size: 21 Copynumber: 4.4 Consensus size: 21
64890 TGCTAGAAGT
64900 TCATTGGAGCAA-GTTCCAAGC
1 TCATTGGAG-AAGGTTCCAAGC
64921 TCATTGGAGAAGGTTCCAAGC
1 TCATTGGAGAAGGTTCCAAGC
*
64942 TCATTGGAGAAGGTTCCAAGA
1 TCATTGGAGAAGGTTCCAAGC
*
64963 TCATTGGAGAAGGTTTCAAGC
1 TCATTGGAGAAGGTTCCAAGC
64984 TCATTGGA
1 TCATTGGA
64992 ATTGCCTAAG
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
20 2 0.03
21 65 0.97
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.26
Consensus pattern (21 bp):
TCATTGGAGAAGGTTCCAAGC
Done.