Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012591.1 Corchorus olitorius cultivar O-4 contig12624, 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: 31243
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:1028 original size:19 final size:19
Alignment explanation
Indices: 1006--1053 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
996 TTTTATCAAT
1006 TGTTTTCTTGATTATTCAC
1 TGTTTTCTTGATTATTCAC
1025 TGTTTTCTTGATTATTCAC
1 TGTTTTCTTGATTATTCAC
*
1044 TGCTTTCTTG
1 TGTTTTCTTG
1054 TTAATTGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.12, C:0.17, G:0.12, T:0.58
Consensus pattern (19 bp):
TGTTTTCTTGATTATTCAC
Found at i:1331 original size:16 final size:17
Alignment explanation
Indices: 1310--1341 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1300 GAAATTACGT
1310 TTTATTTTTCT-TTTTC
1 TTTATTTTTCTATTTTC
1326 TTTATTTTTCTATTTT
1 TTTATTTTTCTATTTT
1342 AATTTGCACT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTATTTTTCTATTTTC
Found at i:11360 original size:194 final size:195
Alignment explanation
Indices: 11091--11486 Score: 573
Period size: 194 Copynumber: 2.0 Consensus size: 195
11081 CAACCGATCA
** *
11091 CCCGCCATATGCATGTTGGGGCAAAAATGACTAACATTTTTGTGAGGATATTCCGTAGCCACTAA
1 CCCGCCATATGCATGTTGCCGCAAAAATGACTAACATTTTTGTGACGATATTCCGTAGCCACTAA
* * * *
11156 TTAGTTGAATTGTTAGTGATACAACTTGTCGTCACAAAA-GTTACACACAAAAGTGACGAGGTAA
66 TTAATTGAATTGTTAGTGACACAACGTGTCGTCACAAAATGTTACACACAAAAGTGACGAGAT-A
11220 ATTTTT-GTCACAGAAAAATGAAACTTGTAGTGACCAATATAGGTTTGGCCACAAAAAGTATCAT
130 ATTTTTCGTCACAGAAAAATGAAACTTGTAGTGACCAATATAGGTTTGGCCACAAAAAGTATCAT
11284 T
195 T
* * **
11285 CCCGCCATAT-CTATGTTGCCGCCAAAATGACTAACGTTTTTGTGACGATATTGTGTAGCCACTA
1 CCCGCCATATGC-ATGTTGCCGCAAAAATGACTAACATTTTTGTGACGATATTCCGTAGCCACTA
* * *
11349 ATTAATTGAATTGTTAGTGACACAACGTGTTGTCACAAAATGTTACACACAAATGTGATGAGATA
65 ATTAATTGAATTGTTAGTGACACAACGTGTCGTCACAAAATGTTACACACAAAAGTGACGAGATA
* * * * * *
11414 CTTTTTCGTCACATAAAAATGAAACTTGTAGTGACCAATATAGGTTTTGCCACAATAATTTTCAT
130 ATTTTTCGTCACAGAAAAATGAAACTTGTAGTGACCAATATAGGTTTGGCCACAAAAAGTATCAT
11479 T
195 T
11480 CCCGCCA
1 CCCGCCA
11487 AATACGTAGT
Statistics
Matches: 179, Mismatches: 20, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
193 1 0.01
194 97 0.54
195 81 0.45
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (195 bp):
CCCGCCATATGCATGTTGCCGCAAAAATGACTAACATTTTTGTGACGATATTCCGTAGCCACTAA
TTAATTGAATTGTTAGTGACACAACGTGTCGTCACAAAATGTTACACACAAAAGTGACGAGATAA
TTTTTCGTCACAGAAAAATGAAACTTGTAGTGACCAATATAGGTTTGGCCACAAAAAGTATCATT
Found at i:11505 original size:195 final size:194
Alignment explanation
Indices: 11114--11489 Score: 565
Period size: 195 Copynumber: 1.9 Consensus size: 194
11104 TGTTGGGGCA
* * *
11114 AAAATGACTAACATTTTTGTGAGGATATTCCGTAGCCACTAATTAGTTGAATTGTTAGTGATACA
1 AAAATGACTAACATTTTTGTGACGATATTCCGTAGCCACTAATTAATTGAATTGTTAGTGACACA
* *
11179 ACTTGTCGTCACAAAAGTTACACACAAAAGTGACGAGGTAAATTTTTGTCACAGAAAAATGAAAC
66 ACGTGTCGTCACAAAAGTTACACACAAAAGTGACGAGATAAATTTTTGTCACAGAAAAATGAAAC
*
11244 TTGTAGTGACCAATATAGGTTTGGCCACAAAAAGTATCATTCCCGCCATATCTATGTTGCCGCC
131 TTGTAGTGACCAATATAGGTTTGGCCACAAAAAGTATCATTCCCGCCAAATCTATGTTGCCGCC
* **
11308 AAAATGACTAACGTTTTTGTGACGATATTGTGTAGCCACTAATTAATTGAATTGTTAGTGACACA
1 AAAATGACTAACATTTTTGTGACGATATTCCGTAGCCACTAATTAATTGAATTGTTAGTGACACA
* * * * *
11373 ACGTGTTGTCACAAAATGTTACACACAAATGTGATGAGAT-ACTTTTTCGTCACATAAAAATGAA
66 ACGTGTCGTCACAAAA-GTTACACACAAAAGTGACGAGATAAATTTTT-GTCACAGAAAAATGAA
* * * *
11437 ACTTGTAGTGACCAATATAGGTTTTGCCACAATAATTTTCATTCCCGCCAAAT
129 ACTTGTAGTGACCAATATAGGTTTGGCCACAAAAAGTATCATTCCCGCCAAAT
11490 ACGTAGTGGC
Statistics
Matches: 162, Mismatches: 18, Indels: 3
0.89 0.10 0.02
Matches are distributed among these distances:
194 79 0.49
195 83 0.51
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (194 bp):
AAAATGACTAACATTTTTGTGACGATATTCCGTAGCCACTAATTAATTGAATTGTTAGTGACACA
ACGTGTCGTCACAAAAGTTACACACAAAAGTGACGAGATAAATTTTTGTCACAGAAAAATGAAAC
TTGTAGTGACCAATATAGGTTTGGCCACAAAAAGTATCATTCCCGCCAAATCTATGTTGCCGCC
Found at i:15012 original size:30 final size:30
Alignment explanation
Indices: 14955--15012 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
14945 TTGATCATTT
*
14955 GCACATCCAAGGGCATTATGGTCATTTTTG
1 GCACATCCAAGGGCATTATGGTAATTTTTG
** * *
14985 GCACATCCTGGGGTATTTTGGTAATTTT
1 GCACATCCAAGGGCATTATGGTAATTTT
15013 CAATGCTTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38
Consensus pattern (30 bp):
GCACATCCAAGGGCATTATGGTAATTTTTG
Found at i:21131 original size:14 final size:14
Alignment explanation
Indices: 21114--21167 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
21104 TTTTGGGACA
21114 CTTGTAATCTGAGG
1 CTTGTAATCTGAGG
* * **
21128 CTTGGAACTCGGACA
1 CTTGTAA-TCTGAGG
21143 CTTGTAATCTGAGG
1 CTTGTAATCTGAGG
21157 CTTGTAATCTG
1 CTTGTAATCTG
21168 TAAATGTACT
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
14 21 0.68
15 10 0.32
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.33
Consensus pattern (14 bp):
CTTGTAATCTGAGG
Found at i:22144 original size:50 final size:50
Alignment explanation
Indices: 22088--22417 Score: 403
Period size: 51 Copynumber: 6.5 Consensus size: 50
22078 CGATCAACTT
* * ***
22088 CTTTGAATTGCCTTCCAATTCAATCTT-CGGGGTATCGTCTTCCACTTACC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGG-ATCGTCTTCCACTTACC
* **
22138 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGATCGTCTTCCGCTTATT
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGATCGTCTTCCACTTACC
* * *
22188 CTTTGAACTGTCTTCCAATTCAATTTTAAAAAGGA-CTGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTT-AAAAGGATC-GTCTTCCACTTACC
* * *
22239 CTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGACCGTCTTCCGCTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTT-AAAAGGATCGTCTTCCACTTACC
** ** *
22290 CTTTGAACTGTCTTGTAATTCAATCTTAAAAAGGATCGTCTTCCGTTTATC
1 CTTTGAACTGTCTTCCAATTCAATCTT-AAAAGGATCGTCTTCCACTTACC
* * *
22341 CTTTGAACTGTCTTCCAATCCAATCTTAAAAGGACCGTCTTCCACTTAAC
1 CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGATCGTCTTCCACTTACC
22391 CTTTGAACTGTCTTCCAATTCAATCTT
1 CTTTGAACTGTCTTCCAATTCAATCTT
22418 GAGAAAATCA
Statistics
Matches: 253, Mismatches: 23, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
50 111 0.44
51 141 0.56
52 1 0.00
ACGTcount: A:0.24, C:0.26, G:0.12, T:0.38
Consensus pattern (50 bp):
CTTTGAACTGTCTTCCAATTCAATCTTAAAAGGATCGTCTTCCACTTACC
Found at i:22243 original size:51 final size:51
Alignment explanation
Indices: 22124--22417 Score: 434
Period size: 51 Copynumber: 5.8 Consensus size: 51
22114 TCGGGGTATC
* *
22124 GTCTTCCACTTACCCTTTGAACTGTCTTCCAATTCAATCTT-AAAAGGA-T
1 GTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGACT
* *
22173 CGTCTTCCGCTTATTCTTTGAACTGTCTTCCAATTCAATTTTAAAAAGGACT
1 -GTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGACT
*
22225 GTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGACC
1 GTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGACT
**
22276 GTCTTCCGCTTATCCTTTGAACTGTCTTGTAATTCAATCTTAAAAAGGA-T
1 GTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGACT
* * *
22326 CGTCTTCCGTTTATCCTTTGAACTGTCTTCCAATCCAATCTT-AAAAGGACC
1 -GTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGACT
* *
22377 GTCTTCCACTTAACCTTTGAACTGTCTTCCAATTCAATCTT
1 GTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTT
22418 GAGAAAATCA
Statistics
Matches: 221, Mismatches: 19, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
50 81 0.37
51 139 0.63
52 1 0.00
ACGTcount: A:0.25, C:0.26, G:0.11, T:0.38
Consensus pattern (51 bp):
GTCTTCCGCTTATCCTTTGAACTGTCTTCCAATTCAATCTTAAAAAGGACT
Found at i:22419 original size:23 final size:23
Alignment explanation
Indices: 22343--22419 Score: 57
Period size: 23 Copynumber: 3.2 Consensus size: 23
22333 CGTTTATCCT
*
22343 TTGAACTGTCTTCCAATCCAATC
1 TTGAACTGTCTTCCAATTCAATC
* * * *
22366 TTAAAAGGACCGTCTTCCACTT-AACC
1 TT----GAACTGTCTTCCAATTCAATC
22392 TTTGAACTGTCTTCCAATTCAATC
1 -TTGAACTGTCTTCCAATTCAATC
22416 TTGA
1 TTGA
22420 GAAAATCATC
Statistics
Matches: 39, Mismatches: 9, Indels: 12
0.65 0.15 0.20
Matches are distributed among these distances:
23 19 0.49
24 3 0.08
26 3 0.08
27 14 0.36
ACGTcount: A:0.27, C:0.27, G:0.10, T:0.35
Consensus pattern (23 bp):
TTGAACTGTCTTCCAATTCAATC
Found at i:22806 original size:64 final size:64
Alignment explanation
Indices: 22650--23006 Score: 473
Period size: 64 Copynumber: 5.5 Consensus size: 64
22640 GCATCTCCTA
* * * *
22650 ACAAGATCGTCTTCCGATCAACTTCTGAAACTTTTTTGAGAAACTATCTTTTGGTGTACTTCTTT
1 ACAAGATCGTCTTCCGATCAACTTCTGAAA-ATTGTTGAGAAACCATCTTCTGGTGTACTT-TTT
22715 G
64 G
* * *
22716 ACAAGATCGTCTTCTGATCAATTTCTGAAAACTGTTGAGAAACCATCTTCTGGTGTACTTTTTG
1 ACAAGATCGTCTTCCGATCAACTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACTTTTTG
* * *
22780 ACAAGATCATCTTCCGATCAACTTCTGAAAATTGTTGA-AAAGCCATCTGCTGGTGTACTTCTTG
1 ACAAGATCGTCTTCCGATCAACTTCTGAAAATTGTTGAGAAA-CCATCTTCTGGTGTACTTTTTG
* * *
22844 ACAAGATCGTCTTCCGATCAATTTCTGAAAATTGTTGAGAAACCATCTTCTAGTGTACCTTTTG
1 ACAAGATCGTCTTCCGATCAACTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACTTTTTG
* * * ** *
22908 ACAAGATCGTCTTCCGATCAACTTCTGAAAATTGTTGAGAAGCCATCTTCCGTTGTGAAAATCTT
1 ACAAGATCGTCTTCCGATCAACTTCTGAAAATTGTTGAGAAACCATCTT-C-TGGTGTACTTTTT
22973 G
64 G
* *
22974 ACGAGATCGTCTTCCGATCAACATCTGAAAATT
1 ACAAGATCGTCTTCCGATCAACTTCTGAAAATT
23007 CTTTCTAGCA
Statistics
Matches: 259, Mismatches: 28, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
63 3 0.01
64 159 0.61
65 29 0.11
66 68 0.26
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.35
Consensus pattern (64 bp):
ACAAGATCGTCTTCCGATCAACTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACTTTTTG
Found at i:23134 original size:68 final size:68
Alignment explanation
Indices: 22983--23173 Score: 303
Period size: 68 Copynumber: 2.8 Consensus size: 68
22973 GACGAGATCG
* * ** * * *
22983 TCTTCCGATCAACATCTGAAAATTCTTTCTAGCAAATAGTCTTCCGATGT-TTTCCTTAATGAGA
1 TCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCGTCTTCCGGTGTACTTCTTTAATGAGA
23047 TTA
66 TTA
*
23050 TCTTCCAACCAACATTTGAAAATTCTTTCTAGCAAACCGTCTTCCGGTGTACTTCTTTAATGAGA
1 TCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCGTCTTCCGGTGTACTTCTTTAATGAGA
23115 TTA
66 TTA
23118 TCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCGTCTTCCGGTGTACTTCT
1 TCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCGTCTTCCGGTGTACTTCT
23174 AATATTCTGT
Statistics
Matches: 114, Mismatches: 9, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
67 44 0.39
68 70 0.61
ACGTcount: A:0.27, C:0.24, G:0.12, T:0.38
Consensus pattern (68 bp):
TCTTCCAATCAACATTTGAAAATTCTTTCTAGCAAACCGTCTTCCGGTGTACTTCTTTAATGAGA
TTA
Found at i:24208 original size:25 final size:25
Alignment explanation
Indices: 24180--24239 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
24170 GCTTGGTGTT
24180 TTCAAGGCAAAGGAGCAAAGA-ATAG
1 TTCAAGGCAAAGGAGCAAAGACA-AG
* * *
24205 TTCAAGGCAAATGCGGAAAGACAAG
1 TTCAAGGCAAAGGAGCAAAGACAAG
24230 TTCAAGGCAA
1 TTCAAGGCAA
24240 GAAGACATGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
25 30 0.97
26 1 0.03
ACGTcount: A:0.45, C:0.15, G:0.27, T:0.13
Consensus pattern (25 bp):
TTCAAGGCAAAGGAGCAAAGACAAG
Found at i:24955 original size:18 final size:17
Alignment explanation
Indices: 24932--24968 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 17
24922 CTAGCCCTAA
24932 AACTAGAAGAAAAACAAG
1 AACTAGAAGAAAAA-AAG
*
24950 AACTAGAAGAGAAAAAG
1 AACTAGAAGAAAAAAAG
24967 AA
1 AA
24969 GAAGAGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.68, C:0.08, G:0.19, T:0.05
Consensus pattern (17 bp):
AACTAGAAGAAAAAAAG
Found at i:27393 original size:32 final size:32
Alignment explanation
Indices: 27357--27417 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
27347 GTCGCGCGGC
*
27357 TGGTGCG-GCAGTGGCCGGGCCATAGCCGGGTA
1 TGGTGCGCG-AGTGGCCAGGCCATAGCCGGGTA
* *
27389 TGGTGCGCGGGTGGCCAGGCCATGGCCGG
1 TGGTGCGCGAGTGGCCAGGCCATAGCCGG
27418 CCTAGAATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
32 24 0.96
33 1 0.04
ACGTcount: A:0.10, C:0.26, G:0.49, T:0.15
Consensus pattern (32 bp):
TGGTGCGCGAGTGGCCAGGCCATAGCCGGGTA
Found at i:29674 original size:26 final size:27
Alignment explanation
Indices: 29627--29679 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
29617 CAGAGCAAAT
*
29627 TTTTTTTTTTAAAATTAAAAACGCAGA
1 TTTTTTTTTTAAAATCAAAAACGCAGA
* *
29654 TTTTTTTTTT-AGATCAGAAACGCAGA
1 TTTTTTTTTTAAAATCAAAAACGCAGA
29680 GACTAAGAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.43
Consensus pattern (27 bp):
TTTTTTTTTTAAAATCAAAAACGCAGA
Found at i:30924 original size:28 final size:28
Alignment explanation
Indices: 30887--30981 Score: 145
Period size: 28 Copynumber: 3.4 Consensus size: 28
30877 TAGGTCATTT
*
30887 AGGGGGATTTTGGTCATTTTGCATATCC
1 AGGGGCATTTTGGTCATTTTGCATATCC
30915 AGGGGCATTTTGGTCATTTTGCATATCC
1 AGGGGCATTTTGGTCATTTTGCATATCC
* * * *
30943 AAGGGCATTTTGGTCATTTTACACATCT
1 AGGGGCATTTTGGTCATTTTGCATATCC
30971 AGGGGCATTTT
1 AGGGGCATTTT
30982 TTTCACTTCA
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 61 1.00
ACGTcount: A:0.20, C:0.16, G:0.25, T:0.39
Consensus pattern (28 bp):
AGGGGCATTTTGGTCATTTTGCATATCC
Done.