Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01000330.1 Corchorus capsularis cultivar CVL-1 contig00330, 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, 774
Length: 1290
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.35
Found at i:93 original size:22 final size:22
Alignment explanation
Indices: 24--295 Score: 172
Period size: 22 Copynumber: 12.5 Consensus size: 22
14 AAAAAGTCTC
* *
24 AATTTCATA-AG-GAGTACCAA
1 AATTTCATAGAGTGATTATCAA
*
44 AATTTGATAGAAG-G-TTATC-A
1 AATTTCATAG-AGTGATTATCAA
* *
64 AATCTCATAGAGTGATTATCGA
1 AATTTCATAGAGTGATTATCAA
86 AATTTCATAGAGATCGGATTATCAA
1 AATTTCATAGAG-T--GATTATCAA
**
111 AATTT-ATAGAAAGATTATCAA
1 AATTTCATAGAGTGATTATCAA
*
132 AATTTCATAGTGTTG-TTATCAA
1 AATTTCATAGAG-TGATTATCAA
154 AATTTCA-A-AGTGAGGTTATCAA
1 AATTTCATAGAGTGA--TTATCAA
* *
176 AATTACATA-ATGTGATTATCAG
1 AATTTCATAGA-GTGATTATCAA
* * * *
198 AATTTCATAGAGGGGTCAACAA
1 AATTTCATAGAGTGATTATCAA
* * *
220 AATTTTATAAAGAGATTATCAA
1 AATTTCATAGAGTGATTATCAA
* * *
242 AATTTCATAAAGAGGTTATCAA
1 AATTTCATAGAGTGATTATCAA
* *
264 ATTTTCA-AAATGTGATTA-CAAA
1 AATTTCATAGA-GTGATTATC-AA
286 AATTTCATAG
1 AATTTCATAG
296 TGGTCTTTCT
Statistics
Matches: 199, Mismatches: 34, Indels: 35
0.74 0.13 0.13
Matches are distributed among these distances:
19 4 0.02
20 19 0.10
21 27 0.14
22 121 0.61
23 6 0.03
24 9 0.05
25 13 0.07
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (22 bp):
AATTTCATAGAGTGATTATCAA
Found at i:195 original size:44 final size:44
Alignment explanation
Indices: 58--799 Score: 263
Period size: 44 Copynumber: 16.9 Consensus size: 44
48 TGATAGAAGG
* * * *
58 TTATC-AAATCTCATAGAGTGATTATCGAAATTTCATAGA-GATCGGA
1 TTATCAAAATTTCATAGAGAGGTTATCAAAATTTCATA-ATG-T--GA
* * *
104 TTATCAAAATTT-ATAGAAAGATTATCAAAATTTCATAGTGTTG-
1 TTATCAAAATTTCATAGAGAGGTTATCAAAATTTCATAATG-TGA
* * *
147 TTATCAAAATTTCAAAGTGAGGTTATCAAAATTACATAATGTGA
1 TTATCAAAATTTCATAGAGAGGTTATCAAAATTTCATAATGTGA
* * * * * * *
191 TTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAGAGA
1 TTATCAAAATTTCATAGAGAGGTTATCAAAATTTCATAATGTGA
* * *
235 TTATCAAAATTTCATAAAGAGGTTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTCATAGAGAGGTTATCAAAATTTCATAATGTGA
* * * * *
279 TTA-CAAAAATTTCATAGTGGTCTTTCTGGGGAGGTTATTAAAATTTCATAGTATGG
1 TTATC-AAAATTTCATA------------GAGAGGTTATCAAAATTTCATAATGTGA
* * * * * *
335 TTA-CCAAA-TT-A-GGA-AGGTTATTAAACTTTTATTATG-GA
1 TTATCAAAATTTCATAGAGAGGTTATCAAAATTTCATAATGTGA
* * **
373 GTAATCAAAATTTCA-AG-GAGGGTATCAAAA-TTCAGGGA-G-GA
1 -TTATCAAAATTTCATAGAGAGGTTATCAAAATTTCA-TAATGTGA
* *
414 -TATCAAAATTTCATATGA-AGGTTATCAAAATTTCATAGT-TTA
1 TTATCAAAATTTCATA-GAGAGGTTATCAAAATTTCATAATGTGA
* * * *
456 GTTTTCAAAATTTCACA-AGAGGGTTATCAAAATTTCATAGTATG-
1 -TTATCAAAATTTCATAGAGA-GGTTATCAAAATTTCATAATGTGA
* * * *
500 TAAGTCAAAATTTCATAGGGAGATTAACAAAATTTCATAGTATGT-A
1 TTA-TCAAAATTTCATAGAGAGGTTATCAAAATTTCATA--ATGTGA
* * * * * *
546 -GATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAGG
1 TTATCAAAATTTCATAGAGAGGTTATCAAAATTTCATAATGTGA
* ** * *
589 TTATAAAAAAAATCATAGGGAGGTTATCAAAATTT-GT-A---G-
1 TTAT-CAAAATTTCATAGAGAGGTTATCAAAATTTCATAATGTGA
* * * ** * *
628 TTATCAAGATTTCATA-AGAATGTTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTCATAGAG-AGGTTATCAAAATTTCATAATG-TGA
** * * * *
673 TTATCAAAATTTTTTAGAAAGATTTATCAAAATTTCA-AAAGATGG
1 TTATCAAAATTTCATAGAGAG-GTTATCAAAATTTCATAATG-TGA
* * * * *
718 TTATTATAATTTCAT-GAGGAGGTTATCAAAATTCCATAGTGTGG
1 TTATCAAAATTTCATAGA-GAGGTTATCAAAATTTCATAATGTGA
* * *
762 TTACCAAAATTTCATAGTGTGGTTA-CTAAAATTTCATA
1 TTATCAAAATTTCATAGAGAGGTTATC-AAAATTTCATA
800 GGATTAGGTT
Statistics
Matches: 521, Mismatches: 119, Indels: 114
0.69 0.16 0.15
Matches are distributed among these distances:
37 1 0.00
38 23 0.04
39 36 0.07
40 7 0.01
41 20 0.04
42 21 0.04
43 19 0.04
44 251 0.48
45 63 0.12
46 45 0.09
47 5 0.01
53 1 0.00
54 2 0.00
55 3 0.01
56 24 0.05
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (44 bp):
TTATCAAAATTTCATAGAGAGGTTATCAAAATTTCATAATGTGA
Found at i:406 original size:19 final size:19
Alignment explanation
Indices: 376--423 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
366 TTATGGAGTA
*
376 ATCAAAATTTCAAGGAGGGT
1 ATCAAAA-TTCAAGGAGGAT
*
396 ATCAAAATTCAGGGAGGAT
1 ATCAAAATTCAAGGAGGAT
415 ATCAAAATT
1 ATCAAAATT
424 TCATATGAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.44, C:0.10, G:0.21, T:0.25
Consensus pattern (19 bp):
ATCAAAATTCAAGGAGGAT
Found at i:442 original size:22 final size:22
Alignment explanation
Indices: 414--817 Score: 154
Period size: 22 Copynumber: 18.4 Consensus size: 22
404 TCAGGGAGGA
414 TATCAAAATTTCATATGAAGGT
1 TATCAAAATTTCATATGAAGGT
**
436 TATCAAAATTTCATAGTTTA-GT
1 TATCAAAATTTCATA-TGAAGGT
* * * *
458 TTTCAAAATTTCACAAGAGGGT
1 TATCAAAATTTCATATGAAGGT
* *
480 TATCAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* * * *
501 AAGTCAAAATTTCATAGGGAGAT
1 TA-TCAAAATTTCATATGAAGGT
* * *
524 TAACAAAATTTCATA-GTATGT
1 TATCAAAATTTCATATGAAGGT
* * * *
545 AGATCAAAATTTCATAGGGAGAT
1 -TATCAAAATTTCATATGAAGGT
*
568 TAACAAAATTTCATAATG-AGGT
1 TATCAAAATTTCAT-ATGAAGGT
* ** * *
590 TATAAAAAAAATCATAGGGAGGT
1 TAT-CAAAATTTCATATGAAGGT
*
613 TATCAAAA--T--T-TGTA-GT
1 TATCAAAATTTCATATGAAGGT
* * *
629 TATCAAGATTTCATAAGAATGT
1 TATCAAAATTTCATATGAAGGT
* * *
651 TATCAAAATTTTATAGGGAGGTT
1 TATCAAAATTTCATATGAAGG-T
** *
674 TATCAAAATTTTTTA-GAAAGATT
1 TATCAAAATTTCATATG-AAG-GT
* * *
697 TATCAAAATTTCAAAAGATGGT
1 TATCAAAATTTCATATGAAGGT
* * *
719 TATTATAATTTCATGA-GGAGGT
1 TATCAAAATTTCAT-ATGAAGGT
* *
741 TATCAAAATTCCATAGTG-TGGT
1 TATCAAAATTTCATA-TGAAGGT
* *
763 TACCAAAATTTCATAGTG-TGGT
1 TATCAAAATTTCATA-TGAAGGT
*
785 TA-CTAAAATTTCATAGGATTAGGT
1 TATC-AAAATTTCATATGA--AGGT
*
809 TATTAAAAT
1 TATCAAAAT
818 CTCTTAGGCT
Statistics
Matches: 286, Mismatches: 69, Indels: 52
0.70 0.17 0.13
Matches are distributed among these distances:
16 9 0.03
17 2 0.01
18 2 0.01
20 2 0.01
21 12 0.04
22 188 0.66
23 60 0.21
24 11 0.04
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (22 bp):
TATCAAAATTTCATATGAAGGT
Found at i:680 original size:23 final size:23
Alignment explanation
Indices: 650--707 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
640 CATAAGAATG
** *
650 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTTATAGAAAGAT
*
673 TTATCAAAATTTTTTAGAAAGAT
1 TTATCAAAATTTTATAGAAAGAT
696 TTATCAAAATTT
1 TTATCAAAATTT
708 CAAAAGATGG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.40, C:0.05, G:0.12, T:0.43
Consensus pattern (23 bp):
TTATCAAAATTTTATAGAAAGAT
Found at i:815 original size:24 final size:22
Alignment explanation
Indices: 696--854 Score: 108
Period size: 22 Copynumber: 7.1 Consensus size: 22
686 TTAGAAAGAT
* * * *
696 TTATCAAAATTTCAAAAGATGG
1 TTATTAAAATTTCATAGGTTGG
* *
718 TTATTATAATTTCATGAGG-AGG
1 TTATTAAAATTTCAT-AGGTTGG
* *
740 TTATCAAAATTCCATA-GTGTGG
1 TTATTAAAATTTCATAGGT-TGG
**
762 TTACCAAAATTTCATA-GTGTGG
1 TTATTAAAATTTCATAGGT-TGG
*
784 TTACTAAAATTTCATAGGATTAGG
1 TTATTAAAATTTCATAGG-TT-GG
* * *
808 TTATTAAAATCTCTTAGGCTGG
1 TTATTAAAATTTCATAGGTTGG
* *
830 TTATTGAAATTTCATAGGGTGG
1 TTATTAAAATTTCATAGGTTGG
852 TTA
1 TTA
855 ATTATCATAA
Statistics
Matches: 111, Mismatches: 20, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
20 1 0.01
21 1 0.01
22 86 0.77
23 5 0.05
24 18 0.16
ACGTcount: A:0.33, C:0.09, G:0.19, T:0.38
Consensus pattern (22 bp):
TTATTAAAATTTCATAGGTTGG
Found at i:1013 original size:22 final size:21
Alignment explanation
Indices: 965--1271 Score: 140
Period size: 22 Copynumber: 13.8 Consensus size: 21
955 TTTCATGGGG
* * *
965 AGGTTATGAAAATTTTATAGTG
1 AGGTTATCAAAATTTCATAG-A
*
987 TGGTTATCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATA-GA
* *
1009 AGGTTAT-AAAAGTCTCAATTTCATA
1 AGGTTATCAAAA-TTTC-A--T-AGA
* * *
1034 AGGAGTACCAAAATTTGATAGA
1 AGG-TTATCAAAATTTCATAGA
*
1056 AGGTTATC-AAATCTCATAG-
1 AGGTTATCAAAATTTCATAGA
*
1075 AGTGATTATCGAAATTTCATAGA
1 AG-G-TTATCAAAATTTCATAGA
1098 GATCGGATTATCAAAATTT-ATAGAA
1 -A--GG-TTATCAAAATTTCATAG-A
*
1123 AGATTATCAAAATTTCATAG-
1 AGGTTATCAAAATTTCATAGA
* * *
1143 TGTTGTTATCAAAATTTCAAAGTG
1 AG--GTTATCAAAATTTCATAG-A
*
1167 AGGTTATCAAAATTACATA-A
1 AGGTTATCAAAATTTCATAGA
* *
1187 TGTGATTATCAGAATTTCATAGA
1 AG-G-TTATCAAAATTTCATAGA
* * * * *
1210 GGGGTCAACAAAATTTTATAAA
1 -AGGTTATCAAAATTTCATAGA
*
1232 GAGGTTATCAAAATTTCATAAA
1 -AGGTTATCAAAATTTCATAGA
*
1254 GAGGTTATCAAATTTTCA
1 -AGGTTATCAAAATTTCA
1272 AAATGTGATT
Statistics
Matches: 220, Mismatches: 40, Indels: 50
0.71 0.13 0.16
Matches are distributed among these distances:
19 2 0.01
20 12 0.05
21 25 0.11
22 138 0.63
23 5 0.02
24 8 0.04
25 20 0.09
26 6 0.03
27 4 0.02
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (21 bp):
AGGTTATCAAAATTTCATAGA
Found at i:1196 original size:44 final size:44
Alignment explanation
Indices: 1103--1287 Score: 171
Period size: 44 Copynumber: 4.2 Consensus size: 44
1093 ATAGAGATCG
* * * *
1103 GATTATCAAAATTT-ATAGAAAGATTATCAAAATTTCATAGTGTT
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATG-T
* *
1147 G-TTATCAAAATTTCAAAGTGAGGTTATCAAAATTACATAATGT
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
* * * * * * * *
1190 GATTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAGA
1 GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
* * *
1234 GGTTATCAAAATTTCATAA-AGAGGTTATCAAATTTTCAAAATGT
1 GATTATCAAAATTTCA-AAGAGAGGTTATCAAAATTTCATAATGT
1278 GATTA-CAAAA
1 GATTATCAAAA
1288 ATT
Statistics
Matches: 110, Mismatches: 28, Indels: 7
0.76 0.19 0.05
Matches are distributed among these distances:
43 19 0.17
44 90 0.82
45 1 0.01
ACGTcount: A:0.43, C:0.09, G:0.14, T:0.34
Consensus pattern (44 bp):
GATTATCAAAATTTCAAAGAGAGGTTATCAAAATTTCATAATGT
Found at i:1222 original size:66 final size:66
Alignment explanation
Indices: 1124--1271 Score: 163
Period size: 66 Copynumber: 2.2 Consensus size: 66
1114 TTTATAGAAA
* ** * * *
1124 GATTATCAAAATTTCATAGTGTTGTTATCAAAATTTCA-AAGTGAGGTTATCAAAATTACATAAT
1 GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAA-AGAGGTTATCAAAATTACATAAT
1188 GT
65 GT
* * * *
1190 GATTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAGAGGTTATCAAAATTTCATAAAG
1 GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAAGAGGTTATCAAAATTACATAATG
*
1255 A
66 T
* *
1256 GGTTATCAAATTTTCA
1 GATTATCAAAATTTCA
1272 AAATGTGATT
Statistics
Matches: 67, Mismatches: 14, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
66 65 0.97
67 2 0.03
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (66 bp):
GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAAGAGGTTATCAAAATTACATAATG
T
Done.