Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020400.1 Corchorus olitorius cultivar O-4 contig20433, 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: 18175
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:6531 original size:2 final size:2
Alignment explanation
Indices: 6492--6517 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6482 AGCTAATTGA
6492 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
6518 CTTACTACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8082 original size:331 final size:325
Alignment explanation
Indices: 7122--8301 Score: 1133
Period size: 331 Copynumber: 3.6 Consensus size: 325
7112 TTGGATTATG
* * * *
7122 AATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTTGGAAAAAATAG
1 AATTTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA-TTGAAAAAAATAT
* *
7187 GAAAAACGATATTAGAAATG-TC-AAAAGCCATTCAATCTTTTTGGCGTTGAATTATATATTTTT
65 GAAAAACAATATTA-AAA-GCTCGAAAAGCCATTCAATCTTTTTGGCGTCGAATTATATA-TTTT
* * *
7250 TATGAGTATTTTAACCAAAAATTGA-GAAAACATCTTTCGGGTCAATTTTTACAAAATTTTAGCC
127 TATGAGTATTTTGA-TAAAAATTGAGGAAAA-ATCTTTCGGGTCAATTTTTGCAAAATTTTAGCC
* * * * *
7314 AAAATCGTGTAATAACCATCAC-AGCTTTTGGCTAAAAATGCGTTTTATGACCCCGACTCAGTTT
190 AAAATCGTGTAATAACCATCACGA-TTTTTGGCTAAAAACGCGTTTT-GGAGCCCGGCTCAGTTT
* * **
7378 TGCCTGATTTTTGGCGCTA-AGACTCCTTGAGATATCCGTATTCATCTAATCAAATCTCAGCCAC
253 TGCATGATTTTTGGCGC-AGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCT-AGCCAC
*
7442 ATTGGATTTAA
316 ATTGCATTT-A
* *
7453 CAATTTGTTTTTACAAGCATCTGAATCTTGTTT-GATTTTGATTAGAAATTAATTGAGAAAAATA
1 -AATTTGTTTTTACAAGCATCTGAATCTTGTTTCGA-TTTAATTAGAAATTAATTGAAAAAAATA
* * *
7517 TGAAAAATAATATTAAAAGCGT-GAAAAGTCC-TCCAAT-TGTTTTGGCG-CTAAATTATATATA
64 TGAAAAACAATATTAAAAGC-TCGAAAAG-CCATTCAATCT-TTTTGGCGTC-GAATTATATAT-
* * *
7578 TTTTATGAGTATTTT-ATCCAAAAAATGAGGAAAAAAT-TTTCGGGTCATTTTTTGCAGAATTTT
124 TTTTATGAGTATTTTGAT--AAAAATTGAGG-AAAAATCTTTCGGGTCAATTTTTGCAAAATTTT
* * * *
7641 AGCCAAAATCGTG---TACCCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGACCCGGCTCAG
186 AGCCAAAATCGTGTAATAACCATCACGATTTTTGGCTAAAAACGCGTTTTGGAG-CCCGGCTCAG
* * * * * *
7703 GTTTGCATGATTTTTGGCGCAGACAATCCTTGAAATATCTAAATTCATCTGATAAAATCATAGCC
250 TTTTGCATGATTTTTGGCGCAGAGACTCCTTGAAATATCTATATTCATCTAATCAAATC-TAGCC
7768 ACATTGCATTTA
314 ACATTGCATTTA
* *
7780 AGGATTTG-TTTTACGAGCATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAA
1 A--ATTTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATT--GAAAAAAA
* *
7844 TATGAAAAACAATATTAAAAGCTCGAAAAGCCCTTCAATCTTTTTGGAGTCGAATTATATA-TTT
62 TATGAAAAACAATATTAAAAGCTCGAAAAGCCATTCAATCTTTTTGGCGTCGAATTATATATTTT
* * * * * *
7908 TATTGTGTATTTTGGATAAAAATTGAGGAAATATCTTTCAGGTCAATTTTTGCAAAATGTCAGTC
127 TA-TGAGTATTTT-GATAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCC
* * * * * * *
7973 GAAATCGTGTAATAATCATCACGATTTTTGGCTAAAACCGTGTTTTGGAGCCCGGTTTAATTTTT
190 AAAATCGTGTAATAACCATCACGATTTTTGGCTAAAAACGCGTTTTGGAGCCCGG-CTCAGTTTT
* * * *
8038 GAATGATTTTTGGTGCCGAGACTCCTTGAAATATCTATATTCATCTAACCAAATC---CCA-A--
254 GCATGATTTTTGGCGCAGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTAGCCACATT
8097 -C---T-
319 GCATTTA
* * * * *
8099 -A-TTCTTTTTACAAGCATCTGAATCATGTTTTGTTTTAATCAGAAATTAATTCGGAAAAAAATA
1 AATTTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATT--GAAAAAAATA
* * * * * **
8162 AGAAAAAACAGTATTAAAAGCTTGAAAAGTCATTCAACCTTTTTGGCGTTTAATTATATATTTTT
64 TG-AAAAACAATATTAAAAGCTCGAAAAGCCATTCAATCTTTTTGGCGTCGAATTATATATTTTT
* * * * * * * * *
8227 ATGAGTATTGTGGCTATAAGTTGAGGAAAAATATTTTGGGTCAATTTTTGCAATATATTAGCCGA
128 ATGAGTATT-TTGATAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCAA
8292 AATCGTGTAA
192 AATCGTGTAA
8302 CATCACGGTT
Statistics
Matches: 707, Mismatches: 104, Indels: 89
0.79 0.12 0.10
Matches are distributed among these distances:
315 2 0.00
316 53 0.07
317 108 0.15
318 6 0.01
320 1 0.00
323 1 0.00
326 2 0.00
327 56 0.08
328 159 0.22
329 57 0.08
330 15 0.02
331 193 0.27
332 50 0.07
333 4 0.01
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (325 bp):
AATTTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTGAAAAAAATATG
AAAAACAATATTAAAAGCTCGAAAAGCCATTCAATCTTTTTGGCGTCGAATTATATATTTTTATG
AGTATTTTGATAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCAAAATC
GTGTAATAACCATCACGATTTTTGGCTAAAAACGCGTTTTGGAGCCCGGCTCAGTTTTGCATGAT
TTTTGGCGCAGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTAGCCACATTGCATTTA
Found at i:9420 original size:330 final size:325
Alignment explanation
Indices: 8658--9804 Score: 1136
Period size: 330 Copynumber: 3.5 Consensus size: 325
8648 ATAGCGGCGG
* *
8658 TTAATTAGAAATTAATTTGGAAAAAATAAGAAAAACGATATTAGAAA-CGTTAAAAGCCAC-TCA
1 TTAATTAGAAATTAATTCGGAAAAAATAAGAAAAACGATATTA-AAAGCGTGAAAAGCC-CTTCA
* * * * * *
8721 ATTTTTTTGGTGTTGAATTATATATTTTTTATGAGTATTTTAACTAAAAATTGGGGAAACATCTT
64 ATCTTTTTGGCGTCGAATTATATATTTTTTA-GAGTATTTTAGCTAAAAATTGAGGAAAAATCTT
*
8786 TCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAACCATCACAGTTTTTGGCTAAAA
128 TCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAACCATCACGGTTTTTGGCTAAAA
* * * * *
8851 ATGCGTTT-TAGGACCCCAGCTCAGTTTTGCCTGATTTTTGGCGCTAAGAC-TCCTTGAGATATC
193 ACGCGTTTCGAGGA-CCCGGCTCAGTTTTGCATGATTTTTGGCGC--AGACATCCTTGAAATATC
** * * *
8914 CGTATTCATCTAATCAAATCTCAGCCACATTGGATTTAACAATTTGTTTTTACAAGTATCTGAAT
255 TATATTCATCT-ATAAAATCT-AGCCACATTGCATTT-A-AATTTG-TTTTACAAGCATCTGAAT
8979 CTTGTTT-GATT
315 CTTGTTTCGA-T
* * * ** * * *
8990 TTGATTAGAAATTAATT--GAGAAAATATGAAAAATAATATTATAAGCGTGAAAAGTCCTCCAAT
1 TTAATTAGAAATTAATTCGGAAAAAATAAGAAAAACGATATTAAAAGCGTGAAAAGCCCTTCAAT
* * * * *
9053 -TGTTTTGGCG-CTAAATTATATATATTTTATGAGTATTTTATCTAAAAAATGAGGAAAAATTTT
66 CT-TTTTGGCGTC-GAATTATATATTTTTTA-GAGTATTTTAGCTAAAAATTGAGGAAAAATCTT
* * * * **
9116 TCGGGTCATTTTTTACAGAATTTTAGCCAAAATCGTGTACTAACCATCACGGGCTTTGGCTAAAA
128 TCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAACCATCACGGTTTTTGGCTAAAA
* * * *
9181 ACGCGTTTCGGGGACCCGGCTCAGGTTTGCATGATTTTTGGCACAGACAATCCTTGAAATATTTA
193 ACGCGTTTCGAGGACCCGGCTCAGTTTTGCATGATTTTTGGCGCAGAC-ATCCTTGAAATATCTA
*
9246 TATTCATCTGATAAAATCTTAGCCACATTGCATTTAAGGATTTGTTTTACGAGCATCTGAATCTT
257 TATTCATCT-ATAAAATC-TAGCCACATTGCATTTAA--ATTTGTTTTACAAGCATCTGAATCTT
9311 GTTTCGAT
318 GTTTCGAT
* * *
9319 TTAATTTGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGC-TCGAAAAGCCCTTCAA
1 TTAATTAGAAATTAATTCGGAAAAAATAAGAAAAACGATATTAAAAGCGT-GAAAAGCCCTTCAA
* * *
9383 TCTTTTTGGCGTCGAATTATATATTTTATTA-AGTATTTTGGATAAAAATTGAGGAAATATCTTT
65 TCTTTTTGGCGTCGAATTATATATTTT-TTAGAGTATTTTAGCTAAAAATTGAGGAAAAATCTTT
* * ** * *
9447 CAGGTCAATTTTTACAAAATTTCAATCGAAATCGTGTAATAATCATTACGGTTTTTTGGCTAAAA
129 CGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAACCATCACGG-TTTTTGGCTAAAA
* * * * * * *
9512 ACACGTTTCGAGG-CCCGGTTCAATTTTTGAATGATTTTTGGTGCCGATACTCCTTGAAATATCT
193 ACGCGTTTCGAGGACCCGGCTC-AGTTTTGCATGATTTTTGGCGCAGACA-TCCTTGAAATATCT
** * * *
9576 ATATTCATCTA-ACCA-C-ATCC-CA--GCCA--T---TCT-TTTTACAAGCATCTGAATCATGT
256 ATATTCATCTATAAAATCTAGCCACATTG-CATTTAAATTTGTTTTACAAGCATCTGAATCTTGT
*
9629 TTCGTT
320 TTCGAT
** * *
9635 TTAATTAGAAATTAATTCGGAGAAAAATAAGAAAAAATAGTATTAGAAGCTTGAAAAGCCCTTCA
1 TTAATTAGAAATTAATTCGGA-AAAAATAAGAAAAACGA-TATTAAAAGCGTGAAAAGCCCTTCA
* * * * * *
9700 ACCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTGTGGCTAAAAGTTGAGGAAAAATATT
64 ATCTTTTTGGCGTCGAATTATATATTTTTTA-GAGTATTTTAGCTAAAAATTGAGGAAAAATCTT
* * *
9765 TTGGGTCAATTTTTGCAAAATATTAGCCGAAATCGTGTAA
128 TCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAA
9805 CATCACGGTT
Statistics
Matches: 682, Mismatches: 107, Indels: 65
0.80 0.13 0.08
Matches are distributed among these distances:
316 45 0.07
317 19 0.03
318 48 0.07
319 61 0.09
322 1 0.00
323 1 0.00
324 2 0.00
325 2 0.00
326 3 0.00
328 6 0.01
329 46 0.07
330 301 0.44
331 126 0.18
332 21 0.03
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (325 bp):
TTAATTAGAAATTAATTCGGAAAAAATAAGAAAAACGATATTAAAAGCGTGAAAAGCCCTTCAAT
CTTTTTGGCGTCGAATTATATATTTTTTAGAGTATTTTAGCTAAAAATTGAGGAAAAATCTTTCG
GGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAACCATCACGGTTTTTGGCTAAAAACG
CGTTTCGAGGACCCGGCTCAGTTTTGCATGATTTTTGGCGCAGACATCCTTGAAATATCTATATT
CATCTATAAAATCTAGCCACATTGCATTTAAATTTGTTTTACAAGCATCTGAATCTTGTTTCGAT
Found at i:9893 original size:319 final size:314
Alignment explanation
Indices: 9290--9902 Score: 711
Period size: 319 Copynumber: 1.9 Consensus size: 314
9280 TAAGGATTTG
* * * * *
9290 TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTTGAAATTAATTCAGAAAAAATATGAAAAAC
1 TTTTACAAGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATAAGAAAAAA
*
9355 GATATTAAAAGCTCGAAAAGCCCTTCAATCTTTTTGGCGTCGAATTATATATTTTATTAAGTATT
66 GATATTAAAAGCTCGAAAAGCCCTTCAACCTTTTTGGCGTCGAATTATATATTTTATTAAGTATT
* * * *
9420 TTGGATAAAAATTGAGGAAATATCTTTCAGGTCAATTTTTACAAAATTTCAATCGAAATCGTGTA
131 GTGGATAAAAATTGAGGAAAAATATTTCAGGTCAATTTTTACAAAATTTCAACCGAAATCGTG--
* *
9485 ATAATCATTACGGTTTTTTGGCTAAAAACACGTTTCGAGGCCCGGTTCAATTTTTGAATGATTTT
194 ATAATCATCACGGTTTTTTGGCTAAAAACACGTTTCGAGGCCCGGTTCAAGTTTTGAATGATTTT
* * * * ** *
9550 TGGTGCCGATACTCCTTGAAATATCTATATTCATCTAACCACATCCCAGCCATTCT
259 TGGCGCCAAAAATCAATGAAATATCCATATTCATCTAACCACATCCCAGCCATTCT
* *
9606 TTTTACAAGCATCTGAATCATGTTTCGTTTTAATTAGAAATTAATTCGGAGAAAAATAAGAAAAA
1 TTTTACAAGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATTCAGA-AAAAATAAGAAAAA
* * * *
9671 ATAGTATTAGAAGCTTGAAAAGCCCTTCAACCTTTTTGGCGTTGAATTATATATTTT-TTATGAG
65 AGA-TATTAAAAGCTCGAAAAGCCCTTCAACCTTTTTGGCGTCGAATTATATATTTTATTA--AG
* * ** * *
9735 TATTGTGGCTAAAAGTTGAGGAAAAATATTTTGGGTCAATTTTTGCAAAATATT-AGCCGAAATC
127 TATTGTGGATAAAAATTGAGGAAAAATATTTCAGGTCAATTTTTACAAAAT-TTCAACCGAAATC
* * *
9799 GTG-TAA-CATCACGGTTTTTTTTTTGGC-GAAAACTGCGTTTCGCGGTCCCGAG-TC-AGTTTT
191 GTGATAATCATCACGG----TTTTTTGGCTAAAAAC-ACGTTTCGAGG-CCCG-GTTCAAGTTTT
* *
9859 GCATGATTTTTTGCGCCAAAAAT-AATGCAAATATCCATATTCAT
249 GAATGATTTTTGGCGCCAAAAATCAATG-AAATATCCATATTCAT
9903 ATAATGGAAT
Statistics
Matches: 248, Mismatches: 36, Indels: 23
0.81 0.12 0.07
Matches are distributed among these distances:
315 7 0.03
316 48 0.19
317 17 0.07
318 56 0.23
319 111 0.45
320 8 0.03
321 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.37
Consensus pattern (314 bp):
TTTTACAAGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATAAGAAAAAA
GATATTAAAAGCTCGAAAAGCCCTTCAACCTTTTTGGCGTCGAATTATATATTTTATTAAGTATT
GTGGATAAAAATTGAGGAAAAATATTTCAGGTCAATTTTTACAAAATTTCAACCGAAATCGTGAT
AATCATCACGGTTTTTTGGCTAAAAACACGTTTCGAGGCCCGGTTCAAGTTTTGAATGATTTTTG
GCGCCAAAAATCAATGAAATATCCATATTCATCTAACCACATCCCAGCCATTCT
Found at i:10975 original size:331 final size:323
Alignment explanation
Indices: 10205--11282 Score: 977
Period size: 329 Copynumber: 3.3 Consensus size: 323
10195 AGCCACACAA
* * * * *
10205 TTTGGCGTTC-AATTATATGTTTTTTATGAGTATTTTAACCAAAAATTGAAGAAACATCTTTC-G
1 TTTGGCG-TCGAATTATATATTTTTTATGAGTATTTTGA-TAAAAATTGAGGAAATATCTTTCAG
* ** *
10268 GATCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAACCATCACAATTTTTGGCTAAAAATG
64 G-TCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACGGTTTTTGGCTAAAAACG
** * * * ** * **
10333 CGTTT-TAGGACCCCCGCTCAGTTTTTCCTGATCTTTCGCACTAAGAC-TCCTTGAGATATCCGT
128 CGTTTCGGGGA--CCCGCTCAGTTTTGCATGAT-TTTTG-ACGCAGACATCCTTGAAATATCTAT
* * *
10396 ATTCATCTAATCAAATCTCAACCACATTGGATTTAACAATTTGTTTTTACAAGCATCTGAATCTT
189 ATTCATCTAAT-AAATCT-TACCACATTGCATTTAA-GATTTG-TTTTACAAGCATCTGAATCTT
* * * **
10461 GTTT-GATTTTGATTAGAAATTAATT-GAGAAAATATGAAAAACAATATTAAAAGCGTGAAAAGT
250 GTTTCGA-TTTAATTAGAAATTAATTCGAAAAAATATGAAAAAAAATATTAAAAGC-TGAAAAAC
* *
10524 CCTCCAATTGT
313 CCTTCAATTTT
* * *
10535 TTT-GCG-CTAAATTATATATATTTTATGAGTATTTT-ATCCAAAAAATGAGGAAAATAT-TTTC
1 TTTGGCGTC-GAATTATATATTTTTTATGAGTATTTTGAT--AAAAATTGAGG-AAATATCTTTC
* * * *
10596 AGGTCATTTTTTGCAGAATTTTAGCCAAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAAC
62 AGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACGGTTTTTGGCTAAAAAC
* *
10661 GCGTTTCGGGGACCCGACTCAGCTTTGCATGATTTTTGACGCAGACAATCCTTGAAATATCTTTA
127 GCGTTTCGGGGACCCG-CTCAGTTTTGCATGATTTTTGACGCAGAC-ATCCTTGAAATATCTATA
** *
10726 TTCATCTAATAAAATCTTAGCCACATTGCATTTAAGGATTTGTTTTATGAGCATATGAATCTTGT
190 TTCATCTAAT-AAATCTTA-CCACATTGCATTTAA-GATTTGTTTTACAAGCATCTGAATCTTGT
10791 TTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAAAATATATTAAAAGCTCGAAAAACC
252 TTCGATTTAATTAGAAATTAATTC-GAAAAAATATGAAAAAAA-ATATTAAAAGCT-GAAAAACC
10856 CTTCAATTTT
314 CTTCAATTTT
* *
10866 TTTGGCGTCGAATTATATATTTTAT-TGAGTATTTTGGATAAAAATTGAGGAAATACCTTTCAGG
1 TTTGGCGTCGAATTATATATTTTTTATGAGTATTTT-GATAAAAATTGAGGAAATATCTTTCAGG
* * * * *
10930 TCAATTTTTGCAAAATTTCAGTCGAAATCGTGTAATAATCATCACGGTTTTTGTCTAAAAACGCA
65 TCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACGGTTTTTGGCTAAAAACGCG
* * * **
10995 TTTCGGTG-CCCGGTTCAGTTTTTGAATGATTTTTGGTGCCGAGAC-TCCTTGAAATATCTATAT
130 TTTCGGGGACCC-GCTCAG-TTTTGCATGATTTTTGACG-C-AGACATCCTTGAAATATCTATAT
*
11058 TCATCTAACTAAA---T-CC-CA--GCCA-TT--G---T-TTTTACAAGCATCTGAATCATGTTT
191 TCATCTAA-TAAATCTTACCACATTG-CATTTAAGATTTGTTTTACAAGCATCTGAATCTTGTTT
* * * ** * *
11109 CGTTTTAATTAGAAATTAATCCGGAAAAAAATAAGAAAAAACGGTATTAGAAGCTTGAAAAACCA
254 CGATTTAATTAGAAATTAATTC-G-AAAAAATATGAAAAAA-AATATTAAAAGC-TGAAAAACCC
**
11174 TTCAACCTT
315 TTCAATTTT
* * * * * * **
11183 TTTGGCGTTGAATTATATATTTTTTATGAGTATTGTGGCTAAAAGTTGAGGAAAAATATTTTGGG
1 TTTGGCGTCGAATTATATATTTTTTATGAGTATT-TTGATAAAAATTGAGGAAATATCTTTCAGG
* *
11248 TCAATTTTTCCAAAATATTAGCCGAAATCGTGTAA
65 TCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAA
11283 CATCACGGAT
Statistics
Matches: 627, Mismatches: 89, Indels: 76
0.79 0.11 0.10
Matches are distributed among these distances:
316 42 0.07
317 63 0.10
318 61 0.10
319 1 0.00
320 1 0.00
323 3 0.00
324 2 0.00
325 2 0.00
326 2 0.00
327 7 0.01
328 50 0.08
329 164 0.26
330 42 0.07
331 162 0.26
332 18 0.03
333 7 0.01
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (323 bp):
TTTGGCGTCGAATTATATATTTTTTATGAGTATTTTGATAAAAATTGAGGAAATATCTTTCAGGT
CAATTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCACGGTTTTTGGCTAAAAACGCGT
TTCGGGGACCCGCTCAGTTTTGCATGATTTTTGACGCAGACATCCTTGAAATATCTATATTCATC
TAATAAATCTTACCACATTGCATTTAAGATTTGTTTTACAAGCATCTGAATCTTGTTTCGATTTA
ATTAGAAATTAATTCGAAAAAATATGAAAAAAAATATTAAAAGCTGAAAAACCCTTCAATTTT
Found at i:12911 original size:825 final size:823
Alignment explanation
Indices: 11298--12932 Score: 2489
Period size: 825 Copynumber: 2.0 Consensus size: 823
11288 CGGATTTTTT
*
11298 TTTTTGGCGAAAACTGCGTTTCGGGGCTCCGGATCAGTTTTGCATGATTTTTGGCGCCAAAAATA
1 TTTTTGGCAAAAACTGCGTTTCGGGGCTCCGGATCAGTTTTGCATGATTTTTGGCG-CAAAAATA
* *
11363 ATGCAAATATCCATATTCATATAATCGAATCTAAGCCATTGGAATTAAGGATTTTGTTTTACAAG
65 ATGCAAATATCCATATTCATATAATCAAATCTAAGCCATTGGAATTAAGGATTGTGTTTTACAAG
* * *
11428 CATCTAGATCTTTACTACTAGAAAATAGTGATATCGCGGCGTTTTTTTTTCTTTTTTACATATAG
130 CATCTAAATCTTCACTACTAGAAAATACTGATATCGCGGCG-----TTTTCTTTTTTACATATAG
* * *
11493 CGGCGTTTTTCACTTCGCCGCCATAGGTGTTGTTATAACAACTGCCTCTATTTTTGCGGCGTTTT
190 CGGCGCTTTTCACTTCGCCGCCAAAGGTGTCGTTATAACAACTGCCTCTATTTTTGCGGCGTTTT
* *
11558 ACCAAAAAACGCCGCTATCTGCATAACGCCGTCATTTAGAGGCGTTTAAACGCCGTTATACTGTT
255 ACCAAAAAACGCCGCTATCCGCATAACGCCGT-ATTAAGAGGCGTTTAAACGCCGTTATACTGTT
*
11623 TGAATCATTTATTTTTTTAAAAAAAATAAATTAAATATAGCGGCGTTTAATTAGAAATTAATTTG
319 TGAATCATTTATTTTTTAAAAAAAAATAAATTAAATATAGCGGCGTTTAATTAGAAATTAATTTG
* * *
11688 GAAAAAATAGGGAAAACGATATTAGAAACGTGAAAAGCCACTCAATTTTTTTGGCGTTGAATTAT
384 GAAAAAAAAGGAAAAACGATATTAGAAACGTCAAAAGCCACTCAATTTTTTTGGCGTTGAATTAT
11753 ATATTTTTTATGAGTATTTTAACCAAAAAATGAGGAAACATCTTTTGGGTCAATTTTTACAAAAT
449 ATATTTTTTATGAGTATTTTAACCAAAAAATGAGGAAACATCTTTTGGGTCAATTTTTACAAAAT
* *
11818 TTTAGCCGAAATCGTGTAATAACCATCACAGTTTTTGACTAAAAATGCGTTTTAGGACCCCGGCT
514 TTTAGCCGAAATCGTGTAATAACCATCACAGTTTTTGACTAAAAATGCGTTTTAGAACCCCGCCT
*
11883 CAGTTTTGCCTGATCTTTGGCACTAAGACTCCTTGAGATATCCATATTCATCTAATCAAATCTCA
579 CAGTTTTGCCTGATCTTTGGCACCAAGACTCCTTGAGATATCCATATTCATCTAATCAAATCTCA
11948 GCCACAATGGATTTAACAATTATTTTTACAAGCATCTGAATCTTGTCTGATTTTGATTAGAAATT
644 GCCACAATGGATTTAACAATTATTTTTACAAGCATCTGAATCTTG--TGATTTTGATTAGAAATT
12013 AATTGAGAAAAATATGAAAAATAATATTAAAAGCGTGAAAAGTCCTCCAATAGTTTTGGCGCTAA
707 AATTGAGAAAAATATGAAAAATAATATTAAAAGCGTGAAAAGTCCTCCAATAGTTTTGGCGCTAA
*
12078 ATTATATATATTTTATGTGTATTTTATCCAAAATCGTGTACTAAACATCACAG
772 ATTATATATATTTTATGAGTA-TTTATCCAAAATCGTGTACTAAACATCACAG
*
12131 TTTTTGGCTAAAAAC-GCGTTTCGGGGAC-CCGGCTCAGTTTTGCATGATTTTTGGCG-AAGACA
1 TTTTTGGC-AAAAACTGCGTTTCGGGG-CTCCGGATCAGTTTTGCATGATTTTTGGCGCAA-A-A
* ** * *
12193 CTCCTTG-AAATATCTATATTCATCTAATCAAATCTAAGCCACATTGGAATTAAGGATTGT-TTT
62 AT-AATGCAAATATCCATATTCATATAATCAAATCTAAG-C-CATTGGAATTAAGGATTGTGTTT
*
12256 TACAAGCATCTAAATCTTCACTACTAGAAAATACTGATATGGCGGCG-TTT-TTTTTTACATATA
124 TACAAGCATCTAAATCTTCACTACTAGAAAATACTGATATCGCGGCGTTTTCTTTTTTACATATA
*
12319 GCGGCGCTTTTCACTTCGCTGCCAAAGGTGTCGTTATAACAAAC-GCC-CATATTTTTGCGGCGT
189 GCGGCGCTTTTCACTTCGCCGCCAAAGGTGTCGTTATAAC-AACTGCCTC-TATTTTTGCGGCGT
* *
12382 TTTA-CAAAAAA-GCACTGCTATCCGCATAACGGCGT-TTAAGAGGCGTTTAAGCGCCGTTATA-
252 TTTACCAAAAAACGC-C-GCTATCCGCATAACGCCGTATTAAGAGGCGTTTAAACGCCGTTATAC
12443 TAGTTT-AGATCATTTATTTTTTAAAAAAAAAATAAATTAAATATAGCGGCGTTTAATTAGAAAT
315 T-GTTTGA-ATCATTTATTTTTT-AAAAAAAAATAAATTAAATATAGCGGCGTTTAATTAGAAAT
* * *
12507 TAATTTGGAAAAAAAATGAAAAACGATATTAGAAACGTCAAACGCCATTCAA-TTTTTTGGCGTT
377 TAATTTGGAAAAAAAAGGAAAAACGATATTAGAAACGTCAAAAGCCACTCAATTTTTTTGGCGTT
* *
12571 GAATTGTATATTTTTTATGAGTATTTTAACCAAAAACTGAGGAAACATCTTTTGGGTCAATTTTT
442 GAATTATATATTTTTTATGAGTATTTTAACCAAAAAATGAGGAAACATCTTTTGGGTCAATTTTT
* * * *
12636 ACAAAATTTTAGCCGGAATCTTTTAATAACCATCACAGTTTTTGGCTAAAAATGCGTTTTCA-AA
507 ACAAAATTTTAGCCGAAATCGTGTAATAACCATCACAGTTTTTGACTAAAAATGCGTTTT-AGAA
* ** *
12700 CCCCGCCTCAGTTTTGCCTGATTTTTGGTGCCAAGGCTCCTTGAGATATCCATATTCATCTAATC
571 CCCCGCCTCAGTTTTGCCTGATCTTTGGCACCAAGACTCCTTGAGATATCCATATTCATCTAATC
*
12765 AAAATCTCAGCCACAATGGATTTGACAATT-TGATTTTACAAGCATCTGAATCTTG-GATTTT-A
636 -AAATCTCAGCCACAATGGATTTAACAATTAT--TTTTACAAGCATCTGAATCTTGTGATTTTGA
*
12827 TTAGAAATTAATTGAGAAAAATATGAAAAATAATATTAAAAGCGTGAAAAGTCCTCCAATTGTTT
698 TTAGAAATTAATTGAGAAAAATATGAAAAATAATATTAAAAGCGTGAAAAGTCCTCCAATAGTTT
12892 TGGCGCTAAATTATATATATTTTATGAGTATTTATCCAAAA
763 TGGCGCTAAATTATATATATTTTATGAGTATTTATCCAAAA
12933 AATGAGGAAA
Statistics
Matches: 740, Mismatches: 44, Indels: 47
0.89 0.05 0.06
Matches are distributed among these distances:
822 11 0.01
823 94 0.13
824 8 0.01
825 236 0.32
826 124 0.17
827 109 0.15
828 6 0.01
831 2 0.00
832 1 0.00
833 76 0.10
834 55 0.07
835 18 0.02
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (823 bp):
TTTTTGGCAAAAACTGCGTTTCGGGGCTCCGGATCAGTTTTGCATGATTTTTGGCGCAAAAATAA
TGCAAATATCCATATTCATATAATCAAATCTAAGCCATTGGAATTAAGGATTGTGTTTTACAAGC
ATCTAAATCTTCACTACTAGAAAATACTGATATCGCGGCGTTTTCTTTTTTACATATAGCGGCGC
TTTTCACTTCGCCGCCAAAGGTGTCGTTATAACAACTGCCTCTATTTTTGCGGCGTTTTACCAAA
AAACGCCGCTATCCGCATAACGCCGTATTAAGAGGCGTTTAAACGCCGTTATACTGTTTGAATCA
TTTATTTTTTAAAAAAAAATAAATTAAATATAGCGGCGTTTAATTAGAAATTAATTTGGAAAAAA
AAGGAAAAACGATATTAGAAACGTCAAAAGCCACTCAATTTTTTTGGCGTTGAATTATATATTTT
TTATGAGTATTTTAACCAAAAAATGAGGAAACATCTTTTGGGTCAATTTTTACAAAATTTTAGCC
GAAATCGTGTAATAACCATCACAGTTTTTGACTAAAAATGCGTTTTAGAACCCCGCCTCAGTTTT
GCCTGATCTTTGGCACCAAGACTCCTTGAGATATCCATATTCATCTAATCAAATCTCAGCCACAA
TGGATTTAACAATTATTTTTACAAGCATCTGAATCTTGTGATTTTGATTAGAAATTAATTGAGAA
AAATATGAAAAATAATATTAAAAGCGTGAAAAGTCCTCCAATAGTTTTGGCGCTAAATTATATAT
ATTTTATGAGTATTTATCCAAAATCGTGTACTAAACATCACAG
Found at i:13382 original size:330 final size:324
Alignment explanation
Indices: 12494--13434 Score: 927
Period size: 328 Copynumber: 2.9 Consensus size: 324
12484 TATAGCGGCG
** * * *
12494 TTTAATTAGAAATTAATTTGGAAAAAAAATGAAAAACGATATTAGAAA-CGTC-AAACGCCATTC
1 TTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTA-AAAGCGTCGAAAAGCCCTTC
** * * *
12557 AATTTTTTGGCGTTGAATTGTATATTTTTTATGAGTATTTTAACCAAAAACTGAGGAAACATCTT
65 AATTTTTTGGCGTCAAATTATATA-TTTTTATGAGTATTTT--CCAAAAAATGAGGAAAAATCTT
* * * * * * *
12622 TTGGGTCAATTTTTACAAAATTTTAGCCGGAATCTTTTAATAACCATCACAGTTTTTGGCTAAAA
127 TCGGGTCAATTTTTGCAAAATTTTAACCGAAATCGTGTAATAACCATCACGGTTTTTGGCTAAAA
**** * * * *
12687 ATGCGTTTTCAAACCCCGCCTCAGTTTTGCCTGATTTTTGGTGCCA-AGGCTCCTTGAGATATCC
192 ATGCG-TTTCGGGGCCCG-CTCAGTTTTGCATGATTTTTGGTG-CAGAGACTCCTTGAAATATCT
* * *
12751 ATATTCATCTAATCAAAATCTCAGCCACAATGGATTTGACAATTTGATTTTACAAGCATCTGAAT
254 ATATTCATATAATCAAAATCTCAGCCACAATGCATTTAACAATTTGATTTTACAAGCATCTGAAT
12816 CTTGGA
319 CTTGGA
* * ** * *
12822 TTTTATTAGAAATTAATTGAG-AAAAATATGAAAAATAATATTAAAAGCGT-GAAAAGTCCTCCA
1 TTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTCGAAAAGCCCTTCA
*
12885 ATTGTTTTGGCG-CTAAATTATATATATTTTATGAGTATTTATCCAAAAAATGAGGAAAAATTTT
66 ATT-TTTTGGCGTC-AAATTATATAT-TTTTATGAGTATTT-TCCAAAAAATGAGGAAAAATCTT
* * * * * *
12949 TCGGGTCATTTTTTGCAGAATTTT-AGCAAAATTGTGTACTATAACCATCACGGTGTTTGGCTAA
127 TCGGGTCAATTTTTGCAAAATTTTAACCGAAATCGTGTA--ATAACCATCACGGTTTTTGGCTAA
* * * *
13013 AAACGCCTTTCGGGGACCCGGCTCAGTTTTGCATGATTTTTGGCGCAGACACTCCTTGAAATATC
190 AAATGCGTTTCGGGG-CCC-GCTCAGTTTTGCATGATTTTTGGTGCAGAGACTCCTTGAAATATC
* ** * *
13078 TATATTCATATAAT-AAAATCTTAGCCAC-ATGCATTTAAGGATTT-ATTTTACGAGCATCTGTA
253 TATATTCATATAATCAAAATCTCAGCCACAATGCATTTAACAATTTGATTTTACAAGCATCTGAA
13140 TCTTGTTTCGA
318 TCTTG----GA
*
13151 TTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATCAAAAGC-TCGAAAAGCCCTTCA
1 TTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTCGAAAAGCCCTTCA
* * *
13215 ATCTTCTTTTGGCGTCAAATTATATA-TTTTATTGAGTATTTTGGCTAAAAATTGAGGAAATATC
66 A--TT-TTTTGGCGTCAAATTATATATTTTTA-TGAGTATTTT--CCAAAAAATGAGGAAAAATC
* * * * *
13279 TTTCAGGTCAATTTTTGTAAAATTTTAATCGAAATCGTGTAATAAACATCACGGTTTTTTGCTAA
125 TTTCGGGTCAATTTTTGCAAAATTTTAACCGAAATCGTGTAATAACCATCACGGTTTTTGGCTAA
* * * * * * * *
13344 AAATGTGTTTCGGGGCCTGCTTCAATTTTGAATGATTTTTGATGCCGAGACACCGTGAAATATCT
190 AAATGCGTTTCGGGGCCCGC-TCAGTTTTGCATGATTTTTGGTGCAGAGACTCCTTGAAATATCT
* * *
13409 ATATTCATCTAA-CCAAATCCCAGCCA
254 ATATTCATATAATCAAAATCTCAGCCA
13435 TTGTTTTCAC
Statistics
Matches: 500, Mismatches: 87, Indels: 50
0.78 0.14 0.08
Matches are distributed among these distances:
325 21 0.04
326 22 0.04
327 92 0.18
328 126 0.25
329 26 0.05
330 101 0.20
331 42 0.08
332 58 0.12
333 12 0.02
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (324 bp):
TTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTAAAAGCGTCGAAAAGCCCTTCA
ATTTTTTGGCGTCAAATTATATATTTTTATGAGTATTTTCCAAAAAATGAGGAAAAATCTTTCGG
GTCAATTTTTGCAAAATTTTAACCGAAATCGTGTAATAACCATCACGGTTTTTGGCTAAAAATGC
GTTTCGGGGCCCGCTCAGTTTTGCATGATTTTTGGTGCAGAGACTCCTTGAAATATCTATATTCA
TATAATCAAAATCTCAGCCACAATGCATTTAACAATTTGATTTTACAAGCATCTGAATCTTGGA
Found at i:14649 original size:323 final size:323
Alignment explanation
Indices: 14057--14941 Score: 865
Period size: 323 Copynumber: 2.7 Consensus size: 323
14047 TAGAAACTTC
* * * ** *
14057 AAAAGCCATTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTAACCAAAAATTG
1 AAAAGCCCTCCAATCCTTTTGGCGTCAAATTATATATATTTTATGAGTATTTTAACCAAAAATTG
* * * * *
14122 AGGAAACATCTTTCAGGTCAATTTTTACAAAATTTTAGCCGAATTCGTGTAATAATCATCACAGT
66 AGGAAAAATTTTTCAGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTG-----A-CATCACGGT
** * * *
14187 TTTTGGCTAAAAATACGTTTTAGGACTCCGGCTCAGTTTTGCCTGATTTTTGGCGCCAAGA-A-T
125 TTTTGGCTAAAAACGCGTTTCAGGAC-CTGGCTCAGTTTTGCATGATTTTT-GC-CC-AGACACT
* * * * *
14250 ACTTGAGATATCCATATTCATCTAATCAAATCTCAGCCACATTCGATTTGACAATTTCTTTTACA
186 CCTTGAAATATCTATATTCATCTAATAAAATCTCAGCCACATTCGATTTAACAATTTCTTTTACA
* * * * *
14315 AGCATCTGAATCTTGTTTCGATTTTATTATAAATTAATT-GAGAAAAATACGAAAAATAATATTA
251 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTAGAAAAAAATACGAAAAACAATATCA
14379 AAAGCGAG
316 AAAGCGAG
* * * * * *
14387 AAAAGTCGTCCAATTCTTTTGGTG-CTAAATTATATATATTTTATGAGTATTTTATCCAAAAAAT
1 AAAAGCCCTCCAATCCTTTTGGCGTC-AAATTATATATATTTTATGAGTATTTTAACCAAAAATT
* * * *
14451 GAGGAAAAATTTTTCGGGTCATTTTTTGCAGAATTTTAGCCAAAATCGTG-CATCACGGTTTTTG
65 GAGGAAAAATTTTTCAGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGACATCACGGTTTTTG
* *
14515 GCTAAAAACGCATTTCGAGGACCTGGCTCAATTTTGCATGATTTTTGCCACAGACACTCCTTGAA
130 GCTAAAAACGCGTTTC-AGGACCTGGCTCAGTTTTGCATGATTTTTGCC-CAGACACTCCTTGAA
* ** * *
14580 ATATCTATATTCATCTAATAAAATCTTAGCCACATT-GCATTTAAGGATTTGTTTTACGAGCATC
193 ATATCTATATTCATCTAATAAAATCTCAGCCACATTCG-ATTTAACAATTTCTTTTACAAGCATC
* *
14644 TGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAATATGAAAAACGATATCAAAAGC
257 TGAATCTTGTTTCGATTTAATTAGAAATTAATT-AGAAAAAAATACGAAAAACAATATCAAAAGC
**
14709 TCG
321 GAG
* * ** *
14712 AAAAGCCCTTCAATCCTTTTGGCGTCGAA-T-TATATATTTTATTGAGTATTTT-GGCTAAAATT
1 AAAAGCCCTCCAATCCTTTTGGCGTCAAATTATATATATTTTA-TGAGTATTTTAACCAAAAATT
** * *
14774 GAGGAAGTATCTTTTCAGGTCAATTTTTGCAAAATTTTAGTCGAAATCGTGTAATAATCATCAAG
65 GAGGAAAAAT-TTTTCAGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTG-----A-CATCACG
* * ** * *
14839 GTTTTTTGTTAAAAACGCGTTTC-GGAGCCTGATTCAGTTTTGAATGATTTTTGGTGCC-GACAC
123 GTTTTTGGCTAAAAACGCGTTTCAGGA-CCTGGCTCAGTTTTGCATGATTTTT-G-CCCAGACAC
* ** *
14902 ACCTTGAAATATCTATATTCATCTAACCAAATCCCAGCCA
185 TCCTTGAAATATCTATATTCATCTAATAAAATCTCAGCCA
14942 TTGTTTTCAC
Statistics
Matches: 457, Mismatches: 77, Indels: 42
0.79 0.13 0.07
Matches are distributed among these distances:
321 4 0.01
322 5 0.01
323 162 0.35
324 51 0.11
325 47 0.10
326 1 0.00
329 3 0.01
330 155 0.34
331 28 0.06
332 1 0.00
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (323 bp):
AAAAGCCCTCCAATCCTTTTGGCGTCAAATTATATATATTTTATGAGTATTTTAACCAAAAATTG
AGGAAAAATTTTTCAGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGACATCACGGTTTTTGG
CTAAAAACGCGTTTCAGGACCTGGCTCAGTTTTGCATGATTTTTGCCCAGACACTCCTTGAAATA
TCTATATTCATCTAATAAAATCTCAGCCACATTCGATTTAACAATTTCTTTTACAAGCATCTGAA
TCTTGTTTCGATTTAATTAGAAATTAATTAGAAAAAAATACGAAAAACAATATCAAAAGCGAG
Found at i:15225 original size:311 final size:308
Alignment explanation
Indices: 14660--15245 Score: 708
Period size: 311 Copynumber: 1.9 Consensus size: 308
14650 TTGTTTCGAT
*
14660 TTAATTAGAAATTAATTCAGAAAAAAATATGAAAAACGATATCAAAAGCTCGAAAAGCCCTTCAA
1 TTAATTAGAAATTAATTCAGAAAAAAATAAGAAAAACGATATCAAAAGCTCGAAAAGCCCTTCAA
* ** *
14725 TCCTTTTGGCGTCGAATTATATATTTTATTGAGTATTTTGGCTAAAATTGAGGAAGTATCTTTTC
66 TCCTTTTGGCGTCGAATTATATATTTTATTGAGTATTGTGGCTAAAATTGAGGAAAAATATTTTC
* *
14790 AGGTCAATTTTTGCAAAATTTTAGTCGAAATCGTGTAATAATCATCAAGGTTTTTTGTTAAAAAC
131 AGGTCAATTTTTGCAAAATATTAGCCGAAATCGTGTAATAATCATCAAGGTTTTTTGTTAAAAAC
* * * * * *
14855 GCGTTTCGGAGCCTGATTCAGTTTTGAATGATTTTTGGTGCCGACACACCTTGAAATATCTATAT
196 GCGTTTCGGAGCCTGAGTCAGTTTTGAATGATTTTTGGCGCCGAAAAACCATGAAATATCAATAT
14920 TCATCTAACCAAATCCCAGCCATTGTTTTCACAAGCATCTGAATCATG
261 TCATCTAACCAAATCCCAGCCATTGTTTTCACAAGCATCTGAATCATG
* * * *
14968 TTAATTAGAAATTAATTCGGAAAAAAAATAAGAAAAAAC-AGTATTAGAAA-CAT-GAATAGCTC
1 TTAATTAGAAATTAATTCAG-AAAAAAATAAG-AAAAACGA-TATCA-AAAGC-TCGAAAAGCCC
* * *
15030 TTCAATCTTTTTGGCGTTGAATTATATATTTT-TCATGAGTATTGTGGCTACAAGTTGAGGAAAA
61 TTCAATCCTTTTGGCGTCGAATTATATATTTTAT--TGAGTATTGTGGCTA-AAATTGAGGAAAA
* * * *
15094 ATATTTT-GGGTCAATTTTTGCAAAATATTAGCCGAAATCGTGTAA-CATCA-C-A-TTTTTTTT
123 ATATTTTCAGGTCAATTTTTGCAAAATATTAGCCGAAATCGTGTAATAATCATCAAGGTTTTTTG
* * * *
15154 TTGCCAAAACTGCGTTTCGGGGCCCCTG-GTCAGTTTTGCATGATTTTTGGCGCC-AAAAATCAT
188 TT--AAAAAC-GCGTTTCGGAG--CCTGAGTCAGTTTTGAATGATTTTTGGCGCCGAAAAACCAT
*
15217 GCAAATATCAATATTCATCTAATCAAATC
248 G-AAATATCAATATTCATCTAACCAAATC
15246 TAAGCCACAT
Statistics
Matches: 235, Mismatches: 29, Indels: 25
0.81 0.10 0.09
Matches are distributed among these distances:
307 8 0.03
308 20 0.09
309 18 0.08
310 68 0.29
311 101 0.43
312 20 0.09
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (308 bp):
TTAATTAGAAATTAATTCAGAAAAAAATAAGAAAAACGATATCAAAAGCTCGAAAAGCCCTTCAA
TCCTTTTGGCGTCGAATTATATATTTTATTGAGTATTGTGGCTAAAATTGAGGAAAAATATTTTC
AGGTCAATTTTTGCAAAATATTAGCCGAAATCGTGTAATAATCATCAAGGTTTTTTGTTAAAAAC
GCGTTTCGGAGCCTGAGTCAGTTTTGAATGATTTTTGGCGCCGAAAAACCATGAAATATCAATAT
TCATCTAACCAAATCCCAGCCATTGTTTTCACAAGCATCTGAATCATG
Found at i:17910 original size:330 final size:331
Alignment explanation
Indices: 17107--18049 Score: 1031
Period size: 331 Copynumber: 2.9 Consensus size: 331
17097 TATAGCAGCG
** * * *
17107 TTTAATTAGAAATTAATTTGGAAAAAATAGGAAAAACTATATTAGAAA-CTTC-AAAAGCCATTC
1 TTTAATTAGAAATTAATTAAG-AAAAATATGAAAAACTATATTA-AAAGCGTCGAAAAGCCCTTC
** * * * *
17170 AATCTTTTTGGTATTGAATTATATATTTTTTATGAGTATATTAACAAAAAATTGAGGAAACATCT
64 AAT-TTTTTGGCGTCGAATTTTATATTTTTTATGAGTATTTTAACAAAAAATTGAGGAAAAATCT
* * * *
17235 TTCGGGTCAATTTTTACAAAATTTTAGCCGAAATTC-TGTATTAACCATCACAGTTTTTGGCTAA
128 TTCGGGTCAATTTTTTCAAAATTTTAGCC-AAAATCGTGTAATAACTATCACAGTTTTTGGCTAA
* ** * * *
17299 AAATGCGTTTTAGGATCCCGGCTCAGTTTTGCCTGATTTTTGGCGTCAG-GACTCCTTGAGATAT
192 AAACGCGTTTCGGGGTCCCGGCTCAGTTTTGCATGATTTTTGGCG-CAGAGACTCCTTGAAATAT
* * *
17363 CCGTATTTATCTAATCAAATCTCAGCCACATTGGATTTAAAATTTTGTTTTTACAAGCATCTGAA
256 CTGTATTCATCTAATCAAATCTCAGCCACATTGCATTTAAAATTTTGTTTTTACAAGCATCTGAA
17428 TCTTGTTTCGA
321 TCTTGTTTCGA
* * *
17439 TTTGATTAGAAATTAATTAAGAAAAATATGAAAAA-TATTATTAAAAGCGT-GAAAAGTCCTCCA
1 TTTAATTAGAAATTAATTAAGAAAAATATGAAAAACTA-TATTAAAAGCGTCGAAAAGCCCTTCA
* *
17502 ATTGTTTTGGCG-CTAATTTATATATTTTTTATGAGTATTTTATCCAAAAAA-TGAGGAAAAAAT
65 ATT-TTTTGGCGTCGAATTT-TATATTTTTTATGAGTATTTTA-ACAAAAAATTGAGG-AAAAAT
* * * *
17565 -TTTTGGGTC-ATTTTTTGCAAAATTTTAGCCAAAATCGTGTACTAACTATCACCGCTTTTGGCT
126 CTTTCGGGTCAATTTTTT-CAAAATTTTAGCCAAAATCGTGTAATAACTATCACAGTTTTTGGCT
*
17628 ACAAACGCGTTTCGGGGTCCCGGCTCAGTTTTGCATGATTTTTGGCGCAGACG-CTCCTTGAAAT
190 AAAAACGCGTTTCGGGGTCCCGGCTCAGTTTTGCATGATTTTTGGCGCAGA-GACTCCTTGAAAT
* * * * * *
17692 ATCTATATTCATCTAAT-AACATCTTAGGCGCATTGCATTTAAAGA-TTTG-TTTTACGAGTATC
254 ATCTGTATTCATCTAATCAA-ATCTCAGCCACATTGCATTTAAA-ATTTTGTTTTTACAAGCATC
17754 TGAATCTTGTTTCGA
317 TGAATCTTGTTTCGA
* *
17769 TTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGC-TCGAAAAGCCCTTCAA
1 TTTAATTAGAAATTAATTAAGAAAAATATGAAAAACTATATTAAAAGCGTCGAAAAGCCCTTCAA
* ** * *
17833 TATTTTTGGCGTCGAATTTTATATTTTAT-TGAGTATTTTGGCTAAAAATTGAGGAAATATCTTT
66 T-TTTTTGGCGTCGAATTTTATATTTTTTATGAGTATTTTAACAAAAAATTGAGGAAAAATCTTT
* * * * *
17897 CAGGTCAATTTTTTCAAAATTTTAGTCGAAATCGTGTAATAA-TCATCACGGTTTTTTGCTAAAA
130 CGGGTCAATTTTTTCAAAATTTTAGCCAAAATCGTGTAATAACT-ATCACAGTTTTTGGCTAAAA
* * ** * * * * * *
17961 ACGTGTTTCGAGG-CCTTGTTCAGTTTTGAAAGATTTTTTGTGCCGAGACTCCTTGAAATATCTG
194 ACGCGTTTCGGGGTCCCGGCTCAGTTTTGCATGATTTTTGGCGCAGAGACTCCTTGAAATATCTG
* * *
18025 TATTCATCTAACCCAATCCCAGCCA
259 TATTCATCTAATCAAATCTCAGCCA
18050 TTGTTTTCAC
Statistics
Matches: 512, Mismatches: 76, Indels: 50
0.80 0.12 0.08
Matches are distributed among these distances:
327 1 0.00
328 69 0.13
329 76 0.15
330 132 0.26
331 202 0.39
332 32 0.06
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (331 bp):
TTTAATTAGAAATTAATTAAGAAAAATATGAAAAACTATATTAAAAGCGTCGAAAAGCCCTTCAA
TTTTTTGGCGTCGAATTTTATATTTTTTATGAGTATTTTAACAAAAAATTGAGGAAAAATCTTTC
GGGTCAATTTTTTCAAAATTTTAGCCAAAATCGTGTAATAACTATCACAGTTTTTGGCTAAAAAC
GCGTTTCGGGGTCCCGGCTCAGTTTTGCATGATTTTTGGCGCAGAGACTCCTTGAAATATCTGTA
TTCATCTAATCAAATCTCAGCCACATTGCATTTAAAATTTTGTTTTTACAAGCATCTGAATCTTG
TTTCGA
Done.