Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020717.1 Corchorus olitorius cultivar O-4 contig20750, 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: 25841
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Found at i:740 original size:331 final size:330
Alignment explanation
Indices: 1--805 Score: 917
Period size: 331 Copynumber: 2.4 Consensus size: 330
* ** * * ** * *
1 CATCTAACTAAATCTCAGCCACATTTTATTTAAGAATTTGTTTGTACGAGTTTCTAAATCTTGTT
1 CATCTAACAAAATCTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTATT
* * * * * *
66 TCGATTTAATCAGAAATTAATTTTGAAATAAAATAGGAAAAACGATATTAGAAGCGTGAAAAAGT
66 TCGATTTAATTAGAAATTAA-TTCG-GA-AAAATAGGAAAAACAATATTAGAAGCATGAAAAAGC
* * * * * * * *
131 CTTTCAATTTTTTTGGTGTTGAATTATTTGTTTTTTATGAGTATTTTCACTAGAAAACGAGGAAA
128 CCTTCAATCTTTTTGATATCGAATTATATATTTTTTATGAGTATTTTCACCAGAAAACGAGGAAA
* *
196 AATCTTTCGGGTCATTTTTTGCATAATTTAGCCGAAATCGTGTACTAACCATCACGGTTTTCGGC
193 AATCTTTCGGGTCAATTTCTGCATAATTTAGCCGAAATCGTGTACTAACCATCACGGTTTTCGGC
* * *** * *
261 TAAAAACGCGTTCCGGAGCCCGACTCAGTTTTGCATGATTTTGGGTGTCAAGACTTCTTGAAGTA
258 TAAAAACGCGTTACAGAGCCCGACTCAGTTTTGCATGATTTTGGCACTCAAGACTCCTTGAAATA
326 TTTGTATT
323 TTTGTATT
* * *
334 CATCTAACCAAATCTTAGCCACATTAGATTTAAGGATTTATTTTTACGAGCATCTGAATCTTATT
1 CATCTAACAAAATCTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTATT
* *
399 TCGATTTAATTAGAAATTAATTCGGAAAAATAGTAAAAGA-AATATTAGAAGCAT-TAAAAGCCC
66 TCGATTTAATTAGAAATTAATTCGGAAAAATAGGAAAA-ACAATATTAGAAGCATGAAAAAGCCC
*
462 TTCAATCTTTTTGATATCGAATTATATATTTTTTATGAGTATTTT-AGCCA-AAAATTGAGGAAA
130 TTCAATCTTTTTGATATCGAATTATATATTTTTTATGAGTATTTTCA-CCAGAAAA-CGAGGAAA
* * **
525 TATCTTTCGGGTCAATTTCTGCA-AAGTTTTAGCCGAAATTGTGTACTAACCATCACGGTTTTTT
193 AATCTTTCGGGTCAATTTCTGCATAA--TTTAGCCGAAATCGTGTACTAACCATCACGGTTTTCG
* *
589 GCTAAAAACGCGTTACAGAGCCACGGCTCTA-TTTTGCATGATTTTTGGCACT-GAGACTCCTTG
256 GCTAAAAACGCGTTACAGAGCC-CGACTC-AGTTTTGCATGA-TTTTGGCACTCAAGACTCCTTG
652 AAATATCTT-TATT
318 AAATAT-TTGTATT
* * * * *
665 CATCTAACAAAATCTCAGTCGCATTGGATTTAAGGATTTGTTTTTATGTGCATCTGAATCTTATT
1 CATCTAACAAAATCTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTATT
* * * * * * *
730 TCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACCATATTAAAATCGTG-AAAAGTCC
66 TCGATTTAATTAGAAATTAATTC-GGAAAAATAGGAAAAACAATATTAGAAGCATGAAAAAGCCC
*
794 TCCAATCTTTTT
130 TTCAATCTTTTT
806 TGGCATCTTT
Statistics
Matches: 400, Mismatches: 60, Indels: 25
0.82 0.12 0.05
Matches are distributed among these distances:
328 7 0.02
329 74 0.19
330 77 0.19
331 116 0.29
332 53 0.13
333 73 0.18
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (330 bp):
CATCTAACAAAATCTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTATT
TCGATTTAATTAGAAATTAATTCGGAAAAATAGGAAAAACAATATTAGAAGCATGAAAAAGCCCT
TCAATCTTTTTGATATCGAATTATATATTTTTTATGAGTATTTTCACCAGAAAACGAGGAAAAAT
CTTTCGGGTCAATTTCTGCATAATTTAGCCGAAATCGTGTACTAACCATCACGGTTTTCGGCTAA
AAACGCGTTACAGAGCCCGACTCAGTTTTGCATGATTTTGGCACTCAAGACTCCTTGAAATATTT
GTATT
Found at i:5980 original size:2 final size:2
Alignment explanation
Indices: 5973--5997 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5963 GGCGTTAAAT
5973 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5998 TATGAGTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7128 original size:333 final size:332
Alignment explanation
Indices: 5146--7996 Score: 1888
Period size: 333 Copynumber: 8.6 Consensus size: 332
5136 ATACTTTACA
* * * * * *
5146 TCATCTAACCAAATTTCAGCAACATTGGATTTAAGAATTTGTTTTTACGAGCATCTAAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * * * *
5211 TTCGATTTAATTAGAAATCAATTTAGAAAAAATAAGAAATACGATATTAAA-AGTGTATAAAGCC
66 TTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATA-TAAAGCGTG-A-AAAGTC
5275 CTCCAATCTTTTTGGC-TTGAATTATATAT-TTTTATGAGTATTTTAGCCAATAATTGAGGAGAA
128 CTCCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTAGCCAA-AATTGAGGA-AA
* * * * *
5338 AT-CTTTCAT-GTCAATTTTTGCAAAATTATAGCCGAAATAGTATACTAACAAACCATCATGGTT
191 ATACTTTC-TGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAAC-TATCA-CA--G-T
* * * * * ** * *
5401 TTTTTTTTTGACTAAAAACGCGTTCCGGGGACCTGACACAATTCCGCATGATTTTTGGCTCCAAG
250 TTTTTTTTTG-CTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCTAAG
*
5466 ACTACTTGAACTATCTATAT
314 ACTCCTTGAA-TATCTATAT
* * *
5486 TCATCTAATCCAAATCTCAGCCACATTGGATTTAAGAATTTGTTTTTACGATCATCTGAATCTTT
1 TCATCTAAT-CAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATC-TT
* * * * *
5551 GTTTCGATCTAATAATTAGAAATTAATT-TGGAAAAATAGGAAAAACGATATTAGAAACGTCAAA
64 GTTTCGAT-T--TAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATA-TA-AAGCGTGAAA
* * * * *
5615 AGCCCTTCAATCTTATTGGCGTTGCATTATATA-ATTTTTATGAGTATTTTAGCTCAAAATTTAG
124 AGTCCTCCAATCTTTTTGGCGTTGAATTATATATA-TTTTATGAGTATTTTAGC-CAAAATTGAG
* * * * *
5679 GAAAA-ACCTTTCGGGTTAATTTTTACAAAATTTTAGCCGAAATCATGTAATAA-TCATCACAG-
187 GAAAATA-CTTTCTGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACT-ATCACAGT
* * * *
5741 ---TTTTTGGCTAAAAAAGCGTTTCGGGGCCCCGGCTCAGTTTTGCACGATTTTTGGCG-TCAAG
250 TTTTTTTTTGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCT-AAG
*
5802 ACTCCTTGAGATATCCATAT
314 ACTCCTTGA-ATATCTATAT
* * * ** * *
5822 TGATCTAATCAAAACTCGGCCATGTTGGATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* *
5887 TTTGATTTAATTAGAAATTAATTCA-AAAAAATATGAAGAACGATATTAAAAGCGTGAAAAGTCC
66 TTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATA-T-AAAGCGTGAAAAGTCC
* * *
5951 TCCAATCTTTTTGGCGTTAAATTATATATATATATATATATATATATTATGAGTATTTTATCTAA
129 TCCAATCTTTTTGGCG--------T-T-GA-AT-TATATATAT-T-TTATGAGTATTTTAGC-CA
* * * * * *
6016 AAATTGAGGAAAA-ACTTT-TCGGTTCATTTTTTACAAAATTTGAGTCAAAATTGTGTAC---C-
179 AAATTGAGGAAAATACTTTCT-GG-TCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACT
* * *
6075 ATCAC-G-----GTTTTGCCTAAAAACGTGTTTCGGGGCCCC-AGCTTAGTTTTGCATGATTTTT
242 ATCACAGTTTTTTTTTTG-CTAAAAACGCGTTTCGGGGCCCCGA-CTCAGTTTTGCATGATTTTT
* * *
6133 GGCGTTGACACTCCTTGAATTATCTATAT
305 GGCGCTAAGACTCCTTGAA-TATCTATAT
* * * * *
6162 TCATCTAATAAAATCTTAGCCACATTGCATTTAAAGATTTGCTTTTACGAGCATCTGAAACTTGT
1 TCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* **
6227 TTCGATTTAATTAGAAATTAATTCAG-AAAAATATGAAAAATGATATTAAA--AAGAAAA-TCCC
66 TTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATA-TAAAGCGTGAAAAGT-CC
* * * * * * *
6288 TTCC-ATTTTTTTGACGTTGAATTATATATTTTTTATGAGTATTATGGCTAAAATTGAGAAAAAT
129 -TCCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTAGCCAAAATTGAGGAAAAT
* * *
6352 A-TTTCGGGTCAATTTTTTTGC-AAATATTAGCCAAAATCGTG---TAAC-ATCAC-GTTTTTTT
193 ACTTTCTGGTCAA--TTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACTATCACAG---TTTT
* * * ** * * * *
6410 TTTTTTGCTAAAAATGTGTTCTGGGGGCCCCGGGTCAGTTTTGCAAGATTTTTTGCGCCAAAACT
253 TTTTTTGCTAAAAACGCGTT-TCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCTAAGACT
6475 CCTTGAAATATC--TA-
317 CCTTG-AATATCTATAT
* * * * *
6489 T-A--T-ATCAAATCTCAACCACATTGGATATAAGGATTTCTTTTTACGAGCATCTAAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * * * * * * * **
6550 TTCCAATTGATTAGATATTAATTCGGAAAAAATAGGAAAAACGATATTAGAAGCATAAAAAAAAC
66 TTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATA-TA-AAGCGT--GAAAAGT
* * * ** *
6615 CCTTCAATATTTTTGGAGTTGAATTATAT-TATTTTTGATGAGTATACTAACCAAAAATTGAGG-
127 CCTCCAATCTTTTTGGCGTTGAATTATATATA-TTTT-ATGAGTATTTTAGCC-AAAATTGAGGA
* * * * **
6678 AAATACCTTTCCGGTCAATTCTTGCAAAATTTTATCTGAAATCGTGTTTTAA-TCATCACAG---
189 AAATA-CTTTCTGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACT-ATCACAGTTT
* * * * * * ** *
6739 -TTTTTTGACTGAAAACACGTTCCAGGGTCCTGGGTCAGTTTTGCATGTTTTTTGGCGCTAAGAC
252 TTTTTTTG-CTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCTAAGAC
* *
6803 TCCTTGAGATATCCATTT
316 TCCTTGA-ATATCTATAT
* ** *
6821 TTATCTAATCAAATCTCAGCCACATCACATTTAAGGATTT-TTTTTACGAGCATCTGAATATTGT
1 TCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * *
6885 TTTGATTTAATTAGAAAATAATTCAGAAAAAACATGAAAAACGATATGCAAAGCGTGAAAAGTCC
66 TTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATAT--AAAGCGTGAAAAGTCC
* * *
6950 TCCAATCTTTTTGGCGTTGAATTATATGTATTTCATGAGTATTTTTGCCAAAATTGAGGAAAATA
129 TCCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTAGCCAAAATTGAGGAAAATA
* * *
7015 -TTTCTGGTCATTTTTTGCAAAATTTTAGCTGAAATCGTATACTAACTATCACAGTTTTTTTTTT
194 CTTTCTGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACTATCACAG-TTTTTTTTT
* *
7079 TGTTAAAAACGCATTTCGGGG-CCCGACTCAGTTTTGCATGATTTTTGGCGTCT-AGACTCCTTG
258 TGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCG-CTAAGACTCCTTG
7142 AAATATCTATAT
322 -AATATCTATAT
* * * * * * *
7154 TCATCTAATCTAGTCTCAGCCATATTGCAGTTAAGGATTTATTTTTACGAGCATATGAATTTTGT
1 TCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * *
7219 TTCGATTTAATTAAAAATTAATTCAGAAAATA-ATGAAAAACGATATTAA---TGAAAAGTCCTC
66 TTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATAAAGCGTGAAAAGTCCTC
** * * *
7280 CAATCTTTTTGAAGTTGAATTAAATATATTTTATGAGTATTGTAGACAAAAATTGA-GAAAA-A-
131 CAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTAG-CCAAAATTGAGGAAAATAC
* * * * * *
7342 ---------AATATTAGACAAAATATTAGCCGAAATTGTGTACGTTAAGTCGAAATCAC-G---A
195 TTTCTGGTCAATTTTTG-CAAAATTTTAGCCGAAATCGTGTAC--TAA--C--TATCACAGTTTT
** * * ** * * * *
7394 TTTTCGGCTAAAAAAGCG-TTCTGGAGCCCCGGTTCAGTGTTGCATGATTTTTCGTGCCAAGACT
253 TTTTTTGCTAAAAACGCGTTTC-GGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCTAAGACT
*
7458 CTTTGAAATATCTATAT
317 CCTTG-AATATCTATAT
* * ** *** * * * *
7475 TTATGTAA-CTAAATCTCAGCCACATTGGTTTTAAGGATTTG-TAAAACAAGCATTTAAATCATG
1 TCATCTAATC-AAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTG
* * * *
7538 TTTCGATTTAATTAGAAATT-ATTTAGGAAAATAATAGGGAAAACGATATTAGAAGCATG-AAAG
65 TTTCGATTTAATTAGAAATTAATTCA-GAAAA-AATATGAAAAACGATA-TA-AAGCGTGAAAAG
* * * * * * *
7601 GCCTTTCAATATTTTTGGCGTTAAATTATAAATATTTTATGAGTATTGCTA-CTAAAAATTGAGG
126 TCC-TCCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATT-TTAGC-CAAAATTGAGG
* * *** * ** * * *
7665 -AATTAACATTCAAATCAATTTTTGCAAAATTCTAGCAAAAAATCATGGAATAA-TCATCAC-G-
188 AAAAT-ACTTTCTGGTCAATTTTTGCAAAATTTTAGC-CGAAATCGTGTACTAACT-ATCACAGT
* * * * * *
7726 --GTTTTTGGCTAACAACGCG-TTCTGGGG-CCCTAGCTAAGTTTTGCATGATTTTTGGTGGC-A
250 TTTTTTTTTGCTAAAAACGCGTTTC-GGGGCCCCGA-CTCAGTTTTGCATGATTTTTGG-CGCTA
* * * *
7786 ATACTCTTTGAGATCTCCATAT
312 AGACTCCTTGA-ATATCTATAT
* * * * * *
7808 TTATGTAATAAAATCTCAGCTACATTGGATTTAAGAATTTGTTTTTAC--G-A---GAATCTTGT
1 TCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
* * *
7867 TTCGATTTAATTAGAAATTAATTC-TAAAAAACATGAAAAACGATATTAAAAGCGTGAAAAGTAC
66 TTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATA-T-AAAGCGTGAAAAGTCC
** * * *
7931 TCCAATCTTTTTGGCACTAAATTATATATACTTTATAAGTATTTTAGCCAAAAATTGACGGAAAA
129 TCCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTAGCC-AAAATTGA-GGAAAA
7996 T
192 T
7997 TTTTTATTGT
Statistics
Matches: 2000, Mismatches: 357, Indels: 320
0.75 0.13 0.12
Matches are distributed among these distances:
318 5 0.00
319 28 0.01
320 56 0.03
321 82 0.04
322 52 0.03
323 91 0.05
324 25 0.01
325 17 0.01
326 76 0.04
327 65 0.03
328 94 0.05
329 107 0.05
330 122 0.06
331 103 0.05
332 33 0.02
333 225 0.11
334 86 0.04
335 122 0.06
336 96 0.05
337 27 0.01
338 13 0.01
339 22 0.01
340 167 0.08
341 54 0.03
342 13 0.01
343 8 0.00
344 51 0.03
345 92 0.05
346 65 0.03
347 3 0.00
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (332 bp):
TCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGT
TTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATAAAGCGTGAAAAGTCCTC
CAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTAGCCAAAATTGAGGAAAATACT
TTCTGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACTATCACAGTTTTTTTTTTGC
TAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCTAAGACTCCTTGAATA
TCTATAT
Found at i:9087 original size:339 final size:328
Alignment explanation
Indices: 8298--9578 Score: 963
Period size: 332 Copynumber: 3.8 Consensus size: 328
8288 TATGGACAAC
* * * * * * * *
8298 TTTTGCAAAATTTTAGCCGAAATTGTGTACCATCACTGTTTTTTTGGTTAAAAACGCGTTTCGGG
1 TTTTGCAAAATTTTAGTCAAAATCGTGTATCATCAC-GGTTTTTCGGCTAAAAACGCGTTACGGG
* * * * *
8363 GCCCCGGGTTAGTTTTGCATGATTTTTGATGACAAAACTCCTTGAAATATCTATATTCATA-TAA
65 G-CCCGGTTTAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAATTATCTATATTCA-ACTAA
* * * * * * * *
8427 CCATATCTTAGCCACATTGGATTTAAGGATTTATTTTTATGAGCAGT-TGAATCATGTTTCAATT
128 CTAAATCTCAG-CACATT-GATTTAAGGATTTGTTTTTACGAG-AATCTGAATCTTGTTTCGATT
* * * *
8491 TAATTAGAAATTAATCTT---AAAAAATAGGAAAAACGATATTATAAGCGTGAGAAGCCCTCCAA
190 TAATTAGAAATTAAT-TTGGAAAAAAATAGGAAAAACAATATTAGAAGAGTGAAAAGCCCTCCAA
* *
8553 TATTTTTGGCATTGAATTATATACTTTTTTATGAGTATTTGTGGCTAAAAATTGAGAAAAATATT
254 TATTTTTGGCATTGAATTATATACTTTATTATGAGTATTTGTCGCTAAAAATTGAGAAAAATATT
8618 TCGGGTCAAT
319 TCGGGTCAAT
* * * * * * * *
8628 TTTTGTAAAATTTTAGTCGAAATCGTGTATTATCATGGTTTTTTTGGCTAAAAACGCATTCCGGT
1 TTTTGCAAAATTTTAGTCAAAATCGTGTATCATCACGG-TTTTTCGGCTAAAAACGCGTTACGGG
* * * *
8693 GCCCTGTGTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTAAAATATATCTATATTCAACTA
65 GCCCGGT-TTAGTTTTGCATGATTTTTGGTGCCAAGACTCCTT-GAAT-TATCTATATTCAACTA
** * *
8758 ACTAAATCTCAGCAACATTGTATTTAAGGATTTGTTTTTACGAGTTTCTAAATCTTGTCTCGATT
127 ACTAAATCTCAGC-ACATTG-ATTTAAGGATTTGTTTTTACGAGAATCTGAATCTTGTTTCGATT
* * * * *
8823 TAATCATAAATTAATTTGGAAATAAAATAGGAAAAAACAATATTAGAAGAGTGACAAAGGCTTTC
190 TAATTAGAAATTAATTTGGAAA-AAAATAGG-AAAAACAATATTAGAAGAGTGA-AAAGCCCTCC
* * * *
8888 AATTTTCTTTTTGCGTTGAATTATATA-TATTATTATGAGTATTT-TCGCT-AGAATTCGAGGAA
252 AA-TAT-TTTTGGCATTGAATTATATACT-TTATTATGAGTATTTGTCGCTAAAAATT-GA-GAA
* *
8950 GAATCTTTCGGGTCAAT
312 AAATATTTCGGGTCAAT
* * *
8967 TTTTAGCAACATTTTATTCAAAATCGTGTACTAACCATCACGG-TTTTCGGGTAAAAACGCGTTA
1 TTTT-GCAAAATTTTAGTCAAAATCGTGTA-T---CATCACGGTTTTTCGGCTAAAAACGCGTTA
*
9031 CGGGGCCCGGTTTAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAATTATCTATATTCATCT
61 CGGGGCCCGGTTTAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAATTATCTATATTCAACT
* * * * *
9096 AA-TCAAATCTCAGGCACATTAGATCTAAGAATTTGTTTTTACGAGCATCTGAATTTTCTTTCGA
126 AACT-AAATCTCA-GCACATT-GATTTAAGGATTTGTTTTTACGAGAATCTGAATCTTGTTTCGA
* * * * *
9160 TTTAATTAGAAATT-ATTTGGAAAAAAAATAAGAAAAACAATATTAGAAGCGTTAAAATCCCTTC
188 TTTAATTAGAAATTAATTTGG-AAAAAAATAGGAAAAACAATATTAGAAGAGTGAAAAGCCCTCC
* ** * * * * * *
9224 AATCTTTTT-TTATGTCGAATTATATA-TTTGTTATCAGTATTT-TAGCCAAAAATTGGGGAAAT
252 AATATTTTTGGCAT-T-GAATTATATACTTTATTATGAGTATTTGTCGCTAAAAATT-GAGAAAA
* *
9286 ATTTTTC--ATCAAT
314 ATATTTCGGGTCAAT
* * * * *
9299 TTTTGTAAAATTTTAGCCGAAATCATGTATTAACCATCACGGTTTTT-GGC-AACAAACGCGTTC
1 TTTTGCAAAATTTTAGTCAAAATCGTGTA-T---CATCACGGTTTTTCGGCTAA-AAACGCGTTA
** * * * * ** * * * *
9362 CATGTCCACGACTCT-GTTTTGCATGATTTCTGGCACCGAGACTCCTTGAAATATCTTTATTCAT
61 CGGGGCC-CG-GTTTAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAATTATCTATATTCAA
* * * * * *
9426 CTGA-TCAAATCTCAACCATATTGGATTTAAGGATTTGCTTTTT--GTGCATATGAATCTTGTTT
124 CTAACT-AAATCTC-AGCACATT-GATTTAAGGATTTG-TTTTTACGAGAATCTGAATCTTGTTT
* * * * * * **
9488 TGATTTAATTAGAAATTAATTTAG-AAAAAATATGAAAAACGATATTAAAAGCA-CGAAAATTCC
185 CGATTTAATTAGAAATTAATTTGGAAAAAAATAGGAAAAACAATATTAGAAG-AGTGAAAAGCCC
* ** *
9551 TCAAATCCTTTTGGCGTTGAATTATATA
249 TCCAATATTTTTGGCATTGAATTATATA
9579 TATACACACA
Statistics
Matches: 771, Mismatches: 140, Indels: 81
0.78 0.14 0.08
Matches are distributed among these distances:
329 15 0.02
330 126 0.16
331 86 0.11
332 167 0.22
333 9 0.01
334 32 0.04
335 27 0.04
336 28 0.04
337 33 0.04
338 23 0.03
339 132 0.17
340 27 0.04
341 34 0.04
342 26 0.03
344 6 0.01
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (328 bp):
TTTTGCAAAATTTTAGTCAAAATCGTGTATCATCACGGTTTTTCGGCTAAAAACGCGTTACGGGG
CCCGGTTTAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAATTATCTATATTCAACTAACTA
AATCTCAGCACATTGATTTAAGGATTTGTTTTTACGAGAATCTGAATCTTGTTTCGATTTAATTA
GAAATTAATTTGGAAAAAAATAGGAAAAACAATATTAGAAGAGTGAAAAGCCCTCCAATATTTTT
GGCATTGAATTATATACTTTATTATGAGTATTTGTCGCTAAAAATTGAGAAAAATATTTCGGGTC
AAT
Found at i:9435 original size:332 final size:326
Alignment explanation
Indices: 8005--9539 Score: 1200
Period size: 315 Copynumber: 4.7 Consensus size: 326
7995 ATTTTTTATT
* ** ** *
8005 GTGTACTAACCATCATAGTTTTTGGCTAAAAACGCGTTTTGGGGCCCTGGAT-TAGTTTTGCATG
1 GTGTATTAACCATCACGGTTTTTGGC-AAAAACGCG-TTCCGGTCCC-GG-TCT-GTTTTGCATG
* * * * * ** *
8069 TTTTTTGACGCCGAGACTCCTTGAAATATCTACATTCATCTAATCAAATCTTAGCCACAACGAAT
61 ATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGAT
*
8134 TTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCT--GAA
126 TTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATT-TAAAAA
* * * * * * **
8197 AAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGCAT-TGAATTATATA
190 AAATAGGAAAAACAATATTAGAAGCGTGAAAAGCCCTTCAATATTTTT-TTATGTGAATTATATA
* * * *
8261 TATT-TTATGAGTA--TT-G---------GGGAAAAATATTAT-GGACAACTTTTGCAAAATTTT
254 T-TTATTATGAGTATTTTAGCCAAAAATTGGGGAAAATATT-TCGGTCAATTTTTGTAAAATTTT
*
8312 AGCCGAAAT-
317 AGTCGAAATC
* * * * *
8321 -TGT-GT-ACCATCACTGTTTTTTTGGTTAAAAACGCGTTTCGGGGCCCCGGGT-TAGTTTTGCA
1 GTGTATTAACCATCAC-G-GTTTTTGG-CAAAAACGCG-TTC-CGGTCCC-GGTCT-GTTTTGCA
** * * * * * *
8382 TGATTTTTGATGACAAAACTCCTTGAAATATCTATATTCATATAACCATATCTTAGCCACATTGG
59 TGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGG
* * * *
8447 ATTTAAGGATTTATTTTTATGAGCAGT-TGAATCATGTTTCAATTTAATTAGAAATTAATCTT--
124 ATTTAAGGATTTGTTTTTACGAGCA-TCTGAATCTTGTTTCGATTTAATTAGAAATTAAT-TTAA
* * * * **
8509 AAAAAATAGGAAAAACGATATTATAAGCGTGAGAAGCCCTCCAATATTTTTGGCAT-TGAATTAT
187 AAAAAATAGGAAAAACAATATTAGAAGCGTGAAAAGCCCTTCAATATTTTT-TTATGTGAATTAT
* * * * *
8573 ATACTTTTTTATGAGTATTTGTGGCTAAAAATTGAGAAAAATATTTCGGGTCAATTTTTGTAAAA
251 ATA-TTTATTATGAGTATTT-TAGCCAAAAATTGGGGAAAATATTTC-GGTCAATTTTTGTAAAA
8638 TTTTAGTCGAAATC
313 TTTTAGTCGAAATC
* * *
8652 GTGTATT----ATCATGGTTTTTTTGGCTAAAAACGCATTCCGGTGCCCTGTGTCAGTTTTGCAT
1 GTGTATTAACCATCACGG--TTTTTGGC-AAAAACGCGTTCCGGT-CCC-G-GTCTGTTTTGCAT
* * *
8713 GATTTTTGGCGCCAAGACTCCTTAAAATATATCTATATTCAACTAA-CTAAATCTCAGCAACATT
60 GATTTTTGGCGCCAAGACTCCTT-GAA-ATATCTATATTCATCTAATC-AAATCTCAGCCACATT
* ** * * * *
8777 GTATTTAAGGATTTGTTTTTACGAGTTTCTAAATCTTGTCTCGATTTAATCATAAATTAATTTGG
122 GGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTT--
* * * * * **
8842 AAATAAAATAGGAAAAAACAATATTAGAAGAGTGACAAAGGCTTTCAATTTTCTTTTTGCGTTGA
185 AAAAAAAATAGG-AAAAACAATATTAGAAGCGTGA-AAAGCCCTTCAATATT-TTTTTATG-TGA
* * * * *
8907 ATTATATATATTATTATGAGTATTTTCG-CTAGAATTCGAGGAAGAATCTTTCGGGTCAATTTTT
246 ATTATATAT-TTATTATGAGTATTTTAGCCAAAAATT-GGGGAA-AATATTTC-GGTCAATTTTT
* * * *
8971 AGCAACATTTTATTCAAAATC
307 -GTAAAATTTTAGTCGAAATC
* * * * * *
8992 GTGTACTAACCATCACGGTTTTCGGGTAAAAACGCGTTACGGGGCCCGGTTTAGTTTTGCATGAT
1 GTGTATTAACCATCACGGTTTT-TGGCAAAAACGCGTT-CCGGTCCCGGTCT-GTTTTGCATGAT
* * * * *
9057 TTTTGGTGCCAAGACTCCTTGAATTATCTATATTCATCTAATCAAATCTCAGGCACATTAGATCT
63 TTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTT
* * *
9122 AAGAATTTGTTTTTACGAGCATCTGAATTTTCTTTCGATTTAATTAGAAATT-ATTTGGAAAAAA
128 AAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTT--AAAAAA
* * * *
9186 AATAAGAAAAACAATATTAGAAGCGTTAAAATCCCTTCAATCTTTTTTTATGTCGAATTATATAT
191 AATAGGAAAAACAATATTAGAAGCGTGAAAAGCCCTTCAATATTTTTTTATGT-GAATTATATAT
* * * *
9251 TTGTTATCAGTATTTTAGCCAAAAATTGGGGAAATATTTTTC-ATCAATTTTTGTAAAATTTTAG
255 TTATTATGAGTATTTTAGCCAAAAATTGGGGAAA-ATATTTCGGTCAATTTTTGTAAAATTTTAG
*
9315 CCGAAATC
319 TCGAAATC
* * *
9323 ATGTATTAACCATCACGGTTTTTGGCAACAAACGCGTTCCATGTCCACGACTCTGTTTTGCATGA
1 GTGTATTAACCATCACGGTTTTTGGCAA-AAACGCGTTCC-GGTCC-CG-GTCTGTTTTGCATGA
* * * * * * *
9388 TTTCTGGCACCGAGACTCCTTGAAATATCTTTATTCATCTGATCAAATCTCAACCATATTGGATT
62 TTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATT
* * * *
9453 TAAGGATTTGCTTTTT--GTGCATATGAATCTTGTTTTGATTTAATTAGAAATTAATTTAGAAAA
127 TAAGGATTTG-TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTAAAAAA
* * *
9516 AATATGAAAAACGATATTAAAAGC
191 AATAGGAAAAACAATATTAGAAGC
9540 ACGAAAATTC
Statistics
Matches: 983, Mismatches: 170, Indels: 118
0.77 0.13 0.09
Matches are distributed among these distances:
313 7 0.01
314 1 0.00
315 203 0.21
316 20 0.02
318 1 0.00
319 1 0.00
320 1 0.00
328 3 0.00
329 19 0.02
330 106 0.11
331 84 0.09
332 168 0.17
333 9 0.01
334 27 0.03
335 32 0.03
336 31 0.03
337 36 0.04
338 27 0.03
339 120 0.12
340 27 0.03
341 32 0.03
342 17 0.02
343 5 0.01
344 6 0.01
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (326 bp):
GTGTATTAACCATCACGGTTTTTGGCAAAAACGCGTTCCGGTCCCGGTCTGTTTTGCATGATTTT
TGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAG
GATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTAAAAAAAATAG
GAAAAACAATATTAGAAGCGTGAAAAGCCCTTCAATATTTTTTTATGTGAATTATATATTTATTA
TGAGTATTTTAGCCAAAAATTGGGGAAAATATTTCGGTCAATTTTTGTAAAATTTTAGTCGAAAT
C
Found at i:10293 original size:31 final size:31
Alignment explanation
Indices: 10255--10317 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
10245 TGATCCCTTC
10255 CTTCTTGTTGATCTGCAAGAGCAATTAAACA
1 CTTCTTGTTGATCTGCAAGAGCAATTAAACA
10286 CTTCTTGTTGATCTGCAAGAGCAATTAAACA
1 CTTCTTGTTGATCTGCAAGAGCAATTAAACA
10317 C
1 C
10318 AAATTAACGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.32
Consensus pattern (31 bp):
CTTCTTGTTGATCTGCAAGAGCAATTAAACA
Found at i:11837 original size:31 final size:31
Alignment explanation
Indices: 11797--11875 Score: 108
Period size: 31 Copynumber: 2.5 Consensus size: 31
11787 ATTTTTAGCC
*
11797 ACCAATTTGAGGCTAAACCTTTCAAAAGTTG
1 ACCAATTTGAGGCTAAACCTTTCAAAACTTG
11828 -CTCAATTTGA-GCTTAAACCTTTCAAAACTTG
1 AC-CAATTTGAGGC-TAAACCTTTCAAAACTTG
*
11859 ACCAATTTGAGTCTAAA
1 ACCAATTTGAGGCTAAA
11876 AATAGAAATA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
30 3 0.07
31 37 0.88
32 2 0.05
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (31 bp):
ACCAATTTGAGGCTAAACCTTTCAAAACTTG
Found at i:24181 original size:24 final size:24
Alignment explanation
Indices: 24138--24183 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
24128 AGTGTCATTT
**
24138 TAAATTCCCTATCTTTTGAGATTG
1 TAAATTCCCTATCTGCTGAGATTG
*
24162 TAAATTCTCTATCTGCTGAGAT
1 TAAATTCCCTATCTGCTGAGAT
24184 AGTTAGAAGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.43
Consensus pattern (24 bp):
TAAATTCCCTATCTGCTGAGATTG
Found at i:24880 original size:23 final size:23
Alignment explanation
Indices: 24852--24899 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
24842 GGCTTTACTT
*
24852 AAAACTAATATAATAAGGATTAA
1 AAAACTAATATAATAAGAATTAA
24875 AAAACTAATATAATAAGAATTAA
1 AAAACTAATATAATAAGAATTAA
24898 AA
1 AA
24900 TCCTCCGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.65, C:0.04, G:0.06, T:0.25
Consensus pattern (23 bp):
AAAACTAATATAATAAGAATTAA
Found at i:25692 original size:2 final size:2
Alignment explanation
Indices: 25685--25715 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
25675 ACTTAACTAC
25685 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
25716 AAAGAAACAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:25785 original size:20 final size:20
Alignment explanation
Indices: 25757--25798 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
25747 AAAAAAAAAA
*
25757 AAAAAAGAAACAAGCTTTAC
1 AAAAAAGAAACAAACTTTAC
* *
25777 AAAATAGAATCAAACTTTAC
1 AAAAAAGAAACAAACTTTAC
25797 AA
1 AA
25799 GGTAAGTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.60, C:0.14, G:0.07, T:0.19
Consensus pattern (20 bp):
AAAAAAGAAACAAACTTTAC
Done.