Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014407.1 Corchorus capsularis cultivar CVL-1 contig14428, 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: 21997
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Found at i:4447 original size:6 final size:6
Alignment explanation
Indices: 4436--4536 Score: 112
Period size: 6 Copynumber: 16.8 Consensus size: 6
4426 TTTCATTGAA
* * * *
4436 ATATAT ATATAT ATATAT ATCTAT ATCTAT ATATAT CTATAT ATATCT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
* * * * * *
4484 ATATCT ATATAT ATCTAT ATATAT ATATCT ATATCT ATATCT ATATCT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
4532 ATATA
1 ATATA
4537 AGTCTAAACT
Statistics
Matches: 85, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 85 1.00
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.50
Consensus pattern (6 bp):
ATATAT
Found at i:4451 original size:10 final size:10
Alignment explanation
Indices: 4436--4536 Score: 112
Period size: 10 Copynumber: 10.1 Consensus size: 10
4426 TTTCATTGAA
4436 ATATATATAT
1 ATATATATAT
4446 ATATATATAT
1 ATATATATAT
* *
4456 CTATATCTAT
1 ATATATATAT
*
4466 ATATATCTAT
1 ATATATATAT
*
4476 ATATATCTAT
1 ATATATATAT
*
4486 ATCTATATAT
1 ATATATATAT
*
4496 ATCTATATAT
1 ATATATATAT
*
4506 ATATATCTAT
1 ATATATATAT
* *
4516 ATCTATATCT
1 ATATATATAT
*
4526 ATATCTATAT
1 ATATATATAT
4536 A
1 A
4537 AGTCTAAACT
Statistics
Matches: 78, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 78 1.00
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.50
Consensus pattern (10 bp):
ATATATATAT
Found at i:4476 original size:26 final size:26
Alignment explanation
Indices: 4437--4529 Score: 145
Period size: 26 Copynumber: 3.6 Consensus size: 26
4427 TTCATTGAAA
*
4437 TATATATATATATATATATCTATATC
1 TATATATATCTATATATATCTATATC
4463 TATATATATCTATATATATCTATATC
1 TATATATATCTATATATATCTATATC
4489 TATATATATCTATATATA--TATATC
1 TATATATATCTATATATATCTATATC
4513 TATATCTATATCTATAT
1 TATA--TATATCTATAT
4530 CTATATAAGT
Statistics
Matches: 64, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
24 10 0.16
26 54 0.84
ACGTcount: A:0.40, C:0.10, G:0.00, T:0.51
Consensus pattern (26 bp):
TATATATATCTATATATATCTATATC
Found at i:4542 original size:16 final size:15
Alignment explanation
Indices: 4436--4542 Score: 96
Period size: 16 Copynumber: 7.1 Consensus size: 15
4426 TTTCATTGAA
* *
4436 ATATATATATATATAT
1 ATATCTATATA-ATCT
* *
4452 ATATCTATATCTATAT
1 ATATCTATAT-AATCT
4468 ATATCTATATATATCT
1 ATATCTATATA-ATCT
4484 ATATCTATATATATCT
1 ATATCTATATA-ATCT
*
4500 ATATATATAT-ATCT
1 ATATCTATATAATCT
4514 ATATC--TAT-ATCT
1 ATATCTATATAATCT
4526 ATATCTATATAAGTCT
1 ATATCTATATAA-TCT
4542 A
1 A
4543 AACTTCAAAA
Statistics
Matches: 79, Mismatches: 6, Indels: 12
0.81 0.06 0.12
Matches are distributed among these distances:
12 12 0.15
14 11 0.14
15 1 0.01
16 55 0.70
ACGTcount: A:0.40, C:0.10, G:0.01, T:0.49
Consensus pattern (15 bp):
ATATCTATATAATCT
Found at i:7426 original size:3 final size:3
Alignment explanation
Indices: 7418--7449 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
7408 TATACTTCTT
7418 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
7450 TAGTAGTACA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:11304 original size:208 final size:209
Alignment explanation
Indices: 10944--11364 Score: 754
Period size: 208 Copynumber: 2.0 Consensus size: 209
10934 GGTCTTTTTA
*
10944 ATACCTAAACATAATTATTAAATTTTAATTTTTTTTAGTTATAACATATATGTAAATAATACTTC
1 ATACCTAAACATAATTATAAAATTTTAA-TTTTTTTAGTTATAACATATATGTAAATAATACTTC
* *
11009 ATAAATTTATATTTACCTATGTCAAATACAAATTAATAATAATGTAGAGGGATTAAAAATATTTA
65 ATAAATTTATATTTACCTACGTCAAATACAAATTAATAATAATGTAGAGGGATTAAAAATATATA
*
11074 ATTAAAGGGATTGAAGTATGTTGACTTTGTTGGGGTTAACCTCTATAGAAATTTTTGTAACATTA
130 ATTAAAGGGATTGAAGTATGTTGACTTTGTTAGGGTTAACCTCTATAGAAATTTTTGTAACATTA
11139 GAGTATTTTACACTC
195 GAGTATTTTACACTC
* *
11154 ATACCTAAACATAATTATAAAATTTTAA-TTTTTTAGTTATAACATATATGTACATAATAGTTCA
1 ATACCTAAACATAATTATAAAATTTTAATTTTTTTAGTTATAACATATATGTAAATAATACTTCA
*
11218 TAAATTTATATTTACCTACGTCAAATACAAATTAATAATAATGTAGAGGGATTAAAAATCTATAA
66 TAAATTTATATTTACCTACGTCAAATACAAATTAATAATAATGTAGAGGGATTAAAAATATATAA
*
11283 TTAAAGGGATTGAAGTATGTTGACTTTGTTAGTGTTAACCTCTATAGAAATTTTTGTAACATTAG
131 TTAAAGGGATTGAAGTATGTTGACTTTGTTAGGGTTAACCTCTATAGAAATTTTTGTAACATTAG
11348 AGTATTTTACACTC
196 AGTATTTTACACTC
11362 ATA
1 ATA
11365 AATTTATTTA
Statistics
Matches: 203, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
208 176 0.87
210 27 0.13
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.40
Consensus pattern (209 bp):
ATACCTAAACATAATTATAAAATTTTAATTTTTTTAGTTATAACATATATGTAAATAATACTTCA
TAAATTTATATTTACCTACGTCAAATACAAATTAATAATAATGTAGAGGGATTAAAAATATATAA
TTAAAGGGATTGAAGTATGTTGACTTTGTTAGGGTTAACCTCTATAGAAATTTTTGTAACATTAG
AGTATTTTACACTC
Found at i:11793 original size:2 final size:2
Alignment explanation
Indices: 11786--11819 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
11776 CTTTAACTAG
11786 TA TA TA TA TA TA TA TA TA 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
11820 AGGCATCATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14849 original size:14 final size:14
Alignment explanation
Indices: 14830--14862 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
14820 CCTAGCCGCT
*
14830 CTCTCCCTTTCTCC
1 CTCTCCCCTTCTCC
14844 CTCTCCCCTTCTCC
1 CTCTCCCCTTCTCC
14858 CTCTC
1 CTCTC
14863 TAGTTTTCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (14 bp):
CTCTCCCCTTCTCC
Found at i:15785 original size:13 final size:13
Alignment explanation
Indices: 15767--15791 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
15757 TTTTCTATCT
15767 TACATCATTAATG
1 TACATCATTAATG
15780 TACATCATTAAT
1 TACATCATTAAT
15792 ATCATAATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.04, T:0.40
Consensus pattern (13 bp):
TACATCATTAATG
Done.