Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012148.1 Corchorus olitorius cultivar O-4 contig12181, 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: 19696
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:672 original size:22 final size:22
Alignment explanation
Indices: 623--752 Score: 102
Period size: 22 Copynumber: 5.9 Consensus size: 22
613 TGACAATCAA
* ** *
623 ACCAAAATTACATAGAAAGATT
1 ACCAAAATTTCATAGTGAGGTT
* * *
645 ATCAAAATTTCTTAGTGTGGTT
1 ACCAAAATTTCATAGTGAGGTT
*
667 ACCAAAATTTCATA-TAGAGATT
1 ACCAAAATTTCATAGT-GAGGTT
* *
689 ATCAAAACTTCATAGTGTA-GTT
1 ACCAAAATTTCATAGTG-AGGTT
* **
711 ATCAAAATTTCATACAGAGGTT
1 ACCAAAATTTCATAGTGAGGTT
*
733 ACCAAAATTTCATAGGGAGG
1 ACCAAAATTTCATAGTGAGG
753 GAGGTTACCA
Statistics
Matches: 84, Mismatches: 20, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
21 2 0.02
22 80 0.95
23 2 0.02
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.32
Consensus pattern (22 bp):
ACCAAAATTTCATAGTGAGGTT
Found at i:688 original size:44 final size:44
Alignment explanation
Indices: 623--747 Score: 160
Period size: 44 Copynumber: 2.8 Consensus size: 44
613 TGACAATCAA
* * * * *
623 ACCAAAATTACATAGAAAGATTATCAAAATTTCTTAGTGTGGTT
1 ACCAAAATTTCATACAGAGATTATCAAAATTTCATAGTGTAGTT
* *
667 ACCAAAATTTCATATAGAGATTATCAAAACTTCATAGTGTAGTT
1 ACCAAAATTTCATACAGAGATTATCAAAATTTCATAGTGTAGTT
* * *
711 ATCAAAATTTCATACAGAGGTTACCAAAATTTCATAG
1 ACCAAAATTTCATACAGAGATTATCAAAATTTCATAG
748 GGAGGGAGGT
Statistics
Matches: 70, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 70 1.00
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.33
Consensus pattern (44 bp):
ACCAAAATTTCATACAGAGATTATCAAAATTTCATAGTGTAGTT
Found at i:838 original size:22 final size:22
Alignment explanation
Indices: 790--849 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 22
780 AATTTCCTAG
790 AGAGGTTAAT-AAAATTTTATAT
1 AGAGGTT-ATGAAAATTTTATAT
*
812 GGAGGTTATGAAAATTTTATGA-
1 AGAGGTTATGAAAATTTTAT-AT
834 AGAGGTTATCGAAAAT
1 AGAGGTTAT-GAAAAT
850 ACATAGAGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
21 2 0.06
22 24 0.73
23 7 0.21
ACGTcount: A:0.42, C:0.02, G:0.22, T:0.35
Consensus pattern (22 bp):
AGAGGTTATGAAAATTTTATAT
Found at i:912 original size:22 final size:23
Alignment explanation
Indices: 878--1094 Score: 73
Period size: 22 Copynumber: 9.8 Consensus size: 23
868 AGTTTCATTC
* * *
878 TCATAGGGAGGTTATCGAAA-TT
1 TCATAGTGCGGTTATCAAAATTT
* *
900 TCATGGTGTGGTTATCAAAATTT
1 TCATAGTGCGGTTATCAAAATTT
*
923 TCATAGTGCGGTTA-C-CAATTT
1 TCATAGTGCGGTTATCAAAATTT
* * * *
944 T-ATTTAGTGTGATTATTAAAACTT
1 TCA--TAGTGCGGTTATCAAAATTT
*
968 T-ATAG-GCAGATTATCAAAA-TT
1 TCATAGTGC-GGTTATCAAAATTT
* * * * *
989 TCACACTGAGATTATCGAAA-TT
1 TCATAGTGCGGTTATCAAAATTT
* * * *
1011 TCATAGTGTGATTACCCAAA-TT
1 TCATAGTGCGGTTATCAAAATTT
* *
1033 TCATAGTGTGGTTATC-GAATTT
1 TCATAGTGCGGTTATCAAAATTT
* * * *
1055 TCATAGGGAGGTAATCGAAA-TT
1 TCATAGTGCGGTTATCAAAATTT
1077 TCATA-T-CAGGTTATCAAA
1 TCATAGTGC-GGTTATCAAA
1095 TTTGCAAAAT
Statistics
Matches: 150, Mismatches: 34, Indels: 23
0.72 0.16 0.11
Matches are distributed among these distances:
20 1 0.01
21 20 0.13
22 106 0.71
23 17 0.11
24 6 0.04
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.37
Consensus pattern (23 bp):
TCATAGTGCGGTTATCAAAATTT
Found at i:1076 original size:44 final size:44
Alignment explanation
Indices: 878--1081 Score: 137
Period size: 44 Copynumber: 4.6 Consensus size: 44
868 AGTTTCATTC
* *
878 TCATAGGGAGGTTATCGAAATTTCATGGTGTGGTTATCAAAATTT
1 TCATAGGGAGGTTATCGAAATTTCATAGTGTGATTATC-AAATTT
* * * * * *
923 TCATAGTGCGGTTA-C-CAATTTTATTTAGTGTGATTATTAAAACTT
1 TCATAGGGAGGTTATCGAAATTTCA--TAGTGTGATTA-TCAAATTT
* * * * * *
968 T-ATAGGCAGATTATCAAAATTTCACACTGAGATTATCGAAA-TT
1 TCATAGGGAGGTTATCGAAATTTCATAGTGTGATTATC-AAATTT
* * * * * * *
1011 TCATAGTGTGATTACCCAAATTTCATAGTGTGGTTATCGAATTT
1 TCATAGGGAGGTTATCGAAATTTCATAGTGTGATTATCAAATTT
*
1055 TCATAGGGAGGTAATCGAAATTTCATA
1 TCATAGGGAGGTTATCGAAATTTCATA
1082 TCAGGTTATC
Statistics
Matches: 117, Mismatches: 34, Indels: 17
0.70 0.20 0.10
Matches are distributed among these distances:
43 12 0.10
44 70 0.60
45 28 0.24
46 7 0.06
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.38
Consensus pattern (44 bp):
TCATAGGGAGGTTATCGAAATTTCATAGTGTGATTATCAAATTT
Found at i:2917 original size:44 final size:44
Alignment explanation
Indices: 2869--2973 Score: 138
Period size: 44 Copynumber: 2.4 Consensus size: 44
2859 ACATAGTAAA
* * **
2869 GTTATTAAAATTTCATAGTGTGATTACCAAAATTTCATATGGAG
1 GTTATCAAAATTTCATAGTGTAATTACCAAAATTTCATACAGAG
* * *
2913 GTTATCAAAACTTCGTAGTGTAATTATCAAAATTTCATACAGAG
1 GTTATCAAAATTTCATAGTGTAATTACCAAAATTTCATACAGAG
*
2957 GTTACCAAAATTTCATA
1 GTTATCAAAATTTCATA
2974 AAAAAAAGGT
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
44 51 1.00
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.36
Consensus pattern (44 bp):
GTTATCAAAATTTCATAGTGTAATTACCAAAATTTCATACAGAG
Found at i:3022 original size:22 final size:22
Alignment explanation
Indices: 2870--3022 Score: 94
Period size: 22 Copynumber: 6.8 Consensus size: 22
2860 CATAGTAAAG
* *
2870 TTATTAAAATTTCATA-GTGTGA
1 TTATCAAAATTTCATATG-GAGA
* *
2892 TTACCAAAATTTCATATGGAGG
1 TTATCAAAATTTCATATGGAGA
* * *
2914 TTATCAAAACTTCGTAGTGTA-A
1 TTATCAAAATTTCATA-TGGAGA
** *
2936 TTATCAAAATTTCATACAGAGG
1 TTATCAAAATTTCATATGGAGA
* *** *
2958 TTACCAAAATTTCATAAAAAAAAGG
1 TTATCAAAATTTCAT---ATGGAGA
* *
2983 TTATCAAAATCTCTTATGGAGA
1 TTATCAAAATTTCATATGGAGA
3005 TTATCAAAATTTCATATG
1 TTATCAAAATTTCATATG
3023 AATGTTATTG
Statistics
Matches: 98, Mismatches: 27, Indels: 12
0.72 0.20 0.09
Matches are distributed among these distances:
21 1 0.01
22 76 0.78
23 4 0.04
25 17 0.17
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (22 bp):
TTATCAAAATTTCATATGGAGA
Found at i:3030 original size:22 final size:22
Alignment explanation
Indices: 2852--3081 Score: 89
Period size: 22 Copynumber: 10.4 Consensus size: 22
2842 ACAATCAAAC
* *
2852 CAAAATTACATA-GTAAAGTTAT
1 CAAAATTTCATATG-AAGGTTAT
* * * *
2874 TAAAATTTCATAGTG-TGATTAC
1 CAAAATTTCATA-TGAAGGTTAT
*
2896 CAAAATTTCATATGGAGGTTAT
1 CAAAATTTCATATGAAGGTTAT
* *
2918 CAAAACTTCGTAGTGTAA--TTAT
1 CAAAATTTCATA-TG-AAGGTTAT
* *
2940 CAAAATTTCATA-CAGAGGTTAC
1 CAAAATTTCATATGA-AGGTTAT
**
2962 CAAAATTTCATAAAAAAAAGGTTAT
1 CAAAATTTCAT---ATGAAGGTTAT
* * * *
2987 CAAAATCTCTTATGGAGATTAT
1 CAAAATTTCATATGAAGGTTAT
*
3009 CAAAATTTCATATGAATGTTAT
1 CAAAATTTCATATGAAGGTTAT
** * * *
3031 TGAAATTTTATAGTG-TGATTAT
1 CAAAATTTCATA-TGAAGGTTAT
* *
3053 CAAAA-TTAAT-TAGAACGTTAT
1 CAAAATTTCATAT-GAAGGTTAT
3074 CAAAATTT
1 CAAAATTT
3082 GTTCTTATCA
Statistics
Matches: 150, Mismatches: 42, Indels: 32
0.67 0.19 0.14
Matches are distributed among these distances:
19 2 0.01
20 2 0.01
21 15 0.10
22 108 0.72
23 4 0.03
24 2 0.01
25 16 0.11
26 1 0.01
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (22 bp):
CAAAATTTCATATGAAGGTTAT
Found at i:3159 original size:81 final size:82
Alignment explanation
Indices: 3069--3243 Score: 316
Period size: 82 Copynumber: 2.1 Consensus size: 82
3059 TAATTAGAAC
**
3069 GTTATCAAAATTTGTTCTTATC-AAATTTCCTAGGATGGTGAACAAAATTTCATAGGGAGCTTAT
1 GTTATCAAAATTTAATCTTATCAAAATTTCCTAGGATGGTGAACAAAATTTCATAGGGAGCTTAT
3133 GAAAATATTATGGAGAG
66 GAAAATATTATGGAGAG
3150 GTTATCAAAATTTAATCTTATCAAAATTTCCTAGGATGGTGAACAAAATTTCATAGGGAGCTTAT
1 GTTATCAAAATTTAATCTTATCAAAATTTCCTAGGATGGTGAACAAAATTTCATAGGGAGCTTAT
*
3215 GAAAATCTTATGGAGAG
66 GAAAATATTATGGAGAG
3232 GTTATCAAAATT
1 GTTATCAAAATT
3244 ACATATAGAG
Statistics
Matches: 90, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
81 20 0.22
82 70 0.78
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.34
Consensus pattern (82 bp):
GTTATCAAAATTTAATCTTATCAAAATTTCCTAGGATGGTGAACAAAATTTCATAGGGAGCTTAT
GAAAATATTATGGAGAG
Found at i:3161 original size:44 final size:43
Alignment explanation
Indices: 3111--3248 Score: 128
Period size: 44 Copynumber: 3.3 Consensus size: 43
3101 GGATGGTGAA
3111 CAAAATTTCATAGGGAGCTTATGAAAATATTATGGAGAGGTTAT
1 CAAAATTTCATAGGGAGCTTATGAAAAT-TTATGGAGAGGTTAT
* * * * * *
3155 CAAAA-TT--TA---ATCTTATCAAAATTTCCTAGGA-TGGTGAA
1 CAAAATTTCATAGGGAGCTTATGAAAATTT-AT-GGAGAGGTTAT
3193 CAAAATTTCATAGGGAGCTTATGAAAATCTTATGGAGAGGTTAT
1 CAAAATTTCATAGGGAGCTTATGAAAAT-TTATGGAGAGGTTAT
*
3237 CAAAATTACATA
1 CAAAATTTCATA
3249 TAGAGAATAT
Statistics
Matches: 71, Mismatches: 13, Indels: 20
0.68 0.12 0.19
Matches are distributed among these distances:
37 2 0.03
38 21 0.30
39 5 0.07
41 4 0.06
43 5 0.07
44 32 0.45
45 2 0.03
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.32
Consensus pattern (43 bp):
CAAAATTTCATAGGGAGCTTATGAAAATTTATGGAGAGGTTAT
Found at i:3314 original size:22 final size:22
Alignment explanation
Indices: 3283--3512 Score: 167
Period size: 22 Copynumber: 10.3 Consensus size: 22
3273 TATAGGGAAT
* *
3283 TTATCGAAATTTCATGGTGTGG
1 TTATCAAAATTTCATAGTGTGG
* *
3305 TTATCAAAATTTTCATAGTGCGA
1 TTATCAAAA-TTTCATAGTGTGG
* * * **
3328 TTA-C-CAATTTTATAATGTAA
1 TTATCAAAATTTCATAGTGTGG
*
3348 TTATCAAAATTTCATAGACAATGAGG
1 TTATCAAAATTTCATAG----TGTGG
* *
3374 TTATCAAAACTTCATTGTGTGG
1 TTATCAAAATTTCATAGTGTGG
* * *
3396 TTATCAGAATTTCACAGTGTGA
1 TTATCAAAATTTCATAGTGTGG
* *
3418 TTATCAAAATTTCACATTGTGG
1 TTATCAAAATTTCATAGTGTGG
* * *
3440 TTATCAAATTTTCATAGGGAGG
1 TTATCAAAATTTCATAGTGTGG
* * *
3462 TTATCAAAATTTCACAATGAGG
1 TTATCAAAATTTCATAGTGTGG
* **
3484 TTATCAAATTTTCGCAGTGTGG
1 TTATCAAAATTTCATAGTGTGG
3506 TTATCAA
1 TTATCAA
3513 TATGTCTACG
Statistics
Matches: 162, Mismatches: 39, Indels: 14
0.75 0.18 0.07
Matches are distributed among these distances:
20 12 0.07
21 3 0.02
22 117 0.72
23 13 0.08
26 17 0.10
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (22 bp):
TTATCAAAATTTCATAGTGTGG
Found at i:4996 original size:19 final size:19
Alignment explanation
Indices: 4972--5009 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
4962 ATTCTAATGT
4972 CTATTCAAATAATTATCTA
1 CTATTCAAATAATTATCTA
4991 CTATTCAAATAATTATCTA
1 CTATTCAAATAATTATCTA
5010 TTGGATCCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.16, G:0.00, T:0.42
Consensus pattern (19 bp):
CTATTCAAATAATTATCTA
Found at i:5814 original size:6 final size:6
Alignment explanation
Indices: 5803--5864 Score: 54
Period size: 6 Copynumber: 10.3 Consensus size: 6
5793 TTACCACTTG
* * * * *
5803 ATTATT ATTATT ATTATA ATTATT GTTATT GTTATT GTTATT GTTATT
1 ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT
*
5851 GA-TATT GTTATT AT
1 -ATTATT ATTATT AT
5865 CAATTAATAT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
6 48 1.00
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (6 bp):
ATTATT
Found at i:5837 original size:12 final size:12
Alignment explanation
Indices: 5822--5862 Score: 73
Period size: 12 Copynumber: 3.4 Consensus size: 12
5812 ATTATTATAA
5822 TTATTGTTATTG
1 TTATTGTTATTG
5834 TTATTGTTATTG
1 TTATTGTTATTG
*
5846 TTATTGATATTG
1 TTATTGTTATTG
5858 TTATT
1 TTATT
5863 ATCAATTAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.20, C:0.00, G:0.15, T:0.66
Consensus pattern (12 bp):
TTATTGTTATTG
Found at i:5843 original size:18 final size:18
Alignment explanation
Indices: 5822--5862 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
5812 ATTATTATAA
*
5822 TTATTGTTATTGTTATTG
1 TTATTGTTATTGATATTG
5840 TTATTGTTATTGATATTG
1 TTATTGTTATTGATATTG
5858 TTATT
1 TTATT
5863 ATCAATTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.20, C:0.00, G:0.15, T:0.66
Consensus pattern (18 bp):
TTATTGTTATTGATATTG
Found at i:19332 original size:6 final size:6
Alignment explanation
Indices: 19321--19375 Score: 51
Period size: 6 Copynumber: 9.5 Consensus size: 6
19311 ACCACACACT
* * * *
19321 GAACCC GAACCC G-ACCC GAGCCC GAGCCC GAGCCC G-ACCC GAGCCC
1 GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC
*
19367 GAAGCC GAA
1 GAACCC GAA
19376 ATAATTTGAA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
5 9 0.21
6 33 0.79
ACGTcount: A:0.25, C:0.47, G:0.27, T:0.00
Consensus pattern (6 bp):
GAACCC
Found at i:19339 original size:11 final size:11
Alignment explanation
Indices: 19323--19368 Score: 74
Period size: 11 Copynumber: 4.1 Consensus size: 11
19313 CACACACTGA
*
19323 ACCCGAACCCG
1 ACCCGAGCCCG
19334 ACCCGAGCCCG
1 ACCCGAGCCCG
19345 AGCCCGAGCCCG
1 A-CCCGAGCCCG
19357 ACCCGAGCCCG
1 ACCCGAGCCCG
19368 A
1 A
19369 AGCCGAAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
11 22 0.67
12 11 0.33
ACGTcount: A:0.22, C:0.52, G:0.26, T:0.00
Consensus pattern (11 bp):
ACCCGAGCCCG
Found at i:19374 original size:12 final size:11
Alignment explanation
Indices: 19325--19374 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
19315 CACACTGAAC
* *
19325 CCGAACCCGAC
1 CCGAGCCCGAG
19336 CCGAGCCCGAG
1 CCGAGCCCGAG
*
19347 CCCGAGCCCGAC
1 -CCGAGCCCGAG
19359 CCGAGCCCGAAG
1 CCGAGCCCG-AG
19371 CCGA
1 CCGA
19375 AATAATTTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
11 18 0.55
12 15 0.45
ACGTcount: A:0.22, C:0.50, G:0.28, T:0.00
Consensus pattern (11 bp):
CCGAGCCCGAG
Found at i:19374 original size:17 final size:16
Alignment explanation
Indices: 19323--19374 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 16
19313 CACACACTGA
* *
19323 ACCCGAACCCGACCCG
1 ACCCGAGCCCGAGCCG
19339 AGCCCGAGCCCGAGCCCG
1 A-CCCGAGCCCGAG-CCG
19357 ACCCGAGCCCGAAGCCG
1 ACCCGAGCCCG-AGCCG
19374 A
1 A
19375 AATAATTTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 1 0.03
17 24 0.77
18 6 0.19
ACGTcount: A:0.23, C:0.50, G:0.27, T:0.00
Consensus pattern (16 bp):
ACCCGAGCCCGAGCCG
Found at i:19374 original size:23 final size:23
Alignment explanation
Indices: 19324--19368 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
19314 ACACACTGAA
19324 CCCGAACCCGACCCGAGCCCGAG
1 CCCGAACCCGACCCGAGCCCGAG
*
19347 CCCGAGCCCGACCCGAGCCCGA
1 CCCGAACCCGACCCGAGCCCGA
19369 AGCCGAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.20, C:0.53, G:0.27, T:0.00
Consensus pattern (23 bp):
CCCGAACCCGACCCGAGCCCGAG
Found at i:19553 original size:2 final size:2
Alignment explanation
Indices: 19546--19580 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
19536 GCTAAACTAC
19546 TA TA TA TA TA T- 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 TA
19581 ACTTAAAGCA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.