Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005780.1 Corchorus capsularis cultivar CVL-1 contig05798, 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: 3777
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Found at i:1053 original size:14 final size:14
Alignment explanation
Indices: 993--1300 Score: 147
Period size: 14 Copynumber: 22.3 Consensus size: 14
983 TGAGAGTTGG
*
993 TCAATTTCAAATCT
1 TCAATTTCAATTCT
1007 TCAATGTTTCAA-T-T
1 TCAA--TTTCAATTCT
1021 TCAATATTTCAA-TCTT
1 TC-A-ATTTCAATTC-T
1037 TCAATTTCAATTCT
1 TCAATTTCAATTCT
1051 TCAATCCTTCGAA---T
1 TCAAT--TTC-AATTCT
*
1065 TCAATCCTTCAATGCT
1 TCAAT--TTCAATTCT
* *
1081 TCTATTCCAATTCT
1 TCAATTTCAATTCT
*
1095 TCAAGTTCAAATTCAT
1 TCAATTTC-AATTC-T
*
1111 TC--TTTCAATGC-
1 TCAATTTCAATTCT
1122 TCAATTTCAATTCT
1 TCAATTTCAATTCT
1136 TCAA--TC----CT
1 TCAATTTCAATTCT
1144 TCAATTTCAATTCT
1 TCAATTTCAATTCT
*
1158 TCAA-TTCAA-CCT
1 TCAATTTCAATTCT
1170 TCAAGTTT-AATTCT
1 TCAA-TTTCAATTCT
* * *
1184 TCAAATGCAATCCT
1 TCAATTTCAATTCT
1198 TCAATTTCAA-T-T
1 TCAATTTCAATTCT
1210 TCAATTTCAATTCT
1 TCAATTTCAATTCT
1224 TCAATCCTTCAA-T-T
1 TCAAT--TTCAATTCT
*
1238 TCAATTCTTCAATGCT
1 TCAA-T-TTCAATTCT
*
1254 TCAATTTCAATCCTT
1 TCAATTTCAATTC-T
* *
1269 TCAAATTCAATCCT
1 TCAATTTCAATTCT
* * *
1283 TCAAATCCAATACT
1 TCAATTTCAATTCT
1297 TCAA
1 TCAA
1301 ACTAAATCAT
Statistics
Matches: 236, Mismatches: 22, Indels: 72
0.72 0.07 0.22
Matches are distributed among these distances:
8 6 0.03
10 2 0.01
11 2 0.01
12 19 0.08
13 23 0.10
14 125 0.53
15 26 0.11
16 31 0.13
17 2 0.01
ACGTcount: A:0.30, C:0.24, G:0.03, T:0.43
Consensus pattern (14 bp):
TCAATTTCAATTCT
Found at i:1140 original size:8 final size:8
Alignment explanation
Indices: 998--1259 Score: 80
Period size: 8 Copynumber: 34.9 Consensus size: 8
988 GTTGGTCAAT
*
998 TTCAAATC
1 TTCAATTC
1006 TTCAATGT-
1 TTCAAT-TC
1014 TTCAA-T-
1 TTCAATTC
1020 TTCAATAT-
1 TTCAAT-TC
1028 TTCAA-TC
1 TTCAATTC
1035 TTTCAA-T-
1 -TTCAATTC
1042 TTCAATTC
1 TTCAATTC
*
1050 TTCAATCC
1 TTCAATTC
1058 TTCGAA---
1 TTC-AATTC
*
1064 TTCAATCC
1 TTCAATTC
*
1072 TTCAATGC
1 TTCAATTC
*
1080 TTCTATTC
1 TTCAATTC
1088 --CAATTC
1 TTCAATTC
1094 TTCAAGTTC
1 TTCAA-TTC
1103 AAATTC-ATTC
1 ---TTCAATTC
*
1113 TTTCAATGC
1 -TTCAATTC
1122 -TCAA-T-
1 TTCAATTC
1127 TTCAATTC
1 TTCAATTC
*
1135 TTCAATCC
1 TTCAATTC
1143 TTCAA-T-
1 TTCAATTC
1149 TTCAATTC
1 TTCAATTC
1157 TTCAATTCAACC
1 TTCAATT----C
*
1169 TTCAAGT-
1 TTCAATTC
1176 TT-AATTC
1 TTCAATTC
*
1183 TTCAA--A
1 TTCAATTC
* *
1189 TGCAATCC
1 TTCAATTC
1197 TTCAA-T-
1 TTCAATTC
1203 TTCAA-T-
1 TTCAATTC
1209 TTCAA-T-
1 TTCAATTC
1215 TTCAATTC
1 TTCAATTC
*
1223 TTCAATCC
1 TTCAATTC
1231 TTCAA-T-
1 TTCAATTC
1237 TTCAATTC
1 TTCAATTC
*
1245 TTCAATGC
1 TTCAATTC
1253 TTCAATT
1 TTCAATT
1260 TCAATCCTTT
Statistics
Matches: 197, Mismatches: 22, Indels: 70
0.68 0.08 0.24
Matches are distributed among these distances:
5 2 0.01
6 58 0.29
7 13 0.07
8 101 0.51
9 9 0.05
10 3 0.02
11 1 0.01
12 10 0.05
ACGTcount: A:0.29, C:0.24, G:0.03, T:0.44
Consensus pattern (8 bp):
TTCAATTC
Found at i:1200 original size:40 final size:40
Alignment explanation
Indices: 1135--1286 Score: 114
Period size: 40 Copynumber: 3.7 Consensus size: 40
1125 ATTTCAATTC
* * * *
1135 TTCAATCCTTCAATTTCAATTCTTCAA-TTCAACCTTCAAGT
1 TTCAATTCTTCAAATGCAATCCTTCAATTTCAA-CTTCAA-T
*
1176 TT-AATTCTTCAAATGCAATCCTTCAATTTCAATTTCAAT
1 TTCAATTCTTCAAATGCAATCCTTCAATTTCAACTTCAAT
* *
1215 TTCAATTCTTCAATCCTTCAAT--TTCAATTCTTCAATGCTTCAAT
1 TTCAATTCTTCAA--ATGCAATCCTTCAA-T-TTCAA--CTTCAAT
* *
1259 TTCAATCCTTTCAAATTCAATCCTTCAA
1 TTCAATTC-TTCAAATGCAATCCTTCAA
1287 ATCCAATACT
Statistics
Matches: 90, Mismatches: 10, Indels: 18
0.76 0.08 0.15
Matches are distributed among these distances:
39 3 0.03
40 40 0.44
41 8 0.09
42 10 0.11
43 6 0.07
44 13 0.14
45 10 0.11
ACGTcount: A:0.30, C:0.25, G:0.02, T:0.43
Consensus pattern (40 bp):
TTCAATTCTTCAAATGCAATCCTTCAATTTCAACTTCAAT
Found at i:1264 original size:22 final size:22
Alignment explanation
Indices: 993--1162 Score: 183
Period size: 22 Copynumber: 7.9 Consensus size: 22
983 TGAGAGTTGG
* *
993 TCAATTTCAAATCTTCAATGTT
1 TCAATTTCAATTCTTCAATGCT
1015 TCAATTTCAATAT-TTCAAT-CTT
1 TCAATTTCAAT-TCTTCAATGC-T
*
1037 TCAATTTCAATTCTTCAATCCT
1 TCAATTTCAATTCTTCAATGCT
*
1059 TCGAA-TTCAATCCTTCAATGCT
1 TC-AATTTCAATTCTTCAATGCT
* *
1081 TCTATTCCAATTCTTCAA-G-T
1 TCAATTTCAATTCTTCAATGCT
*
1101 TCAAATTC-ATTCTTTCAATGC-
1 TCAATTTCAATTC-TTCAATGCT
*
1122 TCAATTTCAATTCTTCAATCCT
1 TCAATTTCAATTCTTCAATGCT
1144 TCAATTTCAATTCTTCAAT
1 TCAATTTCAATTCTTCAAT
1163 TCAACCTTCA
Statistics
Matches: 125, Mismatches: 12, Indels: 22
0.79 0.08 0.14
Matches are distributed among these distances:
19 4 0.03
20 11 0.09
21 18 0.14
22 88 0.70
23 4 0.03
ACGTcount: A:0.29, C:0.24, G:0.03, T:0.45
Consensus pattern (22 bp):
TCAATTTCAATTCTTCAATGCT
Found at i:1293 original size:29 final size:28
Alignment explanation
Indices: 1245--1301 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
1235 ATTTCAATTC
* * * *
1245 TTCAATGCTTCAATTTCAATCCTTTCAAA
1 TTCAATCCTTCAAATCCAATAC-TTCAAA
1274 TTCAATCCTTCAAATCCAATACTTCAAA
1 TTCAATCCTTCAAATCCAATACTTCAAA
1302 CTAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.35, C:0.26, G:0.02, T:0.37
Consensus pattern (28 bp):
TTCAATCCTTCAAATCCAATACTTCAAA
Found at i:1380 original size:17 final size:17
Alignment explanation
Indices: 1339--1394 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
1329 TTTTTTTTTC
*
1339 TTCAATTCTTC-AATTA
1 TTCAATGCTTCAAATTA
*
1355 --CAATTCTTCAAATTA
1 TTCAATGCTTCAAATTA
*
1370 TTCAATGCTTCAATTTA
1 TTCAATGCTTCAAATTA
1387 CTTCAATG
1 -TTCAATG
1395 ATCCAGGGTG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
14 9 0.26
15 5 0.15
17 13 0.38
18 7 0.21
ACGTcount: A:0.32, C:0.20, G:0.04, T:0.45
Consensus pattern (17 bp):
TTCAATGCTTCAAATTA
Found at i:1432 original size:16 final size:15
Alignment explanation
Indices: 1411--1467 Score: 62
Period size: 16 Copynumber: 3.7 Consensus size: 15
1401 GGTGGTCTTC
1411 CTTCAATTCTACAATG
1 CTTCAATT-TACAATG
* *
1427 CTTCAA-TTGCAATT
1 CTTCAATTTACAATG
*
1441 CTTCAATTATCCAATG
1 CTTCAATT-TACAATG
1457 CTTCAATTTAC
1 CTTCAATTTAC
1468 TTCAATGATT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
14 11 0.32
15 4 0.12
16 19 0.56
ACGTcount: A:0.30, C:0.25, G:0.05, T:0.40
Consensus pattern (15 bp):
CTTCAATTTACAATG
Found at i:1444 original size:14 final size:14
Alignment explanation
Indices: 1422--1464 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
1412 TTCAATTCTA
1422 CAATGCTTCAATTG
1 CAATGCTTCAATTG
* *
1436 CAATTCTTCAATTATC
1 CAATGCTTCAA-T-TG
1452 CAATGCTTCAATT
1 CAATGCTTCAATT
1465 TACTTCAATG
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
14 11 0.46
15 2 0.08
16 11 0.46
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (14 bp):
CAATGCTTCAATTG
Found at i:1464 original size:80 final size:81
Alignment explanation
Indices: 1336--1505 Score: 261
Period size: 80 Copynumber: 2.1 Consensus size: 81
1326 CAATTTTTTT
* *
1336 TTCTTCAATTCTTCAATTACAATTCTTCAAATTATTCAATGCTTCAATTTACTTCAATGATCCAG
1 TTCTTCAATGCTTCAATTACAATTCTTCAAATTATCCAATGCTTCAATTTACTTCAATGATCCAG
*
1401 GGTGGTCTTCCTTCAA
66 GGTAGTCTTCCTTCAA
* * **
1417 TTCTACAATGCTTCAATTGCAATTCTTC-AATTATCCAATGCTTCAATTTACTTCAATGATTTAG
1 TTCTTCAATGCTTCAATTACAATTCTTCAAATTATCCAATGCTTCAATTTACTTCAATGATCCAG
*
1481 GGTAGTCTTTCTTCAA
66 GGTAGTCTTCCTTCAA
1497 TTCTTCAAT
1 TTCTTCAAT
1506 CATCCAATGC
Statistics
Matches: 80, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
80 55 0.69
81 25 0.31
ACGTcount: A:0.27, C:0.21, G:0.09, T:0.43
Consensus pattern (81 bp):
TTCTTCAATGCTTCAATTACAATTCTTCAAATTATCCAATGCTTCAATTTACTTCAATGATCCAG
GGTAGTCTTCCTTCAA
Found at i:1501 original size:58 final size:58
Alignment explanation
Indices: 1436--1580 Score: 229
Period size: 58 Copynumber: 2.5 Consensus size: 58
1426 GCTTCAATTG
**
1436 CAATTCTTCAATTATCCAATGCTTCAATTTACTTCAATGATTTAGGGT-AGTCTTTCTT
1 CAATTCTTCAATTATCCAATGCTTCAATTTACTTCAATGATCCAGGGTGA-TCTTTCTT
*
1494 CAATTCTTCAATCATCCAATGCTTCAATTTACTTCAATGATCCAGGGTGATCTTTCTT
1 CAATTCTTCAATTATCCAATGCTTCAATTTACTTCAATGATCCAGGGTGATCTTTCTT
* *
1552 CAATTCTTCAAGTATTCAATGCTTCAATT
1 CAATTCTTCAATTATCCAATGCTTCAATT
1581 CCTCAATTAT
Statistics
Matches: 80, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
58 79 0.99
59 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.10, T:0.42
Consensus pattern (58 bp):
CAATTCTTCAATTATCCAATGCTTCAATTTACTTCAATGATCCAGGGTGATCTTTCTT
Found at i:1560 original size:8 final size:8
Alignment explanation
Indices: 1547--1595 Score: 53
Period size: 8 Copynumber: 6.1 Consensus size: 8
1537 AGGGTGATCT
1547 TTCTTCAA
1 TTCTTCAA
1555 TTCTTCAA
1 TTCTTCAA
* *
1563 GTATTCAA
1 TTCTTCAA
*
1571 TGCTTCAA
1 TTCTTCAA
*
1579 TTCCTCAA
1 TTCTTCAA
*
1587 TTATTCAA
1 TTCTTCAA
1595 T
1 T
1596 GCCTCAATTT
Statistics
Matches: 32, Mismatches: 9, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
8 32 1.00
ACGTcount: A:0.29, C:0.22, G:0.04, T:0.45
Consensus pattern (8 bp):
TTCTTCAA
Found at i:1576 original size:24 final size:24
Alignment explanation
Indices: 1549--1604 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
1539 GGTGATCTTT
*
1549 CTTCAATTCTTCAAGTATTCAATG
1 CTTCAATTCCTCAAGTATTCAATG
*
1573 CTTCAATTCCTCAATTATTCAATG
1 CTTCAATTCCTCAAGTATTCAATG
*
1597 CCTCAATT
1 CTTCAATT
1605 TCAAATCTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.25, G:0.05, T:0.41
Consensus pattern (24 bp):
CTTCAATTCCTCAAGTATTCAATG
Found at i:1604 original size:16 final size:16
Alignment explanation
Indices: 1574--1604 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1564 TATTCAATGC
*
1574 TTCAATTCCTCAATTA
1 TTCAATGCCTCAATTA
1590 TTCAATGCCTCAATT
1 TTCAATGCCTCAATT
1605 TCAAATCTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.26, G:0.03, T:0.42
Consensus pattern (16 bp):
TTCAATGCCTCAATTA
Found at i:1642 original size:14 final size:14
Alignment explanation
Indices: 1619--1652 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1609 ATCTTTAACG
*
1619 CTTCAGTTTCAATA
1 CTTCAATTTCAATA
*
1633 CTTCAATTTCAATT
1 CTTCAATTTCAATA
1647 CTTCAA
1 CTTCAA
1653 ATTCCAAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.29, C:0.24, G:0.03, T:0.44
Consensus pattern (14 bp):
CTTCAATTTCAATA
Found at i:1738 original size:13 final size:13
Alignment explanation
Indices: 1712--1746 Score: 61
Period size: 13 Copynumber: 2.6 Consensus size: 13
1702 ATGCTTCAAT
1712 TTCAATTCTTCGAA
1 TTCAATT-TTCGAA
1726 TTCAATTTTCGAA
1 TTCAATTTTCGAA
1739 TTCAATTT
1 TTCAATTT
1747 CAATGTTCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 14 0.67
14 7 0.33
ACGTcount: A:0.29, C:0.17, G:0.06, T:0.49
Consensus pattern (13 bp):
TTCAATTTTCGAA
Found at i:2584 original size:14 final size:14
Alignment explanation
Indices: 2565--2604 Score: 71
Period size: 14 Copynumber: 2.9 Consensus size: 14
2555 ATATATAAAG
2565 AAAAAGAAAAAGGA
1 AAAAAGAAAAAGGA
*
2579 AAAAAGAAAAAGGG
1 AAAAAGAAAAAGGA
2593 AAAAAGAAAAAG
1 AAAAAGAAAAAG
2605 AGTGCAAATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.78, C:0.00, G:0.23, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAGGA
Found at i:2588 original size:5 final size:6
Alignment explanation
Indices: 2561--2605 Score: 54
Period size: 6 Copynumber: 6.8 Consensus size: 6
2551 ATATATATAT
2561 AAAGAA AAAGAA AAAGGAAA AAAGAA AAAGGGAA AAAGAA AAAGA
1 AAAGAA AAAGAA AAA-G-AA AAAGAA AAA--GAA AAAGAA AAAGA
2606 GTGCAAATGG
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
6 22 0.63
7 2 0.06
8 11 0.31
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:2605 original size:20 final size:20
Alignment explanation
Indices: 2561--2603 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
2551 ATATATATAT
2561 AAAGAAAAAGAAAAAGGAAA
1 AAAGAAAAAGAAAAAGGAAA
2581 AAAGAAAAAGGGAAAAA-GAAA
1 AAAGAAAAA--GAAAAAGGAAA
2602 AA
1 AA
2604 GAGTGCAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 9 0.43
21 6 0.29
22 6 0.29
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (20 bp):
AAAGAAAAAGAAAAAGGAAA
Done.