Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019083.1 Corchorus olitorius cultivar O-4 contig19116, 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: 8288
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Found at i:716 original size:5 final size:5
Alignment explanation
Indices: 706--745 Score: 66
Period size: 5 Copynumber: 8.4 Consensus size: 5
696 TTTTTAATTA
706 ATCTT ATCTT ATCTT ATCTT ATCTT A-C-T ATCTT ATCTT AT
1 ATCTT ATCTT ATCTT ATCTT ATCTT ATCTT ATCTT ATCTT AT
746 TACTATATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 2 0.06
4 2 0.06
5 29 0.88
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (5 bp):
ATCTT
Found at i:930 original size:42 final size:43
Alignment explanation
Indices: 863--944 Score: 107
Period size: 41 Copynumber: 1.9 Consensus size: 43
853 CTTTTTTATT
*
863 AATTATGGAAAGATATTGTAAATCCA-ATAATT-TAATTTTTA
1 AATTATGGAAAGATATTGAAAATCCATATAATTGTAATTTTTA
904 AATTATGGAAATGATA-TGAATAATCCATTATAATTGTAATT
1 AATTATGGAAA-GATATTGAA-AATCCA-TATAATTGTAATT
945 AATAATTTAC
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
41 14 0.40
42 10 0.29
44 6 0.17
45 5 0.14
ACGTcount: A:0.44, C:0.05, G:0.11, T:0.40
Consensus pattern (43 bp):
AATTATGGAAAGATATTGAAAATCCATATAATTGTAATTTTTA
Found at i:1002 original size:16 final size:17
Alignment explanation
Indices: 965--1002 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
955 TTCTACTAAT
965 TATT-TTTAGATTATAA
1 TATTATTTAGATTATAA
981 TA-TATTTA-ATTATAA
1 TATTATTTAGATTATAA
996 TATTATT
1 TATTATT
1003 ATTTATAGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
TATTATTTAGATTATAA
Found at i:1951 original size:335 final size:332
Alignment explanation
Indices: 1340--2043 Score: 866
Period size: 335 Copynumber: 2.1 Consensus size: 332
1330 ATACTTTACA
* * *
1340 TCATCTAACCAAATCTCAGCAACATTGGATTTAAGATTTTGCTTTTACGAGCATCTGAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGATTATGCTTTTACGAGCATCTGAATCTTGT
* * ** *
1405 TTCGATTTAATTAGAAATTAATTTAGAAAAAATAAGAATTATGATATTAAAAGAGTAAAAAGCCC
66 TTCGATATAATTAGAAATTAATTTAGAAAAAATAAAAAAAACGATATTAAAAGAGTAAAAAGCCC
* *
1470 TCCAATCTTTTTGGCATTGAATTATATATTTTTATGAGTATTTTAACCAAAAATTGAGGAGAAAT
131 TCCAATCTTTTTGGCATTGAATTATATATTTTTATGACTATTTTAACCAAAAATTGAGGAAAAAT
* * * * * *
1535 CTTTTGTGTCAATTTTTGCAAAATATTAGCCGAAATTGTGTACTAACAAATCATCACGGTTTTTG
196 CTTTCGAGTCAATTTTTACAAAATATTAGCCGAAATCGTGTAATAAC--A-CATCACAGTTTTTG
** *
1600 GCTAAAAATGCGTTCTGGGGA-CCCGACTCAATTTTGCATGATTTTTG--GCTCCGAGACTACTT
258 GCTAAAAAAACGTTCT-GGGACCCCGACTCAATTTTGCATGATTTTTGATGC-CAG-GACTACTT
1662 GAAATAT-CTATAT
320 GAAATATGC-ATAT
* *
1675 TCATCTAATCAAATCTCAACCACATTGGATTTAAGGA-TATGTTTTTACGAGCATCTGAATCTTG
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAA-GATTATGCTTTTACGAGCATCTGAATCTTG
* * * *
1739 TTTCGATATAATTAGAAATTAATTTTGAAAAACTACAAAAAAACGATATTAGAAA-TGTCAAAAG
65 TTTCGATATAATTAGAAATTAATTTAGAAAAAATA-AAAAAAACGATATTA-AAAGAGTAAAAAG
* ** *
1803 CCCTTCAATCTTTTTGGTGTTGAATTATATATGTTTTTATGACTATTTTAGCCAAAAATTGA-GA
128 CCCTCCAATCTTTTTGGCATTGAATTATATA--TTTTTATGACTATTTTAACCAAAAATTGAGGA
* * * *
1867 AAATATCTTTCGAGTTAATTTTTACAAAATTTTATCTGAAATCGTGTAATAAC-CATCACAGTTT
191 AAA-ATCTTTCGAGTCAATTTTTACAAAATATTAGCCGAAATCGTGTAATAACACATCACAGTTT
* * * *
1931 TTGGCTAAAAAAAACGTTCTGGGACCCCGACTCAGTTTTGCATGATTTTTTATGCCAGGTCTCCT
255 TTGGCT-AAAAAAACGTTCTGGGACCCCGACTCAATTTTGCATGATTTTTGATGCCAGGACTACT
*
1996 TGAGATATGCATAT
319 TGAAATATGCATAT
* *
2010 TCATCTAATCAAATTTTAGCCACATTGGATTTAA
1 TCATCTAATCAAATCTCAGCCACATTGGATTTAA
2044 TTAGAAATTA
Statistics
Matches: 317, Mismatches: 41, Indels: 22
0.83 0.11 0.06
Matches are distributed among these distances:
334 20 0.06
335 170 0.54
336 51 0.16
337 9 0.03
338 67 0.21
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (332 bp):
TCATCTAATCAAATCTCAGCCACATTGGATTTAAGATTATGCTTTTACGAGCATCTGAATCTTGT
TTCGATATAATTAGAAATTAATTTAGAAAAAATAAAAAAAACGATATTAAAAGAGTAAAAAGCCC
TCCAATCTTTTTGGCATTGAATTATATATTTTTATGACTATTTTAACCAAAAATTGAGGAAAAAT
CTTTCGAGTCAATTTTTACAAAATATTAGCCGAAATCGTGTAATAACACATCACAGTTTTTGGCT
AAAAAAACGTTCTGGGACCCCGACTCAATTTTGCATGATTTTTGATGCCAGGACTACTTGAAATA
TGCATAT
Found at i:2291 original size:294 final size:294
Alignment explanation
Indices: 1747--2337 Score: 633
Period size: 294 Copynumber: 2.0 Consensus size: 294
1737 TGTTTCGATA
** * *
1747 TAATTAGAAATTAATTTTGAAAAACTACAAAAAAACGATATTAGAAATGTCAAAAGCCCTTCAAT
1 TAATTAGAAATTAATTCAGAAAAACTACAAAAAAACGATATTAGAAACGTCAAAAGCCCTCCAAT
* * ** *
1812 CTTTTTGGTGTTGAATTATATATGTTTTTATGACTATTTTAGCCAAAAATTGAGAAAATATCTTT
66 CTTCTTGGCGTCAAATTATATATGATTTTATGACTATTTTAGCCAAAAATTGAGAAAATATCTTT
* * **
1877 CGAGTTAATTTTTACAAAATTTTATCTGAAATCGTGTAATAACCATCACAGTTTTTGGCTAAAAA
131 CGAGTTAATTTGTACAAAATTTTAGCCAAAATCGTGTAATAACCATCACAGTTTTTGGCTAAAAA
* * ** *
1942 AAACGTTCTGGGACCCCGACTCAGTTTTGCATGATTTTTTATGCCAGGTCTCCTTGAGATATGC-
196 AAACGTTCTGGGACCCCGACTCAGTTTTGCATGATTTTTGACGCCAGCACTCCTTGAAATAT-CT
* * *
2006 ATATTCATCTAATCAAATTTTAGCCACATTGGATT
260 ATATTCATCTAATAAAATCTTAGCCACATTGCATT
** * *
2041 TAATTAGAAATTAATTCAGAAAAA-TA-TGAAAAGCGATATTA-AAAGCGTGAAAAGCCCTCCAA
1 TAATTAGAAATTAATTCAGAAAAACTACAAAAAAACGATATTAGAAA-CGTCAAAAGCCCTCCAA
* * * * *
2103 TCTTCTTGGCGTCAAATTATATAT-ATTTTATGAGTATTTTATCCAAAACTTGGGGAAAAT-TTT
65 TCTTCTTGGCGTCAAATTATATATGATTTTATGACTATTTTAGCCAAAAATT-GAGAAAATATCT
* * * * * *
2166 TTTGGGTTTTTATTTGTGCAAAATTTTAGCCAAAATCGTGTACTAACCCATCACGGTTTTTTGGC
129 TTCGAG--TTAATTTGTACAAAATTTTAGCCAAAATCGTGTAATAA-CCATCACAG-TTTTTGGC
*** * * * * *
2231 T-AAAAACTTGTT-TCGGGGCCCTGCCTCAGTTTTGCATGGTTTTTGGCGCC-GACACTCCTTGA
190 TAAAAAAAACGTTCT-GGGACCCCGACTCAGTTTTGCATGATTTTTGACGCCAG-CACTCCTTGA
*
2293 AATATCTATATTCATCTGATAAAATCTTAGCCACATTGCATT
253 AATATCTATATTCATCTAATAAAATCTTAGCCACATTGCATT
2335 TAA
1 TAA
2338 GGATTTGTTT
Statistics
Matches: 243, Mismatches: 45, Indels: 18
0.79 0.15 0.06
Matches are distributed among these distances:
291 32 0.13
292 53 0.22
293 36 0.15
294 113 0.47
295 9 0.04
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.37
Consensus pattern (294 bp):
TAATTAGAAATTAATTCAGAAAAACTACAAAAAAACGATATTAGAAACGTCAAAAGCCCTCCAAT
CTTCTTGGCGTCAAATTATATATGATTTTATGACTATTTTAGCCAAAAATTGAGAAAATATCTTT
CGAGTTAATTTGTACAAAATTTTAGCCAAAATCGTGTAATAACCATCACAGTTTTTGGCTAAAAA
AAACGTTCTGGGACCCCGACTCAGTTTTGCATGATTTTTGACGCCAGCACTCCTTGAAATATCTA
TATTCATCTAATAAAATCTTAGCCACATTGCATT
Found at i:3931 original size:330 final size:328
Alignment explanation
Indices: 2037--4071 Score: 1642
Period size: 336 Copynumber: 6.2 Consensus size: 328
2027 AGCCACATTG
* * *
2037 GATTTAATTAGAAATTAATTCAGAAAAATATGAAAAGCGATATTAAAAGCGTGAAAAGCCCTCCA
1 GATTTAATTAGAAATTAATTCAAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCA
* * ** * * * * *
2102 ATCTTCTTGGCGTCAAATTATATATATTTTATGAGTATTTTATCCAAAACTTGGGGAAA-ATTTT
66 ATATTTTTGGCGTTGAATTATATATATTTTATGAGTATTGTAGCCAAAAATT-GAGAAATAATTT
* ** * ** *
2166 TTTGGGTTTTTATTTGTGCAAAATTTTAGCCAAAATCGTGTACTAACCCATCACGGTTTTTTGGC
130 TTCGGG--TCAATTTTTGCAAAATTTTAGCTGAAATCGTG---TAA-CCATCAC-GTTTTTTTGC
** * * * * * * * *
2231 TAAAAACTTGTTTCGGGGCCCTGCCTCAGTTTTGCATGGTTTTTGGCGCCGACACTCCTTGAAAT
188 TAAAAACGCGTTCCAGGGCCCCGCTTCAATTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAAT
* * * * * *
2296 ATCTATATTCATCTGATAAAATCTTAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTA
253 ATCTATATTCATCTAATCAAATCTCAGCCAAATTGGATTTAAGGATTTGTTTTTACGAGCATCTG
*
2361 AATTTTGTTTC
318 AATCTTGTTTC
* * *
2372 GATTTAATTAGAAATTAATTTAGAAAAAAATATGAAAAACGATATTAAAAGCGTG-AAAGCCCTT
1 GATTTAATTAGAAATTAA-TT-CAAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTC
* * * * * * * * *
2436 CAATCTTTTTGGCATTGATTTATATATTTTTTATAAGTATTATGGCTAAAAATTGATGATAT-AT
64 CAATATTTTTGGCGTTGAATTATATATATTTTATGAGTATTGTAGCCAAAAATTGA-GAAATAAT
* * * * * * * * *
2500 CTTTCGGGTCAATTTTTACAAAATTTTAACCGAAATCGTGTAATAATCATTAGGGTTTTTGGCTA
128 TTTTCGGGTCAATTTTTGCAAAATTTTAGCTGAAATCGTG---TAACCATCACGTTTTTTTGCTA
* * * * * *
2565 AAAACGCGTT-CTGGGGCCCGATTCAATTTTGAATGATTTTTGGCACCGAGACTCCTTGAAATAT
190 AAAACGCGTTCCAGGGCCCCGCTTCAATTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATAT
* * * * * **
2629 CTATATTAATCTAAGCAAATCCCAACC--ATT-G-TTTTACCA---------A--A-CATCTGAA
255 CTATATTCATCTAATCAAATCTCAGCCAAATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAA
*
2678 TCATGTTTC
320 TCTTGTTTC
* * * * * * * *
2687 GTTTTAATTAGAAATTAATGCGGAAAAAATAGGAAAAATGATATTAGAAGCGTGAAAAGCCCTTC
1 GATTTAATTAGAAATTAATTC-AAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCC
* * * * * ** *
2752 AATCTTTTTAGCGTTGAATTATATATTTTTTATGAG-ATTGT-GGCTAAAATAAAAGGAAA-ATT
65 AATATTTTTGGCGTTGAATTATATATATTTTATGAGTATTGTAGCCAAAAAT-TGA-GAAATAAT
* * * * *
2814 TTTTCTGGTCATTTTTTTACAAATTTTTAGCTGAAATCGTGTATTAACCATCACGGTTTTCTTTC
128 TTTTCGGGTCA-ATTTTTGCAAAATTTTAGCTGAAATCGTG---TAACCATCAC-GTTTT-TTTG
* * * * * *
2879 CTAAAAATGCGTTTC-GGGACCCGGTTCAATTTTACATGATTTTTGGCGTCAAGACTCCTTGAAA
187 CTAAAAACGCGTTCCAGGGCCCCGCTTCAATTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAA
* * * * * * *
2943 TATCTATATTCATCTAATCAAGTATCATCCAGATTGCATTTAAGGATTTCTTTTTACGTGCATCT
252 TATCTATATTCATCTAATCAAATCTCAGCCAAATTGGATTTAAGGATTTGTTTTTACGAGCATCT
* * *
3008 AAATATTTTTTC
317 GAATCTTGTTTC
* * * * *
3020 GGTTTAATTAGAAATTAATTCAGAAAAATCTCAAAAACGATATTAAATGCGTGAAAAGTCCTCCA
1 GATTTAATTAGAAATTAATTCAAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCA
* * * * * * *
3085 ATCTTTTTTGAGTTGAATTATATATATTTTATAAGTAATT-TAGACAAAAATTGAGAAAAAAATA
66 ATATTTTTGGCGTTGAATTATATATATTTTATGAGT-ATTGTAGCCAAAAATTGAG-AAATAATT
* * * * * * *
3149 TTTCTGGTCAATTTTTGCAAAATATTAGCCGATATCGTGTACGTTAGTCGAAATCACGGTTTTTG
129 TTTCGGGTCAATTTTTGCAAAATTTTAGCTGAAATCGTGTA----A--C--CATCACGTTTTTTT
* * * * * * * *
3214 GCTAAAAACCCGTTCCTGGGCCCAGGTTCAATGTTGCATGATTTTTTGCGTCTAGACTCCTT-AA
186 GCTAAAAACGCGTTCCAGGGCCCCGCTTCAATTTTGCATGATTTTTGGCGCCAAGACTCCTTGAA
* ** * * *** *
3278 ATATCTACATTCATCTAGCCAAATTTCAGCCAAATTGGATTTAAGGATTCG-TAAAACTAGCATC
251 ATATCTATATTCATCTAATCAAATCTCAGCCAAATTGGATTTAAGGATTTGTTTTTACGAGCATC
* *
3342 TGAATCATGTTTT
316 TGAATCTTGTTTC
* * * * * *
3355 GTTTTAATTAGAAATTAATTCGGAAAATAATAGGAAAAATGATATTAGAAGCATGAAAA-TACCT
1 GATTTAATTAGAAATTAATTC--AAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGT-CCT
* * * *
3419 TCAA-ACTTTTTGGCGTTGAATTATATA-ATTTTTATGAGTATTGTGGCTAAAACTTGAGGAAAT
63 CCAATA-TTTTTGGCGTTGAATTATATATA-TTTTATGAGTATTGTAGCCAAAAATTGA-GAAAT
** ** * * * *
3482 AA-CCTTCGAATCAATTTTTGCAAAATTCTAGCCGATCGAAATCATGTAATAATCATCACG-GTT
125 AATTTTTCGGGTCAATTTTTGCAAAATTTTAG-C--T-GAAATC--GT-GTAACCATCACGTTTT
3545 TTTGCCTAAAAACGCGTTCCAGGGCCCCGGC-T-AAGTTTTGCATGATTTTTGGCGCCAAGACTC
183 TTTG-CTAAAAACGCGTTCCAGGGCCCC-GCTTCAA-TTTTGCATGATTTTTGGCGCCAAGACTC
* * * * ** *
3608 TTTGAGATATCCATATTCATATAATCAAATCTCAGGTAAATTGGATTTAAGAATTTGTTTTTACG
245 CTTGAAATATCTATATTCATCTAATCAAATCTCAGCCAAATTGGATTTAAGGATTTGTTTTTACG
3673 AGCATCTGAATCTTGTTTC
310 AGCATCTGAATCTTGTTTC
* * *
3692 GATTTAATTAGAAATTAATTCAAAAAAAATATGAAGAACAATATTAAAAGCTTGAAAAGTCCTCC
1 GATTTAATTAGAAATTAATTC-AAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCC
* * *
3757 AATATTTTTGGCGTTAAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGACGTAATAATT
65 AATATTTTTGGCGTTGAATTATATATATTTTATGAGTATTGTAGCCAAAAATTGA-GAAATAATT
*
3822 TTTCGGGTCATTTTTTGCAAAATTTTAGCTGAAATCGTGT-ACCATCACGATTTTTTTGCTAAAA
129 TTTCGGGTCAATTTTTGCAAAATTTTAGCTGAAATCGTGTAACCATCACG-TTTTTTTGCTAAAA
* *
3886 ACGCGTTTCAGGGCCCCGACTT-AGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCT
193 ACGCGTTCCAGGGCCCCG-CTTCAATTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCT
* * * * *
3950 ATATTAATCTAATCAAATCTCAGCCACATTGAATTGAAGGATTTGTTTTTACGAGCATCTGAATT
257 ATATTCATCTAATCAAATCTCAGCCAAATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATC
4015 TTGTTTC
322 TTGTTTC
* * *
4022 GATTTAATAAGAAATTAATTCAGAAGAATATG-AAAACGATATTAAAAGCG
1 GATTTAATTAGAAATTAATTCAAAAAAATATGAAAAACGATATTAAAAGCG
4072 GGTAATTTTT
Statistics
Matches: 1350, Mismatches: 281, Indels: 145
0.76 0.16 0.08
Matches are distributed among these distances:
313 6 0.00
314 47 0.03
315 107 0.08
316 5 0.00
317 80 0.06
318 2 0.00
319 3 0.00
321 5 0.00
327 5 0.00
328 15 0.01
329 21 0.02
330 147 0.11
331 74 0.05
332 85 0.06
333 70 0.05
334 62 0.05
335 108 0.08
336 276 0.20
337 216 0.16
338 6 0.00
339 1 0.00
340 5 0.00
342 2 0.00
343 2 0.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.37
Consensus pattern (328 bp):
GATTTAATTAGAAATTAATTCAAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCA
ATATTTTTGGCGTTGAATTATATATATTTTATGAGTATTGTAGCCAAAAATTGAGAAATAATTTT
TCGGGTCAATTTTTGCAAAATTTTAGCTGAAATCGTGTAACCATCACGTTTTTTTGCTAAAAACG
CGTTCCAGGGCCCCGCTTCAATTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATAT
TCATCTAATCAAATCTCAGCCAAATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
TTC
Found at i:4336 original size:16 final size:16
Alignment explanation
Indices: 4317--4367 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
4307 TATAAAATAA
4317 AAATTTGATTAATTAT
1 AAATTTGATTAATTAT
* * *
4333 AAATATGA--AA-CAA
1 AAATTTGATTAATTAT
4346 AAATTTGATTAATTAT
1 AAATTTGATTAATTAT
4362 AAATTT
1 AAATTT
4368 AGAGAAATTT
Statistics
Matches: 26, Mismatches: 6, Indels: 6
0.68 0.16 0.16
Matches are distributed among these distances:
13 8 0.31
14 2 0.08
15 2 0.08
16 14 0.54
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.41
Consensus pattern (16 bp):
AAATTTGATTAATTAT
Found at i:4347 original size:29 final size:29
Alignment explanation
Indices: 4305--4365 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
4295 AATTCAAAAG
*
4305 AATATAAAATAAAAATTTGATTAATTATA
1 AATATAAAACAAAAATTTGATTAATTATA
*
4334 AATATGAAACAAAAATTTGATTAATTATA
1 AATATAAAACAAAAATTTGATTAATTATA
4363 AAT
1 AAT
4366 TTAGAGAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (29 bp):
AATATAAAACAAAAATTTGATTAATTATA
Found at i:7424 original size:212 final size:201
Alignment explanation
Indices: 7015--7429 Score: 607
Period size: 212 Copynumber: 2.0 Consensus size: 201
7005 TGAGAAAATT
7015 ATACAAGCAAATTAGCGTGTTGATTTCCATGGAAAATTAATAAGTCAAACAAATTAATTAATGAT
1 ATACAAGCAAATTAGCGTGTTGATTTCCATGGAAAATTAATAAGTCAAACAAATTAATTAATGAT
7080 TTCTCCAAACAAATCAATTAGTCAAACAAATTAATTGATAATAAAGTCTCTACTTTTTGTAAAAT
66 TTCTCCAAACAAATCAATTAGTCAAACAAATTAATTGATAATAAAGTCTCTACTTTTTGTAAAAT
**
7145 TCTCTATTCTTCAATAATTCCCTTGGCAAACAAAATGAGTAGGATCTTAGAGGAGCATATCTTAC
131 TCTCTATTCTTCAATAATTCCCTTGGCAAACAAAATGAGTAAAATCTTAGAGGA-CATATCTTAC
7210 TAACTCA
195 TAACTCA
* * **
7217 ATACAAGTAAATTGGCGTGTTGATTTTGATGGAAAATTAATAAGTCAAACAAATTAATTAATGAT
1 ATACAAGCAAATTAGCGTGTTGATTTCCATGGAAAATTAATAAGTCAAACAAATTAATTAATGAT
*
7282 TTCTACAAACAAATCAATAATCAATTAGTCAAACAAATTAATTGATAATAATAAAGTTTCTACTT
66 TTCT-C---CAAA-C-A-AATCAATTAGTCAAACAAATTAATTG---ATAATAAAGTCTCTACTT
* * * *
7347 TTTGTAAAATTCTCTATTTTTTAATAATTTCTTTGGCAAACAAAATGAGTATAAAATCTTAGAGG
121 TTTGTAAAATTCTCTATTCTTCAATAATTCCCTTGGCAAACAAAATGAG--TAAAATCTTAGAGG
7412 A-ATATCTTACTAACTCA
184 ACATATCTTACTAACTCA
7429 A
1 A
7430 ATTACTAAAC
Statistics
Matches: 190, Mismatches: 11, Indels: 14
0.88 0.05 0.07
Matches are distributed among these distances:
202 65 0.34
203 1 0.01
206 4 0.02
207 1 0.01
208 1 0.01
209 26 0.14
212 79 0.42
214 13 0.07
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.34
Consensus pattern (201 bp):
ATACAAGCAAATTAGCGTGTTGATTTCCATGGAAAATTAATAAGTCAAACAAATTAATTAATGAT
TTCTCCAAACAAATCAATTAGTCAAACAAATTAATTGATAATAAAGTCTCTACTTTTTGTAAAAT
TCTCTATTCTTCAATAATTCCCTTGGCAAACAAAATGAGTAAAATCTTAGAGGACATATCTTACT
AACTCA
Found at i:8284 original size:192 final size:194
Alignment explanation
Indices: 7928--8288 Score: 505
Period size: 192 Copynumber: 1.8 Consensus size: 194
7918 TACACAAACA
* * *
7928 AATTTACACTAAAAGTGTATTGTATAATAATCTTATAAGAAAAATTATACTATACATCGTCGGTC
1 AATTTACACTAAAAGTGTATTGTATAATAATCATATAAGAAAAATTATACTATACACCGTCAGTC
* * * *
7993 GAGTTTAGCAGACTGCATGTGTAGGGTTTAATGGTTGACATGTGTCCCCTTAAGGAACATATATT
66 GAGTTTAACAGACTACACGTGCAGGG--T--T-GTTGACATGTGTCCCCTTAAGGAACATATATT
* *
8058 AATATTAAATATTTAATTTATTATGAAATGAGGTATGTGTCAACTTCTTAACCCGTTTATGGAGT
126 AATATTAAATATTTAATTAATGATGAAATGAGGTATGTGTCAACTTCTTAACCCGTTTATGGAGT
8123 CCAG
191 CCAG
* *
8127 AATTTACACTGACAGTGTATTGTATAAATAATCATATAAGAAAAA-TATACTATACACCGTCAGT
1 AATTTACACTAAAAGTGTATTGTAT-AATAATCATATAAGAAAAATTATACTATACACCGTCAGT
* * *
8191 GGAAGTTTAACAGACTACACGTGCAGGG-T-TTGACATGTGTCCCCTT-AGGAATATGTATTAAT
65 CG-AGTTTAACAGACTACACGTGCAGGGTTGTTGACATGTGTCCCCTTAAGGAACATATATTAAT
8253 ATTAAATATTTAATTAATGATGAAATGAGGTATGTG
129 ATTAAATATTTAATTAATGATGAAATGAGGTATGTG
Statistics
Matches: 146, Mismatches: 14, Indels: 11
0.85 0.08 0.06
Matches are distributed among these distances:
192 48 0.33
193 17 0.12
195 1 0.01
199 41 0.28
200 39 0.27
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (194 bp):
AATTTACACTAAAAGTGTATTGTATAATAATCATATAAGAAAAATTATACTATACACCGTCAGTC
GAGTTTAACAGACTACACGTGCAGGGTTGTTGACATGTGTCCCCTTAAGGAACATATATTAATAT
TAAATATTTAATTAATGATGAAATGAGGTATGTGTCAACTTCTTAACCCGTTTATGGAGTCCAG
Done.