Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019069.1 Corchorus olitorius cultivar O-4 contig19102, 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: 73656
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:615 original size:332 final size:329
Alignment explanation
Indices: 1--2808 Score: 2534
Period size: 332 Copynumber: 8.5 Consensus size: 329
* * * * *
1 TATATAATT-AAAAGCCAAAAATATTGGAGGACTCTTCACGCTTTTAATATCATTTTTTATATTT
1 TATATAATTCAACA-CCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTT
* *
65 TTCTAAATTAATTTCTAATTAAATCG-AACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAAT
65 TTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAAT
** * * * *
129 TGAATGTGGATAAGATTTGATTAGATAAATATAGATATTTTAAGGAGTCTTGGCGCCAAAAATCA
130 CCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCA
* *** ** * *
194 TGCAAAACTAAGCCGGGGTTGCAAAACGCGTTTTTAGCCAAAAAACCGTGATGATTAGTACATGA
195 TGCAAAACTGAGCC-GGGCCCCGGAACGCGTTTTTAGCC-AAAAACCGTGATGATTATTACACGA
* * * * *
259 TTTCGGCTAAAATTTTGTAAAAAATGACTCAAAAAATTTTTCTGTCAATTTTTGGC-ATAAATAC
258 TTTCGGCTAAAATTTTGCAAAAAATGACCCGAAATATTTTTC-CTCAATTTTTGGCTA-AAATAC
*
323 TCATAATATA
321 TCATAA-AAA
* * * *
333 CATATAATTTAACACCAAAAGGATTGGAGGACTTTTCACGCTTTTAATATCGTGTTTCATATTTT
1 TATATAATTCAACACCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTT
* *
398 TCTGAATGAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAATCAAATTCTTAAATC
66 TCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATC
* * * * * * * * * *
463 CAATGTAGATGAGATTTAATTAAATGAATATGGATATCTCAAAGAATTTTGACGCCAAAAATCAT
131 CAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCAT
* * * *
528 GCAAAACTTAGCCGAGGCCCCGGAACACATTTTTAGCCAAAAACCGTGATGATTATTACACGGTT
196 GCAAAACTGAGCCG-GGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGATTATTACACGATT
* * *
593 TCGCCTAAAATTTTACAAAAAAT-A-CCAAAATATTTTTCCTCAATTTTTGGCTAAAATACTCAT
260 TCGGCTAAAATTTTGCAAAAAATGACCCGAAATATTTTTCCTCAATTTTTGGCTAAAATACTCAT
*
656 GAAATA
325 -AAAAA
* * * * *
662 TATATAATTTACCACCAAAAAGATTGGAGGACGTTTCACGATTTTCATATCGTTTTTCATATTTT
1 TATATAATTCAACACCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATA-TTT
* * * *
727 TTCTGAATTAATTTCTAATTTAATCGAAATAAGATTTAGATGCTCGTAAAAACAAATCCTTAAAT
65 TTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAAT
* * * * * * *
792 GCAATGTGTCTGA-A-ATGAATATAGATGAATATGGATATCTCAAGTAGTCTTAGCGCCAAAAAT
130 CCAATGTGGCTGAGATTTG-AT-TAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAAT
* * ** * *
855 CATGCAAAACTAACCCAGGGCCTTGGAACGCATTTTTAGCCAAAAATCGTGATGATTATTACACG
193 CATGCAAAACTGAGCC-GGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGATTATTACACG
* * * * *
920 ATTTCGGCTAAAATTTTGCAAAAAAATGAACGGAAATATATTTCCTCAATTTTTTGCTAAATTAC
257 ATTTCGGCTAAAATTTTGC-AAAAAATGACCCGAAATATTTTTCCTCAATTTTTGGCTAAAATAC
*
985 -CAAAATAAA
321 TCATAA-AAA
* * * * * * *
994 TAATATAATTCTACACCAAAAATATTGAAGGA-TTTTTATGCTTCTAATATAGTTTTTTC-TACT
1 T-ATATAATTCAACACCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCG-TTTTTCATA-T
*
1057 ATTTTC-GAATTAATTTCTAATTAAATCGAAAGAAGAATT-AGATGCTCGTAAAAAC-AATTCCT
63 -TTTTCTGAATTAATTTCTAATTAAATCGAAACAAG-ATTCAGATGCTCGTAAAAACAAATT-CT
* * **
1119 TAAATCCAATGTGGCTGAGATTTGATTAGTAT-AATATAAATAGTTCAAGGAGTCTTGGCGTAAA
125 TAAATCCAATGTGGCTGAGATTTGATTAG-ATGAATATAGATATTTCAAGGAGTCTTGGCGCCAA
* * * ** * * ** *
1183 AAATCTTGCAATACTGACCCGGGGTTCTGGAACGCGTTTTTAGCAAAAAAAAGTGATG----TTG
189 AAATCATGCAAAACTGAGCC-GGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGATTATTA
** * ** * * *
1244 CACGATTTCAACTAATATTTTGCAAAAAATGACTTGAAATATTTTTCCTCAAATTTTAG-TCACA
253 CACGATTTCGGCTAAAATTTTGCAAAAAATGACCCGAAATATTTTTCCTCAATTTTTGGCT-AAA
1308 ATACTCATAAAAA
317 ATACTCATAAAAA
* * * * * * *
1321 TATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCATGCTTCTAATACCGTTTTTCCTATTTT
1 TATATAATTCAACACCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTT
* ** * * * *
1386 TCCGAATTAATTTCTAATTAAAAAGAAACATGATTAAAATGCT--T----ATAAA-----AAA--
66 TCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATC
* * * * *
1438 -AA--TGGTTGAGATTTGGTTAGATGAATATAGACATTTCTAGGAGTCTCGGCGCCAAAAATCAT
131 CAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCAT
* * *** * ** * * *
1500 -TAAATCTGAAATGCGCTTCGGAACGCGTTGTTAGCCAAAACCCGTGATGATTATTACACGATTC
196 GCAAAACTGAGCCGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGATTATTACACGATTT
* * * * * ** * * *
1564 CGGCTAAAATTTTACAAAAATTGACCCGATAGATATTTCCTCAATTTTTACCCATAATATTCATA
261 CGGCTAAAATTTTGCAAAAAATGACCCGAAATATTTTTCCTCAATTTTTGGCTAAAATACTCAT-
1629 AAAAA
325 AAAAA
* * * * *
1634 TATATAATTCAACGCCATAAAGATTGAAGGGCTTTTGACGCTTTTAATATCGTTTTTCATATTTT
1 TATATAATTCAACACCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATA--TT
* * *
1699 TTTCTAAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCGTTAAAAACAAAAAAAATC
64 TTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCG-TAAAAAC----AAATTC
* * * * * * * *
1764 TTAAATGCAATGTGGCTAAGATTTTATTAGATGAATATAGTTATTTCAAGGAGTATCGGTGTCAA
124 TTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAA
* * * * * *
1829 AAATCATGCAAAACTGAACTGGTGCCTCGAAACGCGTTTTTAGCCAAAAACCATGATGATTAATA
189 AAATCATGCAAAACTGAGCCGG-GCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGATTATTA
* * * * * * *
1894 CACGATTTTGGCTAAAATTTTGCAAAATATAACCCGAAAAATTTTTCTTCAATTTTCGGATAAAA
253 CACGATTTCGGCTAAAATTTTGCAAAAAATGACCCGAAATATTTTTCCTCAATTTTTGGCTAAAA
1959 TACTCCTAATATATATATATATATATATA
318 TACT-C------------ATA-A-A-A-A
* * * *
1988 TATATAATTGAACAACAAAAAGATTGGAGGACTTTTTATGCTTTTAATATCGTTTTTCATATTTT
1 TATATAATTCAACACCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTT
* * * * * *
2053 TATGTATTAATTTCTAATTAGATCGAAACAAGATTTAGATGCTTGTAAAAACAAATTTTTAAATC
66 TCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATC
* * * *
2118 CAATGTGGATGTGATTTGATTAGATGAGTATAGATATCTCAAGGAGTCTTGGCGCCAAAAATCAT
131 CAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCAT
* ** ** * * *
2183 GCAAAACTGAGCCGGGGCCACAAAACGTTTTTTTATCCAAAAACTGTGATGGTTATTACACG---
196 GCAAAACTGAGCC-GGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGATTATTACACGATT
* * *
2245 TCGGCTAAAATTTTGTAAAAATTGACCCGAAATA--TTTCCTTAATTTTTGGCTAAAATACTCAT
260 TCGGCTAAAATTTTGCAAAAAATGACCCGAAATATTTTTCCTCAATTTTTGGCTAAAATACTCAT
2308 AAAAAA
325 -AAAAA
* * * * * *
2314 TATATAACTCAACGCCAAAAAGATTGAAGGGCTTTTGACG-TTTCTAATATCGTTTTTCCTATTT
1 TATATAATTCAACACCAAAAAGATTGGAGGACTTTTCACGCTTT-TAATATCGTTTTT-C-ATAT
** * * *
2378 TTTTCCAAATTAATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAGACAAATCCTTAA
63 TTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAA
* * * ** * * * *
2443 ATCTAATGCGGGTGAGATTTGATTAGATGAATATAGATATTTCAAATAGTGTCGGAGCCAGAAAT
128 ATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAAT
* * * * * *
2508 CATGCGAAATTGAGCTGGGTCCCCGGAACGTGTTTTTAGCCAAAAACCGTGATTGTTTGTTAGTA
193 CATGCAAAACTGAGCCGGG-CCCCGGAACGCGTTTTTAGCCAAAAACCGTGA-TG---ATTATTA
* * ** * *
2573 CACGATTTCCGCTAAAATTTTGCAAAAATTGACATGAAAAGATTTTTTCTCAATTTTTGGCTAAA
253 CACGATTTCGGCTAAAATTTTGCAAAAAATGACCCG-AAATATTTTTCCTCAATTTTTGGCTAAA
*
2638 ATACTAATAAAAA
317 ATACTCATAAAAA
* * * * * *
2651 TATCTAATTCAACGCCAAAAAGATTGGAAGACTTTTTACGCTTTTAATATCGTATTTCTTATTTT
1 TATATAATTCAACACCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATA-TTT
* * *
2716 TTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAATAAATTCTTAAAT
65 TTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAAT
* *
2781 CAAATGTTGCTGAGATTTTG-TTAGATGA
130 CCAATGTGGCTGAGA-TTTGATTAGATGA
2809 TGTAAAGTAT
Statistics
Matches: 2020, Mismatches: 360, Indels: 188
0.79 0.14 0.07
Matches are distributed among these distances:
308 28 0.01
309 8 0.00
310 47 0.02
312 59 0.03
313 60 0.03
315 44 0.02
318 1 0.00
320 1 0.00
321 2 0.00
322 1 0.00
324 1 0.00
325 11 0.01
326 114 0.06
327 63 0.03
328 177 0.09
329 87 0.04
330 195 0.10
331 17 0.01
332 288 0.14
333 193 0.10
334 4 0.00
335 26 0.01
336 136 0.07
337 65 0.03
338 117 0.06
339 1 0.00
341 1 0.00
342 22 0.01
344 28 0.01
347 112 0.06
348 2 0.00
350 1 0.00
351 10 0.00
352 43 0.02
353 1 0.00
354 54 0.03
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.34
Consensus pattern (329 bp):
TATATAATTCAACACCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTT
TCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATC
CAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCAT
GCAAAACTGAGCCGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGATTATTACACGATTT
CGGCTAAAATTTTGCAAAAAATGACCCGAAATATTTTTCCTCAATTTTTGGCTAAAATACTCATA
AAAA
Found at i:1974 original size:2 final size:2
Alignment explanation
Indices: 1967--1993 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1957 AATACTCCTA
1967 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 A
1994 ATTGAACAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3110 original size:60 final size:60
Alignment explanation
Indices: 3042--3194 Score: 234
Period size: 60 Copynumber: 2.5 Consensus size: 60
3032 GCTCAAATTG
* * * ** *
3042 GCCTAACGTTTGTCAAAATGCTCAGATAAGGGTCTGATCTTTTAATTTGGCTAAATAAGA
1 GCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCAATCTTTTAATTTGGCCAAATAAGA
* *
3102 GCCTAACGTTTGCCAAAATACTCAAATAAGGGCCCAATCTTTTAATTTGGCCAAATAAGG
1 GCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCAATCTTTTAATTTGGCCAAATAAGA
3162 GCCTAACGTTTGCCAAAATGCTCAAATAAGGGC
1 GCCTAACGTTTGCCAAAATGCTCAAATAAGGGC
3195 ATGGCGTCGA
Statistics
Matches: 84, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 84 1.00
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (60 bp):
GCCTAACGTTTGCCAAAATGCTCAAATAAGGGCCCAATCTTTTAATTTGGCCAAATAAGA
Found at i:3191 original size:31 final size:31
Alignment explanation
Indices: 3094--3194 Score: 102
Period size: 31 Copynumber: 3.3 Consensus size: 31
3084 TAATTTGGCT
* *
3094 AAATAAGAGCCTAACGTTTGCCAAAATACTC
1 AAATAAGGGCCTAACGTTTGCCAAAATGCTC
* * **
3125 AAATAAGGGCCCAATC-TTT--TAATTTGGC-C
1 AAATAAGGGCCTAA-CGTTTGCCAAAAT-GCTC
3154 AAATAAGGGCCTAACGTTTGCCAAAATGCTC
1 AAATAAGGGCCTAACGTTTGCCAAAATGCTC
3185 AAATAAGGGC
1 AAATAAGGGC
3195 ATGGCGTCGA
Statistics
Matches: 54, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
28 1 0.02
29 20 0.37
30 3 0.06
31 29 0.54
32 1 0.02
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (31 bp):
AAATAAGGGCCTAACGTTTGCCAAAATGCTC
Found at i:3405 original size:59 final size:60
Alignment explanation
Indices: 3240--3397 Score: 212
Period size: 59 Copynumber: 2.6 Consensus size: 60
3230 ACGCCAGACA
* * * * * *
3240 CTTATTTGAGTATTTTTGATAACGTTAGACCCTTATTTGGCCAAATTAAAAGATCGGGCT
1 CTTATTTGAGCATTTTCGATAACGTTAGGCTCTTATTTGGCCAAATTAAAAGATCGGACC
*
3300 CTTATTTGAGCATTTTCGATAACGTTATGCTCTTA-TTGGCCAAATTAAAAGATCGGACC
1 CTTATTTGAGCATTTTCGATAACGTTAGGCTCTTATTTGGCCAAATTAAAAGATCGGACC
* *
3359 CTTATTTGAGCATTTTGGCA-AACATTAGGCTCTTATTTG
1 CTTATTTGAGCATTTTCG-ATAACGTTAGGCTCTTATTTG
3398 AGCAATTAGC
Statistics
Matches: 86, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
59 52 0.60
60 34 0.40
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (60 bp):
CTTATTTGAGCATTTTCGATAACGTTAGGCTCTTATTTGGCCAAATTAAAAGATCGGACC
Found at i:3553 original size:15 final size:16
Alignment explanation
Indices: 3535--3564 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
3525 ATAAATAATA
3535 ATATTATAAT-TAAAT
1 ATATTATAATCTAAAT
3550 ATATTATAATCTAAA
1 ATATTATAATCTAAA
3565 AATAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTATAATCTAAAT
Found at i:3973 original size:170 final size:160
Alignment explanation
Indices: 3662--3990 Score: 516
Period size: 170 Copynumber: 2.0 Consensus size: 160
3652 CGCAATATCT
3662 TTTCATAATTAATAAAAAGTTGAATTAATCATCTCAAAAAAATTAAAATAAAGTTAAATGAATAC
1 TTTCATAATTAATAAAAAGTTGAATTAATCATCTCAAAAAAATTAAAATAAAGTTAAATGAATAC
3727 TATTAAAAAACATTATCATACTATAATGCTAAGGGTATTTATGAAATTTCCCAAATAGAATTTTT
66 TATTAAAAAACATTATCATACTATAATGCTAAGGGTATTTATGAAATTTCCCAAATAGAATTTTT
3792 GAGTTCGTGATTTTATATAGTAGTAAGATC
131 GAGTTCGTGATTTTATATAGTAGTAAGATC
3822 TTTCGATAATTAATAAAAAGTTGAATTAATCATCTCAAAAAAATTAAAATAAAGTTAAATGACTA
1 TTTC-ATAATTAATAAAAAGTTGAATTAATCATCTCAAAAAAATTAAAATAAAGTT-AA--A-T-
* *
3887 AAAAGAATACTTATTAAAAAA-ATTATTATACTGTAATGCTAAGGGTATTTATGAAATTTCCCAA
60 ----GAATAC-TATTAAAAAACATTATCATACTATAATGCTAAGGGTATTTATGAAATTTCCCAA
* *
3951 TTATAATTTTTGAGTTCGTGATTTTATATAGTAGTAAGAT
120 ATAGAATTTTTGAGTTCGTGATTTTATATAGTAGTAAGAT
3991 AAGATAACAA
Statistics
Matches: 154, Mismatches: 4, Indels: 12
0.91 0.02 0.07
Matches are distributed among these distances:
160 4 0.03
161 51 0.33
162 2 0.01
164 1 0.01
165 1 0.01
170 85 0.55
171 10 0.06
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.37
Consensus pattern (160 bp):
TTTCATAATTAATAAAAAGTTGAATTAATCATCTCAAAAAAATTAAAATAAAGTTAAATGAATAC
TATTAAAAAACATTATCATACTATAATGCTAAGGGTATTTATGAAATTTCCCAAATAGAATTTTT
GAGTTCGTGATTTTATATAGTAGTAAGATC
Found at i:7600 original size:4 final size:4
Alignment explanation
Indices: 7593--7621 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
7583 CATAATAAGT
7593 AAGA AAGA AAGA AAGA AAGA AAG- AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AA
7622 ATGCTTCTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
3 3 0.12
4 21 0.88
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:12720 original size:334 final size:331
Alignment explanation
Indices: 11309--12781 Score: 1248
Period size: 334 Copynumber: 4.4 Consensus size: 331
11299 TTCCTTTCGG
* * * * ** *
11309 AAAAAGTAGGAAAAACGATATTAGAAGAGTGAAAACCCTT-CAATATTTTTGGCGTTGAATTATA
1 AAAAA-TATGAAAAATGATATTAAAAGCGTGAAAAGTCTTCCAATCTTTTTGGCGTTGAA-T-TA
* * *
11373 TATATATATATTTTTGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGAGTCAATTTTTGCA
63 TATAT-T-T-TTTATGAGTATTTTAGCCAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCA
* * * * * * * *
11438 AATTTTTACCCGAAATCATGTACTAACCA-CA-GTTTTTTTTTTTTTG-CTAGAAACGTGTTTCG
125 AAATTTTAGCCGAAATCGTGTACTAACCATCACG-------GTTTTTGACAAAAAACGCGTTCCG
* ** * * *
11500 GGACTCTC-ACTCAGTTTTGCATGATTTTTGGCATCGACACTCCTTGAAATATTTATATTCATCT
183 GG-C-CTCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCT
* *
11564 AATTAAATCTCAGCCACATTGCATTTAAGGATTTATTTTTACGAGCATCTAAATCTTGTTTTGAT
246 AATCAAATCTCAGCCACATTGCATTTAAGGATTTATTTTTACGAGCATCTAAATCTTGTTTCGAT
* * *
11629 TTAATTAAAAATTAATT-CAG
311 TTAATTAGAAATTAATTGAAT
* **
11649 AAAAATATGAAAAACT-ATATTATAAGCGTGAAAAAGT-TCTCCAATCTTTTTGTAGTTGAATTA
1 AAAAATATGAAAAA-TGATATTAAAAGCGTG-AAAAGTCT-TCCAATCTTTTTGGCGTTGAATTA
* * ** * * *
11712 TATATATTTTATGAGTATTTTTGAAAAAAATTGAGGAAAAATATTTCTGGTTAATTTTTGCAAAA
63 TATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAA
* * * * * *
11777 TATTAGACGAAATCGTGTACGTTAGTCGAAATCACGGTTTTTGGCTAAAAAA-GCGTTCCAGAGC
128 TTTTAGCCGAAATCGTGTAC--TA-AC--CATCACGGTTTTTGAC-AAAAAACGCGTTCC-GGGC
* * * * * *
11841 CCCGGGTCAGTTTTGCAAGATTTTTGGCGCTAAGACTCCTTAAAATATATCTATATTCATCTAAC
186 CTCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTT-GAA-ATATCTATATTCATCTAAT
* * *
11906 CAAATTTCAGCCACATTGTATTTAAGGATTTATTTTTACGAGTATCTAAATCTTGTTTCGATTTA
249 CAAATCTCAGCCACATTGCATTTAAGGATTTATTTTTACGAGCATCTAAATCTTGTTTCGATTTA
* *
11971 ATCAGCAATTAATTTGGAA-
314 ATTAGAAATTAA-TT-GAAT
* * ** * * *
11990 ATAAAATATGAAAAATGCTATTAGAAA-CGTGAAAAAGGCTTTGAATTTTTTTAGCGTTGAATTG
1 A-AAAATATGAAAAATGATATTA-AAAGCGTG-AAAAGTCTTCCAATCTTTTTGGCGTTGAATTA
* * * * * **
12054 TATA-TTTTTATGAGTATTGTCGCTAGAAATTGAGGAAAAATCTTTCGGGTTAATTTTAACAAAA
63 TATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAA
* * * * * * * *
12118 TTTTAGCCAAAATCGTGTACTAACCATCACAG-TTTTCAGCTAGAAATGTGTTCCGGG-TTCGGC
128 TTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGA-CAAAAAACGCGTTCCGGGCCTCGGC
* * *
12181 TTAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAAATGTCTATATTCATCTCAA-CAAATCT
192 TCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCT-AATCAAATCT
* * * * * * *
12245 CA-CCGAAATTGGATTTAATGATTTGTTTTTACGAGCATATGAATCTTCTTTCGATTTAATTAGA
256 CAGCC-ACATTGCATTTAAGGATTTATTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGA
*
12309 AATTAATTCGGAT
320 AATTAATT-GAAT
* * ** * * ** *
12322 AAAAATAGGAAAAA-AATATTTGAAGCGTTAAAAGCCCTT-CAATCTTTTTGATGTCGAATTATA
1 AAAAATATGAAAAATGATATTAAAAGCGTGAAAAG-TCTTCCAATCTTTTTGGCGTTGAATTATA
* *
12385 TATTTTTTATGAGTAGTTTAGCCAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTGCAAAATT
65 TATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATT
* * *
12450 TTAGCTGAAGTCGTGTACTAACCATCACGGTTTTTGACAAAAAAACGCGTTCCGGAGCCACGGCT
130 TTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGAC-AAAAAACGCGTTCCGG-GCCTCGGCT
* ** ** * *
12515 CTGTTTTGCATGATTTTTTACGCCGCGGCTCCTTGAAAATATCTTTATTCATCTAATCAAATCTC
193 CAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTG-AAATATCTATATTCATCTAATCAAATCTC
* * * *
12580 AGCCATATTAG-ATTTAATGATTTGTTTTTAC-ATGCATCTGAATCTTGTTTCGATTTAATTAGA
257 AGCCACATT-GCATTTAAGGATTTATTTTTACGA-GCATCTAAATCTTGTTTCGATTTAATTAGA
12643 AATTAATT-AAT
320 AATTAATTGAAT
* *
12654 AAAAATATGAAAAATGATATTAAAAGCATG-AAAGTCTTCCAATTTTTTTGGCGTTGAATTTTAT
1 AAAAATATGAAAAATGATATTAAAAGCGTGAAAAGTCTTCCAATCTTTTTGGCGTTG-A----AT
* *
12718 ATATATATATATATATTATGAGTATTTT-GCCAGAAATTGAGGAAAAATCTTTCAGGTC-ATTTT
61 -TATATAT-T-T-T-TTATGAGTATTTTAGCCAAAAATTGAGGAAAAATCTTTCGGGTCAATTTT
12781 T
121 T
12782 ACCATCATGG
Statistics
Matches: 910, Mismatches: 170, Indels: 106
0.77 0.14 0.09
Matches are distributed among these distances:
329 26 0.03
330 90 0.10
331 38 0.04
332 112 0.12
333 50 0.05
334 119 0.13
335 13 0.01
336 85 0.09
337 39 0.04
338 18 0.02
339 118 0.13
340 20 0.02
341 114 0.13
342 64 0.07
343 4 0.00
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.38
Consensus pattern (331 bp):
AAAAATATGAAAAATGATATTAAAAGCGTGAAAAGTCTTCCAATCTTTTTGGCGTTGAATTATAT
ATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTT
TAGCCGAAATCGTGTACTAACCATCACGGTTTTTGACAAAAAACGCGTTCCGGGCCTCGGCTCAG
TTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCC
ACATTGCATTTAAGGATTTATTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAA
TTGAAT
Found at i:17255 original size:41 final size:41
Alignment explanation
Indices: 17210--17289 Score: 142
Period size: 41 Copynumber: 2.0 Consensus size: 41
17200 TTTTGAGAAT
*
17210 TTACCATTTACATATTTTTTATTTTGGAATGGGCTAAACAA
1 TTACCATTTACATATTGTTTATTTTGGAATGGGCTAAACAA
*
17251 TTACCATTTACATATTGTTTATTTTGGAATGGGTTAAAC
1 TTACCATTTACATATTGTTTATTTTGGAATGGGCTAAAC
17290 TTTGAACTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.45
Consensus pattern (41 bp):
TTACCATTTACATATTGTTTATTTTGGAATGGGCTAAACAA
Found at i:21312 original size:22 final size:22
Alignment explanation
Indices: 21287--21333 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
21277 ATATATTCAA
* *
21287 ATAATTATCTATCTATATATAT
1 ATAATAATCTACCTATATATAT
* *
21309 ATAATAATTTGCCTATATATAT
1 ATAATAATCTACCTATATATAT
21331 ATA
1 ATA
21334 TATATATAGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.09, G:0.02, T:0.47
Consensus pattern (22 bp):
ATAATAATCTACCTATATATAT
Found at i:21808 original size:15 final size:16
Alignment explanation
Indices: 21783--21812 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
21773 AATAATTATT
21783 TTTAGATTATAATATA
1 TTTAGATTATAATATA
21799 TTTA-ATTATAATAT
1 TTTAGATTATAATAT
21813 TATTATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGATTATAATATA
Found at i:23498 original size:634 final size:639
Alignment explanation
Indices: 22203--23592 Score: 1475
Period size: 634 Copynumber: 2.2 Consensus size: 639
22193 GGATTTATGA
* * *
22203 ATTTGTTTTTACGAGCATATAAATCTTATTTCGATTTAATTAGAAATTAATTTGGAAAAAATATG
1 ATTT-TTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAA-TTCGAAAAAATATG
* * *
22268 AAAAACGATATTACAAA-CGTCAAAAACCATTCAATCTTTTTGGCGTTGAATTATATATTTTTTA
64 AAAAAAGATATTA-AAAGCGTCAAAAACCCTTCAATCTTTTTGGCGTTGAATTATATATTTTATA
* * *
22332 TGAGTATTTTAACCAAAAATTGAGGAAACATCTTCCGGGTCAATTTTTATAAAATTTTAGCCGAA
128 TGAGTATTTGAACCAAAAATTGAGGAAACATCTTCCAGGTCAATTTTTACAAAATTTTAGCCGAA
* * * **
22397 ATCGTGTAATAACCATCACAGTTTTTGGCTAAAAATGCGTTTTAGGATCCCGGCTCAGTTTTGCT
193 ATCGTGTAATAACCATCACAGTTTTTGGCTAAAAACGCGTTTTAGGAGCCCAGCTCAGTTTTGAA
* * **
22462 TGAATTTTGGCGCCAAGACTCCTTGAAATATCCATATTCATCTAATCGAATCTTAGCCACATTGG
258 TGAATTTTGGCGCCAAGACTCCTTGAAATATCCATATTCATCTAACCAAATCCCAGCCACATTGG
* ** * * *
22527 ATTTAAGAATTTGTTTTTACAAGCATCTGAATTTTGTTTCGATTTAATTAGAAATTAATTAAGAA
323 ATTTAAGAATCTG-TGATACAAGCATCTG-ATTTTGTTTAGAATTAATTAGAAA-TAAATAAGAA
* ** *
22592 AAATAATATTAAAAGCGTGAAAATTCCTCCAATTGTTTTGGCCTTCAATTATATATATTTTATGA
385 AAATAATATTAAAAGCATGAAAAGCCCTCCAATTGTTTTGGCATTCAATTATATATATTTTATGA
* * * *
22657 GTATTCTATCCAAAAATTGAGGAAAAATTTTTCGGGTCATTTTTTGCAGAATTTTAGCCAAAATC
450 G---TC-AT-CAAAAATTAAGGAAAAATTTTTCGGGTCAATTTTTGCAAAATATTAGCCAAAATC
* * * *
22722 GTGTACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCAGATCAGTTTTGCATGATTTT
510 GTGTAACATAACGGTTTTTGGCTAAAAACGCGTTCCGGGGCCCCAGATCAATTTTGCATGATTTT
* * * * * *
22787 TGGCGTAGACATTCCTTGAAATAGCTATATTCATTTAATAAAATCTTAGCCACATTGCATTTAAG
575 TGGCGCAAAAATT-CATGAAATAGCTATATTCATCTAATAAAATCTTAGCCACATTGCAATTAAG
22852 G
639 G
* *
22853 ATTTGTTTTACGAGCATCTAAATCTTGTTTCTG-TTTAATTAGAAATTAATTCAAAAAAATATGA
1 ATTTTTTTTACGAGCATCTAAATCTTGTTTC-GATTTAATTAGAAATTAATTCGAAAAAATATGA
* *
22917 AAAATGATATTAAAAGC-TCGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTAT-T
65 AAAAAGATATTAAAAGCGTC-AAAAACCCTTCAATCTTTTTGGCGTTGAATTATATATTTTATAT
* * * * * *
22980 GAGTATTATGGA-TAAAAATTGAGGAAATATCTTTCAGGTCAATTTTTGCAAAATTTTAGTCGAA
129 GAGTATT-TGAACCAAAAATTGAGGAAACATCTTCCAGGTCAATTTTTACAAAATTTTAGCCGAA
* * * * * *
23044 CTCGTGTAATAATCATCACGGTTTTTGGCTAAAAACGCG-TTTCGGGGCCCAGTTCAGTTTTGAA
193 ATCGTGTAATAACCATCACAGTTTTTGGCTAAAAACGCGTTTTAGGAGCCCAGCTCAGTTTTGAA
* * * * * *
23108 T-AATTTTGGTGCCGAGGCTCCTTGATATATCTATATTCATCTAACCAAATCCCAG-C-CATTGT
258 TGAATTTTGGCGCCAAGACTCCTTGAAATATCCATATTCATCTAACCAAATCCCAGCCACATTGG
* * * * * *
23170 TTTTAAAAGCATCTG-GAT-CATG-TTTTG-TTTTAG-TTAGAAATTAATTCGGAAA-AAATAAG
323 ATTT--AAGAATCTGTGATACAAGCATCTGATTTT-GTTTAG-AATTAATT-AGAAATAAATAAG
* * *
23229 AAAAA-ACAGTATTAGAAGCATGAAAAGCCCTTCAATCT-TTTTGGCATTGAATTATATAT-TTT
383 AAAAATA-A-TATTAAAAGCATGAAAAGCCCTCCAAT-TGTTTTGGCATTCAATTATATATATTT
* *
23291 T-T-AG-C-T-AAAAGTTAAGGAAAAATATTTT-GGGTCAATTTTTGCAAAATATTAGCCGAAAT
445 TATGAGTCATCAAAAATTAAGGAAAAAT-TTTTCGGGTCAATTTTTGCAAAATATTAGCCAAAAT
* * * * *
23350 CGTGTAACGTAACGGTTTTTTTTTTTG-TCAAAACTGCGTTCCGGGGCCCCGGGTCAATTTTGCA
509 CGTGTAACATAACGG-----TTTTTGGCTAAAAAC-GCGTTCCGGGGCCCCAGATCAATTTTGCA
* * *
23414 TGATTTTTTGCGCCAAAAATT-ATGCAAATATCTATATTCATCTAATCAAAT-TTCAGCCACATT
568 TGATTTTTGGCG-CAAAAATTCATG-AAATAGCTATATTCATCTAATAAAATCTT-AGCCACATT
*
23477 GGAATTAAGG
630 GCAATTAAGG
* *
23487 ATTTTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTGGAAATTAATTCGGAAAAAATAGGA
1 ATTTTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTC-GAAAAAATATGA
* * *
23552 AAAAAGATATTAGAAGCGTAAAAAAACCCTTCAATATTTTT
65 AAAAAGATATTAAAAGCGT-CAAAAACCCTTCAATCTTTTT
23593 TTCGGTGAAT
Statistics
Matches: 622, Mismatches: 92, Indels: 66
0.80 0.12 0.08
Matches are distributed among these distances:
629 54 0.09
630 4 0.01
631 1 0.00
633 12 0.02
634 130 0.21
635 30 0.05
636 19 0.03
637 2 0.00
638 2 0.00
639 23 0.04
640 49 0.08
641 8 0.01
642 3 0.00
643 9 0.01
644 1 0.00
645 52 0.08
646 19 0.03
647 93 0.15
648 66 0.11
649 40 0.06
650 5 0.01
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (639 bp):
ATTTTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCGAAAAAATATGAA
AAAAGATATTAAAAGCGTCAAAAACCCTTCAATCTTTTTGGCGTTGAATTATATATTTTATATGA
GTATTTGAACCAAAAATTGAGGAAACATCTTCCAGGTCAATTTTTACAAAATTTTAGCCGAAATC
GTGTAATAACCATCACAGTTTTTGGCTAAAAACGCGTTTTAGGAGCCCAGCTCAGTTTTGAATGA
ATTTTGGCGCCAAGACTCCTTGAAATATCCATATTCATCTAACCAAATCCCAGCCACATTGGATT
TAAGAATCTGTGATACAAGCATCTGATTTTGTTTAGAATTAATTAGAAATAAATAAGAAAAATAA
TATTAAAAGCATGAAAAGCCCTCCAATTGTTTTGGCATTCAATTATATATATTTTATGAGTCATC
AAAAATTAAGGAAAAATTTTTCGGGTCAATTTTTGCAAAATATTAGCCAAAATCGTGTAACATAA
CGGTTTTTGGCTAAAAACGCGTTCCGGGGCCCCAGATCAATTTTGCATGATTTTTGGCGCAAAAA
TTCATGAAATAGCTATATTCATCTAATAAAATCTTAGCCACATTGCAATTAAGG
Found at i:25116 original size:332 final size:329
Alignment explanation
Indices: 23592--26604 Score: 2473
Period size: 332 Copynumber: 9.0 Consensus size: 329
23582 TCAATATTTT
* * * * ** * *
23592 TTTC-GGTGAATTTTTGCAAAATTGTAGCCAAAATCGTGTAATAGTCATCACAGTTTTTGACTAA
1 TTTCAGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAA
** ** * *** * *
23656 AAACATGTTCC-AGGGCCCCAAGTCAGCTTTGCATGATTTTT-GCATTAAGAATCCTTGAGATAT
66 AAACGCGTTCCGA-GG-CCCGGGT-AGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATAT
* * * * * * *
23719 CCATATTAATCTAATCAAATCTCATCCACATTGCATTTAATGATTTATTTTTACGAGCATCTGTA
128 CTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAA
* * * * *
23784 TCATGTTTCGATCTAATTACAAATTAATTCAACAAAAAT-ATGAAAAACGATATGAAAAGCGTGA
193 TCTTGTTTCGATTTAATTAGAAATTAATTC-AGAAAAATAATGAAAAACGATATTAAAAGCGTGA
* * *
23848 AAAGTCCTTTAATCTTTTTGGCGTTAAATTATATATATTTTCATGAGTATTTTAGTCAAAAATTG
257 AAAGTCCTTCAATCTTTTTGGCGTTGAATTATATATATTTT-ATGAGTATTTTAGCCAAAAATTG
23913 AGGAAAA-A
321 AGGAAAATA
** * * *
23921 TTTGTCAGGTCTTTTTTTACAAAATTTTAGCCGAAATCGTGTA-TCA-CAGGTTTTTTTTTTTTT
1 -TT-TCAGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCA-------------TC
* ** * * * * * * ** ** *
23984 TCTTTTTTTTTGCGAAAAACACGTTTCTA-GCCTTGACTTAGTACTGCATGATTTTTGGCGTCGA
51 AC-GGTTTTTGGCTAAAAACGCGTTCCGAGGCC-CG-GGTAGTTTTGCATGATTTTTGGCG-CCA
* * * *
24048 A-ACTCCTTGAAAAATCTATATTTATCTAATCAAATCTCAGCCACATTGCATTTTTAAGGATGTG
112 AGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGA--TTTAAGGATTTG
* *
24112 TTTTTACGAGCATCTGAATCTTGTTTTG-TTATAATTTGAAATTAATTCAGAAAAAT-ATGAAAA
175 TTTTTACGAGCATCTGAATCTTGTTTCGATT-TAATTAGAAATTAATTCAGAAAAATAATGAAAA
* **
24175 ACGATATTAAAAGCGTGAAATGTCCCACAATCTTTTTGGCGTTGAAATATATATATATATATATT
239 ACGATATTAAAAGCGTGAAAAGTCCTTCAATCTTTTTGGCGTTG--A-AT-TATATATAT-T-TT
**
24240 ATGAGTATTTTAGAAAAAAATTGAGGAAAAATA
298 ATGAGTATTTTAGCCAAAAATTGAGG-AAAATA
* * * * * *
24273 CTTCTGGTCAATTTTTACAAAATATTAGCCGAAATCGTGTACGTTACTCGAAATTACGGTTTTTT
1 TTTCAGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAC-TAAC-C---ATCACGG------
* * * * *
24338 TTTTTTGCTAAAAACGCGTTCCGGGGTCCC-GGTACAGTGTTGCAAGATTTTTGGCGCTAAGACT
55 TTTTTGGCTAAAAACGCGTTCCGAGG-CCCGGGT--AGTTTTGCATGATTTTTGGCGCCAAGACT
* * * *****
24402 CCTTGAAATATCTATATTCTTTTAACCAAATCTCAGCCACATTGGATTTAAGGATTT-CCAAAAC
117 CCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTAC
* * * * * * *
24466 AAGCATCTGAATCATGTTTCGATTTAATAAAAAATTAATTCA-AAAAATTTAGGAAAAACGATAA
182 GAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAA-TAATGAAAAACGATAT
* * ** * * * *
24530 TAGAAGCATGAAAAACCCTTCAATCTTATTGGCGTTGAATTATATA-ATTTTAATGAGTGTTGTG
246 TAAAAGCGTGAAAAGTCCTTCAATCTTTTTGGCGTTGAATTATATATATTTT-ATGAGTATTTTA
*
24594 GCTAAAAATTGAGG-AAATAA
310 GCCAAAAATTGAGGAAAAT-A
* * * * * *
24614 CTTTC-GAGTCAATTTTTGTAAAATTCTAGCCGAACTCGTTTGA-TAATCATCACGGTGTTTGGC
1 -TTTCAG-GTCAATTTTTGCAAAATTTTAGCCGAAATCGTGT-ACTAACCATCACGGTTTTTGGC
** * * * *** * *
24677 TAAAGTCACGTTTCGAGACCCCAACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCTTTGAGAT
63 TAAAAACGCGTTCCGAG-GCCCGGGT-AGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAAT
* * * * * *
24742 ATCCATATTCATCTAATCAAATATTAGCAACATTGGATTTAAGAATTTGTTTTTATGAGCATCTG
126 ATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTG
* *
24807 AATCTTATTTCGATTTAATTAAAAATTAATTCAGAAAAATAAT-AAAAACGATATTAAAAGCGTG
191 AATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATAATGAAAAACGATATTAAAAGCGTG
* * * *
24871 AAAAGTACTCCAATCTTTTTGGCATTAAATTATATATATTTTATGAGTATTTTAGCCAAAAATTG
256 AAAAGTCCTTCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTAGCCAAAAATTG
* *
24936 TCGGAAAATT
321 -AGGAAAATA
*
24946 TTTCAGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCATGGTTTTTGGCTAA
1 TTTCAGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAA
* * * *
25011 AAACGCGTTTCGAGGCCCGGGCTTAATTTTTGCATGATTTTTTGCGCCAAGACTTCTTGAAATAT
66 AAACGCGTTCCGAGGCCCGGG--T-AGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATAT
* ** *
25076 CTATATTCATCTAATCAAATCTCAACCACATTTAATTTAAGGATTTGTTTTTACGAGCCTCTGAA
128 CTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAA
*
25141 TCTTGTTTTGATTTAATTAGAAATTAATTCAGAAAAAT-ATGAAAAACGATATTAAAAGCGTGAA
193 TCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATAATGAAAAACGATATTAAAAGCGTGAA
* * * * * * * *
25205 AAGTCCTCCAGTCTTTTTGGTGTTGAATTATATATATTTTATGAGTGTTGTGGCTAAAAATCGAG
258 AAGTCCTTCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGAG
*
25270 ACAAAATA
323 -GAAAATA
* * *
25278 TTTCGGGTCAATTTTTGC-AAATTTTAGCCAAAATCGTG---T-ACCATCACAGTTTTTTTGGCT
1 TTTCAGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCAC-G-GTTTTTGGCT
* * * * *
25338 ACAAACGCGTTCCGGAGCCCCGGGTCAGTTTTGCATGATTTTTGGTGGCAAAACTCCTTGAAATA
64 AAAAACGCGTTCC-GAGGCCCGGGT-AGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATA
* * * * *
25403 TCTATATTCATCTTACCAAATCTTAGCCACACTT-GATTTAAGGATTTGTTTTTGCGAGCATTTG
127 TCTATATTCATCTAATCAAATCTCAGCCACA-TTGGATTTAAGGATTTGTTTTTACGAGCATCTG
* *
25467 AATCATGTTTCGATTTAATTAGAAATTAATT-TGAAAAA-AATGGGAAAAACGATATTAGAAA-C
191 AATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATAAT--GAAAAACGATATTA-AAAGC
* * * * * * * *
25529 GTGAGAAGCCCTTCTATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTGTGGCTAAAAT
253 GTGAAAAGTCCTTCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTAGCCAAAAA
*
25594 TTGAGAAAAATA
318 TTGAGGAAAATA
* * * * ***** **
25606 TTTCAGGTTAATTTTTGCAAAATTTTAGCTGAAATCGTGTAC-CATCATTGTTTTTTTTTTTACT
1 TTTCAGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCA-T-CACGGTTTTTGGC-
* * * *
25670 TAAAAACGCGTACCGAGGTCCTGGGTTAGTTTTGCATGATTTTTGGCGCCAAAACTCCTTAAAAT
63 TAAAAACGCGTTCCGAGG-CCCGGG-TAGTTTTGCATGATTTTTGGCGCCAAGACTCCTT-GAA-
* * * *** *
25735 ATATCTATATTCATCTAACCAAATCTCAGCTACATTGTATTTAAGGATTTGTTTTTACGAATTTT
124 ATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATC
* * ** *
25800 TAAATCTTGTTTTGATTTAATTAGAAATTAATTTGGAAAGAA-AAT-AAGGGAAACGATATTAGA
189 TGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAA-AATAATGAA---AAACGATATTAAA
* * * * * * * * *
25863 AGCGTGAAAAATGCTTTCATTTTTTTTGGCATTGAATTATATATTTTTTATGAATATTTTCGCTA
250 AGCGTGAAAAGT-CCTTCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTAGCCA
* * *
25928 GAAATCGAGGAAAAATT
314 AAAATTGAGG-AAAATA
* * * * * * *
25945 TTTCGGGTCAATTTTTGGAAAATTATAGCTGAAATCGTGTACTAACTATCACGATTTTCGGCTAA
1 TTTCAGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAA
***
26010 AAACGCGTT---A----CGGG--G-TTTGCATGATTTTTTTTGCCAAGACTCCTTGAAATATCTA
66 AAACGCGTTCCGAGGCCCGGGTAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTA
* *
26065 TATTCATCTAA-CGAAATCTTAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAATC
131 TATTCATCTAATC-AAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATC
* * * *
26129 TTGTTTCGATTTAATTGGAAATTAATTC-GAAAAGA-AATAGGAAAAACAATATTAGAAGCGTTA
195 TTGTTTCGATTTAATTAGAAATTAATTCAGAAAA-ATAAT--GAAAAACGATATTAAAAGCGTGA
* *** ** * *
26192 AAAGCCCTTCAATC-TTTTGATATCAAATTATATATTTTTTAGGAGTATTTTAGCCAAAAATTGA
257 AAAGTCCTTCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGA
* *
26256 AGAAATATC
322 GGAAA-ATA
* *
26265 TTTCGGGTCAATTTTTGCAAAATTTTAGCCAAAATCGTGTACGT-----T-ACGGTTTTTGGCTA
1 TTTCAGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAC-TAACCATCACGGTTTTTGGCTA
* ** * * *
26324 AAAACGCGTTCCAAGGCCACGACTCTGTTTTGCATGATTTTTGGAGCCAAGACTCCTTGAAATAA
65 AAAACGCGTTCCGAGGCC-CGGGT-AGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATAT
* * * * * *
26389 CTTTATTCATCTAATAAAATCTCAGCCACATTGGATTTAACGATTTGTTTTTATGTGTATCTGAA
128 CTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAA
* * ** * *
26454 TATTGTATCGATTTAATTAGAAATTAATT-TTAAAAA-AATGAAAAACGACATTAAAAACGTGAA
193 TCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATAATGAAAAACGATATTAAAAGCGTGAA
* * *
26517 AAGTCCTTCAATCTTTTTGGGGTTGAATTATATATATTTTATGAGTATTTTTGTCAAAAATTGAG
258 AAGTCCTTCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGAG
*
26582 GAAAAATC
323 G-AAAATA
26590 TTTC-GGATCAATTTT
1 TTTCAGG-TCAATTTT
26605 ACAATCATGG
Statistics
Matches: 2170, Mismatches: 388, Indels: 255
0.77 0.14 0.09
Matches are distributed among these distances:
315 22 0.01
316 1 0.00
318 1 0.00
319 3 0.00
320 81 0.04
321 8 0.00
322 30 0.01
323 87 0.04
324 35 0.02
325 85 0.04
326 9 0.00
327 134 0.06
328 140 0.06
329 118 0.05
330 20 0.01
331 251 0.12
332 317 0.15
333 58 0.03
334 8 0.00
335 84 0.04
336 6 0.00
337 40 0.02
338 55 0.03
339 44 0.02
340 7 0.00
341 6 0.00
342 55 0.03
343 20 0.01
344 72 0.03
345 58 0.03
346 55 0.03
347 37 0.02
348 56 0.03
349 31 0.01
350 122 0.06
351 9 0.00
352 3 0.00
354 1 0.00
357 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (329 bp):
TTTCAGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAA
AAACGCGTTCCGAGGCCCGGGTAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTA
TATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCT
TGTTTCGATTTAATTAGAAATTAATTCAGAAAAATAATGAAAAACGATATTAAAAGCGTGAAAAG
TCCTTCAATCTTTTTGGCGTTGAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGAGGAA
AATA
Found at i:28561 original size:58 final size:58
Alignment explanation
Indices: 28466--28575 Score: 141
Period size: 58 Copynumber: 1.9 Consensus size: 58
28456 GTTAATCAAA
* *
28466 TATCAAGTGACATGTTCTTTATTAAATGCATAAAAAAAGACGTTTTCGGACCACGGCT
1 TATCAAGTGACAAGTTCTTTATTAAATGCATAAAAAAAGACGTTTTAGGACCACGGCT
* * * * *
28524 TATCGAGTGACAAGTTTTTTTATTAGATGCCT-AAAAAAGAGGTTTTAGGACC
1 TATCAAGTGACAAG-TTCTTTATTAAATGCATAAAAAAAGACGTTTTAGGACC
28576 GAGGCATGAT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
58 30 0.68
59 14 0.32
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.33
Consensus pattern (58 bp):
TATCAAGTGACAAGTTCTTTATTAAATGCATAAAAAAAGACGTTTTAGGACCACGGCT
Found at i:29896 original size:36 final size:36
Alignment explanation
Indices: 29849--29918 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
29839 TTCAATAACC
* *
29849 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
29885 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
29919 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:30654 original size:203 final size:204
Alignment explanation
Indices: 30254--30665 Score: 713
Period size: 203 Copynumber: 2.0 Consensus size: 204
30244 GCTTAATAAC
30254 TTTATCAAAGGTGAATGTTATTAATTTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATA
1 TTTATCAAAGGTGAATGTTATTAATTTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATA
* *
30319 AGATACAACACATTATTATTATATATATAACTATACCAAAAAAAAGTGGTTGAACATTAGTGGTT
66 AGATACAACACATTACTATTATATATATAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTT
*
30384 GATTTAATAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAAATTATAAAAGATATTAAAGA
131 GATTTAATAAATTAAATTAGATCAATGTCAAAAAAAATTTCAAAAATTATAAAAGATATTAAAGA
30449 TCCGATATA
196 TCCGATATA
*
30458 TTTATCAATGGTGAATGTTATTAA-TTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATA
1 TTTATCAAAGGTGAATGTTATTAATTTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATA
* *
30522 AGATACAACACATTACTATTATATATATAGAACTATACCTAAAAAAATTAGTTGAACATTAGTGG
66 AGATACAACACATTACTATTATATATAT--AACTATACCAAAAAAAAGTAGTTGAACATTAGTGG
*
30587 TTGATTTATTAAATTAAATTAGATCAATGTCAAAAAAAATTTC-AAAATTATAAAAGATATT-AA
129 TTGATTTAATAAATTAAATTAGATCAATGTCAAAAAAAATTTCAAAAATTATAAAAGATATTAAA
*
30650 GATCCGATTTA
194 GATCCGATATA
30661 TTTAT
1 TTTAT
30666 TATTAAGGAA
Statistics
Matches: 198, Mismatches: 8, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
203 84 0.42
204 41 0.21
205 73 0.37
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.36
Consensus pattern (204 bp):
TTTATCAAAGGTGAATGTTATTAATTTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATA
AGATACAACACATTACTATTATATATATAACTATACCAAAAAAAAGTAGTTGAACATTAGTGGTT
GATTTAATAAATTAAATTAGATCAATGTCAAAAAAAATTTCAAAAATTATAAAAGATATTAAAGA
TCCGATATA
Found at i:30829 original size:39 final size:41
Alignment explanation
Indices: 30775--30855 Score: 121
Period size: 39 Copynumber: 2.0 Consensus size: 41
30765 TACCTAAGAG
*
30775 TTTAATTAATGTAAG-TATTTCAGTTATTATA-GTATTACA
1 TTTAATTAATGTAAGTTATTTCAGTTATTATATATATTACA
* *
30814 TTTAATTAATGTAAGTTTTTTTAGTTATTATATATATTACA
1 TTTAATTAATGTAAGTTATTTCAGTTATTATATATATTACA
30855 T
1 T
30856 AAAAATTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
39 15 0.41
40 14 0.38
41 8 0.22
ACGTcount: A:0.35, C:0.04, G:0.09, T:0.53
Consensus pattern (41 bp):
TTTAATTAATGTAAGTTATTTCAGTTATTATATATATTACA
Found at i:32449 original size:15 final size:15
Alignment explanation
Indices: 32424--32503 Score: 55
Period size: 15 Copynumber: 5.6 Consensus size: 15
32414 ATATTAACCC
**
32424 TTATA-TTAATTTGT
1 TTATATTTAATTTAA
32438 TTATATTTAATTTAA
1 TTATATTTAATTTAA
*
32453 TTATCTTTAATTCATAA
1 TTATATTTAATT--TAA
*
32470 TGA-A-TTAA--TAA
1 TTATATTTAATTTAA
*
32481 TTATATTTGATTTAA
1 TTATATTTAATTTAA
32496 -TATATTTA
1 TTATATTTA
32504 TAATAATTTA
Statistics
Matches: 51, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
11 5 0.10
12 1 0.02
13 3 0.06
14 12 0.24
15 25 0.49
17 5 0.10
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.56
Consensus pattern (15 bp):
TTATATTTAATTTAA
Found at i:34269 original size:22 final size:22
Alignment explanation
Indices: 34180--34347 Score: 121
Period size: 22 Copynumber: 7.6 Consensus size: 22
34170 TATAGGAAAA
* * *
34180 TTATCAAAATTTCATACTAAGG
1 TTATCAAATTTTCATAATGAGG
* * * *
34202 TTGTCAAGA-TTTCTTAGTGTGG
1 TTATCAA-ATTTTCATAATGAGG
* *
34224 TTATCAAAATTTCAT-ATTATGG
1 TTATCAAATTTTCATAATGA-GG
**
34246 TTATCAAATTTTCATAGGGAGG
1 TTATCAAATTTTCATAATGAGG
*
34268 TTATCGAAA-TTTAATAATGAGG
1 TTATC-AAATTTTCATAATGAGG
* *
34290 TTATCAAATTTTCACAGAT-AGA
1 TTATCAAATTTTCATA-ATGAGG
*
34312 TTATTGAAA-TTTCATAATGAGG
1 TTA-TCAAATTTTCATAATGAGG
34334 TTATCAAATTTTCA
1 TTATCAAATTTTCA
34348 CAGTGTGATT
Statistics
Matches: 112, Mismatches: 24, Indels: 20
0.72 0.15 0.13
Matches are distributed among these distances:
21 11 0.10
22 90 0.80
23 11 0.10
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (22 bp):
TTATCAAATTTTCATAATGAGG
Found at i:34270 original size:44 final size:44
Alignment explanation
Indices: 34158--34347 Score: 170
Period size: 44 Copynumber: 4.3 Consensus size: 44
34148 TATATCGTGA
* * * *
34158 TTATCAAAATTTT-ATAGGAAAATTATCAAAATTTCATACTAAGG
1 TTATC-AAATTTTCATAGGGAGATTATCAAAATTTCATAATGAGG
* * * * * *
34202 TTGTCAAGA-TTTCTTAGTGTGGTTATCAAAATTTCAT-ATTATGG
1 TTATCAA-ATTTTCATAGGGAGATTATCAAAATTTCATAATGA-GG
* * *
34246 TTATCAAATTTTCATAGGGAGGTTATCGAAATTTAATAATGAGG
1 TTATCAAATTTTCATAGGGAGATTATCAAAATTTCATAATGAGG
* ** **
34290 TTATCAAATTTTCACAGATAGATTATTGAAATTTCATAATGAGG
1 TTATCAAATTTTCATAGGGAGATTATCAAAATTTCATAATGAGG
34334 TTATCAAATTTTCA
1 TTATCAAATTTTCA
34348 CAGTGTGATT
Statistics
Matches: 119, Mismatches: 22, Indels: 10
0.79 0.15 0.07
Matches are distributed among these distances:
43 8 0.07
44 108 0.91
45 3 0.03
ACGTcount: A:0.37, C:0.09, G:0.14, T:0.40
Consensus pattern (44 bp):
TTATCAAATTTTCATAGGGAGATTATCAAAATTTCATAATGAGG
Found at i:39651 original size:15 final size:15
Alignment explanation
Indices: 39633--39673 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
39623 ATATCATCAT
39633 AATATATTCTTAAAA
1 AATATATTCTTAAAA
* *
39648 AATAAATCCTTTAAAA
1 AATATATTC-TTAAAA
39664 AATATATTCT
1 AATATATTCT
39674 CAAATATCCT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (15 bp):
AATATATTCTTAAAA
Found at i:40951 original size:41 final size:42
Alignment explanation
Indices: 40879--40965 Score: 131
Period size: 41 Copynumber: 2.1 Consensus size: 42
40869 TTGTTAAAGG
* *
40879 ATATTTAAGAATATATTTTTTTAAAGGATTTATTTTTGAAAA
1 ATATTTAAGAATATATTTCTTTAAAAGATTTATTTTTGAAAA
* *
40921 ATATTTAAGAATGTA-TTCTTTAAAAGATTTATTTTTGAAGA
1 ATATTTAAGAATATATTTCTTTAAAAGATTTATTTTTGAAAA
40962 ATAT
1 ATAT
40966 ATTATGATGA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 27 0.66
42 14 0.34
ACGTcount: A:0.40, C:0.01, G:0.10, T:0.48
Consensus pattern (42 bp):
ATATTTAAGAATATATTTCTTTAAAAGATTTATTTTTGAAAA
Found at i:42232 original size:19 final size:19
Alignment explanation
Indices: 42208--42245 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
42198 TCTCTTGTAA
42208 TCTGTTTGATAAGTGTATT
1 TCTGTTTGATAAGTGTATT
42227 TCTGTTTGATAAGTGTATT
1 TCTGTTTGATAAGTGTATT
42246 ATAGTTTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.05, G:0.21, T:0.53
Consensus pattern (19 bp):
TCTGTTTGATAAGTGTATT
Found at i:43898 original size:17 final size:17
Alignment explanation
Indices: 43878--43916 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
43868 TTTTTTGAGG
43878 TTAATTATGAAAAGATA
1 TTAATTATGAAAAGATA
43895 TTAATTATGAAAAGATA
1 TTAATTATGAAAAGATA
43912 TTAAT
1 TTAAT
43917 GATCTGCTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.38
Consensus pattern (17 bp):
TTAATTATGAAAAGATA
Found at i:44429 original size:35 final size:35
Alignment explanation
Indices: 44383--44452 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
44373 TAGAATTTTC
44383 AATGGAAATTTTGTTTAACCCCATAAACAAAGAAA
1 AATGGAAATTTTGTTTAACCCCATAAACAAAGAAA
44418 AATGGAAATTTTGTTTAACCCCATAAACAAAGAAA
1 AATGGAAATTTTGTTTAACCCCATAAACAAAGAAA
44453 GTAATATGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.26
Consensus pattern (35 bp):
AATGGAAATTTTGTTTAACCCCATAAACAAAGAAA
Found at i:46932 original size:22 final size:22
Alignment explanation
Indices: 46793--47181 Score: 140
Period size: 22 Copynumber: 17.5 Consensus size: 22
46783 ACAATCAAAC
* *
46793 CAAAATTACATGAGAAGGTTAT
1 CAAAATTTCATAAGAAGGTTAT
*
46815 CAAAATTTCATAAAAAGGTTAT
1 CAAAATTTCATAAGAAGGTTAT
* * *
46837 CAAAATTTCTTAAGGAGGTTAA
1 CAAAATTTCATAAGAAGGTTAT
*
46859 CACAATTTCATACA-AAGGTTAT
1 CAAAATTTCATA-AGAAGGTTAT
* * **
46881 CGAAATTTTAT-AGTGTGGTTAT
1 CAAAATTTCATAAG-AAGGTTAT
* *
46903 CAAAATTTAATAAGAAGGTTAA
1 CAAAATTTCATAAGAAGGTTAT
* *
46925 CAAAATTTTATAGGGAGGAAAGTTAT
1 CAAAATTTCATA---A-GAAGGTTAT
* *
46951 CAAAA-TT--T--G-TGCTTAT
1 CAAAATTTCATAAGAAGGTTAT
* * *
46967 TAAAATTTCCTAAGAAGGTTAA
1 CAAAATTTCATAAGAAGGTTAT
* *
46989 CAAAATTTCATAGGGAGGTTAT
1 CAAAATTTCATAAGAAGGTTAT
* * *
47011 GAAAATTT--TATGGAGAGTTAT
1 CAAAATTTCATAAGAAG-GTTAT
*
47032 CAAAATTAT-ATAGAGAA-GATAT
1 CAAAATT-TCATA-AGAAGGTTAT
** * *
47054 CACGGTTTCATTCTCATAGGGAGGTTAT
1 CA-----AAATT-TCATAAGAAGGTTAT
* ** *
47082 CTAAATTTCATGGTGTA-GTTAT
1 CAAAATTTCAT-AAGAAGGTTAT
* * *
47104 CAAAATTTTATGAGGAGGTTAT
1 CAAAATTTCATAAGAAGGTTAT
* * * *
47126 CAAAATTTTATAGGGAGATTAT
1 CAAAATTTCATAAGAAGGTTAT
* *
47148 CAAAATTTCACAATG-AGTTTAT
1 CAAAATTTCATAA-GAAGGTTAT
47170 CAAAATTTCATA
1 CAAAATTTCATA
47182 GTGTCGTTAT
Statistics
Matches: 273, Mismatches: 66, Indels: 56
0.69 0.17 0.14
Matches are distributed among these distances:
16 8 0.03
17 3 0.01
19 1 0.00
20 7 0.03
21 15 0.05
22 196 0.72
23 12 0.04
24 2 0.01
25 3 0.01
26 12 0.04
27 6 0.02
28 8 0.03
ACGTcount: A:0.40, C:0.09, G:0.17, T:0.34
Consensus pattern (22 bp):
CAAAATTTCATAAGAAGGTTAT
Found at i:47148 original size:44 final size:45
Alignment explanation
Indices: 47073--47289 Score: 162
Period size: 44 Copynumber: 4.9 Consensus size: 45
47063 ATTCTCATAG
* * **
47073 GGAGGTTATCTAAATTTCAT-GGTGTAGTTATCAAAATTTTATGA
1 GGAGGTTATCAAAATTTCATAGGTGTAGTTATCAAAATTTCACAA
*
47117 GGAGGTTATCAAAATTTTATAGG-G-AGATTATCAAAATTTCACAA
1 GGAGGTTATCAAAATTTCATAGGTGTAG-TTATCAAAATTTCACAA
* * * * * *
47161 TGAGTTTATCAAAATTTCATA-GTGTCGTTATTAAGATTTCAC-C
1 GGAGGTTATCAAAATTTCATAGGTGTAGTTATCAAAATTTCACAA
* * * * *
47204 GTGTGGTTATCAAATTTTCACACG-G-AGCTTATCAAAATTTCATAA
1 G-GAGGTTATCAAAATTTCATAGGTGTAG-TTATCAAAATTTCACAA
* * * * *
47249 TGAGGTTATCAAATTTTCACA-GTGTTGTTATCAATATTTCA
1 GGAGGTTATCAAAATTTCATAGGTGTAGTTATCAAAATTTCA
47290 ACGTTGGAGC
Statistics
Matches: 137, Mismatches: 26, Indels: 20
0.75 0.14 0.11
Matches are distributed among these distances:
43 5 0.04
44 127 0.93
45 5 0.04
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.39
Consensus pattern (45 bp):
GGAGGTTATCAAAATTTCATAGGTGTAGTTATCAAAATTTCACAA
Found at i:47191 original size:22 final size:22
Alignment explanation
Indices: 47077--47289 Score: 134
Period size: 22 Copynumber: 9.7 Consensus size: 22
47067 TCATAGGGAG
* *
47077 GTTATCTAAATTTCATGGTGTA
1 GTTATCAAAATTTCATAGTGTA
*
47099 GTTATCAAAATTTTATGAG-G-A
1 GTTATCAAAATTTCAT-AGTGTA
* *
47120 GGTTATCAAAATTTTATAG-GGA
1 -GTTATCAAAATTTCATAGTGTA
* *
47142 GATTATCAAAATTTCACAATG-A
1 G-TTATCAAAATTTCATAGTGTA
*
47164 GTTTATCAAAATTTCATAGTGTC
1 G-TTATCAAAATTTCATAGTGTA
* * ** *
47187 GTTATTAAGATTTCACCGTGTG
1 GTTATCAAAATTTCATAGTGTA
* *
47209 GTTATCAAATTTTCACACG-G-A
1 GTTATCAAAATTTCATA-GTGTA
*
47230 GCTTATCAAAATTTCATAATG-A
1 G-TTATCAAAATTTCATAGTGTA
* * *
47252 GGTTATCAAATTTTCACAGTGTT
1 -GTTATCAAAATTTCATAGTGTA
*
47275 GTTATCAATATTTCA
1 GTTATCAAAATTTCA
47290 ACGTTGGAGC
Statistics
Matches: 151, Mismatches: 29, Indels: 22
0.75 0.14 0.11
Matches are distributed among these distances:
21 6 0.04
22 140 0.93
23 5 0.03
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.39
Consensus pattern (22 bp):
GTTATCAAAATTTCATAGTGTA
Found at i:47191 original size:66 final size:65
Alignment explanation
Indices: 47069--47265 Score: 173
Period size: 66 Copynumber: 3.0 Consensus size: 65
47059 TTTCATTCTC
* *** *
47069 ATAGGGAGGTTATCTAAATTTCATGGTGTAGTTATCAAAATTTTATGAG-GAGGTTATCAAAATT
1 ATAGGGAGGTTATCAAAATTTCACAATG-AGTTATCAAAATTTCAT-AGTGAGGTTATCAAAATT
47133 TT
64 TT
* ** * *
47135 ATAGGGAGATTATCAAAATTTCACAATGAGTTTATCAAAATTTCATAGTGTCGTTATTAAGATTT
1 ATAGGGAGGTTATCAAAATTTCACAATGAG-TTATCAAAATTTCATAGTGAGGTTATCAAAATTT
*
47200 C
65 T
** * * * ** *
47201 ACCGTGTGGTTATCAAATTTTCACACGGAGCTTATCAAAATTTCATAATGAGGTTATC-AAATTT
1 ATAGGGAGGTTATCAAAATTTCACAATGAG-TTATCAAAATTTCATAGTGAGGTTATCAAAATTT
47265 T
65 T
47266 CACAGTGTTG
Statistics
Matches: 103, Mismatches: 26, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
65 9 0.09
66 94 0.91
ACGTcount: A:0.34, C:0.11, G:0.17, T:0.38
Consensus pattern (65 bp):
ATAGGGAGGTTATCAAAATTTCACAATGAGTTATCAAAATTTCATAGTGAGGTTATCAAAATTTT
Found at i:47267 original size:66 final size:66
Alignment explanation
Indices: 47100--47287 Score: 182
Period size: 66 Copynumber: 2.8 Consensus size: 66
47090 CATGGTGTAG
* * * * * * * * *
47100 TTATCAAAATTTTATGAGGAGGTTATCAAAATTTT-ATAGGGAGATTATCAAAATTTCACAATGA
1 TTATCAAAATTTCATAATGAGGTTATC-AAATTTTCACAGTGTGGTTATCAAATTTTCACAAGGA
*
47164 GT
65 GC
* ** * * *
47166 TTATCAAAATTTCATAGTGTCGTTATTAAGA-TTTCACCGTGTGGTTATCAAATTTTCACACGGA
1 TTATCAAAATTTCATAATGAGGTTATCAA-ATTTTCACAGTGTGGTTATCAAATTTTCACAAGGA
47230 GC
65 GC
*
47232 TTATCAAAATTTCATAATGAGGTTATCAAATTTTCACAGTGTTGTTATCAATATTT
1 TTATCAAAATTTCATAATGAGGTTATCAAATTTTCACAGTGTGGTTATCAA-ATTT
47288 CAACGTTGGA
Statistics
Matches: 96, Mismatches: 22, Indels: 7
0.77 0.18 0.06
Matches are distributed among these distances:
65 6 0.06
66 86 0.90
67 4 0.04
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.39
Consensus pattern (66 bp):
TTATCAAAATTTCATAATGAGGTTATCAAATTTTCACAGTGTGGTTATCAAATTTTCACAAGGAG
C
Found at i:51285 original size:12 final size:14
Alignment explanation
Indices: 51252--51291 Score: 57
Period size: 12 Copynumber: 3.0 Consensus size: 14
51242 TACTCCCTCC
51252 GTCCCTTTTTATCT
1 GTCCCTTTTTATCT
*
51266 GTCGCTTTTT-T-T
1 GTCCCTTTTTATCT
51278 GTCCCTTTTTATCT
1 GTCCCTTTTTATCT
51292 CTCATTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 10 0.45
13 2 0.09
14 10 0.45
ACGTcount: A:0.05, C:0.25, G:0.10, T:0.60
Consensus pattern (14 bp):
GTCCCTTTTTATCT
Found at i:51300 original size:26 final size:26
Alignment explanation
Indices: 51252--51301 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
51242 TACTCCCTCC
* *
51252 GTCCCTTTTTATCTGTCGCTTTTTTT
1 GTCCCTTTTTATCTCTCACTTTTTTT
51278 GTCCCTTTTTATCTCTCA-TTTTTT
1 GTCCCTTTTTATCTCTCACTTTTTT
51302 GATATAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.06, C:0.24, G:0.08, T:0.62
Consensus pattern (26 bp):
GTCCCTTTTTATCTCTCACTTTTTTT
Found at i:55884 original size:12 final size:12
Alignment explanation
Indices: 55867--55891 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55857 TAAACTCTAA
55867 TACTTTTGCTAT
1 TACTTTTGCTAT
55879 TACTTTTGCTAT
1 TACTTTTGCTAT
55891 T
1 T
55892 GTGCCATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.16, G:0.08, T:0.60
Consensus pattern (12 bp):
TACTTTTGCTAT
Found at i:57011 original size:19 final size:19
Alignment explanation
Indices: 56987--57024 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
56977 TCTCTTTTAA
56987 TCTGTTTGATAAGTGTATT
1 TCTGTTTGATAAGTGTATT
57006 TCTGTTTGATAAGTGTATT
1 TCTGTTTGATAAGTGTATT
57025 ATAGTTTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.05, G:0.21, T:0.53
Consensus pattern (19 bp):
TCTGTTTGATAAGTGTATT
Found at i:59462 original size:330 final size:326
Alignment explanation
Indices: 58105--60967 Score: 2479
Period size: 330 Copynumber: 8.7 Consensus size: 326
58095 CCATAATGGT
* *
58105 AAAAA-TGACCCGAAAGATTTTTCCTCAATTTTT-GACAAAAAATACTCATAAAATATATATAAT
1 AAAAATTGACCCGAAAAATTTTTCCTCAATTTTTAG-C-TAAAATACTCATAAAATATATATAAT
* * * *
58168 TAAACGCCAAAAAAATTTG-AGGACTTTTCACGCTTTTAATATCATTTTTCATTTTTTTCTGAAT
64 TCAACGCCAAAAAGA-TTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAAT
* * * * *
58232 CAA-TTCTTAATTAAATCGATACAAGATTCAAATGCACATAAAAACAAATCCTTAAATCCAATGT
128 TAATTTC-TAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTT-AATCCAATGT
* * * *
58296 TGCTGAGATTTTATTAGATGAATAAAGATATTTCAAGGAGTCTCGGTGCCAAAAATCATGCAAAA
191 GGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCAG-G-CAAAAATCATGCAAAA
** ** * * * * *
58361 CAAAGTTGTGGCCTTGGAACGCATTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTTGACT
254 CTGAGCCG-GGCC-CGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCT
58426 AAAATTTTGC
317 AAAATTTTGC
* *
58436 AAAAATTGACCC-AAAAGATATTTT--TACAATTTTTGGCTAAAATACTCATGAAAA-ATATATG
1 AAAAATTGACCCGAAAA-AT-TTTTCCT-CAATTTTTAGCTAAAATACTCAT-AAAATATATATA
*** * * * * * * *
58497 ATTCAATATCAAAAAGATTGAAGGGCTTTTAACGCTTCTAATATTGCTTTTCCTATTTCTTTCCG
62 ATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCATA-TT-TTTCTG
* * *
58562 AATTAATTTCTAATTAAATCG-AACAAAGATTCAGATGCTCGTAAAAATAAATTCTTAAATCTAA
125 AATTAATTTCTAATTAAATCGAAAC-AAGATTCAGATGCTCGTAAAAACAAATCCTT-AATCCAA
* * * *
58626 TGTGGCTAAGATTTGGTTAGAT-TATATAGATATTTCAAGGAGTCTTGGCA-CCAAAAATCATGC
188 TGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTC-T--CAGGCAAAAATCATGC
** * * ** *
58689 AAAACTGAGCCTGACCCCGGAACGCGTTTTTAGCCGAAAACTGTGATGGTTAGTACAATATTTCA
250 AAAACTGAGCC-GGGCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCG
58754 GCTAAAATTTT-C
314 GCTAAAATTTTGC
* * * * *
58766 AAAAAATTGACCCGAAATATTTTTCCTCGATTTCTAGCGAAAATACTCATAAAAAATATATAATT
1 -AAAAATTGACCCGAAAAATTTTTCCTCAATTTTTAGCTAAAATACTCATAAAATATATATAATT
* * * * * *
58831 CAACGCCAAAAA-AATGAAAGCCTTTTTCACGCTTTTAATATCGTTTTCCCTATTTTATTTCTAA
65 CAACGCCAAAAAGATTGAAGGAC-TTTTCACGCTTTTAATATCGTTTT-TC-ATATT-TTTCTGA
* * * *** *
58895 ATTAATTTCTGATTAAATCAAAACAAGATTTAGAAATTCGTAAAAACAAATCCTTAAATACAATG
126 ATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTT-AATCCAATG
* * *
58960 TGGCTGAGATTTGGTTAGATGAATATAGATATATTTTAAGGAGTCTTGGCA-CCAAAAATCATGC
190 TGGCTGAGATTTGATTAGATGAATATAG--ATATTTCAAGGAGTC-T--CAGGCAAAAATCATGC
* * ** *
59024 AAAACTGACCCAGGATCCCGGAACGCGTTTTTAGCCAAAAAACAATTAT-G--A-TACACGATTT
250 AAAACTGAGCC-GG-GCCCGGAACGCGTTTTTAGCC-AAAAACCGTGATGGTTAGTACACGATTT
*
59085 CGGTTAAAATTTTGC
312 CGGCTAAAATTTTGC
* * * * *
59100 AAAAATTGACCCGAAATATTTTGT-CTCAATTTTAAGCCACAACACTCATAAAATATATATAATT
1 AAAAATTGACCCGAAAAATTTT-TCCTCAATTTTTAGCTAAAATACTCATAAAATATATATAATT
* * *
59164 CAACACCAAAAAGACTGGAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTA
65 CAACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTA
* *
59229 ATTTCTAATTAAATCGAAACAAGATTCAGAGGCTCGTAAAAACAAATCCTTATATTCAATGTGGC
130 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTA-ATCCAATGTGGC
* *
59294 TGAGATTTGATTAGATGAATATAGATATTTCAAGAAGTCTCAGTGCAAAAATTCATGCAAAACTA
194 TGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCAG-GCAAAAA-TCATGCAAAACTG
* * *
59359 AGCCGGGCCTCGAAATGCGTTTTTAGCC-AAAACCGTGATGGTTAGTACACGATTTCTGCTAAAA
257 AGCCGGGCC-CGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAA
*
59423 TTTTGT
321 TTTTGC
* *
59429 AAAAATTGACCCGAAAAATTTTTCCGACAATTTTTGGCTAAAATACTCAT--AATATATATAATT
1 AAAAATTGACCCGAAAAATTTTTCC-TCAATTTTTAGCTAAAATACTCATAAAATATATATAATT
* * * * *
59492 TAATGCCAAAAAGATTGGAGAACTTTTCACGCTTTTAATATCATTTTT-ATTATTTTTCTGAATT
65 CAACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCA-TATTTTTCTGAATT
* * * * *
59556 AATTTCTAATTAAATCGAAATAAGATTCAGATGTTCATAAAAACAAATTCTTAAATCCAATGTTG
129 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTT-AATCCAATGTGG
* * * * * **
59621 CTAATATTTGATTAGATGAATAT-GAATATCTCAAAGAGTTTTGGCGCCAAAAATCATGCAAAAC
193 CTGAGATTTGATTAGATGAATATAG-ATATTTCAAGGAGTCTCAG-G-CAAAAATCATGCAAAAC
* * * *
59685 TGAGCCGGGGTCCCGAAATGCGATTTTAGCCAAAAACCGTGATGATTA-T-CA--A--------A
255 TGAGCC-GGG-CCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTA
*
59738 CAATTTT--
318 AAATTTTGC
* *
59745 ----A--G--CC--AAAATTATTTCCTCAATTTTTAGCCACAATACTCATTAAAAT-TATATAAT
1 AAAAATTGACCCGAAAAATT-TTTCCTCAATTTTTAGCTAAAATACTCA-TAAAATATATATAAT
* * * * * *
59799 TCAATGCCAATAAGATTGAAGGGCTTTTCATGCTTCTAATATCTTTTTTCCTATTATTTTT-TGA
64 TCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTT-C-A-TATTTTTCTGA
* * ** * *
59863 ATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTTGCT--TTAGAAATCCTTGAATCCAAA
126 ATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCG-TAAAAACAAATCCTT-AATCCAAT
* * * * *
59926 GTGGCCGAGATTTGGTTAGATAAATATAGATATTTTAAGGAGTCTAAGCGCCAAAAATCATGCAA
189 GTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCAG-G-CAAAAATCATGCAA
* * * * * * *
59991 CACTGTA-CTGGGACACCGGAACGCGTTTTTAACAACAAAAAAAACGTAATTTCGACTAACGTAC
252 AACTG-AGCCGGG-C-CCGGAACGCGTTTTTAGC--C--AAAAACCGTGA--T-G-GTTA-GTAC
*
60055 ACGATTTCGGCTAATATTTTGC
305 ACGATTTCGGCTAAAATTTTGC
* *** * *
60077 AAAAATTGACCAGAATTCTTTTTCCTCAATTTTT-GTCTAAAATACTCATAAAAAATATATATTT
1 AAAAATTGACCCGAAAAATTTTTCCTCAATTTTTAG-CTAAAATACTCATAAAATATATATAATT
* * * * * * * *
60141 TAATGCCTAAAAGATTGCAGAATTTTTCACGCTTTTAATATTGTTTTTTCATGTTTTTCTGAATT
65 CAACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCG-TTTTTCATATTTTTCTGAATT
* * * * *
60206 GATTTCAAATTAAATC---A-AA-ATTCAGATGCTCGTAAAAACACATCCTTAAGTGCAATGTAG
129 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAA-TCCAATGTGG
* * * *
60266 CAGACATTTGATTAAATAAATATAGATATTTCAAGGAGTCTCGACGGCAAAAATCATGCAAAACT
193 CTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTC-A-GGCAAAAATCATGCAAAACT
* * * * *
60331 GAGTCGGGGCCCCGAAACACGTTTTTAGCAAAAAAAAACCGTGATGCTTAGTACACGATTTCGGC
256 GAG-CCGGG-CCCGGAACGCGTTTTTAGC---CAAAAACCGTGATGGTTAGTACACGATTTCGGC
*
60396 TAAAATTTTGT
316 TAAAATTTTGC
* * * *
60407 AAAAAATGACCAGAAAAATTTTTCCTTAATTTTT-GTCTAAAATACTCATGAAATATATATAATT
1 AAAAATTGACCCGAAAAATTTTTCCTCAATTTTTAG-CTAAAATACTCATAAAATATATATAATT
* * * * *
60471 TAACGCCAAAAAGATTGGAGGACTTTTCACGCTTTTCATATCATTTTTCATATTTTTTTTGAATT
65 CAACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCATA-TTTTTCTGAATT
* * * * *
60536 AATTTGTAATTAAATCGAAACAAGATACAGATGCTCGTAAAAACAAATCATTAAATGCTATGTGG
129 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTT-AATCCAATGTGG
* * * * *
60601 ATGAGATTTGATTAGATTAATATGGATATATCTCAAGGATTCTTAGTGCAAAAAATCATGCAAAA
193 CTGAGATTTGATTAGATGAATATAGATAT-T-TCAAGGAGTCTCAG-GC-AAAAATCATGCAAAA
** * * * *
60666 CTGA-CCTGGGGCCCTGGATTGCGTCTTTAGCCAAAAACCGTGATGATTTATTAGACGATTTCGG
254 CTGAGCC--GGGCCC-GGAACGCGTTTTTAGCCAAAAACCGTGATG-GTTAGTACACGATTTCGG
*
60730 CTAACATTTTGC
315 CTAAAATTTTGC
* * * * *
60742 AAAAATTGA-CCGAAAAAAAATATTTCCCCAATTTTTGGCTAAAATACTTATAAAAAAATATATA
1 AAAAATTGACCCG---AAAAATTTTTCCTCAATTTTTAGCTAAAATACTCAT-AAAATATATATA
* * ** * * * * *
60806 ATTCATCGCCAAAAATATTGAAGGGTTTTTTACGCTTCTAATAT-TTTTTTCCTACTTTTTCCGA
62 ATTCAACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCATA-TTTTTCTGA
*
60870 ATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAA-AAATCCTTAATTCCAATG
126 ATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAA-TCCAATG
*
60934 TGGTTGAGATTTGATTAGATGAATATAGATATTT
190 TGGCTGAGATTTGATTAGATGAATATAGATATTT
60968 GCATGATTTT
Statistics
Matches: 2067, Mismatches: 338, Indels: 251
0.78 0.13 0.09
Matches are distributed among these distances:
306 25 0.01
307 6 0.00
308 55 0.03
309 88 0.04
310 41 0.02
311 11 0.01
312 1 0.00
313 9 0.00
315 1 0.00
316 1 0.00
317 2 0.00
318 7 0.00
319 1 0.00
320 2 0.00
322 1 0.00
325 10 0.00
326 4 0.00
327 27 0.01
328 208 0.10
329 81 0.04
330 288 0.14
331 193 0.09
332 150 0.07
333 200 0.10
334 31 0.01
335 163 0.08
336 157 0.08
337 149 0.07
338 48 0.02
339 6 0.00
340 28 0.01
341 65 0.03
342 8 0.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.34
Consensus pattern (326 bp):
AAAAATTGACCCGAAAAATTTTTCCTCAATTTTTAGCTAAAATACTCATAAAATATATATAATTC
AACGCCAAAAAGATTGAAGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAA
TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAATCCAATGTGGCTG
AGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCAGGCAAAAATCATGCAAAACTGAGCC
GGGCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTG
C
Found at i:72301 original size:44 final size:42
Alignment explanation
Indices: 72244--72360 Score: 154
Period size: 37 Copynumber: 2.9 Consensus size: 42
72234 TTCTTCAAGA
*
72244 ATAATAATTCTCCACATACGTGGATCTTCTTTCAATCTTCTTTG
1 ATAATAATACTCCACATACGTGGATCTTCTTTCAA--TTCTTTG
72288 ATAATAATACTCCACATACGTGGA---TC-TTCAA-TCTTTG
1 ATAATAATACTCCACATACGTGGATCTTCTTTCAATTCTTTG
* *
72325 AAAATAATCCTCCACATACGTGGATCTTCTTTCAAT
1 ATAATAATACTCCACATACGTGGATCTTCTTTCAAT
72361 AATCCTCATT
Statistics
Matches: 65, Mismatches: 3, Indels: 12
0.81 0.04 0.15
Matches are distributed among these distances:
37 28 0.43
40 7 0.11
41 7 0.11
44 23 0.35
ACGTcount: A:0.30, C:0.23, G:0.09, T:0.38
Consensus pattern (42 bp):
ATAATAATACTCCACATACGTGGATCTTCTTTCAATTCTTTG
Found at i:73465 original size:334 final size:333
Alignment explanation
Indices: 72754--73646 Score: 1050
Period size: 334 Copynumber: 2.7 Consensus size: 333
72744 TTGCTCTACA
* * * * * * *
72754 GCTCGTAAAAACAAATTCTTAAATCTAATGTGGCTAAGATTAGGTTAGATGACTATAGATATTTG
1 GCTCGT-AAAACAAATACTTAAATCAAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTC
** * * * * *
72819 AAGGAGT-TTTGCTACAAAAAATCATGTAAAACTGGCCCGGGACCCCGGAACGCGTTTTTAGCAA
65 AAGGAGTCTCGGC-ACCAAAAATCATGCAAAACTAG-CCGGGGCCCCGGAACGCGTTTTTAGC-C
* * *
72883 AAAAATCGTGAT-G---GTACACGATTTCGGCTAAAATTTTGCAAAAATA-GACCCGAAACATTT
127 AAAAACCGTGATGGTTAGTATACGATTTCGGCTAAAATTTTGCAAAAAAATGACCCGAAA-ATTT
* * * *
72943 TTCCTCAATTTTTAGCCACAATACTC---ATA-ATATATATAATTCAACTCCAAAAAGATTGGAG
191 TTCCTCAATTTTTAGCTAAAATACTCATAATATATATATATAATTCAACACAAAAAAGATTGGAG
*
73004 AACTTTTCACGCTTTTAATATCGTTTTCCATATTTTCCTGAATATCAATTTCTAATTAAATCAAA
256 AACTTTTCACGCTTTTAATATCGTTTTCCATATTTTCCTGAATATCAATGTCTAATTAAATCAAA
*
73069 ACAAGATTCAGAT
321 ACAAGATTCAAAT
* * * *
73082 GCTCGTAAAA-AAATAATTAAATTCAAATATGGCTGAGATTTGATTAGATGAGTATGGATATTTC
1 GCTCGTAAAACAAATACTTAAA-TCAAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTC
* * * *
73146 AAGAAGTCTCGGCGCCAAAAATCATGCAAAACTAAGCCGGGGCCCCGAAACACGTTTTTAGCCAA
65 AAGGAGTCTCGGCACCAAAAATCATGCAAAACT-AGCCGGGGCCCCGGAACGCGTTTTTAGCCAA
* * *
73211 AAACCGTGATGGTTAGTATACGATTCCAGCTTAAATTTTGCAAAAAAATGACCCGACAAATTTTT
129 AAACCGTGATGGTTAGTATACGATTTCGGCTAAAATTTTGCAAAAAAATGACCCGA-AAATTTTT
* *
73276 CCTCAATTTTTAGCTAAAATACTCATAATATATATATATAATTTAACACAAAAAAGATTGGAGTA
193 CCTCAATTTTTAGCTAAAATACTCATAATATATATATATAATTCAACACAAAAAAGATTGGAGAA
* *
73341 -TTTTCACGCTTTTAATATCGCTTTT-CATATTTTTTCTGAAT-T-AATGTCTAATTAAATCGAA
258 CTTTTCACGCTTTTAATATCG-TTTTCCATA-TTTTCCTGAATATCAATGTCTAATTAAATCAAA
*
73402 ATAAGATTCAAAT
321 ACAAGATTCAAAT
* * *
73415 GCTCGTATAAACAAATCCTTAAATGC-AATGTGACTGAGATTTGATTAGATGAATGTAGATATTT
1 GCTCGTA-AAACAAATACTTAAAT-CAAATGTGGCTGAGATTTGATTAGATGAATATAGATATTT
* * *
73479 CAAGGAGTCTCGACACCAAAAATCATGCAAAACTGAGCCTGGGCCCCGGAATGCGTTTTTAG-CA
64 CAAGGAGTCTCGGCACCAAAAATCATGCAAAACT-AGCCGGGGCCCCGGAACGCGTTTTTAGCCA
* *
73543 AAAACTAGTGAATGGTTAGT-TCATGATTTCGGCTAAAATTTTGC-AAAAAATGACCCGATAAAT
128 AAAAC-CGTG-ATGGTTAGTAT-ACGATTTCGGCTAAAATTTTGCAAAAAAATGACCCGA-AAAT
* *
73606 TTTTCTTCAATTTTTTGCTAAAATACTCATGAATATATATA
189 TTTTCCTCAATTTTTAGCTAAAATACTCAT-AATATATATA
73647 ATTTAACACC
Statistics
Matches: 482, Mismatches: 61, Indels: 37
0.83 0.11 0.06
Matches are distributed among these distances:
326 20 0.04
327 85 0.18
328 10 0.02
330 28 0.06
331 35 0.07
332 2 0.00
333 42 0.09
334 169 0.35
335 91 0.19
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (333 bp):
GCTCGTAAAACAAATACTTAAATCAAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCA
AGGAGTCTCGGCACCAAAAATCATGCAAAACTAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAA
ACCGTGATGGTTAGTATACGATTTCGGCTAAAATTTTGCAAAAAAATGACCCGAAAATTTTTCCT
CAATTTTTAGCTAAAATACTCATAATATATATATATAATTCAACACAAAAAAGATTGGAGAACTT
TTCACGCTTTTAATATCGTTTTCCATATTTTCCTGAATATCAATGTCTAATTAAATCAAAACAAG
ATTCAAAT
Done.