Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024916.1 Corchorus olitorius cultivar O-4 contig24949, 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: 47596
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:5416 original size:7 final size:7
Alignment explanation
Indices: 5406--5430 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5396 GAAGAAAATG
5406 AAAAAGA
1 AAAAAGA
5413 AAAAAGA
1 AAAAAGA
5420 AAAAAGA
1 AAAAAGA
5427 AAAA
1 AAAA
5431 GAAGAGAGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:6993 original size:321 final size:318
Alignment explanation
Indices: 5823--7035 Score: 1125
Period size: 322 Copynumber: 3.7 Consensus size: 318
5813 GATAAAATTT
* ** *
5823 TTTTTTCTCAATTTTATGGGACAATAGTCA-TAAAAATATATAAATT-AACGGCAAAAAA-ATTG
1 TTTTTTCTCAATTTTTTGCCACAATAGTCAGAAAAAATATAT-AATTCAAC-GCAAAAAATATTG
* * ** *
5885 AAGGATTTTTCAAACTTCTAATATCGTTTTTCCA-TTTTTCCGAATTAATTTCTAATTAAAACGA
64 AAAGACTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTCCGAATTAATTTCTAATTAAATCGA
* * * * * * *
5949 AACAAGATTCAGATGCTCGTAAAAATAAATCGTTAAATCGAATTTGGCTGCGATTTGATTCGATG
129 AACAAGATTCAGATGCTCGTAAAAACAAAACCTTAAATCTAATGTGGCTGGGATTTGGTTCGATG
* * *
6014 GATATAGATATTTCAAGGAGTCTTTACG-CTAAAATCATGCAAAACTGAGCCGGGGTCCCGGAAC
194 AATATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAGCCGGGCT-CCGGAAC
* * * *
6078 GTGGTTTTAGCAAAAAACCGTGATGGTTAGTACATGATTTCAGCGAAAGTTTTGCAAAAACTAAC
258 G-CGTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTT-AGC--------T--AAAAACTGAC
6143 CCGAAAAA
311 CCGAAAAA
* * *
6151 TATTTTCTCAATTTTTTTGCCACAATAGTCAGAAAAAATACACAATTCAACGCAAAAAAATATTG
1 TTTTTTCTCAA-TTTTTTGCCACAATAGTCAGAAAAAATATATAATTCAACGC-AAAAAATATTG
* * * * *
6216 AAATATTTTTCTCGCTT-TAAATATCATTTTTTTCATTTTTTTCCGAATCT-ATTTCTAATTAAA
64 AAAGACTTTTCACGCTTCT-AATATC-GTTTTTCCA-TTTTTTCCGAAT-TAATTTCTAATTAAA
* * * * * *
6279 TCCAAACAATATTTAGATGTTCGTAAAAACAAATCCTTAAATCTAATGTGGCTGAAAGCCTGAGA
125 TCGAAACAAGATTCAGATGCTCGTAAAAACAAAACCTTAAATCTAATGTGGCTG---G---GA-T
**
6344 TTGGTTAAATGAATATAGATATTTCAAGGAGTCTTT-CTGCCAAAAATCATGCAAAACTGAGCCG
183 TTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTAC-GCCAAAAATCATGCAAAACTGAGCC-
* * * * * *
6408 GGGACCCCGAAACGCATTTTTAGCCCAAAAACCATGATGGTT--T--TCG-----GCTAAAAATT
246 GGG-CTCCGGAACGC-GTTTTAG-CCAAAAACCGTGATGGTTAGTACACGATTTAGCTAAAAACT
*
6464 GACCCG--AAT
308 GACCCGAAAAA
* * * * *
6473 TTTTTTCTCCTGATTTTTTTGCCACAATACTTAGAAAAAATATATAATTCAACACAAAAAAGATT
1 TTTTTTCT-C--AATTTTTTGCCACAATAGTCAGAAAAAATATATAATTCAACGCAAAAAATATT
* * * *
6538 GACAGTCTTTTCACGCTTTTAATATCATTTTTCCAATTTTTTCCGAATTAATTTCTAATTAAATC
63 GAAAGACTTTTCACGCTTCTAATATCGTTTTTCC-ATTTTTTCCGAATTAATTTCTAATTAAATC
* * * * * *** *
6603 GAAACAAGATTTAGATGCTCGTAAAAACAGATCCTTATATCTAATGTGCCTTACATTTGGTTTGA
127 GAAACAAGATTCAGATGCTCGTAAAAACAAAACCTTAAATCTAATGTGGCTGGGATTTGGTTCGA
* * * *
6668 TGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGTCGTGGCTCGGGA
192 TGAATATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAGCCG-GGCTCCGGA
* * * * *
6733 ACGCGTTATCAGCCAACAACCGTGATGGTTAGTACACGATTTTAGCTAAAAACTGATCGGAAAAG
256 ACGCGTT-TTAGCCAAAAACCGTGATGGTTAGTACACGA-TTTAGCTAAAAACTGACCCGAAAAA
* * * *
6798 TTTTTTCTCAATTTTTTGCCACAATAATCATAAAAAATATATAATTCAACGCCAAAAATATTGAC
1 TTTTTTCTCAATTTTTTGCCACAATAGTCAGAAAAAATATATAATTCAACGCAAAAAATATTGAA
* * * * *
6863 GGGCTTTTCACGCTTCTAATGTCGTTTTTCCATTTTTTCCGAATTAATTTTTAATTAAATTGAAA
66 AGACTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTCCGAATTAATTTCTAATTAAATCGAAA
* * * *
6928 CAAGATTCAGATGCTCGTAAAAATAAAAACTTAAAT-TGAACGTGGCTGGGATTTTGTTCGATGA
131 CAAGATTCAGATGCTCGTAAAAACAAAACCTTAAATCT-AATGTGGCTGGGATTTGGTTCGATGA
* *
6992 ATATAGATATTTCAAGGAGTATTTACGTCAAAAATCATGCAAAA
195 ATATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAA
7036 GCAAAAAAAT
Statistics
Matches: 727, Mismatches: 113, Indels: 97
0.78 0.12 0.10
Matches are distributed among these distances:
313 18 0.02
314 12 0.02
315 60 0.08
316 2 0.00
317 2 0.00
320 1 0.00
321 123 0.17
322 162 0.22
323 43 0.06
324 49 0.07
325 11 0.02
326 1 0.00
328 10 0.01
329 22 0.03
330 18 0.02
331 22 0.03
332 7 0.01
334 71 0.10
335 1 0.00
340 4 0.01
341 33 0.05
342 23 0.03
343 16 0.02
344 16 0.02
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34
Consensus pattern (318 bp):
TTTTTTCTCAATTTTTTGCCACAATAGTCAGAAAAAATATATAATTCAACGCAAAAAATATTGAA
AGACTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTCCGAATTAATTTCTAATTAAATCGAAA
CAAGATTCAGATGCTCGTAAAAACAAAACCTTAAATCTAATGTGGCTGGGATTTGGTTCGATGAA
TATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAGCCGGGCTCCGGAACGCG
TTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTAGCTAAAAACTGACCCGAAAAA
Found at i:7726 original size:323 final size:325
Alignment explanation
Indices: 7150--7767 Score: 770
Period size: 323 Copynumber: 1.9 Consensus size: 325
7140 TTTTAGCCCC
* * * *
7150 AAAACCATGATGGTTAGTACACGATTTTTGGCTAAAAACTGACCCGATTTTTTTTTTCTGATTTT
1 AAAACCATGATGGTTAGTACACGATTTTCGGCTAAAAACTGACCCGAGTTTTTTTTTCTCAATTT
* * * *
7215 TTTGCCATCAATATCTCAGAAAAAAATATATAATTCAACATAAAAAACATTGATGGTCTTTTCAC
66 TTTGCCATCAATATCTCAGAAAAAAATATATAATTCAACACAAAAAACATTGACGGGCATTTCAC
* *
7280 GCTTTTAAATATCATTTTTCCAATTTTTTCCCGAATTAATTTCTAATTAAATCGAACAAGATTCA
131 GATTCTAAATATCA-TTTTCCAATTTTTTCCCGAATTAATTTCTAATTAAATCGAACAAGATTCA
* * * * *
7345 GATGCTCCAAAAAACAAATCCTTATATTCAATGTGGCTGACATTTGGTTTGATGAATATAGATAT
195 AATGCTCCAAAAAACAAATACTTATAATCAACGTGGCTGACATTTGGTTCGATGAATATAGATAT
* *
7410 TTCAA-AGAGTCTTTGCGCCAAAAATCATGAAAAATTGAGTCGGGGCTCGGGAACGCGTCTTTAG
260 TTCAAGA-AGTATTTACGCCAAAAATCATGAAAAATTGAGTCGGGGCTCGGGAACGCGTCTTTAG
7474 CA
324 CA
* *
7476 AAAACCGTGATGGTTAGTACACGA-TTTCGGCTAAAAACTGA-TCGAAAAAGTTTTTTTTTCTCA
1 AAAACCATGATGGTTAGTACACGATTTTCGGCTAAAAACTGACCCG----AGTTTTTTTTTCTCA
* * * * *
7539 ATTTTTTGTCA-CAATA-CTCAG-AAAAAATATATAATTCAACGCCAAAAAGATTTACGGGCATT
62 ATTTTTTGCCATCAATATCTCAGAAAAAAATATATAATTCAACACAAAAAACATTGACGGGCATT
* * * *
7601 TCACGATTCT-AATATCGA-TTTCC-ATTTTTTTCCGAATTAATTTTTAATTAAATTGAAATAAG
127 TCACGATTCTAAATATC-ATTTTCCAATTTTTTCCCGAATTAATTTCTAATTAAATCG-AACAAG
** ** *
7663 ATTCAAATGCTCGTAAAAACAAATACTTA-AATCGAACGTGGCTGGGATTTTGTTCGATGAATAT
190 ATTCAAATGCTCCAAAAAACAAATACTTATAATC-AACGTGGCTGACATTTGGTTCGATGAATAT
* *
7727 AGATATTTCAAGAAGTATTTACGTCAAAAATCATGCAAAAT
254 AGATATTTCAAGAAGTATTTACGCCAAAAATCATGAAAAAT
7768 AAAAAAAAAA
Statistics
Matches: 249, Mismatches: 35, Indels: 19
0.82 0.12 0.06
Matches are distributed among these distances:
322 32 0.13
323 95 0.38
324 9 0.04
325 58 0.23
326 28 0.11
327 5 0.02
328 22 0.09
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.35
Consensus pattern (325 bp):
AAAACCATGATGGTTAGTACACGATTTTCGGCTAAAAACTGACCCGAGTTTTTTTTTCTCAATTT
TTTGCCATCAATATCTCAGAAAAAAATATATAATTCAACACAAAAAACATTGACGGGCATTTCAC
GATTCTAAATATCATTTTCCAATTTTTTCCCGAATTAATTTCTAATTAAATCGAACAAGATTCAA
ATGCTCCAAAAAACAAATACTTATAATCAACGTGGCTGACATTTGGTTCGATGAATATAGATATT
TCAAGAAGTATTTACGCCAAAAATCATGAAAAATTGAGTCGGGGCTCGGGAACGCGTCTTTAGCA
Found at i:7746 original size:731 final size:715
Alignment explanation
Indices: 6360--7775 Score: 2162
Period size: 731 Copynumber: 2.0 Consensus size: 715
6350 AAATGAATAT
* *
6360 AGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCGGGGACCCCGAAACGCAT
1 AGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCGGAGACCCCGAAACACAT
*
6425 TTTTAGCCCAAAAACCATGATGGTTTTCGGCTAAAAATTGACCCGAATTTTTTTCTCCTGATTTT
66 TTTTAGCCCAAAAACCATGATGGTTTTCGGCTAAAAACTGACCCGAATTTTTTTCTCCTGATTTT
* *
6490 TTTGCCACAATACTTAGAAAAAATATATAATTCAACACAAAAAAGATTGACAGTCTTTTCACGCT
131 TTTGCCACAATACTCAGAAAAAATATATAATTCAACACAAAAAACATTGACAGTCTTTTCACGCT
*
6555 TTTAATATCATTTTTCCAATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATG
196 TTTAATATCATTTTTCCAATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATG
** * *
6620 CTCGTAAAAACAGATCCTTATATCTAATGTGCCTTACATTTGGTTTGATGAATATAGATATTTCA
261 CTCCAAAAAACAAATCCTTATATCTAATGTGCCTGACATTTGGTTTGATGAATATAGATATTTCA
* * * *
6685 AGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGTCGTGGCTCGGGAACGCGTTATCAGCCAAC
326 AAGAGTCTTTGCGCCAAAAATCATGAAAAATTGAGTCGGGGCTCGGGAACGCGTTATCAGCCAAA
* *
6750 AACCGTGATGGTTAGTACACGATTTTAGCTAAAAACTGATCGGAAAAGTTTTTTCTCAATTTTTT
391 AACCGTGATGGTTAGTACACGATTTCAGCTAAAAACTGATCGAAAAAGTTTTTTCTCAATTTTTT
* * * *
6815 GCCACAATAATCATAAAAAATATATAATTCAACGCCAAAAATATTGACGGGCTTTTCACGCTTCT
456 GCCACAATAATCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCATTTCACGATTCT
* * *
6880 AATGTCGTTTTTCCATTTTTTCCGAATTAATTTTTAATTAAATTGAAACAAGATTCAGATGCTCG
521 AATATCGTATTTCCATTTTTTCCGAATTAATTTTTAATTAAATTGAAACAAGATTCAAATGCTCG
* * *
6945 TAAAAATAAAAACTTAAATTGAACGTGGCTGGGATTTTGTTCGATGAATATAGATATTTCAAGGA
586 TAAAAACAAAAACTTAAATCGAACGTGGCTGGGATTTTGTTCGATGAATATAGATATTTCAAGAA
*
7010 GTATTTACGTCAAAAATCATGCAAAAGCAAAAAAATATTTTCGGCAAAAATTACACAATTTAAAA
651 GTATTTACGTCAAAAATCATGCAAAAGAAAAAAAATATTTTCGGCAAAAATTACACAATTTAAAA
* * *
7075 AGATATTTCAAGGAGTCTTTCTGCCAAAATTCATGCAAAACTGAG-CTGAGACCCCCGAAACACG
1 AGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCGGAGA-CCCCGAAACACA
* *
7139 TTTTTAGCCCCAAAACCATGATGGTTAGTACACGATTTTTGGCTAAAAACTGACCCG-ATTTTTT
65 TTTTTAGCCCAAAAACCATGA----T-G-----G-TTTTCGGCTAAAAACTGACCCGAATTTTTT
* * *
7203 TTTTCTGATTTTTTTGCCATCAATATCTCAGAAAAAAATATATAATTCAACATAAAAAACATTGA
119 TCTCCTGATTTTTTTGCCA-CAATA-CTCAG-AAAAAATATATAATTCAACACAAAAAACATTGA
**
7268 TGGTCTTTTCACGCTTTTAAATATCATTTTTCCAATTTTTTCCCGAATTAATTTCTAATTAAATC
181 CAGTCTTTTCACGCTTTT-AATATCATTTTTCCAATTTTTT-CCGAATTAATTTCTAATTAAATC
*
7333 G-AACAAGATTCAGATGCTCCAAAAAACAAATCCTTATAT-TCAATGTGGCTGACATTTGGTTTG
244 GAAACAAGATTCAGATGCTCCAAAAAACAAATCCTTATATCT-AATGTGCCTGACATTTGGTTTG
7396 ATGAATATAGATATTTCAAAGAGTCTTTGCGCCAAAAATCATGAAAAATTGAGTCGGGGCTCGGG
308 ATGAATATAGATATTTCAAAGAGTCTTTGCGCCAAAAATCATGAAAAATTGAGTCGGGGCTCGGG
* *
7461 AACGCGTCT-TTAG-CAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGATCGAAAA
373 AACGCGT-TATCAGCCAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAAACTGATCGAAAA
* *
7524 AGTTTTTTTTTCTCAATTTTTTGTCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGA
437 AG---TTTTTTCTCAATTTTTTGCCACAATAATCAGAAAAAATATATAATTCAACGCCAAAAAGA
*
7589 TTTACGGGCATTTCACGATTCTAATATCG-ATTTCCATTTTTTTCCGAATTAATTTTTAATTAAA
499 TTGACGGGCATTTCACGATTCTAATATCGTATTTCCA-TTTTTTCCGAATTAATTTTTAATTAAA
* *
7653 TTGAAATAAGATTCAAATGCTCGTAAAAACAAATACTTAAATCGAACGTGGCTGGGATTTTGTTC
563 TTGAAACAAGATTCAAATGCTCGTAAAAACAAAAACTTAAATCGAACGTGGCTGGGATTTTGTTC
*
7718 GATGAATATAGATATTTCAAGAAGTATTTACGTCAAAAATCATGCAAAATAAAAAAAA
628 GATGAATATAGATATTTCAAGAAGTATTTACGTCAAAAATCATGCAAAAGAAAAAAAA
7776 AATCAGCAAA
Statistics
Matches: 632, Mismatches: 46, Indels: 30
0.89 0.06 0.04
Matches are distributed among these distances:
714 4 0.01
715 74 0.12
719 1 0.00
720 1 0.00
725 25 0.04
726 25 0.04
727 4 0.01
728 96 0.15
729 148 0.23
730 31 0.05
731 223 0.35
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (715 bp):
AGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCGGAGACCCCGAAACACAT
TTTTAGCCCAAAAACCATGATGGTTTTCGGCTAAAAACTGACCCGAATTTTTTTCTCCTGATTTT
TTTGCCACAATACTCAGAAAAAATATATAATTCAACACAAAAAACATTGACAGTCTTTTCACGCT
TTTAATATCATTTTTCCAATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATG
CTCCAAAAAACAAATCCTTATATCTAATGTGCCTGACATTTGGTTTGATGAATATAGATATTTCA
AAGAGTCTTTGCGCCAAAAATCATGAAAAATTGAGTCGGGGCTCGGGAACGCGTTATCAGCCAAA
AACCGTGATGGTTAGTACACGATTTCAGCTAAAAACTGATCGAAAAAGTTTTTTCTCAATTTTTT
GCCACAATAATCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCATTTCACGATTCT
AATATCGTATTTCCATTTTTTCCGAATTAATTTTTAATTAAATTGAAACAAGATTCAAATGCTCG
TAAAAACAAAAACTTAAATCGAACGTGGCTGGGATTTTGTTCGATGAATATAGATATTTCAAGAA
GTATTTACGTCAAAAATCATGCAAAAGAAAAAAAATATTTTCGGCAAAAATTACACAATTTAAAA
Found at i:8325 original size:558 final size:545
Alignment explanation
Indices: 7273--8325 Score: 1312
Period size: 558 Copynumber: 1.9 Consensus size: 545
7263 ATTGATGGTC
7273 TTTTCACGCTTTTAAATATCATTTTTCCAATTTTTTCCCGAATTAATTTCTAATTAAATCGAACA
1 TTTTCACGCTTTTAAATATCATTTTTCCAATTTTTTCCCGAATTAATTTCTAATTAAATCGAACA
* * *
7338 AGATTCAGATGCTCCAAAAAACAAATCCTTATATTCAATGTGGCTGACATTTGGTTTGATGAATA
66 AGATTCAGATGCTCCAAAAAACAAATCCTTAAATTCAATGTGGCTGACAATTGGTTAGATGAATA
* * * * * *
7403 TAGATATTTCAAAGAGTCTTTGCGCCAAAAATCATGAAAAATTGAGTCGGGGCTCGGGAACGCGT
131 TAGATATTTCAAAGAGTCTTTGCACAAAAAATCATGAAAAACTGAGTCGGGGCCCCGAAACGCGT
* * * * *
7468 CTTTAGCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGATCGAAAAAGTTTTTTT
196 CTTTAGCAAAAACCATGATAGTTACTACACGATTTCGGCTAAAAACTGACCG--AAAGTTCTTTT
* * * * * *
7533 TTCTCAATTTTTTGTCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTTACGGGC
259 TCCTCAATTTTTAGCCACAATACTCAGAAAAAATATATAATTCAACACCAAAAAAATTGACGGGC
* * * *
7598 ATTTCACGATTCTAATATCGATTTCCATTTTTTTCCGAATTAATTTTTAATTAAATTGAAATAAG
324 ATTTCACGATTCTAATATCGATTTCCATTTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAG
* * ** *
7663 ATTCAAATGCTCGTAAAAACAAATACTTAAATCGAACGTGGCTGGGATTTTGTTCGATGAATATA
389 ATTCAAATGCTCGTAAAAACAAATACTTAAACCCAACGTGGCTGACATTTGGTTCGATGAATATA
*
7728 GATATTTCAAGAAGTATTTACGTCAAAAATCATGCAAAATAAAAAAAAAATCAGCAAAAAATACA
454 GATATTTCAAGAAGTATTTACGCCAAAAATCATGCAAAATAAAAAAAAAATCAGCAAAAAATACA
7793 CAATTCATCGCCAAAAAAAAAGAAATA
519 CAATTCATCGCCAAAAAAAAAGAAATA
* * * *
7820 TTTTCTCGC-TTTAAATATCATTTTT-CTATTTGTTTTCCGAATCT-ATTTCTAATTAGATCGAA
1 TTTTCACGCTTTTAAATATCATTTTTCCAATTT-TTTCCCGAAT-TAATTTCTAATTAAATCGAA
* * **
7882 CCAATATTTAGATGCTCGTAAAAACAAATCCTTAAA-TCTAATGTGGCTGAGAGCCTGAGATTGG
64 -CAAGATTCAGATGCTCCAAAAAACAAATCCTTAAATTC-AATGTGGCT--GA--C--A-ATTGG
* * *
7946 TTAGATGAATATATATATATTTCAAGGAGTCTTT-CTACAAAAAATTATGAAAAACTGAGTCGGG
120 TTAGATG-A-ATATAGATATTTCAAAGAGTCTTTGC-ACAAAAAATCATGAAAAACTGAGTCGGG
* * *
8010 GCCCCGAAACGCGTTTTTAGCCAAAAAACCATGATAGTTACTATATGATTTTCGGCTAAAAACTG
182 GCCCCGAAACGCGTCTTTAG-C-AAAAACCATGATAGTTACTACACGA-TTTCGGCTAAAAACTG
* *
8075 ACCCG-AA-TTCTTTTTCCTGAATTTTTAGCCACAATGCTCAGAAAAAATATATAATTCAACACC
244 A-CCGAAAGTTCTTTTTCCTCAATTTTTAGCCACAATACTCAGAAAAAATATATAATTCAACACC
* * * * *
8138 AAAAAAATTGATGGTCTTTTCACGCTTTTAATATC-ATTTTCCAATTTTTTTTCCAAATTAATTT
308 AAAAAAATTGACGGGCATTTCACGATTCTAATATCGA-TTTCC-A-TTTTTTTCCAAATTAATTT
* * * *
8202 CTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATACCCAATGTGGCTGAC
370 CTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATACTTAAACCCAACGTGGCTGAC
* * * *
8267 ATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAAT
435 ATTTGGTTCGATGAATATAGATATTTCAAGAAGTATTTACGCCAAAAATCATGCAAAAT
8326 TGAGTCGGGG
Statistics
Matches: 426, Mismatches: 59, Indels: 31
0.83 0.11 0.06
Matches are distributed among these distances:
545 5 0.01
546 44 0.10
547 48 0.11
549 2 0.00
551 1 0.00
553 1 0.00
554 10 0.02
555 3 0.01
556 144 0.34
557 4 0.01
558 145 0.34
559 17 0.04
560 2 0.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (545 bp):
TTTTCACGCTTTTAAATATCATTTTTCCAATTTTTTCCCGAATTAATTTCTAATTAAATCGAACA
AGATTCAGATGCTCCAAAAAACAAATCCTTAAATTCAATGTGGCTGACAATTGGTTAGATGAATA
TAGATATTTCAAAGAGTCTTTGCACAAAAAATCATGAAAAACTGAGTCGGGGCCCCGAAACGCGT
CTTTAGCAAAAACCATGATAGTTACTACACGATTTCGGCTAAAAACTGACCGAAAGTTCTTTTTC
CTCAATTTTTAGCCACAATACTCAGAAAAAATATATAATTCAACACCAAAAAAATTGACGGGCAT
TTCACGATTCTAATATCGATTTCCATTTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGAT
TCAAATGCTCGTAAAAACAAATACTTAAACCCAACGTGGCTGACATTTGGTTCGATGAATATAGA
TATTTCAAGAAGTATTTACGCCAAAAATCATGCAAAATAAAAAAAAAATCAGCAAAAAATACACA
ATTCATCGCCAAAAAAAAAGAAATA
Found at i:9114 original size:890 final size:872
Alignment explanation
Indices: 7075--9793 Score: 3904
Period size: 890 Copynumber: 3.1 Consensus size: 872
7065 CAATTTAAAA
** * * *
7075 AGATATTTCAAGGAGTCTTTCTGCCAAAATTCATGCAAAACTGAGCTGAGACCCCCGAAACA-CG
1 AGATATTTCAAGGAGTCTTTCTG-CAAAAAACATGAAAAACTGAGCCGAGGCCCCCGAAA-AGCG
* * *
7139 TTTTTAGCCCCAAAACCATGATGGTTAGTACACGATTTTTGGCTAAAAACTGACCCGATTTTTTT
64 TTTTTAGCCCAAAAACCATGATGGTTAGTACACGATTTTCGGCTAAAAACTGACCCGA-ATTTTT
* * *
7204 TTTCTGATTTTTTTGCCATCAATATCTCAGAAAAAAATATATAATTCAACATAAAAAACATTGAT
128 TTTCTGAATTTTTTACCA-CAATA-CTCAG-AAAAAATATATAATTCAACACAAAAAA-ATTGAT
*
7269 GGTCTTTTCACGCTTTTAAATATCATTTTTCCAATTTTTTCCCGAATTAATTTCTAATTAAATCG
189 GGTCTTTTCACGCTTTT-AATATCATTTTTCCAATTTTTTTCCGAATTAATTTCTAATTAAATCG
** **
7334 -AACAAGATTCAGATGCTCCAAAAAACAAATCCTTATATTCAATGTGGCTGACATTTGGTTTGAT
253 AAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATACCCAATGTGGCTGACATTTGGTTTGAT
* * *
7398 GAATATAGATATTTCAAAGAGTCTTTGCGCCAAAAATCATGAAAAATTGAGTCGGGGCTCGGGAA
318 GAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGTCGGGGCTAGGGAA
* * *
7463 CGCGTCTTTAG-CAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGATCGAAAAAGT
383 CACGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGATCGGAAAAG-
* *
7527 TTTTTTTTCTCAATTTTTTGTCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTT
447 ---TTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTG
* *
7592 ACGGGCATTTCACGATTCTAATATCGA--TTTCCATTTTTTTCCGAATTAATTTTTAATTAAATT
509 ACGGGCTTTTCACGCTTCTAATATC-ATTTTTCCATTTTTTTCCGAATTAATTTTTAATTAAATT
* *
7655 GAAATAAGATTCAAATGCTCGTAAAAACAAATACTTAAATCGAACGTGGCTGGGATTTTGTTCGA
573 GAAACAAGATTC-AATGCTCGTAAAAA-AAATACTTAAATCGAACGAGGCTGGGATTTTGTTCGA
* **
7720 TGAATATAGATATTTCAAGAAGTATTTACGTCAAAAATCATGCAAA-ATAAAAAAAAAATCAGCA
636 TGAATATAGATATTTCAAGGAGTATTTACGTCAAAAATCATGCAAACA-AAAAAAAATTTCAGCA
* **
7784 AAAAATACACAATTCATCGCCAAAAAAAAAGAAATA-TTTTCTCGCTTTAAATATCATTTTTCTA
700 AAAAATACACAATTCAACG-CAAAAAAATTGAAATATTTTTCTCGCTTTAAATATCATTTTTCTA
* * * * * *
7848 TTTGTTTTCCGAATCTATTTCTAATTAGATCGAACCAATATTTAGATGCTCGTAAAAACAAATCC
764 -TTATTTTCCGAATCTATTTCTAATTAAATTGAAACAATATTAAGATGCTCGTAAAAACAAATCT
7913 TTAAATCTAATGTGGCTGAGAGCCTGAGATTGGTTAGATGAATATAT
828 TTAAATCTAATGTGGCTGAGAGCCTGAGATTGGTTAGATG-A-ATAT
* * * * * *
7960 ATATATTTCAAGGAGTCTTTCTACAAAAAATTATGAAAAACTGAGTCG-GGGCCCCGAAACGCGT
1 AGATATTTCAAGGAGTCTTTCTGCAAAAAA-CATGAAAAACTGAGCCGAGGCCCCCGAAAAGCGT
* * * * *
8024 TTTTAGCCAAAAAACCATGATAGTTACTATATGATTTTCGGCTAAAAACTGACCCGAATTCTTTT
65 TTTTAGCCCAAAAACCATGATGGTTAGTACACGATTTTCGGCTAAAAACTGACCCGAATT-TTTT
* *
8089 TCCTGAA-TTTTTAGCCACAATGCTCAGAAAAAATATATAATTCAACACCAAAAAAATTGATGGT
129 TTCTGAATTTTTTA-CCACAATACTCAGAAAAAATATATAATTCAACA-CAAAAAAATTGATGGT
*
8153 CTTTTCACGCTTTTAATATCA-TTTTCCAATTTTTTTTCCAAATTAATTTCTAATTAAATCGAAA
192 CTTTTCACGCTTTTAATATCATTTTTCCAA-TTTTTTTCCGAATTAATTTCTAATTAAATCGAAA
8217 CAAGATTCAGATGCTCGTAAAAACAAATCCTTATACCCAATGTGGCTGACATTTGGTTTGATGAA
256 CAAGATTCAGATGCTCGTAAAAACAAATCCTTATACCCAATGTGGCTGACATTTGGTTTGATGAA
8282 TATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGTCGGGGCTAGGGAACAC
321 TATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGTCGGGGCTAGGGAACAC
* *
8347 GTTTTTAGCCAAAAACCGTGAAGGTTAGTACATC-ATTTCGGCTAAAAACTAATCGGAAAAGTGT
386 GTTTTTAGCCAAAAACCGTGATGGTTAGTACA-CGATTTCGGCTAAAAACTGATCGGAAAAGT-T
** * * *
8411 TTTCTCAAAATTTTCCCACAATACTCAAAAAATATATATATATATATAATTCAACGCCGAAAAGA
449 TTTCTCAATTTTTTGCCACAATACTC---AGA-A-A-A-A-ATATATAATTCAACGCCAAAAAGA
*
8476 TTGACGGGCTTTTCATGCTTCTAATATCATTTTTCCA-TTTTTTCCGAATTAATTTTTAATTAAA
506 TTGACGGGCTTTTCACGCTTCTAATATCATTTTTCCATTTTTTTCCGAATTAATTTTTAATTAAA
*
8540 TTGAAACAAGATTCGAATACTCGTAAAAAAAATACTTAAATCGAACGAGGCTGGGATTTTGTTCG
571 TTGAAACAAGATTC-AATGCTCGTAAAAAAAATACTTAAATCGAACGAGGCTGGGATTTTGTTCG
* *
8605 ATGAATATAGATATTTCAAGGAGTATTAACGTCAAAAACCATGGACAAACGAAAAAAAATACTTT
635 ATGAATATAGATATTTCAAGGAGTATTTACGTCAAAAATCAT-G-CAAAC-AAAAAAAA-A-TTT
*
8670 CAGCAAAAAATACACAATTCAACGCATAAAAAATTGAAATATTTTTCTCGCTTTAAATATAATTT
695 CAGCAAAAAATACACAATTCAACGCA-AAAAAATTGAAATATTTTTCTCGCTTTAAATATCATTT
* *
8735 TTCTATTATTTTCGGAATTTATTTCTAATTAAATTGAAACAATATTAAGATGCTCGTAAAAACAA
759 TTCTATTATTTTCCGAATCTATTTCTAATTAAATTGAAACAATATTAAGATGCTCGTAAAAACAA
* *
8800 ATTTTTAAATCTAATGTGGCTGAGAGCCAGAGATTGGTTAGATGAATAT
824 ATCTTTAAATCTAATGTGGCTGAGAGCCTGAGATTGGTTAGATGAATAT
* *
8849 AGATATTTCAAGGAGTTTTTCTGTCAAAAAACATGAAAAACTGAGCCG-GGGCCCCGAAAAGCGT
1 AGATATTTCAAGGAGTCTTTCTG-CAAAAAACATGAAAAACTGAGCCGAGGCCCCCGAAAAGCGT
* *
8913 TTTTAGCCCAAAAACCATGATGGTTGGTACACGATTTTCGGCTAAAAACTTACCCGAATTTATAT
65 TTTTAGCCCAAAAACCATGATGGTTAGTACACGATTTTCGGCTAAAAACTGACCCGAATTT-T-T
*
8978 TTTCTGAATTTTTTACCACAATACTCAGAAAAAATATATAATTCAACACAAGAAAGATTGATGGT
128 TTTCTGAATTTTTTACCACAATACTCAGAAAAAATATATAATTCAACACAA-AAAAATTGATGGT
* * *
9043 CATTTCAAGCTTTTAATATCATTTTTCTAATTTTTTTCCGAATTAATTTCTAATTAAATCGAAAC
192 CTTTTCACGCTTTTAATATCATTTTTCCAATTTTTTTCCGAATTAATTTCTAATTAAATCGAAAC
*
9108 AAGATTCAGATGCTCGTAAAAACAAATCCTTATACCCAATGTGGCTGATATTTGGTTTGATGAAT
257 AAGATTCAGATGCTCGTAAAAACAAATCCTTATACCCAATGTGGCTGACATTTGGTTTGATGAAT
* * *
9173 ATAAATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGTGTCGAGGCTAGGGAACACG
322 ATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGTCGGGGCTAGGGAACACG
9238 TTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGATCGGAAAAGTTTTT
387 TTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGATCGGAAAAGTTTTT
* * *
9303 CTCAATTTTTTGCCACAATACCCTGAAAAAATATATAATTCAACGTCAAAAAGATTGACGGGCTT
452 CTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTT
* * *
9368 TTCACGCTTGTAATATCGTTTTTCCATTTTCTTTCCGAATTAATTTCTAATTAAATTGAAACAAG
517 TTCACGCTTCTAATATCATTTTTCCATTTT-TTTCCGAATTAATTTTTAATTAAATTGAAACAAG
* * * *
9433 ATTCAGATGCTCGTCAAAACAAATTCTTAAATCGAACGCGGCTGGGATTTTGTTTGATGAATATA
581 ATTCA-ATGCTCGT-AAAAAAAATACTTAAATCGAACGAGGCTGGGATTTTGTTCGATGAATATA
* * *
9498 GATATTTCAAGGAGTATTTTCGTCAAAAATCATG--AACAAAAAAAAATTTCGGCGAAAAATACA
644 GATATTTCAAGGAGTATTTACGTCAAAAATCATGCAAACAAAAAAAAATTTCAGCAAAAAATACA
* * * * * *
9561 CAATTTAATGCAAAAAAATTGAAATATTTCTCTTGTTTTAAATATCATTTTTCTATTTTTTTCCG
709 CAATTCAACGCAAAAAAATTGAAATATTTTTCTCGCTTTAAATATCATTTTTCTATTATTTTCCG
* * *
9626 AATCTATGTT-TAATTAAATTGAAACAATATTCAGATTCTCGTAAAAATAAATCTTTAAATCTAA
774 AATCTAT-TTCTAATTAAATTGAAACAATATTAAGATGCTCGTAAAAACAAATCTTTAAATCTAA
9690 TGTGGCTGAGAGCCTGAGATTGGTTAGATGAATAT
838 TGTGGCTGAGAGCCTGAGATTGGTTAGATGAATAT
* * *
9725 AGATATTTCAAGGAGTCTTTCTGCTAAAAATCATGCAAAACTGAGCCGAGGCCCCCGAAATGCGT
1 AGATATTTCAAGGAGTCTTTCTGC-AAAAAACATGAAAAACTGAGCCGAGGCCCCCGAAAAGCGT
9790 TTTT
65 TTTT
9794 CATAAATTTT
Statistics
Matches: 1654, Mismatches: 138, Indels: 92
0.88 0.07 0.05
Matches are distributed among these distances:
875 1 0.00
876 180 0.11
877 45 0.03
878 2 0.00
879 39 0.02
880 39 0.02
881 230 0.14
882 65 0.04
883 59 0.04
884 157 0.09
885 36 0.02
886 77 0.05
887 101 0.06
888 11 0.01
889 142 0.09
890 300 0.18
891 143 0.09
892 27 0.02
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.33
Consensus pattern (872 bp):
AGATATTTCAAGGAGTCTTTCTGCAAAAAACATGAAAAACTGAGCCGAGGCCCCCGAAAAGCGTT
TTTAGCCCAAAAACCATGATGGTTAGTACACGATTTTCGGCTAAAAACTGACCCGAATTTTTTTT
CTGAATTTTTTACCACAATACTCAGAAAAAATATATAATTCAACACAAAAAAATTGATGGTCTTT
TCACGCTTTTAATATCATTTTTCCAATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGA
TTCAGATGCTCGTAAAAACAAATCCTTATACCCAATGTGGCTGACATTTGGTTTGATGAATATAG
ATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGTCGGGGCTAGGGAACACGTTTT
TAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGATCGGAAAAGTTTTTCTCA
ATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCA
CGCTTCTAATATCATTTTTCCATTTTTTTCCGAATTAATTTTTAATTAAATTGAAACAAGATTCA
ATGCTCGTAAAAAAAATACTTAAATCGAACGAGGCTGGGATTTTGTTCGATGAATATAGATATTT
CAAGGAGTATTTACGTCAAAAATCATGCAAACAAAAAAAAATTTCAGCAAAAAATACACAATTCA
ACGCAAAAAAATTGAAATATTTTTCTCGCTTTAAATATCATTTTTCTATTATTTTCCGAATCTAT
TTCTAATTAAATTGAAACAATATTAAGATGCTCGTAAAAACAAATCTTTAAATCTAATGTGGCTG
AGAGCCTGAGATTGGTTAGATGAATAT
Found at i:9384 original size:322 final size:322
Alignment explanation
Indices: 8712--9533 Score: 963
Period size: 322 Copynumber: 2.5 Consensus size: 322
8702 ATTGAAATAT
* * * * *
8712 TTTTCTCGCTTTAAATATAATTTTTCTATTATTTTCGGAATTTATTTCTAATTAAATTGAAACAA
1 TTTTCACGCTTT-AATATCATTTTTCTATTTTTTTCCGAATTAATTTCTAATTAAATTGAAACAA
* * * * * *
8777 TATTAAGATGCTCGTAAAAACAAATTTTTAAATCTAATGTGGCTGAGAGCCAGAGATTGGTTAGA
65 GATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGCT----G--AGA-TTTGGTTTGA
* * *
8842 TGAATATAGATATTTCAAGGAGTTTTTCTGTCAAAAAACATGAAAAACTGAGCCGGGGCCCCGAA
123 TGAATATAGATATTTCAAGGAGTTTTTC-GTCAAAAATCATGAAAAACTGAGCCGAGGCACCGAA
* *
8907 AAGCGTTTTTAGCCCAAAAACCATGATGGTTGGTACACGATTTTCGGCTAAAAACTTACCCGAAT
187 AAGCGTTTTTAGCCCAAAAACCATGATGGTTAGTACACGATTTTCGGCTAAAAACTGACCCGAA-
* * *
8972 TTATATTTTCTGAATTTTTTACCACAATACTCAGAAAAAATATATAATTCAACACAAGAAAGATT
251 TAATATTTTCTCAATTTTTTACCACAATACCCAGAAAAAATATATAATTCAACACAAGAAAGATT
* *
9037 GATGGTC
316 GACGGGC
* * *
9044 ATTTCAAGCTTTTAATATCATTTTTCTAATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACA
1 TTTTCACGC-TTTAATATCATTTTTCT-ATTTTTTTCCGAATTAATTTCTAATTAAATTGAAACA
* * * *
9109 AGATTCAGATGCTCGTAAAAACAAATCCTTATACCCAATGTGGCTGATATTTGGTTTGATGAATA
64 AGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTGGTTTGATGAATA
* * * * * * * ** *
9174 TAAATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGTGTCGAGGCTAGGGAACA-CG
129 TAGATATTTCAAGGAGT-TTTTCGTCAAAAATCATGAAAAACTGAGCCGAGGC-ACCGAAAAGCG
* * *
9238 TTTTTAG-CCAAAAACCGTGATGGTTAGTACACGA-TTTCGGCTAAAAACTGATCGGAA-AAGT-
192 TTTTTAGCCCAAAAACCATGATGGTTAGTACACGATTTTCGGCTAAAAACTGACCCGAATAA-TA
* * *
9299 TTTTCTCAATTTTTTGCCACAATACCCTGAAAAAATATATAATTCAACGTCAA-AAAGATTGACG
256 TTTTCTCAATTTTTTACCACAATACCCAGAAAAAATATATAATTCAAC-ACAAGAAAGATTGACG
9363 GGC
320 GGC
* *
9366 TTTTCACGCTTGTAATATCGTTTTTCCATTTTCTTTCCGAATTAATTTCTAATTAAATTGAAACA
1 TTTTCACGCTT-TAATATCATTTTTCTATTTT-TTTCCGAATTAATTTCTAATTAAATTGAAACA
* * * * * *
9431 AGATTCAGATGCTCGTCAAAACAAATTCTTAAATCGAACGCGGCTGGGATTTTGTTTGATGAATA
64 AGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTGGTTTGATGAATA
9496 TAGATATTTCAAGGAGTATTTTCGTCAAAAATCATGAA
129 TAGATATTTCAAGGAGT-TTTTCGTCAAAAATCATGAA
9534 CAAAAAAAAA
Statistics
Matches: 418, Mismatches: 64, Indels: 26
0.82 0.13 0.05
Matches are distributed among these distances:
321 7 0.02
322 196 0.47
323 4 0.01
324 20 0.05
325 25 0.06
326 62 0.15
327 10 0.02
329 1 0.00
332 19 0.05
333 74 0.18
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Consensus pattern (322 bp):
TTTTCACGCTTTAATATCATTTTTCTATTTTTTTCCGAATTAATTTCTAATTAAATTGAAACAAG
ATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTGGTTTGATGAATATA
GATATTTCAAGGAGTTTTTCGTCAAAAATCATGAAAAACTGAGCCGAGGCACCGAAAAGCGTTTT
TAGCCCAAAAACCATGATGGTTAGTACACGATTTTCGGCTAAAAACTGACCCGAATAATATTTTC
TCAATTTTTTACCACAATACCCAGAAAAAATATATAATTCAACACAAGAAAGATTGACGGGC
Found at i:11145 original size:323 final size:321
Alignment explanation
Indices: 10440--11233 Score: 951
Period size: 323 Copynumber: 2.4 Consensus size: 321
10430 ATTTTCTATT
* * * *
10440 TTTTTTTCCGAATCT-ATTTCTAATTAAATGGAAGA-AATATATATAGATGCTCGTAAAAAGAAA
1 TTTTTTTCCGAAT-TAATTTCTAATTAAATCGAA-ACAAGAT-T-CAGATGCTCGTAAAAACAAA
* * * *
10503 TCCTTAAATCTAATGTGGCTGAGAGTTTGAGATTGGTTAGATGAATATAAAAATTTCAAGGAGTC
62 TCCTTAAATCAAATGTGGCTGAGAGTTT--GA-T--TT-GATGAATATAGATATTTCAAGGAGTA
* *
10568 TTTTTGCCAAAAATCATG-AAATATTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCCAAAAACCA
121 TTTATGCCAAAAATCATGCAAA-ATTGAGCCGGGGCCACGAAACGCGTTTTTAGCCCAAAAACCA
* * ***
10632 TGATGGTTAGTGCACGATATTCGGCTAAAAACTTACTCGAATTTTTTTTCTAAATTTTTTGCCAC
185 TGATGGTTAGTACACGATATTCGGCTAAAAACTGACTCGAAAAGTTTTTCTAAATTTTTTGCCAC
* * * * * *
10697 AGTATTAAAAAAAATATAATTCAACACCAAAAAGATTGATGGTCTTTTCATGCTTTTAATATCAT
250 AATATCAAAAAAAATATAATTCAACACCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCAT
10762 TTTCCCA
315 TTTCCCA
10769 TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCT
1 TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCT
* * * *
10834 TATATCCAATGTGGCTGACA-TTTGATTTGATGAATATAGATATTTCAAGGAGTATTTGTGCCAA
66 TAAATCAAATGTGGCTGAGAGTTTGATTTGATGAATATAGATATTTCAAGGAGTATTTATGCCAA
* * * * *
10898 AAATCATGCAAAATTGAGTCGGGGCTAGGGAACGCGTTTTTAG-CCAAAAACCGTGATGGTTTAG
131 AAATCATGCAAAATTGAGCCGGGGCCACGAAACGCGTTTTTAGCCCAAAAACCATGATGG-TTAG
*
10962 TACACGAT-TTCGGCTAAAAACTGA-TCGAAAAGTTTTTCTCAATTTTTTGCCACAATACTCAGA
195 TACACGATATTCGGCTAAAAACTGACTCGAAAAGTTTTTCTAAATTTTTTGCCACAATA-TCA-A
* * *
11025 GAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCCT
258 -AAAAAATATAATTCAACACCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATC-ATTTTCC-
11090 TC-
320 -CA
* * *
11092 TTTTTTTCCGAATTAATTTTTAATTAAA-CTGAAACAAGATTCAGATGCTCGTAAAAACCAATAC
1 TTTTTTTCCGAATTAATTTCTAATTAAATC-GAAACAAGATTCAGATGCTCGTAAAAACAAATCC
* * * * * *
11156 TTAAATCAAACGTGGCTGGGATTTTG-TTCGATGAATATAGATATTTCAAGGAGTATTTACGTCA
65 TTAAATCAAATGTGGCTGAGAGTTTGATTTGATGAATATAGATATTTCAAGGAGTATTTATGCCA
*
11220 AAAATCATACAAAA
130 AAAATCATGCAAAA
11234 AAAAATATTT
Statistics
Matches: 408, Mismatches: 45, Indels: 30
0.84 0.09 0.06
Matches are distributed among these distances:
318 28 0.07
319 32 0.08
320 78 0.19
321 54 0.13
322 7 0.02
323 123 0.30
324 7 0.02
326 3 0.01
327 39 0.10
328 3 0.01
329 34 0.08
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.34
Consensus pattern (321 bp):
TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCT
TAAATCAAATGTGGCTGAGAGTTTGATTTGATGAATATAGATATTTCAAGGAGTATTTATGCCAA
AAATCATGCAAAATTGAGCCGGGGCCACGAAACGCGTTTTTAGCCCAAAAACCATGATGGTTAGT
ACACGATATTCGGCTAAAAACTGACTCGAAAAGTTTTTCTAAATTTTTTGCCACAATATCAAAAA
AAATATAATTCAACACCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCATTTTCCCA
Found at i:11771 original size:877 final size:875
Alignment explanation
Indices: 9789--12109 Score: 3311
Period size: 877 Copynumber: 2.6 Consensus size: 875
9779 CCGAAATGCG
9789 TTTTTCATAAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACACCAAAAAGATTGAT
1 TTTTTC-TAAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACACCAAAAAGATTGAT
* * * *
9854 GGTCTTTTCACGCTTTTAATATCGTTTTTCTAATTTTTTTCCAAATTAATTTCTAACTAAATCGA
65 GGTCTTTTCACGCTTTTAATATCATTTTTCCAATTTTTTTCCGAATTAATTTCTAATTAAATCGA
* * *
9919 AACAAGATTCAAATGCTCGTAAAAACAAATCCTTATACCCAATGTGGCTGACATTTGGTTTGATG
130 AACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGACATTTGATTTGATG
* * * *
9984 AATATAGATATTTCAAGGAGTCTTTGCGCAAAAAATAATGCAAAATTGAGTTGGGGCTAGGGAAC
195 AATATAGATATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAATTGAGTCGGGGCTAGGGAAC
* * *
10049 ACGTTTTTAGCCAAAAACCGTGAAGGTAACGTACACGA-TTCGGCTAAAAACTGATTGGAAAAGT
260 ACGTTTTTAGCCAAAAACCGTGATGGTTA-GTACACGATTTCGGCTAAAAACTGA-TCGAAAAGT
* * * * * *
10113 GTTTTATCAATTCTTTCCCACAGTACTCAGATAAAATATATAATTCAATGCCGAAAAGATATACG
323 -TTTTCTCAATTTTTTGCCACAATACTCAGA-AAAATATATAATTCAACGCCAAAAAGAT-TACG
* *
10178 GGCTTTTCACGCTTCTAATATCATTTTTCC-ATTTTTTTCTGAATTAATTTTAAATTAAATTGAA
385 GGCTTTTCACGCTTCTAATATCATTTTTCCTATTTTTTTCCGAATTAATTTTTAATTAAA-TGAA
* * **
10242 ACAAGATTCAGATGCTCGTAAAAATAAATACTTAAATCGAACGTGGCTTTGATTTAGTTCGATGA
449 ACAAGATTCAGATGCTCGTAAAAACAAATACTTAAATCAAACGTGGCTGGGATTTAGTTCGATGA
* *
10307 ATATAGATACTTCAAGGAGTATTTACGTCAAAAATTATGCAAAAACAAAAAAAAATTATTTTCGG
514 ATATAGATATTTCAAGGAGTATTTACGTC-AAAA--AT-C--ATACAAAAAAAAATTATTTTCGG
* *
10372 CAAAAAATACACATTTCAACGCAAAAAAAAATTTGAAATATTTTTCACTTTAAATATCATTTTCT
573 CAAAAAATACACAATTCAACGCAAAAAAAAATTTGAAATATTTTTCACATTAAATATCATTTTCT
* * *
10437 ATTTTTTTTTCCGAATCTATTTCTAATTAAATGGAAGAAATATATATAGATGCTCGTAAAAAGAA
638 A-TTTTTTTTCCGAATCTATTTCTAATTAAATCGAAGAAATATATACAGATGCTCGTAAAAACAA
* ** *
10502 ATCCTTAAATCTAATGTGGCTGAGAGTTTGAGATTGGTTAGATGAATATAAAAATTTCAAGGAGT
702 ATCCTTAAATCTAATGTGGCTAAGAGCATGAGATTGGTTAGATAAATATAAAAATTTCAAGGAGT
* *
10567 CTTTTTGCCAAAAATCATGAAATATTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCCAAAAACCA
767 CTTTCTGCCAAAAATCATGAAAAATTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCCAAAAACCA
* * * *
10632 TGATGGTTAGTGCACGATATTCGGCTAAAAACTTACTCGAATTT
832 TGATGGTTAGTACACGATATTCGGCAAAAAACTGACCCGAATTT
* *
10676 TTTTTCTAAATTTTTTGCCACAGTA-TTA-AAAAAA-ATATAATTCAACACCAAAAAGATTGATG
1 TTTTTCTAAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACACCAAAAAGATTGATG
* *
10738 GTCTTTTCATGCTTTTAATATCA-TTTTCCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAA
66 GTCTTTTCACGCTTTTAATATCATTTTTCCAATTTTTTTCCGAATTAATTTCTAATTAAATCGAA
10802 ACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGACATTTGATTTGATGA
131 ACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGACATTTGATTTGATGA
* *
10867 ATATAGATATTTCAAGGAGTATTTGTGCCAAAAATCATGCAAAATTGAGTCGGGGCTAGGGAACG
196 ATATAGATATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAATTGAGTCGGGGCTAGGGAACA
10932 CGTTTTTAGCCAAAAACCGTGATGGTTTAGTACACGATTTCGGCTAAAAACTGATCGAAAAGTTT
261 CGTTTTTAGCCAAAAACCGTGATGG-TTAGTACACGATTTCGGCTAAAAACTGATCGAAAAGTTT
10997 TTCTCAATTTTTTGCCACAATACTCAGAGAAAATATATAATTCAACGCCAAAAAGATTGACGGGC
325 TTCTCAATTTTTTGCCACAATACTCAGA-AAAATATATAATTCAACGCCAAAAAGATT-ACGGGC
* *
11062 TTTTCACGCTTCTAATATCGTTTTTCCTTCTTTTTTTCCGAATTAATTTTTAATTAAACTGAAAC
388 TTTTCACGCTTCTAATATCATTTTTCC-TATTTTTTTCCGAATTAATTTTTAATTAAA-TGAAAC
* *
11127 AAGATTCAGATGCTCGTAAAAACCAATACTTAAATCAAACGTGGCTGGGATTTTGTTCGATGAAT
451 AAGATTCAGATGCTCGTAAAAACAAATACTTAAATCAAACGTGGCTGGGATTTAGTTCGATGAAT
11192 ATAGATATTTCAAGGAGTATTTACGTCAAAAATCATACAAAAAAAAA-TATTTTCGGCAAAAAAT
516 ATAGATATTTCAAGGAGTATTTACGTCAAAAATCATACAAAAAAAAATTATTTTCGGCAAAAAAT
** *
11256 ACACAATTCAAC-CCCAAAAAAATTTGAAATATTTTTCTCGCATTAAATATCATTTTTCTA-TTT
581 ACACAATTCAACGCAAAAAAAAATTTGAAATA-TTTT-TCACATTAAATATCA-TTTTCTATTTT
* *
11319 TTTTCTGAATCTATTTCTAATTAAATCTAA-ACAATAT-T-CAGATGCTCGTAAAAACAAATCCT
643 TTTTCCGAATCTATTTCTAATTAAATCGAAGA-AATATATACAGATGCTCGTAAAAACAAATCCT
* *
11381 TAAATCTAATGTGGCTAAGAGCATGAGATTGGTTAGATAAATATAGATATTTCAAGGAGTCTTTC
707 TAAATCTAATGTGGCTAAGAGCATGAGATTGGTTAGATAAATATAAAAATTTCAAGGAGTCTTTC
** *
11446 TGCCAAAAATCATGAAAAACTT-AGCCGGGGCCCCGAAACTTGTTTTTAGCTCAAAAACCATGAT
772 TGCCAAAAATCATGAAAAA-TTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCCAAAAACCATGAT
*
11510 GGTTAGTACATGAT-TGTCGGCAAAAAACTGACCCGAA-TT
836 GGTTAGTACACGATAT-TCGGCAAAAAACTGACCCGAATTT
*
11549 TTTTTCTGAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACACCAAAAAGATTGATG
1 TTTTTCTAAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACACCAAAAAGATTGATG
*
11614 GTCTTTTTACGCTTTTAATATCATTTTTCCAATTTTTTTCCGAATTAATTTCTAATTAAATCGAA
66 GTCTTTTCACGCTTTTAATATCATTTTTCCAATTTTTTTCCGAATTAATTTCTAATTAAATCGAA
* * * *
11679 ACAATATTCAGATGCTCGTAAAAATAAATCCTTATATCCAATGCGACTGACATTTGATTTGATGA
131 ACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGACATTTGATTTGATGA
*
11744 ATATAGATATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAATTGAGTCGGGGCTCGGGAACA
196 ATATAGATATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAATTGAGTCGGGGCTAGGGAACA
* * *
11809 CGTTTTTAGCC-AAAACGGTGATGGTTAGTACACGATTTCAGCTAAAAACTTATCGGAAAAGTTT
261 CGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGATC-GAAAAG-TT
* * * * *
11873 TTTCTCAATTTTTGGCCACAATACTCAGAAAAATATATTATTCAACGCCAAAAATAATA----TT
324 TTTCTCAATTTTTTGCCACAATACTCAGAAAAATATATAATTCAACGCCAAAAAGATTACGGGCT
* * * *
11934 TTTCTCGCTT-TAAATATCATTTTT-CTATTTTTTTCCGATTTTATTTCTAATTAAATCGAAACA
389 TTTCACGCTTCT-AATATCATTTTTCCTATTTTTTTCCGAATTAATTTTTAATTAAAT-GAAACA
* * * * * * *
11997 ATATTCAGATGCTCGTAAAAACAAATCCTTAAATCTAATGTGGCTGAGAGCCTGAGATTGGTTAG
452 AGATTCAGATGCTCGTAAAAACAAATACTTAAATCAAACGTGGCT--G-G---GA-TTTAGTTCG
* * *
12062 ATGAATATAGATATTTCAAGGAGT-TTTTCTGCCAAAAATCATGCAAAA
510 ATGAATATAGATATTTCAAGGAGTATTTAC-GTCAAAAATCATACAAAA
12110 CTGAGTCGGG
Statistics
Matches: 1303, Mismatches: 104, Indels: 65
0.89 0.07 0.04
Matches are distributed among these distances:
868 1 0.00
869 72 0.06
870 2 0.00
871 22 0.02
872 1 0.00
873 26 0.02
874 169 0.13
875 62 0.05
876 206 0.16
877 229 0.18
878 7 0.01
879 1 0.00
880 3 0.00
881 84 0.06
882 202 0.16
883 184 0.14
884 6 0.00
885 2 0.00
886 18 0.01
887 6 0.00
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (875 bp):
TTTTTCTAAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACACCAAAAAGATTGATG
GTCTTTTCACGCTTTTAATATCATTTTTCCAATTTTTTTCCGAATTAATTTCTAATTAAATCGAA
ACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGACATTTGATTTGATGA
ATATAGATATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAATTGAGTCGGGGCTAGGGAACA
CGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGATCGAAAAGTTTT
TCTCAATTTTTTGCCACAATACTCAGAAAAATATATAATTCAACGCCAAAAAGATTACGGGCTTT
TCACGCTTCTAATATCATTTTTCCTATTTTTTTCCGAATTAATTTTTAATTAAATGAAACAAGAT
TCAGATGCTCGTAAAAACAAATACTTAAATCAAACGTGGCTGGGATTTAGTTCGATGAATATAGA
TATTTCAAGGAGTATTTACGTCAAAAATCATACAAAAAAAAATTATTTTCGGCAAAAAATACACA
ATTCAACGCAAAAAAAAATTTGAAATATTTTTCACATTAAATATCATTTTCTATTTTTTTTCCGA
ATCTATTTCTAATTAAATCGAAGAAATATATACAGATGCTCGTAAAAACAAATCCTTAAATCTAA
TGTGGCTAAGAGCATGAGATTGGTTAGATAAATATAAAAATTTCAAGGAGTCTTTCTGCCAAAAA
TCATGAAAAATTGAGCCGGGGCCCCGAAACGCGTTTTTAGCCCAAAAACCATGATGGTTAGTACA
CGATATTCGGCAAAAAACTGACCCGAATTT
Found at i:12553 original size:647 final size:643
Alignment explanation
Indices: 11283--12755 Score: 2203
Period size: 647 Copynumber: 2.3 Consensus size: 643
11273 AAAAATTTGA
* * * *
11283 AATATTTTTCTCGCATTAAATATCATTTTTCTATTTTTTTCTGAATCTATTTCTAATTAAATCTA
1 AATATTTTTCTCGCTTTAAATATCATTTTTCTATTTTTTTCCGAATTTATTTCTAATTAAATCGA
11348 AACAATATTCAGATGCTCGTAAAAACAAATCCTTAAATCTAATGTGGCTAAGAGCATGAGATTGG
66 AACAATATTCAGATGCTCGTAAAAACAAATCCTTAAATCTAATGTGGCT-AGAGC-TGAGATTGG
* * * *
11413 TTAGATAAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGAAAAACTTAGCCGGGGCC
129 TTAGATGAATATAGATATTTCAAGGAGTTTTTCTGCCAAAAATCATGCAAAACTGAGCCGGGGCC
* * *
11478 CCGAAACTTGTTTTTAGCTCAAAAACCATGATGGTTAGTACATGATTGTCGGCAAAAAACTGACC
194 CCGAAACTCGTTTTTAGCCCAAAAACCATGATGGTTAGTACACGATTGTCGGCAAAAAACTGACC
11543 CGAATTTTTTTCTGAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACACCAAAAAGA
259 CGAATTTTTTTCTGAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACACCAAAAAGA
* *
11608 TTGATGGTCTTTTTACGCTTTTAATATCATTTTTCCAATTTTTTTCCGAATTAATTTCTAATTAA
324 TTGATGGTCTTTTCACACTTTTAATATCATTTTTCCAATTTTTTTCCGAATTAATTTCTAATTAA
* * * *
11673 ATCGAAACAATATTCAGATGCTCGTAAAAATAAATCCTTATATCCAATGCGACTGACATTTGATT
389 ATCGAAACAAGATTCAGATGCTCATAAAAACAAATCCTTATACCCAATGCGACTGACATTTGATT
* *
11738 TGATGAATATAGATATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAAATTGAGTCGGGGCTCG
454 TGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGTCGGGGCTAG
* *
11803 GGAACACGTTTTTAGCCAAAACGGTGATGGTTAGTACACGATTTCAGCTAAAAACTTATCGGAAA
519 GGAACACGTTTTTAGCCAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAAACTGATCGGAAA
* * * *
11868 AGTTTTTTCTCAATTTTTGGCCACAATACTCAGAAAAATATATTATTCAACGCCAAAAAT
584 AGTGTTTTCACAATTTTTGGCCACAATACTCAGAAAAATATATAAGTCAACGCCAAAAAT
*
11928 AATATTTTTCTCGCTTTAAATATCATTTTTCTATTTTTTTCCGATTTTATTTCTAATTAAATCGA
1 AATATTTTTCTCGCTTTAAATATCATTTTTCTATTTTTTTCCGAATTTATTTCTAATTAAATCGA
11993 AACAATATTCAGATGCTCGTAAAAACAAATCCTTAAATCTAATGTGGCTGAGAGCCTGAGATTGG
66 AACAATATTCAGATGCTCGTAAAAACAAATCCTTAAATCTAATGTGGCT-AGAG-CTGAGATTGG
*
12058 TTAGATGAATATAGATATTTCAAGGAGTTTTTCTGCCAAAAATCATGCAAAACTGAGTCGGGGCC
129 TTAGATGAATATAGATATTTCAAGGAGTTTTTCTGCCAAAAATCATGCAAAACTGAGCCGGGG-C
* * * *
12123 CCCGAGACTCGTTTTTAGCCCAAAAACTATGATGGTTAGTACACGATTTTCGGCTAAAAACTGAC
193 CCCGAAACTCGTTTTTAGCCCAAAAACCATGATGGTTAGTACACGATTGTCGGCAAAAAACTGAC
12188 CCGAATTTTTTTTTCTGAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACACCAAAA
258 CCGAA--TTTTTTTCTGAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACACCAAAA
12253 AGATTGATGGTCTTTTCACACTTTTAATATCATTTTTCCAA-TTTTTTCCGAATTAATTTCTAAT
321 AGATTGATGGTCTTTTCACACTTTTAATATCATTTTTCCAATTTTTTTCCGAATTAATTTCTAAT
* * **
12317 TAAATCGAAATAAGATTCAGATGCTCATAAAAACAAATCCTTATACCCAATGTGGTTGACATTTG
386 TAAATCGAAACAAGATTCAGATGCTCATAAAAACAAATCCTTATACCCAATGCGACTGACATTTG
* *
12382 GTTTGATGAATATAGATATTTGAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGTCGGGGC
451 ATTTGATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGTCGGGGC
* * *
12447 TAGGGAACGCGTTTTTAGCCAAAAGCCGTGATGGTTAGTACATGATTTCGGCTAAAAACTGATCG
516 TAGGGAACACGTTTTTAGCCAAAA-CCGTGATGGTTAGTACACGATTTCAGCTAAAAACTGATCG
* *
12512 GAAAAGTGTTTTCACAATTTTT-TCCACAATACTCAGAAAAATATATAAGTCAATGCCAAAAAT
580 GAAAAGTGTTTTCACAATTTTTGGCCACAATACTCAGAAAAATATATAAGTCAACGCCAAAAAT
* * * *
12575 ATTGACAGGCTTTTCAT-GCTTCT-AATATCATTTTTAC-ATTTTTTTTCCGAATTAATTTTTAA
1 A---ATA--TTTTTC-TCGCTT-TAAATATCATTTTT-CTA-TTTTTTTCCGAATTTATTTCTAA
* * * * *
12637 TTAAATTGAAACAAGATTCAGATGCTCGTAAAAACAAATACTTAAATCGAACGTGGCT-G-G--G
57 TTAAATCGAAACAATATTCAGATGCTCGTAAAAACAAATCCTTAAATCTAATGTGGCTAGAGCTG
* * * * *
12698 A-TTTTGTTCGATGAATATAGATATTTCAAGGAGTATTTACT-TCAAAAATCATGCAAAA
122 AGATTGGTTAGATGAATATAGATATTTCAAGGAGT-TTTTCTGCCAAAAATCATGCAAAA
12756 AAAATATTTT
Statistics
Matches: 755, Mismatches: 58, Indels: 29
0.90 0.07 0.03
Matches are distributed among these distances:
645 180 0.24
646 111 0.15
647 209 0.28
648 153 0.20
650 3 0.00
651 1 0.00
652 22 0.03
653 76 0.10
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Consensus pattern (643 bp):
AATATTTTTCTCGCTTTAAATATCATTTTTCTATTTTTTTCCGAATTTATTTCTAATTAAATCGA
AACAATATTCAGATGCTCGTAAAAACAAATCCTTAAATCTAATGTGGCTAGAGCTGAGATTGGTT
AGATGAATATAGATATTTCAAGGAGTTTTTCTGCCAAAAATCATGCAAAACTGAGCCGGGGCCCC
GAAACTCGTTTTTAGCCCAAAAACCATGATGGTTAGTACACGATTGTCGGCAAAAAACTGACCCG
AATTTTTTTCTGAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACACCAAAAAGATT
GATGGTCTTTTCACACTTTTAATATCATTTTTCCAATTTTTTTCCGAATTAATTTCTAATTAAAT
CGAAACAAGATTCAGATGCTCATAAAAACAAATCCTTATACCCAATGCGACTGACATTTGATTTG
ATGAATATAGATATTTCAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTGAGTCGGGGCTAGGG
AACACGTTTTTAGCCAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAAACTGATCGGAAAAG
TGTTTTCACAATTTTTGGCCACAATACTCAGAAAAATATATAAGTCAACGCCAAAAAT
Found at i:12657 original size:321 final size:322
Alignment explanation
Indices: 11301--12755 Score: 1661
Period size: 321 Copynumber: 4.5 Consensus size: 322
11291 TCTCGCATTA
* *
11301 AATATCATTTTTC-TATTTTTTTCTGAATCT-ATTTCTAATTAAATCTAAACAATATTCAGATGC
1 AATATCATTTTTCAT-TTTTTTTCCGAAT-TAATTTCTAATTAAATCGAAACAATATTCAGATGC
* * *
11364 TCGTAAAAACAAATCCTTAAATCTAATGTGGCTAAGAGCATGAGATTGGTTAGATAAATATAGAT
64 TCGTAAAAACAAATCCTTAAATCCAATGTGG-T-TGA-CAT----TTGGTTAGATGAATATAGAT
* * * *
11429 ATTTCAAGGAGTCTTT-CTGCCAAAAATCATGAAAAACTT-AGCCGGGGCCCCGAAACTTGTTTT
122 ATTTCAAGGAGTCTTTGC-GCCAAAAATCATGCAAAA-TTGAGTCGGGGCCCCGGAACTCGTTTT
* * *
11492 TAGCTCAAAAACCATGATGGTTAGTACATGATTGTCGGCAAAAAACTGACCCG--AATTTTTTTC
185 TAGC-CAAAAACCATGATGGTTAGTACACGATT-TCGGCTAAAAACTGACCCGAAAAGTTTTTTC
* *
11555 TGAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACACCAAAAAGATTGATGGTCTTT
248 TCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACACCAAAAAGATTGAAGGTCTTT
*
11620 TTACGCTTTT
313 TCACGCTTTT
*
11630 AATATCATTTTTCCAATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAATATTCAGATGCT
1 AATATCATTTTT-CATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAATATTCAGATGCT
* * * ** * *
11695 CGTAAAAATAAATCCTTATATCCAATGCGACTGACATTTGATTTGATGAATATAGATATTTCAAG
65 CGTAAAAACAAATCCTTAAATCCAATGTGGTTGACATTTGGTTAGATGAATATAGATATTTCAAG
* * * *
11760 GAGTCTTTGTGCCAAAAATCATGCAAAATTGAGTCGGGGCTCGGGAACACGTTTTTAGCC-AAAA
130 GAGTCTTTGCGCCAAAAATCATGCAAAATTGAGTCGGGGCCCCGGAACTCGTTTTTAGCCAAAAA
** * * * * *
11824 CGGTGATGGTTAGTACACGATTTCAGCTAAAAACTTATCGGAAAAGTTTTTTCTCAATTTTTGGC
195 CCATGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAAGTTTTTTCTCAATTTTTTGC
* * ** * *
11889 CACAATACTCAG-AAAAATATATTATTCAACGCC-AAAA-A-T-AATAT-TTTTCTCGCTTTA
260 CACAATACTCAGAAAAAATATATAATTCAACACCAAAAAGATTGAAGGTCTTTTCACGCTTTT
* *
11946 AATATCATTTTTC-TATTTTTTTCCGATTTTATTTCTAATTAAATCGAAACAATATTCAGATGCT
1 AATATCATTTTTCAT-TTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAATATTCAGATGCT
* * *
12010 CGTAAAAACAAATCCTTAAATCTAATGTGGCTGAGAGCCTGAGATTGGTTAGATGAATATAGATA
65 CGTAAAAACAAATCCTTAAATCCAATGTGG-T-TGA--C--A-TTTGGTTAGATGAATATAGATA
* * *
12075 TTTCAAGGAGT-TTTTCTGCCAAAAATCATGCAAAACTGAGTCGGGGCCCCCGAGACTCGTTTTT
123 TTTCAAGGAGTCTTTGC-GCCAAAAATCATGCAAAATTGAGTCGGGGCCCCGGA-ACTCGTTTTT
* ***
12139 AGCCCAAAAACTATGATGGTTAGTACACGATTTTCGGCTAAAAACTGACCCGAATTTTTTTTTCT
186 AG-CCAAAAACCATGATGGTTAGTACACGA-TTTCGGCTAAAAACTGACCCGAAAAGTTTTTTCT
* *
12204 GAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACACCAAAAAGATTGATGGTCTTTT
249 CAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACACCAAAAAGATTGAAGGTCTTTT
*
12269 CACACTTTT
314 CACGCTTTT
* * *
12278 AATATCATTTTTCCA-ATTTTTTCCGAATTAATTTCTAATTAAATCGAAATAAGATTCAGATGCT
1 AATATCATTTTT-CATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAATATTCAGATGCT
* * * * *
12342 CATAAAAACAAATCCTTATACCCAATGTGGTTGACATTTGGTTTGATGAATATAGATATTTGAAG
65 CGTAAAAACAAATCCTTAAATCCAATGTGGTTGACATTTGGTTAGATGAATATAGATATTTCAAG
*** * *
12407 GAGTCTTTGCGCCAAAAATCATGCAAAATTGAGTCGGGGCTAGGGAACGCGTTTTTAGCCAAAAG
130 GAGTCTTTGCGCCAAAAATCATGCAAAATTGAGTCGGGGCCCCGGAACTCGTTTTTAGCCAAAAA
* * * * * *
12472 CCGTGATGGTTAGTACATGATTTCGGCTAAAAACTGATCGGAAAAGTGTTTTCACAATTTTTT-C
195 CCATGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAAGTTTTTTCTCAATTTTTTGC
* ** * * *
12536 CACAATACTCAG-AAAAATATATAAGTCAATGCCAAAAATATTGACAGG-CTTTTCATGCTTCT
260 CACAATACTCAGAAAAAATATATAATTCAACACCAAAAAGATTGA-AGGTCTTTTCACGCTTTT
* * *
12598 AATATCATTTTTACATTTTTTTTCCGAATTAATTTTTAATTAAATTGAAACAAGATTCAGATGCT
1 AATATCATTTTT-CATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAATATTCAGATGCT
* * * * ** * *
12663 CGTAAAAACAAATACTTAAATCGAACGTGGCTGGGATTTTGTTCGATGAATATAGATATTTCAAG
65 CGTAAAAACAAATCCTTAAATCCAATGTGGTTGACATTTGGTTAGATGAATATAGATATTTCAAG
* * **
12728 GAGTATTTACTTCAAAAATCATGCAAAA
130 GAGTCTTTGCGCCAAAAATCATGCAAAA
12756 AAAATATTTT
Statistics
Matches: 955, Mismatches: 140, Indels: 70
0.82 0.12 0.06
Matches are distributed among these distances:
315 73 0.08
316 22 0.02
317 4 0.00
318 1 0.00
319 2 0.00
320 71 0.07
321 183 0.19
322 131 0.14
323 106 0.11
324 13 0.01
325 83 0.09
326 53 0.06
327 22 0.02
328 7 0.01
329 14 0.01
330 74 0.08
331 3 0.00
332 92 0.10
333 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (322 bp):
AATATCATTTTTCATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAATATTCAGATGCTC
GTAAAAACAAATCCTTAAATCCAATGTGGTTGACATTTGGTTAGATGAATATAGATATTTCAAGG
AGTCTTTGCGCCAAAAATCATGCAAAATTGAGTCGGGGCCCCGGAACTCGTTTTTAGCCAAAAAC
CATGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAAAGTTTTTTCTCAATTTTTTGCC
ACAATACTCAGAAAAAATATATAATTCAACACCAAAAAGATTGAAGGTCTTTTCACGCTTTT
Found at i:13271 original size:554 final size:543
Alignment explanation
Indices: 12278--13309 Score: 1306
Period size: 554 Copynumber: 1.9 Consensus size: 543
12268 TCACACTTTT
* *
12278 AATATCATTTTTCCAATTTTTTCCGAATTAATTTCTAATTAAATCGAAATAAGATTCAGATGCTC
1 AATATCATTTTTCCAATTTTTTCCGAACTAATTTCTAATTAAATCGAAATAAGATACAGATGCTC
* ** * * *
12343 ATAAAAACAAATCCTTATACCCAATGTGGTTGACATTTGGTTTGATGAATATAGATATTTGAAGG
66 ATAAAAACAAATCCTTAAACCCAATGTGGGAGACAATTGGTTAGATGAATATAGATATTTCAAGG
* * * * * * *
12408 AGTCTTTGCGCCAAAAATCATGCAAAATTGAGTCGGGGCTAGGGAACGCGTTTTTAGCCAAAAGC
131 AGTCTTTGCGCCAAAAATCATGAAAAACTAAGCCGGGGCCACGAAACGCGTTTTTAGCCAAAAGC
* * ** ** *
12473 CGTGATGGTTAGTACATGATTTCGGCTAAAAACTGATCGGAAAAGTGTTTTCACAATTTTTTCCA
196 CATGATGGTTAGTACACGATTTCGGCTAAAAACTGATCCCAAAAGTGTTTTCACAATTACTGCCA
** * **
12538 CAATACTCAGAAAAATATATAAGTCAATGCCAAAAATATTGACAGGCTTTTCATGCTTCTAATAT
261 CAATACTCAGAAAAATATATAAGTCAACACCAAAAAGATTGACAGGCTTTTCACACTTCTAATAT
* * *
12603 CATTTTTACATTTTTTTTCCGAATTAATTTTTAATTAAATTGAAACAAGATTCAGATGCTCGTAA
326 CATTTTTACATATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAA
* * ** *
12668 AAACAAATACTTAAATCGAACGTGGCTGGGATTTTGTTCGATGAATATAGATATTTCAAGGAGTA
391 AAACAAATACTTAAACCCAACGTGGCTGACATTTGGTTCGATGAATATAGATATTTCAAGGAGTA
*
12733 TTTACTTC-AAAAATCATGCAAAAAAAATATTTTCGGTAAAAAATACACAATTCAACCCCAAAAA
456 TTTAC-GCGAAAAATCATGCAAAAAAAATATTTTCGGTAAAAAATACACAATTCAACCCCAAAAA
12797 AATTGAAATATTTTTCTAGCATTA
520 AATTGAAATATTTTTCTAGCATTA
* * * *
12821 AATATCATTTTTCTATTTTTTTCCGAACCT-ATTTCTAATTAATTCGAAGA-AATATACAGATGC
1 AATATCATTTTTCCAATTTTTTCCGAA-CTAATTTCTAATTAAATCGAA-ATAAGATACAGATGC
* * *
12884 TCGTAAAAACAAATCCTTAAATCTAATGTGGCCGAGAGCCTGAGATTGGTTAGATGAATATAGAT
64 TCATAAAAACAAATCCTTAAACCCAATGTGG--GAGA--C--A-ATTGGTTAGATGAATATAGAT
*
12949 ATTTCAAGGAGTCTTT-CTGCCAAAAATCATGAAAAACTAAGCCGGGGCCCCGAAACGCGTTTTT
122 ATTTCAAGGAGTCTTTGC-GCCAAAAATCATGAAAAACTAAGCCGGGGCCACGAAACGCGTTTTT
* * *
13013 CGCCCAAAAGCCATGATGGTTAGTACACGATTTTCGGCTAAAAACTGA-CCCAAAATTTTTTTTT
186 AG-CCAAAAGCCATGATGGTTAGTACACGA-TTTCGGCTAAAAACTGATCCCAAAA--GTGTTTT
* *
13077 CTGA-AATTACTGCCACAATACTCAGAAAAAATATATAATTCAACACCAAAAAGATTGA-TGGTC
247 C--ACAATTACTGCCACAATACTCAG-AAAAATATATAAGTCAACACCAAAAAGATTGACAGG-C
* * *
13140 TTTTCACACTTTTAATATCATTTTTCCA-ATTTTTTCCGAATTAATTTCTAATTAAATCGAAATA
308 TTTTCACACTTCTAATATCATTTTTACATATTTTTTCCGAATTAATTTCTAATTAAATCGAAACA
* * * * *
13204 AGATTCAGATGCTCGTAAAAACAAATCCTTATACCCAATGTGGTTGACATTTGGTTTGATGAATA
373 AGATTCAGATGCTCGTAAAAACAAATACTTAAACCCAACGTGGCTGACATTTGGTTCGATGAATA
* *
13269 TAGATATTTCAAGGAGTCTTTGCGCGAAAAATCATGCAAAA
438 TAGATATTTCAAGGAGTATTTACGCGAAAAATCATGCAAAA
13310 TTGAGTCGGG
Statistics
Matches: 411, Mismatches: 59, Indels: 27
0.83 0.12 0.05
Matches are distributed among these distances:
543 80 0.19
544 2 0.00
545 2 0.00
547 1 0.00
549 2 0.00
550 73 0.18
551 30 0.07
552 17 0.04
553 7 0.02
554 143 0.35
555 54 0.13
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (543 bp):
AATATCATTTTTCCAATTTTTTCCGAACTAATTTCTAATTAAATCGAAATAAGATACAGATGCTC
ATAAAAACAAATCCTTAAACCCAATGTGGGAGACAATTGGTTAGATGAATATAGATATTTCAAGG
AGTCTTTGCGCCAAAAATCATGAAAAACTAAGCCGGGGCCACGAAACGCGTTTTTAGCCAAAAGC
CATGATGGTTAGTACACGATTTCGGCTAAAAACTGATCCCAAAAGTGTTTTCACAATTACTGCCA
CAATACTCAGAAAAATATATAAGTCAACACCAAAAAGATTGACAGGCTTTTCACACTTCTAATAT
CATTTTTACATATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAA
AAACAAATACTTAAACCCAACGTGGCTGACATTTGGTTCGATGAATATAGATATTTCAAGGAGTA
TTTACGCGAAAAATCATGCAAAAAAAATATTTTCGGTAAAAAATACACAATTCAACCCCAAAAAA
ATTGAAATATTTTTCTAGCATTA
Found at i:14262 original size:8 final size:8
Alignment explanation
Indices: 14249--14274 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
14239 TTTTATATAG
14249 TAGTAAGA
1 TAGTAAGA
14257 TAGTAAGA
1 TAGTAAGA
14265 TAGTAAGA
1 TAGTAAGA
14273 TA
1 TA
14275 AGATAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.23, T:0.27
Consensus pattern (8 bp):
TAGTAAGA
Found at i:14888 original size:21 final size:21
Alignment explanation
Indices: 14862--14905 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
14852 TCGACGGTGA
14862 TCAAATAAATCTTTCTTTTCT
1 TCAAATAAATCTTTCTTTTCT
14883 TCAAATAAATCTTTCTTTTCT
1 TCAAATAAATCTTTCTTTTCT
14904 TC
1 TC
14906 TTTTTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.20, G:0.00, T:0.52
Consensus pattern (21 bp):
TCAAATAAATCTTTCTTTTCT
Found at i:14913 original size:14 final size:13
Alignment explanation
Indices: 14894--14933 Score: 55
Period size: 12 Copynumber: 3.1 Consensus size: 13
14884 CAAATAAATC
14894 TTTCTTTTCTTCTT
1 TTTCTTTT-TTCTT
14908 TTTCTTTTTTCTT
1 TTTCTTTTTTCTT
*
14921 TTT-TTCTTTCTT
1 TTTCTTTTTTCTT
14933 T
1 T
14934 AATACTTGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 9 0.36
13 8 0.32
14 8 0.32
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.82
Consensus pattern (13 bp):
TTTCTTTTTTCTT
Found at i:14924 original size:15 final size:16
Alignment explanation
Indices: 14898--14929 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
14888 TAAATCTTTC
14898 TTTTCTTCTTTTTCTT
1 TTTTCTTCTTTTTCTT
14914 TTTTCTT-TTTTTCTT
1 TTTTCTTCTTTTTCTT
14929 T
1 T
14930 CTTTAATACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
TTTTCTTCTTTTTCTT
Found at i:25601 original size:60 final size:60
Alignment explanation
Indices: 25527--25693 Score: 173
Period size: 60 Copynumber: 2.8 Consensus size: 60
25517 AGCGGTTTGG
* * *
25527 TTAA-TTGTTCAAATAAGAG-CTTAATGTT-T-GTTAAAATATTTAAATAAGGGCTCC-ATCTT
1 TTAATTTGATCAAATAAGAGTC-TAATGTTATCG--AAAATACTCAAATAAGGGC-CCGATCTT
*
25586 TTAATTTGGTCAAATAAGAGTCTAATGTTATCGAAAATACTCAAATAAGGGCCCGATCTT
1 TTAATTTGATCAAATAAGAGTCTAATGTTATCGAAAATACTCAAATAAGGGCCCGATCTT
* * * * * *
25646 TTAATTTGACCAAATAAGGGCCTAACGTTATTGAAAATTCTCAAATAA
1 TTAATTTGATCAAATAAGAGTCTAATGTTATCGAAAATACTCAAATAA
25694 AGGCTTGGCA
Statistics
Matches: 93, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
59 6 0.06
60 84 0.90
61 2 0.02
62 1 0.01
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (60 bp):
TTAATTTGATCAAATAAGAGTCTAATGTTATCGAAAATACTCAAATAAGGGCCCGATCTT
Found at i:25813 original size:59 final size:60
Alignment explanation
Indices: 25742--25897 Score: 230
Period size: 57 Copynumber: 2.7 Consensus size: 60
25732 GACGACAAGT
** *
25742 CCTTATTTGAGCATTTTGGC-AACATTAGGCCCTTATTTGGCCAAATTAAAAGATTGGGC
1 CCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGGCCAAATTAAAAGATCAGAC
25801 CCTTATTTGAGCATTTTGGCAAACATTAGGCCC---TTTGGCCAAATTAAAAGATCAGAC
1 CCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGGCCAAATTAAAAGATCAGAC
* * *
25858 CCTTATTTGAGCATTTTGTCAAACGTTAGACCCTTATTTG
1 CCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTG
25898 AGTAATTGGC
Statistics
Matches: 87, Mismatches: 6, Indels: 7
0.87 0.06 0.07
Matches are distributed among these distances:
57 51 0.59
59 20 0.23
60 16 0.18
ACGTcount: A:0.28, C:0.20, G:0.18, T:0.35
Consensus pattern (60 bp):
CCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGGCCAAATTAAAAGATCAGAC
Done.