Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011125.1 Corchorus olitorius cultivar O-4 contig11158, 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: 76920
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:632 original size:20 final size:20
Alignment explanation
Indices: 568--888 Score: 227
Period size: 20 Copynumber: 16.0 Consensus size: 20
558 ACTCATATTA
*
568 AACTTTCCCAATTGACATTG
1 AACTTTCCCAATTCACATTG
* ** *
588 AACTTGCCTTGATTCACATTC
1 AACTTTCC-CAATTCACATTG
*
609 AACTTTCCCAATTGACATTG
1 AACTTTCCCAATTCACATTG
* ** *
629 AACTTGCCTTGATTCACATTC
1 AACTTTCC-CAATTCACATTG
650 AACTTT-CCAATTCACATTG
1 AACTTTCCCAATTCACATTG
* ** **
669 AACTTGCCTTATTCACATCC
1 AACTTTCCCAATTCACATTG
*
689 AACATTCCCAATTCACATTG
1 AACTTTCCCAATTCACATTG
* ** *
709 AACTTGCCTTATTCACATTC
1 AACTTTCCCAATTCACATTG
*
729 AATTTTCCCAATTCACATTG
1 AACTTTCCCAATTCACATTG
* * * *
749 AACTTGCCTTAA-CCACATTC
1 AACTTTCC-CAATTCACATTG
*
769 AATTTTCCCAATTCACATTG
1 AACTTTCCCAATTCACATTG
* * * *
789 AACTTGCCTTAA-CCACATTC
1 AACTTTCC-CAATTCACATTG
809 AA-TTTCCCAATTCACATTG
1 AACTTTCCCAATTCACATTG
* ** * *
828 AACTTGCCTTATCCACATTC
1 AACTTTCCCAATTCACATTG
*
848 AATTTTCCCAATTCACATTG
1 AACTTTCCCAATTCACATTG
* *
868 AACTTGCCTTAATTCACATTG
1 AACTTTCC-CAATTCACATTG
889 GCCCTCAATG
Statistics
Matches: 219, Mismatches: 73, Indels: 17
0.71 0.24 0.06
Matches are distributed among these distances:
18 2 0.01
19 28 0.13
20 146 0.67
21 43 0.20
ACGTcount: A:0.29, C:0.29, G:0.07, T:0.36
Consensus pattern (20 bp):
AACTTTCCCAATTCACATTG
Found at i:671 original size:40 final size:40
Alignment explanation
Indices: 568--887 Score: 491
Period size: 40 Copynumber: 8.0 Consensus size: 40
558 ACTCATATTA
*
568 AACTTTCCCAATTGACATTGAACTTGCCTTGATTCACATTC
1 AACTTTCCCAATTCACATTGAACTTGCCTT-ATTCACATTC
*
609 AACTTTCCCAATTGACATTGAACTTGCCTTGATTCACATTC
1 AACTTTCCCAATTCACATTGAACTTGCCTT-ATTCACATTC
*
650 AACTTT-CCAATTCACATTGAACTTGCCTTATTCACATCC
1 AACTTTCCCAATTCACATTGAACTTGCCTTATTCACATTC
*
689 AACATTCCCAATTCACATTGAACTTGCCTTATTCACATTC
1 AACTTTCCCAATTCACATTGAACTTGCCTTATTCACATTC
* **
729 AATTTTCCCAATTCACATTGAACTTGCCTTAACCACATTC
1 AACTTTCCCAATTCACATTGAACTTGCCTTATTCACATTC
* **
769 AATTTTCCCAATTCACATTGAACTTGCCTTAACCACATTC
1 AACTTTCCCAATTCACATTGAACTTGCCTTATTCACATTC
*
809 AA-TTTCCCAATTCACATTGAACTTGCCTTATCCACATTC
1 AACTTTCCCAATTCACATTGAACTTGCCTTATTCACATTC
*
848 AATTTTCCCAATTCACATTGAACTTGCCTTAATTCACATT
1 AACTTTCCCAATTCACATTGAACTTGCCTT-ATTCACATT
888 GGCCCTCAAT
Statistics
Matches: 266, Mismatches: 10, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
39 52 0.20
40 159 0.60
41 55 0.21
ACGTcount: A:0.29, C:0.29, G:0.06, T:0.36
Consensus pattern (40 bp):
AACTTTCCCAATTCACATTGAACTTGCCTTATTCACATTC
Found at i:1169 original size:122 final size:122
Alignment explanation
Indices: 952--1195 Score: 357
Period size: 122 Copynumber: 2.0 Consensus size: 122
942 GTCGAGCCAG
* *
952 GAAGGCAATCCTTGCTGCCACAAGGATATGCTCAGCTCCAATGGGGAGACAACTGCAAAGGAGAA
1 GAAGGCAATCCTAGCTGCCACAAGGATACGCTCAGCTCCAATGGGGAGACAACTGCAAAGGAGAA
** * * *
1017 GAAACGTTATCTAGAAACCATCAAAGCAGAATAAGGAAACTCACAACAAGCAAATCT
66 GAAACACTATCAAGAAACCATCAAAGCAGAAAAAGGAAAATCACAACAAGCAAATCT
* *
1074 GAAGGCAATCCTAGCTGCCACAGGGATACGCTCAGCTCCTATGGGGAGACAACTGCAGAA-GAGA
1 GAAGGCAATCCTAGCTGCCACAAGGATACGCTCAGCTCCAATGGGGAGACAACTGCA-AAGGAGA
* *
1138 AGAAACACTATCAAGAAACCAAT-AGAGCAGAAAAAGGAAAATCACAGCAAGCAAATCT
65 AGAAACACTATCAAGAAACC-ATCAAAGCAGAAAAAGGAAAATCACAACAAGCAAATCT
1196 ATGCAATGGC
Statistics
Matches: 109, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
122 105 0.96
123 4 0.04
ACGTcount: A:0.42, C:0.22, G:0.22, T:0.14
Consensus pattern (122 bp):
GAAGGCAATCCTAGCTGCCACAAGGATACGCTCAGCTCCAATGGGGAGACAACTGCAAAGGAGAA
GAAACACTATCAAGAAACCATCAAAGCAGAAAAAGGAAAATCACAACAAGCAAATCT
Found at i:13836 original size:18 final size:19
Alignment explanation
Indices: 13813--13848 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
13803 GAAGTTACAG
13813 AGAAGACAGAG-AAAAATA
1 AGAAGACAGAGTAAAAATA
*
13831 AGAAGAGAGAGTAAAAAT
1 AGAAGACAGAGTAAAAAT
13849 TGAGAAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.64, C:0.03, G:0.25, T:0.08
Consensus pattern (19 bp):
AGAAGACAGAGTAAAAATA
Found at i:13854 original size:20 final size:18
Alignment explanation
Indices: 13812--13854 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
13802 GGAAGTTACA
13812 GAGAAGACAGAGAAAAAT
1 GAGAAGACAGAGAAAAAT
* *
13830 AAGAAGAGAGAGTAAAAATT
1 GAGAAGACAGAG-AAAAA-T
13850 GAGAA
1 GAGAA
13855 AATGAGAAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 10 0.50
19 5 0.25
20 5 0.25
ACGTcount: A:0.60, C:0.02, G:0.28, T:0.09
Consensus pattern (18 bp):
GAGAAGACAGAGAAAAAT
Found at i:15384 original size:40 final size:40
Alignment explanation
Indices: 15327--15418 Score: 166
Period size: 40 Copynumber: 2.2 Consensus size: 40
15317 GTACATGGTA
15327 TTAACTTTGACAAAAACTACATATTTGATTATTATATCTCCC
1 TTAACTTT--CAAAAACTACATATTTGATTATTATATCTCCC
15369 TTAACTTTCAAAAACTACATATTTGATTATTATATCTCCC
1 TTAACTTTCAAAAACTACATATTTGATTATTATATCTCCC
15409 TTAACTTTCA
1 TTAACTTTCA
15419 TGTCATGGTC
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
40 42 0.84
42 8 0.16
ACGTcount: A:0.35, C:0.20, G:0.03, T:0.42
Consensus pattern (40 bp):
TTAACTTTCAAAAACTACATATTTGATTATTATATCTCCC
Found at i:15540 original size:12 final size:12
Alignment explanation
Indices: 15523--15554 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
15513 TCATCTCATC
15523 TAAATATATATA
1 TAAATATATATA
15535 TAAATATATATA
1 TAAATATATATA
*
15547 TATATATA
1 TAAATATA
15555 ATAGGTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TAAATATATATA
Found at i:16187 original size:18 final size:17
Alignment explanation
Indices: 16149--16187 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
16139 TTGAACTTGG
* *
16149 ATTTGTTTTTTATTTTT
1 ATTTGTTTTTTATTCTC
16166 ATTTGTTGTTTTATTCTC
1 ATTTGTT-TTTTATTCTC
16184 ATTT
1 ATTT
16188 TTCTGAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.13, C:0.05, G:0.08, T:0.74
Consensus pattern (17 bp):
ATTTGTTTTTTATTCTC
Found at i:20099 original size:25 final size:25
Alignment explanation
Indices: 20071--20120 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
20061 ATAATCACAA
20071 ACACTTCATTAACCATGAAAAACCC
1 ACACTTCATTAACCATGAAAAACCC
20096 ACACTTCATTAACCATGAAAAACCC
1 ACACTTCATTAACCATGAAAAACCC
20121 GCAGCGAAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.44, C:0.32, G:0.04, T:0.20
Consensus pattern (25 bp):
ACACTTCATTAACCATGAAAAACCC
Found at i:36369 original size:31 final size:31
Alignment explanation
Indices: 36331--36393 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
36321 TTAACTTTTG
36331 ACAGTTAATAATAGTTGGGGTCTTCCAATTT
1 ACAGTTAATAATAGTTGGGGTCTTCCAATTT
36362 ACAGTTAATAATAGTTGGGGTCTTCCAATTT
1 ACAGTTAATAATAGTTGGGGTCTTCCAATTT
36393 A
1 A
36394 TTCCGCCGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.38
Consensus pattern (31 bp):
ACAGTTAATAATAGTTGGGGTCTTCCAATTT
Found at i:41367 original size:33 final size:33
Alignment explanation
Indices: 41325--41421 Score: 176
Period size: 33 Copynumber: 2.9 Consensus size: 33
41315 GACTGAGTTC
*
41325 TTGGATACTCGTGAGATGGCGGCGGAGGTGAAG
1 TTGGATACTCGTGAGATGGTGGCGGAGGTGAAG
41358 TTGGATACTCGTGAGATGGTGGCGGAGGTGAAG
1 TTGGATACTCGTGAGATGGTGGCGGAGGTGAAG
*
41391 TTGGATACTGGTGAGATGGTGGCGGAGGTGA
1 TTGGATACTCGTGAGATGGTGGCGGAGGTGA
41422 CGGAGTGTAT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 62 1.00
ACGTcount: A:0.21, C:0.09, G:0.46, T:0.24
Consensus pattern (33 bp):
TTGGATACTCGTGAGATGGTGGCGGAGGTGAAG
Found at i:41716 original size:27 final size:27
Alignment explanation
Indices: 41671--41722 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
41661 ACTTTGTCGG
** * *
41671 TGGTGGTGGTGTGTTGTAGTTATGGCT
1 TGGTGGTGGTGAATGGTAGTAATGGCT
41698 TGGTGGTGGTGAATGGTAGTAATGG
1 TGGTGGTGGTGAATGGTAGTAATGG
41723 TGCTCTGATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.13, C:0.02, G:0.46, T:0.38
Consensus pattern (27 bp):
TGGTGGTGGTGAATGGTAGTAATGGCT
Found at i:44762 original size:8 final size:8
Alignment explanation
Indices: 44749--44775 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
44739 ATAAACTCCC
44749 GGCACTGT
1 GGCACTGT
44757 GGCACTGT
1 GGCACTGT
44765 GGCACTGT
1 GGCACTGT
44773 GGC
1 GGC
44776 CAAGAGGCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.11, C:0.26, G:0.41, T:0.22
Consensus pattern (8 bp):
GGCACTGT
Found at i:73709 original size:11 final size:11
Alignment explanation
Indices: 73666--73703 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
73656 TTCCTATATA
*
73666 AAATAAATTAT
1 AAATTAATTAT
73677 CAAA-TAATTAT
1 -AAATTAATTAT
73688 AAATTAATTAT
1 AAATTAATTAT
73699 AAATT
1 AAATT
73704 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Done.