Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017565.1 Corchorus olitorius cultivar O-4 contig17598, 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: 5442
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:2017 original size:215 final size:211
Alignment explanation
Indices: 1604--2031 Score: 615
Period size: 215 Copynumber: 2.0 Consensus size: 211
1594 AAATAAAATT
*
1604 GACCCGAAAATGTTTTTCTCATTTTTTGCCACACAACTCTAACAAAATATATGATTCAAAGCCAA
1 GACCCGAAAATGTTTTTCTCATTTTTTGCCACACAACTCTAAAAAAATATATGATTCAAAGCCAA
* *
1669 AAAAAATTGAAGGGTTTTTCACGCTTCGAATATCAGTTTTCTATTTTTTTCCGAATTTATTTCTA
66 AAAAAATTGAAGGGTCTTTCACGCTTCGAATATCAGTTTTCAATTTTTTTCCGAATTTATTTCTA
* * *
1734 ATCAAATCGAAACAAAATTTAGATGCTCGTAAAAAGAAATACATAAATCCAAATTAGCTGAGATT
131 ATCAAATCGAAACAAAATTCAAATGCTCGTAAAAACAAATACATAAATCCAAATTAGCTGAGATT
1799 TGGTTATATGAATATA
196 TGGTTATATGAATATA
* * *
1815 GACCCGAAGAATTTTTTTTCTCATTTCTTTGCCACACAACTGTAAAAAAATATATGATTCAACGC
1 GACCCGAA-AA-TGTTTTTCTCATTT-TTTGCCACACAACTCTAAAAAAATATATGATTCAAAGC
* * * *
1880 CAAAAAAACTTTAAGGGTCTTTCACGCTTTGAATAT-TGTTTTTCCAATTTTTTTCCGAATTTAT
63 CAAAAAAAATTGAAGGGTCTTTCACGCTTCGAATATCAG-TTTT-CAATTTTTTTCCGAATTTAT
* * * * * *
1944 TTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATCTAAATTGGCTG
126 TTCTAATCAAATCGAAACAAAATTCAAATGCTCGTAAAAACAAATACATAAATCCAAATTAGCTG
* *
2009 ATATTTGGTTATATGACTATA
191 AGATTTGGTTATATGAATATA
2030 GA
1 GA
2032 TATTTTAAGG
Statistics
Matches: 191, Mismatches: 21, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
211 8 0.04
212 2 0.01
213 14 0.07
214 71 0.37
215 96 0.50
ACGTcount: A:0.36, C:0.16, G:0.12, T:0.36
Consensus pattern (211 bp):
GACCCGAAAATGTTTTTCTCATTTTTTGCCACACAACTCTAAAAAAATATATGATTCAAAGCCAA
AAAAAATTGAAGGGTCTTTCACGCTTCGAATATCAGTTTTCAATTTTTTTCCGAATTTATTTCTA
ATCAAATCGAAACAAAATTCAAATGCTCGTAAAAACAAATACATAAATCCAAATTAGCTGAGATT
TGGTTATATGAATATA
Found at i:2981 original size:322 final size:319
Alignment explanation
Indices: 1815--4118 Score: 3031
Period size: 324 Copynumber: 7.1 Consensus size: 319
1805 TATGAATATA
* * * * *
1815 GACCCGAAGAATTTTTTTTCTCATTTCTTTGCCACACAACTGTAAAAAAATATATGATTCAACGC
1 GACCCG-A-AATTTTTTTT-TCATTT-TTTGCCACACTACTCTGAAAAAATATATAATTCAAAGC
* * *
1880 CAAAAAAACTTTAAGGGTCTTTCACGCTTTGAATATTGTTTTTCCAATTTTTTTCCGAATTTATT
62 CAAAAAAA-TTTAAGGGTTTTTCACGCTTCGAATA-TCTTTTT-CAATTTTTTTCCGAATTTATT
* * * *
1945 TCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATCTAAATTGGCTGA
124 TCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCAAATTGGCTGA
* * * ** * *
2010 TATTTGGTTATATGACTATAGATATTTTAAGGAAACTTTCTGCCAAAAATCATGCAAAATTTAG-
189 GATTTGGTTATATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGT
* * * * * * **
2074 CAGAGGCTCCGGAACGCGTTTTTAGCAAAAAACCGTGATGATTAGTTCACGATTTCTGCTAAAAA
254 C-GGGGCCCCGAAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTACACGATTTCGGCCCAAAA
2139 TT
318 TT
* *
2141 GACCCGAAAGTTTTTATTTTTTCA-TTTTTGCCTCGCTACTCTGAAAAAATATATAATTCAAAGC
1 GACCCGAAA---TTT-TTTTTTCATTTTTTGCCACACTACTCTGAAAAAATATATAATTCAAAGC
* * * * *
2205 CAAAAAAATTGAAGGG-TTTTCATGCTTCCAATATCGTTTTTCGATTTTTGTTTTTCGAATTTAT
62 CAAAAAAATTTAAGGGTTTTTCACGCTTCGAATATC-TTTTTC-A-ATTT-TTTTCCGAATTTAT
* ** *
2269 TTCT-ATTAAAATCGAAACAAAATTTAGATGCTTTTAAAAAGAAATCCTTCAATCCAAATTGGCT
123 TTCTAATT-AAATCGAAACAAAATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCAAATTGGCT
* * *
2333 GAGATTTGGTTATATGAATATAGATATTTCAACGAGTCTTTCTGCCAAAAATCATGTAAAAGTGA
187 GAGATTTGGTTATATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGA
* * * * * * *** **
2398 GCCGGGGTCCCGAAACGCGTTTTTGGCCAAAAATCCGTGATTGTTATTACACGATTTTTACTAAA
252 GTCGGGGCCCCGAAACGCGTTTTTAG-CAAAAAACCGTGATGGTTAGTACACGATTTCGGCCCAA
2463 AATT
316 AATT
* * *
2467 GACCCGAAATTTTTTTTCTCATTTGTTTGCCACACAACTCTAAAAAAATATATAATTCAACGCCA
1 GACCCGAAATTTTTTTT-TCATTT-TTTGCCACACTACTCTGAAAAAATATATAATTCAAAGCCA
* * * * ** *
2532 AAGAAAATTGAAGGGGTTTTCACACTTCCAATATAGTTTTCTATTTTTTTCCCGAATTTATTTC-
64 AA-AAAATTTAAGGGTTTTTCACGCTTCGAATATCTTTTTCAATTTTTTT-CCGAATTTATTTCT
* *
2596 AAATAAATTCGAAACAAAATTCAGATGCTCGTAAAAAGAAATCCTTAAATTCAAATTGGCTGAGA
127 AATTAAA-TCGAAACAAAATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCAAATTGGCTGAG-
* *
2661 ATTTGGTTATATGAATATAGATATTTCAAGAAGTCTTTCTGCCAAAAATCATGCAAAACTTAGTC
190 ATTTGGTTATATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTC
*
2726 GGGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCCCAAAATT
255 GGGGCCCCGAAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTACACGATTTCGGCCCAAAATT
* *
2791 GACTCGAAATTTTTTTTTCAATTTTTT-CCACACTACTCTGGAAAAATATATAATTCAAAGCCAA
1 GACCCGAAATTTTTTTTTC-ATTTTTTGCCACACTACTCTGAAAAAATATATAATTCAAAGCCAA
*
2855 AATAAATTTAAGGGTTTTTCACGCTTCGAATATCTCTTTTCAAATTTTTTCCGAATTTATTTCTA
65 AA-AAATTTAAGGGTTTTTCACGCTTCGAATATCT-TTTTCAATTTTTTTCCGAATTTATTTCTA
* *
2920 ATTAAATCGTAACGAAATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCAAATTGGCTGAGATT
128 ATTAAATCGAAACAAAATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCAAATTGGCTGAGATT
2985 TGGTTATATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCGGG
193 TGGTTATATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCGGG
* *
3050 GCCCCGAAACGCGTTTTTAGTAAAAAAAACCGTGA-----CGTACACGATTTCGGCCCAAAATT
258 GCCCCGAAACGCGTTTTTAG--CAAAAAACCGTGATGGTTAGTACACGATTTCGGCCCAAAATT
* *
3109 GACGC-AAATTTTTTTTTTATAATTTTTTGCCACACTACTCTGGAAAAAATATATAATTCAAAGC
1 GACCCGAAA--TTTTTTTT-TCATTTTTTGCCACACTACTCT-GAAAAAATATATAATTCAAAGC
*
3173 CAAAAAAAATTTAAGGGTTTTTCACGCTTCGAATATCGTTTTTCTAATTTTTTGCCGAATTTATT
62 C-AAAAAAATTTAAGGGTTTTTCACGCTTCGAATATC-TTTTTC-AATTTTTTTCCGAATTTATT
* * *
3238 TCTAATTAAATCGTAACGAAATTTAGATGCTCGTAAAAAGAAATCCTTAAATCCAAATTGGCTGA
124 TCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCAAATTGGCTGA
*
3303 GATTTGGTTATATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACGGAGT
189 GATTTGGTTATATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGT
* * * *
3368 CGGGGCCCCGAAACGAGTTTTTAGCAAAAAAACCGTTATGGTTCGTACACGATTTC-GCTCAAAA
254 CGGGGCCCCGAAACGCGTTTTTAGC-AAAAAACCGTGATGGTTAGTACACGATTTCGGCCCAAAA
*
3432 AT
318 TT
* * *
3434 GACCCGAAGTTTTATTTTTTTCATTTTTTGCCACACTAATCTGAAAAAATATATAATTTAAAGCC
1 GACCCGAA--ATT-TTTTTTTCATTTTTTGCCACACTACTCTGAAAAAATATATAATTCAAAGCC
* * *
3499 AAAAAAATTTAAGGGTTTTTCACACTTCGAATATCTTTTTTCCAATTTTTTTCTGAATTTTTTTC
63 AAAAAAATTTAAGGGTTTTTCACGCTTCGAATATC-TTTTT-CAATTTTTTTCCGAATTTATTTC
* *
3564 TAATTAAATTGAAACGAAATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCAAATTGGCTGAGA
126 TAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCAAATTGGCTGAGA
* * *
3629 TTTGGTTATATGAATATAGACATTTCAAGGAGTCTTTCTGCCAAAACTCATGCAAAACTTAGTCG
191 TTTGGTTATATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCG
* * * * * * *
3694 GGGCCCCAAAAAGCATTTTTAGCCAAAAACCGTGATGGTTATTACACGATTTCTG-CTAAATATT
256 GGGCCCCGAAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTACACGATTTCGGCCCAAA-ATT
*
3758 GACCCG-AATTTTTTTTTCAATTTTTT-CCACACTACTCTGGAAAAATATATAATTCAAAGCCAA
1 GACCCGAAATTTTTTTTTC-ATTTTTTGCCACACTACTCTGAAAAAATATATAATTCAAAGCCAA
*
3821 AATAAATTTAAGGGTTTTTCACGCTTCGAATATCTCTTTTCAAATTTTTTCCGAATTTATTTCTA
65 AA-AAATTTAAGGGTTTTTCACGCTTCGAATATCT-TTTTCAATTTTTTTCCGAATTTATTTCTA
3886 ATTAAATCGAAACAAAATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCAAATTGGCTGAGATT
128 ATTAAATCGAAACAAAATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCAAATTGGCTGAGATT
* *
3951 TGGTTATATGAATATAGATATTTCAACGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCGGG
193 TGGTTATATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCGGG
** * *
4016 GCCCCGAAACTTGTTTTTAGCAAAAAAACCGTGATGGTTTGTACACGATTTCGGCCCGAAATT
258 GCCCCGAAACGCGTTTTTAGC-AAAAAACCGTGATGGTTAGTACACGATTTCGGCCCAAAATT
* *
4079 GACTCGGAATTTTTTTTTCAATTTTTT-CCACACTACTCTG
1 GACCCGAAATTTTTTTTTC-ATTTTTTGCCACACTACTCTG
4119 GAATCAGTTC
Statistics
Matches: 1757, Mismatches: 168, Indels: 110
0.86 0.08 0.05
Matches are distributed among these distances:
317 3 0.00
318 27 0.02
319 15 0.01
320 219 0.12
321 235 0.13
322 343 0.20
323 96 0.05
324 347 0.20
325 332 0.19
326 107 0.06
327 28 0.02
328 5 0.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (319 bp):
GACCCGAAATTTTTTTTTCATTTTTTGCCACACTACTCTGAAAAAATATATAATTCAAAGCCAAA
AAAATTTAAGGGTTTTTCACGCTTCGAATATCTTTTTCAATTTTTTTCCGAATTTATTTCTAATT
AAATCGAAACAAAATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCAAATTGGCTGAGATTTGG
TTATATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCGGGGCC
CCGAAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTACACGATTTCGGCCCAAAATT
Found at i:3454 original size:646 final size:638
Alignment explanation
Indices: 1826--4118 Score: 3025
Period size: 646 Copynumber: 3.6 Consensus size: 638
1816 ACCCGAAGAA
* * * * * *
1826 TTTTTTTTCTCATTTCTTTGCCACACAACTGTAAAAAAATATATGATTCAACGCCAAAAAAACTT
1 TTTTTTTTATAATTT-TTTGCCACACAACTCTAAAAAAATATATAATTCAAAGCCAAAAAAAATT
* * * *
1891 TAAGGGTCTTTCACGCTTTGAATATTGTTTTTCCAATTTTTTTCCGAATTTATTTCTAATTAAAT
65 TAAGGGTTTTTCACGCTTCGAATATCGTTTTTCTAA-TTTTTTCCGAATTTATTTCTAATTAAAT
* * * * *
1956 CGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTTAAATCTAAATTGGCTGATATTTGGTTAT
129 CGAAACAAAATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCAAATTGGCTGAGATTTGGTTAT
* * ** * * * *
2021 ATGACTATAGATATTTTAAGGAAACTTTCTGCCAAAAATCATGCAAAATTTAG-CAGAGGCTCCG
194 ATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTC-GGGGCCCCG
* * * * *
2085 GAACGCGTTTTTAGCAAAAAACCGTGATGATTAGTTCACGATTTCTG-CTAAAAATTGACCCGAA
258 AAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTACACGATTTCGGCCCAAAAA-TGACCCG-A
* * *
2149 AGTTTTTATTTTTTCATTTTTGCCTCGCTACTCTGAAAAAATATATAATTCAAAGCCAAAAAAAT
321 A--TTTT-TTTTTTCATTTTTTCCACACTACTCTGAAAAAATATATAATTCAAAGCCAAAAAAAT
* * * * *
2214 TGAAGGG-TTTTCATGCTTCCAATATCGTTTTTCGATTTTTGTTTTTCGAATTTATTTCT-ATTA
383 TTAAGGGTTTTTCACGCTTCGAATATC-TTTTTC-A-ATTT-TTTTCCGAATTTATTTCTAATT-
* * ** *
2277 AAATCGAAACAAAATTTAGATGCTTTTAAAAAGAAATCCTTCAATCCAAATTGGCTGAGATTTGG
443 AAATCGAAACGAAATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCAAATTGGCTGAGATTTGG
* * * * *
2342 TTATATGAATATAGATATTTCAACGAGTCTTTCTGCCAAAAATCATGTAAAAGTGAGCCGGGGTC
508 TTATATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCGGGGCC
* * * * * *
2407 CCGAAACGCGTTTTTGGCCAAAAATCCGTGATTGTTATTACACGATTTTTACTAAAAATTGACCC
573 CCGAAACGCGTTTTTAG-CAAAAAACCGTGATCG---TTACACGATTTCTGCCAAAAATTGACCC
2472 GAAATT
634 -AAATT
* * * *
2478 TTTTTTCTCAT--TTGTTTGCCACACAACTCTAAAAAAATATATAATTCAACGCCAAAGAAAATT
1 TTTTTT-TTATAATTTTTTGCCACACAACTCTAAAAAAATATATAATTCAAAGCCAAAAAAAATT
* * * * * * *
2541 GAAGGGGTTTTCACACTTCCAATATAG-TTTTCTATTTTTTTCCCGAATTTATTTC-AAATAAAT
65 TAAGGGTTTTTCACGCTTCGAATATCGTTTTTCTAATTTTTT-CCGAATTTATTTCTAATTAAA-
*
2604 TCGAAACAAAATTCAGATGCTCGTAAAAAGAAATCCTTAAATTCAAATTGGCTGAGAATTTGGTT
128 TCGAAACAAAATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCAAATTGGCTGAG-ATTTGGTT
* *
2669 ATATGAATATAGATATTTCAAGAAGTCTTTCTGCCAAAAATCATGCAAAACTTAGTCGGGGCCCC
192 ATATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCGGGGCCCC
* * *
2734 GAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCCCAAAATTGACTCGAA
257 GAAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTACACGATTTCGGCCCAAAAATGACCCGAA
* *
2799 ATTTTTTTTTCAATTTTTTCCACACTACTCTGGAAAAATATATAATTCAAAGCCAAAATAAATTT
322 TTTTTTTTTTC-ATTTTTTCCACACTACTCTGAAAAAATATATAATTCAAAGCCAAAA-AAATTT
*
2864 AAGGGTTTTTCACGCTTCGAATATCTCTTTTCAAATTTTTTCCGAATTTATTTCTAATTAAATCG
385 AAGGGTTTTTCACGCTTCGAATATCT-TTTTCAATTTTTTTCCGAATTTATTTCTAATTAAATCG
*
2929 TAACGAAATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCAAATTGGCTGAGATTTGGTTATAT
449 AAACGAAATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCAAATTGGCTGAGATTTGGTTATAT
2994 GAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCGGGGCCCCGAAA
514 GAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCGGGGCCCCGAAA
* * * *
3059 CGCGTTTTTAGTAAAAAAAACCGTGA-CG-TACACGATTTCGGCCCAAAATTGACGCAAATT
579 CGCGTTTTTAG--CAAAAAACCGTGATCGTTACACGATTTCTGCCAAAAATTGACCCAAATT
* *
3119 TTTTTTTTATAATTTTTTGCCACACTACTCTGGAAAAAATATATAATTCAAAGCCAAAAAAAATT
1 TTTTTTTTATAATTTTTTGCCACACAACTCT-AAAAAAATATATAATTCAAAGCCAAAAAAAATT
3184 TAAGGGTTTTTCACGCTTCGAATATCGTTTTTCTAATTTTTTGCCGAATTTATTTCTAATTAAAT
65 TAAGGGTTTTTCACGCTTCGAATATCGTTTTTCTAATTTTTT-CCGAATTTATTTCTAATTAAAT
* * *
3249 CGTAACGAAATTTAGATGCTCGTAAAAAGAAATCCTTAAATCCAAATTGGCTGAGATTTGGTTAT
129 CGAAACAAAATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCAAATTGGCTGAGATTTGGTTAT
*
3314 ATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACGGAGTCGGGGCCCCGA
194 ATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCGGGGCCCCGA
* * * *
3379 AACGAGTTTTTAGCAAAAAAACCGTTATGGTTCGTACACGATTTC-GCTCAAAAATGACCCGAAG
259 AACGCGTTTTTAGC-AAAAAACCGTGATGGTTAGTACACGATTTCGGCCCAAAAATGACCCGAA-
* *
3443 TTTTATTTTTTTCATTTTTTGCCACACTAATCTGAAAAAATATATAATTTAAAGCCAAAAAAATT
322 -TTT-TTTTTTTCATTTTTT-CCACACTACTCTGAAAAAATATATAATTCAAAGCCAAAAAAATT
* * *
3508 TAAGGGTTTTTCACACTTCGAATATCTTTTTTCCAATTTTTTTCTGAATTTTTTTCTAATTAAAT
384 TAAGGGTTTTTCACGCTTCGAATATC-TTTTT-CAATTTTTTTCCGAATTTATTTCTAATTAAAT
*
3573 TGAAACGAAATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCAAATTGGCTGAGATTTGGTTAT
447 CGAAACGAAATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCAAATTGGCTGAGATTTGGTTAT
* * * *
3638 ATGAATATAGACATTTCAAGGAGTCTTTCTGCCAAAACTCATGCAAAACTTAGTCGGGGCCCCAA
512 ATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCGGGGCCCCGA
* * * * * * *
3703 AAAGCATTTTTAGCCAAAAACCGTGATGGTTATTACACGATTTCTGCTAAATATTGACCCGAA-T
577 AACGCGTTTTTAGCAAAAAACCGTGATCG---TTACACGATTTCTGCCAAAAATTGACCCAAATT
* * ** *
3767 TTTTTTTT-CAATTTTTT-CCACACTACTCTGGAAAAATATATAATTCAAAGCCAAAATAAATTT
1 TTTTTTTTATAATTTTTTGCCACACAACTCTAAAAAAATATATAATTCAAAGCCAAAAAAAATTT
*
3830 AAGGGTTTTTCACGCTTCGAATATC-TCTTTTCAAATTTTTTCCGAATTTATTTCTAATTAAATC
66 AAGGGTTTTTCACGCTTCGAATATCGT-TTTTCTAATTTTTTCCGAATTTATTTCTAATTAAATC
3894 GAAACAAAATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCAAATTGGCTGAGATTTGGTTATA
130 GAAACAAAATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCAAATTGGCTGAGATTTGGTTATA
* *
3959 TGAATATAGATATTTCAACGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGAA
195 TGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCGGGGCCCCGAA
** * * * *
4024 ACTTGTTTTTAGCAAAAAAACCGTGATGGTTTGTACACGATTTCGGCCCGAAATTGACTCGGAA-
260 ACGCGTTTTTAGC-AAAAAACCGTGATGGTTAGTACACGATTTCGGCCCAAAAATGAC-CCGAAT
4088 TTTTTTTTTCAATTTTTTCCACACTACTCTG
323 TTTTTTTTTC-ATTTTTTCCACACTACTCTG
4119 GAATCAGTTC
Statistics
Matches: 1464, Mismatches: 144, Indels: 76
0.87 0.09 0.05
Matches are distributed among these distances:
640 3 0.00
641 11 0.01
642 58 0.04
643 161 0.11
644 304 0.21
645 130 0.09
646 385 0.26
647 69 0.05
648 33 0.02
649 117 0.08
650 177 0.12
651 8 0.01
652 6 0.00
653 2 0.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (638 bp):
TTTTTTTTATAATTTTTTGCCACACAACTCTAAAAAAATATATAATTCAAAGCCAAAAAAAATTT
AAGGGTTTTTCACGCTTCGAATATCGTTTTTCTAATTTTTTCCGAATTTATTTCTAATTAAATCG
AAACAAAATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCAAATTGGCTGAGATTTGGTTATAT
GAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCGGGGCCCCGAAA
CGCGTTTTTAGCAAAAAACCGTGATGGTTAGTACACGATTTCGGCCCAAAAATGACCCGAATTTT
TTTTTTCATTTTTTCCACACTACTCTGAAAAAATATATAATTCAAAGCCAAAAAAATTTAAGGGT
TTTTCACGCTTCGAATATCTTTTTCAATTTTTTTCCGAATTTATTTCTAATTAAATCGAAACGAA
ATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCAAATTGGCTGAGATTTGGTTATATGAATATA
GATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCGGGGCCCCGAAACGCGTTT
TTAGCAAAAAACCGTGATCGTTACACGATTTCTGCCAAAAATTGACCCAAATT
Found at i:3557 original size:12 final size:11
Alignment explanation
Indices: 3534--3568 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
3524 TTCGAATATC
*
3534 TTTTTTCCAAT
1 TTTTTTCTAAT
3545 TTTTTTCTGAAT
1 TTTTTTCT-AAT
3557 TTTTTTCTAAT
1 TTTTTTCTAAT
3568 T
1 T
3569 AAATTGAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.17, C:0.11, G:0.03, T:0.69
Consensus pattern (11 bp):
TTTTTTCTAAT
Done.