Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024477.1 Corchorus olitorius cultivar O-4 contig24510, 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: 47335
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.32
Found at i:642 original size:30 final size:31
Alignment explanation
Indices: 606--672 Score: 93
Period size: 30 Copynumber: 2.2 Consensus size: 31
596 GTTTGTGATG
*
606 AGAAATTTCAGTATTTAACA-A-AAAAAAGAA
1 AGAAATTTCAGTACTTAA-ATACAAAAAAGAA
636 AGAAATTTCAGTACTTAAATACAAAAAAGAA
1 AGAAATTTCAGTACTTAAATACAAAAAAGAA
*
667 ATAAAT
1 AGAAAT
673 AAATGAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 1 0.03
30 18 0.55
31 14 0.42
ACGTcount: A:0.60, C:0.07, G:0.09, T:0.24
Consensus pattern (31 bp):
AGAAATTTCAGTACTTAAATACAAAAAAGAA
Found at i:5542 original size:1 final size:1
Alignment explanation
Indices: 5536--5567 Score: 55
Period size: 1 Copynumber: 32.0 Consensus size: 1
5526 TTATGGGAAG
*
5536 AAAAAAAAAACAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
5568 CAAACAAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.97, C:0.03, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:5552 original size:8 final size:8
Alignment explanation
Indices: 5539--5578 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
5529 TGGGAAGAAA
5539 AAAAAAAC
1 AAAAAAAC
5547 AAAAAAA-
1 AAAAAAAC
5554 AAAAAAA-
1 AAAAAAAC
5561 AAAAAAAC
1 AAAAAAAC
*
5569 AAACAAAC
1 AAAAAAAC
5577 AA
1 AA
5579 TGGGTCACAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
7 14 0.47
8 16 0.53
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAAAAC
Found at i:5552 original size:11 final size:11
Alignment explanation
Indices: 5536--5571 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
5526 TTATGGGAAG
5536 AAAAAAAAAAC
1 AAAAAAAAAAC
*
5547 AAAAAAAAAAA
1 AAAAAAAAAAC
5558 AAAAAAAAAAC
1 AAAAAAAAAAC
5569 AAA
1 AAA
5572 CAAACAATGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:16973 original size:3 final size:3
Alignment explanation
Indices: 16965--17071 Score: 196
Period size: 3 Copynumber: 35.7 Consensus size: 3
16955 TTTTAATTTC
*
16965 AAT AAT AAT AGT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
17013 AAT AAT AAT AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
17061 AAT AAT AAT AA
1 AAT AAT AAT AA
17072 AGCATGTTTA
Statistics
Matches: 100, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 100 1.00
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:18915 original size:21 final size:21
Alignment explanation
Indices: 18888--19094 Score: 240
Period size: 21 Copynumber: 9.9 Consensus size: 21
18878 TATATGAAAC
*
18888 TTTGGGGTTTGACTATTAAAA
1 TTTGGGGTTTGACTATCAAAA
* * * *
18909 TTCGGGGGTTGACCATCAAAC
1 TTTGGGGTTTGACTATCAAAA
*
18930 TTTGGGCTTTGACTATCAAAA
1 TTTGGGGTTTGACTATCAAAA
* * *
18951 TTTGGGGGTTGACCATCAAAC
1 TTTGGGGTTTGACTATCAAAA
*
18972 TTTGAGGTTTGACTATCAAAA
1 TTTGGGGTTTGACTATCAAAA
* *
18993 TTTGGGGTTTGACAATCAAAC
1 TTTGGGGTTTGACTATCAAAA
19014 TTT-GGGTGTTGACTATCAAAA
1 TTTGGGGT-TTGACTATCAAAA
* *
19035 TTTGGGG-TTGACCATCAAAC
1 TTTGGGGTTTGACTATCAAAA
19055 TTTGGGGTTTGACTATCAAAA
1 TTTGGGGTTTGACTATCAAAA
*
19076 TTTGAGGG-TTGACCATCAA
1 TTTG-GGGTTTGACTATCAA
19095 TGGGATTTGA
Statistics
Matches: 154, Mismatches: 28, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
20 22 0.14
21 126 0.82
22 6 0.04
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (21 bp):
TTTGGGGTTTGACTATCAAAA
Found at i:18930 original size:42 final size:42
Alignment explanation
Indices: 18884--19094 Score: 336
Period size: 42 Copynumber: 5.0 Consensus size: 42
18874 GAAATATATG
* *
18884 AAACTTTGGGGTTTGACTATTAAAATTCGGGGGTTGACCATC
1 AAACTTTGGGGTTTGACTATCAAAATTTGGGGGTTGACCATC
*
18926 AAACTTTGGGCTTTGACTATCAAAATTTGGGGGTTGACCATC
1 AAACTTTGGGGTTTGACTATCAAAATTTGGGGGTTGACCATC
* * *
18968 AAACTTTGAGGTTTGACTATCAAAATTTGGGGTTTGACAATC
1 AAACTTTGGGGTTTGACTATCAAAATTTGGGGGTTGACCATC
19010 AAACTTT-GGGTGTTGACTATCAAAATTT-GGGGTTGACCATC
1 AAACTTTGGGGT-TTGACTATCAAAATTTGGGGGTTGACCATC
*
19051 AAACTTTGGGGTTTGACTATCAAAATTTGAGGGTTGACCATC
1 AAACTTTGGGGTTTGACTATCAAAATTTGGGGGTTGACCATC
19093 AA
1 AA
19095 TGGGATTTGA
Statistics
Matches: 155, Mismatches: 11, Indels: 6
0.90 0.06 0.03
Matches are distributed among these distances:
41 37 0.24
42 118 0.76
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (42 bp):
AAACTTTGGGGTTTGACTATCAAAATTTGGGGGTTGACCATC
Found at i:19218 original size:17 final size:17
Alignment explanation
Indices: 19192--19246 Score: 56
Period size: 17 Copynumber: 3.0 Consensus size: 17
19182 TAATTAAATT
19192 TTGATAGTCAAACCCCA
1 TTGATAGTCAAACCCCA
* *
19209 TTGATGGTCAAATCCCAAA
1 TTGATAGTCAAA-CCC-CA
19228 TTTTGATAGTCAAACCCCA
1 --TTGATAGTCAAACCCCA
19247 AAGTTTGATA
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
17 11 0.37
18 3 0.10
19 2 0.07
20 3 0.10
21 11 0.37
ACGTcount: A:0.35, C:0.25, G:0.13, T:0.27
Consensus pattern (17 bp):
TTGATAGTCAAACCCCA
Found at i:19233 original size:21 final size:21
Alignment explanation
Indices: 19209--19261 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
19199 TCAAACCCCA
* * *
19209 TTGATGGTCAAATCCCAAATT
1 TTGATAGTCAAACCCCAAAGT
19230 TTGATAGTCAAACCCCAAAGT
1 TTGATAGTCAAACCCCAAAGT
19251 TTGATAGTCAA
1 TTGATAGTCAA
19262 CACGTTAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.30
Consensus pattern (21 bp):
TTGATAGTCAAACCCCAAAGT
Found at i:22099 original size:16 final size:16
Alignment explanation
Indices: 22080--22113 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
22070 TGTTTTTGTT
*
22080 TTTTATTTTTGTTTCG
1 TTTTATTTTTGTTGCG
*
22096 TTTTGTTTTTGTTGCG
1 TTTTATTTTTGTTGCG
22112 TT
1 TT
22114 GTCAATTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.03, C:0.06, G:0.18, T:0.74
Consensus pattern (16 bp):
TTTTATTTTTGTTGCG
Found at i:22773 original size:18 final size:18
Alignment explanation
Indices: 22750--22786 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
22740 TTTGATCAAA
22750 AAGAGTATACTAATTTCT
1 AAGAGTATACTAATTTCT
22768 AAGAGTATACTAATTTCT
1 AAGAGTATACTAATTTCT
22786 A
1 A
22787 CTCCATATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.38
Consensus pattern (18 bp):
AAGAGTATACTAATTTCT
Found at i:24018 original size:30 final size:32
Alignment explanation
Indices: 23966--24027 Score: 101
Period size: 30 Copynumber: 2.0 Consensus size: 32
23956 CAATTATCAT
23966 TTTAACATGCTTTTTCTTGGCCAAAAAAAAAAA
1 TTTAACATGC-TTTTCTTGGCCAAAAAAAAAAA
23999 TTTAACATGC-TTT-TTGGCCAAAAAAAAAA
1 TTTAACATGCTTTTCTTGGCCAAAAAAAAAA
24028 TACTAACATG
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
30 16 0.55
31 3 0.10
33 10 0.34
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.32
Consensus pattern (32 bp):
TTTAACATGCTTTTCTTGGCCAAAAAAAAAAA
Found at i:24035 original size:30 final size:32
Alignment explanation
Indices: 23968--24037 Score: 92
Period size: 30 Copynumber: 2.2 Consensus size: 32
23958 ATTATCATTT
*
23968 TAACATGCTTTTTCTTGGCCAAAAAAAAAAATT
1 TAACATGC-TTTTCTTGGCCAAAAAAAAAAATC
24001 TAACATGC-TTT-TTGGCC-AAAAAAAAAATAC
1 TAACATGCTTTTCTTGGCCAAAAAAAAAAAT-C
24031 TAACATG
1 TAACATG
24038 ATTTCCATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
29 11 0.31
30 13 0.37
31 3 0.09
33 8 0.23
ACGTcount: A:0.44, C:0.16, G:0.10, T:0.30
Consensus pattern (32 bp):
TAACATGCTTTTCTTGGCCAAAAAAAAAAATC
Found at i:34535 original size:17 final size:17
Alignment explanation
Indices: 34500--34537 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
34490 CACCCCCCAA
*
34500 ATCACTAGTGATCTTAG
1 ATCACTAGTGATCTAAG
34517 ATCACTAGTGATGC-AAG
1 ATCACTAGTGAT-CTAAG
34534 ATCA
1 ATCA
34538 ATGGTAATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 18 0.95
18 1 0.05
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Consensus pattern (17 bp):
ATCACTAGTGATCTAAG
Found at i:35251 original size:14 final size:14
Alignment explanation
Indices: 35232--35279 Score: 55
Period size: 14 Copynumber: 3.5 Consensus size: 14
35222 GTCAAGCATG
35232 ACAGGAAAATCAAA
1 ACAGGAAAATCAAA
*
35246 ACAGGAAGAA--AAT
1 ACAGGAA-AATCAAA
*
35259 CCAGGAAAATCAAA
1 ACAGGAAAATCAAA
35273 ACAGGAA
1 ACAGGAA
35280 GAAAAATCTG
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
12 2 0.07
13 8 0.30
14 15 0.56
15 2 0.07
ACGTcount: A:0.60, C:0.15, G:0.19, T:0.06
Consensus pattern (14 bp):
ACAGGAAAATCAAA
Found at i:35267 original size:27 final size:27
Alignment explanation
Indices: 35233--35284 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
35223 TCAAGCATGA
35233 CAGGAAAATCAAAACAGGAAGAAAATC
1 CAGGAAAATCAAAACAGGAAGAAAATC
35260 CAGGAAAATCAAAACAGGAAGAAAA
1 CAGGAAAATCAAAACAGGAAGAAAA
35285 ATCTGACACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.62, C:0.13, G:0.19, T:0.06
Consensus pattern (27 bp):
CAGGAAAATCAAAACAGGAAGAAAATC
Found at i:35301 original size:15 final size:14
Alignment explanation
Indices: 35281--35312 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
35271 AAACAGGAAG
35281 AAAAATCTGACACAA
1 AAAAATCTGACA-AA
35296 AAAAATCTGACAAA
1 AAAAATCTGACAAA
35310 AAA
1 AAA
35313 CAGAAACAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.66, C:0.16, G:0.06, T:0.12
Consensus pattern (14 bp):
AAAAATCTGACAAA
Found at i:37063 original size:17 final size:17
Alignment explanation
Indices: 37041--37082 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
37031 TTTGCAAAAT
*
37041 ATCAGAAACATTTATAA
1 ATCAGAAACATATATAA
37058 ATCAGAAACATATATAA
1 ATCAGAAACATATATAA
37075 ATCAGAAA
1 ATCAGAAA
37083 TACATAGACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.57, C:0.12, G:0.07, T:0.24
Consensus pattern (17 bp):
ATCAGAAACATATATAA
Found at i:37763 original size:17 final size:17
Alignment explanation
Indices: 37743--37802 Score: 63
Period size: 17 Copynumber: 3.6 Consensus size: 17
37733 CAATTGCACG
37743 AGAAAATCAAAACAGGA
1 AGAAAATCAAAACAGGA
*
37760 AGAAAATCAATTGACA-G-
1 AGAAAATCAA--AACAGGA
37777 -GAAAATCAAAACAGGA
1 AGAAAATCAAAACAGGA
*
37793 ATAAAATCAA
1 AGAAAATCAA
37803 TTGACCAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 3 0.09
15 1 0.03
16 9 0.26
17 18 0.51
18 1 0.03
19 3 0.09
ACGTcount: A:0.62, C:0.12, G:0.15, T:0.12
Consensus pattern (17 bp):
AGAAAATCAAAACAGGA
Found at i:37783 original size:33 final size:33
Alignment explanation
Indices: 37744--37807 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
37734 AATTGCACGA
37744 GAAAATCAAAACAGGAAGAAAATCAATTGACAG
1 GAAAATCAAAACAGGAAGAAAATCAATTGACAG
*
37777 GAAAATCAAAACAGGAATAAAATCAATTGAC
1 GAAAATCAAAACAGGAAGAAAATCAATTGAC
37808 CAAACAAAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.58, C:0.12, G:0.16, T:0.14
Consensus pattern (33 bp):
GAAAATCAAAACAGGAAGAAAATCAATTGACAG
Done.