Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020800.1 Corchorus olitorius cultivar O-4 contig20833, 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: 70631
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:2590 original size:331 final size:330
Alignment explanation
Indices: 1--3685 Score: 4615
Period size: 330 Copynumber: 11.3 Consensus size: 330
*
1 CTGGGATTCAGATCGGTGAATATACATATTTCGAGGAGTCTTTACGCCAAAAATCATGCAAAACT
1 CTGGGATTCAGATCGGTGAATATACGTATTTCGAGGAGTCTTTACGCCAAAAATCATGCAAAACT
* * * *
66 GAGTCGGGGCCTCGGAATGCGTTTTTAGGCAAAAACCGTGATGGTTATTACACGATTTCCGCTAA
66 GAGTCGGGGCCCCGGAACGCGTTTTTAGGCAAAAACCGTGATGGTTAATACACGATTTCGGCTAA
* * *
131 AA--TT------A-T-CCCGAAAATTTTTTTCCCCAATTTTCTGCAACAATATTCAGGAAAAACA
131 AATTTTGCGAAAATTACCCGAAAATTTTTTTCCTCAATTTTCTGCCACAATACTCAGGAAAAACA
* *
186 TATAATCCAACGCCAAAAAGACTGAAGCGTTTTTCACGCTTCTAATATCGTTTTTCCATTCTTTC
196 TATAATTCAACGCCAAAAAGACTGAAGCGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTC
* * * * *
251 GAATTAATTTCCATTTAAATCGAAATAAGATTCAGATGCTCGTAAAAACTAATCCAGAAATCCAA
261 GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTGAAATCCAA
316 TGTGG
326 TGTGG
* * *
321 CTTGGATTCAGATCGGTGAATATACGTATTTCGAGGAGTTTTTACGCCAAAAATCATTCAAAACT
1 CTGGGATTCAGATCGGTGAATATACGTATTTCGAGGAGTCTTTACGCCAAAAATCATGCAAAACT
* * *
386 GAGTCGGGGCCTCGGAACGCGTTTTTAGGCAAAAATCGTGATGGTTAATACACGATTTCAGCTAA
66 GAGTCGGGGCCCCGGAACGCGTTTTTAGGCAAAAACCGTGATGGTTAATACACGATTTCGGCTAA
* *
451 AATTTTGCGAAACTTATCCCGAAAA--TTTTTCCTCAACTTTCTGCCACAATACTCAGGAAAAAC
131 AATTTTGCGAAAATTA-CCCGAAAATTTTTTTCCTCAATTTTCTGCCACAATACTCAGGAAAAAC
* *
514 ATATAATTCAACGCCAAAAATACTGAAGCGTTTTTCACGCTTCTAATGTCGTTTTTCCATTTTTT
195 ATATAATTCAACGCCAAAAAGACTGAAGCGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTT
* * * * * *
579 CGAATTAATTTTTAATTAAATCGAAACAAGATTCAAATACTTGTAAAAACAAATCCAGAATTCCA
260 CGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTGAAATCCA
644 ATGTGG
325 ATGTGG
* * * * *
650 CTGGGATTCAGATCGGTGAATATACATATTTCCAAGAGTCTTTACGCCAAAAGTCATGCGAAACT
1 CTGGGATTCAGATCGGTGAATATACGTATTTCGAGGAGTCTTTACGCCAAAAATCATGCAAAACT
* *
715 GAATCGGGGGCCCGGAACGCGTTTTTA-GCAAAAAACCGTGATGGTTAATACACGATTTCGGCTA
66 GAGTCGGGGCCCCGGAACGCGTTTTTAGGC-AAAAACCGTGATGGTTAATACACGATTTCGGCTA
* * *
779 AAATTTTGCG-AAATTACCTCGAAAATTTTTTTCTTCAATTTTCTGCTACAATACTCAAGAAAAA
130 AAATTTTGCGAAAATTACC-CGAAAATTTTTTTCCTCAATTTTCTGCCACAATACTCAGGAAAAA
* * *
843 TATATAATTCAACGCCAAAAAGACTGAAGCGTTTTTCACGCTTCTGATATCGTTTTTCCATTCTT
194 CATATAATTCAACGCCAAAAAGACTGAAGCGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTT
* * * *
908 TCGAATTAATTTCTTATTAAATCGTAACAAGATTCAGATACACGTAAAAACAAATCCTGAAATCC
259 TCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTGAAATCC
*
973 ACTGTGG
324 AATGTGG
* * * *
980 CTGGGATTCAGATCGGTGAATATATGTATTTCGAAGAGTATTTACGCCAAAAATCATGCAAAATT
1 CTGGGATTCAGATCGGTGAATATACGTATTTCGAGGAGTCTTTACGCCAAAAATCATGCAAAACT
* * *
1045 GAGTCGGGGTCCCGGAACGCGTTCTTAGGCAAAAACCGTGATGGTTAATACAAGATTTCGGCTAA
66 GAGTCGGGGCCCCGGAACGCGTTTTTAGGCAAAAACCGTGATGGTTAATACACGATTTCGGCTAA
* * *
1110 AATTTTGCG-AAATTACCCCGAAAATTTTTTTCCTCAACTTTCTGCTACAATACTCAGGAAAAAT
131 AATTTTGCGAAAATTA-CCCGAAAATTTTTTTCCTCAATTTTCTGCCACAATACTCAGGAAAAAC
* *
1174 ATATAATTCAACGCCAAAAAGACTGAATCGTTTTTCACGCTTCTAATATCGTTTTTCCATTCTTT
195 ATATAATTCAACGCCAAAAAGACTGAAGCGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTT
* * * * *
1239 CGAATTAATTTCTTATTAAATCGTAACAAGATTCATATGCTCGTAAAAACAAATCCAGAAATCCG
260 CGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTGAAATCCA
1304 ATGTGG
325 ATGTGG
* * * *
1310 CTGGGATTCAGATCGTTGAATATACGTATTTCGAGGAGTTTTTACGCCAAAAAGCATGCAAAATT
1 CTGGGATTCAGATCGGTGAATATACGTATTTCGAGGAGTCTTTACGCCAAAAATCATGCAAAACT
* * * ** *
1375 GAGTCGGGGCCTCGGAACGTGTTTTTAGGCAAATACAATGATGGTTAATACACGATTTCAGCTAA
66 GAGTCGGGGCCCCGGAACGCGTTTTTAGGCAAAAACCGTGATGGTTAATACACGATTTCGGCTAA
*
1440 AATTTTGCGAAAATTATCCCGAAAA-TTTTTTCCTCAACTTTCTGCCACAATACTCAGGAAAAAC
131 AATTTTGCGAAAATTA-CCCGAAAATTTTTTTCCTCAATTTTCTGCCACAATACTCAGGAAAAAC
* *
1504 ATCTAATTTAACGCCAAAAAGACTGAAGCGTTTTTCACGCTTCTAA-ATCGTTTTTCCATTCTTT
195 ATATAATTCAACGCCAAAAAGACTGAAGCGTTTTTCACGCTTCTAATATCGTTTTTCCATT-TTT
* * *
1568 T-GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAAACAAATCCAGAAATCA
259 TCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTGAAATCC
1632 AATGTGG
324 AATGTGG
*
1639 CTGGGATTCAGATCGGTGAATATACATATTTCGAGGAGTCTTTACGCCAAAAATCATGCAAAACT
1 CTGGGATTCAGATCGGTGAATATACGTATTTCGAGGAGTCTTTACGCCAAAAATCATGCAAAACT
* * *
1704 GAGTCGGGGCCTCGGAATGCGGTTTTA-GCAAAAACCGTGATGGTTAATACACGATTTCGGCTAA
66 GAGTCGGGGCCCCGGAACGCGTTTTTAGGCAAAAACCGTGATGGTTAATACACGATTTCGGCTAA
* * *
1768 AA--TT------A-T-CCCGAAAATTTTTTTCCCCAATTTTCTGCAACAATATTCAGGAAAAACA
131 AATTTTGCGAAAATTACCCGAAAATTTTTTTCCTCAATTTTCTGCCACAATACTCAGGAAAAACA
* * *
1823 TATAATTCAACGCCAAAAAGACTGAAGAGTTTTTCACGCTTCTAATATCATTTTTCCATTCTTTC
196 TATAATTCAACGCCAAAAAGACTGAAGCGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTC
* * *
1888 GAATTAATTTTTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCTTGAAATCCAT
261 GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTGAAATCCAA
1953 TGTGG
326 TGTGG
*
1958 CTGGGATTCAGATCGGTGAATATACGTATTTCGAGGAGTCTCTACGCCAAAAATCATGCAAAACT
1 CTGGGATTCAGATCGGTGAATATACGTATTTCGAGGAGTCTTTACGCCAAAAATCATGCAAAACT
*
2023 GAGTCGGGGCCTCGGAACGCGTTTTTAGGC-AAAACCGTGATGG---ATACACGATTTCGGCTAA
66 GAGTCGGGGCCCCGGAACGCGTTTTTAGGCAAAAACCGTGATGGTTAATACACGATTTCGGCTAA
* * * * *
2084 AATTTTGC-AATAATTATCCCGAAAA-TTTTTTCCTCGACTTCCTGCCACAATCCTTAGGAAAAA
131 AATTTTGCGAA-AATTA-CCCGAAAATTTTTTTCCTCAATTTTCTGCCACAATACTCAGGAAAAA
* * * * *
2147 CATATAATTCAACGCAAAAAATATTGAAGCGTTTTTCACGCTTCTAATGTCGTTTTTCTATTTTT
194 CATATAATTCAACGCCAAAAAGACTGAAGCGTTTTTCACGCTTCTAATATCGTTTTTCCA-TTTT
* *
2212 TTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCTTGAAATC
258 TTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTGAAATC
*
2277 CATTGTGG
323 CAATGTGG
*
2285 CTGGGATTCAGATCGGTGAATATACGTATTTCGAGGAGTCTCTACGCCAAAAATCATGCAAAACT
1 CTGGGATTCAGATCGGTGAATATACGTATTTCGAGGAGTCTTTACGCCAAAAATCATGCAAAACT
* * *
2350 GAGTCGGGACCCCGGAACGCGTTTTTAGGCAAAAACCGTGAT-ATAACATACACGATTTCGGCTA
66 GAGTCGGGGCCCCGGAACGCGTTTTTAGGCAAAAACCGTGATGGTTA-ATACACGATTTCGGCTA
* * * * *
2414 AAATTTTGTGAAAATTACCCCAAAATTTTTTTCCTCAATTTTCTACTACAATACTCAGGAAAAAT
130 AAATTTTGCGAAAATTACCCGAAAATTTTTTTCCTCAATTTTCTGCCACAATACTCAGGAAAAAC
* * *
2479 ATATGATTCAACGCCAAAAAGACTGAAGCGTTTTTCATGCTTCTAATATCGTTTTCCCATTTTTT
195 ATATAATTCAACGCCAAAAAGACTGAAGCGTTTTTCACGCTTCTAATATCGTTTTTCCA-TTTTT
* * * *
2544 TCGAATTAAATTATAATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAAATCCAGAAATCC
259 TCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTGAAATCC
2609 AATGTGG
324 AATGTGG
* *
2616 CTGGGATTCAGATCGGTGAATATACGTATTTCGAGGAGTCTTTACGCCAAAAATAATGTAAAACT
1 CTGGGATTCAGATCGGTGAATATACGTATTTCGAGGAGTCTTTACGCCAAAAATCATGCAAAACT
* * *
2681 GAATCGGGG-CCTGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAATACACGATTTCGGCTAA
66 GAGTCGGGGCCCCGGAACGCGTTTTTAGGCAAAAACCGTGATGGTTAATACACGATTTCGGCTAA
* * * *
2745 AATTTTGCGAAAATTATCCCGAAATTTTTTTTCCTCAATTTTCTACTACAATATTCAGCG-AAAA
131 AATTTTGCGAAAATTA-CCCGAAAATTTTTTTCCTCAATTTTCTGCCACAATACTCAG-GAAAAA
* * *
2809 CATATAATTCAATGCGAAAAAGACTGAAGCGTTTTTCACGCTTCTAATATCGTTTTTCCATTCTT
194 CATATAATTCAACGCCAAAAAGACTGAAGCGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTT
* * *
2874 TCGACTTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATCC
259 TCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTGAAATCC
*
2939 AATGTGC
324 AATGTGG
** * ** * * * *
2946 CTTAGACTC-GCATCACTGAATATA-GATATTTCAAGGAGTCTTTACGCTAAAAATCGTGAAAAA
1 CTGGGATTCAG-ATCGGTGAATATACG-TATTTCGAGGAGTCTTTACGCCAAAAATCATGCAAAA
* * * * *
3009 CTAAGTCGAGGCGCCGGAACGCGTTTTTAGCCAAAAAACC---AT-GTTAGTACACGA-TT-GGC
64 CTGAGTCGGGGCCCCGGAACGCGTTTTTAGGC-AAAAACCGTGATGGTTAATACACGATTTCGGC
* ** * * * * * *
3068 TAAAA-ATT--G------ACCCGAAAA-AATTTTCTTCAATCCTT-AGCCACATTACTTAGAAAA
128 TAAAATTTTGCGAAAATTACCCGAAAATTTTTTTCCTCAAT-TTTCTGCCACAATACTCAGGAAA
* * * * *
3122 AATATATAATTCAACGCTAAAAA-ATTGAAGGGTTTTTTACGCTTCTAATATCGTTTTTTCCATT
192 AACATATAATTCAACGCCAAAAAGACTGAAGCGTTTTTCACGCTTCTAATATCG-TTTTTCCA-T
* ** * * ** *
3186 TTTTTCTGAATTTATTTCTAATTAAATTTAAACATGATTCAGATGCTCGTAAAAAGAAAAGCTTA
255 TTTTTC-GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTGA
3251 AATCCAATGTGG
319 AATCCAATGTGG
* ** * ** * *
3263 CTGAGATTC-GATTCAATGAATATA-GATATTTCAAGGAGTGGTTGCGCAAAAAATCATGCAAAA
1 CTGGGATTCAGA-TCGGTGAATATACG-TATTTCGAGGAGTCTTTACGCCAAAAATCATGCAAAA
*** ** * * ** * * *
3326 CTGAGTCGGGGCCGTAGAACGCGTTTTTAACCAAAAACCGTAACGGTTTGTACTCTATTTTGGCT
64 CTGAGTCGGGGCCCCGGAACGCGTTTTTAGGCAAAAACCGTGATGGTTAATACACGATTTCGGCT
* * **
3391 AAAATTTTGCAAAAACTGACCC--AAATTCTTTTTCCTCAATCCT-TGCCACAATACTCA-GAAA
129 AAAATTTTGCGAAAA-TTACCCGAAAATT-TTTTTCCTCAATTTTCTGCCACAATACTCAGGAAA
* * * * * *
3452 AAAATATAATTCAACACTAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGATTTTT-CATT
192 AACATATAATTCAACGCCAAAAAGACTGAAGCGTTTTTCACGCTTCTAATATCG-TTTTTCCATT
** * * * *
3516 TTCCCCCGAATTTATTTCCAACTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTA
256 TT--TTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTGA
*
3581 AACCCAATGTGG
319 AATCCAATGTGG
* ** * * * * *
3593 CTGAGATTTGGTTCGATGAATATA-GATATTTCAAGGATTCTTT-CTGCCAAAAATCATACAAAA
1 CTGGGATTCAGATCGGTGAATATACG-TATTTCGAGGAGTCTTTAC-GCCAAAAATCATGCAAAA
* *
3656 CTGAGTCGGGGCCCCGAAACGAGTTTTTAG
64 CTGAGTCGGGGCCCCGGAACGCGTTTTTAG
3686 AACAGTGATG
Statistics
Matches: 2970, Mismatches: 317, Indels: 146
0.87 0.09 0.04
Matches are distributed among these distances:
314 27 0.01
315 49 0.02
316 43 0.01
317 146 0.05
318 83 0.03
319 180 0.06
320 136 0.05
321 2 0.00
322 10 0.00
323 3 0.00
324 1 0.00
325 3 0.00
326 93 0.03
327 179 0.06
328 70 0.02
329 452 0.15
330 1026 0.35
331 443 0.15
332 24 0.01
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (330 bp):
CTGGGATTCAGATCGGTGAATATACGTATTTCGAGGAGTCTTTACGCCAAAAATCATGCAAAACT
GAGTCGGGGCCCCGGAACGCGTTTTTAGGCAAAAACCGTGATGGTTAATACACGATTTCGGCTAA
AATTTTGCGAAAATTACCCGAAAATTTTTTTCCTCAATTTTCTGCCACAATACTCAGGAAAAACA
TATAATTCAACGCCAAAAAGACTGAAGCGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTC
GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTGAAATCCAA
TGTGG
Found at i:4257 original size:269 final size:268
Alignment explanation
Indices: 3771--4259 Score: 709
Period size: 269 Copynumber: 1.8 Consensus size: 268
3761 CAACTCAAAT
* * *
3771 TTTGCGAAAACTGACCCGAAAATTTTTTTATTCTCAATTCCTTGCCAGAATACTAAGAAAAAATA
1 TTTGCAAAAACTGACCCGAAAA-TTTTTTATCCTCAATTCCTTGCCACAATACTAAGAAAAAATA
* * * * *
3836 TATAATTCAACGCCAAAAGATTTATGGGTTTTTCATGCTTCTAATAACGTTTTTCAATTTTTCTA
65 TATAATTCAACACCAAAAGATTAAAGGGTTTTTCACGCTTCTAATAACGTTTTTCAATTTTTCGA
* *
3901 ATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAGAATTCCTTAAATCCAATG
130 ATTAATTTCTAATCAAATCGAAACAAAATTCAGATGCTCGTAAAAAGAATTCCTTAAATCCAATG
**
3966 TGGCTTAGATTTGGTTCGATGAATACATATAATTTAAGGAGTCTTTACCCGAAAACCGCGATTTC
195 TGGCTTAGATTTGGCACGATGAATACATATAATTTAAGGAGTCTTTACCCGAAAACCGCGATTTC
4031 GGCTAAAAC
260 GGCTAAAAC
* *
4040 TTTGCAAAAACTGACCCGAAAA-TTTTT-TCCTCAATTCTTTGCCACATTACTCAA-AAAAAATA
1 TTTGCAAAAACTGACCCGAAAATTTTTTATCCTCAATTCCTTGCCACAATACT-AAGAAAAAATA
* *
4102 TATAATTCAACACCAAATGATTAAAGGGTTTTTCACGCTTCTAATATCGTTTTTCAATTATTTTT
65 TATAATTCAACACCAAAAGATTAAAGGGTTTTTCACGCTTCTAATAACGTTTTTC-A--ATTTTT
* * *
4167 CGAATTAATTTCTAATCATATCGAAACAAAATTCAGATGCTCGTAAGAAGAAATT-TTTAAATCC
127 CGAATTAATTTCTAATCAAATCGAAACAAAATTCAGATGCTCGTAAAAAG-AATTCCTTAAATCC
4231 AATGTGG-TTGAGATTTGGCACGATGAATA
191 AATGTGGCTT-AGATTTGGCACGATGAATA
4260 TAGATATTCT
Statistics
Matches: 195, Mismatches: 19, Indels: 12
0.86 0.08 0.05
Matches are distributed among these distances:
266 77 0.39
267 8 0.04
268 2 0.01
269 104 0.53
270 4 0.02
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.35
Consensus pattern (268 bp):
TTTGCAAAAACTGACCCGAAAATTTTTTATCCTCAATTCCTTGCCACAATACTAAGAAAAAATAT
ATAATTCAACACCAAAAGATTAAAGGGTTTTTCACGCTTCTAATAACGTTTTTCAATTTTTCGAA
TTAATTTCTAATCAAATCGAAACAAAATTCAGATGCTCGTAAAAAGAATTCCTTAAATCCAATGT
GGCTTAGATTTGGCACGATGAATACATATAATTTAAGGAGTCTTTACCCGAAAACCGCGATTTCG
GCTAAAAC
Found at i:4623 original size:325 final size:323
Alignment explanation
Indices: 4024--6476 Score: 2100
Period size: 325 Copynumber: 7.6 Consensus size: 323
4014 CCGAAAACCG
*
4024 CGATTTCGGCTAAAACTTTGCAAAAACTGACCCGAAAATTTTTTCCTCAATTCTTTGCCACATTA
1 CGATTTCGGCTAAAA-TTTGCAAAAACT-ACCCGAAAATTTTTTCCTCAATTCTTTGCCACAATA
* * ** *
4089 CTCAAAAAAAATATATAATTCAACAC-CAAATGATTAAAGGGTTTTTCACGCTTCTAATATCGTT
64 CTC-AAAAAAATATATAATTCAACGCTAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTT
* * * * * * *
4153 TTTCAATTATTTT-TCGAATTAATTTCTAATCATATCGAAACAAAATTCAGATGCTCGTAAGAAG
128 TTTCCATTTTTTTCTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAC
** * * *
4217 AAATTTTTAAATCCAATGTGGTTGAGATTTGG-CACGATGAATATAGATA-TTCTGAGGAG--TT
193 AAATCCTTAAATCCAATGTGGCTGAGATTTGGTTA-GATGAATATAGATATTTC-AAGGAGCCTT
* * * * * *
4278 TTTGCGCAAAAAATCATGCAAAATTTAGCCG-GGGCCCTAGAACGCGTTTTTAGCCAAAAACCG-
256 TATGC-C-AAAAATCATGCAAAACTGAGTCGAGGCCCCGA-AACGCGTTTTTAGCCAAAAACCGA
4341 TGGTACA
318 TGGTA-A
* **
4348 CGATTTTGGCTAAAATTTTGCAAAAACTAGCCCGAAAATTTTTTAATCAATTCTTTGCCACAATA
1 CGATTTCGGCTAAAA-TTTGCAAAAACTA-CCCGAAAATTTTTTCCTCAATTCTTTGCCACAATA
** * *
4413 CT-TTAAAAA-ATATAATTCAACGCTAAAAAAATTGAAGGGTTTTTCACGATTCTAATATTGTTT
64 CTCAAAAAAATATATAATTCAACGCTAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTT
* * *
4476 TTCCATTTTTTTCCTCTGAATTTATTTTTAATTAAATTGAAACAAGATTCAGATGCTCGTAAAAA
129 TTCCATTTTTTT-CTC-GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA
* * *
4541 CAAATCCTTAAATCCAATGTGGGTGACATTTGGTTAGATGAATATAGATATGTCAAGGAGCCTTT
192 CAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGCCTTT
* *
4606 ATGCCAAAAACCATGCAAAACTGAGTCGAGGCCCCGAAACGCGTATTTAGCCAAAAACCGTGATG
257 ATGCCAAAAATCATGCAAAACTGAGTCGAGGCCCCGAAACGCGTTTTTAGCCAAAAACC--GATG
4671 GT--
320 GTAA
* * * * *
4673 -G--TT-AG-TACACGATTTCGGCTAAAAACTGACCCGAAAAATATTTT-CTCAATTGTTTGCGA
1 CGATTTCGGCTA-A-AATTT--GC-AAAAACT-ACCCG-AAAATTTTTTCCTCAATTCTTTGCCA
* ** * *
4732 TAATACTCAGGAAAATATATAATTCAA-GAC-AATAAATATTGAAGCGTTTTTCACGCTTCTAAT
59 CAATACTCAAAAAAATATATAATTCAACG-CTAA-AAAAATTGAAGGGTTTTTCACGCTTCTAAT
* * * * * *
4795 ATAGTTTTTGCTTCTTTTTTTTC-CGAATTTATTTATAATTAAATCGAAACAAGATTTATATGCT
122 ATCGTTTTT-C--CATTTTTTTCTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCT
* *
4859 CGTAAAAACAAATCCTT-AATCCAATGTGGCTGGGATTTGGATCA-ATGAATATAGATATTTCAA
184 CGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGG-TTAGATGAATATAGATATTTCAA
** * * *
4922 GGAGTGTTTACGCCAAAAATCATGCAAAACTGAGTCGAGGCTCCGAAACACGTTTTTAGCC-AAA
248 GGAGCCTTTATGCCAAAAATCATGCAAAACTGAGTCGAGGCCCCGAAACGCGTTTTTAGCCAAAA
4986 ACCGTGATGGTACA
313 ACC--GATGGTA-A
* * *
5000 CGATTTCGGCTAAAA-CTG--------ACCCGAAAAATTTTTCCTCAATTCTTTGTCACAATACT
1 CGATTTCGGCTAAAATTTGCAAAAACTACCCGAAAATTTTTTCCTCAATTCTTTGCCACAATACT
*
5056 CAGAAAAATATATAATTCAACGCT-AAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTT
66 CAAAAAAATATATAATTCAACGCTAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTT
* * *
5120 CTATTTTTTTC-CGAATTTATTTTTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAA
131 CCATTTTTTTCTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAA
* *
5184 TCCTTAAATCCAATGTGGCT-AGAATTTGGTTCGATGAAAATAGATATTTCAAGGAGCCTTTATG
196 TCCTTAAATCCAATGTGGCTGAG-ATTTGGTTAGATGAATATAGATATTTCAAGGAGCCTTTATG
* * * * * * *
5248 CCAAAAACCGTGCAAAACTAAATCGAGGCCCCGAAACACGTTTTTACGCAAAAAACATGATGAGT
260 CCAAAAATCATGCAAAACTGAGTCGAGGCCCCGAAACGCGTTTTTA-GCCAAAAAC-CGATG-GT
5313 AAA
322 -AA
* ** * * *
5316 CGATTTCGACTAAAAACTG-----ACT---CAAAAATTTTTTTCTCAATTCTTTGCCACAATGCT
1 CGATTTCGGCTAAAATTTGCAAAAACTACCCGAAAATTTTTTCCTCAATTCTTTGCCACAATACT
** * * *
5373 CAGAAAAAATATATAATTCAA-TTTCAAAAATTTGAAGGGTTTTTCATGCTTCTAATATCGTTTT
66 CA-AAAAAATATATAATTCAACGCTAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTT
* *
5437 TCCATTTTATTTC-CGAATTAATTTCTAATTAAATCGAAACAAGATTCAGGTGCTCGTAAACA-A
130 TCCATTTT-TTTCTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACA
** * * * *
5500 AATCCCAAAATCCAATGTGGCT-AGGATTTGGATCGATGAATATACATATTTCAAGGAGACTTTA
194 AATCCTTAAATCCAATGTGGCTGA-GATTTGGTTAGATGAATATAGATATTTCAAGGAGCCTTTA
* * *
5564 GGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGAAACGCGTTTTTAGCC-AAAACCTGTGATG
258 TGCCAAAAATCATGCAAAACTGAGTCGAGGCCCCGAAACGCGTTTTTAGCCAAAAACC---GAT-
5628 GTTAGTATA
319 G---GTA-A
*
5637 CGATTTCGGCTAAAATTTTGCAAAAACTAACCCGAAATTTTTTTTCCTCAATTCTTTGCCACAAT
1 CGATTTCGGCTAAAA-TTTGCAAAAACT-ACCCGAAA-ATTTTTTCCTCAATTCTTTGCCACAAT
* * * * *
5702 ATTCAGAAAAAACATATAATTCAATGCCAAAAAAATTGAAGGCTTTTTCACGCTTCTAATATCGT
63 ACTCA-AAAAAATATATAATTCAACGCTAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGT
* * * * *
5767 TTTTCAATTGTTTTC-CGAATTAATTTCTAATTAAATCTAAACAAGATTCAGATACCCGTAAAAA
127 TTTTCCATTTTTTTCTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA
* ** * * * *
5831 GAAGCCCTTAAATCCAATGTGTCTGATATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTT
192 CAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGCCTTT
** * * *
5896 ACACCAAAAATTTATGCAAAACTGAGTCGGGGCCCCGCAACGCGTTTTTAGCCAAAAACCG--GG
257 ATGCCAAAAA-TCATGCAAAACTGAGTCGAGGCCCCGAAACGCGTTTTTAGCCAAAAACCGATGG
5959 CTAA
321 -TAA
* ** * * * *
5963 -AATTTTTG-TAAAAGTTG--------ACCCGAAAGA-TATTTCCTCAATT-TTTGGCTAAAATA
1 CGATTTCGGCTAAAATTTGCAAAAACTACCCGAAA-ATTTTTTCCTCAATTCTTT-GCCACAATA
* * * * * * * * **
6016 ATCATAAAAATATATGTATTTCAACGCCAGAAAGATTGAAGGGCTTTTGACATTTCTAATATCGT
64 CTCA-AAAAA-ATATATAATTCAACGCTAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGT
* * * *
6081 TTTTCCAATTTTTT-TCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCATAAAAA
127 TTTTCCATTTTTTTCTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA
** * * *
6145 CAAATCCTTAAATCCAATGTTACTGAGATTTGATTAGATGAATATAGATATATTTCAAGTAGTC-
192 CAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAG--ATATTTCAAGGAGCCT
* * * * * * * *
6209 TCAGAGCAAAAAATCATGCAAAATTGAGGT-GAGTCCCCGGAATGCGTTTTTAGCCAAAAACTGT
255 TTA-TGCCAAAAATCATGCAAAACTGA-GTCGAGGCCCCGAAACGCGTTTTTAGCCAAAAAC--C
6273 GATGGTTAGTTAGTTCA
316 GAT-G---G-TA----A
* * * * *
6290 CGATTTCGGCTAAAATTTTGCAAAAATTGACACGAAAGA-TTTCTCCTCAATT-TTTGGCTATAA
1 CGATTTCGGCTAAAA-TTTGCAAAAACT-ACCCGAAA-ATTTTTTCCTCAATTCTTT-GCCACAA
* * * * * *
6353 TACTCATAAAATTATATAATTTAATG-TCAAAAAGATTTG-AGGGCTTTTCACGCTAT-TAATAT
62 TACTCAAAAAAATATATAATTCAACGCT-AAAAA-AATTGAAGGGTTTTTCACGCT-TCTAATAT
* * * * * *
6415 TGTATTTCTTATTTTTTT-TCTAAATTAATTTCTAATTAAATCGAAATAAGATTTAGATGCTC
124 CGTTTTTC-CATTTTTTTCTC-GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTC
6477 AATTTTTTTA
Statistics
Matches: 1764, Mismatches: 250, Indels: 215
0.79 0.11 0.10
Matches are distributed among these distances:
312 3 0.00
313 92 0.05
314 234 0.13
315 48 0.03
316 93 0.05
317 84 0.05
318 162 0.09
319 51 0.03
320 4 0.00
321 36 0.02
322 53 0.03
323 9 0.01
324 111 0.06
325 242 0.14
326 114 0.06
327 16 0.01
328 11 0.01
329 15 0.01
330 6 0.00
331 6 0.00
332 97 0.05
333 103 0.06
334 40 0.02
335 6 0.00
337 38 0.02
338 17 0.01
339 73 0.04
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (323 bp):
CGATTTCGGCTAAAATTTGCAAAAACTACCCGAAAATTTTTTCCTCAATTCTTTGCCACAATACT
CAAAAAAATATATAATTCAACGCTAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTT
CCATTTTTTTCTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAA
TCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGCCTTTATGC
CAAAAATCATGCAAAACTGAGTCGAGGCCCCGAAACGCGTTTTTAGCCAAAAACCGATGGTAA
Found at i:6132 original size:965 final size:956
Alignment explanation
Indices: 4046--6195 Score: 2328
Period size: 965 Copynumber: 2.2 Consensus size: 956
4036 AAACTTTGCA
* * * * * * *
4046 AAAACTGACCCGAAAATTTTTTCCTCAATTCTTTGCCACATTACTCAAAAAAAATATATAATTCA
1 AAAACTGACCCGAAAAATATTTCCTCAATTCTTTGGCAAAATAATC-AGAAAAATATATAATTCA
* ** * * * *
4111 ACACCAAATGATTAAAGGGTTTTTCACGCTTCTAATATCGTTTTTCAATTATTTTT-CGAATTAA
65 ACGCCAAAAAATTGAAGGGCTTTTCACACTTCTAATATCGTTTTTCAATT-TTTTTCCAAATTAA
* * * * * * * ** **
4175 TTTCTAATCATATCGAAACAAAATTCAGATGCTCGTAAGAAGAAATTTTTAAATCCAATGTGGTT
129 TTTCTAATTAAATCGAAACAAGATTCAGATACTCATAAAAACAAATCCTTAAATCCAATGTGACT
** * * * * *
4240 GAGATTTG-GCACGATGAATATAGATA-TTCTGAGGAG--TTTTTGCGCAAAAAATCATGCAAAA
194 GAGATTTGATTA-GATGAAAATAGATATTTC-AAGGAGCCTTTATGC-C-AAAAACCGTGCAAAA
* * ** * * * * * * * *
4301 TTTAGCCG-GGGCCCTAGAACGCGTTTTTA-GCCAAAAAC-CG-TG-GTACACGATTTTGGCTAA
255 CTAAATCGAGGCCCCGA-AACACGTTTTTACGCAAAAAACATGATGAGTAAACGATTTCGACTAA
** * **
4361 AATTTTGCAAAAACTAGCCCGAAAATTTTTTAATCAATTCTTTGCCACAATACTTTAAAAAATAT
319 AA-ACTG-----ACT----CAAAAATTTTTTAATCAATTCTTTGCCACAATACTGAAAAAAATAT
*
4426 AATTCAACGCTAAAAAAATTGAAGGGTTTTTCACGATTCTAATATTGTTTTTCCATTTTTTTCCT
374 AATTCAACGCTAAAAAAATTGAAGGGTTTTTCACGATTCTAATATCGTTTTTCCATTTTTTTCCT
* * * **
4491 CTGAATTTATTTTTAATTAAATTGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCC
439 CTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCCAAAATCC
* * * * *
4556 AATGTGGGTGACATTTGGTTAGATGAATATAGATATGTCAAGGAGCCTTTATGCCAAAAACCATG
504 AATGTGGCTGACATTTGGATAGATGAATATACATATGTCAAGGAGACTTTAGGCCAAAAACCATG
*
4621 CAAAACTGAGTCGAGGCCCCGAAACGCGTATTTAGCCAAAAACCGTGATGGTGTTAGTACACGAT
569 CAAAACTGAGCCGAGGCCCCGAAACGCGTATTTAGCCAAAAACCGTGATGGTGTTAGTACACGAT
* * * * * *
4686 TTCGGCTAAAAACTGACCCGAAAAATATTTTCTCAATTGTTTGCGATAATACTCAGGAAAATATA
634 TTCGGCTAAAAACTAACCCGAAAAATATTTTCTCAATTCTTTGCCACAATACTCAGAAAAACATA
* ** *
4751 TAATTCAAGACAATAAATATTGAAGCGTTTTTCACGCTTCTAATATAGTTTTTGCTTCTTTTTTT
699 TAATTCAAGACAATAAAAATTGAAGCGTTTTTCACGCTTCTAATATAGTTTTTGC-TAATTGTTT
* * * * * *
4816 TCCGAATTTATTTATAATTAAATCGAAACAAGATTTATATGCTCGTAAAAACAAATCCTTAATCC
763 TCCGAATTAATTTATAATTAAATCGAAACAAGATTCAGATACCCGTAAAAACAAACCCTTAATCC
* * *
4881 AATGTGGCTGGGATTTGGATCAATGAATATAGATATTTCAAGGAGTGTTTACGCCAAAAATCATG
828 AATGTGGCTGAGATTTGGATCAATGAATATAGATATTTCAAGGAGTCTTTACACCAAAAATCATG
* * *
4946 CAAAACTGAGTCGAGGCTCCGAAACACGTTTTTAGCCAAAACCGTGATGGTACACGATTTCGGCT
893 CAAAACTGAGTCGAGGCCCCGAAACACGTTTTTAGCCAAAACCGTGA-GCTACACAATTTCGGCT
* * * *
5011 AAAACTGACCCGAAAAATTTTTCCTCAATTCTTTGTCACAATACTCAGAAAAATATATAATTCAA
1 AAAACTGACCCGAAAAATATTTCCTCAATTCTTTGGCAAAATAATCAGAAAAATATATAATTCAA
* * * * * *
5076 CGCTAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCTATTTTTTTCCGAATTTATT
66 CGCCAAAAAATTGAAGGGCTTTTCACACTTCTAATATCGTTTTTCAATTTTTTTCCAAATTAATT
* * * *
5141 TTTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCT-A
131 TCTAATTAAATCGAAACAAGATTCAGATACTCATAAAAACAAATCCTTAAATCCAATGTGACTGA
* *
5205 GAATTTGGTTCGATGAAAATAGATATTTCAAGGAGCCTTTATGCCAAAAACCGTGCAAAACTAAA
196 G-ATTTGATTAGATGAAAATAGATATTTCAAGGAGCCTTTATGCCAAAAACCGTGCAAAACTAAA
5270 TCGAGGCCCCGAAACACGTTTTTACGCAAAAAACATGATGAGTAAACGATTTCGACTAAAAACTG
260 TCGAGGCCCCGAAACACGTTTTTACGCAAAAAACATGATGAGTAAACGATTTCGACTAAAAACTG
** * ** *
5335 ACTCAAAAATTTTTTTCTCAATTCTTTGCCACAATGCTCAGAAAAAATATATAATTCAA-TTTCA
325 ACTCAAAAATTTTTTAATCAATTCTTTGCCACAATACT--GAAAAAA-ATATAATTCAACGCTAA
* * *
5399 AAAATTTGAAGGGTTTTTCATGCTTCTAATATCGTTTTTCCATTTTATTT-C-C-GAATTAATTT
387 AAAAATTGAAGGGTTTTTCACGATTCTAATATCGTTTTTCCATTTT-TTTCCTCTGAATTAATTT
* *
5461 CTAATTAAATCGAAACAAGATTCAGGTGCTCGTAAACA-AAATCCCAAAATCCAATGTGGCT-AG
451 CTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCCAAAATCCAATGTGGCTGA-
* * * *
5524 GATTTGGATCGATGAATATACATATTTCAAGGAGACTTTAGGCCAAAAATCATGCAAAACTGAGC
515 CATTTGGATAGATGAATATACATATGTCAAGGAGACTTTAGGCCAAAAACCATGCAAAACTGAGC
* * *
5589 CGGGGCCCCGAAACGCGTTTTTAGCC-AAAACCTGTGAT-G-GTTAGTATACGATTTCGGCTAAA
580 CGAGGCCCCGAAACGCGTATTTAGCCAAAAACC-GTGATGGTGTTAGTACACGATTTCGGC----
** * *
5651 ATTTTGCAAAAACTAACCCGAAATTTTTTTTCCTCAATTCTTTGCCACAATATTCAGAAAAAACA
640 ----T--AAAAACTAACCCGAAAAATATTTT-CTCAATTCTTTGCCACAATACTCAG-AAAAACA
* *
5716 TATAATTCAATGCCAA-AAAAATTGAAG-GCTTTTTCACGCTTCTAATATCGTTTTT-C-AATTG
697 TATAATTCAA-GACAATAAAAATTGAAGCG-TTTTTCACGCTTCTAATATAGTTTTTGCTAATTG
* * * *
5777 TTTTCCGAATTAATTTCTAATTAAATCTAAACAAGATTCAGATACCCGTAAAAAGAAGCCCTTAA
760 TTTTCCGAATTAATTTATAATTAAATCGAAACAAGATTCAGATACCCGTAAAAACAAACCCTT-A
* * * *
5842 ATCCAATGTGTCTGATATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACACCAAAAAT
824 ATCCAATGTGGCTGAGATTTGGATCAATGAATATAGATATTTCAAGGAGTCTTTACACCAAAAA-
* * * *
5907 TTATGCAAAACTGAGTCGGGGCCCCGCAACGCGTTTTTAGCCAAAAACCG-G-GCTA-A-AATTT
888 TCATGCAAAACTGAGTCGAGGCCCCGAAACACGTTTTTAGCC-AAAACCGTGAGCTACACAATTT
**
5968 TTG-T
952 CGGCT
* * * *
5972 AAAAGTTGACCCGAAAGATATTTCCTCAATT-TTTGGCTAAAATAATCATAAAAATATATGTATT
1 AAAA-CTGACCCGAAAAATATTTCCTCAATTCTTTGGC-AAAATAATCAGAAAAATATA--TAAT
* * *
6036 TCAACGCCAGAAAGATTGAAGGGCTTTTGACATTTCTAATATCGTTTTTCCAATTTTTTT-CAAA
62 TCAACGCCA-AAAAATTGAAGGGCTTTTCACACTTCTAATATCGTTTTT-CAATTTTTTTCCAAA
6100 TTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCATAAAAACAAATCCTTAAATCCAATGT
125 TTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCATAAAAACAAATCCTTAAATCCAATGT
* *
6165 TACTGAGATTTGATTAGATGAATATAGATAT
190 GACTGAGATTTGATTAGATGAAAATAGATAT
6196 ATTTCAAGTA
Statistics
Matches: 1002, Mismatches: 142, Indels: 82
0.82 0.12 0.07
Matches are distributed among these distances:
955 18 0.02
956 8 0.01
957 105 0.10
958 74 0.07
959 1 0.00
960 50 0.05
961 24 0.02
962 48 0.05
963 9 0.01
964 244 0.24
965 260 0.26
966 79 0.08
967 61 0.06
968 21 0.02
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (956 bp):
AAAACTGACCCGAAAAATATTTCCTCAATTCTTTGGCAAAATAATCAGAAAAATATATAATTCAA
CGCCAAAAAATTGAAGGGCTTTTCACACTTCTAATATCGTTTTTCAATTTTTTTCCAAATTAATT
TCTAATTAAATCGAAACAAGATTCAGATACTCATAAAAACAAATCCTTAAATCCAATGTGACTGA
GATTTGATTAGATGAAAATAGATATTTCAAGGAGCCTTTATGCCAAAAACCGTGCAAAACTAAAT
CGAGGCCCCGAAACACGTTTTTACGCAAAAAACATGATGAGTAAACGATTTCGACTAAAAACTGA
CTCAAAAATTTTTTAATCAATTCTTTGCCACAATACTGAAAAAAATATAATTCAACGCTAAAAAA
ATTGAAGGGTTTTTCACGATTCTAATATCGTTTTTCCATTTTTTTCCTCTGAATTAATTTCTAAT
TAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCCAAAATCCAATGTGGCTGACATTTG
GATAGATGAATATACATATGTCAAGGAGACTTTAGGCCAAAAACCATGCAAAACTGAGCCGAGGC
CCCGAAACGCGTATTTAGCCAAAAACCGTGATGGTGTTAGTACACGATTTCGGCTAAAAACTAAC
CCGAAAAATATTTTCTCAATTCTTTGCCACAATACTCAGAAAAACATATAATTCAAGACAATAAA
AATTGAAGCGTTTTTCACGCTTCTAATATAGTTTTTGCTAATTGTTTTCCGAATTAATTTATAAT
TAAATCGAAACAAGATTCAGATACCCGTAAAAACAAACCCTTAATCCAATGTGGCTGAGATTTGG
ATCAATGAATATAGATATTTCAAGGAGTCTTTACACCAAAAATCATGCAAAACTGAGTCGAGGCC
CCGAAACACGTTTTTAGCCAAAACCGTGAGCTACACAATTTCGGCT
Found at i:6372 original size:651 final size:644
Alignment explanation
Indices: 4045--6472 Score: 2037
Period size: 651 Copynumber: 3.8 Consensus size: 644
4035 AAAACTTTGC
* * * * * *
4045 AAAAACTGACCCGAAAATTTTTTCCTCAATTCTTTGCCACATTACTCAAAAAAAATATATAATTC
1 AAAAACTGACCCAAAAATTATTTCCTCAATTCTTTGCCAAAATAATCAGAAAAAATATATAATTC
* * * * * * *
4110 AACACCAAATGA-TTAAAGGGTTTTTCACGCTTCTAATATCGTTTTTCAATTATT-TTT-CGAAT
66 AACGCCAAA-AATTTGAAGGGTTTTACA-TCTTCTAATATCGTTTTTCCATT-TTATTTCCAAAT
* * * * * * ****
4172 TAATTTCTAATCATATCGAAACAAAATTCAGATGCTCGTAAGAAGAAATTTTTAAATCCAATGTG
128 TAATTTCTAATTAAATCGAAACAAGATTCAGATACTCATAA-AAAAAATCCCAAAATCCAATGTG
* * * * * * **
4237 -GTTGAGATTTGGCA-CGATGAATATAGATA-TTCTGAGGAG-TTTTTGCGCAAAAAATCATGCA
192 ACTAG-GATTTGG-ATAGATGAATATACATATTTC-AAGGAGACTTCAG-GCAAAAAATCATGCA
* * * * * * *
4298 AAATTTAGCCG-GGGCCCTAGAACGCGTTTTTAGCCAAAAAC--CG-T-G---GTACACGATTTT
253 AAACTGAGCCGAGGCCCCGA-AACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTATACGATTTC
* ** * **
4355 GGCTAAAATTTTGCAAAAACT-AGCCCGAAAATTTTTTAATCAATTCTTTGCCACAATACT-TTA
317 GGCTAAAATTTTGCAAAAACTGA-CCCGAAAAATTTTTCCTCAATTCTTTGGCACAATACTCAAA
* * * * *
4418 AAAA-ATATAATTCAACGCTAAAAAAATTGAAGGGTTTTTCACGATTCTAATATTGTTTTTCCAT
381 AAAATATATAATTCAATGC-AAAAAAATTGAAGGCTTTTTCACGCTTCTAATATCGTTTTTCAAT
* * * * * *
4482 TTTTTTCCTCTGAATTTATTTTTAATTAAATTGAAACAAGATTCAGATGCTCGTAAAAACAAATC
445 TTTTTT-C-C-GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACCCGTAAAAACAAACC
* * * * **
4547 CTTAAATCCAATGTGGGT-GACATTTGGTTAGATGAATATAGATATGTCAAGGAGCCTTTATGCC
507 CTTAAATCCAATGTGGCTAGA-ATTTGGTTCGATGAAAATAGATATTTCAAGGAGCCTTTACACC
* * * * *
4611 AAAAACCATGCAAAACTGAGTCGAGGCCCCGAAACGCGTATTTA-GCCAAAAAC-CGTGATGGTG
571 AAAAACCATGCAAAACTAAATCGAGGCCCCGAAACACGTTTTTACGCAAAAAACAC--GA----G
* *
4674 TTAGTACACGATTTCGGCT
630 --AGTAAAC-ATTTC-GAT
* * * * * *
4693 AAAAACTGACCCGAAAAA-TATTTTCTCAATTGTTTGCGATAATACTCAG-GAAAATATATAATT
1 AAAAACTGACCC-AAAAATTATTTCCTCAATTCTTTGCCAAAATAATCAGAAAAAATATATAATT
* * * * * *
4756 CAA-GACAATAAATATTGAAGCGTTTTTCACGCTTCTAATATAGTTTTTGCTTC-TTTTTTTTCC
65 CAACGCCAA-AAAT-TTGAAGGGTTTTACA-TCTTCTAATATCGTTTTT-C--CATTTTATTTCC
* * * * * * * **
4819 GAATTTATTTATAATTAAATCGAAACAAGATTTATATGCTCGTAAAAACAAAT-CCTTAATCCAA
124 AAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCATAAAAA-AAATCCCAAAATCCAA
* * * ** * * *
4883 TGTGGCTGGGATTTGGATCA-ATGAATATAGATATTTCAAGGAGTGTTTACGCCAAAAATCATGC
188 TGTGACTAGGATTTGGAT-AGATGAATATACATATTTCAAGGAGACTTCAGGCAAAAAATCATGC
* * * * *
4947 AAAACTGAGTCGAGGCTCCGAAACACGTTTTTAGCC-AAAACCGTGAT-G---GTACACGATTTC
252 AAAACTGAGCCGAGGCCCCGAAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTATACGATTTC
* *
5007 GGC--------T---AAAACTGACCCGAAAAATTTTTCCTCAATTCTTTGTCACAATACTCAGAA
317 GGCTAAAATTTTGCAAAAACTGACCCGAAAAATTTTTCCTCAATTCTTTGGCACAATACTCAAAA
* * * *
5061 AAATATATAATTCAACGCTAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCTATTT
382 AAATATATAATTCAATGCAAAAAAATTGAAGGCTTTTTCACGCTTCTAATATCGTTTTTCAATTT
* * * * *
5126 TTTTCCGAATTTATTTTTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAA
447 TTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACCCGTAAAAACAAACCCTTAA
**
5191 ATCCAATGTGGCTAGAATTTGGTTCGATGAAAATAGATATTTCAAGGAGCCTTTATGCCAAAAAC
512 ATCCAATGTGGCTAGAATTTGGTTCGATGAAAATAGATATTTCAAGGAGCCTTTACACCAAAAAC
* *
5256 CGTGCAAAACTAAATCGAGGCCCCGAAACACGTTTTTACGCAAAAAACATGATGAGTAAACGATT
577 CATGCAAAACTAAATCGAGGCCCCGAAACACGTTTTTACGCAAAAAACACGA-GAGTAAAC-ATT
5321 TCGACT
640 TCGA-T
* * * * **
5327 AAAAACTGACTCAAAAATTTTTTTCTCAATTCTTTGCCACAATGCTCAGAAAAAATATATAATTC
1 AAAAACTGACCCAAAAATTATTTCCTCAATTCTTTGCCAAAATAATCAGAAAAAATATATAATTC
*** * *
5392 AATTTCAAAAATTTGAAGGGTTTTTCATGCTTCTAATATCGTTTTTCCATTTTATTTCCGAATTA
66 AACGCCAAAAATTTGAAGGGTTTTACAT-CTTCTAATATCGTTTTTCCATTTTATTTCCAAATTA
* * * * *
5457 ATTTCTAATTAAATCGAAACAAGATTCAGGTGCTCGTAAACAAAATCCCAAAATCCAATGTGGCT
130 ATTTCTAATTAAATCGAAACAAGATTCAGATACTCATAAAAAAAATCCCAAAATCCAATGTGACT
* * *
5522 AGGATTTGGATCGATGAATATACATATTTCAAGGAGACTTTAGGCCAAAAATCATGCAAAACTGA
195 AGGATTTGGATAGATGAATATACATATTTCAAGGAGACTTCAGGCAAAAAATCATGCAAAACTGA
* *
5587 GCCGGGGCCCCGAAACGCGTTTTTAGCCAAAACCTGTGATGGTTAGTATACGATTTCGGCTAAAA
260 GCCGAGGCCCCGAAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTATACGATTTCGGCTAAAA
* ** * * *
5652 TTTTGCAAAAACTAACCCGAAATTTTTTTTCCTCAATTCTTTGCCACAATATTCAGAAAAAACAT
325 TTTTGCAAAAACTGACCCGAAA-AATTTTTCCTCAATTCTTTGGCACAATACTCA-AAAAAATAT
*
5717 ATAATTCAATGCCAAAAAAATTGAAGGCTTTTTCACGCTTCTAATATCGTTTTTCAATTGTTTTC
388 ATAATTCAATG-CAAAAAAATTGAAGGCTTTTTCACGCTTCTAATATCGTTTTTCAATTTTTTTC
* * *
5782 CGAATTAATTTCTAATTAAATCTAAACAAGATTCAGATACCCGTAAAAAGAAGCCCTTAAATCCA
452 CGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACCCGTAAAAACAAACCCTTAAATCCA
* * * **
5847 ATGTGTCT-GATATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACACCAAAAATTTAT
517 ATGTGGCTAGA-ATTTGGTTCGATGAAAATAGATATTTCAAGGAGCCTTTACACCAAAAA-CCAT
* * * * * * *
5911 GCAAAACTGAGTCGGGGCCCCGCAACGCGTTTTTA-GCCAAAAAC-CG-G-GCTAAA-ATTTTTG
580 GCAAAACTAAATCGAGGCCCCGAAACACGTTTTTACGCAAAAAACACGAGAG-TAAACA-TTTCG
5971 -T
643 AT
** * * * * *
5972 AAAAGTTGACCCGAAAGA-TATTTCCTCAATT-TTTGGCTAAAATAATCATAAAAATATATGTAT
1 AAAAACTGACCC-AAAAATTATTTCCTCAATTCTTT-GCCAAAATAATCAGAAAAA-ATATATAA
6035 TTCAACGCCAGAAAGA-TTGAAGGGCTTTTGACAT-TTCTAATATCGTTTTTCCAATTTT-TTT-
63 TTCAACGCCA-AAA-ATTTGAAGGG-TTTT-ACATCTTCTAATATCGTTTTTCC-ATTTTATTTC
**
6096 CAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCATAAAAACAAATCCTTAAATCCA
123 CAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATACTCATAAAAA-AAATCCCAAAATCCA
* * * *
6161 ATGTTACT-GAGATTT-GATTAGATGAATATAGATATATTTCAAGTAGTC-TCAGAGCAAAAAAT
187 ATGTGACTAG-GATTTGGA-TAGATGAATAT--ACATATTTCAAGGAGACTTCAG-GCAAAAAAT
* ** * * *
6223 CATGCAAAATTGAGGTGAGTCCCCGGAATGCGTTTTTAGCCAAAAACTGTGATGGTTAGTTAGTT
247 CATGCAAAACTGAGCCGAGGCCCCGAAACGCGTTTTTAGCCAAAAACTGTGATGGTTAG-TA--T
* * * * *
6288 CACGATTTCGGCTAAAATTTTGCAAAAATTGACACGAAAGATTTCTCCTCAATT-TTTGGCTATA
309 -ACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAAAATTTTTCCTCAATTCTTTGGC-ACA
* * * * *
6352 ATACTCATAAAATTATATAATTTAATGTCAAAAAGATTTGAGGGC-TTTTCACGCTAT-TAATAT
372 ATACTCAAAAAAATATATAATTCAATG-CAAAAA-AATTGAAGGCTTTTTCACGCT-TCTAATAT
* * * ** * *
6415 TGTATTTCTTATTTTTTTTCTAAATTAATTTCTAATTAAATCGAAATAAGATTTAGAT
434 CGT-TTT-TCAATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGAT
6473 GCTCAATTTT
Statistics
Matches: 1498, Mismatches: 203, Indels: 153
0.81 0.11 0.08
Matches are distributed among these distances:
631 5 0.00
632 149 0.10
633 16 0.01
634 81 0.05
635 20 0.01
636 5 0.00
637 14 0.01
639 151 0.10
640 11 0.01
641 40 0.03
642 53 0.04
643 14 0.01
644 4 0.00
645 36 0.02
646 69 0.05
647 88 0.06
648 99 0.07
649 117 0.08
650 102 0.07
651 267 0.18
652 80 0.05
653 77 0.05
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (644 bp):
AAAAACTGACCCAAAAATTATTTCCTCAATTCTTTGCCAAAATAATCAGAAAAAATATATAATTC
AACGCCAAAAATTTGAAGGGTTTTACATCTTCTAATATCGTTTTTCCATTTTATTTCCAAATTAA
TTTCTAATTAAATCGAAACAAGATTCAGATACTCATAAAAAAAATCCCAAAATCCAATGTGACTA
GGATTTGGATAGATGAATATACATATTTCAAGGAGACTTCAGGCAAAAAATCATGCAAAACTGAG
CCGAGGCCCCGAAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTATACGATTTCGGCTAAAAT
TTTGCAAAAACTGACCCGAAAAATTTTTCCTCAATTCTTTGGCACAATACTCAAAAAAATATATA
ATTCAATGCAAAAAAATTGAAGGCTTTTTCACGCTTCTAATATCGTTTTTCAATTTTTTTCCGAA
TTAATTTCTAATTAAATCGAAACAAGATTCAGATACCCGTAAAAACAAACCCTTAAATCCAATGT
GGCTAGAATTTGGTTCGATGAAAATAGATATTTCAAGGAGCCTTTACACCAAAAACCATGCAAAA
CTAAATCGAGGCCCCGAAACACGTTTTTACGCAAAAAACACGAGAGTAAACATTTCGAT
Found at i:14067 original size:18 final size:18
Alignment explanation
Indices: 14030--14086 Score: 55
Period size: 20 Copynumber: 3.1 Consensus size: 18
14020 AAATAATTAA
* *
14030 AAAGGTAG-TTTATGTTT
1 AAAGGTAGTTTTTTTTTT
14047 AAA-GTAGTTTTCTTTTTT
1 AAAGGTAGTTTT-TTTTTT
14065 AAATGGGTAGTTTTTTTTTT
1 AAA--GGTAGTTTTTTTTTT
14085 AA
1 AA
14087 TTATATAGAC
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
16 4 0.12
17 6 0.18
18 7 0.21
20 8 0.24
21 8 0.24
ACGTcount: A:0.26, C:0.02, G:0.18, T:0.54
Consensus pattern (18 bp):
AAAGGTAGTTTTTTTTTT
Found at i:20061 original size:7 final size:7
Alignment explanation
Indices: 20049--20082 Score: 50
Period size: 7 Copynumber: 4.6 Consensus size: 7
20039 CCTTCCTCTC
20049 ATATTAT
1 ATATTAT
20056 ATATTAT
1 ATATTAT
20063 ATATTAGAT
1 ATATT--AT
20072 ATATTAT
1 ATATTAT
20079 ATAT
1 ATAT
20083 AGGAGTAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
7 18 0.72
9 7 0.28
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (7 bp):
ATATTAT
Found at i:50723 original size:36 final size:36
Alignment explanation
Indices: 50671--50742 Score: 126
Period size: 36 Copynumber: 2.0 Consensus size: 36
50661 CATGGTTGTT
*
50671 TGCTTTATGCATGCAGCACTAGTTGTACAAAGTCGA
1 TGCTATATGCATGCAGCACTAGTTGTACAAAGTCGA
*
50707 TGCTATATGCATGCAGCACTAGTTGTACAAATTCGA
1 TGCTATATGCATGCAGCACTAGTTGTACAAAGTCGA
50743 CATCACTTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.29, C:0.19, G:0.21, T:0.31
Consensus pattern (36 bp):
TGCTATATGCATGCAGCACTAGTTGTACAAAGTCGA
Found at i:56765 original size:2 final size:2
Alignment explanation
Indices: 56758--56789 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
56748 ATGTGCATGC
56758 AT AT AT 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 AT AT AT
56790 GCATGAGTCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:65662 original size:16 final size:16
Alignment explanation
Indices: 65637--65667 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
65627 CATCTGTTTT
65637 TTTATCCCAAATTCTA
1 TTTATCCCAAATTCTA
*
65653 TTTATTCCAAATTCT
1 TTTATCCCAAATTCT
65668 GCAAAGTCTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.23, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTATCCCAAATTCTA
Found at i:67959 original size:14 final size:14
Alignment explanation
Indices: 67940--67973 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
67930 TTTTATAATT
67940 ATTTTATTTTTACC
1 ATTTTATTTTTACC
*
67954 ATTTTATTTTTACT
1 ATTTTATTTTTACC
67968 ATTTTA
1 ATTTTA
67974 ATTTAAAAGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.68
Consensus pattern (14 bp):
ATTTTATTTTTACC
Found at i:68745 original size:8 final size:8
Alignment explanation
Indices: 68732--68757 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
68722 TGATGACTAG
68732 TATATCTA
1 TATATCTA
68740 TATATCTA
1 TATATCTA
68748 TATATCTA
1 TATATCTA
68756 TA
1 TA
68758 GTACTTTAAA
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:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (8 bp):
TATATCTA
Found at i:69316 original size:13 final size:13
Alignment explanation
Indices: 69298--69347 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
69288 GTAACTAATT
69298 AATTTCCTTTTGA
1 AATTTCCTTTTGA
**
69311 AATTTCCTTTAAAA
1 AATTTCCTTT-TGA
**
69325 AAAATCCTTTTGA
1 AATTTCCTTTTGA
69338 AATTTCCTTT
1 AATTTCCTTT
69348 AAAAAAAATC
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
13 19 0.68
14 9 0.32
ACGTcount: A:0.32, C:0.16, G:0.04, T:0.48
Consensus pattern (13 bp):
AATTTCCTTTTGA
Found at i:69332 original size:27 final size:27
Alignment explanation
Indices: 69302--69365 Score: 128
Period size: 27 Copynumber: 2.4 Consensus size: 27
69292 CTAATTAATT
69302 TCCTTTTGAAATTTCCTTTAAAAAAAA
1 TCCTTTTGAAATTTCCTTTAAAAAAAA
69329 TCCTTTTGAAATTTCCTTTAAAAAAAA
1 TCCTTTTGAAATTTCCTTTAAAAAAAA
69356 TCCTTTTGAA
1 TCCTTTTGAA
69366 TTAGTAAAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.42
Consensus pattern (27 bp):
TCCTTTTGAAATTTCCTTTAAAAAAAA
Found at i:69334 original size:14 final size:14
Alignment explanation
Indices: 69315--69361 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
69305 TTTTGAAATT
69315 TCCTTTAAAAAAAA
1 TCCTTTAAAAAAAA
** **
69329 TCCTTT-TGAAATT
1 TCCTTTAAAAAAAA
69342 TCCTTTAAAAAAAA
1 TCCTTTAAAAAAAA
69356 TCCTTT
1 TCCTTT
69362 TGAATTAGTA
Statistics
Matches: 24, Mismatches: 8, Indels: 2
0.71 0.24 0.06
Matches are distributed among these distances:
13 9 0.38
14 15 0.62
ACGTcount: A:0.40, C:0.17, G:0.02, T:0.40
Consensus pattern (14 bp):
TCCTTTAAAAAAAA
Found at i:70611 original size:2 final size:2
Alignment explanation
Indices: 70604--70631 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
70594 CAAATAGAAC
70604 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.