Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007970.1 Corchorus capsularis cultivar CVL-1 contig07991, 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: 4602
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Found at i:67 original size:22 final size:22
Alignment explanation
Indices: 42--215 Score: 115
Period size: 22 Copynumber: 7.8 Consensus size: 22
32 TGTCTCTATG
*
42 TGGTTATCAAAATTTCATAAAA
1 TGGTTATCAAAATTTCATAGAA
* * *
64 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AGAA
**
87 -GGTTATCAAAA-TTCTATAGTG
1 TGGTTATCAAAATTTC-ATAGAA
* *
108 TGATTACCAAAATTTCATATGGAA
1 TGGTTATCAAAATTTCATA--GAA
132 --GTTATCAAAATTTCATA-ATA
1 TGGTTATCAAAATTTCATAGA-A
*
152 TGGTTACCAAAATTTCATAGAA
1 TGGTTATCAAAATTTCATAGAA
* * * **
174 TCAAGTTATTAAAATTTCTTAGGT
1 T--GGTTATCAAAATTTCATAGAA
*
198 TGGTTATTAAAATTTCAT
1 TGGTTATCAAAATTTCAT
216 TGGGTGGTTA
Statistics
Matches: 117, Mismatches: 23, Indels: 24
0.71 0.14 0.15
Matches are distributed among these distances:
19 1 0.01
20 1 0.01
21 5 0.04
22 87 0.74
23 6 0.05
24 17 0.15
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.40
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAGAA
Found at i:93 original size:44 final size:44
Alignment explanation
Indices: 43--170 Score: 145
Period size: 44 Copynumber: 2.9 Consensus size: 44
33 GTCTCTATGT
** *
43 GGTTATCAAAATTTCATAAAATGGTTATTATAATTTCATGA-GGA
1 GGTTATCAAAATTTCATAAAATGGTTACCAAAATTTCAT-ATGGA
* *
87 GGTTATCAAAA-TTC-TATAGTGTGATTACCAAAATTTCATATGGA
1 GGTTATCAAAATTTCATAAAATG-G-TTACCAAAATTTCATATGGA
* *
131 AGTTATCAAAATTTCATAATATGGTTACCAAAATTTCATA
1 GGTTATCAAAATTTCATAAAATGGTTACCAAAATTTCATA
171 GAATCAAGTT
Statistics
Matches: 70, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
42 5 0.07
43 5 0.07
44 52 0.74
45 4 0.06
46 4 0.06
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (44 bp):
GGTTATCAAAATTTCATAAAATGGTTACCAAAATTTCATATGGA
Found at i:223 original size:22 final size:22
Alignment explanation
Indices: 178--225 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
168 ATAGAATCAA
*
178 GTTATTAAAATTTCTTAGGTTG
1 GTTATTAAAATTTCTTAGGGTG
200 GTTATTAAAATTTCATT-GGGTG
1 GTTATTAAAATTTC-TTAGGGTG
222 GTTA
1 GTTA
226 ATTATCACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 22 0.92
23 2 0.08
ACGTcount: A:0.27, C:0.04, G:0.21, T:0.48
Consensus pattern (22 bp):
GTTATTAAAATTTCTTAGGGTG
Found at i:378 original size:22 final size:23
Alignment explanation
Indices: 329--384 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 23
319 TTAGACTTAC
*
329 AAGGTTATCAAAATTTTATAGTG
1 AAGGTTATCAAAATTTCATAGTG
*
352 -TGGTTATCAAAATTTCATA-TG
1 AAGGTTATCAAAATTTCATAGTG
373 AAGGTTAT-AAAA
1 AAGGTTATCAAAA
385 GTCTCAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 6 0.21
22 23 0.79
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.38
Consensus pattern (23 bp):
AAGGTTATCAAAATTTCATAGTG
Found at i:695 original size:22 final size:22
Alignment explanation
Indices: 670--798 Score: 88
Period size: 22 Copynumber: 5.9 Consensus size: 22
660 TGTCTCTATG
670 TGGTTATCAAAATTTCATAAAA
1 TGGTTATCAAAATTTCATAAAA
* * **
692 TGGTTATTATAATTTCATGAGGA
1 TGGTTATCAAAATTTCAT-AAAA
* *
715 -GGTTATCAAAA-TTC-TATAG
1 TGGTTATCAAAATTTCATAAAA
* *
734 TGTGATTACCAAAATTTCATATGGAA
1 TG-G-TTATCAAAATTTCATA--AAA
*
760 --GTTATCAAAATTTCATAATA
1 TGGTTATCAAAATTTCATAAAA
*
780 TGGTTACCAAAATTTCATA
1 TGGTTATCAAAATTTCATA
799 GAATCAAGTT
Statistics
Matches: 81, Mismatches: 16, Indels: 20
0.69 0.14 0.17
Matches are distributed among these distances:
19 1 0.01
20 3 0.04
21 4 0.05
22 64 0.79
23 6 0.07
24 2 0.02
26 1 0.01
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAAA
Found at i:721 original size:44 final size:44
Alignment explanation
Indices: 671--798 Score: 145
Period size: 44 Copynumber: 2.9 Consensus size: 44
661 GTCTCTATGT
** *
671 GGTTATCAAAATTTCATAAAATGGTTATTATAATTTCATGA-GGA
1 GGTTATCAAAATTTCATAAAATGGTTACCAAAATTTCAT-ATGGA
* *
715 GGTTATCAAAA-TTC-TATAGTGTGATTACCAAAATTTCATATGGA
1 GGTTATCAAAATTTCATAAAATG-G-TTACCAAAATTTCATATGGA
* *
759 AGTTATCAAAATTTCATAATATGGTTACCAAAATTTCATA
1 GGTTATCAAAATTTCATAAAATGGTTACCAAAATTTCATA
799 GAATCAAGTT
Statistics
Matches: 70, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
42 5 0.07
43 5 0.07
44 52 0.74
45 4 0.06
46 4 0.06
ACGTcount: A:0.39, C:0.10, G:0.13, T:0.38
Consensus pattern (44 bp):
GGTTATCAAAATTTCATAAAATGGTTACCAAAATTTCATATGGA
Found at i:831 original size:46 final size:46
Alignment explanation
Indices: 672--819 Score: 128
Period size: 44 Copynumber: 3.3 Consensus size: 46
662 TCTCTATGTG
* ** * ** *
672 GTTATCAAAATTTCATAAAATGGTTATTATAATTTCAT-G-AGGAG
1 GTTATCAAAATTTCATAATATGGTTACCAAAATTTCATAGAATCAA
* * * *
716 GTTATCAAAA-TTCTATAGTGTGATTACCAAAATTTCAT---ATGGAA
1 GTTATCAAAATTTC-ATAATATGGTTACCAAAATTTCATAGAAT-CAA
760 GTTATCAAAATTTCATAATATGGTTACCAAAATTTCATAGAATCAA
1 GTTATCAAAATTTCATAATATGGTTACCAAAATTTCATAGAATCAA
*
806 GTTATTAAAATTTC
1 GTTATCAAAATTTC
820 TTAGGTTGGT
Statistics
Matches: 84, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
43 4 0.05
44 60 0.71
45 3 0.04
46 15 0.18
47 2 0.02
ACGTcount: A:0.40, C:0.10, G:0.12, T:0.38
Consensus pattern (46 bp):
GTTATCAAAATTTCATAATATGGTTACCAAAATTTCATAGAATCAA
Found at i:838 original size:22 final size:22
Alignment explanation
Indices: 669--853 Score: 86
Period size: 22 Copynumber: 8.3 Consensus size: 22
659 TTGTCTCTAT
* **
669 GTGGTTATCAAAATTTCATAAA
1 GTGGTTATTAAAATTTCATAGG
* *
691 ATGGTTATTATAATTTCAT-GAG
1 GTGGTTATTAAAATTTCATAG-G
* * *
713 GAGGTTATCAAAA-TTCTATAGT
1 GTGGTTATTAAAATTTC-ATAGG
* ** *
735 GTGATTACCAAAATTTCATATG
1 GTGGTTATTAAAATTTCATAGG
** * **
757 GAAGTTATCAAAATTTCATAAT
1 GTGGTTATTAAAATTTCATAGG
* ** *
779 ATGGTTACCAAAATTTCATAGA
1 GTGGTTATTAAAATTTCATAGG
* * *
801 ATCAAGTTATTAAAATTTCTTAGG
1 GT--GGTTATTAAAATTTCATAGG
* *
825 TTGGTTATTGAAATTTCATAGG
1 GTGGTTATTAAAATTTCATAGG
847 GTGGTTA
1 GTGGTTA
854 ATTATCACAA
Statistics
Matches: 120, Mismatches: 37, Indels: 12
0.71 0.22 0.07
Matches are distributed among these distances:
21 3 0.03
22 97 0.81
23 4 0.03
24 16 0.13
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (22 bp):
GTGGTTATTAAAATTTCATAGG
Found at i:914 original size:22 final size:22
Alignment explanation
Indices: 889--1306 Score: 122
Period size: 22 Copynumber: 18.9 Consensus size: 22
879 ATCAAAAAGA
* *
889 TTATCAAAATGTCATAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
* *
911 TTAT-AACAATTTCGTAGTGTGG
1 TTATCAA-AATTTCATAGTGAGG
* *
933 TTAACAAAATTTCATTAG-AAGG
1 TTATCAAAATTTCA-TAGTGAGG
* * *
955 TTA-CTAATATTTCATGGGGAGG
1 TTATC-AAAATTTCATAGTGAGG
* *
977 TTATCAAAATTTTATAGTGTGG
1 TTATCAAAATTTCATAGTGAGG
999 TTATCAAAATTTCATA-TGAAGG
1 TTATCAAAATTTCATAGTG-AGG
* * *
1021 TTATAAGAGTCTCAATTTCATA-AGAAG
1 TTATCA-A-----AATTTCATAGTGAGG
* * ** *
1048 -TACCAAAATTTGATA-CAATG
1 TTATCAAAATTTCATAGTGAGG
* * * *
1068 TTATC-AAATCTCATAGAGTGA
1 TTATCAAAATTTCATAGTGAGG
* * * * **
1089 TTATCGATATTCCATAGAGAACAA
1 TTATCAAAATTTCATAGTG-A-GG
* ** *
1113 ATATCAAAATTT-ATAGAAAGA
1 TTATCAAAATTTCATAGTGAGG
***
1134 TTATCAAAATTTCATAGTTTTG
1 TTATCAAAATTTCATAGTGAGG
* *
1156 TTATCAAAATTTCAAAGCGAGG
1 TTATCAAAATTTCATAGTGAGG
* * * * *
1178 TTATCAAAATTACTTAATGTGA
1 TTATCAAAATTTCATAGTGAGG
*
1200 TTATCAGAAA-TTCATAG-AAGGG
1 TTATCA-AAATTTCATAGTGA-GG
* * **
1222 TTAACAAAATTTTATAAAGAGG
1 TTATCAAAATTTCATAGTGAGG
**
1244 TTATCAAAATTTCATAAAGAGG
1 TTATCAAAATTTCATAGTGAGG
* * * * *
1266 TTATCAAATTTTCAAAATGTGA
1 TTATCAAAATTTCATAGTGAGG
1288 TTA-CAAAAATTTCATAGTG
1 TTATC-AAAATTTCATAGTG
1307 GTATTTCTGG
Statistics
Matches: 288, Mismatches: 84, Indels: 48
0.69 0.20 0.11
Matches are distributed among these distances:
20 18 0.06
21 31 0.11
22 198 0.69
23 16 0.06
24 9 0.03
25 1 0.00
26 3 0.01
27 2 0.01
28 10 0.03
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGAGG
Found at i:1211 original size:88 final size:87
Alignment explanation
Indices: 1114--1304 Score: 197
Period size: 88 Copynumber: 2.2 Consensus size: 87
1104 AGAGAACAAA
* ***** *
1114 TATCAAAATTTATAGAAAGATTATCAAAATTTCATAGTTTTGTTATCAAAATTTCA-AAGCGAGG
1 TATCAAAATTTATAGAAAGATTAACAAAATTTCATAAAGAGGTTATCAAAATTTCATAA-AGAGG
**
1178 TTATCAAAATTACTTAATGTGAT
65 TTATCAAAATTACAAAATGTGAT
* * * *
1201 TATCAGAAATTCATAGAAGGGTTAACAAAATTTTATAAAGAGGTTATCAAAATTTCATAAAGAGG
1 TATCA-AAATTTATAGAAAGATTAACAAAATTTCATAAAGAGGTTATCAAAATTTCATAAAGAGG
* *
1266 TTATCAAATTTTCAAAATGTGAT
65 TTATCAAAATTACAAAATGTGAT
1289 TA-CAAAAATTTCATAG
1 TATC-AAAATTT-ATAG
1305 TGGTATTTCT
Statistics
Matches: 84, Mismatches: 16, Indels: 7
0.79 0.15 0.07
Matches are distributed among these distances:
87 11 0.13
88 71 0.85
89 2 0.02
ACGTcount: A:0.43, C:0.09, G:0.13, T:0.35
Consensus pattern (87 bp):
TATCAAAATTTATAGAAAGATTAACAAAATTTCATAAAGAGGTTATCAAAATTTCATAAAGAGGT
TATCAAAATTACAAAATGTGAT
Found at i:1600 original size:23 final size:23
Alignment explanation
Indices: 1550--1656 Score: 94
Period size: 23 Copynumber: 4.7 Consensus size: 23
1540 AAATTCGTAG
* * * *
1550 TTATCAAGATTTCATAAGAAAG-
1 TTATCAAAATTTCATAGGGAGGT
*
1572 TTATCAAAATTTTATAGGGAGGT
1 TTATCAAAATTTCATAGGGAGGT
* * *
1595 TTATCAAAATTTTATAGGAAGAT
1 TTATCAAAATTTCATAGGGAGGT
*
1618 TTATC-AAATCTTCATAGCGAGG-
1 TTATCAAAAT-TTCATAGGGAGGT
*
1640 TTATCACAATTTCATAG
1 TTATCAAAATTTCATAG
1657 TATTATTATC
Statistics
Matches: 70, Mismatches: 12, Indels: 6
0.80 0.14 0.07
Matches are distributed among these distances:
22 33 0.47
23 37 0.53
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.36
Consensus pattern (23 bp):
TTATCAAAATTTCATAGGGAGGT
Found at i:1656 original size:22 final size:21
Alignment explanation
Indices: 1385--1675 Score: 175
Period size: 22 Copynumber: 13.6 Consensus size: 21
1375 TTATGGTGTA
*
1385 ATCAAAATTTCA-AGGAGGAT
1 ATCAAAATTTCATAGGAGGTT
* *
1405 ATCACAATTTCATAGTTTA-GTT
1 ATCAAAATTTCATAG--GAGGTT
* *
1427 TTCAAAATTTCATAAGAAGGTT
1 ATCAAAATTTCAT-AGGAGGTT
* * *
1449 ATCAAAATTTCATAGTATGTAG
1 ATCAAAATTTCATAGGAGGT-T
*
1471 ATCAAAATTTCATAAGGAGATT
1 ATCAAAATTTCAT-AGGAGGTT
* **
1493 AACAAAATTTCATAATAAGGTT
1 ATCAAAATTTCAT-AGGAGGTT
**
1515 ATCAAAAAATCATAGGAGGTT
1 ATCAAAATTTCATAGGAGGTT
*
1536 ATCAAAA-TTC---GTA-GTT
1 ATCAAAATTTCATAGGAGGTT
* * *
1552 ATCAAGATTTCATAAGAAAGTT
1 ATCAAAATTTCAT-AGGAGGTT
*
1574 ATCAAAATTTTATAGGGAGGTTT
1 ATCAAAATTTCATA-GGAGG-TT
* *
1597 ATCAAAATTTTATAGGAAGATTT
1 ATCAAAATTTCATAGG-AG-GTT
1620 ATC-AAATCTTCATAGCGAGGTT
1 ATCAAAAT-TTCATAG-GAGGTT
* * **
1642 ATCACAATTTCATAGTATTATT
1 ATCAAAATTTCATAGGA-GGTT
1664 ATCAAAATTTCA
1 ATCAAAATTTCA
1676 GAGTGTGATT
Statistics
Matches: 211, Mismatches: 39, Indels: 40
0.73 0.13 0.14
Matches are distributed among these distances:
16 9 0.04
17 5 0.02
20 13 0.06
21 25 0.12
22 117 0.55
23 41 0.19
24 1 0.00
ACGTcount: A:0.41, C:0.10, G:0.13, T:0.35
Consensus pattern (21 bp):
ATCAAAATTTCATAGGAGGTT
Found at i:1686 original size:22 final size:22
Alignment explanation
Indices: 1640--1686 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
1630 CATAGCGAGG
* * *
1640 TTATCACAATTTCATAGTATTA
1 TTATCAAAATTTCAGAGTATGA
*
1662 TTATCAAAATTTCAGAGTGTGA
1 TTATCAAAATTTCAGAGTATGA
1684 TTA
1 TTA
1687 CTAACAATTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.43
Consensus pattern (22 bp):
TTATCAAAATTTCAGAGTATGA
Found at i:1764 original size:22 final size:22
Alignment explanation
Indices: 1738--1825 Score: 72
Period size: 22 Copynumber: 4.0 Consensus size: 22
1728 TTACAATATA
*
1738 TCATATGGAGGTTATCAACATC
1 TCATATGGAGGTTATCAAAATC
** *
1760 TCATAGTGTTGGTTATCAAAATT
1 TCATA-TGGAGGTTATCAAAATC
* *
1783 TC-TTTGGGAAGTTATCAAAATC
1 TCATAT-GGAGGTTATCAAAATC
*
1805 TCATATTGAGGTCT-TCAAAAT
1 TCATATGGAGGT-TATCAAAAT
1826 TCCTTATGGA
Statistics
Matches: 50, Mismatches: 12, Indels: 8
0.71 0.17 0.11
Matches are distributed among these distances:
21 1 0.02
22 31 0.62
23 18 0.36
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.38
Consensus pattern (22 bp):
TCATATGGAGGTTATCAAAATC
Found at i:2046 original size:2 final size:2
Alignment explanation
Indices: 2039--2068 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2029 AAAACTAGTG
2039 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2069 CACTACGTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3978 original size:27 final size:27
Alignment explanation
Indices: 3927--3978 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
3917 TACTCAACTT
* **
3927 TTCCTACTCCTTTACATTACCAAACGA
1 TTCCTACTCCTTAACAACACCAAACGA
*
3954 TTCCTACTCCTTAACAACACTAAAC
1 TTCCTACTCCTTAACAACACCAAAC
3979 TACACCAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.33, C:0.35, G:0.02, T:0.31
Consensus pattern (27 bp):
TTCCTACTCCTTAACAACACCAAACGA
Done.