Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008109.1 Corchorus capsularis cultivar CVL-1 contig08130, 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: 66498
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:555 original size:19 final size:19
Alignment explanation
Indices: 524--623 Score: 73
Period size: 19 Copynumber: 5.4 Consensus size: 19
514 CCTAGATGTG
524 AAAATG-ACCAAAATGCCCC
1 AAAATGCACCAAAATG-CCC
* * *
543 TAAATGCA-GAAAATGACC
1 AAAATGCACCAAAATGCCC
* **
561 AAAATGCACCTAAATGCAG
1 AAAATGCACCAAAATGCCC
580 AAAATG-ACCAAAATGCCCC
1 AAAATGCACCAAAATG-CCC
* * *
599 TAAATGCA-GAAAATGACC
1 AAAATGCACCAAAATGCCC
617 AAAATGC
1 AAAATGC
624 CCCTAGGCGA
Statistics
Matches: 61, Mismatches: 16, Indels: 9
0.71 0.19 0.10
Matches are distributed among these distances:
18 25 0.41
19 34 0.56
20 2 0.03
ACGTcount: A:0.49, C:0.23, G:0.14, T:0.14
Consensus pattern (19 bp):
AAAATGCACCAAAATGCCC
Found at i:561 original size:28 final size:28
Alignment explanation
Indices: 497--628 Score: 221
Period size: 28 Copynumber: 4.8 Consensus size: 28
487 GAATGCAAAA
* * *
497 AAAATGACCTAAATGCCCCTAGATG-TG
1 AAAATGACCAAAATGCCCCTAAATGCAG
524 AAAATGACCAAAATGCCCCTAAATGCAG
1 AAAATGACCAAAATGCCCCTAAATGCAG
*
552 AAAATGACCAAAATGCACCTAAATGCAG
1 AAAATGACCAAAATGCCCCTAAATGCAG
580 AAAATGACCAAAATGCCCCTAAATGCAG
1 AAAATGACCAAAATGCCCCTAAATGCAG
608 AAAATGACCAAAATGCCCCTA
1 AAAATGACCAAAATGCCCCTA
629 GGCGACCCTA
Statistics
Matches: 99, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
27 23 0.23
28 76 0.77
ACGTcount: A:0.45, C:0.24, G:0.14, T:0.16
Consensus pattern (28 bp):
AAAATGACCAAAATGCCCCTAAATGCAG
Found at i:577 original size:10 final size:10
Alignment explanation
Indices: 524--623 Score: 79
Period size: 9 Copynumber: 10.7 Consensus size: 10
514 CCTAGATGTG
524 AAAATG-ACC
1 AAAATGCACC
*
533 AAAATGCCCC
1 AAAATGCACC
* *
543 TAAATGCA-G
1 AAAATGCACC
552 AAAATG-ACC
1 AAAATGCACC
561 AAAATGCACC
1 AAAATGCACC
* *
571 TAAATGCA-G
1 AAAATGCACC
580 AAAATG-ACC
1 AAAATGCACC
*
589 AAAATGCCCC
1 AAAATGCACC
* *
599 TAAATGCA-G
1 AAAATGCACC
608 AAAATG-ACC
1 AAAATGCACC
617 AAAATGC
1 AAAATGC
624 CCCTAGGCGA
Statistics
Matches: 68, Mismatches: 16, Indels: 13
0.70 0.16 0.13
Matches are distributed among these distances:
8 3 0.04
9 39 0.57
10 26 0.38
ACGTcount: A:0.49, C:0.23, G:0.14, T:0.14
Consensus pattern (10 bp):
AAAATGCACC
Found at i:1533 original size:21 final size:21
Alignment explanation
Indices: 1509--1559 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
1499 ATGTTGGAGG
1509 TTTATTTTACATTGTTAGTT-A
1 TTTATTTTACATTGTT-GTTAA
* * *
1530 TTTAATTTACTTTGTTTTTAA
1 TTTATTTTACATTGTTGTTAA
1551 TTTATTTTA
1 TTTATTTTA
1560 ATTTAGAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.24, C:0.04, G:0.06, T:0.67
Consensus pattern (21 bp):
TTTATTTTACATTGTTGTTAA
Found at i:8682 original size:6 final size:6
Alignment explanation
Indices: 8671--8700 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
8661 CAGATAAATC
8671 TAGATT TAGATT TAGATT TAGATT T-GATT T
1 TAGATT TAGATT TAGATT TAGATT TAGATT T
8701 GCTTTGTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.21
6 19 0.79
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (6 bp):
TAGATT
Found at i:13155 original size:21 final size:20
Alignment explanation
Indices: 13126--13173 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
13116 ATAGTTTAGA
* *
13126 TTTAATTTACTTTGCTTTGTT
1 TTTAATTTA-ATTGCTTTCTT
*
13147 TTTAGTTTAATTGCTTTCTT
1 TTTAATTTAATTGCTTTCTT
13167 TTTAATT
1 TTTAATT
13174 AATCTGTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.17, C:0.08, G:0.08, T:0.67
Consensus pattern (20 bp):
TTTAATTTAATTGCTTTCTT
Found at i:14490 original size:59 final size:59
Alignment explanation
Indices: 14418--14531 Score: 192
Period size: 59 Copynumber: 1.9 Consensus size: 59
14408 GATCAAAACA
*
14418 AAATAAGAAAATGTTTGTTGGTATAAATTAAATCTCATGTCTAAAGAACAAAATAATCC
1 AAATAAGAAAATGTTTGTTGGTACAAATTAAATCTCATGTCTAAAGAACAAAATAATCC
* * *
14477 AAATAAGAAAATGTTTGTTGTTACAAATTAAATTTCATGTCTATAGAACAAAATA
1 AAATAAGAAAATGTTTGTTGGTACAAATTAAATCTCATGTCTAAAGAACAAAATA
14532 CCGAAATCAT
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 51 1.00
ACGTcount: A:0.47, C:0.09, G:0.11, T:0.32
Consensus pattern (59 bp):
AAATAAGAAAATGTTTGTTGGTACAAATTAAATCTCATGTCTAAAGAACAAAATAATCC
Found at i:14506 original size:122 final size:121
Alignment explanation
Indices: 14256--14488 Score: 357
Period size: 122 Copynumber: 2.0 Consensus size: 121
14246 TAATAATTCA
* *
14256 TTAATTAGAACAAAATTAAACATGATTGATGATCAACACAAAATAATAAAATGTTTGTTGGTACA
1 TTAATTAGAACAAAATTAAACATGATTGATGATCAAAACAAAATAAGAAAATGTTTGTTGGTACA
* *
14321 AATTAAATCCCATGCCTAAAAAACAAAATCAATACCCAAATTATATAAACTAATATT
66 AATTAAATCCCATGCCTAAAAAACAAAATCAATA-CCAAATTATAGAAAATAATATT
*
14378 TTAATTAGAACAAAATTAAACATGATTGATGATCAAAACAAAATAAGAAAATGTTTGTTGGTATA
1 TTAATTAGAACAAAATTAAACATGATTGATGATCAAAACAAAATAAGAAAATGTTTGTTGGTACA
* * *
14443 AATTAAATCTCATGTCTAAAGAACAAAAT-AAT-CCAAA-TA-AGAAAAT
66 AATTAAATCCCATGCCTAAAAAACAAAATCAATACCAAATTATAGAAAAT
14489 GTTTGTTGTT
Statistics
Matches: 103, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
117 5 0.05
118 2 0.02
119 5 0.05
121 3 0.03
122 88 0.85
ACGTcount: A:0.51, C:0.12, G:0.09, T:0.28
Consensus pattern (121 bp):
TTAATTAGAACAAAATTAAACATGATTGATGATCAAAACAAAATAAGAAAATGTTTGTTGGTACA
AATTAAATCCCATGCCTAAAAAACAAAATCAATACCAAATTATAGAAAATAATATT
Found at i:15179 original size:2 final size:2
Alignment explanation
Indices: 15172--15212 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
15162 ATGTTAAGGC
* * *
15172 AT AT AT AT AT AT AC AT AT AT AT AA AT AT AT AT TT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15213 ACAGACAAAG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:15583 original size:19 final size:18
Alignment explanation
Indices: 15559--15594 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
15549 TGAAGATTTC
15559 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
15578 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
15595 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:31864 original size:21 final size:21
Alignment explanation
Indices: 31840--31880 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
31830 ACTGAAGCAG
31840 TCACAAGAAGAAATGAGGCAT
1 TCACAAGAAGAAATGAGGCAT
* *
31861 TCACAGGAAGAGATGAGGCA
1 TCACAAGAAGAAATGAGGCA
31881 GGAACAGGGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.15, G:0.29, T:0.12
Consensus pattern (21 bp):
TCACAAGAAGAAATGAGGCAT
Found at i:33439 original size:15 final size:16
Alignment explanation
Indices: 33407--33440 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
33397 AAGAAGAATT
*
33407 TAAAATTAAATCTAAC
1 TAAAAGTAAATCTAAC
33423 TAAAAGTAAAT-TAAC
1 TAAAAGTAAATCTAAC
33438 TAA
1 TAA
33441 GAAAGCAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.59, C:0.09, G:0.03, T:0.29
Consensus pattern (16 bp):
TAAAAGTAAATCTAAC
Found at i:34750 original size:19 final size:18
Alignment explanation
Indices: 34717--34752 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
34707 TTGAAATAAT
34717 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
34735 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
34753 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:41010 original size:11 final size:10
Alignment explanation
Indices: 40992--41025 Score: 50
Period size: 11 Copynumber: 3.2 Consensus size: 10
40982 AATTGTCTTC
40992 AAATCTTCAA
1 AAATCTTCAA
41002 AATATCTTCAA
1 AA-ATCTTCAA
41013 GAAATCTTCAA
1 -AAATCTTCAA
41024 AA
1 AA
41026 CACGAACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 4 0.18
11 16 0.73
12 2 0.09
ACGTcount: A:0.50, C:0.18, G:0.03, T:0.29
Consensus pattern (10 bp):
AAATCTTCAA
Found at i:51432 original size:30 final size:30
Alignment explanation
Indices: 51370--51429 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
51360 TTTGCGTCGA
*
51370 TAAAAAAAATTTCTTTTCCGTTTTTCCTTT
1 TAAAAAAAATTTATTTTCCGTTTTTCCTTT
* *
51400 TAAAAAAAA-TTATTTTCTGTTTTTGCTTT
1 TAAAAAAAATTTATTTTCCGTTTTTCCTTT
51429 T
1 T
51430 TAATTTATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 18 0.67
30 9 0.33
ACGTcount: A:0.28, C:0.12, G:0.05, T:0.55
Consensus pattern (30 bp):
TAAAAAAAATTTATTTTCCGTTTTTCCTTT
Done.