Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005866.1 Corchorus capsularis cultivar CVL-1 contig05884, 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: 3627
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Found at i:415 original size:33 final size:32
Alignment explanation
Indices: 225--442 Score: 149
Period size: 33 Copynumber: 6.6 Consensus size: 32
215 GTCACCCATA
* *
225 ATCATATAATTCATATTCAGTAGGGTCACCGGC
1 ATCATATAGTTCATATTCAGTA-GGTCATCGGC
* * * *
258 ATCGTATAATTCATATTTAGTAGGTTCACCGGC
1 ATCATATAGTTCATATTCAGTAGG-TCATCGGC
*
291 ATCATATA-TATCATTTTCAGTAGCGTCATC--C
1 ATCATATAGT-TCATATTCAGTAG-GTCATCGGC
* * *
322 -GCATATAGTTCATATTCAATAAGGTCAACGAG-
1 ATCATATAGTTCATATTCAGT-AGGTCATCG-GC
* * *
354 GTCATATAGTTCATAATCAGTACGGTCATCTGC
1 ATCATATAGTTCATATTCAGTA-GGTCATCGGC
* *
387 ATCATATGGTTCATATTCAGTACGGTCATTCATCAGC
1 ATCATATAGTTCATATTCAGTA-GG----TCATCGGC
*
424 ATCATATAGATCATATTCA
1 ATCATATAGTTCATATTCA
443 ATAAGAGCCA
Statistics
Matches: 149, Mismatches: 21, Indels: 26
0.76 0.11 0.13
Matches are distributed among these distances:
30 20 0.13
31 4 0.03
32 5 0.03
33 95 0.64
34 1 0.01
37 24 0.16
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.34
Consensus pattern (32 bp):
ATCATATAGTTCATATTCAGTAGGTCATCGGC
Found at i:465 original size:26 final size:26
Alignment explanation
Indices: 435--1333 Score: 452
Period size: 26 Copynumber: 32.5 Consensus size: 26
425 TCATATAGAT
* *
435 CATATTCAATAAGAGCCATGTAGTTG
1 CATATTCAGTAGGAGCCATGTAGTTG
* *
461 CATATTTAGTAGGGGCCATGTAGTTG
1 CATATTCAGTAGGAGCCATGTAGTTG
* * *
487 TATATTCAGTAGGAACCATATAGTTG
1 CATATTCAGTAGGAGCCATGTAGTTG
* * *
513 CATATATTTAGTAGG-GATCATATAGTTG
1 C--ATATTCAGTAGGAG-CCATGTAGTTG
* *
541 CATATTCAGTAGG-TCTCATATAGTTG
1 CATATTCAGTAGGAGC-CATGTAGTTG
567 CATATTCAGTAAGG-GCCATGATCATATAGTTG
1 CATATTCAGT-AGGAGCCATG------TAGTTG
*
599 CATATTCAGTAGG-GCTCATATAGTTG
1 CATATTCAGTAGGAGC-CATGTAGTTG
* *
625 CATATTCAGTAGGGGCCATTATCATATAGTTG
1 CATATTCAGTAGGAG-C-----CATGTAGTTG
* *
657 CATATTCAATAGG-GCTCATATAGTTG
1 CATATTCAGTAGGAGC-CATGTAGTTG
* *
683 CATATTCAGTAGG-GATCATATAGTTG
1 CATATTCAGTAGGAG-CCATGTAGTTG
* *
709 CCTATTCAGTAGGGGCCATGATCATATAGTTG
1 CATATTCAGTAGGAGCCATG------TAGTTG
*
741 CATATTCAGTAGG-GCTCATATAGTTG
1 CATATTCAGTAGGAGC-CATGTAGTTG
767 CATATTCAGTAAGG-GCCATGATCATATAGTTG
1 CATATTCAGT-AGGAGCCATG------TAGTTG
*
799 CATATTCAGTAGG-GCTCATATAGTTG
1 CATATTCAGTAGGAGC-CATGTAGTTG
* *
825 CATATTCAGTAGGGGCCATTATCATATAGTTG
1 CATATTCAGTAGGAG-C-----CATGTAGTTG
* *
857 CATATTCAATAGG-GCTCATATAGTTG
1 CATATTCAGTAGGAGC-CATGTAGTTG
* *
883 CATATTCAGTAGG-GATCATATAGTTG
1 CATATTCAGTAGGAG-CCATGTAGTTG
* *
909 CCTATTCAGTAGGGGCCATGATCATATAGTTG
1 CATATTCAGTAGGAGCCATG------TAGTTG
* *
941 CATATTCAGTA-GAGATCATATAGTTG
1 CATATTCAGTAGGAG-CCATGTAGTTG
* * *
967 CATATTCAGTA-GAGATCATATAGCTG
1 CATATTCAGTAGGAG-CCATGTAGTTG
* * *
993 TATATTCAGTAGGGGCCATAATCATATAGTTG
1 CATATTCAGTAGGAG-C-----CATGTAGTTG
* * * *
1025 CATATTCAATAGGGGTCATATAGTTG
1 CATATTCAGTAGGAGCCATGTAGTTG
* *
1051 CATATTCAATAGGGGCCATGATCATATAGTTG
1 CATATTCAGTAGGAGCCATG------TAGTTG
* * *
1083 CATATTTAGTAGGGGCCACGTAGTTG
1 CATATTCAGTAGGAGCCATGTAGTTG
* *
1109 CATATTCAATA-GAGCTCATATAGTTG
1 CATATTCAGTAGGAGC-CATGTAGTTG
* *
1135 CATATTCAGTAGG-GTTCAT-AAGTTG
1 CATATTCAGTAGGAG-CCATGTAGTTG
* *
1160 CATATTCAGTAGG-GATCATATAGTTG
1 CATATTCAGTAGGAG-CCATGTAGTTG
*
1186 CATATTCAGTAGGAGCCATATAGTTG
1 CATATTCAGTAGGAGCCATGTAGTTG
*
1212 CATATTCAGTAGG-GCTCATATAGTTG
1 CATATTCAGTAGGAGC-CATGTAGTTG
1238 CATATTCAGTAGG-GACCATGATCATATAGTTG
1 CATATTCAGTAGGAG-CCATG------TAGTTG
* * *
1270 CATATTTAGTAGGGGCCACGTAGTTG
1 CATATTCAGTAGGAGCCATGTAGTTG
*
1296 CATATTCAGTAGGA-CCATGTAATTG
1 CATATTCAGTAGGAGCCATGTAGTTG
1321 CATATTCAGTAGG
1 CATATTCAGTAGG
1334 TGCATATTCT
Statistics
Matches: 726, Mismatches: 71, Indels: 153
0.76 0.07 0.16
Matches are distributed among these distances:
25 50 0.07
26 424 0.58
27 18 0.02
28 24 0.03
30 2 0.00
31 16 0.02
32 191 0.26
33 1 0.00
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.33
Consensus pattern (26 bp):
CATATTCAGTAGGAGCCATGTAGTTG
Found at i:607 original size:58 final size:54
Alignment explanation
Indices: 455--1333 Score: 777
Period size: 58 Copynumber: 15.9 Consensus size: 54
445 AAGAGCCATG
* * * * * *
455 TAGTTGCATATTTAGTAGGG-G-CCATGTAGTTGTATATTCAGTAGGAACCATA
1 TAGTTGCATATTCAGTAGGGCGATCATATAGTTGCATATTCAGTAGGGATCATA
* **
507 TAGTTGCATATATTTAGTA-GG-GATCATATAGTTGCATATTCAGTAGGTCTCATA
1 TAGTTGC--ATATTCAGTAGGGCGATCATATAGTTGCATATTCAGTAGGGATCATA
*
561 TAGTTGCATATTCAGTAAGGGCCATGATCATATAGTTGCATATTCAGTAGGGCTCATA
1 TAGTTGCATATTCAGT-AGGG-C--GATCATATAGTTGCATATTCAGTAGGGATCATA
* * *
619 TAGTTGCATATTCAGTAGGGGCCATTATCATATAGTTGCATATTCAATAGGGCTCATA
1 TAGTTGCATATTCAGTA-GGG-C--GATCATATAGTTGCATATTCAGTAGGGATCATA
*
677 TAGTTGCATATTCAGTA-GG-GATCATATAGTTGCCTATTCAGTAGGGGCCATGATCATA
1 TAGTTGCATATTCAGTAGGGCGATCATATAGTTGCATATTCAGTA--GG----GATCATA
735 TAGTTGCATATTCAGTAGGGC--TCATATAGTTGCATATTCAGTAAGGGCCATGATCATA
1 TAGTTGCATATTCAGTAGGGCGATCATATAGTTGCATATTCAGT-A-GG----GATCATA
793 TAGTTGCATATTCAGTAGGGC--TCATATAGTTGCATATTCAGTAGGGGCCATTATCATA
1 TAGTTGCATATTCAGTAGGGCGATCATATAGTTGCATATTCAGTA-GGG-----ATCATA
*
851 TAGTTGCATATTCAATAGGGC--TCATATAGTTGCATATTCAGTAGGGATCATA
1 TAGTTGCATATTCAGTAGGGCGATCATATAGTTGCATATTCAGTAGGGATCATA
* *
903 TAGTTGCCTATTCAGTAGGGGCCATGATCATATAGTTGCATATTCAGTAGAGATCATA
1 TAGTTGCATATTCAGTA-GGG-C--GATCATATAGTTGCATATTCAGTAGGGATCATA
* * *
961 TAGTTGCATATTCAGTA--GAGATCATATAGCTGTATATTCAGTAGGGGCCATAATCATA
1 TAGTTGCATATTCAGTAGGGCGATCATATAGTTGCATATTCAGTA-GGG-----ATCATA
* *
1019 TAGTTGCATATTCAATAGGG-G-TCATATAGTTGCATATTCAATAGGGGCCATGATCATA
1 TAGTTGCATATTCAGTAGGGCGATCATATAGTTGCATATTCAGTA--GG----GATCATA
* * ** * * *
1077 TAGTTGCATATTTAGTAGGG-G-CCACGTAGTTGCATATTCAATAGAGCTCATA
1 TAGTTGCATATTCAGTAGGGCGATCATATAGTTGCATATTCAGTAGGGATCATA
*
1129 TAGTTGCATATTCAGTA-GG-GTTCATA-AGTTGCATATTCAGTAGGGATCATA
1 TAGTTGCATATTCAGTAGGGCGATCATATAGTTGCATATTCAGTAGGGATCATA
*
1180 TAGTTGCATATTCAGTAGGAGC---CATATAGTTGCATATTCAGTAGGGCTCATA
1 TAGTTGCATATTCAGTAGG-GCGATCATATAGTTGCATATTCAGTAGGGATCATA
* ** **
1232 TAGTTGCATATTCAGTAGGGACCATGATCATATAGTTGCATATTTAGTAGGGGCCACG
1 TAGTTGCATATTCAGTAGGG--C--GATCATATAGTTGCATATTCAGTAGGGATCATA
* * *
1290 TAGTTGCATATTCAGTA--G-GACCATGTAATTGCATATTCAGTAGG
1 TAGTTGCATATTCAGTAGGGCGATCATATAGTTGCATATTCAGTAGG
1334 TGCATATTCT
Statistics
Matches: 720, Mismatches: 52, Indels: 111
0.82 0.06 0.13
Matches are distributed among these distances:
51 69 0.10
52 147 0.20
53 12 0.02
54 47 0.07
55 1 0.00
56 4 0.01
57 8 0.01
58 423 0.59
59 7 0.01
60 1 0.00
63 1 0.00
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.34
Consensus pattern (54 bp):
TAGTTGCATATTCAGTAGGGCGATCATATAGTTGCATATTCAGTAGGGATCATA
Found at i:626 original size:84 final size:84
Alignment explanation
Indices: 503--1331 Score: 838
Period size: 84 Copynumber: 9.9 Consensus size: 84
493 CAGTAGGAAC
* * *
503 CATATAGTTGCATATATTTAGTAGGGATCATATAGTTGCATATTCAGTAGGTCTCATATAGTTGC
1 CATATAGTTGC--ATATTCAGTAGGGCTCATATAGTTGCATATTCAGTAGGTATCATATAGTTGC
568 ATATTCAGTAAGGGCCATGAT
64 ATATTCAGTAAGGGCCATGAT
589 CATATAGTTGCATATTCAGTAGGGCTCATATAGTTGCATATTCAGTAGGGGCCATTATCATATAG
1 CATATAGTTGCATATTCAGTAGGGCTCATATAGTTGCATATTCAGTA--GG----TATCATATAG
*
654 TTGCATATTCAAT-AGGG-C----T
60 TTGCATATTCAGTAAGGGCCATGAT
* *
673 CATATAGTTGCATATTCAGTAGGGATCATATAGTTGCCTATTCAGTAGGGGCCATGATCATATAG
1 CATATAGTTGCATATTCAGTAGGGCTCATATAGTTGCATATTCAGTA--GG---T-ATCATATAG
738 TTGCATATTCAGT-AGGG-C----T
60 TTGCATATTCAGTAAGGGCCATGAT
**
757 CATATAGTTGCATATTCAGTAAGGGCCATGATCATATAGTTGCATATTCAGTAGGGCTCATATAG
1 CATATAGTTGCATATTCAGT-AGGG-C----TCATATAGTTGCATATTCAGTAGGTATCATATAG
* *
822 TTGCATATTCAGTAGGGGCCATTAT
60 TTGCATATTCAGTAAGGGCCATGAT
* * *
847 CATATAGTTGCATATTCAATAGGGCTCATATAGTTGCATATTCAGTAGGGATCATATAGTTGCCT
1 CATATAGTTGCATATTCAGTAGGGCTCATATAGTTGCATATTCAGTAGGTATCATATAGTTGCAT
*
912 ATTCAGTAGGGGCCATGAT
66 ATTCAGTAAGGGCCATGAT
* * * *
931 CATATAGTTGCATATTCAGTAGAGATCATATAGTTGCATATTCAGTAGAG-ATCATATAGCTGTA
1 CATATAGTTGCATATTCAGTAGGGCTCATATAGTTGCATATTCAGTAG-GTATCATATAGTTGCA
* *
995 TATTCAGTAGGGGCCATAAT
65 TATTCAGTAAGGGCCATGAT
* * *
1015 CATATAGTTGCATATTCAATAGGGGTCATATAGTTGCATATTCAATAGGGGCCATGATCATATAG
1 CATATAGTTGCATATTCAGTAGGGCTCATATAGTTGCATATTCAGTA--GG---T-ATCATATAG
* *
1080 TTGCATATTTAGTAGGGGCC---A-
60 TTGCATATTCAGTAAGGGCCATGAT
* * *
1101 C--GTAGTTGCATATTCAATAGAGCTCATATAGTTGCATATTCAGTAGGGT-TCATA-AGTTGCA
1 CATATAGTTGCATATTCAGTAGGGCTCATATAGTTGCATATTCAGTA-GGTATCATATAGTTGCA
1162 TATTCAGT-A-GG----GAT
65 TATTCAGTAAGGGCCATGAT
**
1176 CATATAGTTGCATATTCAGTAGGAGC-CATATAGTTGCATATTCAGTAGGGCTCATATAGTTGCA
1 CATATAGTTGCATATTCAGTAGG-GCTCATATAGTTGCATATTCAGTAGGTATCATATAGTTGCA
1240 TATTCAGT-AGGGACCATGAT
65 TATTCAGTAAGGG-CCATGAT
* ** * * *
1260 CATATAGTTGCATATTTAGTAGGGGC-CACGTAGTTGCATATTCAGTAGG-ACCATGTAATTGCA
1 CATATAGTTGCATATTCAGTA-GGGCTCATATAGTTGCATATTCAGTAGGTATCATATAGTTGCA
1323 TATTCAGTA
65 TATTCAGTA
1332 GGTGCATATT
Statistics
Matches: 652, Mismatches: 49, Indels: 86
0.83 0.06 0.11
Matches are distributed among these distances:
74 1 0.00
75 3 0.00
76 2 0.00
77 57 0.09
78 23 0.04
79 2 0.00
80 1 0.00
83 23 0.04
84 412 0.63
85 11 0.02
86 16 0.02
87 1 0.00
88 4 0.01
89 8 0.01
90 88 0.13
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.34
Consensus pattern (84 bp):
CATATAGTTGCATATTCAGTAGGGCTCATATAGTTGCATATTCAGTAGGTATCATATAGTTGCAT
ATTCAGTAAGGGCCATGAT
Found at i:3443 original size:324 final size:321
Alignment explanation
Indices: 2785--3627 Score: 1180
Period size: 324 Copynumber: 2.6 Consensus size: 321
2775 GGGGCCCGAA
* * * * * * *
2785 AACGCATTTTTAACCTAAAACCGTGAT-GCTTAGTACACGATTTCGGTTAAAAACTGACCAGAAA
1 AACGCGTTTTTAGCCAAAAACCATGATAG-TTTGTACACGATTTCGG-CAAAAACTGACCCGAAA
* *
2849 TATTTTTCTCAATTTTTTGCCACAATACTCAG--AAAAAATATATAATTC-GACGCAAAAAAAAA
64 TATTTTTCTCAATTTTTTTCCACAATACTTAGAAAAAAAATATATAATTCAG-CGC--AAAAAAA
* * * *
2911 AATTTGTAGGGCTTTTCA-CACTTCT-AATATCGTTTTCCATTCTTTTCAGAATTTATTTCTAAT
126 AA-TTGTAGGGGTTTTCAGCA-TT-TAAATATCGTTTTTCTTTTTTTTCAGAATTTATTTCTAAT
* *
2974 TATATCGAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTG
188 TATATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTCG
* *
3039 GTTAGATGAATATACATATTTCAAGGAGACATTTTGCCAAAAACCATGCAAAACTGGGCCGTGGC
253 GTTAGATGAATATACATATTTCAAGGAGACATTCTGCCAAAAACAATGCAAAACTGGGCCGTGGC
*
3104 CCGG
318 CCCG
* *
3108 AACGTGTTTTTAGCCAAAAACCAATGATAGTTTCGTACACGATTTTTGGCAAAAACTGACCCGAA
1 AACGCGTTTTTAGCCAAAAACC-ATGATAGTTT-GTACACGA-TTTCGGCAAAAACTGACCCG-A
* *
3173 AATTTTTTTCTCAATTTTTTTCCACAATAGTTAGAAAAAAAATATATAATTCAGCGCAAAAAAAA
62 AATATTTTTCTCAATTTTTTTCCACAATACTTAGAAAAAAAATATATAATTCAGCGCAAAAAAAA
*
3238 ATT-TAGGGGTTTTCAGTATTTAAATATCGTTTTTCTTTTTTTTCAGAATTTATTTCTAATTATA
127 ATTGTAGGGGTTTTCAGCATTTAAATATCGTTTTTCTTTTTTTTCAGAATTTATTTCTAATTATA
*
3302 TCGAAACAAGATTCAGATTCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTCGGTTC
192 TCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTCGGTT-
* * *
3367 A-TTGAATATAGATATTTCAAGGAGACATTCTGCCAAAAACAATGCAAAACTGGGTCGTGGCCCC
256 AGATGAATATACATATTTCAAGGAGACATTCTGCCAAAAACAATGCAAAACTGGGCCGTGGCCCC
3431 G
321 G
* * *
3432 AACGCGTTTTTAGCCAAAAACCGTGATAGTTTGTACACGATTTCGGCTAAAACAGACCCGAAATA
1 AACGCGTTTTTAGCCAAAAACCATGATAGTTTGTACACGATTTCGGCAAAAACTGACCCGAAATA
* *
3497 TTTTTCTCAATTTTTTTCCACAATACTTAGAAAAAAAAATATATAATTCAGGGCAAAAAAAATTT
66 TTTTTCTCAATTTTTTTCCACAATACTTAG-AAAAAAAATATATAATTCAGCGCAAAAAAAA-AT
3562 TGTAGGGGTTTTCAGCATTTAAATATCGTTTTTCATTTTTTTTTTCAGAATTTATTTCTAATTAT
129 TGTAGGGGTTTTCAGCATTTAAATATCGTTTTTC---TTTTTTTTCAGAATTTATTTCTAATTAT
3627 A
191 A
Statistics
Matches: 466, Mismatches: 37, Indels: 31
0.87 0.07 0.06
Matches are distributed among these distances:
320 33 0.07
321 47 0.10
322 10 0.02
323 59 0.13
324 198 0.42
325 25 0.05
326 74 0.16
328 19 0.04
329 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.34
Consensus pattern (321 bp):
AACGCGTTTTTAGCCAAAAACCATGATAGTTTGTACACGATTTCGGCAAAAACTGACCCGAAATA
TTTTTCTCAATTTTTTTCCACAATACTTAGAAAAAAAATATATAATTCAGCGCAAAAAAAAATTG
TAGGGGTTTTCAGCATTTAAATATCGTTTTTCTTTTTTTTCAGAATTTATTTCTAATTATATCGA
AACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTCGGTTAGATG
AATATACATATTTCAAGGAGACATTCTGCCAAAAACAATGCAAAACTGGGCCGTGGCCCCG
Done.