Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007978.1 Corchorus capsularis cultivar CVL-1 contig07999, 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: 7993
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Found at i:606 original size:37 final size:37
Alignment explanation
Indices: 558--956 Score: 430
Period size: 37 Copynumber: 10.8 Consensus size: 37
548 CATTCTCGTC
*
558 AAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTCATCA
1 AAAT-CTTGTTTAAGATCCCTGTTTAGGTGTCTCATCA
*
596 AAATCTTGTTTAAGATACCTGTTTAGGTGTCTCATCA
1 AAATCTTGTTTAAGATCCCTGTTTAGGTGTCTCATCA
* * * *
633 AAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTAT-T
1 AAATCTTGTTTAAGATCCCTGTTTAGGTGTCTCATCA
*
669 AAATCCTTGTTTAAGATCCCTGTTTAGGTGTCTCGTCA
1 AAAT-CTTGTTTAAGATCCCTGTTTAGGTGTCTCATCA
* * * * * *
707 AAATCTTGTTTAAGATTCTTGTTTAGATTTCTTAT-T
1 AAATCTTGTTTAAGATCCCTGTTTAGGTGTCTCATCA
*
743 AAATCCTTGTTTAA-AGTCCCTGTTTAGGTGTCTCGTCA
1 AAAT-CTTGTTTAAGA-TCCCTGTTTAGGTGTCTCATCA
* * * * **
781 AAATCTTGTTTAAGATTCCTATTTAGGTTTCT-TTTT
1 AAATCTTGTTTAAGATCCCTGTTTAGGTGTCTCATCA
* **
817 AAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTCGCCA
1 AAAT-CTTGTTTAAGATCCCTGTTTAGGTGTCTCATCA
* * * * * *
855 AAGTCTTGTTTAAGATTCCTGTTTAGATTTCTTAT-T
1 AAATCTTGTTTAAGATCCCTGTTTAGGTGTCTCATCA
*
891 AAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTCATCA
1 AAAT-CTTGTTTAAGATCCCTGTTTAGGTGTCTCATCA
*
929 AAATCTTGTTTAAGATTCCTGTTTAGGT
1 AAATCTTGTTTAAGATCCCTGTTTAGGT
957 TTAACAAATC
Statistics
Matches: 294, Mismatches: 57, Indels: 21
0.79 0.15 0.06
Matches are distributed among these distances:
36 17 0.06
37 257 0.87
38 20 0.07
ACGTcount: A:0.22, C:0.16, G:0.16, T:0.45
Consensus pattern (37 bp):
AAATCTTGTTTAAGATCCCTGTTTAGGTGTCTCATCA
Found at i:644 original size:74 final size:74
Alignment explanation
Indices: 551--958 Score: 615
Period size: 74 Copynumber: 5.5 Consensus size: 74
541 AAAAATTCAT
* * * * * *
551 TCTCGTC-AAATCCTTGTTTAAGGTCCCTGTTTAGGTGTCTCATCAAAAT-CTTGTTTAAGATAC
1 TCTCGTCAAAAT-CTTGTTTAAGATTCCTGTTTAGGTTTCTTAT-TAAATCCTTGTTTAAGATCC
614 CTGTTTAGGTG
64 CTGTTTAGGTG
*
625 TCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATTAAATCCTTGTTTAAGATCCCT
1 TCTCGTCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATTAAATCCTTGTTTAAGATCCCT
690 GTTTAGGTG
66 GTTTAGGTG
* *
699 TCTCGTCAAAATCTTGTTTAAGATTCTTGTTTAGATTTCTTATTAAATCCTTGTTTAA-AGTCCC
1 TCTCGTCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATTAAATCCTTGTTTAAGA-TCCC
763 TGTTTAGGTG
65 TGTTTAGGTG
* * *
773 TCTCGTCAAAATCTTGTTTAAGATTCCTATTTAGGTTTCTTTTTAAATCCTTGTTTAAGGTCCCT
1 TCTCGTCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATTAAATCCTTGTTTAAGATCCCT
838 GTTTAGGTG
66 GTTTAGGTG
* * * *
847 TCTCGCCAAAGTCTTGTTTAAGATTCCTGTTTAGATTTCTTATTAAATCCTTGTTTAAGGTCCCT
1 TCTCGTCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATTAAATCCTTGTTTAAGATCCCT
912 GTTTAGGTG
66 GTTTAGGTG
*
921 TCTCATCAAAATCTTGTTTAAGATTCCTGTTTAGGTTT
1 TCTCGTCAAAATCTTGTTTAAGATTCCTGTTTAGGTTT
959 AACAAATCCT
Statistics
Matches: 306, Mismatches: 24, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
73 5 0.02
74 297 0.97
75 4 0.01
ACGTcount: A:0.22, C:0.17, G:0.16, T:0.45
Consensus pattern (74 bp):
TCTCGTCAAAATCTTGTTTAAGATTCCTGTTTAGGTTTCTTATTAAATCCTTGTTTAAGATCCCT
GTTTAGGTG
Found at i:728 original size:13 final size:13
Alignment explanation
Indices: 636--756 Score: 51
Period size: 13 Copynumber: 9.8 Consensus size: 13
626 CTCATCAAAA
636 TCTTGTTTAAGAT
1 TCTTGTTTAAGAT
* * *
649 TCCTGTTTAGGTT
1 TCTTGTTTAAGAT
*
662 TCTT-ATTAA-AT
1 TCTTGTTTAAGAT
*
673 CCTTGTTTAAGAT
1 TCTTGTTTAAGAT
* * *
686 CCCTGTTT-AGGT
1 TCTTGTTTAAGAT
* * *
698 GTCTCG-TCAA-AA
1 -TCTTGTTTAAGAT
710 TCTTGTTTAAGAT
1 TCTTGTTTAAGAT
723 TCTTGTTT-AGATT
1 TCTTGTTTAAGA-T
*
736 TCTT-ATTAA-AT
1 TCTTGTTTAAGAT
*
747 CCTTGTTTAA
1 TCTTGTTTAA
757 AGTCCCTGTT
Statistics
Matches: 76, Mismatches: 23, Indels: 19
0.64 0.19 0.16
Matches are distributed among these distances:
11 12 0.16
12 24 0.32
13 40 0.53
ACGTcount: A:0.22, C:0.14, G:0.14, T:0.50
Consensus pattern (13 bp):
TCTTGTTTAAGAT
Found at i:1052 original size:28 final size:28
Alignment explanation
Indices: 1000--1058 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
990 TATTCAAAAA
* *
1000 TCAAATTTCAAAATCAGCATCTCATAGT
1 TCAAAATTCAAAATCACCATCTCATAGT
* * *
1028 TCAAAATTCAAAATCTCCATTTCATGGT
1 TCAAAATTCAAAATCACCATCTCATAGT
1056 TCA
1 TCA
1059 TTCTTCAAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.37, C:0.22, G:0.07, T:0.34
Consensus pattern (28 bp):
TCAAAATTCAAAATCACCATCTCATAGT
Found at i:1123 original size:43 final size:42
Alignment explanation
Indices: 1028--1123 Score: 106
Period size: 42 Copynumber: 2.3 Consensus size: 42
1018 ATCTCATAGT
* *
1028 TCAAAATTCAAAATCTCCATTTCATGGTTCATTCTTCAAAAA
1 TCAAAATTCAAAATCTCCATTTCATGATTCATTATTCAAAAA
* *
1070 TCAAATTTCAAAA-CTCTCATTTCA-GTATTCCATTATTCGAAAA
1 TCAAAATTCAAAATCTC-CATTTCATG-ATT-CATTATTCAAAAA
*
1113 TCAAAGTTCAA
1 TCAAAATTCAA
1124 TATTTGCATC
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
41 4 0.09
42 21 0.46
43 21 0.46
ACGTcount: A:0.39, C:0.21, G:0.05, T:0.35
Consensus pattern (42 bp):
TCAAAATTCAAAATCTCCATTTCATGATTCATTATTCAAAAA
Found at i:1136 original size:62 final size:59
Alignment explanation
Indices: 1069--1191 Score: 167
Period size: 62 Copynumber: 2.0 Consensus size: 59
1059 TTCTTCAAAA
* * * *
1069 ATCAAATTTCAAAAC-TCTCATTTCAGTATTCCATTATTCGAAAATCAAAGTTCAATATTTGC
1 ATCAAAATTCAAAACAT-GCATTTCAGTATTCC---ATCCGAAAATCAAAGTTCAAAATTTGC
1131 ATCAAAATTCAAAACATGCATTTCAGTATTCCATCCGAAAATCAAAGTTCAAAATTTGC
1 ATCAAAATTCAAAACATGCATTTCAGTATTCCATCCGAAAATCAAAGTTCAAAATTTGC
1190 AT
1 AT
1192 TTCATTATTC
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
59 27 0.48
62 28 0.50
63 1 0.02
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (59 bp):
ATCAAAATTCAAAACATGCATTTCAGTATTCCATCCGAAAATCAAAGTTCAAAATTTGC
Found at i:1207 original size:35 final size:35
Alignment explanation
Indices: 1131--1604 Score: 194
Period size: 34 Copynumber: 13.2 Consensus size: 35
1121 CAATATTTGC
** *
1131 ATCAAAATTCAAAACATGCATTTCAGTATTCCATCCGAAA
1 ATCAAAATTCAAAATTTGCATTTCATTATT-CA----AAA
*
1171 ATCAAAGTTCAAAATTTGCATTTCATTATTCAAAA
1 ATCAAAATTCAAAATTTGCATTTCATTATTCAAAA
** * **
1206 ATCAAAATTCAAAATCAGCATCTCATGGTTCAAAA
1 ATCAAAATTCAAAATTTGCATTTCATTATTCAAAA
* * *** *
1241 TTCAAAA-CCTGCATTT-CATGTTCATTCTTCAAAA
1 ATCAAAATTCAAAATTTGCAT-TTCATTATTCAAAA
* * *
1275 GTCAAAATTCAAAACTTGCATTTCAGCATTCTATTCTTCGAAA
1 ATCAAAATTCAAAATTTGCATTT---CA-T-TA---TTCAAAA
*
1318 ATCAAAGTTCAAAATTTGCATTTCATTATTCAAAA
1 ATCAAAATTCAAAATTTGCATTTCATTATTCAAAA
* ** * **
1353 ATCAAAGTTCAAAATCAGCATCTCATGGTTCAAAA
1 ATCAAAATTCAAAATTTGCATTTCATTATTCAAAA
* * *** * *
1388 TTCAAAA-CCTGCATTTCACAATTT-ATTCTTCAAAA
1 ATCAAAATTCAAAATTT-GC-ATTTCATTATTCAAAA
* * * *
1423 GTCAAAATTCAAAACTTGCATTTCAGCATTCCTTTCGAAA
1 ATCAAAATTCAAAATTTGCATTT---CATT--ATTCAAAA
1463 ATCAAAATTC-AAATTTGCATTTCA-T-TTCAAAA
1 ATCAAAATTCAAAATTTGCATTTCATTATTCAAAA
* * * * * *
1495 TTTAAAGTTCAAAATCTGCATCTCA-TGTTCAAAA
1 ATCAAAATTCAAAATTTGCATTTCATTATTCAAAA
* * * * * *
1529 CTCAAAATCCAGAATCTGCATCTCA-TGTTCAAAA
1 ATCAAAATTCAAAATTTGCATTTCATTATTCAAAA
* * * * * *
1563 CTCAAAATCCAGAATCTGCATTTTA-TGTTCAAAA
1 ATCAAAATTCAAAATTTGCATTTCATTATTCAAAA
*
1597 CTCAAAAT
1 ATCAAAAT
1605 CATAATTGTT
Statistics
Matches: 339, Mismatches: 73, Indels: 50
0.73 0.16 0.11
Matches are distributed among these distances:
32 13 0.04
33 16 0.05
34 103 0.30
35 103 0.30
36 12 0.04
38 7 0.02
39 15 0.04
40 44 0.13
43 26 0.08
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (35 bp):
ATCAAAATTCAAAATTTGCATTTCATTATTCAAAA
Found at i:1238 original size:28 final size:27
Alignment explanation
Indices: 1207--1264 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 27
1197 TATTCAAAAA
*
1207 TCAAAATTCAAAATCAGCATCTCATGGT
1 TCAAAATTCAAAACCAGCATCTCAT-GT
* *
1235 TCAAAATTCAAAACCTGCATTTCATGT
1 TCAAAATTCAAAACCAGCATCTCATGT
1262 TCA
1 TCA
1265 TTCTTCAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.38, C:0.22, G:0.09, T:0.31
Consensus pattern (27 bp):
TCAAAATTCAAAACCAGCATCTCATGT
Found at i:1329 original size:43 final size:41
Alignment explanation
Indices: 1235--1343 Score: 141
Period size: 43 Copynumber: 2.6 Consensus size: 41
1225 ATCTCATGGT
*
1235 TCAAAATTCAAAACCTGCATTTCATGTTCATTCTTCAAAAG
1 TCAAAATTCAAAACTTGCATTTCATGTTCATTCTTCAAAAG
1276 TCAAAATTCAAAACTTGCATTTCA-GCATTCTATTCTTCGAAAA-
1 TCAAAATTCAAAACTTGCATTTCATG--TTC-ATTCTTC-AAAAG
* *
1319 TCAAAGTTCAAAATTTGCATTTCAT
1 TCAAAATTCAAAACTTGCATTTCAT
1344 TATTCAAAAA
Statistics
Matches: 60, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
40 1 0.02
41 23 0.38
42 3 0.05
43 29 0.48
44 4 0.07
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.36
Consensus pattern (41 bp):
TCAAAATTCAAAACTTGCATTTCATGTTCATTCTTCAAAAG
Found at i:1347 original size:147 final size:146
Alignment explanation
Indices: 1132--1535 Score: 617
Period size: 147 Copynumber: 2.8 Consensus size: 146
1122 AATATTTGCA
* *
1132 TCAAAATTCAAAACATGCATTTCAGTATTCCATC--CGAAAATCAAAGTTCAAAATTTGCATTTC
1 TCAAAATTCAAAACTTGCATTTCAGCATT-CATCTTCGAAAATCAAAGTTCAAAATTTGCATTTC
*
1195 ATTATTCAAAAATCAAAATTCAAAATCAGCATCTCATGGTTCAAAATTCAAAACCTGCATTTCA-
65 ATTATTCAAAAATCAAAGTTCAAAATCAGCATCTCATGGTTCAAAATTCAAAACCTGCATTTCAC
**
1259 TGTTCATTCTTCAAAAG
130 AATTCATTCTTCAAAAG
1276 TCAAAATTCAAAACTTGCATTTCAGCATTCTATTCTTCGAAAATCAAAGTTCAAAATTTGCATTT
1 TCAAAATTCAAAACTTGCATTTCAGCATTC-A-TCTTCGAAAATCAAAGTTCAAAATTTGCATTT
1341 CATTATTCAAAAATCAAAGTTCAAAATCAGCATCTCATGGTTCAAAATTCAAAACCTGCATTTCA
64 CATTATTCAAAAATCAAAGTTCAAAATCAGCATCTCATGGTTCAAAATTCAAAACCTGCATTTCA
*
1406 CAATTTATTCTTCAAAAG
129 CAATTCATTCTTCAAAAG
* *
1424 TCAAAATTCAAAACTTGCATTTCAGCATTCCT-TTCGAAAATCAAAATTC-AAATTTGCATTTCA
1 TCAAAATTCAAAACTTGCATTTCAGCATTCATCTTCGAAAATCAAAGTTCAAAATTTGCATTTCA
* * * *
1487 -T-TTCAAAATTTAAAGTTCAAAATCTGCATCTCAT-GTTCAAAACTCAAAA
66 TTATTCAAAAATCAAAGTTCAAAATCAGCATCTCATGGTTCAAAATTCAAAA
1536 TCCAGAATCT
Statistics
Matches: 243, Mismatches: 12, Indels: 13
0.91 0.04 0.05
Matches are distributed among these distances:
141 14 0.06
142 30 0.12
143 2 0.01
144 42 0.17
145 18 0.07
146 1 0.00
147 92 0.38
148 44 0.18
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (146 bp):
TCAAAATTCAAAACTTGCATTTCAGCATTCATCTTCGAAAATCAAAGTTCAAAATTTGCATTTCA
TTATTCAAAAATCAAAGTTCAAAATCAGCATCTCATGGTTCAAAATTCAAAACCTGCATTTCACA
ATTCATTCTTCAAAAG
Found at i:4571 original size:15 final size:14
Alignment explanation
Indices: 4535--4578 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 14
4525 AAATGGGGTT
4535 GAAGGAAAGAGAAGAA
1 GAAGGAAA-AGAA-AA
4551 GAAGGAAAAGAAAA
1 GAAGGAAAAGAAAA
4565 GACAGGAAAAGAAA
1 GA-AGGAAAAGAAA
4579 GGAAAGCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.15
15 15 0.56
16 8 0.30
ACGTcount: A:0.66, C:0.02, G:0.32, T:0.00
Consensus pattern (14 bp):
GAAGGAAAAGAAAA
Done.