Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011904.1 Corchorus olitorius cultivar O-4 contig11937, 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: 30475
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.34
Found at i:16962 original size:6 final size:6
Alignment explanation
Indices: 16953--16978 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
16943 TTATTGATGA
16953 TCAGCC TCAGCC TCAGCC TCAGCC TC
1 TCAGCC TCAGCC TCAGCC TCAGCC TC
16979 TTGTTGTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.50, G:0.15, T:0.19
Consensus pattern (6 bp):
TCAGCC
Found at i:18389 original size:48 final size:48
Alignment explanation
Indices: 18318--18411 Score: 179
Period size: 48 Copynumber: 2.0 Consensus size: 48
18308 ACGACTCTAG
18318 AAAACATAGGAGAAAAGACAAAAATAAGTTAGTTATCTCAATCCTTGT
1 AAAACATAGGAGAAAAGACAAAAATAAGTTAGTTATCTCAATCCTTGT
*
18366 AAAACATAGGAGAAAAGACAAAAATAAGTTAGTTATTTCAATCCTT
1 AAAACATAGGAGAAAAGACAAAAATAAGTTAGTTATCTCAATCCTT
18412 ATGAGAAGTA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.49, C:0.12, G:0.14, T:0.26
Consensus pattern (48 bp):
AAAACATAGGAGAAAAGACAAAAATAAGTTAGTTATCTCAATCCTTGT
Found at i:18468 original size:2 final size:2
Alignment explanation
Indices: 18461--18490 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
18451 TAGGAAAATA
18461 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
18491 AAATCACGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21078 original size:22 final size:22
Alignment explanation
Indices: 21053--21246 Score: 94
Period size: 22 Copynumber: 8.8 Consensus size: 22
21043 TACATAGAAA
*
21053 GGTTATCAATATTTTATAGTGT
1 GGTTATCAAAATTTTATAGTGT
* * *
21075 GGTTACCAAAATTTCATA-TGGC
1 GGTTATCAAAATTTTATAGT-GT
* *
21097 GGTTATCAAAACTTAATAGTGT
1 GGTTATCAAAATTTTATAGTGT
* *
21119 AGTTATCAAAATTTTATA-TAGA
1 GGTTATCAAAATTTTATAGT-GT
* * ****
21141 GATTA-CAAAAATTTCATAAAAA
1 GGTTATC-AAAATTTTATAGTGT
* *
21163 GATTATCAAAATTTCT-TAGAGAT
1 GGTTATCAAAATTT-TATAGTG-T
** * **
21186 -GTTAAAAAAATTTCATACG-AA
1 GGTTATCAAAATTTTATA-GTGT
*
21207 GGTTATCGAAATTTTATAGTGT
1 GGTTATCAAAATTTTATAGTGT
21229 GGTTATCAAAATTTTATA
1 GGTTATCAAAATTTTATA
21247 AGGATGTTAA
Statistics
Matches: 126, Mismatches: 34, Indels: 24
0.68 0.18 0.13
Matches are distributed among these distances:
21 4 0.03
22 119 0.94
23 3 0.02
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.38
Consensus pattern (22 bp):
GGTTATCAAAATTTTATAGTGT
Found at i:21104 original size:44 final size:44
Alignment explanation
Indices: 21053--21137 Score: 116
Period size: 44 Copynumber: 1.9 Consensus size: 44
21043 TACATAGAAA
* * * *
21053 GGTTATCAATATTTTATAGTGTGGTTACCAAAATTTCATATGGC
1 GGTTATCAAAACTTAATAGTGTAGTTACCAAAATTTCATATGGC
* *
21097 GGTTATCAAAACTTAATAGTGTAGTTATCAAAATTTTATAT
1 GGTTATCAAAACTTAATAGTGTAGTTACCAAAATTTCATAT
21138 AGAGATTACA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.34, C:0.09, G:0.15, T:0.41
Consensus pattern (44 bp):
GGTTATCAAAACTTAATAGTGTAGTTACCAAAATTTCATATGGC
Found at i:21169 original size:44 final size:45
Alignment explanation
Indices: 21121--21224 Score: 124
Period size: 44 Copynumber: 2.4 Consensus size: 45
21111 AATAGTGTAG
*
21121 TTATCAAAATTTTATATAGAGA-TTACAAAAATTTCATAAAAAGA
1 TTATCAAAATTTTATATAGAGAGTTAAAAAAATTTCATAAAAAGA
* ** *
21165 TTATCAAAA-TTTCT-TAGAGATGTTAAAAAAATTTCATACGAAGG
1 TTATCAAAATTTTATATAGAGA-GTTAAAAAAATTTCATAAAAAGA
*
21209 TTATCGAAATTTTATA
1 TTATCAAAATTTTATA
21225 GTGTGGTTAT
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
42 6 0.12
43 4 0.08
44 35 0.71
45 4 0.08
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.37
Consensus pattern (45 bp):
TTATCAAAATTTTATATAGAGAGTTAAAAAAATTTCATAAAAAGA
Found at i:21255 original size:22 final size:22
Alignment explanation
Indices: 21165--21290 Score: 71
Period size: 22 Copynumber: 5.5 Consensus size: 22
21155 CATAAAAAGA
21165 TTATCAAAATTTCT-T-AGAGATG
1 TTATCAAAATTT-TATAAG-GATG
** * * * *
21187 TTAAAAAAATTTCATACGAAGG
1 TTATCAAAATTTTATAAGGATG
*
21209 TTATCGAAATTTTAT-AGTG-TGG
1 TTATCAAAATTTTATAAG-GAT-G
21231 TTATCAAAATTTTATAAGGATG
1 TTATCAAAATTTTATAAGGATG
* *
21253 TTAACAAAATTTCATAGGGAGGGATG
1 TTATCAAAATTTTATA---A-GGATG
21279 TTATCAAAATTT
1 TTATCAAAATTT
21291 GTGCTTATCA
Statistics
Matches: 77, Mismatches: 17, Indels: 16
0.70 0.15 0.15
Matches are distributed among these distances:
21 1 0.01
22 55 0.71
23 4 0.05
25 1 0.01
26 16 0.21
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (22 bp):
TTATCAAAATTTTATAAGGATG
Found at i:21512 original size:22 final size:22
Alignment explanation
Indices: 21409--21662 Score: 173
Period size: 22 Copynumber: 11.7 Consensus size: 22
21399 CTCATATGGA
* *
21409 GGTTATCGAAATTTCATGGTGT
1 GGTTATCAAAATTTCATAGTGT
** *
21431 AATTA-CAAAATTTCATGAG-GA
1 GGTTATCAAAATTTCAT-AGTGT
*
21452 GGTTA-CAAAATTTTTATAGTGT
1 GGTTATCAAAA-TTTCATAGTGT
* *
21474 GGTTA-C-CAATTTTATAGTGT
1 GGTTATCAAAATTTCATAGTGT
* * * *
21494 GATTATCAAAATTTAATAGGGA
1 GGTTATCAAAATTTCATAGTGT
* * * * *
21516 GATTATCACAATTTCACACTGA
1 GGTTATCAAAATTTCATAGTGT
21538 GGTTATCAAAATTTCATAGTGT
1 GGTTATCAAAATTTCATAGTGT
*
21560 GGTTATCAAAATTTCACAGTGT
1 GGTTATCAAAATTTCATAGTGT
*
21582 GGTTATCAAATTTTCATAAG-GT
1 GGTTATCAAAATTTCAT-AGTGT
* * *
21604 GGTTATCCAGATTTCATAAT-T
1 GGTTATCAAAATTTCATAGTGT
* * *
21625 ACGTTATCAAATTTTCACAGTGT
1 -GGTTATCAAAATTTCATAGTGT
*
21648 GATTAT-AAATATTTC
1 GGTTATCAAA-ATTTC
21663 TACTTTGGAG
Statistics
Matches: 181, Mismatches: 41, Indels: 20
0.75 0.17 0.08
Matches are distributed among these distances:
20 15 0.08
21 29 0.16
22 134 0.74
23 3 0.02
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.39
Consensus pattern (22 bp):
GGTTATCAAAATTTCATAGTGT
Found at i:23085 original size:2 final size:2
Alignment explanation
Indices: 23078--23127 Score: 75
Period size: 2 Copynumber: 24.5 Consensus size: 2
23068 AAAATACTAG
23078 TA TA TA TA TA CTA GTA TA TA TA TA TA TA TA T- TA TA TA TA TA TA
1 TA TA TA TA TA -TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
23121 TA TA TA T
1 TA TA TA T
23128 TTTGTGATAG
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
1 1 0.02
2 40 0.89
3 4 0.09
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:23274 original size:19 final size:19
Alignment explanation
Indices: 23247--23285 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
23237 CTCAACTCCA
23247 AATCAAATA-GGTTTACCGG
1 AATCAAATATGG-TTACCGG
*
23266 AATCTAATATGGTTACCGG
1 AATCAAATATGGTTACCGG
23285 A
1 A
23286 TAAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 16 0.89
20 2 0.11
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (19 bp):
AATCAAATATGGTTACCGG
Found at i:25786 original size:144 final size:144
Alignment explanation
Indices: 25523--25841 Score: 401
Period size: 144 Copynumber: 2.2 Consensus size: 144
25513 AATGAGTTAT
** * * * *
25523 ATGAAAGAGAAAGATGCCTAAGAGAAGTCAGGTTCCCTATCAAACTTGAAATTTCACCTACCAAG
1 ATGAAAGATCAAGATGCATAAGAGAAGTCAGATTCCCTATCAAACCTGAAATTTCACCTACCAAC
* * *
25588 TTGTTATAGCCAAGGTTAAGAAACTGAAGAGAATTGAGGCGGAACAACTCGTCAGGTATTGAAGA
66 TTGTTAAAGCCAAGGTCAAGAAACTGAAGAGAATTGAGGCGGAACAACTCGTCAGGTATCGAAGA
25653 GTTGAAAGAGTTGA
131 GTTGAAAGAGTTGA
* * * *
25667 ATGAAAGATCAAGATGCATAAGAAAAGTCATATTCCCTAT-AGCACCTGAAATTTCACCTTCCAA
1 ATGAAAGATCAAGATGCATAAGAGAAGTCAGATTCCCTATCA-AACCTGAAATTTCACCTACCAA
* * * ***
25731 CTTGTTAAAGCCAAGGTCAAGAAACTGGAGGGAGTTGAGTTTGAA-AAGC-CAGTCAGGTATCGA
65 CTTGTTAAAGCCAAGGTCAAGAAACTGAAGAGAATTGAGGCGGAACAA-CTC-GTCAGGTATCGA
*
25794 AGAGTTGAAAGAGTTGG
128 AGAGTTGAAAGAGTTGA
*
25811 ATGAAAGATCAAGATGCGTAAGAGAAGTCAG
1 ATGAAAGATCAAGATGCATAAGAGAAGTCAG
25842 GTTCTGAAGG
Statistics
Matches: 149, Mismatches: 23, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
143 4 0.03
144 145 0.97
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.23
Consensus pattern (144 bp):
ATGAAAGATCAAGATGCATAAGAGAAGTCAGATTCCCTATCAAACCTGAAATTTCACCTACCAAC
TTGTTAAAGCCAAGGTCAAGAAACTGAAGAGAATTGAGGCGGAACAACTCGTCAGGTATCGAAGA
GTTGAAAGAGTTGA
Found at i:26816 original size:31 final size:30
Alignment explanation
Indices: 26751--26816 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 30
26741 ATAAGCATTT
* * * *
26751 TTAATTTCCCTTGTTTTTTTTTTGTCCAAT
1 TTAATTTCCCTTGTTATATTTTTGTCAAAA
26781 TTAATTTCCCTTGTTAATATTTTTG-CTAAAA
1 TTAATTTCCCTTGTT-ATATTTTTGTC-AAAA
26812 TTAAT
1 TTAAT
26817 CAATACATCA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
30 16 0.53
31 14 0.47
ACGTcount: A:0.23, C:0.14, G:0.06, T:0.58
Consensus pattern (30 bp):
TTAATTTCCCTTGTTATATTTTTGTCAAAA
Done.