Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014129.1 Corchorus olitorius cultivar O-4 contig14162, 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: 71340
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:8501 original size:19 final size:19
Alignment explanation
Indices: 8477--8517 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
8467 TGATATTCAT
*
8477 TCCAAGTTTTGTAATTAAC
1 TCCAAGTTCTGTAATTAAC
*
8496 TCCAAGTTCTGTAATTCAC
1 TCCAAGTTCTGTAATTAAC
8515 TCC
1 TCC
8518 TAGCTCACTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.27, C:0.24, G:0.10, T:0.39
Consensus pattern (19 bp):
TCCAAGTTCTGTAATTAAC
Found at i:8830 original size:29 final size:29
Alignment explanation
Indices: 8798--8856 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
8788 TGTGTTTGGA
8798 AGCTCATATCTTCAGTAGATGTATCTGAT
1 AGCTCATATCTTCAGTAGATGTATCTGAT
8827 AGCTCATATCTTCAGTAGATGTATCTGAT
1 AGCTCATATCTTCAGTAGATGTATCTGAT
8856 A
1 A
8857 TACAAATTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (29 bp):
AGCTCATATCTTCAGTAGATGTATCTGAT
Found at i:24247 original size:76 final size:76
Alignment explanation
Indices: 24145--24290 Score: 274
Period size: 76 Copynumber: 1.9 Consensus size: 76
24135 AAGTTTGATG
*
24145 TTCTAGTTACATCTACAATTTTTTTTTAAAAAAAGCATATTAATTTATGAAAATGTTTACAATTA
1 TTCTAGTTACATCGACAATTTTTTTTTAAAAAAAGCATATTAATTTATGAAAATGTTTACAATTA
24210 AATTCCCTCCC
66 AATTCCCTCCC
*
24221 TTCTAGTTACATCGACAATTTTTTTTTTAAAAAAGCATATTAATTTATGAAAATGTTTACAATTA
1 TTCTAGTTACATCGACAATTTTTTTTTAAAAAAAGCATATTAATTTATGAAAATGTTTACAATTA
24286 AATTC
66 AATTC
24291 TCTCGGGGAG
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
76 68 1.00
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.43
Consensus pattern (76 bp):
TTCTAGTTACATCGACAATTTTTTTTTAAAAAAAGCATATTAATTTATGAAAATGTTTACAATTA
AATTCCCTCCC
Found at i:25907 original size:12 final size:12
Alignment explanation
Indices: 25890--25914 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
25880 ATACAAAGAT
25890 ACTCAGAGAGAA
1 ACTCAGAGAGAA
25902 ACTCAGAGAGAA
1 ACTCAGAGAGAA
25914 A
1 A
25915 GAGAACCTGG
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:0.52, C:0.16, G:0.24, T:0.08
Consensus pattern (12 bp):
ACTCAGAGAGAA
Found at i:27469 original size:6 final size:6
Alignment explanation
Indices: 27460--27485 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
27450 GGAAGAATAG
27460 GAATCA GAATCA GAATCA GAATCA GA
1 GAATCA GAATCA GAATCA GAATCA GA
27486 GTCGGAGCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.19, T:0.15
Consensus pattern (6 bp):
GAATCA
Found at i:30083 original size:21 final size:21
Alignment explanation
Indices: 30054--30102 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
30044 TAAACAAAAC
30054 AAATACTGCATGCCCTACCTAA
1 AAAT-CTGCATGCCCTACCTAA
30076 AAATCTGCATGCCCTACCTAA
1 AAATCTGCATGCCCTACCTAA
30097 AAATCT
1 AAATCT
30103 ACGAAAATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.37, C:0.31, G:0.08, T:0.24
Consensus pattern (21 bp):
AAATCTGCATGCCCTACCTAA
Found at i:30680 original size:64 final size:64
Alignment explanation
Indices: 30609--30733 Score: 160
Period size: 64 Copynumber: 2.0 Consensus size: 64
30599 ACTTATTTTT
* * ** *
30609 ATCATTCACAAAACTCAATTGGAGATTTTACTTAAAATATATTGAACTTCCTCAACTCAATTTC
1 ATCATTCACAAAACTCAACTCGAGACCTTACTTAAAATACATTGAACTTCCTCAACTCAATTTC
* * ** *
30673 ATCATTCACAAAACTCGACTCGAGACCTTATTTAAGGTACATTGAACTTCCTCGACTCAAT
1 ATCATTCACAAAACTCAACTCGAGACCTTACTTAAAATACATTGAACTTCCTCAACTCAAT
30734 CCAATTGGTG
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
64 51 1.00
ACGTcount: A:0.35, C:0.23, G:0.09, T:0.33
Consensus pattern (64 bp):
ATCATTCACAAAACTCAACTCGAGACCTTACTTAAAATACATTGAACTTCCTCAACTCAATTTC
Found at i:60800 original size:322 final size:323
Alignment explanation
Indices: 60300--63730 Score: 2766
Period size: 322 Copynumber: 10.5 Consensus size: 323
60290 CAAGGAATCT
* * * **
60300 CGGAATGCGTTTTTAGTCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTAACCCGA
1 CGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTTAAAACTTGCCCGA
* * *
60365 AACGTTTTTTTCTCAATTTTTTGCCACAATACTCAGAAGAAACATATAATTCAACGCCACAAAA-
66 AAAG-TTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCA-AAAAG
* * * * *
60429 ATTGACGGGTTTTTCACGTTTCTAATATCATTTTTCCA--TTTTTTCCGAATTAATTTTTAATTA
129 ATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTTCCGAATTAATTTATAATTA
** ** * *
60492 TTTCGAAACAAGATTCAGATATTCGTAAAAACAAATCTTTAAATCCATTGTGGCTGACATTTGGT
194 AATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCTTTAAATCCAATGTGGCTGAGATTTGGT
* * * ** *
60557 TCA-ATGAATATAGACATTTGAAGGAGT-TTT-TGCACCAAAAATCTTGCAAATTTGAGCCGGGG
259 T-AGATGAATATAGATATTTCAAGGAGTCTTTCTG--CCAAAAATCATGCAAAACTGAGTCGGGG
60619 CTC
321 CTC
*
60622 CGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTTAAAACTTGTCCGA
1 CGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTTAAAACTTGCCCGA
* * * **
60687 AAAGTTTTTTCTCAATTTTTTG-CAAAATATTTAGAATTAATATATAATTCAACGCCAAAAAGAT
66 AAAGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGAT
* * * * * * * *
60751 TGACGGACTTTTCATGCTTTTAATATCGTTTTCCCATTTTCTATCCGAATTAATTTCTAATTAAA
131 TGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTTCCGAATTAATTTATAATTAAA
* * *
60816 TCCGAAACAAGATTCAGATGCTCGTATAAAAAAAATCTGTATATCCAATGTGGCTGAGATTTGGT
196 T-CGAAACAAGATTCAGATGCTCGTA-AAAACAAATCTTTAAATCCAATGTGGCTGAGATTTGGT
* * * * *
60881 TCGATGAATATAGATATTTCAAAGAGTCTTTGTGCCAAAAATCATGCAAAATTGAGTAGGGGCTC
259 TAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCGGGGCTC
* * * * *
60946 CGGAACGCGTTTTTAGCCAAAAACTGTAATGGTTAGTACAAGATTTTGGGTAAAATTTTGCAAAA
1 CGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGA-TTTCGG------CTT---AAA
* * * * * ** *
61011 AC-TGACCCAAAAAGTTTTTCCTCAATTTTTTGCCACAATACTAAAAAAAAATATAAAACACATC
56 ACTTG-CCCGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAAC
* * * *
61075 GCCAAAAAAACTGAAGGG-TTTCTCACTCTTCTAATTTCGTTTTTCC-TTTCTTTTTCCCGAATT
120 GCCAAAAAGATTGAAGGGCTTT-TCACGCTTCTAATATCGTTTTTCCATTT-TTTTT-CCGAATT
* * * * * * **
61138 TATTTATAATTAAATGGAAACAAGATTCAGACGCTCGTAAAAATAATTCCTTAAATCCAATGTCA
182 AATTTATAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCTTTAAATCCAATGTGG
* * * *
61203 CT-AGATTTGGTTAGATGAATATAGATATTTCAAAGAGTCTTTATGCCAAAAACCATGCAAAACA
247 CTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACT
*
61267 GAGTCGAGG-TC
312 GAGTCGGGGCTC
** * * *
61278 CTAAAACGCGTTTTTAGCCAAAAAAGCGTGA----TCGTACACGATTTC-GCCTAAAA-TCTGAC
1 C-GGAACGCGTTTTTAGCC-AAAAACCGTGATGGTTAGTACACGATTTCGGCTTAAAACT-TG-C
* * * * * * *
61337 TCGAAAATTTTTTTCTCAACTTTTTGCCACAGTACTCATAAAAAATATATAATTTCAAAGCCGAA
62 CCGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAA-TTCAACGCCAAA
* *
61402 AAGATTGAAGGGGTTTTCACGCTTCTAATATCGTTTTTCCTATCTTTTTTTTTCCGAATTTATTT
126 AAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCC-A---TTTTTTTTCCGAATTAATTT
* * * * * * *
61467 ATATTTAAATCGAAACAAGAGATTTACATGCTGGTAAACATAAATCTTTAAATCCATTGTGGCTG
187 ATAATTAAATCGAAAC-A-AGATTCAGATGCTCGTAAAAACAAATCTTTAAATCCAATGTGGCTG
* * *
61532 AGATTTAGTTAGATGAATATAGATATTTTAAGTAGTCTTTCTGCCAAAAATCATGCAAAACTGAG
250 AGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAG
* *
61597 TTGGGCCT-
315 TCGGGGCTC
** * * * * * * *
61605 CAAAACGCATATTTAGCCAAAAATCGTGATTGTTAGTATACGGTTTCGGCTTAAAACTTACCCGA
1 CGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTTAAAACTTGCCCGA
* * * *
61670 AAAGTTTTTTCTCATTTTTTTG-CAAAATA-TTATGAAAAAATATATAATTCAACGCCAAAAATA
66 AAAGTTTTTTCTCAATTTTTTGCCACAATACTCA-GAAAAAATATATAATTCAACGCCAAAAAGA
* * * * * ** * * *
61733 TTTACGGACTTTTCACGTTTCTAATATCATTTTTCCATTTTTAGTCCGAGTTAATTTCTTATTAA
130 TTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTTCCGAATTAATTTATAATTAA
* * ** *
61798 ATCAAAACAAGATTCAGATGCTCGTATAAAATAAATCCGTATATCCAATGTGGCTGAGATTTGGT
195 ATCGAAACAAGATTCAGATGCTCGTA-AAAACAAATCTTTAAATCCAATGTGGCTGAGATTTGGT
* * * * * *
61863 TCGATGAATATAGATATTTTAAGGAGTTTTTGC-GCCAAAAATTATTCAAAATTGAGTCGGGGCT
259 TAGATGAATATAGATATTTCAAGGAGTCTTT-CTGCCAAAAATCATGCAAAACTGAGTCGGGGCT
61927 C
323 C
** ** * * *
61928 TAGAACGCGTTTTTAGCCAAAAATTGTAATGGTTAGTACATGATTTCAGCTAAAATTTTGCAAAA
1 CGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGC-------TT---AAA
* * **
61993 AC-TGACCCGAAAAGTTTTTCCTCAATTTCTTGCCACAATACTCAGAAAAAAAAATATATAACAC
56 ACTTG-CCCGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCAG---AAAAAATATATAATTC
* *
62057 AACGCCAAAAAAATTGAAGGG--TTT-A----TC-AATTTCGTTTTTCCA--TTTTTTCCGAATT
117 AACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTTCCGAATT
* * * * * **
62112 TATTTATAATCAAATCGAAACAAGATTCAGACGCTCGTAAAAGCAAATCCTTAAATCCAATGTCA
182 AATTTATAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCTTTAAATCCAATGTGG
* * * * *
62177 CTGAGATTTGGTTAGATTAATATAGATATTTCAAAGAGTCTTTATGCCAAAAACCATGCAAAACA
247 CTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACT
* *
62242 AAGTCGAGG-TCC
312 GAGTCGGGGCT-C
* * * * * * *
62254 CGAAACGCGTTTTTAGTCAAAAAAC---AAGGATCA-TACACGATTTCGCCTAAAAAC-TGACCC
1 CGGAACGCGTTTTTAGCCAAAAACCGTGATGG-TTAGTACACGATTTCGGCTTAAAACTTG-CCC
* * *
62314 -AAAATTTTTTTTCTCAA--TTTT----C--TGC-C------AATATATAATTCAAAGCCAAAAA
64 GAAAA-GTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAA
* * * *
62363 GATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCTATCTTTTTTTTTTCGAATTTATTTCT
128 GATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCC-A---TTTTTTTTCCGAATTAATTTAT
* * * * *
62428 AATTAAATTGAAACAAGAGATGCAGATGCTGGTAAAAATAAATCTTTAAATCCATTGTGGCTGAG
189 AATTAAATCGAAAC-A-AGATTCAGATGCTCGTAAAAACAAATCTTTAAATCCAATGTGGCTGAG
* * * *
62493 ATTTGATTAGATGAATATAGACATCTCAAGGAGTCTTTCTGCAAAAAATCATGCAAAACTGAG-C
252 ATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTC
** *
62557 CAGGCAC
317 GGGGCTC
** * * ** * ** * *
62564 CAAAACACGTTTTTAGCCAAAAACTGTGATTCTTCGTTTACGATTTCGGTTTAAAACTTACCCGA
1 CGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTTAAAACTTGCCCGA
* * * *
62629 AAAG--TTTTCTCAATTTTTTG-CAAAATATTTAGAAAAAATATATAATTCAACGCCAGAAAGAT
66 AAAGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGAT
** * * * *
62691 TGTCGGACTTTTCACGCTTCTAATATGGTTTTTCCATTTTTTATCCGAATTAATTTCTAATTAAA
131 TGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTTCCGAATTAATTTATAATTAAA
* * * * *
62756 TCGAAACAAGATTTAGATGCTCGTATAAAAAAAATCTGTATATCCAATGCGGCTGAGATTTGGTT
196 TCGAAACAAGATTCAGATGCTCGTA-AAAACAAATCTTTAAATCCAATGTGGCTGAGATTTGGTT
** * * * *
62821 CCATGAATATAGATTTTTCAAGGAGTTTTTGTGCCAAAAATCATGCAAAATTGAGTCGGGGCTC
260 AGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCGGGGCTC
** * *
62885 CGGAACGCGTTTTTAGCCAAAAATTGTAATGGGTTAGTACACGAATTCGGCTAAAATTTTGCAAA
1 CGGAACGCGTTTTTAGCCAAAAACCGTGAT-GGTTAGTACACGATTTCGGC-------TT--AAA
* * * * * * *
62950 AATTGACACGAAAAGTTTTTCCACTATTTTTTGCCACAATATTCAGAAAAAATATA-ACA--AAA
56 ACTTG-CCCGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATA-ATTCAA
* * * * * *
63012 TGTCAAAAAAATTGAAGGG-TTTATCACGCTTCTAATTTTGTTTTTCCATTTTTTTTCCGAATTT
119 CGCCAAAAAGATTGAAGGGCTTT-TCACGCTTCTAATATCGTTTTTCCATTTTTTTTCCGAATTA
* * * *
63076 ATTTATAATTAAATCGAAACAAGATTTAGATGCTTGTAAAAACAAATCTCTAAATCCAATATGGC
183 ATTTATAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCTTTAAATCCAATGTGGC
* *
63141 CGAGATTTGGTTAGATGAATATAGGA-ATTTCAAGGAGTCTTTCTGCCAAAAATCTTGCAAAACT
248 TGAGATTTGGTTAGATGAATATA-GATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACT
*
63205 GAGTTGGGGC-C
312 GAGTCGGGGCTC
* * * * * *
63216 TCGAAATGCCTTTTTAGCCCAAAAACCGTGATGGTT--TATACGATTTCGGCTAAAAAC-TGACA
1 -CGGAACGCGTTTTTAG-CCAAAAACCGTGATGGTTAGTACACGATTTCGGCTTAAAACTTG-CC
* **** * * * * *
63278 TGATTTTTTTTTTTTCTGAATTTTTGGCCATAATACTCA-TAAAAATATAAAATTCAACGCCAAA
63 CGA--AAAGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAA
* * * * ** *
63342 AAGATTGACGGGCTTTTGATGCTTCTAATATTGTTTTTCCATTTTTTTTGTGAATTAA-TTCTAA
126 AAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTTCCGAATTAATTTATAA
* * * * * * *
63406 TTAAATCGAAACAAGATTTAGATGCTCATAAAAACAAATCCTAAAATCCAGTGTAGCTAAGATTT
191 TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCTTTAAATCCAATGTGGCTGAGATTT
* * * * * *
63471 GGTTCGATGAATATAGATATTTCAAGGAATGTTTAC-GGCAAAAATCATGC-AAATTGAGACGGG
256 GGTTAGATGAATATAGATATTTCAAGGAGTCTTT-CTGCCAAAAATCATGCAAAACTGAGTCGGG
*
63534 ACTC
320 GCTC
63538 CGGAACAG-GTTTTTAGCCAAAAGCCCAAAACCCGTGATGGTTAGTACACGATTTCGGCTAAAAT
1 CGGAAC-GCGTTTTTAGCC---A----AAAA-CCGTGATGGTTAGTACACGATTTCGGC------
* * *
63602 TTTTCAAAAATTGAGCCGAAAA-TCTTATTT-TCAATTTTTTGCCGCAATACTC-GTAAAAAACT
51 --TT-AAAACTTG-CCCGAAAAGT-TT-TTTCTCAATTTTTTGCCACAATACTCAG-AAAAAA-T
* * * * * *
63664 ATATAACTCAACGCCAAAAAAATTGAAGGGTTTTTTCACACTTCTAATATCGTTTTTTCATATTT
108 ATATAATTCAACGCCAAAAAGATTGAAGGG-CTTTTCACGCTTCTAATATCGTTTTTCCATTTTT
63729 TT
172 TT
63731 CCTCAATTCT
Statistics
Matches: 2478, Mismatches: 469, Indels: 305
0.76 0.14 0.09
Matches are distributed among these distances:
295 29 0.01
297 3 0.00
298 1 0.00
302 2 0.00
303 13 0.01
304 2 0.00
305 2 0.00
307 1 0.00
309 30 0.01
310 26 0.01
311 104 0.04
312 5 0.00
313 45 0.02
314 5 0.00
316 1 0.00
318 1 0.00
319 22 0.01
320 196 0.08
321 171 0.07
322 315 0.13
323 160 0.06
324 154 0.06
325 79 0.03
326 156 0.06
327 154 0.06
328 31 0.01
329 52 0.02
330 45 0.02
331 10 0.00
332 116 0.05
333 210 0.08
334 86 0.03
335 105 0.04
336 20 0.01
337 32 0.01
338 21 0.01
339 12 0.00
340 32 0.01
341 29 0.01
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (323 bp):
CGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTTAAAACTTGCCCGA
AAAGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGAT
TGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTTCCGAATTAATTTATAATTAAA
TCGAAACAAGATTCAGATGCTCGTAAAAACAAATCTTTAAATCCAATGTGGCTGAGATTTGGTTA
GATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGTCGGGGCTC
Found at i:64324 original size:335 final size:334
Alignment explanation
Indices: 63726--65771 Score: 2280
Period size: 337 Copynumber: 6.2 Consensus size: 334
63716 TTTTTTCATA
* * * * * ** *
63726 TTTTTCCTCAATTCTTTGTCATAATACTCGTAATAAATATATAATTCAACGGCTGAAAAGTTGAA
1 TTTTTCCTCAATTTTTTGCCACAATACTCGTAAAAAATATATAATTCAACGCCAAAAAAATTGAA
* *
63791 GGGTTTTTCACGCTTCT-A-AT-A----T-C---GTTTTTCGATTTAATATCTAATTAAATCAAA
66 GGGTTTTTCACGCTTCTAATATCATTTTTCCATATTTTTTCGATTTAATTTCTAATTAAATCAAA
* * * *
63845 ACAAGATTAAGATACTCGTAAAAACAAATCCTTAAATCTAATGT-TTCTGGAATTTGGTTCAATA
131 ACAAGATTAAGATACTCGTAAAAACAAATCCTTAAATCTAATGTGGT-TGGGATTTGGTTCGATG
* * * * * *
63909 AATATAGATATATCAAGAAGTCTTTACGCCAAAAATAATGCAAAACTAAGCCAGAGCCCCTGGAT
195 AATATAGATATTTCAAGAAGTCTTTACGCAAAAAATAATGCAAAACTGAGCCGGGGCCCCTGAAT
* * *
63974 GCGTTTTAAGCAAAAAACTGTGATGGTAAATATACACGATTTCGGCTAAAATTTTGAAAAAACTA
260 GCGTTTTTAGCAAAAAACCGTGATGGTAAA-ATACACGATTTCGGCTAAAATTTTGAAAAAACTG
**
64039 ACACGAAAAAA
324 ACACGAAAATT
* *
64050 TTTTTCCTGAATTTTTTGCCACAATACTCGTAAAAATTATATAATTCAACGCCAAAAAAATTGAA
1 TTTTTCCTCAATTTTTTGCCACAATACTCGTAAAAAATATATAATTCAACGCCAAAAAAATTGAA
* * * *
64115 CGGTTTTTAACACTTCTAATATCATTTTTCCATATTTTTTCGATTTAATTTCTAATTAGATCAAA
66 GGGTTTTTCACGCTTCTAATATCATTTTTCCATATTTTTTCGATTTAATTTCTAATTAAATCAAA
* * *
64180 ACAAGATTAAGATACTTGTAAAAATAAATCATTAAATCTAATGTGGTTGGGATTTGGTTCGATGA
131 ACAAGATTAAGATACTCGTAAAAACAAATCCTTAAATCTAATGTGGTTGGGATTTGGTTCGATGA
* *
64245 ATATAGATATTTCAAGAAGACTTTACGCAAAAAATAATGCAAAACTGAGCCGGGGCCCTTGAATG
196 ATATAGATATTTCAAGAAGTCTTTACGCAAAAAATAATGCAAAACTGAGCCGGGGCCCCTGAATG
* **
64310 CGTTTTTAGCAAAAACCCGTGATGGTTAGTTTATACACGATTTCGGCTAAAATTTTGAAAAAACT
261 CGTTTTTAGCAAAAAACCGTGATGG-TA--AAATACACGATTTCGGCTAAAATTTTGAAAAAACT
64375 GACACGAAAATT
323 GACACGAAAATT
* * *
64387 TTTTTCCTCAATTCTTTGCCACAATACTCGTAAAAATTATATGATTCAACGCCAAAAAAATTTGA
1 TTTTTCCTCAATTTTTTGCCACAATACTCGTAAAAAATATATAATTCAACGCCAAAAAAA-TTGA
* *
64452 AGGGGTTTTCACGCTTCTAATATCGTTTTTCCATATTTTTTCGATTTAATTTTTCTAATTAAATC
65 AGGGTTTTTCACGCTTCTAATATCATTTTTCCATATTTTTTCGATTTAA--TTTCTAATTAAATC
* *
64517 AAAACACGATTAAGATACTCGTAAAAACAAATCCTTAAATCTAATGTGGCTGGGATTTGGTTCGA
128 AAAACAAGATTAAGATACTCGTAAAAACAAATCCTTAAATCTAATGTGGTTGGGATTTGGTTCGA
* * * * *
64582 TGAATATAGATGTTTTAACAAGTCTTTACGCCAAAAATAATGCAAAACTAAGCCGGGGCCCCTGA
193 TGAATATAGATATTTCAAGAAGTCTTTACGCAAAAAATAATGCAAAACTGAGCCGGGGCCCCTGA
** * *
64647 ATGCGGTCATTAGTAAAAAACTGTGATGGT-AAATACACGATTTCGGCTAAAATTTTGAAAAAAC
258 ATGC-GTTTTTAGCAAAAAACCGTGATGGTAAAATACACGATTTCGGCTAAAATTTTGAAAAAAC
*
64711 TGATACGAAAATT
322 TGACACGAAAATT
* * *
64724 TTTTTCCTCAATTTTTTGCCACGATATTCGTAAAAAATATATAATTCAATGCCAAAAAAAATT-A
1 TTTTTCCTCAATTTTTTGCCACAATACTCGTAAAAAATATATAATTCAACGCC-AAAAAAATTGA
*
64788 AGGGGTTTTTCACGCTTCCAATATCATTTTTCCATATTTTTTTTCGATTTAATTTCTAATTAAAT
65 A-GGGTTTTTCACGCTTCTAATATCATTTTTCCATA--TTTTTTCGATTTAATTTCTAATTAAAT
* ** * *
64853 CAAAAGAAGATTAAGATACTTATAAAAATAAATCCTTAAATCTAATATGG-TGGGAATTTGGTTC
127 CAAAACAAGATTAAGATACTCGTAAAAACAAATCCTTAAATCTAATGTGGTTGGG-ATTTGGTTC
* * * *
64917 GATGAATATAGATATTTGAAGAAGTCTTTACGTAAAAAAATAATGC-AAACAGAGCCGGGGACCC
191 GATGAATATAGATATTTCAAGAAGTCTTTACG-CAAAAAATAATGCAAAACTGAGCCGGGGCCCC
* * * * *
64981 TTAACGCGTTTTTAGCAAAAAACCGTGATGGT-AAATACACGATTTCGACTAAAATTTTGCACAA
255 TGAATGCGTTTTTAGCAAAAAACCGTGATGGTAAAATACACGATTTCGGCTAAAATTTTGAAAAA
* *
65045 ACTGAAAC-ATAAA-G
320 ACTGACACGA-AAATT
* * * *
65059 TTTTTCCTCTATTTTTTACCATAATACTCGTAAAAGATATATAATTCAACGCCAAAAAAATTGAA
1 TTTTTCCTCAATTTTTTGCCACAATACTCGTAAAAAATATATAATTCAACGCCAAAAAAATTGAA
* *
65124 -GGTTTTTCACGCTTCTAATATCGTTTTTCCATATTTTTTTTCGATTTAATTTCTTATTAAATCA
66 GGGTTTTTCACGCTTCTAATATCATTTTTCCATA--TTTTTTCGATTTAATTTCTAATTAAATCA
* * *
65188 AAACAAGATTAAGATACTTGTAAAAACAAATCCTTAAATCTAACGTGGTTGGGATTTGCTTCGAT
129 AAACAAGATTAAGATACTCGTAAAAACAAATCCTTAAATCTAATGTGGTTGGGATTTGGTTCGAT
* * * *
65253 GAATATAGATATTTCGAGAAATCTTTACGGAAAAAATAATGCAAAACTGAGCCGGGTCCCCTGAA
194 GAATATAGATATTTCAAGAAGTCTTTACGCAAAAAATAATGCAAAACTGAGCCGGGGCCCCTGAA
* * *
65318 CGCGGTTTTAGCAAAAACCCGTGATGGTTAGTAAATACACGATTTCGGCTAAAATTTT-AAAAAT
259 TGCGTTTTTAGCAAAAAACCGTGATGG-TA--AAATACACGATTTCGGCTAAAATTTTGAAAAA-
*
65382 ACTGACACGAATATT
320 ACTGACACGAAAATT
* * * *
65397 TTTTTCCTCAATTCTTTGCCACAAAACTAC--AAAAAATATATAATACAACG-CAAAAAGAATTA
1 TTTTTCCTCAATTTTTTGCCACAATACT-CGTAAAAAATATATAATTCAACGCCAAAAA-AATTG
* * * * *
65459 AAGGGTTTTTCACACTT-T--TA--A--TGT-CGTTTTTTTTCGAAATTT-ATTTTTAATTAAAT
64 AAGGGTTTTTCACGCTTCTAATATCATTTTTCCATATTTTTTCG--ATTTAATTTCTAATTAAAT
* * * * * * ** * *
65515 CGAAACAAGATTCAA-ATGCTCGTAAAAATAAATCCTTAAATCCAATATGGCTCAGAATTGGTTA
127 CAAAACAAGATT-AAGATACTCGTAAAAACAAATCCTTAAATCTAATGTGGTTGGGATTTGGTTC
* * * * ** *
65579 GATGAATATAGAAATTTCAAGGAGTCTTT-CTGCCAAAAATCATGCAAAACTGAG-CGGGATCCA
191 GATGAATATAGATATTTCAAGAAGTCTTTAC-GCAAAAAATAATGCAAAACTGAGCCGGGGCCCC
* * * * * * * * *
65642 AGAAACGCCTTTTTACCTCAAAAACCGTGACGGT-TAGTACATGATTTCGG--------TT--AA
255 TG-AATGCGTTTTTAGC-AAAAAACCGTGATGGTAAAATACACGATTTCGGCTAAAATTTTGAAA
* * *
65696 AAATTGACCCGAAAA-A
318 AAACTGACACGAAAATT
* *
65712 TTTTTCCTCAATTTTTTTCCACAATACTCGTAAAAAACTATATAATTCAACTCCAAAAAA
1 TTTTTCCTCAATTTTTTGCCACAATACTCGTAAAAAA-TATATAATTCAACGCCAAAAAA
65772 GTCTCTAGAG
Statistics
Matches: 1482, Mismatches: 191, Indels: 105
0.83 0.11 0.06
Matches are distributed among these distances:
314 1 0.00
315 25 0.02
316 16 0.01
317 17 0.01
318 8 0.01
324 69 0.05
325 1 0.00
326 15 0.01
327 1 0.00
328 16 0.01
329 117 0.08
330 20 0.01
331 3 0.00
332 13 0.01
333 184 0.12
334 14 0.01
335 214 0.14
336 78 0.05
337 397 0.27
338 103 0.07
339 15 0.01
340 136 0.09
341 19 0.01
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (334 bp):
TTTTTCCTCAATTTTTTGCCACAATACTCGTAAAAAATATATAATTCAACGCCAAAAAAATTGAA
GGGTTTTTCACGCTTCTAATATCATTTTTCCATATTTTTTCGATTTAATTTCTAATTAAATCAAA
ACAAGATTAAGATACTCGTAAAAACAAATCCTTAAATCTAATGTGGTTGGGATTTGGTTCGATGA
ATATAGATATTTCAAGAAGTCTTTACGCAAAAAATAATGCAAAACTGAGCCGGGGCCCCTGAATG
CGTTTTTAGCAAAAAACCGTGATGGTAAAATACACGATTTCGGCTAAAATTTTGAAAAAACTGAC
ACGAAAATT
Found at i:66327 original size:323 final size:322
Alignment explanation
Indices: 65784--66389 Score: 1061
Period size: 323 Copynumber: 1.9 Consensus size: 322
65774 CTCTAGAGCC
*
65784 CCTGCTAAATTTTGCATGATTTTAGGCAGAAAGTCTCCTTTAAATATTTATATTCATATAACCAA
1 CCTGCTAAATTTTGCATGATTTTAGGCAGAAAGTCTCCTTAAAATATTTATATTCATATAACCAA
*
65849 ATCTCAGTCAACTTAGATTTAAGGATTTGTTTTTACGAGTATTTGAATCTTGTTTCGATTTAATT
66 ATCTCAGTCAACTTAGATTTAAGGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATT
*
65914 AAAAATAAATTCGAGAAAAAATCGAAAAACGATATTGGAAGCGTGAAAAACCCTTAAATTTTTTT
131 AAAAATAAATTCGAAAAAAAATCGAAAAACGATATTGGAAGCGTGAAAAACCCTTAAATTTTTTT
* * *
65979 GGCTTTGAAATATATATATTTTTTCAGAGTTGTGTGGTAAAAATTAGAAAAAAAGTTTTCGGGTA
196 GGCTTTGAAATATATATATTTTTTCAAAGTAGTGTGGCAAAAATTAGAAAAAAA-TTTTCGGGTA
* *
66044 AATTTTTATCCGAAATCGTGTACTAACCATCACGGTTTTTGGTTAAAAACGCGTTCCAGAACG
260 AATTTTTAGCAGAAATCGTGTACTAACCATCACGGTTTTTGGTTAAAAACGCGTTCCAGAACG
*
66107 CCTGCTAAATTTTGCATGATTTTAGGCAGAAAGTCTCCTTAAAATATTTATATTCATTTAACCAA
1 CCTGCTAAATTTTGCATGATTTTAGGCAGAAAGTCTCCTTAAAATATTTATATTCATATAACCAA
66172 ATCTCAGTCAACTTAGATTTAAGGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATT
66 ATCTCAGTCAACTTAGATTTAAGGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATT
* *
66237 AAAAATAAATTCGAAAAAAAAATCGAAAAACGATATTGGAAGCGTGAAAGACCCTTCAATTTTTT
131 AAAAATAAATTCG-AAAAAAAATCGAAAAACGATATTGGAAGCGTGAAAAACCCTTAAATTTTTT
* * *
66302 TGGCTTTTAATTATATATA-TTTTTCAAAGTAGTGTGGCAAAAATTAGAAAAAAATTTTCGTGTA
195 TGGCTTTGAAATATATATATTTTTTCAAAGTAGTGTGGCAAAAATTAGAAAAAAATTTTCGGGTA
66366 AATTTTTAGCAGAAATCGTGTACT
260 AATTTTTAGCAGAAATCGTGTACT
66390 GGGGCCCTGA
Statistics
Matches: 268, Mismatches: 14, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
322 31 0.12
323 172 0.64
324 65 0.24
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (322 bp):
CCTGCTAAATTTTGCATGATTTTAGGCAGAAAGTCTCCTTAAAATATTTATATTCATATAACCAA
ATCTCAGTCAACTTAGATTTAAGGATTTGTTTTTACGAGCATTTGAATCTTGTTTCGATTTAATT
AAAAATAAATTCGAAAAAAAATCGAAAAACGATATTGGAAGCGTGAAAAACCCTTAAATTTTTTT
GGCTTTGAAATATATATATTTTTTCAAAGTAGTGTGGCAAAAATTAGAAAAAAATTTTCGGGTAA
ATTTTTAGCAGAAATCGTGTACTAACCATCACGGTTTTTGGTTAAAAACGCGTTCCAGAACG
Found at i:69482 original size:323 final size:319
Alignment explanation
Indices: 67375--69644 Score: 2791
Period size: 324 Copynumber: 7.0 Consensus size: 319
67365 TAATGCAAAA
* * * *
67375 CTAAAAACGCGTTTCCGGGCTCCAGCTTAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAA
1 CTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAA
* * * *
67440 TATCTATATTCGTATAACCAAATCTCAGCTAATTTGGATTTAAGGATATCTTTTTAAGAGCATCT
66 TATCTATATTCATATAACCAAATCTCAGCCAATTTGGATTTAAGGATTTCTTTTTACGAGCATCT
*
67505 GAATTTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAAAAATGGAAAAACGATATTGGAAGCG
131 GAATTTTGTTTCGATTTAATTAGAAATAAATTC-G-AAAAAAATGGAAAAACGATATTCGAAGCG
* * * *
67570 TGAAAACCCCTTCAATTTTTGTTGGCGTTGAATTATATATTTTGTAGAGTTGTGTGGCAAATAAA
194 TGAAAAACCCTTCAATTTTTTTTGGCGTTGAATTATATATTTTTTAGAGTTGTGTGGCAAAAAAA
* * * *
67635 TGAGAAGAAAGTTTTCGGGTCAACTTTTAGCAGAAATCGTGT-ACCATCACGGTTTTTGT-
259 TGAGAAAAAAGTTTTCGGGTCAATTTTTAGCCGAAATCGTGTAACCATCACGGTTTTTTTG
* * ** *
67694 CTAAAAATGCGTTTCGGGGCCCCGACTCAGTTTTATATGATTTTTGGCAGAAAGACTCCTTGAGA
1 CTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAA
* *
67759 TATCTATATTCATATAACCAAATCTCAGCCAATTTGCATTTCAGGATTTCTTTTTACGAGCATCT
66 TATCTATATTCATATAACCAAATCTCAGCCAATTTGGATTTAAGGATTTCTTTTTACGAGCATCT
* *
67824 GAATTTTGTTTCGATTTAATCAGAAATAAATTCGAAAAAAAAATGGAAAAACGATATTGGAAGCG
131 GAATTTTGTTTCGATTTAATTAGAAATAAATTCG--AAAAAAATGGAAAAACGATATTCGAAGCG
* * *
67889 TGAAAACCCCTTCAA-TTTTTTTGGCATTGAATTATATATTTTGTAGAGTTGTGTGGCAAAAACA
194 TGAAAAACCCTTCAATTTTTTTTGGCGTTGAATTATATATTTTTTAGAGTTGTGTGGC-AAAA-A
*** * * * *
67953 AATGAGAAGTTAGTTTTTGGGTCAACTTTTAGCAGAAATCGTGT-ACGTTACATCCCGG-TTTTT
257 AATGAGAAAAAAGTTTTCGGGTCAATTTTTAGCCGAAATCGTGTAAC----CATCACGGTTTTTT
*
68016 GG
318 TG
* * ** * * * * * *
68018 CTAAAAACGCGTTTCTGGGTCCTAGCTTAGTTTTGCATGATTTTAGCCTGGAAGTCTCCTTGAAA
1 CTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAA
* * * * *
68083 TATCTATTTTCATATAAACAAATCTCAGCCATTTTGGATTTAAAGATTCCTTTTTACGAGCATCT
66 TATCTATATTCATATAACCAAATCTCAGCCAATTTGGATTTAAGGATTTCTTTTTACGAGCATCT
* * * *
68148 GAATTTTGTTTCGATTTAATTAGAAATAAATTCGAAAAAATTGGAAAAATGATATTCTAAGCATG
131 GAATTTTGTTTCGATTTAATTAGAAATAAATTCGAAAAAAATGGAAAAACGATATTCGAAGCGTG
* *
68213 AAAAACGCTTCAATTTTTTTTGGGCGTTGAATCATATATTTTTTAAGAGTTGTGTGGCAAAAAAA
196 AAAAACCCTTCAATTTTTTTT-GGCGTTGAATTATATATTTTTT-AGAGTTGTGTGGCAAAAAAA
* * ** *
68278 TGAGAAATAAAGTTTTTGGGACAATTTTTAGTTGAAATCGTGT-ACCATCGCGGTTTTTTTTG
259 TGAGAAA-AAAGTTTTCGGGTCAATTTTTAGCCGAAATCGTGTAACCATCACGG-TTTTTTTG
* * * * *
68340 TTTATAACGCGTTTCGTGGCCCCGGCTCAGTTTTGCATGATTTTTTGCAGAAAGACTCCTTGAAA
1 CTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAA
* * * * *
68405 TATCAATATTCATATAACCAAATCTCAGCCTATTTGGATTAAAGGATTTGTTTTTACGAGTATCT
66 TATCTATATTCATATAACCAAATCTCAGCCAATTTGGATTTAAGGATTTCTTTTTACGAGCATCT
* * *
68470 GAATTTTGTTTCAAGTTAATTAGAAA-AAACTTTGGAAAAAAATTGGAAAAACGATATTCGAAGC
131 GAATTTTGTTTCGATTTAATTAGAAATAAA--TTCGAAAAAAA-TGGAAAAACGATATTCGAAGC
* * * *
68534 GTGAAAAAACCTTGAAATTTTTTTTGGCGTTGAATCATATATGTTTTTTTAGAGTTGTGCGGCAA
193 GTGAAAAACCCTT-CAATTTTTTTTGGCGTTGAAT--TATAT-ATTTTTTAGAGTTGTGTGGC--
* * *
68599 AAAAAAATAAGAAAAAAAGTTTT-GTGTCAATTTTTAGCCGAAATCGTGTACAAACCATCAGGGT
252 AAAAAAATGAG-AAAAAAGTTTTCGGGTCAATTTTTAGCCGAAATCGTGT---AACCATCACGGT
68663 TTTTTTG
313 TTTTTTG
**** * *
68670 CTAAAAACGCGTTTCGGGGATTTGGCTAAATTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAA
1 CTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAA
* * *
68735 TATCTATATTCATATAACCAAATCTCAACCAATTTGGATTTCAGGATTTCATTTTACGAGCATCT
66 TATCTATATTCATATAACCAAATCTCAGCCAATTTGGATTTAAGGATTTCTTTTTACGAGCATCT
* * * * **
68800 TAATTATGTTTCGATTTAATTAGAAATATATTTGGAAAAAAAATGGAAAAACGATATTCGAAATG
131 GAATTTTGTTTCGATTTAATTAGAAATA-AATTCG-AAAAAAATGGAAAAACGATATTCGAAGCG
* * *
68865 TGAAAAACCCTTCAA-TTTTTTTGGCATTGAATTACATATTTTGTAGAGTTGTGTGGCTAAAAAA
194 TGAAAAACCCTTCAATTTTTTTTGGCGTTGAATTATATATTTTTTAGAGTTGTGTGGC-AAAAAA
* * *
68929 ATGA-AAAGAAAGTTTTCGGGTCAACTTTTGGCCGAAATCGTGT---CAT---GGTTTTTTGG
258 ATGAGAAA-AAAGTTTTCGGGTCAATTTTTAGCCGAAATCGTGTAACCATCACGGTTTTTTTG
* *
68985 CTAAAAACGCGTTTCGAGGCCCCAGCTCAGTTTTGCATGATTCTTT-GCAGAAAGACTCCTT-AA
1 CTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATT-TTTGGCAGAAAGACTCCTTGAA
* * * * *
69048 GAAATCTATATTCATATAGCCAATTCTCAGCCAATTTGGACTTCAGGATTTCTTTTTACGAGCAT
65 -ATATCTATATTCATATAACCAAATCTCAGCCAATTTGGATTTAAGGATTTCTTTTTACGAGCAT
* * * *
69113 CTTAATTATGTTTCGATTTAATTAGAAATATATTCGGAAAAAATGGAAAAACGATATTCGAAGCG
129 CTGAATTTTGTTTCGATTTAATTAGAAATAAATTCGAAAAAAATGGAAAAACGATATTCGAAGCG
* *
69178 TGAAAAACCCTTCAATTTTTTTTAGCGTTGAATCATATATTTTTTTAGAGTTGTGTGGC-AAAAA
194 TGAAAAACCCTTCAATTTTTTTTGGCGTTGAATTATATA-TTTTTTAGAGTTGTGTGGCAAAAAA
69242 ATGAGAACAAAAGTTTTCGGGTCAATTTTTAGCCGAAATCGTGTACAAACCATCACGGTTTTTTT
258 ATGAGAA-AAAAGTTTTCGGGTCAATTTTTAGCCGAAATCGTGT---AACCATCACGGTTTTTTT
69307 G
319 G
** * * * *
69308 CTAAAAACGCGCCTCGGGGCCTCGGCTCAGTTTTGCATTATTTTTGGCAGGAAGACTCCTTAAAA
1 CTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTT-GAA
* * * *
69373 AGATCTATATTCATATAACCAAATCTCAGTCAATTTGGATTTAAGGATTTCTTTTTAAGATCATC
65 ATATCTATATTCATATAACCAAATCTCAGCCAATTTGGATTTAAGGATTTCTTTTTACGAGCATC
* *
69438 TGAATTTTGTTTCGATTTTATTAGAAATAAATTCG-AAAAAATGGAAAAACGATATTGGAAGCGT
130 TGAATTTTGTTTCGATTTAATTAGAAATAAATTCGAAAAAAATGGAAAAACGATATTCGAAGCGT
* * *
69502 -AAAAACCCCTTCAATTTTCTTTGGCGTTGAATTATATATATTTTAGAGTTGTGAGGCAAAAAAA
195 GAAAAA-CCCTTCAATTTTTTTTGGCGTTGAATTATATATTTTTTAGAGTTGTGTGGCAAAAAAA
*
69566 TGAGAAAAAAGTTTTCGGGTCAATTTTTAATCCGAAATCGTGTATTAACCATCACGGTTTTTTTG
259 TGAGAAAAAAGTTTTCGGGTCAATTTTT-AGCCGAAATCGTG---TAACCATCACGGTTTTTTT-
69631 G
319 G
69632 CTAAAAACGCGTT
1 CTAAAAACGCGTT
69645 CCGGAGCTCC
Statistics
Matches: 1686, Mismatches: 207, Indels: 111
0.84 0.10 0.06
Matches are distributed among these distances:
313 50 0.03
314 59 0.03
315 165 0.10
316 3 0.00
318 44 0.03
319 195 0.12
320 54 0.03
321 3 0.00
322 222 0.13
323 195 0.12
324 373 0.22
325 42 0.02
326 21 0.01
327 28 0.02
328 34 0.02
329 5 0.00
330 176 0.10
331 16 0.01
332 1 0.00
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (319 bp):
CTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAA
TATCTATATTCATATAACCAAATCTCAGCCAATTTGGATTTAAGGATTTCTTTTTACGAGCATCT
GAATTTTGTTTCGATTTAATTAGAAATAAATTCGAAAAAAATGGAAAAACGATATTCGAAGCGTG
AAAAACCCTTCAATTTTTTTTGGCGTTGAATTATATATTTTTTAGAGTTGTGTGGCAAAAAAATG
AGAAAAAAGTTTTCGGGTCAATTTTTAGCCGAAATCGTGTAACCATCACGGTTTTTTTG
Found at i:71218 original size:321 final size:320
Alignment explanation
Indices: 70143--71340 Score: 1575
Period size: 320 Copynumber: 3.7 Consensus size: 320
70133 CTGTGTTACA
* * * * * *
70143 TGCATGATTTTAGGTAG-AAGTCTCCTTAAAATACCTATATTCATATAACCAAATCTCAGCCAAC
1 TGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATATAACCAAATCTCAGCCAAT
* * * *
70207 TTAGATTTAAGGATTTGTTTTTACGAGCATTTAAATCTTGTTTCGATTTAATTAAAAATAAATTC
66 TTAGATTTAAGGATTTCTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAAAAATAAATTC
* *
70272 GGCAAAAAAAATCGAAATACGATATTGGAAGCGTGAAAAACCCTTCCATTTTTTTGGCTTTGAAT
131 GG--AAAAAAATCGAAAAACGATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTGGCTTTGAAT
** *
70337 TATATATTTTTTCAGAGTAGTGTGGCAAAAATTGAGAAAAAAAATTTTCGGGAAAAGTTTTAGCA
194 TATATATTTTTTCAGAGTAGTGTGGCAAAAATTGAG--AAAAAATTTTCGGGTCAACTTTTAGCA
* * * * *
70402 TAAATCGTGTACTAAGCATCGCAGTTTTTGGCTAAAAACGCGTTTCGGGGCCTCGGCTCAGTTT
257 GAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTT
* * *
70466 TGCATGATTTTTGGCAGAAAGGCTCCTTGAAATATCTATATTCATATAACCAAATCTCATCTAAT
1 TGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATATAACCAAATCTCAGCCAAT
* * * *
70531 TTGGATTTAAGGATTTCTTTTTATGAGCATCTGAATTTTGTTTTGATTTAATTAGAAATAAATTC
66 TTAGATTTAAGGATTTCTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAAAAATAAATTC
* * *
70596 -GAAAAAAATGGAAAAATGATATTGGAAGCGTGAAAAACCCTTCAATTCTTTTGGCTTTGAATTA
131 GGAAAAAAATCGAAAAACGATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTGGCTTTGAATTA
* *
70660 TATATTTTTTCAGAGTAGTGTGGCCAAAAA-TGAGAAAAAAGTTTTTGGGTCAATTTTTAAG-AG
196 TATATTTTTTCAGAGTAGTGTGG-CAAAAATTGAGAAAAAA-TTTTCGGGTCAACTTTT-AGCAG
* * * *
70723 AAATCATATACTAACCATCACGATTTTTGGCTAAAAACGCGTTTTGGGGCCCCGGCTCAGTTT
258 AAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTT
** * * *
70786 TGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTTTTACAACCAAATATCAGCTAAT
1 TGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATATAACCAAATCTCAGCCAAT
* * * *
70851 TTGGATTTAAGGATTTCTTTTTACAAGCATCTGAATTTTGTTTCGATTTAATTACAAATAAACTC
66 TTAGATTTAAGGATTTCTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAAAAATAAATTC
* ** * *** *
70916 -GAAAAAAATGGAAAATTGATATTGGAAGCGTGAAAACCCCTTCAATTTTTTTTTGAAGTTGAAC
131 GGAAAAAAATCGAAAAACGATATTGGAAGCGTGAAAAACCCTTCAA--TTTTTTTGGCTTTGAAT
* * * * *
70980 TATGTGTTTTTT-AGAGTTGTGTGGCAAAAAATTGAGAAGAAATTTTCGGGTCAACTTTTAGCCG
194 TATATATTTTTTCAGAGTAGTGTGGC-AAAAATTGAGAAAAAATTTTCGGGTCAACTTTTAGCAG
* * * *
71044 AAATCGCGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCAGGGCCCCGACACAGTTTT
258 AAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAG-TTT
*
71108 TGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATTTTCATATAACCAAATCTCAGCCAAT
1 TGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATATAACCAAATCTCAGCCAAT
** * *
71173 TTAGATTTATTGATCTCTTTTTACGAGCATTTG-ATTCTT-TTTCGATTTAATTAAAAATAAATT
66 TTAGATTTAAGGATTTCTTTTTACGAGCATCTGAATT-TTGTTTCGATTTAATTAAAAATAAATT
*
71236 CGGAAAAAGTATCGAAAAACGATATTGGAAGCGTGAAAAACCCTTCAATTCTTTTTGGCTTTGAA
130 CGGAAAAA-AATCGAAAAACGATATTGGAAGCGTGAAAAACCCTTCAATT-TTTTTGGCTTTGAA
* * *
71301 TTAAATATTTTTTCAGAGTGGTGTGGCGAAAATTGAGAAA
193 TTATATATTTTTTCAGAGTAGTGTGGCAAAAATTGAGAAA
Statistics
Matches: 764, Mismatches: 96, Indels: 31
0.86 0.11 0.03
Matches are distributed among these distances:
319 6 0.01
320 234 0.31
321 199 0.26
322 165 0.22
323 62 0.08
324 98 0.13
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (320 bp):
TGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATATAACCAAATCTCAGCCAAT
TTAGATTTAAGGATTTCTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAAAAATAAATTC
GGAAAAAAATCGAAAAACGATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTGGCTTTGAATTA
TATATTTTTTCAGAGTAGTGTGGCAAAAATTGAGAAAAAATTTTCGGGTCAACTTTTAGCAGAAA
TCGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTT
Done.