Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006240.1 Corchorus capsularis cultivar CVL-1 contig06259, 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, 641
Length: 1069
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.22
Found at i:399 original size:155 final size:154
Alignment explanation
Indices: 1--1067 Score: 1538
Period size: 158 Copynumber: 6.8 Consensus size: 154
*
1 ATGAGCTAAAAACTTCACAATGGACTAATCTCACTAAAATGATTATAGTTAGGTCGTAAACAATT
1 ATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGTCGTAAACAATT
* *
66 GAAAGAAAAGCTTTTGTGGTTTGACCAAAATCGAAGCCGATTTCAAAACAACACTAATGGGCCCC
66 AAAAGAAAAGC-TTTGTGGTTTG-CC-AAATCGAAGCCGA-TTCAAAACAGCACTAATGGGCCCC
* *
131 GAAAGGCCCGAAATAACAAGGGTTCTGA
127 GAAAGGCCCAAAATAACAAGTGTTCTGA
*
159 ATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAAACAAT
1 ATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGTCGT-AAACAAT
*
224 TGAAAAG-AAAGCTTTATGGTTTGCCAAATCGAAGCCGATTCAAAACAGCACTAATGGGCCCCGA
65 T-AAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGCCGATTCAAAACAGCACTAATGGGCCCCGA
288 AAGGCCCAAAATAACAAGTGTTCTGA
129 AAGGCCCAAAATAACAAGTGTTCTGA
*
314 AGTGAGACTAAAAACTTCACAACGGACTAATCTCACCAAAATGATTATAGTTAGGTCGTAAAACA
1 A-TGAG-CTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGTCGT-AAACA
*
379 ATT-AAAG-AAAGCTTTGTGGTTTGCCAAATCGAAGCCGATTCAAAACAGCACTAACGGGCCCC-
63 ATTAAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGCCGATTCAAAACAGCACTAATGGGCCCCG
* *
441 AAAGACCCGAAATAACAAGTGTTCTGA
128 AAAGGCCCAAAATAACAAGTGTTCTGA
* * *
468 ATGAGCTAAAAACTTCACAACGGACTAATCTCACCAAAATGATTATAGTTAGGCCGTAAAAAAAT
1 ATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGTCGT-AAACAAT
* * * *
533 TGAAAGAAAAGCTTTGCGCTTTCCCAAACTCGAAGCCGATTCAAAACAGCACTAATGGGCCCCCG
65 TAAAAGAAAAGCTTTGTGGTTTGCCAAA-TCGAAGCCGATTCAAAACAGCACTAATGGG-CCCCG
598 AAAAGGCCCCGAAAA-AACAAGTGTTCTGA
128 -AAAGG-CCC-AAAATAACAAGTGTTCTGA
** * *
627 ATGAGCTAAAAACTTCACGTTGGACTAGTCTCACCAAAATGATTATTGTTAGGTCGTAAACAATT
1 ATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGTCGTAAACAATT
* **
692 AAAAGAAAAGCTTTGTAGGTTTGCCAAATCGAAGCCGATTACAAAACAGCACTAACGGGTTCCGA
66 AAAAGAAAAGCTTTGT-GGTTTGCCAAATCGAAGCCGATT-CAAAACAGCACTAATGGGCCCCGA
* *
757 AAGACCCGAAATAACAAGTGTTCTGA
129 AAGGCCCAAAATAACAAGTGTTCTGA
* * * *
783 ATGAGCGAAAAACTTCACAGTGGACTAATCTCACCAAAATGATAATACGTTAGGCCGTAAACAAT
1 ATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATA-GTTAGGTCGTAAACAAT
* *
848 TAGAAAGAAAAGCTTTATGG-TTCCCAAATCGGAACGACCGACTTACAAAACAGCACTAATGGGC
65 TA-AAAGAAAAGCTTTGTGGTTTGCCAAATC-GAA-G-CCGA-TT-CAAAACAGCACTAATGGGC
912 CCCGAAAGGCCCGAAAA-AACAAGTGTTCTGA
124 CCCGAAAGGCCC-AAAATAACAAGTGTTCTGA
*
943 ATGAGCTAAAAACTTCACGATGGACTAATCTCACC-AAATGATTATAGTTAGGTCGTAAACAATT
1 ATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGTCGTAAACAATT
*
1007 AAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGCCGATTCAAAACAGCACTAACGGGCCCC
66 AAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGCCGATTCAAAACAGCACTAATGGGCCCC
1068 CG
Statistics
Matches: 827, Mismatches: 59, Indels: 51
0.88 0.06 0.05
Matches are distributed among these distances:
152 59 0.07
153 29 0.04
154 46 0.06
155 143 0.17
156 89 0.11
157 107 0.13
158 147 0.18
159 121 0.15
160 83 0.10
161 3 0.00
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.22
Consensus pattern (154 bp):
ATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGTCGTAAACAATT
AAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGCCGATTCAAAACAGCACTAATGGGCCCCGAAA
GGCCCAAAATAACAAGTGTTCTGA
Found at i:817 original size:315 final size:307
Alignment explanation
Indices: 1--1066 Score: 1649
Period size: 315 Copynumber: 3.4 Consensus size: 307
*
1 ATGAGCTAAAAACTTCACAATGGACTAATCTCACTAAAATGATTATAGTTAGGTCGTAAACAATT
1 ATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGTCGTAAACAATT
* * *
66 GAAAGAAAAGCTTTTGTGGTTTGACCAAAATCGAAGCCGATTTCAAAACAACACTAATGGGCCCC
66 AAAAGAAAAGC-TTTGTGGTTTG-CC-AAATCGAAGCCGA-TTCAAAACAGCACTAACGGG-CCC
* *
131 GAAAGGCCCGAAATAACAAGGGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCACCAA
126 GAAAGACCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCACCAA
*
196 AATGATTATAGTTAGGCCGTAAAACAATTGAAA-AGAAAGCTTTATGGTTTGCCAAATCGAAGCC
191 AATGATTATAGTTAGGCCGTAAAACAATTGAAAGA-AAAGCTTTAT-GTTTCCCAAATCGAAGCC
260 GATTCAAAACAGCACTAATGGGCCCCGAAAGGCCC-AAAATAACAAGTGTTCTGA
254 GATTCAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAAA-AACAAGTGTTCTGA
*
314 AGTGAGACTAAAAACTTCACAACGGACTAATCTCACCAAAATGATTATAGTTAGGTCGTAAAACA
1 A-TGAG-CTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGTCGT-AAACA
*
379 ATT-AAAG-AAAGCTTTGTGGTTTGCCAAATCGAAGCCGATTCAAAACAGCACTAACGGGCCCCA
63 ATTAAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGCCGATTCAAAACAGCACTAACGGGCCCGA
*
442 AAGACCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAACGGACTAATCTCACCAAAA
128 AAGACCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAA
* **
507 TGATTATAGTTAGGCCGTAAAAAAATTGAAAGAAAAGCTTTGCGCTTTCCCAAACTCGAAGCCGA
193 TGATTATAGTTAGGCCGTAAAACAATTGAAAGAAAAGCTTTATG-TTTCCCAAA-TCGAAGCCGA
572 TTCAAAACAGCACTAATGGGCCCCCGAAAAGGCCCCGAAAAAACAAGTGTTCTGA
256 TTCAAAACAGCACTAATGGG-CCCCG-AAAGG-CCCGAAAAAACAAGTGTTCTGA
** * *
627 ATGAGCTAAAAACTTCACGTTGGACTAGTCTCACCAAAATGATTATTGTTAGGTCGTAAACAATT
1 ATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGTCGTAAACAATT
*
692 AAAAGAAAAGCTTTGTAGGTTTGCCAAATCGAAGCCGATTACAAAACAGCACTAACGGGTTCCGA
66 AAAAGAAAAGCTTTGT-GGTTTGCCAAATCGAAGCCGATT-CAAAACAGCACTAACGGG-CCCGA
* *
757 AAGACCCGAAATAACAAGTGTTCTGAATGAGCGAAAAACTTCACAGTGGACTAATCTCACCAAAA
128 AAGACCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAA
* *
822 TGATAATACGTTAGGCCGT-AAACAATTAGAAAGAAAAGCTTTATGGTTCCCAAATCGGAACGAC
193 TGATTATA-GTTAGGCCGTAAAACAATT-GAAAGAAAAGCTTTATGTTTCCCAAATC-GAA-G-C
886 CGACTTACAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAAAAACAAGTGTTCTGA
253 CGA-TT-CAAAACAGCACTAATGGGCCCCGAAAGGCCCGAAAAAACAAGTGTTCTGA
*
943 ATGAGCTAAAAACTTCACGATGGACTAATCTCACC-AAATGATTATAGTTAGGTCGTAAACAATT
1 ATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGTCGTAAACAATT
1007 AAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGCCGATTCAAAACAGCACTAACGGGCCC
66 AAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGCCGATTCAAAACAGCACTAACGGGCCC
1067 CCG
Statistics
Matches: 700, Mismatches: 31, Indels: 45
0.90 0.04 0.06
Matches are distributed among these distances:
308 1 0.00
309 112 0.16
310 57 0.08
311 69 0.10
312 23 0.03
313 71 0.10
314 56 0.08
315 188 0.27
316 89 0.13
317 9 0.01
318 7 0.01
319 18 0.03
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.22
Consensus pattern (307 bp):
ATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGATTATAGTTAGGTCGTAAACAATT
AAAAGAAAAGCTTTGTGGTTTGCCAAATCGAAGCCGATTCAAAACAGCACTAACGGGCCCGAAAG
ACCCGAAATAACAAGTGTTCTGAATGAGCTAAAAACTTCACAATGGACTAATCTCACCAAAATGA
TTATAGTTAGGCCGTAAAACAATTGAAAGAAAAGCTTTATGTTTCCCAAATCGAAGCCGATTCAA
AACAGCACTAATGGGCCCCGAAAGGCCCGAAAAAACAAGTGTTCTGA
Done.