Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016413.1 Corchorus olitorius cultivar O-4 contig16446, 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: 16585
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Found at i:10 original size:2 final size:2
Alignment explanation
Indices: 4--44 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
1 CTC
*
4 TA TA TA T- TA TA CA TA TA -A TA TA -A TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
43 TA
1 TA
45 ATTTGAACAC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
1 3 0.09
2 31 0.91
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:1220 original size:51 final size:49
Alignment explanation
Indices: 1164--1260 Score: 160
Period size: 51 Copynumber: 1.9 Consensus size: 49
1154 CTTGAGTCAC
1164 ATGACTTATAATTTTTACCTAGT-TAAAAGACTAATTTTATTAGTCAAAAGA
1 ATGACTTATAATTTTTACCTAGTCT---AGACTAATTTTATTAGTCAAAAGA
1215 ATGACTTATAATTTTTACCTAGTCTAGACTAATTTTATTAGTCAAA
1 ATGACTTATAATTTTTACCTAGTCTAGACTAATTTTATTAGTCAAA
1261 GATGGGCACT
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
49 21 0.47
51 23 0.51
52 1 0.02
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.41
Consensus pattern (49 bp):
ATGACTTATAATTTTTACCTAGTCTAGACTAATTTTATTAGTCAAAAGA
Found at i:1329 original size:12 final size:12
Alignment explanation
Indices: 1312--1336 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1302 TTCTGTTTGT
1312 TAAATTAAGTAC
1 TAAATTAAGTAC
1324 TAAATTAAGTAC
1 TAAATTAAGTAC
1336 T
1 T
1337 GAAAATCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.08, T:0.36
Consensus pattern (12 bp):
TAAATTAAGTAC
Found at i:2176 original size:22 final size:22
Alignment explanation
Indices: 2150--2200 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
2140 GCGGATGATC
*
2150 AAAATGTGAT-AAGATGAAATAA
1 AAAAT-TGATGAAGATGAAAAAA
*
2172 AAAATTGGTGAAGATGAAAAAA
1 AAAATTGATGAAGATGAAAAAA
2194 AAAATTG
1 AAAATTG
2201 GTGTAAGTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
21 3 0.12
22 23 0.88
ACGTcount: A:0.59, C:0.00, G:0.20, T:0.22
Consensus pattern (22 bp):
AAAATTGATGAAGATGAAAAAA
Found at i:2201 original size:22 final size:22
Alignment explanation
Indices: 2160--2203 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
2150 AAAATGTGAT
*
2160 AAGATGAAATAAAAAATTGGTG
1 AAGATGAAAAAAAAAATTGGTG
2182 AAGATGAAAAAAAAAATTGGTG
1 AAGATGAAAAAAAAAATTGGTG
2204 TAAGTGAGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.57, C:0.00, G:0.23, T:0.20
Consensus pattern (22 bp):
AAGATGAAAAAAAAAATTGGTG
Found at i:2686 original size:16 final size:16
Alignment explanation
Indices: 2665--2695 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2655 TTGAATATCT
2665 ATAAATCTAGAAATAA
1 ATAAATCTAGAAATAA
*
2681 ATAAATCTATAAATA
1 ATAAATCTAGAAATA
2696 TACATATTAC
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:0.61, C:0.06, G:0.03, T:0.29
Consensus pattern (16 bp):
ATAAATCTAGAAATAA
Found at i:10472 original size:18 final size:17
Alignment explanation
Indices: 10438--10484 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
10428 TTAAGGCCGA
* *
10438 AATTATTAATGAATAAT
1 AATTATTATTTAATAAT
10455 AATTATTTATTTAATAAT
1 AATTA-TTATTTAATAAT
*
10473 TATTATTATTTA
1 AATTATTATTTA
10485 CCCATATATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 12 0.46
18 14 0.54
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (17 bp):
AATTATTATTTAATAAT
Found at i:12896 original size:36 final size:36
Alignment explanation
Indices: 12849--12920 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
12839 GAAGCTAAAC
*
12849 TCATCCTTAGACATTAAGATGCTGTCGAGAAAGTTG
1 TCATCCCTAGACATTAAGATGCTGTCGAGAAAGTTG
*
12885 TCATCCCTAGACATTAAGATGCTGTCGAGAACGTTG
1 TCATCCCTAGACATTAAGATGCTGTCGAGAAAGTTG
12921 CTGACAACGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.29
Consensus pattern (36 bp):
TCATCCCTAGACATTAAGATGCTGTCGAGAAAGTTG
Found at i:15308 original size:21 final size:20
Alignment explanation
Indices: 15284--15351 Score: 68
Period size: 21 Copynumber: 3.4 Consensus size: 20
15274 GATAATATAA
15284 CTAATAATAATTTTACTACTT
1 CTAATAATAATTTTACTA-TT
* *
15305 CTAATAAT--TATTATTATT
1 CTAATAATAATTTTACTATT
* *
15323 ATAATAATAAGTTTACTAATT
1 CTAATAATAATTTTACT-ATT
15344 CTAATAAT
1 CTAATAAT
15352 TGAGATGTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
18 9 0.24
19 6 0.16
20 4 0.11
21 18 0.49
ACGTcount: A:0.43, C:0.09, G:0.01, T:0.47
Consensus pattern (20 bp):
CTAATAATAATTTTACTATT
Found at i:15309 original size:18 final size:17
Alignment explanation
Indices: 15288--15352 Score: 58
Period size: 18 Copynumber: 3.5 Consensus size: 17
15278 ATATAACTAA
15288 TAATAATTTTACTACTTC
1 TAATAATTTTACTA-TTC
* *
15306 TAATAATTATTATTATTA
1 TAATAATT-TTACTATTC
15324 TAATAATAAGTTTACTAATTC
1 TAATAAT---TTTACT-ATTC
15345 TAATAATT
1 TAATAATT
15353 GAGATGTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
18 18 0.47
19 5 0.13
20 4 0.11
21 11 0.29
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.49
Consensus pattern (17 bp):
TAATAATTTTACTATTC
Found at i:15642 original size:3 final size:3
Alignment explanation
Indices: 15634--15739 Score: 107
Period size: 3 Copynumber: 35.3 Consensus size: 3
15624 AAAGATTTAT
15634 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
15681 TACA ATA A-A ATA ATA A-A ATAA ATA A-A TATA ATA AT- ATA TATA AT-
1 -ATA ATA ATA ATA ATA ATA AT-A ATA ATA -ATA ATA ATA ATA -ATA ATA
15725 ATA TATA ATA CATA A
1 ATA -ATA ATA -ATA A
15740 AGATATTTCT
Statistics
Matches: 89, Mismatches: 2, Indels: 24
0.77 0.02 0.21
Matches are distributed among these distances:
2 11 0.12
3 63 0.71
4 15 0.17
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:15721 original size:2 final size:2
Alignment explanation
Indices: 15706--15797 Score: 70
Period size: 2 Copynumber: 49.0 Consensus size: 2
15696 AAATAAATAA
* * *
15706 AT AT A- AT A- AT AT AT AT A- AT AT AT AT A- AT AC AT AA AG AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
15744 AT TT CT AT AT AT AA AT AA AG AT A- AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
15785 AT AT A- AT AT AT AT
1 AT AT AT AT AT AT AT
15798 GGTTAGGGTT
Statistics
Matches: 71, Mismatches: 13, Indels: 12
0.74 0.14 0.12
Matches are distributed among these distances:
1 6 0.08
2 65 0.92
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (2 bp):
AT
Found at i:15775 original size:23 final size:23
Alignment explanation
Indices: 15720--15797 Score: 88
Period size: 23 Copynumber: 3.5 Consensus size: 23
15710 AATAATATAT
*
15720 ATAATATATATA-ATACATAAAG
1 ATAATATATATATATAAATAAAG
* *
15742 AT-ATTTCTATATATAAATAAAG
1 ATAATATATATATATAAATAAAG
* * *
15764 ATAATATATATATATATATATAT
1 ATAATATATATATATAAATAAAG
15787 ATAATATATAT
1 ATAATATATAT
15798 GGTTAGGGTT
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
21 7 0.15
22 13 0.28
23 26 0.57
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.41
Consensus pattern (23 bp):
ATAATATATATATATAAATAAAG
Found at i:15795 original size:9 final size:9
Alignment explanation
Indices: 15640--15797 Score: 81
Period size: 9 Copynumber: 18.2 Consensus size: 9
15630 TTATATAATA
15640 ATAATA-AT
1 ATAATATAT
15648 AATAATA-AT
1 -ATAATATAT
15657 AATAATA-AT
1 -ATAATATAT
15666 AATAATA-AT
1 -ATAATATAT
* *
15675 AAAATATACA
1 ATAATATA-T
*
15685 ATAAAATA-
1 ATAATATAT
* *
15693 ATAAAATAA
1 ATAATATAT
15702 ATAA-ATAT
1 ATAATATAT
15710 AATAATATAT
1 -ATAATATAT
15720 ATAATATAT
1 ATAATATAT
*
15729 ATAATACAT
1 ATAATATAT
*
15738 A-AAGATAT
1 ATAATATAT
**
15746 -TTCTATAT
1 ATAATATAT
15754 ATAA-ATA-
1 ATAATATAT
15761 A-AGATA-AT
1 ATA-ATATAT
15769 AT-ATATAT
1 ATAATATAT
15777 ATATATATAT
1 ATA-ATATAT
15787 ATAATATAT
1 ATAATATAT
15796 AT
1 AT
15798 GGTTAGGGTT
Statistics
Matches: 122, Mismatches: 13, Indels: 28
0.75 0.08 0.17
Matches are distributed among these distances:
6 1 0.01
7 6 0.05
8 34 0.28
9 62 0.51
10 19 0.16
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.36
Consensus pattern (9 bp):
ATAATATAT
Done.