Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005889.1 Corchorus capsularis cultivar CVL-1 contig05907, 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, 933
Length: 1555
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.38
Found at i:98 original size:30 final size:31
Alignment explanation
Indices: 44--108 Score: 114
Period size: 30 Copynumber: 2.1 Consensus size: 31
34 AACTTTATGT
*
44 TTTCCGATTGTACCCTTATTTTTAAAACATA
1 TTTCCAATTGTACCCTTATTTTTAAAACATA
75 TTTCCAATTGTACCCTT-TTTTTAAAACATA
1 TTTCCAATTGTACCCTTATTTTTAAAACATA
105 TTTC
1 TTTC
109 TAAATAGCCA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 17 0.52
31 16 0.48
ACGTcount: A:0.28, C:0.20, G:0.05, T:0.48
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTATTTTTAAAACATA
Found at i:235 original size:22 final size:22
Alignment explanation
Indices: 209--329 Score: 154
Period size: 22 Copynumber: 5.5 Consensus size: 22
199 GGTTAATTAT
* *
209 AATTCCATGAG-GAGGTTATCAA
1 AATTCCAT-AGTGTGGTTACCAA
231 AATTCCATAGTGTGGTTACCAA
1 AATTCCATAGTGTGGTTACCAA
253 AATTCCATAGTGTGGTTACCAA
1 AATTCCATAGTGTGGTTACCAA
* *
275 AATTTCATAGTGTAGTTACCAA
1 AATTCCATAGTGTGGTTACCAA
* * *
297 AATTTCATAGAGTGGATACCAA
1 AATTCCATAGTGTGGTTACCAA
*
319 AATTTCATAGT
1 AATTCCATAGT
330 ATCAAGTTAT
Statistics
Matches: 90, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
21 2 0.02
22 88 0.98
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (22 bp):
AATTCCATAGTGTGGTTACCAA
Found at i:550 original size:22 final size:22
Alignment explanation
Indices: 502--808 Score: 104
Period size: 22 Copynumber: 13.8 Consensus size: 22
492 CTTCATCGGG
* *
502 AGGTTATCAAAATTTTATA-GCG
1 AGGTTATCAAAATTTCATATG-A
*
524 TGGTTATCAAAATTTCATATGA
1 AGGTTATCAAAATTTCATATGA
*
546 AGGTTAT-AAAAGTCTCAATTTCAT-A
1 AGGTTATCAAAA-TTTC-A--T-ATGA
* * *
571 AGGAGTACCAAAATTTGATA-GA
1 AGG-TTATCAAAATTTCATATGA
* *
593 AGGTTATC-AAGTCTCATA-G-
1 AGGTTATCAAAATTTCATATGA
* *
612 AGTGATTATCGAAATTTCATAAAGA
1 AG-G-TTATCAAAATTTCAT-ATGA
*
637 TATGATTATCAAAATTT-ATATGA
1 -A-GGTTATCAAAATTTCATATGA
*
660 AGATTATCAAAATTTCATAGTG-
1 AGGTTATCAAAATTTCATA-TGA
** *
682 TTGTTATCAAAATTTCA-AAGCA
1 AGGTTATCAAAATTTCATATG-A
* *
704 AGGTTATAAAAATTACATAATG-
1 AGGTTATCAAAATTTCAT-ATGA
* *
726 TGATTATCAAAATTTCATA-GA
1 AGGTTATCAAAATTTCATATGA
* * * *
747 GGGGTCAACAAAATTT--TATAA
1 -AGGTTATCAAAATTTCATATGA
*
768 AGATGTTATCAAAATTTCATA-AA
1 AG--GTTATCAAAATTTCATATGA
*
791 GAGGTTATCAAATTTTCA
1 -AGGTTATCAAAATTTCA
809 AAATCTGATT
Statistics
Matches: 213, Mismatches: 41, Indels: 62
0.67 0.13 0.20
Matches are distributed among these distances:
19 2 0.01
20 14 0.07
21 29 0.14
22 119 0.56
23 11 0.05
24 9 0.04
25 17 0.08
26 7 0.03
27 5 0.02
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.35
Consensus pattern (22 bp):
AGGTTATCAAAATTTCATATGA
Found at i:642 original size:25 final size:24
Alignment explanation
Indices: 614--808 Score: 107
Period size: 22 Copynumber: 8.7 Consensus size: 24
604 TCTCATAGAG
*
614 TGATTATCGAAATTTCATAAAGATA
1 TGATTATCAAAATTTCATAAAGA-A
*
639 TGATTATCAAAATTT-AT-ATGAA
1 TGATTATCAAAATTTCATAAAGAA
** *
661 -GATTATCAAAATTTCATAGTG-T
1 TGATTATCAAAATTTCATAAAGAA
683 TG-TTATCAAAATTTC--AAAGCAA
1 TGATTATCAAAATTTCATAAAG-AA
* * * *
705 -GGTTATAAAAATTACATAATG--
1 TGATTATCAAAATTTCATAAAGAA
*
726 TGATTATCAAAATTTCAT--AGAG
1 TGATTATCAAAATTTCATAAAGAA
* * * * *
748 GGGTCAACAAAATTTTATAAAG-A
1 TGATTATCAAAATTTCATAAAGAA
771 TG-TTATCAAAATTTCATAAAG-A
1 TGATTATCAAAATTTCATAAAGAA
* *
793 -GGTTATCAAATTTTCA
1 TGATTATCAAAATTTCA
809 AAATCTGATT
Statistics
Matches: 131, Mismatches: 25, Indels: 31
0.70 0.13 0.17
Matches are distributed among these distances:
20 3 0.02
21 16 0.12
22 84 0.64
23 7 0.05
24 7 0.05
25 14 0.11
ACGTcount: A:0.43, C:0.09, G:0.12, T:0.36
Consensus pattern (24 bp):
TGATTATCAAAATTTCATAAAGAA
Found at i:659 original size:18 final size:19
Alignment explanation
Indices: 636--674 Score: 53
Period size: 21 Copynumber: 2.0 Consensus size: 19
626 TTTCATAAAG
636 ATAT-GATTATCAAAATTT
1 ATATAGATTATCAAAATTT
654 ATATGAAGATTATCAAAATTT
1 ATAT--AGATTATCAAAATTT
675 CATAGTGTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 4 0.22
21 14 0.78
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (19 bp):
ATATAGATTATCAAAATTT
Found at i:734 original size:44 final size:45
Alignment explanation
Indices: 639--744 Score: 130
Period size: 44 Copynumber: 2.4 Consensus size: 45
629 CATAAAGATA
* * * *
639 TGATTATCAAAATTT-ATATGAAGATTATCAAAATTTCATAGTGT
1 TGATTATCAAAATTTCATAAGAAGATTATAAAAATTACATAATGT
*
683 TG-TTATCAAAATTTCA-AAGCAAGGTTATAAAAATTACATAATG-
1 TGATTATCAAAATTTCATAAG-AAGATTATAAAAATTACATAATGT
726 TGATTATCAAAATTTCATA
1 TGATTATCAAAATTTCATA
745 GAGGGGTCAA
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
43 16 0.30
44 36 0.68
45 1 0.02
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.38
Consensus pattern (45 bp):
TGATTATCAAAATTTCATAAGAAGATTATAAAAATTACATAATGT
Found at i:943 original size:20 final size:20
Alignment explanation
Indices: 918--966 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
908 ATGGAGTAAT
*
918 CAAAATTTTAGGGAGGATAC
1 CAAAATTTCAGGGAGGATAC
* *
938 CAAAA-TTCAGTGAGGATAT
1 CAAAATTTCAGGGAGGATAC
957 CAAAATTTCA
1 CAAAATTTCA
967 TATGAAGGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 16 0.64
20 9 0.36
ACGTcount: A:0.43, C:0.12, G:0.18, T:0.27
Consensus pattern (20 bp):
CAAAATTTCAGGGAGGATAC
Found at i:982 original size:22 final size:21
Alignment explanation
Indices: 948--1250 Score: 139
Period size: 22 Copynumber: 13.8 Consensus size: 21
938 CAAAATTCAG
*
948 TGAGGATATCAAAATTTCATA
1 TGAGGTTATCAAAATTTCATA
*
969 TGAAGGTTATCAAATTTTCATA
1 TG-AGGTTATCAAAATTTCATA
* *
991 GTTTA-GTTTTCAAAATTTCATA
1 --TGAGGTTATCAAAATTTCATA
*
1013 AGAGAGTTATCAAAATTTCATA
1 TGAG-GTTATCAAAATTTCATA
* *
1035 -GTATGTAGATCAAAATTTCATA
1 TG-AGGT-TATCAAAATTTCATA
* * *
1057 GGGAGATTAACAAAATTTCATAA
1 -TGAGGTTATCAAAATTTCAT-A
**
1080 TGAGGTTATCAAAAAATCATAA
1 TGAGGTTATCAAAATTTCAT-A
* * *
1102 GGAGCTTATCAAAATTT-GTA
1 TGAGGTTATCAAAATTTCATA
* ** *
1122 GTTATATT-TCAAGATTTCATA
1 -TGAGGTTATCAAAATTTCATA
* ** *
1143 AGAAATTTATCAAAATTTTATA
1 TG-AGGTTATCAAAATTTCATA
* * *
1165 GGGAGGTTCATTAAAATTTTATA
1 -TGAGGTT-ATCAAAATTTCATA
*
1188 -GAAAGATTTATCAAAATTTCATA
1 TG--AG-GTTATCAAAATTTCATA
*
1211 GTGAGGTTATCACAATTTCATA
1 -TGAGGTTATCAAAATTTCATA
* *
1233 GTGTGATTATCAAAATTT
1 -TGAGGTTATCAAAATTT
1251 TAAAGTGTGA
Statistics
Matches: 213, Mismatches: 48, Indels: 41
0.71 0.16 0.14
Matches are distributed among these distances:
20 10 0.05
21 15 0.07
22 149 0.70
23 34 0.16
24 4 0.02
25 1 0.00
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (21 bp):
TGAGGTTATCAAAATTTCATA
Found at i:1031 original size:66 final size:64
Alignment explanation
Indices: 954--1250 Score: 224
Period size: 66 Copynumber: 4.5 Consensus size: 64
944 TCAGTGAGGA
* *
954 TATCAAAATTTCATATGAAGGTTATCAAATTTTCATAGTTTAG-TTTTCAAAATTTCATAAGAGA
1 TATCAAAATTTCATA-GGAGGTTATCAAAATTT-ATAG-TTAGATTTTCAAAATTTCATAAGAGA
1018 GT
63 GT
* * * ** **
1020 TATCAAAATTTCATAGTATGTAGATCAAAATTTCATAGGGAGATTAACAAAATTTCATAATGAG-
1 TATCAAAATTTCATAGGAGGT-TATCAAAATTT-ATAGTTAGATTTTCAAAATTTCATAA-GAGA
1084 GT
63 GT
** * * * * * *
1086 TATCAAAAAATCATAAGGAGCTTATCAAAATTTGTAGTTATA-TTTCAAGATTTCATAAGAAATT
1 TATCAAAATTTCAT-AGGAGGTTATCAAAATTTATAGTTAGATTTTCAAAATTTCATAAGAGAGT
* * ** *
1150 TATCAAAATTTTATAGGGAGGTTCATTAAAATTTTATAGAAAGATTTATCAAAATTTCAT-AGTG
1 TATCAAAATTTCATA-GGAGGTT-ATCAAAA-TTTATAGTTAGATTT-TCAAAATTTCATAAGAG
1214 AGGT
62 A-GT
* * *
1218 TATCACAATTTCATAGTGTGATTATCAAAATTT
1 TATCAAAATTTCATAG-GAGGTTATCAAAATTT
1251 TAAAGTGTGA
Statistics
Matches: 178, Mismatches: 41, Indels: 24
0.73 0.17 0.10
Matches are distributed among these distances:
63 3 0.02
64 31 0.17
65 17 0.10
66 79 0.44
67 19 0.11
68 29 0.16
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (64 bp):
TATCAAAATTTCATAGGAGGTTATCAAAATTTATAGTTAGATTTTCAAAATTTCATAAGAGAGT
Found at i:1048 original size:44 final size:44
Alignment explanation
Indices: 955--1212 Score: 154
Period size: 44 Copynumber: 5.9 Consensus size: 44
945 CAGTGAGGAT
* *
955 ATCAAAATTTCATATGA-AGGTTATCAAATTTTCATAGT-T-TAG
1 ATCAAAATTTCATAAGAGA-GTTATCAAAATTTCATAGTATGTAG
*
997 TTTTCAAAATTTCATAAGAGAGTTATCAAAATTTCATAGTATGTAG
1 --ATCAAAATTTCATAAGAGAGTTATCAAAATTTCATAGTATGTAG
* * * * *
1043 ATCAAAATTTCAT-AGGGAGATTAACAAAATTTCATAATGAGGT-T
1 ATCAAAATTTCATAAGAGAG-TTATCAAAATTTCATAGT-ATGTAG
** * * *
1087 ATCAAAAAATCATAAG-GAGCTTATCAAAATTT-GTAGT-TATAT
1 ATCAAAATTTCATAAGAGAG-TTATCAAAATTTCATAGTATGTAG
* * * * * * * **
1129 TTCAAGATTTCATAAGAAATTTATCAAAATTTTATAGGGAGGTTC
1 ATCAAAATTTCATAAGAGAGTTATCAAAATTTCATA-GTATGTAG
* * * *
1174 ATTAAAATTTTATAGAAAGATTTATCAAAATTTCATAGT
1 ATCAAAATTTCATA-AGAGAGTTATCAAAATTTCATAGT
1213 GAGGTTATCA
Statistics
Matches: 165, Mismatches: 37, Indels: 23
0.73 0.16 0.10
Matches are distributed among these distances:
41 1 0.01
42 25 0.15
43 11 0.07
44 87 0.53
45 19 0.12
46 22 0.13
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.37
Consensus pattern (44 bp):
ATCAAAATTTCATAAGAGAGTTATCAAAATTTCATAGTATGTAG
Found at i:1203 original size:23 final size:23
Alignment explanation
Indices: 1147--1211 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
1137 TTCATAAGAA
**
1147 ATTTATCAAAATTTTATAGGGAG
1 ATTTATCAAAATTTTATAGAAAG
* * *
1170 GTTCATTAAAATTTTATAGAAAG
1 ATTTATCAAAATTTTATAGAAAG
*
1193 ATTTATCAAAATTTCATAG
1 ATTTATCAAAATTTTATAG
1212 TGAGGTTATC
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.40
Consensus pattern (23 bp):
ATTTATCAAAATTTTATAGAAAG
Found at i:1232 original size:132 final size:131
Alignment explanation
Indices: 946--1250 Score: 319
Period size: 132 Copynumber: 2.3 Consensus size: 131
936 ACCAAAATTC
* * * * *
946 AGTGAGGATATCAAAATTTCATATGAAGGTTATCAAATTTTCATAGTTTAGTTTTCAAAATTTCA
1 AGTGAGGTTATCAAAATTTCATAAGGAGATTATCAAAATTTCATAGTTTAG-TTTCAAAATTTCA
* * * * **
1011 TAAGAGAGTTATCAAAATTTCATAGTATGTAGATCAAAATTTCATAGGGAGATTAACAAAATTTC
65 TAAGAAAGTTATCAAAATTTCATAGGAGGTACATCAAAATTTCATAGAAAGATTAACAAAATTTC
1076 AT
130 AT
* ** * * *
1078 AATGAGGTTATCAAAAAATCATAAGGAGCTTATCAAAATTT-GTAGTTATA-TTTCAAGATTTCA
1 AGTGAGGTTATCAAAATTTCATAAGGAGATTATCAAAATTTCATAGTT-TAGTTTCAAAATTTCA
* * * * * *
1141 TAAGAAATTTATCAAAATTTTATAGGGAGGTTCATTAAAATTTTATAGAAAGATTTATCAAAATT
65 TAAGAAAGTTATCAAAATTTCATA-GGAGGTACATCAAAATTTCATAGAAAGA-TTAACAAAATT
1206 TCAT
128 TCAT
* *
1210 AGTGAGGTTATCACAATTTCAT-AGTGTGATTATCAAAATTT
1 AGTGAGGTTATCAAAATTTCATAAG-GAGATTATCAAAATTT
1251 TAAAGTGTGA
Statistics
Matches: 141, Mismatches: 28, Indels: 8
0.80 0.16 0.05
Matches are distributed among these distances:
130 33 0.23
131 27 0.19
132 81 0.57
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (131 bp):
AGTGAGGTTATCAAAATTTCATAAGGAGATTATCAAAATTTCATAGTTTAGTTTCAAAATTTCAT
AAGAAAGTTATCAAAATTTCATAGGAGGTACATCAAAATTTCATAGAAAGATTAACAAAATTTCA
T
Done.