Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022222.1 Corchorus olitorius cultivar O-4 contig22255, 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: 17376
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:2953 original size:22 final size:22
Alignment explanation
Indices: 2928--3517 Score: 375
Period size: 22 Copynumber: 27.0 Consensus size: 22
2918 GATAATCTTT
*
2928 CTATGAAATTTTGTTAACCACA
1 CTATGAAATTTTGATAACCACA
* *
2950 CTAT-AAAATTTGATAACCTC-
1 CTATGAAATTTTGATAACCACA
* *
2970 CTTATGAAATTTCGATAAGCACA
1 C-TATGAAATTTTGATAACCACA
* ** * *
2993 CCATGAAACATGGATAACCTTC-
1 CTATGAAATTTTGATAACC-ACA
*
3015 CTATGTAATTTTTG-TAACCACA
1 CTATG-AAATTTTGATAACCACA
* * *
3037 TTGTGAAATTTTGATAACCTC-
1 CTATGAAATTTTGATAACCACA
***
3058 CATATGAAA-TTTGATAACCTTT
1 C-TATGAAATTTTGATAACCACA
3080 CTATGAAATTTTGATAACCACA
1 CTATGAAATTTTGATAACCACA
3102 CTATGAAATTTT-AGTAA-CATC-
1 CTATGAAATTTTGA-TAACCA-CA
* * *
3123 CTTATAAAATTTTGTTAA-CA-T
1 C-TATGAAATTTTGATAACCACA
* * *
3144 CTATGAAAATTTAATAATCACA
1 CTATGAAATTTTGATAACCACA
* *
3166 CTATGAAATTTTGGTAACCTCA
1 CTATGAAATTTTGATAACCACA
* * *
3188 TTATAAAATTTTAATAACCACA
1 CTATGAAATTTTGATAACCACA
*
3210 CTATGAAAATTTTGAT-ACTCTCA
1 CTATG-AAATTTTGATAAC-CACA
*
3233 CTATTAAAATTTTGATAACCACA
1 CTA-TGAAATTTTGATAACCACA
*
3256 TTATGAAAATTTT-ATAA-CATTC-
1 CTATG-AAATTTTGATAACCA--CA
* **
3278 CT-TAAAATTTTGATAACC-TT
1 CTATGAAATTTTGATAACCACA
* * *
3298 CTCA-AAACATTTTGATAACCTCC
1 CT-ATGAA-ATTTTGATAACCACA
*
3321 CTATGAAATTTCGAT-ACCACA
1 CTATGAAATTTTGATAACCACA
*
3342 CTATGAAATTTTGATAACCTTC-
1 CTATGAAATTTTGATAACC-ACA
*
3364 CTATG-AATTTTGGTAACCACA
1 CTATGAAATTTTGATAACCACA
*
3385 CTATGAAATTTTGATAACCACC
1 CTATGAAATTTTGATAACCACA
*
3407 CTATGAAATTTTTG-TAACTACA
1 CTATGAAA-TTTTGATAACCACA
* * **
3429 CTA-CAAGATTGTGATAACTTC-
1 CTATGAA-ATTTTGATAACCACA
* *
3450 CTTACGAAATTTTGATAACTACA
1 C-TATGAAATTTTGATAACCACA
*
3473 GTATGAAATTTTGATAA-CAGCA
1 CTATGAAATTTTGATAACCA-CA
*
3495 CTATGAAATTTTGATAACTACA
1 CTATGAAATTTTGATAACCACA
3517 C
1 C
3518 AGAGACGACA
Statistics
Matches: 442, Mismatches: 82, Indels: 88
0.72 0.13 0.14
Matches are distributed among these distances:
20 23 0.05
21 102 0.23
22 257 0.58
23 57 0.13
24 3 0.01
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCACA
Found at i:2963 original size:43 final size:44
Alignment explanation
Indices: 2915--3517 Score: 385
Period size: 43 Copynumber: 13.8 Consensus size: 44
2905 GTTCATCACT
* * *
2915 TTTGATAATCTTTCTATGAAATTTTGTTAACCACACTAT-AAAA
1 TTTGATAACCTTCCTATGAAATTTTGATAACCACACTATGAAAA
* * *
2958 TTTGATAACC-TCCTTATGAAATTTCGATAAGCACACCATGAAACA
1 TTTGATAACCTTCC-TATGAAATTTTGATAACCACACTATGAAA-A
* * * * *
3003 -TGGATAACCTTCCTATGTAATTTTTG-TAACCACATTGTGAAAT
1 TTTGATAACCTTCCTATG-AAATTTTGATAACCACACTATGAAAA
*** *
3046 TTTGATAACC-TCCATATGAAA-TTTGATAACCTTTCTATGAAAT
1 TTTGATAACCTTCC-TATGAAATTTTGATAACCACACTATGAAAA
*
3089 TTTGATAACC-ACACTATGAAATTTT-AGTAA-CATC-CTTAT-AAAA
1 TTTGATAACCTTC-CTATGAAATTTTGA-TAACCA-CAC-TATGAAAA
* * * * * *
3132 TTTTGTTAA-CAT-CTATGAAAATTTAATAATCACACTATGAAAT
1 -TTTGATAACCTTCCTATGAAATTTTGATAACCACACTATGAAAA
* * * *
3175 TTTGGTAACC-TCATTATAAAATTTTAATAACCACACTATGAAAA
1 TTTGATAACCTTC-CTATGAAATTTTGATAACCACACTATGAAAA
* *
3219 TTTTGAT-A-CTCTCACTATTAAAATTTTGATAACCACATTATGAAAA
1 -TTTGATAACCT-TC-CTA-TGAAATTTTGATAACCACACTATGAAAA
* * * **
3265 TTTTATAACATTCCT-TAAAATTTTGATAACC-TTCTCA--AAACA
1 TTTGATAACCTTCCTATGAAATTTTGATAACCACACT-ATGAAA-A
* * *
3307 TTTTGATAACCTCCCTATGAAATTTCGAT-ACCACACTATGAAAT
1 -TTTGATAACCTTCCTATGAAATTTTGATAACCACACTATGAAAA
* *
3351 TTTGATAACCTTCCTATG-AATTTTGGTAACCACACTATGAAAT
1 TTTGATAACCTTCCTATGAAATTTTGATAACCACACTATGAAAA
** * * *
3394 TTTGATAACCACCCTATGAAATTTTTG-TAACTACACTA-CAAGA
1 TTTGATAACCTTCCTATGAAA-TTTTGATAACCACACTATGAAAA
* * * *
3437 TTGTGATAA-CTTCCTTACGAAATTTTGATAACTACAGTATGAAAT
1 TT-TGATAACCTTCC-TATGAAATTTTGATAACCACACTATGAAAA
** *
3482 TTTGATAA-CAGCACTATGAAATTTTGATAACTACAC
1 TTTGATAACCTTC-CTATGAAATTTTGATAACCACAC
3518 AGAGACGACA
Statistics
Matches: 445, Mismatches: 72, Indels: 85
0.74 0.12 0.14
Matches are distributed among these distances:
41 3 0.01
42 41 0.09
43 174 0.39
44 157 0.35
45 40 0.09
46 29 0.07
47 1 0.00
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (44 bp):
TTTGATAACCTTCCTATGAAATTTTGATAACCACACTATGAAAA
Found at i:3098 original size:65 final size:65
Alignment explanation
Indices: 2929--3512 Score: 260
Period size: 65 Copynumber: 8.9 Consensus size: 65
2919 ATAATCTTTC
* ** * * * * *
2929 TATGAAATTTTGTTAACCACACTAT-AAAATTTGATAACCTCCTTATGAAATTTCGATAAGCACA
1 TATGAAA-TTTGATAACCTTACTATGAAATTTTGATAACCACATTATGAAATTTTGATAA-C-CT
2993 CC-
63 CCA
* * * * *
2995 -ATGAAACATGGATAACCTTCCTATGTAATTTTTG-TAACCACATTGTGAAATTTTGATAACCTC
1 TATGAAA-TTTGATAACCTTACTATG-AAATTTTGATAACCACATTATGAAATTTTGATAACCTC
3058 CA
64 CA
* * *
3060 TATGAAATTTGATAACCTTTCTATGAAATTTTGATAACCACACTATGAAATTTT-AGTAACATCC
1 TATGAAATTTGATAACCTTACTATGAAATTTTGATAACCACATTATGAAATTTTGA-TAACCTCC
*
3124 T
65 A
* * * * * * * *
3125 TATAAAATTTTGTTAA-CAT-CTATGAAAATTTAATAATCACACTATGAAATTTTGGTAACCT-C
1 TATGAAA-TTTGATAACCTTACTATGAAATTTTGATAACCACATTATGAAATTTTGATAACCTCC
3187 A
65 A
* * ** *
3188 TTATAAAATTTTAATAACCACACTATGAAAATTTTGATACTCTCACTATTA--AAATTTTGATAA
1 -TATGAAA-TTTGATAACCTTACTATG-AAATTTTGATA-AC-CAC-ATTATGAAATTTTGATAA
*
3251 CC-ACA
60 CCTCCA
* * * * * * *
3256 TTATGAAAATTTTATAACATTCCT-TAAAATTTTGATAACCTTC-TCA-AAACATTTTGATAACC
1 -TATG-AAATTTGATAACCTTACTATGAAATTTTGATAACC-ACATTATGAA-ATTTTGATAACC
*
3318 TCCC
62 TCCA
** * * * *
3322 TATGAAATTTCGAT-ACCACACTATGAAATTTTGATAACCTTC-CTATG-AATTTTGGTAACC-A
1 TATGAAATTT-GATAACCTTACTATGAAATTTTGATAACC-ACATTATGAAATTTTGATAACCTC
3383 CA
64 CA
*** * * * * *
3385 CTATGAAATTTTGATAACCACCCTATGAAATTTTTG-TAACTACACTA-CAAGATTGTGATAACT
1 -TATGAAA-TTTGATAACCTTACTATGAAA-TTTTGATAACCACATTATGAA-ATTTTGATAACC
*
3448 TCCT
62 TCCA
* *
3452 TACGAAATTTTGATAA-C-TACAGTATGAAATTTTGATAA-CAGCACTATGAAATTTTGATAAC
1 TATGAAA-TTTGATAACCTTAC--TATGAAATTTTGATAACCA-CATTATGAAATTTTGATAAC
3513 TACACAGAGA
Statistics
Matches: 402, Mismatches: 79, Indels: 74
0.72 0.14 0.13
Matches are distributed among these distances:
63 4 0.01
64 97 0.24
65 139 0.35
66 105 0.26
67 19 0.05
68 29 0.07
69 6 0.01
70 3 0.01
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (65 bp):
TATGAAATTTGATAACCTTACTATGAAATTTTGATAACCACATTATGAAATTTTGATAACCTCCA
Found at i:3173 original size:64 final size:64
Alignment explanation
Indices: 3079--3199 Score: 188
Period size: 64 Copynumber: 1.9 Consensus size: 64
3069 TGATAACCTT
* * *
3079 TCTATGAAATTTTGATAACCACACTATGAAATTTTAGTAACATCCTTATAAAATTTTGTTAACA
1 TCTATGAAAATTTAATAACCACACTATGAAATTTTAGTAACATCATTATAAAATTTTGTTAACA
* * *
3143 TCTATGAAAATTTAATAATCACACTATGAAATTTTGGTAACCTCATTATAAAATTTT
1 TCTATGAAAATTTAATAACCACACTATGAAATTTTAGTAACATCATTATAAAATTTT
3200 AATAACCACA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
64 51 1.00
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.40
Consensus pattern (64 bp):
TCTATGAAAATTTAATAACCACACTATGAAATTTTAGTAACATCATTATAAAATTTTGTTAACA
Found at i:4176 original size:13 final size:13
Alignment explanation
Indices: 4158--4183 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4148 GGTTTATATT
4158 ATACTAGTACTAG
1 ATACTAGTACTAG
4171 ATACTAGTACTAG
1 ATACTAGTACTAG
4184 TATTTAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATACTAGTACTAG
Found at i:4447 original size:42 final size:44
Alignment explanation
Indices: 4396--4489 Score: 140
Period size: 45 Copynumber: 2.2 Consensus size: 44
4386 AGTGCATTAC
*
4396 CTAA-ATTCTA-C-TCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTTCCATCTCTAGATAATTCATCAAAATAAAG
4437 CTAATATTCTACTCTTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTAC-CTTCCATCTCTAGATAATTCATCAAAATAAAG
*
4482 TTAATATT
1 CTAATATT
4490 AATTGTTGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
44 1 0.02
45 36 0.77
ACGTcount: A:0.38, C:0.20, G:0.05, T:0.36
Consensus pattern (44 bp):
CTAATATTCTACCTTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:5258 original size:22 final size:23
Alignment explanation
Indices: 5232--5277 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
5222 TAATTTCTAT
5232 ACACAATTAAT-ATATAAT-TAAA
1 ACACAATTAATCATA-AATATAAA
*
5254 ACACACTTAATCATAAATATAAA
1 ACACAATTAATCATAAATATAAA
5277 A
1 A
5278 ATAGTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.59, C:0.13, G:0.00, T:0.28
Consensus pattern (23 bp):
ACACAATTAATCATAAATATAAA
Found at i:6032 original size:97 final size:102
Alignment explanation
Indices: 5836--6037 Score: 263
Period size: 104 Copynumber: 2.0 Consensus size: 102
5826 TAATGGCCCA
* *
5836 CTTCCTAGACTAAAGACTAAAGAGCAAAAGTGGTTCCAGAAAAGAACCAAAATAAAAGGGATGAC
1 CTTCCTAGACCAAAGACTAAAGAGCAAAAGGGGTTCCAGAAAAGAACCAAAATAAAA--GATGAC
* *
5901 ATTTATATGACACTAAGCATAGCATAATTTCAAATAATG
64 ATCTATATGACACTAAACATAGCATAATTTCAAATAATG
** * *
5940 CTTCCTAGACCAAAGACTAAAGAGCAAGTGGGGTTCCA-AAAA-ACCCCAAAA-CAAA-ATGACA
1 CTTCCTAGACCAAAGACTAAAGAGCAAAAGGGGTTCCAGAAAAGA-ACCAAAATAAAAGATGACA
6001 -CTA-ATGACACTAAACATAGCATAATTTCAAATAATG
65 TCTATATGACACTAAACATAGCATAATTTCAAATAATG
6037 C
1 C
6038 ATATCTTTGC
Statistics
Matches: 89, Mismatches: 8, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
97 33 0.37
98 2 0.02
99 6 0.07
102 4 0.04
103 10 0.11
104 34 0.38
ACGTcount: A:0.46, C:0.19, G:0.15, T:0.20
Consensus pattern (102 bp):
CTTCCTAGACCAAAGACTAAAGAGCAAAAGGGGTTCCAGAAAAGAACCAAAATAAAAGATGACAT
CTATATGACACTAAACATAGCATAATTTCAAATAATG
Found at i:8107 original size:18 final size:19
Alignment explanation
Indices: 8086--8121 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
8076 TTCTATTTCT
*
8086 ATTG-ATTTTATTTTTAAA
1 ATTGCATTTCATTTTTAAA
8104 ATTGCATTTCATTTTTAA
1 ATTGCATTTCATTTTTAA
8122 TATTTTTGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.58
Consensus pattern (19 bp):
ATTGCATTTCATTTTTAAA
Found at i:14335 original size:30 final size:29
Alignment explanation
Indices: 14239--14399 Score: 98
Period size: 29 Copynumber: 5.4 Consensus size: 29
14229 GCTAATCACC
*
14239 CAAATAAAGGCCTAACGTTTGTCAAAATGCT
1 CAAATAAGGGCCTAACG-TT-TCAAAATGCT
** * * *
14270 CAAATAAGGGTTTGATC-TTTTAATATGAC-
1 CAAATAAGGGCCT-AACGTTTCAAAATG-CT
14299 CAAATAAGGGCCTAACGTTATCAAAATGCT
1 CAAATAAGGGCCTAACGTT-TCAAAATGCT
* * * **
14329 CAAATAAGGGACCGATC-TTTTAATTTGAC-
1 CAAATAAGGG-CCTAACGTTTCAAAATG-CT
* *
14358 CAAATAAGGGCCTAATG-TTCGAAAATTCT
1 CAAATAAGGGCCTAACGTTTC-AAAATGCT
14387 CAAATAAGGGCCT
1 CAAATAAGGGCCT
14400 GGTGTCAATT
Statistics
Matches: 97, Mismatches: 23, Indels: 22
0.68 0.16 0.15
Matches are distributed among these distances:
28 8 0.08
29 51 0.53
30 22 0.23
31 14 0.14
32 2 0.02
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.28
Consensus pattern (29 bp):
CAAATAAGGGCCTAACGTTTCAAAATGCT
Found at i:14337 original size:59 final size:58
Alignment explanation
Indices: 14238--14396 Score: 212
Period size: 59 Copynumber: 2.7 Consensus size: 58
14228 GGCTAATCAC
* ***
14238 CCAAATAAAGGCCTAACGTTTGTCAAAATGCTCAAATAAGGGTTTGATCTTTTAATATGA
1 CCAAATAAGGGCCTAACG-TT-TCAAAATGCTCAAATAAGGGACCGATCTTTTAATATGA
*
14298 CCAAATAAGGGCCTAACGTTATCAAAATGCTCAAATAAGGGACCGATCTTTTAATTTGA
1 CCAAATAAGGGCCTAACGTT-TCAAAATGCTCAAATAAGGGACCGATCTTTTAATATGA
* *
14357 CCAAATAAGGGCCTAATG-TTCGAAAATTCTCAAATAAGGG
1 CCAAATAAGGGCCTAACGTTTC-AAAATGCTCAAATAAGGG
14397 CCTGGTGTCA
Statistics
Matches: 90, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
57 2 0.02
58 18 0.20
59 53 0.59
60 17 0.19
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.28
Consensus pattern (58 bp):
CCAAATAAGGGCCTAACGTTTCAAAATGCTCAAATAAGGGACCGATCTTTTAATATGA
Found at i:14536 original size:31 final size:29
Alignment explanation
Indices: 14498--14604 Score: 94
Period size: 31 Copynumber: 3.6 Consensus size: 29
14488 CTAAAAGACC
*
14498 AGACCCTTATTTGAGCATTTTCGATAACGTT
1 AGACCCTTATTTGAGCATTTT-GA-AAAGTT
** *
14529 AGACCCTTATTTG-GCCAAATT-AAAAGATG
1 AGACCCTTATTTGAG-CATTTTGAAAAG-TT
14558 AGA-CCTTATTTGAGCATTTTGGAAAATGTT
1 AGACCCTTATTTGAGCATTTT-GAAAA-GTT
*
14588 AGGCCCTTATTTGAGCA
1 AGACCCTTATTTGAGCA
14605 ATTAGCCTAC
Statistics
Matches: 61, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
28 16 0.26
29 6 0.10
30 8 0.13
31 31 0.51
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35
Consensus pattern (29 bp):
AGACCCTTATTTGAGCATTTTGAAAAGTT
Found at i:14536 original size:60 final size:60
Alignment explanation
Indices: 14436--14600 Score: 224
Period size: 60 Copynumber: 2.8 Consensus size: 60
14426 ATTTTTTAAG
* * * *
14436 CCAGACCCTTATTTGAACATTTTCAATAACGCTAGGCCCTTATTTGGCTAAACTAAAAGA
1 CCAGACCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAACTAAAAGA
* *
14496 CCAGACCCTTATTTGAGCATTTTCGATAACGTTAGACCCTTATTTGGCCAAATTAAAAGA
1 CCAGACCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAACTAAAAGA
** * * *
14556 TGAGA-CCTTATTTGAGCATTTTGGAAAATGTTAGGCCCTTATTTG
1 CCAGACCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTG
14601 AGCAATTAGC
Statistics
Matches: 93, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
59 36 0.39
60 57 0.61
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.33
Consensus pattern (60 bp):
CCAGACCCTTATTTGAGCATTTTCGATAACGTTAGGCCCTTATTTGGCCAAACTAAAAGA
Found at i:15640 original size:24 final size:24
Alignment explanation
Indices: 15593--15643 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
15583 GAAGGAAAAA
*
15593 AAAAACTTGCACTAGGGAAGGACT
1 AAAAACTTGCACTAGGGAAAGACT
15617 AAAAACTTGCACTA-GGACAAGACT
1 AAAAACTTGCACTAGGGA-AAGACT
15641 AAA
1 AAA
15644 CTCTAAATCT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 3 0.12
24 22 0.88
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.16
Consensus pattern (24 bp):
AAAAACTTGCACTAGGGAAAGACT
Done.