Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013656.1 Corchorus capsularis cultivar CVL-1 contig13677, 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: 5518
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.35
Found at i:705 original size:193 final size:195
Alignment explanation
Indices: 329--719 Score: 554
Period size: 195 Copynumber: 2.0 Consensus size: 195
319 TCTCGGCTCC
* * * * * *
329 ATTTTACATGATTATTGGCGCAATGACTCTTTGAAATATTTATATTCATCGAAACAAATGTCAGT
1 ATTTTACATGATTATTGACGCAAAGACTCCTTAAAATATCTATATTCATCGAAACAAATCTCAGT
* * * *
394 CATATTGGATATATGGATTTATTTTTACGAGCATCTGAGTATTATTTCGATTTAATTAGAAATTA
66 CATATTGAATATAAGGATTTATTTTTACGAGCATCTCAATATTATTTCGATTTAATTAGAAATTA
*
459 ATTCGGAAAAAAATGGAAAAACGATGTTAGAAGTGTGAAAAACCTATCAATCTTTTTGGCGTTGA
131 ATTCGGAAAAAAATGGAAAAACGATGTTAGAAGCGTGAAAAACCTATCAATCTTTTTGGCGTTGA
* * *
524 ATTTTGCATGATTTTTGACGCAAAGACTCCTTAAAATATCTATATTCATCGAACCAAATCTCAGT
1 ATTTTACATGATTATTGACGCAAAGACTCCTTAAAATATCTATATTCATCGAAACAAATCTCAGT
* * * *
589 CATATTGAATATAAGGATTTGTTTTTTCGCGCATCTCAATCTT-TTTCGATTTAATTAGAAATTA
66 CATATTGAATATAAGGATTTATTTTTACGAGCATCTCAATATTATTTCGATTTAATTAGAAATTA
* * **
653 ATTC-GATAAAAATGGAAAAACGATTTTAGAAGCGTGAAATGCC-AGTCAATCTTTTTGGCGTTG
131 ATTCGGAAAAAAATGGAAAAACGATGTTAGAAGCGTGAAAAACCTA-TCAATCTTTTTGGCGTTG
716 A
195 A
717 ATT
1 ATT
720 ATATATTGTT
Statistics
Matches: 173, Mismatches: 22, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
192 1 0.01
193 56 0.32
194 25 0.14
195 91 0.53
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (195 bp):
ATTTTACATGATTATTGACGCAAAGACTCCTTAAAATATCTATATTCATCGAAACAAATCTCAGT
CATATTGAATATAAGGATTTATTTTTACGAGCATCTCAATATTATTTCGATTTAATTAGAAATTA
ATTCGGAAAAAAATGGAAAAACGATGTTAGAAGCGTGAAAAACCTATCAATCTTTTTGGCGTTGA
Found at i:1126 original size:516 final size:515
Alignment explanation
Indices: 4--1235 Score: 1806
Period size: 516 Copynumber: 2.4 Consensus size: 515
1 GCA
* * *
4 TTGAATTTTGCATGATTTTTGGCGCAAATACTCCTTGAAATATCTATATTTATCGAAACAAATCT
1 TTGAATTTTGCATGATTTTTGGCGCAAAAACTCCTTGAAATATCTATATTCATCGAACCAAATCT
* * * * * * *
69 CAACAACATTGGATATAAGGATTTGTTTTTTTGAGCATCTCAATCTTGTTTCGAATTAATAAGAA
66 CAGCCATATTGAATATAAGGATTTGTTTTTTCGAGCATCTCAATCTT-TTTCGATTTAATTAGAA
* * * * *
134 ATTAATTTG-GAAAAATGGAAAAACGATATTAGAAGCGTGCAAAGCCCGTCATTCTTTTCGGCGT
130 ATTAATTCGAAAAAAATGGAAAAACGATATTAGAAGCGTG-AAAGCCAGTCAATCTTTTTGGCGT
* * *
198 TGAATTATATAATTTTTTCTGTGTATTGTGGTAAAAAAGTGAGAAAAAAATTTTCGGGTCAGTTT
194 TGAATTATATAATTGTTTCTGTGTATTGTGGCAAAAAAGTGAGAAAAAAATTTTCGGGTCAATTT
* * *
263 TTAGCCGAAATCGTATACTTACCATCACGGGTTTTTGATAAAAACGCGTTCCGGAGTCTCGGCTC
259 TTAGCCGAAATCGTATACTTACCATCACGGGTTTTTGATAAAAACACGTTCCGGAGCCCCGGCTC
* * *
328 CATTTTACATGATTATTGGCGCAATGACTCTTTGAAATATTTATATTCATCGAAACAAATGTCAG
324 AATTTTACATGATTATTGGCGCAAAGACTCTTTGAAATATCTATATTCATCGAAACAAATGTCAG
* * * * *
393 TCATATTGGATATATGGATTTATTTTTACGAGCATCTGAGTATTATTTCGATTTAATTAGAAATT
389 CCACATTGGATATAAGGATTTACTTTTACGAGCATCTGAATATTATTTCGATTTAATTAGAAATT
* *
458 AATTCGGAAAAAAATGGAAAAACGATGTTAGAAGTGTGAAAAACCTATCAATCTTTTTGGCG
454 AATTCGGAAAAAAATCGAAAAACGATGTTAGAAGTGTGAAAAACCTATCAATCTTTTTGACG
* * *
520 TTGAATTTTGCATGATTTTTGACGCAAAGACTCCTTAAAATATCTATATTCATCGAACCAAATCT
1 TTGAATTTTGCATGATTTTTGGCGCAAAAACTCCTTGAAATATCTATATTCATCGAACCAAATCT
* *
585 CAGTCATATTGAATATAAGGATTTGTTTTTTCGCGCATCTCAATCTTTTTCGATTTAATTAGAAA
66 CAGCCATATTGAATATAAGGATTTGTTTTTTCGAGCATCTCAATCTTTTTCGATTTAATTAGAAA
* *
650 TTAATTCGATAAAAATGGAAAAACGATTTTAGAAGCGTGAAATGCCAGTCAATCTTTTTGGCGTT
131 TTAATTCGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAA-GCCAGTCAATCTTTTTGGCGTT
* * * *
715 GAATTATAT-ATTGTTTCTGTGTATTGTGGCGAAAAATTGAGAAAAAATTTTTTGGGTCAATTTT
195 GAATTATATAATTGTTTCTGTGTATTGTGGCAAAAAAGTGAGAAAAAAATTTTCGGGTCAATTTT
* * * *
779 TAGCTGAAATCGTGTACTTACCATCAC-GGTTTTTAGCTAAAAACACGTTCCGGAGCCCCGGCTG
260 TAGCCGAAATCGTATACTTACCATCACGGGTTTTT-GATAAAAACACGTTCCGGAGCCCCGGCTC
* * * *
843 AATTTTGCATGATTTTTTGCGTAAAGACTCTTTGAAATATCTACT-TTCATCGAAACAAATGTCA
324 AATTTTACATGATTATTGGCGCAAAGACTCTTTGAAATATCTA-TATTCATCGAAACAAATGTCA
* *
907 GCCACATTGGATATAAGGATTTCCTTTTACGAGCATCTGAATATTGTTTCGATTTAATTAGAAAT
388 GCCACATTGGATATAAGGATTTACTTTTACGAGCATCTGAATATTATTTCGATTTAATTAGAAAT
* * * *
972 TAATTCGGAAAAAAAATCGAAAAACGATGTTAGAAGTGTTAAAAGCCTGTCAATCTTTTTGATG
453 TAATTCGG-AAAAAAATCGAAAAACGATGTTAGAAGTGTGAAAAACCTATCAATCTTTTTGACG
* * *
1036 TTGAATTTTGCATTATTTCTGGCGCAAAAATTCCTTGAAATATCTATATTCATCGAACCAAATCT
1 TTGAATTTTGCATGATTTTTGGCGCAAAAACTCCTTGAAATATCTATATTCATCGAACCAAATCT
1101 CAGCCATATTGAATATAAGGATTTGTTTTTTCGAGCATCTCAATCTTTTTCGATTTAATTAGAAA
66 CAGCCATATTGAATATAAGGATTTGTTTTTTCGAGCATCTCAATCTTTTTCGATTTAATTAGAAA
* * * *
1166 TTAACTCGAAAAAAATGGAAAAACGATATTACAAGCGGGAAAAGCCAGTCAATCTTTTTGGTGTT
131 TTAATTCGAAAAAAATGGAAAAACGATATTAGAAGCGTG-AAAGCCAGTCAATCTTTTTGGCGTT
1231 GAATT
195 GAATT
1236 TTTTCATTAT
Statistics
Matches: 642, Mismatches: 68, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
514 7 0.01
515 244 0.38
516 388 0.60
517 3 0.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (515 bp):
TTGAATTTTGCATGATTTTTGGCGCAAAAACTCCTTGAAATATCTATATTCATCGAACCAAATCT
CAGCCATATTGAATATAAGGATTTGTTTTTTCGAGCATCTCAATCTTTTTCGATTTAATTAGAAA
TTAATTCGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAGCCAGTCAATCTTTTTGGCGTTG
AATTATATAATTGTTTCTGTGTATTGTGGCAAAAAAGTGAGAAAAAAATTTTCGGGTCAATTTTT
AGCCGAAATCGTATACTTACCATCACGGGTTTTTGATAAAAACACGTTCCGGAGCCCCGGCTCAA
TTTTACATGATTATTGGCGCAAAGACTCTTTGAAATATCTATATTCATCGAAACAAATGTCAGCC
ACATTGGATATAAGGATTTACTTTTACGAGCATCTGAATATTATTTCGATTTAATTAGAAATTAA
TTCGGAAAAAAATCGAAAAACGATGTTAGAAGTGTGAAAAACCTATCAATCTTTTTGACG
Found at i:1306 original size:194 final size:193
Alignment explanation
Indices: 872--1428 Score: 715
Period size: 194 Copynumber: 2.9 Consensus size: 193
862 CGTAAAGACT
* * * ** *
872 CTTTGAAATATCTACT-TTCATCGAAACAAATGTCAGCCACATTGGATATAAGGATTTCCTTTTA
1 CTTT-AAATATCTA-TATTCATCG-AACAAATCTCAGCCATATTGAATATAAGGATTTGTTTTTT
* * * * *
936 CGAGCATCTGAATATTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATCGAAAAACGATG
63 CGAGCATCTCAATCTT-TTTCGATTTAATTAGAAATTAAATC-G-AAAAAAATGGAAAAACGATA
* * * * *
1001 TTAGAAGTGTTAAAAGCCTGTCAATCTTTTTGATGTTGAA-TTTTGCATTATTTCTGGCGCAAAA
125 TTAGAAGCGTGAAAAGCCAGTCAATCTTTTTGGTGTTGAATTTTTGCATTATTTCTGGCCCAAAA
*
1065 ATTC
190 ACTC
*
1069 CTTGAAATATCTATATTCATCGAACCAAATCTCAGCCATATTGAATATAAGGATTTGTTTTTTCG
1 CTTTAAATATCTATATTCATCGAA-CAAATCTCAGCCATATTGAATATAAGGATTTGTTTTTTCG
* *
1134 AGCATCTCAATCTTTTTCGATTTAATTAGAAATTAACTCGAAAAAAATGGAAAAACGATATTACA
65 AGCATCTCAATCTTTTTCGATTTAATTAGAAATTAAATCGAAAAAAATGGAAAAACGATATTAGA
* * * *
1199 AGCGGGAAAAGCCAGTCAATCTTTTTGGTGTTGAATTTTTTCATTATTTTTGGCCCAAATACTC
130 AGCGTGAAAAGCCAGTCAATCTTTTTGGTGTTGAATTTTTGCATTATTTCTGGCCCAAAAACTC
* * *
1263 CTTTAAATATCTATATTAATCGAACTAAATCTCAGCTATATTGAATATAAGGATTTGTTTTTTGG
1 CTTTAAATATCTATATTCATCGAAC-AAATCTCAGCCATATTGAATATAAGGATTTGTTTTTTCG
* * * * *
1328 AGCATCTCAATCATTTTCAATTTAATTAGGAATTAAATCG-GAAAAATGGAAAAACTATATTAGA
65 AGCATCTCAATCTTTTTCGATTTAATTAGAAATTAAATCGAAAAAAATGGAAAAACGATATTAGA
* *
1392 AGCATGAAAAGCCAGTCAATCTTTTTGGCGTTGAATT
130 AGCGTGAAAAGCCAGTCAATCTTTTTGGTGTTGAATT
1429 ATATATTGTT
Statistics
Matches: 319, Mismatches: 37, Indels: 12
0.87 0.10 0.03
Matches are distributed among these distances:
193 108 0.34
194 119 0.37
195 27 0.08
196 62 0.19
197 3 0.01
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (193 bp):
CTTTAAATATCTATATTCATCGAACAAATCTCAGCCATATTGAATATAAGGATTTGTTTTTTCGA
GCATCTCAATCTTTTTCGATTTAATTAGAAATTAAATCGAAAAAAATGGAAAAACGATATTAGAA
GCGTGAAAAGCCAGTCAATCTTTTTGGTGTTGAATTTTTGCATTATTTCTGGCCCAAAAACTC
Found at i:2221 original size:195 final size:194
Alignment explanation
Indices: 1875--2460 Score: 768
Period size: 195 Copynumber: 3.0 Consensus size: 194
1865 CCTGACTCCG
* * * * * * *
1875 TTTTACA-TGATTTTTGGCGCAAAGACTCTTTGAAATATTTACATTCATCAAAAAAAATTTCAGC
1 TTTTACACT-ATTTTTGGTGCAAAAACTCCTTGAAATATCTATATTCATGAAAAAAAATCTCAGC
** * *
1939 CACGTTGGATATAAGGATTTGTTTTTTCGAGCATCTAAAT-ATTGTTTCGATTTAATTAGAAATT
65 CATATTGAATATAAGGATTTGTTTTTTCGAGCATCTCAATCA-T-TTTCGATTTAATTAGAAATT
* * *
2003 AATTCGGAAAAAAATGGAAAAACGATGTTAGAAGTTTGAAAAGCCTGTCAATCTTTTTGGTGTTG
128 AATTCGGAAAAAAATGAAAAAACGATGTTAGAAGTGTGAAAAGCCTGTCAATCTTTTTGGCGTTG
2068 AA
193 AA
* * * *
2070 TTTTGCACTATTTTTGGTGCAAAAACTCCTAGAAATATCTATATTCATGGAAATAAATCTCAGCC
1 TTTTACACTATTTTTGGTGCAAAAACTCCTTGAAATATCTATATTCATGAAAAAAAATCTCAGCC
* *
2135 ATATTGAATATAAGGATTTGTTTTTTCGAGAATCTCAATCATTTTCGATTTAATTAGAAATTATT
66 ATATTGAATATAAGGATTTGTTTTTTCGAGCATCTCAATCATTTTCGATTTAATTAGAAATTAAT
** *
2200 TCGGAAAAAAAATGAAAAAACGATGTTAGAAGTGTGAAAAGCCTAACAACCTTTTTGGCGTTGAA
131 TCGG-AAAAAAATGAAAAAACGATGTTAGAAGTGTGAAAAGCCTGTCAATCTTTTTGGCGTTGAA
* **
2265 TTTTACATTATTTTTGGCT-CAAAAACTCCTTGAAATATCTATATTCA-GCAAACCAAATCTCAG
1 TTTTACACTATTTTTGG-TGCAAAAACTCCTTGAAATATCTATATTCATG-AAAAAAAATCTCAG
* ** *
2328 TCATATTGAATATAAGGATTTGTTTTTTTTTAGCATCTCAATCTTTTTCGATTTAATTAGAAATT
64 CCATATTGAATATAAGGATTTG-TTTTTTCGAGCATCTCAATCATTTTCGATTTAATTAGAAATT
* * * *
2393 AATTCGG-AAAAAATGAAAAAATGATATTAGAAGCGTGAAAAGCCAGTCAATCTTTTTGGCGTTG
128 AATTCGGAAAAAAATGAAAAAACGATGTTAGAAGTGTGAAAAGCCTGTCAATCTTTTTGGCGTTG
2457 AA
193 AA
2459 TT
1 TT
2461 ATATATTGTT
Statistics
Matches: 343, Mismatches: 42, Indels: 13
0.86 0.11 0.03
Matches are distributed among these distances:
194 81 0.24
195 215 0.63
196 47 0.14
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (194 bp):
TTTTACACTATTTTTGGTGCAAAAACTCCTTGAAATATCTATATTCATGAAAAAAAATCTCAGCC
ATATTGAATATAAGGATTTGTTTTTTCGAGCATCTCAATCATTTTCGATTTAATTAGAAATTAAT
TCGGAAAAAAATGAAAAAACGATGTTAGAAGTGTGAAAAGCCTGTCAATCTTTTTGGCGTTGAA
Found at i:2981 original size:323 final size:321
Alignment explanation
Indices: 2263--3094 Score: 1081
Period size: 323 Copynumber: 2.6 Consensus size: 321
2253 TTTGGCGTTG
* * *
2263 AATTTTACATTATTTTTGGCTCAAAAACTCCTTGAAATATCTATATTCAGC-AAACCAAATCTCA
1 AATTTTACATGATTTTTGGCTCAAAGACTCCTTGAAATATCTATATTCATCGAAA-CAAATCTCA
* * * *
2327 GTCATATTGAATATAAGGATTTGTTTTTTTTTAGCATCTCAATCTT-TTTCGATTTAATTAGAAA
65 GTCACATTGGATATAAGGATTTG--TTTTTTGAGCATCTCAATCTTGTTTCGAATTAATTAGAAA
* * * *
2391 TTAATTCGGAAAAAATGAAAAAATGATATTAGAAGCGTGAAAAGCCAGTCAATCTTTTTGGCGTT
128 TTAATTCGGAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCAGTCAATCTTTTCGGCGTT
* * *
2456 GAATTATATATTGTTTCTGTGTATTGTGGGAAAAAATTGAGAAAAAAACTTTTTGGGTCAATTTT
193 GAATTATATATTGTTTCTGTGTATTGTGGCAAAAAATTGAGAAAAAAACTTTTCGGGTCAAGTTT
* * *
2521 TAGCCGAATTCGTGTACTTACCATCACGGTTTCTGACTAAAAACTCGTTTCGGTGCCCCAATTC
258 TAGCCGAAATCGTGTACTTACCATCACGGTTTCTGACTAAAAACTCGTTCCGGTGCCCCAACTC
* * * *
2585 AATTTTGCATGTTTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAG
1 AATTTTACATGATTTTTGGCTCAAAGACTCCTTGAAATATCTATATTCATCGAAACAAATCTCAG
* *
2650 TAACATTGGATATAAGGATTTGTTTTTTCGAGCATCTCAATCTTGTTTCGAATAAATTAGAAATT
66 TCACATTGGATATAAGGATTTGTTTTTT-GAGCATCTCAATCTTGTTTCGAATTAATTAGAAATT
2715 AATTCGGAAAAAATGGAAAAACGATATTAGAAGCGT-ATAAAACTC-GTCAATCTTTTCGGCGTT
130 AATTCGGAAAAAATGGAAAAACGATATTAGAAGCGTGA-AAAAC-CAGTCAATCTTTTCGGCGTT
* * *
2778 GAATTATATAATATTTTTTTGTGTATTGTGGCAAAAAATTGAGAAGAAAA-TTTTCGGGT-AAGG
193 GAATTATAT-AT-TGTTTCTGTGTATTGTGGCAAAAAATTGAGAAAAAAACTTTTCGGGTCAA-G
* *
2841 TTTTAGCCGAAATCGTGTACTTACTATCACGGTTTTTTG-CTAAAAACGT-GTTCCGGTGCCCCA
255 TTTTAGCCGAAATCGTGTACTTACCATCACGG-TTTCTGACTAAAAAC-TCGTTCCGGTGCCCCA
2904 ACTC
318 ACTC
* * * * *
2908 CATTTTACATGATTTTTGGCTCAAAGACTCTTTGAAATATTTACATTCATCGAAACAAATGTCAG
1 AATTTTACATGATTTTTGGCTCAAAGACTCCTTGAAATATCTATATTCATCGAAACAAATCTCAG
* * *
2973 CCACATTGGATATAAGGATTTGTTTTTATGAGCATCTAAATATTGTTTC-AATTTAATTAGAAAT
66 TCACATTGGATATAAGGATTTGTTTTT-TGAGCATCTCAATCTTGTTTCGAA-TTAATTAGAAAT
* * * * * *
3037 TAATTCAGAAAAAAATGGAAAAGCGATGTTA-AGAGTGTGAAAAGCCTGTCAATCTTTT
129 TAATTC-GGAAAAAATGGAAAAACGATATTAGA-AGCGTGAAAAACCAGTCAATCTTTT
3095 TGATGTTGAA
Statistics
Matches: 447, Mismatches: 47, Indels: 30
0.85 0.09 0.06
Matches are distributed among these distances:
320 6 0.01
321 15 0.03
322 160 0.36
323 185 0.41
324 80 0.18
325 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.36
Consensus pattern (321 bp):
AATTTTACATGATTTTTGGCTCAAAGACTCCTTGAAATATCTATATTCATCGAAACAAATCTCAG
TCACATTGGATATAAGGATTTGTTTTTTGAGCATCTCAATCTTGTTTCGAATTAATTAGAAATTA
ATTCGGAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAACCAGTCAATCTTTTCGGCGTTGAA
TTATATATTGTTTCTGTGTATTGTGGCAAAAAATTGAGAAAAAAACTTTTCGGGTCAAGTTTTAG
CCGAAATCGTGTACTTACCATCACGGTTTCTGACTAAAAACTCGTTCCGGTGCCCCAACTC
Found at i:3301 original size:196 final size:194
Alignment explanation
Indices: 2939--3493 Score: 823
Period size: 196 Copynumber: 2.9 Consensus size: 194
2929 CAAAGACTCT
* * * * *
2939 TTGAAATATTTACATTCATCGAAACAAATGTCAGCCACATTGGATATAAGGATTTGTTTTTATGA
1 TTGAAATATCTACATTCATCGAACCAAATCTCAGCCATATTGAATATAAGGATTTGTTTTT-TGA
* * * * *
3004 GCATCTAAATATTGTTTCAATTTAATTAGAAATTAATTCAG-AAAAAAATGGAAAAGCGATGTTA
65 GCATCTCAATCTT-TTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATGGAAAAACGATGTTA
**
3068 -AGAGTGTGAAAAGCCTGTCAATCTTTTTGATGTTGAATTTTGCATTATTTCTGGCGCAAAAAAT
129 GA-AGTGTGAAAAGCCTGTCAATCTTTTTGGCGTTGAATTTTGCATTATTTCTGGCGCAAAAAAT
3132 CC
193 CC
*
3134 TTGAAATATCTATATTCATCGAACCAAATCTCAGCCATATTGAATATAAGGATTTGTTTTTTCGA
1 TTGAAATATCTACATTCATCGAACCAAATCTCAGCCATATTGAATATAAGGATTTGTTTTTT-GA
* * *
3199 GAATCTCAATCCTTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAAATGAAAAAACGATGTTA
65 GCATCTCAATCTTTTTCGATTTAATTAGAAATTAATTCGG-AAAAAAAATGGAAAAACGATGTTA
* *
3264 GAAGTGTGAAAAGCCTGTCAATCTTTTTGGCGTTGAATTTTGCATTATTTTTGGCGCAAAAACTC
129 GAAGTGTGAAAAGCCTGTCAATCTTTTTGGCGTTGAATTTTGCATTATTTCTGGCGCAAAAAATC
3329 C
194 C
* *
3330 TTGAAATATCTACATTCATTGAACCAAATCTCAGTCATATTGAATATAAGGATTTGTTTTTTGAG
1 TTGAAATATCTACATTCATCGAACCAAATCTCAGCCATATTGAATATAAGGATTTGTTTTTTGAG
*
3395 CATCTCAATCTTTTTCGATTTAATTAGAAATTAATTCGG---AAAAATGGAAAAACGATATTAGA
66 CATCTCAATCTTTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATGGAAAAACGATGTTAGA
* *
3457 AGCGTGAAAAGCCAGTCAATCTTTTTGGCGTTGAATT
131 AGTGTGAAAAGCCTGTCAATCTTTTTGGCGTTGAATT
3494 ATATATTGTT
Statistics
Matches: 329, Mismatches: 27, Indels: 12
0.89 0.07 0.03
Matches are distributed among these distances:
191 56 0.17
194 26 0.08
195 106 0.32
196 140 0.43
197 1 0.00
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (194 bp):
TTGAAATATCTACATTCATCGAACCAAATCTCAGCCATATTGAATATAAGGATTTGTTTTTTGAG
CATCTCAATCTTTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATGGAAAAACGATGTTAGA
AGTGTGAAAAGCCTGTCAATCTTTTTGGCGTTGAATTTTGCATTATTTCTGGCGCAAAAAATCC
Found at i:4006 original size:320 final size:313
Alignment explanation
Indices: 3310--4107 Score: 1032
Period size: 320 Copynumber: 2.5 Consensus size: 313
3300 ATTTTGCATT
* * * *
3310 ATTTTTGGCGCAAAAACTCCTTGAAATATCTACATTCATTGAACCAAATCTCAGTCATATTGAAT
1 ATTTTTGGCGCAAAAACTCCTTGAAATATCTACATTCATCGAACCAAATCTCAGCCACATTGGAT
*
3375 ATAAGGATTTGTTTTTTGAGCATCTCAATCTT-TTTCGATTTAATTAGAAATTAATTCGGAAAAA
66 ATAA-GATTTGTTTTTTGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAA
* *
3439 TGGAAAAACGATATTAGAAGCGTGAAAAGCCAGTCAATCTTTTTGGCGTTGAATTATATATTGTT
130 TGGAAAAACGATATTAGAAGCGTGAAAAGCCAGTCAATCTTTTCGACGTTGAATTATATATTGTT
* *
3504 TCTGTGTATTGTGGGAAAAAATTGAGAAAAAAACATTTCGGGTCAATTTTTAGCCGAATTCGTGT
195 TCTGTGTATTGTGGCAAAAAATTGAGAAAAAAACATTTCGGATCAATTTTTAGCCGAATTCGTGT
* * * * *
3569 ACTTCACGGTTTCTGGCTAAAAACGCGTTTCGGAGCCCCAAATCAATTTTGCATG
260 ACATCACGGTTTCTGGCTAAAAACACGTTTC-AAGCCCCAAATCAATTTTACAAG
* * *
3624 ATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCAACATTGGAT
1 ATTTTTGGCGCAAAAACTCCTTGAAATATCTACATTCATCGAACCAAATCTCAGCCACATTGGAT
3689 ATAAGTATTTGGTTTTTTGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCTGAAAA
66 ATAAG-ATTT-GTTTTTTGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTC-GAAAA
3754 AATGGAAAAACGATATTAGAAGCGTGAAAAGCTC-GTCAATCTTTTCGACGTTGAATTATATAAT
128 AATGGAAAAACGATATTAGAAGCGTGAAAAGC-CAGTCAATCTTTTCGACGTTGAATTATAT-AT
* * * *
3818 AT-TTTTTGTGTATTGTGGCAAAAAATTGAGAAAAAAGA-TTTTCGGATCAGTTTTTAGCTGAAA
191 -TGTTTCTGTGTATTGTGGCAAAAAATTGAGAAAAAA-ACATTTCGGATCAATTTTTAGCCG-AA
* * * * *
3881 TT-GTGTACAGATCACGGTTTTTTGCTAAAAACATGTTAT-AATGCCCCGACTCAATTTTACAAG
253 TTCGTGTAC--ATCACGGTTTCTGGCTAAAAACACGTT-TCAA-GCCCCAAATCAATTTTACAAG
* * * * * *
3944 ATTTTTGGCACAAATACTCTTTGAAATATTTACATTCATCGAAACAAATGTCAGCCACATTGGAT
1 ATTTTTGGCGCAAAAACTCCTTGAAATATCTACATTCATCGAACCAAATCTCAGCCACATTGGAT
* * * * *
4009 ATAAAGATTTGTTTTTACGAGTATCTGAATATTGTTTCGATTTAATTAAAAATTAATTCAGAAAA
66 AT-AAGATTTGTTTTT-TGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTC-G--AA
* *
4074 AAAATGGAAAAACGATGTTAGAAGTGTGAAAAGC
126 AAAATGGAAAAACGATATTAGAAGCGTGAAAAGC
4108 ATGTGAATCA
Statistics
Matches: 425, Mismatches: 42, Indels: 26
0.86 0.09 0.05
Matches are distributed among these distances:
313 1 0.00
314 66 0.16
315 22 0.05
316 25 0.06
317 61 0.14
318 59 0.14
319 13 0.03
320 140 0.33
321 4 0.01
322 34 0.08
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.35
Consensus pattern (313 bp):
ATTTTTGGCGCAAAAACTCCTTGAAATATCTACATTCATCGAACCAAATCTCAGCCACATTGGAT
ATAAGATTTGTTTTTTGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAAT
GGAAAAACGATATTAGAAGCGTGAAAAGCCAGTCAATCTTTTCGACGTTGAATTATATATTGTTT
CTGTGTATTGTGGCAAAAAATTGAGAAAAAAACATTTCGGATCAATTTTTAGCCGAATTCGTGTA
CATCACGGTTTCTGGCTAAAAACACGTTTCAAGCCCCAAATCAATTTTACAAG
Found at i:4784 original size:320 final size:320
Alignment explanation
Indices: 4129--4966 Score: 1057
Period size: 320 Copynumber: 2.6 Consensus size: 320
4119 TTTGGCGTTA
* * *
4129 AATTTTGCATGATTTTTGGCGCAAAGACTCCTTAAAATATCTATATTCATCAAACCAAATCTCAG
1 AATTTTGCATGATTTTTGGCGCAAAGACTTCTTGAAATATCTATATTCATCGAACCAAATCTCAG
* ** * *
4194 CCATATTAAATATAATGATTTGTTTTTAGGAGCATCTCAATCTT-TTTCGATTTAATTAGAAATT
66 CCACATTGGATATAAGGATTTGTTTTTACGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATT
* * * ** *
4258 AAATCGGAAAAATGG-AAAACGTTATTAGAAGTGAGAAAAGCAAGGCAATCTTTTTGGCGTTGAA
131 AATTCGGAAAAATGGAAAAACGATATTAGAAGTGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAA
*
4322 TTATATATTGTTTCTGTGTATTGTGGCAAAAAATTGAGAAAAAAAATTCCGGGCCAATTATCAGT
196 TTATATATTGTTTCTGTGTATTATGGCAAAAAATTGAGAAAAAAAATTCCGGGCCAATTATCAGT
* * ** * *
4387 CAAATTCGTGTACTTACCATCACGGTTTCTGGCTAAAAACGCGTTTTGGAGCCCCGTCTC
261 CAAATTCGTGTACGTAACATCACGGTTTCTGGCTAAAAACGCGTTCCGGAGACCCGACTC
*
4447 AATTTTGCATGATTTTTGGCACAAAGACTTCTTGAAATATCTATATTCATCGAACCAAATCTCAG
1 AATTTTGCATGATTTTTGGCGCAAAGACTTCTTGAAATATCTATATTCATCGAACCAAATCTCAG
* * *
4512 CAACATTGGATATAAGGATTTGTTTTTTCGAGCATCTCAATCTTGTTTCGAATTAATTAGAAATT
66 CCACATTGGATATAAGGATTTGTTTTTACGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATT
* *
4577 AATTCGGAAAAATGGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTCGGCGTTGAA
131 AATTCGGAAAAATGGAAAAACGATATTAGAAGTGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAA
* * * * * * * *
4642 TTATATAATAT-TTTCTGTGTATTATGGCGAAAAAGTTGAGAAGAAAATTTTCGGGTCAGTTTTT
196 TTATAT-AT-TGTTTCTGTGTATTATGGC-AAAAAATTGAGAAAAAAAATTCCGGGCCAATTATC
** * *
4706 AG-CCGA-TCGTGTACGTAACATCACGGATTT-TTGCTAAAAACGTGTTCCGGAGACCCGACTTC
258 AGTCAAATTCGTGTACGTAACATCACGG-TTTCTGGCTAAAAACGCGTTCCGGAGACCCGAC-TC
* * * * *
4768 -ATTTTAG-ATGATTTTTGGCGCAAAGAC-TCTTTGAAATATTTACATTCGTCGAAACAAATGTC
1 AATTTT-GCATGATTTTTGGCGCAAAGACTTC-TTGAAATATCTATATTCATCGAACCAAATCTC
* * *
4830 AGCCACATTGGATATAAGGATTTGTTTTTACGAGCATATAAATATTGTTTCGATTTAATTAGAAA
64 AGCCACATTGGATATAAGGATTTGTTTTTACGAGCATCTCAATCTTGTTTCGATTTAATTAGAAA
* * *
4895 TTAATCCGGAAAAAAAATGGAAAAACGATGTTAGAAGTGTGAAAAGCCTC-TTAATCTTTTTGGC
129 TTAATTCGG---AAAAATGGAAAAACGATATTAGAAGTGTGAAAAGCC-CGTCAATCTTTTTGGC
4959 GTTGAATT
190 GTTGAATT
4967 TTGCATTATT
Statistics
Matches: 451, Mismatches: 56, Indels: 21
0.85 0.11 0.04
Matches are distributed among these distances:
318 98 0.22
319 35 0.08
320 207 0.46
321 26 0.06
322 30 0.07
323 54 0.12
324 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (320 bp):
AATTTTGCATGATTTTTGGCGCAAAGACTTCTTGAAATATCTATATTCATCGAACCAAATCTCAG
CCACATTGGATATAAGGATTTGTTTTTACGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATT
AATTCGGAAAAATGGAAAAACGATATTAGAAGTGTGAAAAGCCCGTCAATCTTTTTGGCGTTGAA
TTATATATTGTTTCTGTGTATTATGGCAAAAAATTGAGAAAAAAAATTCCGGGCCAATTATCAGT
CAAATTCGTGTACGTAACATCACGGTTTCTGGCTAAAAACGCGTTCCGGAGACCCGACTC
Found at i:4822 original size:834 final size:829
Alignment explanation
Indices: 3114--5052 Score: 2915
Period size: 834 Copynumber: 2.3 Consensus size: 829
3104 ATTTTGCATT
* * * * * * * * *
3114 ATTTCTGGCGCAAAAAATCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCATATTGAAT
1 ATTTTTGGCGCAAAAACTCTTTGAAATATTTACATTCATCGAAACAAATGTCAGCCACATTGGAT
* * **
3179 ATAAGGATTTGTTTTTTCGAGAATCTCAATCCT-TTTCGATTTAATTAGAAATTAATTCGGAAAA
66 ATAAGGATTTGTTTTTACGAGAATCTAAATATTGTTTCGATTTAATTAGAAATTAATTCGG-AAA
*
3243 AAAAATGAAAAAACGATGTTAGAAGTGTGAAAAGCCTGTCAATCTTTTTGGCGTTGAATTTTGCA
130 AAAAATGGAAAAACGATGTTAGAAGTGTGAAAAGCCTGTCAATCTTTTTGGCGTTGAATTTTGCA
* *
3308 TTATTTTTGGCGCAAAAACTCCTTGAAATATCTACATTCATTGAACCAAATCTCAGTCATATTGA
195 TTATTTTTGGCGCAAAAACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGTCATATTGA
* * *
3373 ATATAAGGATTTGTTTTTTGAGCATCTCAATCTTTTTCGATTTAATTAGAAATTAATTCGGAAAA
260 ATATAAAGATTTGTTTTTGGAGCATCTCAATCTTTTTCGATTTAATTAGAAATTAAATCGGAAAA
* * *
3438 ATGGAAAAACGATATTAGAAGCGTGAAAAGCCAGTCAATCTTTTTGGCGTTGAATTATATATTGT
325 ATGGAAAAACGATATTAGAAGCGAGAAAAGCAAGGCAATCTTTTTGGCGTTGAATTATATATTGT
* * * * * *
3503 TTCTGTGTATTGTGGGAAAAAATTGAGAAAAAAACATTTCGGGTCAATTTTTAGCCGAATTCGTG
390 TTCTGTGTATTGTGGCAAAAAATTGAGAAAAAAACATTCCGGGCCAATTATCAGCCAAATTCGTG
3568 TACTTCACGGTTTCTGGCTAAAAACGCGTTTCGGAGCCCCAAATCAATTTTGCATGATTTTTGGC
455 TACTTCACGGTTTCTGGCTAAAAACGCGTTTCGGAGCCCCAAATCAATTTTGCATGATTTTTGGC
* *
3633 GCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCAACATTGGATATAAGTATT
520 ACAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCAACATTGGATATAAGGATT
*
3698 TGGTTTTTTGAGCATCTCAATCTTGTTTCGATTTAATTAGAAATTAATTCTGAAAAAATGGAAAA
585 TGGTTTTTTGAGCATCTCAATCTTGTTTCGAATTAATTAGAAATTAATTCTGAAAAAATGGAAAA
* *
3763 ACGATATTAGAAGCGTGAAAAGCTCGTCAATCTTTTCGACGTTGAATTATATAATATTTTTTGTG
650 ACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTCGACGTTGAATTATATAATATTTTCTGTG
* * * *
3828 TATTGTGGCAAAAAATTGAGAAAAAAGATTTTCGGATCAGTTTTTAGCTGAAATTGTGTACAGAT
715 TATTATGGCAAAAAATTGAGAAAAAAGATTTTCGGATCAGTTTTTAGCCG-AATCGTGTACACAT
* * *
3893 CACGGTTTTTTGCTAAAAACATGTTATAATGCCCCGACTCAATTTTACAAG
779 CACGGATTTTTGCTAAAAACATGTTAGAATGACCCGACTCAATTTTACAAG
* *
3944 ATTTTTGGCACAAATACTCTTTGAAATATTTACATTCATCGAAACAAATGTCAGCCACATTGGAT
1 ATTTTTGGCGCAAAAACTCTTTGAAATATTTACATTCATCGAAACAAATGTCAGCCACATTGGAT
* * * * *
4009 ATAAAGATTTGTTTTTACGAGTATCTGAATATTGTTTCGATTTAATTAAAAATTAATTCAGAAAA
66 ATAAGGATTTGTTTTTACGAGAATCTAAATATTGTTTCGATTTAATTAGAAATTAATTCGGAAAA
* * * *
4074 AAAATGGAAAAACGATGTTAGAAGTGTGAAAAGCATGTGAATCATTTTGGCGTTAAATTTTGCAT
131 AAAATGGAAAAACGATGTTAGAAGTGTGAAAAGCCTGTCAATCTTTTTGGCGTTGAATTTTGCAT
* * * * * *
4139 GATTTTTGGCGCAAAGACTCCTTAAAATATCTATATTCATCAAACCAAATCTCAGCCATATTAAA
196 TATTTTTGGCGCAAAAACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGTCATATTGAA
*
4204 TATAATGATTTGTTTTTAGGAGCATCTCAATCTTTTTCGATTTAATTAGAAATTAAATCGGAAAA
261 TATAAAGATTTGTTTTT-GGAGCATCTCAATCTTTTTCGATTTAATTAGAAATTAAATCGGAAAA
* *
4269 ATGG-AAAACGTTATTAGAAGTGAGAAAAGCAAGGCAATCTTTTTGGCGTTGAATTATATATTGT
325 ATGGAAAAACGATATTAGAAGCGAGAAAAGCAAGGCAATCTTTTTGGCGTTGAATTATATATTGT
*
4333 TTCTGTGTATTGTGGCAAAAAATTGAGAAAAAAA-ATTCCGGGCCAATTATCAGTCAAATTCGTG
390 TTCTGTGTATTGTGGCAAAAAATTGAGAAAAAAACATTCCGGGCCAATTATCAGCCAAATTCGTG
* ***
4397 TACTTACCATCACGGTTTCTGGCTAAAAACGCGTTTTGGAGCCCCGTCTCAATTTTGCATGATTT
455 TAC-T----TCACGGTTTCTGGCTAAAAACGCGTTTCGGAGCCCCAAATCAATTTTGCATGATTT
*
4462 TTGGCACAAAGACTTCTTGAAATATCTATATTCATCGAACCAAATCTCAGCAACATTGGATATAA
515 TTGGCACAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCAACATTGGATATAA
*
4527 GGATTT-GTTTTTTCGAGCATCTCAATCTTGTTTCGAATTAATTAGAAATTAATTC-GGAAAAAT
580 GGATTTGGTTTTTT-GAGCATCTCAATCTTGTTTCGAATTAATTAGAAATTAATTCTGAAAAAAT
*
4590 GGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTCGGCGTTGAATTATATAATATTT
644 GGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTCGACGTTGAATTATATAATATTT
* * *
4655 TCTGTGTATTATGGCGAAAAAGTTGAGAAGAAA-ATTTTCGGGTCAGTTTTTAGCCG-ATCGTGT
709 TCTGTGTATTATGGC-AAAAAATTGAGAAAAAAGATTTTCGGATCAGTTTTTAGCCGAATCGTGT
* * * * *
4718 ACGTAACATCACGGATTTTTGCTAAAAACGTGTTCCGGA-GACCCGACTTC-ATTTTAGATG
773 AC---ACATCACGGATTTTTGCTAAAAACATGTT-AGAATGACCCGAC-TCAATTTTACAAG
* *
4778 ATTTTTGGCGCAAAGACTCTTTGAAATATTTACATTCGTCGAAACAAATGTCAGCCACATTGGAT
1 ATTTTTGGCGCAAAAACTCTTTGAAATATTTACATTCATCGAAACAAATGTCAGCCACATTGGAT
* * *
4843 ATAAGGATTTGTTTTTACGAGCATATAAATATTGTTTCGATTTAATTAGAAATTAATCCGGAAAA
66 ATAAGGATTTGTTTTTACGAGAATCTAAATATTGTTTCGATTTAATTAGAAATTAATTCGGAAAA
* *
4908 AAAATGGAAAAACGATGTTAGAAGTGTGAAAAGCCTCTTAATCTTTTTGGCGTTGAATTTTGCAT
131 AAAATGGAAAAACGATGTTAGAAGTGTGAAAAGCCTGTCAATCTTTTTGGCGTTGAATTTTGCAT
* *
4973 TATTTTTGGCGCAAAAACTGCTTGAAATATCTATATTCATCGAATCAAATCTCAGTCATATTGAA
196 TATTTTTGGCGCAAAAACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGTCATATTGAA
5038 TATAAAGATTTGTTT
261 TATAAAGATTTGTTT
5053 CTGTGTATTG
Statistics
Matches: 997, Mismatches: 98, Indels: 24
0.89 0.09 0.02
Matches are distributed among these distances:
829 27 0.03
830 307 0.31
831 82 0.08
833 111 0.11
834 467 0.47
835 3 0.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (829 bp):
ATTTTTGGCGCAAAAACTCTTTGAAATATTTACATTCATCGAAACAAATGTCAGCCACATTGGAT
ATAAGGATTTGTTTTTACGAGAATCTAAATATTGTTTCGATTTAATTAGAAATTAATTCGGAAAA
AAAATGGAAAAACGATGTTAGAAGTGTGAAAAGCCTGTCAATCTTTTTGGCGTTGAATTTTGCAT
TATTTTTGGCGCAAAAACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGTCATATTGAA
TATAAAGATTTGTTTTTGGAGCATCTCAATCTTTTTCGATTTAATTAGAAATTAAATCGGAAAAA
TGGAAAAACGATATTAGAAGCGAGAAAAGCAAGGCAATCTTTTTGGCGTTGAATTATATATTGTT
TCTGTGTATTGTGGCAAAAAATTGAGAAAAAAACATTCCGGGCCAATTATCAGCCAAATTCGTGT
ACTTCACGGTTTCTGGCTAAAAACGCGTTTCGGAGCCCCAAATCAATTTTGCATGATTTTTGGCA
CAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCAACATTGGATATAAGGATTT
GGTTTTTTGAGCATCTCAATCTTGTTTCGAATTAATTAGAAATTAATTCTGAAAAAATGGAAAAA
CGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTCGACGTTGAATTATATAATATTTTCTGTGT
ATTATGGCAAAAAATTGAGAAAAAAGATTTTCGGATCAGTTTTTAGCCGAATCGTGTACACATCA
CGGATTTTTGCTAAAAACATGTTAGAATGACCCGACTCAATTTTACAAG
Done.