Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015189.1 Corchorus olitorius cultivar O-4 contig15222, 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: 52365
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Found at i:5403 original size:35 final size:35
Alignment explanation
Indices: 5357--5427 Score: 142
Period size: 35 Copynumber: 2.0 Consensus size: 35
5347 AGTCTGCTAA
5357 ACTCCATTGACAATCTACAACAAGCTAAAAGGCCT
1 ACTCCATTGACAATCTACAACAAGCTAAAAGGCCT
5392 ACTCCATTGACAATCTACAACAAGCTAAAAGGCCT
1 ACTCCATTGACAATCTACAACAAGCTAAAAGGCCT
5427 A
1 A
5428 GAAATATGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.41, C:0.28, G:0.11, T:0.20
Consensus pattern (35 bp):
ACTCCATTGACAATCTACAACAAGCTAAAAGGCCT
Found at i:8142 original size:13 final size:13
Alignment explanation
Indices: 8124--8148 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
8114 TTTAAGCATA
8124 AAGAAGCAGAGTC
1 AAGAAGCAGAGTC
8137 AAGAAGCAGAGT
1 AAGAAGCAGAGT
8149 TTTCAAACTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.12, G:0.32, T:0.08
Consensus pattern (13 bp):
AAGAAGCAGAGTC
Found at i:10960 original size:30 final size:30
Alignment explanation
Indices: 10924--10998 Score: 134
Period size: 30 Copynumber: 2.5 Consensus size: 30
10914 TCATCATTTT
10924 CCTTGTCCATGATATGCTGCAGGCTTGGCA
1 CCTTGTCCATGATATGCTGCAGGCTTGGCA
10954 CCTTGTCCATGATATGCTGCAGGCTTGGCA
1 CCTTGTCCATGATATGCTGCAGGCTTGGCA
10984 CCTTGT-CATTGATAT
1 CCTTGTCCA-TGATAT
10999 AGTCTCCAAG
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
29 2 0.05
30 42 0.95
ACGTcount: A:0.17, C:0.25, G:0.24, T:0.33
Consensus pattern (30 bp):
CCTTGTCCATGATATGCTGCAGGCTTGGCA
Found at i:11565 original size:28 final size:29
Alignment explanation
Indices: 11492--11568 Score: 120
Period size: 29 Copynumber: 2.7 Consensus size: 29
11482 CATTAGGCTG
11492 AGGGGGCAAAATGTCCCAAAATTGAAGTTC
1 AGGGGGCAAAATGT-CCAAAATTGAAGTTC
11522 AGGGGGCAAAATGTCCAAAATTGAAGTTC
1 AGGGGGCAAAATGTCCAAAATTGAAGTTC
* *
11551 A-TGGGCAAAACGTCCAAA
1 AGGGGGCAAAATGTCCAAA
11569 CGTTACAAGT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
28 15 0.33
29 16 0.36
30 14 0.31
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.18
Consensus pattern (29 bp):
AGGGGGCAAAATGTCCAAAATTGAAGTTC
Found at i:15476 original size:36 final size:36
Alignment explanation
Indices: 15429--15502 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
15419 ACATCATATG
15429 CAAGCCCTTCATTTAACCAGAAATGATGCCAATAAA
1 CAAGCCCTTCATTTAACCAGAAATGATGCCAATAAA
15465 CAAGCCCTTCATTTAACCAGAAATGATGCCAATAAA
1 CAAGCCCTTCATTTAACCAGAAATGATGCCAATAAA
15501 CA
1 CA
15503 GACTCACTGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.42, C:0.26, G:0.11, T:0.22
Consensus pattern (36 bp):
CAAGCCCTTCATTTAACCAGAAATGATGCCAATAAA
Found at i:18255 original size:48 final size:48
Alignment explanation
Indices: 18200--18464 Score: 485
Period size: 48 Copynumber: 5.5 Consensus size: 48
18190 ATTACATACA
18200 GCGCACACTGTTTTAGTAGCATAAATACAAGACAGCGAGTTACATGAG
1 GCGCACACTGTTTTAGTAGCATAAATACAAGACAGCGAGTTACATGAG
18248 GCGCACACTGTTTTAGTAGCATAAATACAAGACAGCGAGTTACATGAG
1 GCGCACACTGTTTTAGTAGCATAAATACAAGACAGCGAGTTACATGAG
*
18296 GCGCACACTGTTTTAGTAGCATATATACAAGACAGCGAGTTACATGAG
1 GCGCACACTGTTTTAGTAGCATAAATACAAGACAGCGAGTTACATGAG
18344 GCGCACACTGTTTTAGTAGCATAAATACAAGACAGCGAGTTACATGAG
1 GCGCACACTGTTTTAGTAGCATAAATACAAGACAGCGAGTTACATGAG
*
18392 GCGCACACTGTTTTAGTAGCATAAATACAAAACAGCGAGTTACATGAG
1 GCGCACACTGTTTTAGTAGCATAAATACAAGACAGCGAGTTACATGAG
* * *
18440 GCGCGCACTGTTTTAATGGCATAAA
1 GCGCACACTGTTTTAGTAGCATAAA
18465 GATACTACTT
Statistics
Matches: 211, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
48 211 1.00
ACGTcount: A:0.35, C:0.19, G:0.23, T:0.24
Consensus pattern (48 bp):
GCGCACACTGTTTTAGTAGCATAAATACAAGACAGCGAGTTACATGAG
Found at i:20940 original size:4 final size:4
Alignment explanation
Indices: 20931--20986 Score: 112
Period size: 4 Copynumber: 14.0 Consensus size: 4
20921 GAAAATGGTT
20931 CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTCC
1 CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTCC
20979 CTCC CTCC
1 CTCC CTCC
20987 ATGCTTATAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 52 1.00
ACGTcount: A:0.00, C:0.75, G:0.00, T:0.25
Consensus pattern (4 bp):
CTCC
Found at i:21640 original size:28 final size:28
Alignment explanation
Indices: 21591--21644 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
21581 TCCCTTATTC
*
21591 AAATGTTCCTATTTTCTCGTGATTTCTT
1 AAATGTTCCTATTTTCTAGTGATTTCTT
*
21619 AAATGTTCCTGTTATT-TAGTGATTTC
1 AAATGTTCCTATT-TTCTAGTGATTTC
21645 AGTTTCTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 21 0.91
29 2 0.09
ACGTcount: A:0.20, C:0.15, G:0.13, T:0.52
Consensus pattern (28 bp):
AAATGTTCCTATTTTCTAGTGATTTCTT
Found at i:23708 original size:325 final size:323
Alignment explanation
Indices: 22821--24079 Score: 933
Period size: 325 Copynumber: 3.9 Consensus size: 323
22811 ATATCAGAAG
* * *
22821 CGTGAAAAACTCTTCAATCTTTTTGGCGTT-AATTATATATTTTTTTATGAGTATTGTGGCTAAA
1 CGTGAAAAACTCTTCAATCTTTTTGACGTTGAATTATATATCTTTTTACGAGTATTGTGGCTAAA
** * *
22885 AATTGAGGAAAAATCTTAT-GGACCATTTTTTGCAAAAATTTTGCCGAAATCGTGTACTAACCCT
66 AATTGAGGAAAAATCTT-TCGGATTA-ATTTTGCAAAATTTTTGCCGAAATCGTG---T-A---T
* ** * * * *
22949 CACGGTTTTTGGCTAAAAACATGTTCCGAGG-CTCCGGCTCAGTTTTACATGATTTTTGGTGCCA
122 CACGATTTTTAACTAAAAACGTGTTCCG-GGCCT-C-GTTCAGTTTTGCATGATTTTTTGTGCCA
* * * * * * *
23013 AGACTCATTGAAATAACTATATTCATCTAACGAAATCTTAGCCACATTATATTTAAGTATTTGTT
184 AGACTCATTGAAATATCTATATTAATCTAACCAAATCTCAGACACATTAGATTTAAGAATTTGTT
* * * * *
23078 TTTACGAA-CATCATAATCTAGTTTTGATTTAATCAGAAATTAATTTGGAGAAAAAATAGGAAAA
249 TTTA-GAAGCATCTTAATCTTGTTTCGATTTAATTAGAAATTAA-TT-AAGAAAAAATAGGAAAA
* *
23142 ACGATATTA-GAA
311 ATGATATTAGGCA
* * * * *
23154 GCGTGAAAAACACTTCAATCTTTTTGGA-ATTGAATCATATAT-TATTTTATGAGTATTGTGGGT
1 -CGTGAAAAACTCTTCAATCTTTTT-GACGTTGAATTATATATCT-TTTTACGAGTATTGTGGCT
* * *
23217 AAAAATTGAGGAAAAATCTTTC-G----A--GT-C--AATTTTTGCCGAAAATC---CATTACGA
63 AAAAATTGAGGAAAAATCTTTCGGATTAATTTTGCAAAATTTTTGCCG-AAATCGTGTATCACGA
* * * * * *
23269 TTTTTTAGA-TAAAAACGCGTTTCGAGCCCCGTCTCAGTTTTGTATGA-TTTTTGATGACAAGAC
127 -TTTTTA-ACTAAAAACGTGTTCCGGGCCTCGT-TCAGTTTTGCATGATTTTTTG-TGCCAAGAC
* * *
23332 TCATT-AATATATCTATATTGATCTAACCAAATCTCAGACATATTTGATTTAAGAATTTGTTTTT
188 TCATTGAA-ATATCTATATTAATCTAACCAAATCTCAGACACATTAGATTTAAGAATTTGTTTTT
* ** * * *
23396 AGAAGCATCTTAATCTTGTTTGGAGCTAATTAGAAATTAATTAAGTAAAAATCGAAAAAATGATA
252 AGAAGCATCTTAATCTTGTTTCGATTTAATTAGAAATTAATTAAGAAAAAATAGGAAAAATGATA
*
23461 TCAGGCA
317 TTAGGCA
* * * *
23468 CGTGAAAAGCTCTTCAATATTTTTGACGTTGAATTATATA-CTTTTCACGATTATTGTGGCTAAA
1 CGTGAAAAACTCTTCAATCTTTTTGACGTTGAATTATATATCTTTTTACGAGTATTGTGGCTAAA
*
23532 AATTGAGGAAAAATATTTCGGATTAATTTTCGCAAAATTTTTGCCGAAATCGTGTATCACGATTT
66 AATTGAGGAAAAATCTTTCGGATTAATTTT-GCAAAATTTTTGCCGAAATCGTGTATCACGATTT
* * * * *
23597 TTAACTAAAAACGTGTTCCGGGCCTCGATTTAGTTTTGGATGATTTTTTGCGCCAATAGTCATTG
130 TTAACTAAAAACGTGTTCCGGGCCTCG-TTCAGTTTTGCATGATTTTTTGTGCCAAGACTCATTG
* * * *
23662 AAATATCTAATATTAATCTAACCAAATCTCAGACACATTGGATTTAAGAGTTTGTTTTTGGGAGC
194 AAATATCT-ATATTAATCTAACCAAATCTCAGACACATTAGATTTAAGAATTTGTTTTTAGAAGC
* * *** * * * *
23727 AT-TTGAATCTTATTTCGATTTAATTAAAAATTAATCCGGGAAAAATTGGAAAAATGGTATTAGA
258 ATCTT-AATCTTGTTTCGATTTAATTAGAAATTAATTAAGAAAAAATAGGAAAAATGATATTAGG
*
23791 CG
322 CA
* * ** *
23793 CGT-AAAAGGCT-TTTAATCTTTTCAACGTTGAATTATATAT-TCTTTTACGAGTATTGTGACTA
1 CGTGAAAA-ACTCTTCAATCTTTTTGACGTTGAATTATATATCT-TTTTACGAGTATTGTGGCTA
* * * ** * *
23855 AAAATTGAGAAAAAATCTTTTGGCTTAATTTTTGCCGAA-GTTT-----AATC----ATCACCAT
64 AAAATTGAGGAAAAATCTTTCGGATTAA-TTTTGCAAAATTTTTGCCGAAATCGTGTATCACGA-
*** * ** ** * *** **
23910 TTTTTGGGTTAAAAACGCGTTATAGGGTTTCGGCTCAGTTTTGCATGATTTTTACCGATAAGACT
127 TTTTT-AACTAAAAACGTGTT-CCGGGCCTC-GTTCAGTTTTGCATGATTTTTTGTGCCAAGACT
* * *
23975 CCTTGAAATATCTATATTAATCTAACCAAATCTCAGACACATT-GAATTTAAGGATTTGTTTTAA
189 CATTGAAATATCTATATTAATCTAACCAAATCTCAGACACATTAG-ATTTAAGAATTTGTTTTTA
* **
24039 GCAGCAT-TTGAATCTTGTTTTAATTTAATTAGAAATTAATT
253 GAAGCATCTT-AATCTTGTTTCGATTTAATTAGAAATTAATT
24080 CGGGAAAAAC
Statistics
Matches: 749, Mismatches: 132, Indels: 105
0.76 0.13 0.11
Matches are distributed among these distances:
312 38 0.05
313 54 0.07
314 15 0.02
315 114 0.15
316 24 0.03
317 92 0.12
318 41 0.05
319 6 0.01
321 1 0.00
322 5 0.01
323 12 0.02
324 96 0.13
325 169 0.23
326 5 0.01
327 1 0.00
334 28 0.04
335 48 0.06
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (323 bp):
CGTGAAAAACTCTTCAATCTTTTTGACGTTGAATTATATATCTTTTTACGAGTATTGTGGCTAAA
AATTGAGGAAAAATCTTTCGGATTAATTTTGCAAAATTTTTGCCGAAATCGTGTATCACGATTTT
TAACTAAAAACGTGTTCCGGGCCTCGTTCAGTTTTGCATGATTTTTTGTGCCAAGACTCATTGAA
ATATCTATATTAATCTAACCAAATCTCAGACACATTAGATTTAAGAATTTGTTTTTAGAAGCATC
TTAATCTTGTTTCGATTTAATTAGAAATTAATTAAGAAAAAATAGGAAAAATGATATTAGGCA
Found at i:24638 original size:19 final size:19
Alignment explanation
Indices: 24614--24650 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
24604 CTGTTTAGCA
24614 ACTGTACAGATGAGATTAC
1 ACTGTACAGATGAGATTAC
*
24633 ACTGTACAGATTAGATTA
1 ACTGTACAGATGAGATTA
24651 AGTACTGCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (19 bp):
ACTGTACAGATGAGATTAC
Found at i:25828 original size:12 final size:12
Alignment explanation
Indices: 25811--25836 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
25801 TAGATTAACT
25811 TCGAGTGCTTCA
1 TCGAGTGCTTCA
25823 TCGAGTGCTTCA
1 TCGAGTGCTTCA
25835 TC
1 TC
25837 AAAGAGAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.27, G:0.23, T:0.35
Consensus pattern (12 bp):
TCGAGTGCTTCA
Found at i:26725 original size:40 final size:40
Alignment explanation
Indices: 26633--26951 Score: 480
Period size: 40 Copynumber: 7.9 Consensus size: 40
26623 ACTCACATTT
26633 AACTTTCCCAA-TCGACATTGAACTTGCCTTGATTCACATCC
1 AACTTTCCCAATTC-ACATTGAACTTGCCTT-ATTCACATCC
*
26674 ATA-TTTTCCAATTCACATTGAACTTGCCTTATTCACATCC
1 A-ACTTTCCCAATTCACATTGAACTTGCCTTATTCACATCC
26714 AACTTTCCCAATTCACATTGAACTTGCCTTATTCACATCC
1 AACTTTCCCAATTCACATTGAACTTGCCTTATTCACATCC
* *
26754 AACTTTCCCAAATGACATTGAACTTGCCTTATTCACATCC
1 AACTTTCCCAATTCACATTGAACTTGCCTTATTCACATCC
* * *
26794 AAATTTCCCAAATAACATTGAACTTGCCTTATTCACATCC
1 AACTTTCCCAATTCACATTGAACTTGCCTTATTCACATCC
* * * *
26834 AAATTTCCCAAATGACATTGAACTTGCCTTATTCACATTC
1 AACTTTCCCAATTCACATTGAACTTGCCTTATTCACATCC
* *
26874 AACTTTTCCAATTCACATTGAACTTGCCTTATTCACATTC
1 AACTTTCCCAATTCACATTGAACTTGCCTTATTCACATCC
26914 AACTTTCCCAATTCACATTGAACTTGCCTTAATTCACA
1 AACTTTCCCAATTCACATTGAACTTGCCTT-ATTCACA
26952 ATGGCCCTCA
Statistics
Matches: 261, Mismatches: 13, Indels: 8
0.93 0.05 0.03
Matches are distributed among these distances:
39 1 0.00
40 226 0.87
41 31 0.12
42 3 0.01
ACGTcount: A:0.30, C:0.29, G:0.06, T:0.35
Consensus pattern (40 bp):
AACTTTCCCAATTCACATTGAACTTGCCTTATTCACATCC
Found at i:28713 original size:46 final size:45
Alignment explanation
Indices: 28615--28765 Score: 266
Period size: 45 Copynumber: 3.3 Consensus size: 45
28605 AAAGCTTAGT
28615 CTCCATGATTGCCGAATACTTGAAGGAGATCAAAGAGAGCTTTGG
1 CTCCATGATTGCCGAATACTTGAAGGAGATCAAAGAGAGCTTTGG
28660 CTCCATGATTGCCGAATACTTGAAGGAGATCAAAAGAGAGCTTTGG
1 CTCCATGATTGCCGAATACTTGAAGGAGATC-AAAGAGAGCTTTGG
* *
28706 CTCCATGATTTCCGAAAACTTGAAGGAGATCAAAGAGAGCTTTGG
1 CTCCATGATTGCCGAATACTTGAAGGAGATCAAAGAGAGCTTTGG
*
28751 CTGCATGATTGCCGA
1 CTCCATGATTGCCGA
28766 GTGCTCCAAG
Statistics
Matches: 101, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
45 58 0.57
46 43 0.43
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.25
Consensus pattern (45 bp):
CTCCATGATTGCCGAATACTTGAAGGAGATCAAAGAGAGCTTTGG
Found at i:30496 original size:14 final size:14
Alignment explanation
Indices: 30477--30503 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
30467 ACAACCAAAA
30477 GGCCCAATTAATAT
1 GGCCCAATTAATAT
30491 GGCCCAATTAATA
1 GGCCCAATTAATA
30504 GAACCTGAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (14 bp):
GGCCCAATTAATAT
Found at i:32140 original size:34 final size:34
Alignment explanation
Indices: 32093--32167 Score: 125
Period size: 34 Copynumber: 2.2 Consensus size: 34
32083 GTAAAGTTTT
*
32093 TAAC-CAAATGGAGAAAATGGCCATTCACAATCC
1 TAACACAAATGGAGAAAATGACCATTCACAATCC
*
32126 TAACACAAATGGAGAAAATGACCATTCTCAATCC
1 TAACACAAATGGAGAAAATGACCATTCACAATCC
32160 TAACACAA
1 TAACACAA
32168 GCAAGAAAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 4 0.10
34 35 0.90
ACGTcount: A:0.45, C:0.24, G:0.12, T:0.19
Consensus pattern (34 bp):
TAACACAAATGGAGAAAATGACCATTCACAATCC
Found at i:33236 original size:51 final size:51
Alignment explanation
Indices: 33155--33251 Score: 142
Period size: 51 Copynumber: 1.9 Consensus size: 51
33145 TACGGTTTGT
* * *
33155 CGATAATTCTGAGGATATGTCTGATAAATTATCCCCAACTTCTTCAGCGAG
1 CGATAATTCTGAGGACATGTCTCATAAATTATACCCAACTTCTTCAGCGAG
*
33206 CGATAATTCTGAGGACATGTCCTCA-GAATTATACCCAACTTCTTCA
1 CGATAATTCTGAGGACATGT-CTCATAAATTATACCCAACTTCTTCA
33252 CCATTCACAA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
51 38 0.93
52 3 0.07
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.31
Consensus pattern (51 bp):
CGATAATTCTGAGGACATGTCTCATAAATTATACCCAACTTCTTCAGCGAG
Found at i:41007 original size:36 final size:36
Alignment explanation
Indices: 40960--41033 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
40950 TCCATTCCAA
40960 TCTGCGTAACGGAAACTTAATGTCGTTATTTCTATT
1 TCTGCGTAACGGAAACTTAATGTCGTTATTTCTATT
40996 TCTGCGTAACGGAAACTTAATGTCGTTATTTCTATT
1 TCTGCGTAACGGAAACTTAATGTCGTTATTTCTATT
41032 TC
1 TC
41034 AAACATAACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (36 bp):
TCTGCGTAACGGAAACTTAATGTCGTTATTTCTATT
Done.