Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010333.1 Corchorus capsularis cultivar CVL-1 contig10354, 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: 113475
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1100 original size:25 final size:25
Alignment explanation
Indices: 1054--1111 Score: 66
Period size: 26 Copynumber: 2.4 Consensus size: 25
1044 AAGAAAACAT
*
1054 AATTT-TTTAATGTTTAATTATT-A
1 AATTTATTTAATATTTAATTATTCA
*
1077 AATTTATTTAATATATTTATTATTCA
1 AATTTATTTAATAT-TTAATTATTCA
*
1103 ATTTTATTT
1 AATTTATTT
1112 TACAATTCAC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.17
24 7 0.24
25 8 0.28
26 9 0.31
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (25 bp):
AATTTATTTAATATTTAATTATTCA
Found at i:5250 original size:7 final size:7
Alignment explanation
Indices: 5238--5264 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
5228 TATTGTATAG
5238 TTGCAAC
1 TTGCAAC
5245 TTGCAAC
1 TTGCAAC
5252 TTGCAAC
1 TTGCAAC
5259 TTGCAA
1 TTGCAA
5265 ATACATCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.30
Consensus pattern (7 bp):
TTGCAAC
Found at i:5632 original size:2 final size:2
Alignment explanation
Indices: 5625--5655 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
5615 CCATTAAGCT
5625 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5656 GAACCTTTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5972 original size:30 final size:31
Alignment explanation
Indices: 5902--5972 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
5892 GCACGTATCC
*
5902 TTTTGTACACGTGGCATGCCACGTGTCACTT
1 TTTTGTACACGTGACATGCCACGTGTCACTT
* *
5933 TTTGGTACACGTGACATGCCACGTGTC-GTT
1 TTTTGTACACGTGACATGCCACGTGTCACTT
*
5963 TTTTTTACAC
1 TTTTGTACAC
5973 ATGTCGCTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
30 10 0.29
31 25 0.71
ACGTcount: A:0.17, C:0.24, G:0.21, T:0.38
Consensus pattern (31 bp):
TTTTGTACACGTGACATGCCACGTGTCACTT
Found at i:8626 original size:17 final size:17
Alignment explanation
Indices: 8604--8652 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
8594 ATAAACTCAT
8604 GTAATCTTTGATCACCG
1 GTAATCTTTGATCACCG
*
8621 GTAATC-TTGCATCACTG
1 GTAATCTTTG-ATCACCG
* *
8638 GTGATCTTAGATCAC
1 GTAATCTTTGATCAC
8653 TAGTGATGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 3 0.11
17 22 0.81
18 2 0.07
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.35
Consensus pattern (17 bp):
GTAATCTTTGATCACCG
Found at i:8653 original size:17 final size:16
Alignment explanation
Indices: 8611--8659 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
8601 CATGTAATCT
* *
8611 TTGATCACCGGTAATC
1 TTGATCACTGGTGATC
8627 TTGCATCACTGGTGATC
1 TTG-ATCACTGGTGATC
*
8644 TTAGATCACTAGTGAT
1 TT-GATCACTGGTGAT
8660 GGAGGGTGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 3 0.11
17 24 0.86
18 1 0.04
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.35
Consensus pattern (16 bp):
TTGATCACTGGTGATC
Found at i:36731 original size:18 final size:18
Alignment explanation
Indices: 36708--36744 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
36698 GAGGAGGAGC
*
36708 AAGCGGAGCTGGCGAAGA
1 AAGCGGAGCAGGCGAAGA
*
36726 AAGCGGAGGAGGCGAAGA
1 AAGCGGAGCAGGCGAAGA
36744 A
1 A
36745 GAAGCAGAGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.38, C:0.14, G:0.46, T:0.03
Consensus pattern (18 bp):
AAGCGGAGCAGGCGAAGA
Found at i:36734 original size:33 final size:33
Alignment explanation
Indices: 36675--36737 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
36665 AAGGTGACGG
*
36675 AAGCGGAGCTGAGGAAGAGGAGGGAGGAGGAGC
1 AAGCGGAGCTGAGGAAGAGAAGGGAGGAGGAGC
36708 AAGCGGAGCTG-GCGAAGA-AAGCGGAGGAGG
1 AAGCGGAGCTGAG-GAAGAGAAG-GGAGGAGG
36738 CGAAGAAGAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
32 3 0.11
33 24 0.89
ACGTcount: A:0.33, C:0.11, G:0.52, T:0.03
Consensus pattern (33 bp):
AAGCGGAGCTGAGGAAGAGAAGGGAGGAGGAGC
Found at i:42661 original size:2 final size:2
Alignment explanation
Indices: 42648--42677 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
42638 TGAAGATCAT
42648 TA TA TCA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA T
42678 TTACCATCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:43366 original size:2 final size:2
Alignment explanation
Indices: 43359--43387 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
43349 CAAATAATCA
43359 AT 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 AT A
43388 GACCAAGCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:52768 original size:6 final size:6
Alignment explanation
Indices: 52750--52780 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
52740 AAAATCTTTG
52750 AATAGT AAATAGT AATAGT AATAGT AATAGT
1 AATAGT -AATAGT AATAGT AATAGT AATAGT
52781 GTTTTTCATG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.75
7 6 0.25
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (6 bp):
AATAGT
Found at i:59628 original size:5 final size:5
Alignment explanation
Indices: 59618--59645 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
59608 GTTGTTCTGC
59618 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
59646 TAAAAGGTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:69432 original size:14 final size:15
Alignment explanation
Indices: 69408--69439 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
69398 ACCCTAGCCG
69408 CTCCTCTCTCCCCTT
1 CTCCTCTCTCCCCTT
69423 CTCC-CTCTCCCCTT
1 CTCCTCTCTCCCCTT
69437 CTC
1 CTC
69440 GTTGGTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (15 bp):
CTCCTCTCTCCCCTT
Found at i:81362 original size:24 final size:24
Alignment explanation
Indices: 81335--81380 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
81325 ATCCAAACAG
81335 GAGACAACCATAAAAAGGAAATAA
1 GAGACAACCATAAAAAGGAAATAA
* **
81359 GAGATAATGATAAAAAGGAAAT
1 GAGACAACCATAAAAAGGAAAT
81381 CTGGTAGCAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.61, C:0.07, G:0.20, T:0.13
Consensus pattern (24 bp):
GAGACAACCATAAAAAGGAAATAA
Found at i:83078 original size:45 final size:45
Alignment explanation
Indices: 83005--83092 Score: 131
Period size: 45 Copynumber: 2.0 Consensus size: 45
82995 CCATACGTAT
* * *
83005 CGATCTTGATCCTTCTATGGATCTTAAGCCTCCCATGGATCGTGA
1 CGATCTTGAGCCTTCTATAGATCGTAAGCCTCCCATGGATCGTGA
* *
83050 CGATCTTGCGCCTTCTATATATCGTAAGCCTCCCATGGATCGT
1 CGATCTTGAGCCTTCTATAGATCGTAAGCCTCCCATGGATCGT
83093 AAGGAAGAGG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.19, C:0.28, G:0.19, T:0.33
Consensus pattern (45 bp):
CGATCTTGAGCCTTCTATAGATCGTAAGCCTCCCATGGATCGTGA
Found at i:88742 original size:34 final size:34
Alignment explanation
Indices: 88703--88767 Score: 130
Period size: 34 Copynumber: 1.9 Consensus size: 34
88693 TCAAATTTAC
88703 TTACTTCAAAAAAGTTAACAATATATATATAATG
1 TTACTTCAAAAAAGTTAACAATATATATATAATG
88737 TTACTTCAAAAAAGTTAACAATATATATATA
1 TTACTTCAAAAAAGTTAACAATATATATATA
88768 TATATATAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.51, C:0.09, G:0.05, T:0.35
Consensus pattern (34 bp):
TTACTTCAAAAAAGTTAACAATATATATATAATG
Found at i:91406 original size:104 final size:104
Alignment explanation
Indices: 91252--91580 Score: 541
Period size: 104 Copynumber: 3.2 Consensus size: 104
91242 AACTCAAGTA
* * *
91252 TTCATCAATTAATACTGGCTCCGGGTTCGTTGTCAACACTGCCATTTTTTCAAAGTGAAGACTTG
1 TTCATCGATTAATACTGCCTCCGGGTTCGCTGTCAACACTGCCATTTTTTCAAAGTGAAGACTTG
91317 GAGTTTTAGTCGATTAATACTAAAACTCAAACTGGAGTT
66 GAGTTTTAGTCGATTAATACTAAAACTCAAACTGGAGTT
91356 TTCATCGATTAATACTGCCTCCGGGTTCGCTGTCAACACTGCCATTTTTTCAAAGTGAAGACTTG
1 TTCATCGATTAATACTGCCTCCGGGTTCGCTGTCAACACTGCCATTTTTTCAAAGTGAAGACTTG
91421 GAGTTTTAGTCGATTAATACTAAAACTCAAACTGGAGTT
66 GAGTTTTAGTCGATTAATACTAAAACTCAAACTGGAGTT
* *
91460 TTCATCGATTAATACTGCCTCCGGGTTCGCTGTCAACACTGCCACTTTTTTAAAAGAGAAGACTT
1 TTCATCGATTAATACTGCCTCCGGGTTCGCTGTCAACACTGCCA-TTTTTTCAAAGTGAAGACTT
** * * * *
91525 GGAGTTTTAGTCGATTAATACTGGAATTAAAACTGAAGTA
65 GGAGTTTTAGTCGATTAATACTAAAACTCAAACTGGAGTT
*
91565 TTCATCGACTAATACT
1 TTCATCGATTAATACT
91581 TTTCTGACAG
Statistics
Matches: 212, Mismatches: 12, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
104 145 0.68
105 67 0.32
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (104 bp):
TTCATCGATTAATACTGCCTCCGGGTTCGCTGTCAACACTGCCATTTTTTCAAAGTGAAGACTTG
GAGTTTTAGTCGATTAATACTAAAACTCAAACTGGAGTT
Found at i:99750 original size:321 final size:319
Alignment explanation
Indices: 98712--100536 Score: 1635
Period size: 321 Copynumber: 5.6 Consensus size: 319
98702 TCAGTTTTTA
* * * * *
98712 GCCCCGACTCAGTTTTGCATGATTTTTGGCGTAAAGATTTC-TTTAAATATCTATATTAAATCGA
1 GCCCCGACTCAGTTTTGCATGATTTTTGGCATAAAGA-CTCATTGAAATATCTATATT-CATCAA
* * * * * * *
98776 ATCAAATCACAGT-CACACTCGATTTAAGGATTT-GTTTTACGAGCATCTAAATCTTGTTTCGAT
64 ACCAAATCTCA-TCCAAATTGGATTTAAGGATTTATTTTTACGAGCATCTGAATCTTGTTTCGAT
* *
98839 TTAATTAGAAATTAATTCCGGAAAAAAAGGAAAAAAGATATTAGATA-CGTGAAAAACCTTTCAA
128 TTAATTAGAAATTAATT-CGGAAAAAAAGGAAAAACGATATTAGA-AGCGTGAAAAACCCTTCAA
* * * *
98903 TCTTTTTTGGGGTTAAACTATATATTTTTTATGAGTATTGTGGTGAAAAAATTGAGAAAAAAAAT
191 T-TTTTTTGGCGTTAAATTATATATTTTTTATGAGTATTGTGG-CAAAAAATTGAG--AAAAAAC
* * * *
98968 ATTTCGGGTCAGTTTTTAGCCGAAAATCGGGTACTAACCATCACAGTTTTTGGCTAAAAACGCAT
252 ATTTCGGGTAAGTTTTTAGCCG-AAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAA-G-AG
**
99033 TTTGGG
314 TTCCGG
** * * *
99039 GCCTTGACTCAGTTTTGCATGGTTTTTGGCATAAAGACTCATTGAAATGTCTATATTCATCTAAC
1 GCCCCGACTCAGTTTTGCATGATTTTTGGCATAAAGACTCATTGAAATATCTATATTCATCAAAC
* * * * * *
99104 CAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGTATATATGAATCTTGTTTCAATT
66 CAAATCTCATCCAAATTGGATTTAAGGATTTATTTTTACGAG--CATCTGAATCTTGTTTCGATT
* * * * * *
99169 TAATTAGAAATAAATTTGAAAAAAAAAAGGAAAAATGATATTGGAAGCGAGAAAAACCCTTCAAT
129 TAATTAGAAATTAATTCG--GAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAAT
* * * * * * * *
99234 TTTTTTGGTGTTGAATTATATATTTTTTTCTGAGTATTATAGCCAAAAATTAAGAAAAAACTTTT
192 TTTTTTGGCGTTAAATTATATA-TTTTTTATGAGTATTGTGGCAAAAAATTGAGAAAAAACATTT
* * * * * * *
99299 CAAGTCAGTTTTTGCAAATTTTTGGCTGAAATCTTGTACTAACCTTCACGGTTTTTGACTAAAAA
256 C--G---G-----GTAAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAA
*
99364 CATGTTCCGG
311 GA-GTTCCGG
* * * * * * *
99374 AGCCCCGGCTCAAG-TTTGCATCATGTTTGACGA-AAAGACTCCTTCAAATATCTATATTCATCG
1 -GCCCCGACTC-AGTTTTGCATGATTTTTGGC-ATAAAGACTCATTGAAATATCTATATTCATCA
* * * *
99437 AACCAAATCTCATCAAAACTGGATATAAGGATTTATTTTTACGAGCATCTGGATCTTGTTTCGAT
63 AACCAAATCTCATCCAAATTGGATTTAAGGATTTATTTTTACGAGCATCTGAATCTTGTTTCGAT
* * * * * * *
99502 TTAATTAGAAATTAATTCGGAAAAACAGGAAAAACGATATTGGAAACGTTAAAAGCCCGTCAATA
128 TTAATTAGAAATTAATTCGGAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATT
99567 TTTTTGGCGTTAAATTATATACTTTTTT-TGAGTATTGTGGCAAAAAATTGAGAAAAAACATTTC
193 TTTTTGGCGTTAAATTATATA-TTTTTTATGAGTATTGTGGCAAAAAATTGAGAAAAAACATTTC
* ** * * *
99631 GGGTAAGTTTTTAGCCGAAATCATAAACCAACCATCACGGTTTTTCGCTAAAAATGAGTTACGAG
257 GGGTAAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAA-GAGTTCCG-G
* * *
99696 GCCCC-AGTTCAGTTTTGCATGATTTTTGGCATAAAAACTCATTGAAATATCTATATTGATCAAA
1 GCCCCGA-CTCAGTTTTGCATGATTTTTGGCATAAAGACTCATTGAAATATCTATATTCATCAAA
* * *
99760 CCAAATCTCATCCAAGTTAGATTTAAGGATTTATTTTTACGAGCATCTGAATCTTGTTTCGAATT
65 CCAAATCTCATCCAAATTGGATTTAAGGATTTATTTTTACGAGCATCTGAATCTTGTTTCGATTT
* * * * * *
99825 AATTAGAGATTAATTCGG----GAA--AAAAATGATATTAGAAGCGTGGAAAATCCTTCATCTTT
130 AATTAGAAATTAATTCGGAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCA-ATTT
* * * *
99884 TTTTGGCATTGAATTATATA-TTTTT-TGAGTATTGTGGCTAAGAATTGAGGAGAAATTTCACGG
194 TTTTGGCGTTAAATTATATATTTTTTATGAGTATTGTGGCAAAAAATTGA-GA-AAA----A---
* * * * *
99947 ATCAGTTTTC--GCAAATTTTTAGCCGAAATCGTTTACT---CATCGCGGTTTATGGCTAAAAAC
250 A-CA--TTTCGGGTAAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAA-
*
100007 GCGTTCCGG
311 GAGTTCCGG
* * * * * *
100016 GTTCCCGACTCAGTTTTGCATGATTTTTGGCGTAAAGACTCCTTAAAATATCTATATTTATAAAA
1 G-CCCCGACTCAGTTTTGCATGATTTTTGGCATAAAGACTCATTGAAATATCTATATTCATCAAA
* * * ** * *
100081 CCAAATCCCAACCAAATTTGATTTAACAATTTATTTTTACGAGCATCTCAATCTTGTTTCAATTT
65 CCAAATCTCATCCAAATTGGATTTAAGGATTTATTTTTACGAGCATCTGAATCTTGTTTCGATTT
* * * *
100146 AATTATAAATTAATTTGGAAAAAAATGGAAAAACGATATTAGAAGCATGAAAAACCCTTCAATCT
130 AATTAGAAATTAATTCGGAAAAAAA-GGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTT
* * * *
100211 TTTTGGCGTTTAATTATATATTTTTTACGAGTATTGTGGAAAAAAATTAAGAAAAAA-ATTTTCG
194 TTTTGGCGTTAAATTATATATTTTTTATGAGTATTGTGGCAAAAAATTGAGAAAAAACA-TTTCG
* * ** * *
100275 GGTCAGTTTTTAGCCGAAATCGTGTACTAGCCATCACGAATTTTGGCTAAAAACACGTTTCGG
258 GGTAAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAAGA-GTTCCGG
* * * * * * *
100338 GCCTCGACTCAGTTTCT-CATGGTTTTTGACATATAGACTCTTTTAAATATCTATATTCATCTAA
1 GCCCCGACTCAGTTT-TGCATGATTTTTGGCATAAAGACTCATTGAAATATCTATATTCATCAAA
*** * * * * * * *
100402 GTGAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTATGAGCATTTGAATCTTATTTCGATTT
65 CCAAATCTCATCCAAATTGGATTTAAGGATTTATTTTTACGAGCATCTGAATCTTGTTTCGATTT
* *
100467 AATTAGAAATAAATTCGGGAAAAAAAAGGAAAAACGATATTAGAAGTGTGAAAAACCCTTCAATT
130 AATTAGAAATTAATTC-GG-AAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATT
*
100532 ATTTT
193 TTTTT
100537 CAAGTCAGTT
Statistics
Matches: 1208, Mismatches: 229, Indels: 127
0.77 0.15 0.08
Matches are distributed among these distances:
314 26 0.02
315 27 0.02
316 23 0.02
317 6 0.00
318 1 0.00
319 23 0.02
320 7 0.01
321 430 0.36
322 70 0.06
323 9 0.01
324 23 0.02
325 2 0.00
326 38 0.03
327 89 0.07
328 37 0.03
329 81 0.07
330 54 0.04
331 31 0.03
332 63 0.05
334 34 0.03
335 4 0.00
336 117 0.10
337 13 0.01
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35
Consensus pattern (319 bp):
GCCCCGACTCAGTTTTGCATGATTTTTGGCATAAAGACTCATTGAAATATCTATATTCATCAAAC
CAAATCTCATCCAAATTGGATTTAAGGATTTATTTTTACGAGCATCTGAATCTTGTTTCGATTTA
ATTAGAAATTAATTCGGAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTT
TTGGCGTTAAATTATATATTTTTTATGAGTATTGTGGCAAAAAATTGAGAAAAAACATTTCGGGT
AAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAAAGAGTTCCGG
Found at i:100352 original size:642 final size:640
Alignment explanation
Indices: 98711--100492 Score: 1994
Period size: 642 Copynumber: 2.7 Consensus size: 640
98701 ATCAGTTTTT
* * *
98711 AGCCCCGACTCAGTTTTGCATGATTTTTGGCGTAAAGATTTCTTTAAATATCTATATTAAATCGA
1 AGCCCCGACTCAGTTTTGCATGATTTTTGGCGTAAAGACTCCTTAAAATATCTATATT-AATCGA
* ** * *
98776 ATCAAATCACAGTCACACTCGATTTAAGGATTT-GTTTTACGAGCATCTAAATCTTGTTTCGATT
65 ACCAAATCACAACCAAACTCGATTTAAGGATTTATTTTTACGAGCATCTAAATCTTGTTTCGATT
* *
98840 TAATTAGAAATTAATTCCGGAAAAAAAGGAAAAAAGATATTAGATACGTGAAAAACCTTTCAATC
130 TAATTAGAAATTAATT-CGGAAAAAAAGGAAAAACGATATTAGA-ACGTGAAAAACCCTTCAATC
* * *
98905 TTTTTTGGGGTTAAACTATATATTTTTTATGAGTATTGTGGTGAAAAAATTGAGAAAAAAAATAT
193 -TTTTTGGCGTTAAATTATATATTTTTTATGAGTATTGTGG-AAAAAAATTGAG-AAAAAAAT-T
* * *
98970 TTCGGGTCAGTTTTTAGCCGAAAATCGGGTACTAACCATCAC-AGTTTTTGGCTAAAAACGCATT
254 TTCGGGTCAGTTTTTAGCCG-AAATCGTGTACTAACCATCACGA-TTTTTGGCTAAAAACAC-GT
* * *
99034 TTGGGGCCTTGACTCAGTTTTGCATGGTTTTTGGCATAAAGACTCATTGAAATGTCTATATTCAT
316 TTCGGGCCTCGACTCAGTTTTGCATGGTTTTTGGCATAAAGACTCATTGAAATATCTATATTCAT
*
99099 CTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGTATATATGAATCTTGTTT
381 CTAACCAAATCTCAGCCACATT-GATTTAAGGATTTGTTTTTACGAG--CATATGAATCTTGTTT
* ** *
99164 C-AATTTAATTAGAAATAAATTTGAAAAAAAAAAGGAAAAATGATATTGGAAGCGAGAAAAACCC
443 CGAA-TTAATTAGAAATAAATTCG------GGAA--AAAAATGATATTAGAAGCGAGAAAAACCC
**
99228 TTCAATTTTTTTGGTGTTGAATTATATATTTTTTTCTGAGTATTATAGCCAAAAATTAAGAAAAA
499 TTCAATTTTTTTGGCATTGAATTATATA-TTTTTTCTGAGTATTATAGCCAAAAATTAAGAAAAA
* * * * *
99293 ACTTTTCAAGTCAGTTTTTGCAAATTTTTGGCTGAAATCTTGTACTAACCTTCACGGTTTTTGAC
563 AC-TTTCAAGTCAGTTTTCGCAAATTTTTAGCCGAAATCTTGTACT-A-CATCACGGTTTATGAC
*
99358 TAAAAACATGTTCCGG
625 TAAAAACACGTTCCGG
* * * * * * *
99374 AGCCCCGGCTCAAG-TTTGCATCATGTTTGACGAAAAGACTCCTTCAAATATCTATATTCATCGA
1 AGCCCCGACTC-AGTTTTGCATGATTTTTGGCGTAAAGACTCCTTAAAATATCTATATTAATCGA
* * * * * **
99438 ACCAAATCTCATCAAAACTGGATATAAGGATTTATTTTTACGAGCATCTGGATCTTGTTTCGATT
65 ACCAAATCACAACCAAACTCGATTTAAGGATTTATTTTTACGAGCATCTAAATCTTGTTTCGATT
* * * * * *
99503 TAATTAGAAATTAATTCGGAAAAACAGGAAAAACGATATTGGAAACGTTAAAAGCCCGTCAATAT
130 TAATTAGAAATTAATTCGGAAAAAAAGGAAAAACGATATTAG-AACGTGAAAAACCCTTCAATCT
*
99568 TTTTGGCGTTAAATTATATACTTTTTT-TGAGTATTGTGGCAAAAAATTGAGAAAAAACA-TTTC
194 TTTTGGCGTTAAATTATATA-TTTTTTATGAGTATTGTGGAAAAAAATTGAGAAAAAA-ATTTTC
* * ** * * * * *
99631 GGGTAAGTTTTTAGCCGAAATCATAAACCAACCATCACGGTTTTTCGCTAAAAATGA-GTTACGA
257 GGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAA-CACGTTTCG-
* * * * * *
99695 GGCC-CCAGTTCAGTTTTGCATGATTTTTGGCATAAAAACTCATTGAAATATCTATATTGATCAA
320 GGCCTCGA-CTCAGTTTTGCATGGTTTTTGGCATAAAGACTCATTGAAATATCTATATTCATCTA
* * *
99759 ACCAAATCTCATCCA-AGTTAGATTTAAGGATTTATTTTTACGAGCATCTGAATCTTGTTTCGAA
384 ACCAAATCTCAGCCACA-TT-GATTTAAGGATTTGTTTTTACGAGCATATGAATCTTGTTTCGAA
* * * * * *
99823 TTAATTAGAGATTAATTCGGGAAAAAAATGATATTAGAAGCGTGGAAAATCCTTCATCTTTTTTT
447 TTAATTAGAAATAAATTCGGGAAAAAAATGATATTAGAAGCGAGAAAAACCCTTCA-ATTTTTTT
* * * * * * * *
99888 GGCATTGAATTATATA-TTTTT-TGAGTATTGTGGCTAAGAATTGAGGAGAAA-TTTCACGGATC
511 GGCATTGAATTATATATTTTTTCTGAGTATTATAGCCAAAAATTAAGAAAAAACTTTCA-AG-TC
* * *
99950 AGTTTTCGCAAATTTTTAGCCGAAATCGTT-TACT-CATCGCGGTTTATGGCTAAAAACGCGTTC
574 AGTTTTCGCAAATTTTTAGCCGAAATC-TTGTACTACATCACGGTTTATGACTAAAAACACGTTC
100013 CGG
638 CGG
* * **
100016 -GTTCCCGACTCAGTTTTGCATGATTTTTGGCGTAAAGACTCCTTAAAATATCTATATTTATAAA
1 AG-CCCCGACTCAGTTTTGCATGATTTTTGGCGTAAAGACTCCTTAAAATATCTATATTAATCGA
* * * ** * *
100080 ACCAAATCCCAACCAAATTTGATTTAACAATTTATTTTTACGAGCATCTCAATCTTGTTTCAATT
65 ACCAAATCACAACCAAACTCGATTTAAGGATTTATTTTTACGAGCATCTAAATCTTGTTTCGATT
* * *
100145 TAATTATAAATTAATTTGGAAAAAAATGGAAAAACGATATTAGAAGCATGAAAAACCCTTCAATC
130 TAATTAGAAATTAATTCGGAAAAAAA-GGAAAAACGATATTAGAA-CGTGAAAAACCCTTCAATC
* * *
100210 TTTTTGGCGTTTAATTATATATTTTTTACGAGTATTGTGGAAAAAAATTAAGAAAAAAATTTTCG
193 TTTTTGGCGTTAAATTATATATTTTTTATGAGTATTGTGGAAAAAAATTGAGAAAAAAATTTTCG
* *
100275 GGTCAGTTTTTAGCCGAAATCGTGTACTAGCCATCACGAATTTTGGCTAAAAACACGTTTCGGGC
258 GGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAACACGTTTCGGGC
* * * * **
100340 CTCGACTCAGTTTCT-CATGGTTTTTGACATATAGACTCTTTTAAATATCTATATTCATCTAAGT
323 CTCGACTCAGTTT-TGCATGGTTTTTGGCATAAAGACTCATTGAAATATCTATATTCATCTAACC
* * * * *
100404 GAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTATGAGCATTTGAATCTTATTTCGATTTAA
387 AAATCTCAGCCACATTG-ATTTAAGGATTTGTTTTTACGAGCATATGAATCTTGTTTCGAATTAA
100469 TTAGAAATAAATTCGGGAAAAAAA
451 TTAGAAATAAATTCGGGAAAAAAA
100493 AGGAAAAACG
Statistics
Matches: 941, Mismatches: 152, Indels: 73
0.81 0.13 0.06
Matches are distributed among these distances:
641 4 0.00
642 288 0.31
643 139 0.15
644 1 0.00
645 53 0.06
646 7 0.01
647 29 0.03
648 21 0.02
649 2 0.00
655 31 0.03
656 7 0.01
657 122 0.13
658 20 0.02
659 6 0.01
660 12 0.01
661 31 0.03
662 74 0.08
663 92 0.10
664 2 0.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35
Consensus pattern (640 bp):
AGCCCCGACTCAGTTTTGCATGATTTTTGGCGTAAAGACTCCTTAAAATATCTATATTAATCGAA
CCAAATCACAACCAAACTCGATTTAAGGATTTATTTTTACGAGCATCTAAATCTTGTTTCGATTT
AATTAGAAATTAATTCGGAAAAAAAGGAAAAACGATATTAGAACGTGAAAAACCCTTCAATCTTT
TTGGCGTTAAATTATATATTTTTTATGAGTATTGTGGAAAAAAATTGAGAAAAAAATTTTCGGGT
CAGTTTTTAGCCGAAATCGTGTACTAACCATCACGATTTTTGGCTAAAAACACGTTTCGGGCCTC
GACTCAGTTTTGCATGGTTTTTGGCATAAAGACTCATTGAAATATCTATATTCATCTAACCAAAT
CTCAGCCACATTGATTTAAGGATTTGTTTTTACGAGCATATGAATCTTGTTTCGAATTAATTAGA
AATAAATTCGGGAAAAAAATGATATTAGAAGCGAGAAAAACCCTTCAATTTTTTTGGCATTGAAT
TATATATTTTTTCTGAGTATTATAGCCAAAAATTAAGAAAAAACTTTCAAGTCAGTTTTCGCAAA
TTTTTAGCCGAAATCTTGTACTACATCACGGTTTATGACTAAAAACACGTTCCGG
Found at i:101286 original size:328 final size:319
Alignment explanation
Indices: 100540--102134 Score: 1296
Period size: 328 Copynumber: 4.9 Consensus size: 319
100530 TTATTTTCAA
** *
100540 GTCAGTTTTTGCAAATTTTTAGTTGAAATCGTGTACTAACCATCACGGTTT-TGACTAAAAACGC
1 GTCAG-TTTTGCAAATTTTTAGCCGAAATCGTGTACT---CATCACGGTTTATGGCTAAAAACGC
* **
100604 GTTCCGGAGCGCCGGCTCAAG-TTTGCATGATAT-TTGGCGA-AAAGACTCCTTGAAATA-CTAT
62 GTTCCGG-GCCCCAACTC-AGTTTTGCATGAT-TGTTGGC-ATAAAGACTCCTTGAAATATCTAT
* *
100665 ATTCATCGAACCAAATCTCAGCCAAATTGGATATAAGGA-TT-TTTTTACGAGTATCTGAATCTT
123 ATTCATCGAACCAAATCTCAGCC-AATTGAAT-TAAGGATTTATTTTTACGAGTATCTAAATCTT
* * * * * *
100728 GCTTCGATTTAATTAGAAATTAATTCGAAAAAAAAAGAAAAACGATATTAGAAACGTTAAAAGCC
186 GTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAAGAAAAATGATATTAGAAGCGTGAAAAACC
* * *
100793 CGTCAA--TATTGGCGTTAAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTG-GGAAAAA
251 CTTCAATTTTTTGGCGTTGAATTATATA-TTTTT-TGAGTATTGTGGC-AAAAATTGAGGAAAAA
100855 CTTTTCTG
313 C-TTTCTG
* * * * * * *
100863 GTCA-----G----TTTTTAGCCTAAATCGTGAACCAACCATCACGGTTTTTCGTTAAAAACGAG
1 GTCAGTTTTGCAAATTTTTAGCCGAAATCGTGTA-C--TCATCACGGTTTATGGCTAAAAACGCG
* * * * * *
100919 TTACGGGGCCCAAGTTCAGTTTTGCATGATTTTTGGCATAATGACTCATTGAAATATCTATATTC
63 TTCCGGGCCCCAA-CTCAGTTTTGCATGATTGTTGGCATAAAGACTCCTTGAAATATCTATATTC
* * *
100984 ATCTAACCAAATCTCATCCAAGTTAGAATTAAGGATTTATTTTTATGAGTATCTAAATCTTGTTT
127 ATCGAACCAAATCTCAGCCAA-TT-GAATTAAGGATTTATTTTTACGAGTATCTAAATCTTGTTT
* * *
101049 CGATTTAATTAGAAATTAACTCGGGAAAAAAAAGAAAAATGATATTAGAAGCGTGGAAAATCCTT
190 CGATTTAATTAGAAATTAATTC-GGAAAAAAAAGAAAAATGATATTAGAAGCGTGAAAAACCCTT
* *
101114 CAATTTATTTTGGCATTGAATTATACATTTTTTGAGTATTGTGGCAAAGAATTGAGGAAAAA-TT
254 CAA-TT-TTTTGGCGTTGAATTATATATTTTTTGAGTATTGTGGCAAA-AATTGAGGAAAAACTT
101178 TCTTG
316 TC-TG
*
101183 GATCAGTTTTCGCAAATTTTTAGCCGAAATCGTTTACTCATCACGGTTTATGGCTAAAAACGCGT
1 G-TCAGTTTT-GCAAATTTTTAGCCGAAATCGTGTACTCATCACGGTTTATGGCTAAAAACGCGT
* *
101248 TCCGGGTCCCCAACTCAGTTTTGCATGATTGTTGGCATAAAGACTCCTTAAAATATCTATATTTA
64 TCCGGG-CCCCAACTCAGTTTTGCATGATTGTTGGCATAAAGACTCCTTGAAATATCTATATTCA
** * * * * * *
101313 TAAAACCAAATCCCAACAAAATTTGATTTAACGATTTATTTTTACGAGTATCTCAATCTTGTTTC
128 TCGAACCAAATCTCAGC-CAA-TTGAATTAAGGATTTATTTTTACGAGTATCTAAATCTTGTTTC
* *
101378 GATTTAATTAGAAATTAATTC-G--------GAAAAATGATATTAGAAGCATGAAAAAGCCTTCA
191 GATTTAATTAGAAATTAATTCGGAAAAAAAAGAAAAATGATATTAGAAGCGTGAAAAACCCTTCA
* * * *
101434 ATCTTTCTGGCGTTAAATTATATATTTTTTACGAGTATTGTGGCATAAAATTGAGAAAAAAAATT
256 AT-TTTTTGGCGTTGAATTATATATTTTTT--GAGTATTGTGGCA-AAAATTGAG-GAAAAACTT
101499 TCT-
316 TCTG
* * * *
101502 G---G--TT---AGTTTTTAGCCGAAATCGTGTACTAGCCATAACGG-CTATTGGCTAAAAACAC
1 GTCAGTTTTGCAAATTTTTAGCCGAAATCGTGTACT---CATCACGGTTTA-TGGCTAAAAACGC
* * * * * * * *
101558 GTTTCGGGGCCTCGACTCAGTTTTTCATGGTTTTTGACATATAGACTCCTTGAAATATCTATATT
62 G-TTCCGGGCCCCAACTCAGTTTTGCATGATTGTTGGCATAAAGACTCCTTGAAATATCTATATT
* * * ** * *
101623 TATCTAAGCAAATCTTTGCCACATTGAATTTAAGGATTTATTTTTACGAGCAT-TCGAATCTTGT
126 CATCGAACCAAATCTCAGCCA-ATTGAA-TTAAGGATTTATTTTTACGAGTATCT-AAATCTTGT
* ** * *
101687 TTCGATTTAATTAGAAATAAATTCCGG-AAAAATGGAAAAACGATATTAGAAGTGTGAAAAACCC
188 TTCGATTTAATTAGAAATTAATT-CGGAAAAAAAAGAAAAATGATATTAGAAGCGTGAAAAACCC
* * * *
101751 TTCAATTTTTTGGTGTTGAGTTATATATTTTTCTAGAGTATTGTGGGAAAATATTGAAGAAAAAC
252 TTCAATTTTTTGGCGTTGAATTATATATTTTT-T-GAGTATTGTGGCAAAA-ATTGAGGAAAAAC
*
101816 TCTTCAG
314 T-TTCTG
* * * * * * * *
101823 GTAAGTTTTTGCAAAATTTTAGTCAAAATCGTGTACTAATCATCCCAGTTTTTGGCTAAAAACGA
1 GTCAG-TTTTGCAAATTTTTAGCCGAAATCGTGTAC---TCATCACGGTTTATGGCTAAAAACGC
* * * * ** *
101888 GTTCTGGAGCCCC-GCATCAATTTTGCAGGATTTTTGTTTGGCATAAAGACTTTTTGAAATTTCT
62 GTTCCGG-GCCCCAAC-TCAGTTTTGCATGA---TTG-TTGGCATAAAGACTCCTTGAAATATCT
* * * *
101952 ATAGTCATCGAACCAAATCTCAGCCACATT-AGATATAAGGATTTGTTTTTACGAGCATTTAAAT
121 ATATTCATCGAACCAAATCTCAGCCA-ATTGA-AT-TAAGGATTTATTTTTACGAGTATCTAAAT
* * * * * * *
102016 TTTATTTCAATCTAATTAGAAATTAATTCAGAAAAAAAAAGGAAAATGATATTAGAAGCATGAAA
183 CTTGTTTCGATTTAATTAGAAATTAATTC-GGAAAAAAAAGAAAAATGATATTAGAAGCGTGAAA
* ** * *
102081 AGCCAGTCAATTTTTTGGCGTTGAATTATATTTTTTTTTAGTATTGTGGCAAAA
247 AACCCTTCAATTTTTTGGCGTTGAATTATATATTTTTTGAGTATTGTGGCAAAA
102135 TTTTCAGAAT
Statistics
Matches: 1023, Mismatches: 164, Indels: 160
0.76 0.12 0.12
Matches are distributed among these distances:
309 22 0.02
311 8 0.01
312 133 0.13
313 43 0.04
314 51 0.05
315 34 0.03
316 5 0.00
317 68 0.07
318 70 0.07
319 37 0.04
320 71 0.07
321 53 0.05
322 16 0.02
323 4 0.00
324 1 0.00
326 1 0.00
327 3 0.00
328 144 0.14
329 15 0.01
330 51 0.05
331 18 0.02
333 20 0.02
334 97 0.09
335 58 0.06
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (319 bp):
GTCAGTTTTGCAAATTTTTAGCCGAAATCGTGTACTCATCACGGTTTATGGCTAAAAACGCGTTC
CGGGCCCCAACTCAGTTTTGCATGATTGTTGGCATAAAGACTCCTTGAAATATCTATATTCATCG
AACCAAATCTCAGCCAATTGAATTAAGGATTTATTTTTACGAGTATCTAAATCTTGTTTCGATTT
AATTAGAAATTAATTCGGAAAAAAAAGAAAAATGATATTAGAAGCGTGAAAAACCCTTCAATTTT
TTGGCGTTGAATTATATATTTTTTGAGTATTGTGGCAAAAATTGAGGAAAAACTTTCTG
Found at i:101663 original size:312 final size:305
Alignment explanation
Indices: 100555--101814 Score: 1044
Period size: 312 Copynumber: 4.0 Consensus size: 305
100545 TTTTTGCAAA
** * * * * **
100555 TTTTTAGTTGAAATCGTGTACTAACCATCACGGTTTTGACTAAAAACGCGTTCCGGAGCGCCGGC
1 TTTTTAGCCGAAATCGTGTACT-ACCATCACGGTTTTGGCTAAAAACACGTTACGGGGC-CCAAC
* * *
100620 TCAAG-TTTGCATGATATTTGGCGAAAAGACTCCTTGAAATA-CTATATTCATCGAACCAAATCT
64 TC-AGTTTTGCATGATTTTTGGC-ATAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCT
* * * *
100683 CAGCCAAA-TTGGATATAAGGA-TT-TTTTTACGAGTATCTGAATCTTGCTTCGATTTAATTAGA
127 CAGCCAAAGTTGAATTTAAGGATTTATTTTTACGAGTATCTCAATCTTGTTTCGATTTAATTAGA
* * * * *
100745 AATTAATTCGAAAAAAAAAGAAAAACGATATTAGAAACGT-TAAAAGCCCGTCAA-TATTGGCGT
192 AATTAATTCG--------AGAAAAATGATATTAGAAGCGTGAAAAAG-CCTTCAATTTTTGGCGT
* ** *
100808 TAAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGGGAAAAACTTTTCTGGTCAG
248 TAAATTATATATTTTTTC-GAGTATTGTGGC-AAAAATTGAGAAAAAAATTTCTGGTTAG
* * * * *
100868 TTTTTAGCCTAAATCGTGAACCAACCATCACGGTTTTTCGTTAAAAACGA-GTTACGGGGCCCAA
1 TTTTTAGCCGAAATCGTGTA-CTACCATCACGG-TTTTGGCTAAAAAC-ACGTTACGGGGCCCAA
* *
100932 GTTCAGTTTTGCATGATTTTTGGCATAATGACTCATTGAAATATCTATATTCATCTAACCAAATC
63 -CTCAGTTTTGCATGATTTTTGGCATAA-GACTCCTTGAAATATCTATATTCATCTAACCAAATC
* * *
100997 TCATCC-AAGTTAGAA-TTAAGGATTTATTTTTATGAGTATCTAAATCTTGTTTCGATTTAATTA
126 TCAGCCAAAGTT-GAATTTAAGGATTTATTTTTACGAGTATCTCAATCTTGTTTCGATTTAATTA
* * *
101060 GAAATTAACTCGGGAAAAAAAAGAAAAATGATATTAGAAGCGTGGAAAATCCTTCAATTTATTTT
190 GAAATTAATTC--G-------AGAAAAATGATATTAGAAGCGTGAAAAAGCCTTCAA--T-TTTT
* * * *
101125 GGCATTGAATTATACATTTTTT-GAGTATTGTGGCAAAGAATTGAG-GAAAAATTTCTTGGATCA
243 GGCGTTAAATTATATATTTTTTCGAGTATTGTGGCAAA-AATTGAGAAAAAAATTTC-T-G----
*
101188 GTTTTCGCAAA
301 G--TT----AG
* * * *
101199 TTTTTAGCCGAAATCGTTTACT--CATCACGGTTTATGGCTAAAAACGCGTTCCGGGTCCCCAAC
1 TTTTTAGCCGAAATCGTGTACTACCATCACGGTTT-TGGCTAAAAACACGTTACGGG-GCCCAAC
* * * ** *
101262 TCAGTTTTGCATGATTGTTGGCATAAAGACTCCTTAAAATATCTATATTTATAAAACCAAATCCC
64 TCAGTTTTGCATGATTTTTGGCAT-AAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTC
* * * *
101327 AACAAAATTTG-ATTTAACGATTTATTTTTACGAGTATCTCAATCTTGTTTCGATTTAATTAGAA
128 AGCCAAAGTTGAATTTAAGGATTTATTTTTACGAGTATCTCAATCTTGTTTCGATTTAATTAGAA
*
101391 ATTAATTCG-GAAAAATGATATTAGAAGCATGAAAAAGCCTTCAATCTTTCTGGCGTTAAATTAT
193 ATTAATTCGAGAAAAATGATATTAGAAGCGTGAAAAAGCCTTCAAT-TTT-TGGCGTTAAATTAT
101455 ATATTTTTTACGAGTATTGTGGCATAAAATTGAGAAAAAAAATTTCTGGTTAG
256 ATATTTTTT-CGAGTATTGTGGCA-AAAATTGAG-AAAAAAATTTCTGGTTAG
* * * *
101508 TTTTTAGCCGAAATCGTGTACTAGCCATAACGGCTATTGGCTAAAAACACGTTTCGGGGCCTCGA
1 TTTTTAGCCGAAATCGTGTACTA-CCATCACGG-TTTTGGCTAAAAACACGTTACGGGGCC-CAA
* * * * *
101573 CTCAGTTTTTCATGGTTTTTGACATATAGACTCCTTGAAATATCTATATTTATCTAAGCAAATCT
63 CTCAGTTTTGCATGATTTTTGGCATA-AGACTCCTTGAAATATCTATATTCATCTAACCAAATCT
** * *
101638 TTGCCACA-TTGAATTTAAGGATTTATTTTTACGAGCAT-TCGAATCTTGTTTCGATTTAATTAG
127 CAGCCAAAGTTGAATTTAAGGATTTATTTTTACGAGTATCTC-AATCTTGTTTCGATTTAATTAG
* * * * *
101701 AAATAAATTCCGGAAAAATGGAAAAACGATATTAGAAGTGTGAAAAACCCTTCAATTTTTTGGTG
191 AAATTAATT-C-G----A--GAAAAATGATATTAGAAGCGTGAAAAAGCCTTCAA-TTTTTGGCG
* * * *
101766 TTGAGTTATATATTTTTCTAGAGTATTGTGGGAAAATATTGAAGAAAAA
247 TTAAATTATATATTTTT-TCGAGTATTGTGGCAAAA-ATTG-AGAAAAA
101815 CTCTTCAGGT
Statistics
Matches: 777, Mismatches: 106, Indels: 121
0.77 0.11 0.12
Matches are distributed among these distances:
309 22 0.03
311 8 0.01
312 139 0.18
313 38 0.05
314 54 0.07
315 34 0.04
316 8 0.01
317 64 0.08
318 65 0.08
319 39 0.05
320 62 0.08
321 47 0.06
322 23 0.03
325 1 0.00
326 1 0.00
327 5 0.01
328 137 0.18
329 11 0.01
330 1 0.00
331 18 0.02
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (305 bp):
TTTTTAGCCGAAATCGTGTACTACCATCACGGTTTTGGCTAAAAACACGTTACGGGGCCCAACTC
AGTTTTGCATGATTTTTGGCATAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGC
CAAAGTTGAATTTAAGGATTTATTTTTACGAGTATCTCAATCTTGTTTCGATTTAATTAGAAATT
AATTCGAGAAAAATGATATTAGAAGCGTGAAAAAGCCTTCAATTTTTGGCGTTAAATTATATATT
TTTTCGAGTATTGTGGCAAAAATTGAGAAAAAAATTTCTGGTTAG
Found at i:103005 original size:321 final size:313
Alignment explanation
Indices: 102241--103239 Score: 1026
Period size: 321 Copynumber: 3.1 Consensus size: 313
102231 AATTTTTGCA
* * * *
102241 AATTTTTAGCTGAAATCGTGTACTAACAACCATCACGGTTTTTGACTAAAAACACGTTCCGGAGT
1 AATTTTTAGCCGAAATCGTGTACT----ACCATCAC-GCTTTTGACTAAAAACACGTTTCGGGGT
* * *
102306 GCCGGCTCA-TGTTTGCATGATATTTGGCGAAAAGACTCCTTGAAATATCTATATTCATCGAACC
61 CCCGACTCAGT-TTTGCATGATTTTTGGC-AAAAGACTCCTTGAAATATCTATATTCATCGAACC
*
102370 AAATCTCAGCCAAATTGGATATAAGGATTTTTTTTACGAGCATCTGAATTTTGTTTCGATTTAAT
124 AAATCTCAGCCAAATTGGATATAAGGATTTTTTTTACGAGCATCTGAATCTTGTTTCGATTTAAT
* *
102435 TAGAAATTAATTCGGGAAAAAAATTGAAAAATGATATTAGAAGCGTGGAAAATCCTTCAATTTCT
189 TAGAAATTAATTC-GG-AAAAAATGGAAAAATGATATTAGAAGCGT-GAAAAGCCTTCAA--TCT
* ****
102500 TTTGGCATTGAATTATATATTTTTTGAGTATTGTGGCAAAGAATTGAGGAAAAATTTCTCGTATC
249 TTTGGCATTGAATTATATATTTTTTTAGTATTGTGGCAAA-AATTGA-GAAAAAAAAAT--T-TC
*
102565 AGTTTT
309 AG-GTT
* * * **
102571 CGCAAATTTTTAGCCGAAATCGTTTACT--CATCACGGTTTATGGCT-AAAA-ACGTGTTCCTGG
1 ----AATTTTTAGCCGAAATCGTGTACTACCATCACGCTTT-TGACTAAAAACACGT-TTCGGGG
* * * * * *
102632 TCCCCGACCCAGTTTTGCATGATTTTTGGCGTAAAGAATCCTTAAAATATCTATATTTA-CAAAA
60 T-CCCGACTCAGTTTTGCATGATTTTTGGC-AAAAGACTCCTTGAAATATCTATATTCATC-GAA
* * * * * *
102696 CCAAAT-TCCAACCAAATTTGATTTAACGATTTATTTTTACGACCATCTCAATCTTGTTTCGATT
122 CCAAATCT-CAGCCAAATTGGATATAAGGATTT-TTTTTACGAGCATCTGAATCTTGTTTCGATT
*
102760 TAATTAGAAATTAATTCGG-AAAAATGGAAAAATGATATTAGAAGCATGAAAAAGCCTTCAATCT
185 TAATTAGAAATTAATTCGGAAAAAATGGAAAAATGATATTAGAAGCGTG-AAAAGCCTTCAATCT
* *
102824 TTCTGGCATTAAATTATATATTTTTTACTAGTATTGTGGCATAAAATTGAGAAAAAAAAATTTCT
249 TT-TGGCATTGAATTATATATTTTTT--TAGTATTGTGGCA-AAAATTGAGAAAAAAAAATTTCA
102889 GGTT
310 GGTT
* * *
102893 AGTTTTTAGCCGAAATCATGTACTAGCCATCACGACTTTTGACTAAAAACACGTTTCGGGGTCTC
1 AATTTTTAGCCGAAATCGTGTACTA-CCATCACG-CTTTTGACTAAAAACACGTTTCGGGGTCCC
* * ** *
102958 GACTCAGTTTTTCATGGTTTTTGGCACAAAGACTTTTTGAAATATCTATATTCATCGAACCAGAT
64 GACTCAGTTTTGCATGATTTTTGGCA-AAAGACTCCTTGAAATATCTATATTCATCGAACCAAAT
* * *
103023 CTCAGCCACATTGGATATAAGGATTTGTTTTTACGAGCATTTGAATCTTATTTC-ACTTTAATTA
128 CTCAGCCAAATTGGATATAAGGATTT-TTTTTACGAGCATCTGAATCTTGTTTCGA-TTTAATTA
* * *
103087 GAAATTAATTCGGAAAAAAAGAGAAAAATGATATTAAAAGCGTGAAAAGCCTGTCAATTTTTTGG
191 GAAATTAATTCGGAAAAAATG-GAAAAATGATATTAGAAGCGTGAAAAGCCT-TCAATCTTTTGG
* * * * * *
103152 CGTTGAATTATATATTTTTTTGAGTATTATGACAAAAATTTAAGAAAAAAAAAATTTCGGGTC
254 CATTGAATTATATATTTTTTT-AGTATTGTGGCAAAAA-TTGAG-AAAAAAAAATTTCAGGTT
*
103215 ATTTTTTAGCCGAAATCGTGTACTA
1 AATTTTTAGCCGAAATCGTGTACTA
103240 ATCGTCACAG
Statistics
Matches: 560, Mismatches: 77, Indels: 68
0.79 0.11 0.10
Matches are distributed among these distances:
318 21 0.04
320 6 0.01
321 141 0.25
322 91 0.16
323 35 0.06
324 6 0.01
325 23 0.04
326 48 0.09
327 32 0.06
328 89 0.16
329 46 0.08
334 22 0.04
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (313 bp):
AATTTTTAGCCGAAATCGTGTACTACCATCACGCTTTTGACTAAAAACACGTTTCGGGGTCCCGA
CTCAGTTTTGCATGATTTTTGGCAAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTC
AGCCAAATTGGATATAAGGATTTTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAAT
TAATTCGGAAAAAATGGAAAAATGATATTAGAAGCGTGAAAAGCCTTCAATCTTTTGGCATTGAA
TTATATATTTTTTTAGTATTGTGGCAAAAATTGAGAAAAAAAAATTTCAGGTT
Found at i:104777 original size:334 final size:326
Alignment explanation
Indices: 103745--104877 Score: 1207
Period size: 320 Copynumber: 3.5 Consensus size: 326
103735 AGTTATATTC
* *
103745 AAGGATTTATTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTATTTCGGGAAAAA
1 AAGGATTTATTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTC-GGAAAAA
* * * * *
103810 AATTGAAAAATGATATTAGAAGCGTGGAAAATCCTTCAATTTATTTTGGCATTGAATTATATATT
65 AATGGAAAAACGATATTAGAAGCGTGAAAAAGCCTTCAATTT-TTTTGGCGTTGAATTATATATT
* *
103875 TTTT-GAGTATTGTGGC-AAAGATTTGAGGAAAAATTTCTCGGATAAGTTTTCGCAAATTTTTAG
129 TTTTAGAGTATTGTGGCAAAAGA-TTGAGGAAAAATTTC-AGG-TAAGTTTTTGCAAA-TTTTAG
* * *
103938 CCGAAATCGTTTACT--CATCACGGTTTATGGCTAAAAACGTGTTCCT-GGTCCCCGACTCAGTT
190 CCGAAATCGTGTACTACCATCACGGTTTTTGGCTAAAAACGAGTT-CTGGGT-CCCGACTCAGTT
* * * * * *
104000 TTACATGATTTTTGGCGTAAAAACTCCTTAAAATATCTATATTTATAAAACCAAATC-CCAACCA
253 TTACATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCC-GCCA
* *
104064 AATTTGATTT
317 CATTGGATTT
* * * *
104074 AACGATTTATTTTTACGACCATCTCAATCTTGTTTCGATTGAATTAGAAATTAATTCGG--AAAA
1 AAGGATTTATTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAA
* * *
104137 ATCGAAAAACGATATTAGAAGCATGAAAAA-CTCGTCAATTTTTTTGGCGTT-AAGTTATATATT
66 ATGGAAAAACGATATTAGAAGCGTGAAAAAGC-CTTCAATTTTTTTGGCGTTGAA-TTATATATT
* *
104200 TTTTACGAGTATTGTGGCAAAAAATTGAGAAAAAAGTTTTCAGGTAAG----T-----TTTTAGC
129 TTTTA-GAGTATTGTGGCAAAAGATTGAGGAAAAA--TTTCAGGTAAGTTTTTGCAAATTTTAGC
* * * *
104256 CGAAATCGTGTACTAGCCATCACGGCTTTTGGCTAAAAAC-ACGTTTCGGGGTCTCGACTTAGTT
191 CGAAATCGTGTACTA-CCATCACGGTTTTTGGCTAAAAACGA-G-TTCTGGGTCCCGACTCAGTT
* * * * * * *
104320 TTTCATGGTTTTTGACATATAGACTCCTTGAAATATCTATATTCATCTAAGCAAATCTCAGCCAC
253 TTACATGATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCCGCCAC
*
104385 ATTGAATTT
318 ATTGGATTT
* * * *
104394 AAGGATTTGTTTTTACGAGCATTTGAATCCTGTTTCGATTTAATTAGAAATAAATTCGGGAAAAA
1 AAGGATTTATTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTC-GGAAAAA
* * *
104459 AATGGAAAAACGATATTAGAAGTGTGAAAAAGCCTTCAATTTTTTTGGTGTTGAGTTATATATTT
65 AATGGAAAAACGATATTAGAAGCGTGAAAAAGCCTTCAATTTTTTTGGCGTTGAATTATATATTT
* *
104524 TTCTAGAGTATTGTGGGAAAAGATTGAGGAAAAACTCTTCAGGTCAGTTTTTGCAAAATTTTAGC
130 TT-TAGAGTATTGTGGCAAAAGATTGAGGAAAAA-T-TTCAGGTAAGTTTTTGC-AAATTTTAGC
* * *
104589 CGAAATCGTGCACTAACCATC-CTAGTTTTTGGCTAAAAACGAGTTCTGGAGTCCCGCCTCAGTT
191 CGAAATCGTGTACT-ACCATCAC-GGTTTTTGGCTAAAAACGAGTTCTGG-GTCCCGACTCAGTT
* * * ** *
104653 TTGCATGTTTTTTTGGCACAAAGACTTTTTGAAATATCTATATTCATCGAACCAAATCTCCGCCA
253 TTACATG-ATTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCCGCCA
* *
104718 CATTGGCTAT
317 CATTGGATTT
* * * * *
104728 AAGGATTTGTTTTTACGAGCATTTGAATCTTATTTCAATCTAATTAGAAATTAATTCGGAAAAAA
1 AAGGATTTATTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAA
* *
104793 AAGAGAAAAATGATATTAGAAGCGTG-AAAAGCCCGTT-AA-TTTTTTGGCGTTGAATTATATAT
66 ATG-GAAAAACGATATTAGAAGCGTGAAAAAG-CC-TTCAATTTTTTTGGCGTTGAATTATATAT
*
104855 TGTTTTTGAGTATTGTGGCAAAA
128 T-TTTTAGAGTATTGTGGCAAAA
104878 ATTTCAGAAA
Statistics
Matches: 675, Mismatches: 89, Indels: 76
0.80 0.11 0.09
Matches are distributed among these distances:
317 20 0.03
320 138 0.20
321 8 0.01
322 1 0.00
323 95 0.14
324 6 0.01
325 23 0.03
326 38 0.06
327 27 0.04
328 8 0.01
329 56 0.08
332 6 0.01
333 111 0.16
334 136 0.20
335 2 0.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (326 bp):
AAGGATTTATTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAA
ATGGAAAAACGATATTAGAAGCGTGAAAAAGCCTTCAATTTTTTTGGCGTTGAATTATATATTTT
TTAGAGTATTGTGGCAAAAGATTGAGGAAAAATTTCAGGTAAGTTTTTGCAAATTTTAGCCGAAA
TCGTGTACTACCATCACGGTTTTTGGCTAAAAACGAGTTCTGGGTCCCGACTCAGTTTTACATGA
TTTTTGGCATAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCCGCCACATTGGATT
T
Found at i:106270 original size:654 final size:649
Alignment explanation
Indices: 104960--106668 Score: 1905
Period size: 654 Copynumber: 2.6 Consensus size: 649
104950 AAAATTAAGA
* * * * * * *
104960 AAAAACTTTTCAAGTCAATTTTTGCAAATTTTTAGCTGCAATCGTGTACTAACCATCACGGTTTT
1 AAAAACTCTTCAGGTCAGTTTTCGCAAAATTTTAGCCGAAATCGTGTACT-A-CATCACGGTTTT
* * * *
105025 TGACTAAAAAC-ACGTTCCGGAGCACCGGCTCATGTTTGCATGATATTTGGCGAAAAGACTCCTT
64 TGGCTAAAAACGA-GTTCCGGAGCCCCGACTCAT-TTTGCATGATTTTTGGC-AAAAGACTCCTT
*
105089 GAAATATCTATATTCATTGAACCAAATCTCAGCCAAATTGGATATAAGGATTTTTTTTACGAGCA
126 GAAATATCTATATTCATAGAACCAAATCTCAGCCAAATTGGATATAAGGATTTTTTTTACGAGCA
*
105154 TCTGAATCCTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAAGGAAAAACGATATTAGAAA
191 TCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAAGGAAAAACGATATTAG--A
* * *
105219 TG-TTAAAAGCCCGTCAACCTTTTTGGTGTTAAATTATATATTTTTTCTGAGTATTGTGGC-AAA
254 TGCTGAAAAGCCCGTCAATCTTTTTGGCGTTAAATTATATATTTTTTC-GAGTATTGTGGCAAAA
* * *
105282 AATTGAGAAAAAAACTTTTCGGGTCAGTTTTTAGCCGAAATCGTGAACCAACAACCATCACGGTT
318 AATTGAGAAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTA-C--TAACCATCACGGTT
* * * * * * * *
105347 TTTCGCTTAAAACGAGTTACGGGGCCCCAGTTCAGTTTTGCATGATTTTTGGCACTAAGACTCAT
380 TTTGGCTAAAAACGAATTACGGGGCCCCAGATAAGTTTTGCATGACTTTTGACACTAACACTCAT
* *
105412 TGAAATATCTATATTCATCAAACCAAATCTCATCCAAGTTAGATTTGAGGATTTATTTTTACGAG
445 TGAAATATCTATATTCATCAAACCAAATCTCAGCCAAGTTAGATTTAAGGATTTATTTTTACGAG
* * * *
105477 CATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCGGGAAAAAAATTGAAAAATGATATTAG
510 CATCTAAATCTTGTTTCGATCTAATTAGAAATAAATTCGGGAAAAAAATGGAAAAACGATATTAG
* * * * * * * *
105542 AAGCGTGGAAAATCCTTCAATTTATTTTGGCATTGAATTATATATTTTTTTGAGTATTGTGGCAA
575 AAGCGTGAAAAAACCTTCAAATTATTTTGGCACTGAATTACATATTTTTTAGAATATTGTGGAAA
105607 AGAATTGAGG
640 AGAATTGAGG
* * * * * *
105617 AAAAA-T-TTCTCGGATCAGTTTTCGTAAATTTTTAGCCGAAATTGTTTACT-CATCACGGTTTA
1 AAAAACTCTTC-AGG-TCAGTTTTCGCAAAATTTTAGCCGAAATCGTGTACTACATCACGGTTTT
* *
105679 TGGCTAAAAACGTGTTCCGG-GTCCCCGACTCAGTTTTGCATGATTTTTGACATAAAGACTCCTT
64 TGGCTAAAAACGAGTTCCGGAG-CCCCGACTCA-TTTTGCATGATTTTTGGCA-AAAGACTCCTT
* * * * * * * * *
105743 AAAATATCTATATTTATAAAACCAAATCCCAACCAAATTTGATTTAACGATTTATTTTTACGACC
126 GAAATATCTATATTCATAGAACCAAATCTCAGCCAAATTGGATATAAGGATTT-TTTTTACGAGC
** *
105808 ATCTCTATCTTGTTTCGATTTAATTAGAAATTAATTCGG-AAAAAATGGAAAAACGATATTAGAT
190 ATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAAGGAAAAACGATATTAGAT
* * *
105872 GCATGAAAAACCCTTCAATCTTTCTGGCGTTAAATTATATATTTTTTACGAGTATTGTGGCAAAA
255 GC-TGAAAAGCCCGTCAATCTTTTTGGCGTTAAATTATATATTTTTT-CGAGTATTGTGGCAAAA
* *
105937 AATTGAGAAAAAAAAAATTTT-GGGTCAGTTTTTTGCCGAAATCGTGTACTAGA-CATCATGGTT
318 AATTGAG--AAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTA-ACCATCACGGTT
* * * * * *
106000 TTTGGCTAAAAAC-ACATTTCGGGGTCTC-GAATAAGTTTTTCATGGCTTTTGACA-TATACTCT
380 TTTGGCTAAAAACGA-ATTACGGGGCCCCAG-ATAAGTTTTGCATGACTTTTGACACTA-ACACT
* * * * *
106062 CCTTGAAATATCTATATTTATCTAAGCAAATCTCAGCCACA-TT-GAATTTAAGGATTTGTTTTT
442 CATTGAAATATCTATATTCATCAAACCAAATCTCAGCCA-AGTTAG-ATTTAAGGATTTATTTTT
* * * *
106125 ATGAGCATTTGAATCTTGTTTCGATCTAATTAGAAATAAATTCGGGAAAAAAATGGGAAAACGAT
505 ACGAGCATCTAAATCTTGTTTCGATCTAATTAGAAATAAATTCGGGAAAAAAATGGAAAAACGAT
* ** *
106190 ATTAGAAGTGTGAAAAAAACCTTCAAATT-TTTTGGTGCTGGATTACATATTTTTCTAGATTATA
570 ATTAGAAGCGTG-AAAAAACCTTCAAATTATTTTGGCACTGAATTACATATTTTT-TAGA--ATA
106254 TTG-GGAAAAG-ATTGAGG
631 TTGTGGAAAAGAATTGAGG
* * *
106271 AAAAACTCTTCAGGTCAGTTTTTGCAAAATTTTAGCCGAAATCGTGTACTAACCATCCCAGTTTT
1 AAAAACTCTTCAGGTCAGTTTTCGCAAAATTTTAGCCGAAATCGTGTACT-A-CATCACGGTTTT
* * **
106336 TGGCTAAAAACGAGTTCTGGAGCCCCGCCTCAATTTTGCATGATTTTTGGCACAAAGACTTTTTG
64 TGGCTAAAAACGAGTTCCGGAGCCCCGACTC-ATTTTGCATGATTTTTGGCA-AAAGACTCCTTG
* * * *
106401 AAATATCTATATTCATCGAACCAAATCTCAGTCACATTGGATATAAGGATTTGTTTTTAGGAGCA
127 AAATATCTATATTCATAGAACCAAATCTCAGCCAAATTGGATATAAGGATTT-TTTTTACGAGCA
* * * * * * *
106466 TTTGAATCTTATTTCAATCTAATTAGAAATTAATTTGGAAAAAAACAAAAGAAAAATGATATTAG
191 TCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGG--AAAAA-AAAGGAAAAACGATATTAG
* * * *
106531 AAGCGTGAAAAGCCCGTCAAT-TTTTTGGCGTTGAATTATATATTTTTT-TAGTATTGT-GTAAA
253 ATGC-TGAAAAGCCCGTCAATCTTTTTGGCGTTAAATTATATATTTTTTCGAGTATTGTGGCAAA
* *
106593 AAATTTTAG-AAAAAATTTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTT
317 AAA-TTGAGAAAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTT
106657 TTGGTCTAAAAA
381 TTGG-CTAAAAA
106669 TTAAGAAAAA
Statistics
Matches: 880, Mismatches: 134, Indels: 76
0.81 0.12 0.07
Matches are distributed among these distances:
652 8 0.01
653 193 0.22
654 239 0.27
655 82 0.09
656 78 0.09
657 204 0.23
658 14 0.02
660 29 0.03
661 33 0.04
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Consensus pattern (649 bp):
AAAAACTCTTCAGGTCAGTTTTCGCAAAATTTTAGCCGAAATCGTGTACTACATCACGGTTTTTG
GCTAAAAACGAGTTCCGGAGCCCCGACTCATTTTGCATGATTTTTGGCAAAAGACTCCTTGAAAT
ATCTATATTCATAGAACCAAATCTCAGCCAAATTGGATATAAGGATTTTTTTTACGAGCATCTGA
ATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAAGGAAAAACGATATTAGATGCTGAA
AAGCCCGTCAATCTTTTTGGCGTTAAATTATATATTTTTTCGAGTATTGTGGCAAAAAATTGAGA
AAAAAAATTTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACGGTTTTTGGCTAAAA
ACGAATTACGGGGCCCCAGATAAGTTTTGCATGACTTTTGACACTAACACTCATTGAAATATCTA
TATTCATCAAACCAAATCTCAGCCAAGTTAGATTTAAGGATTTATTTTTACGAGCATCTAAATCT
TGTTTCGATCTAATTAGAAATAAATTCGGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAA
AACCTTCAAATTATTTTGGCACTGAATTACATATTTTTTAGAATATTGTGGAAAAGAATTGAGG
Found at i:107449 original size:321 final size:317
Alignment explanation
Indices: 106664--109078 Score: 1685
Period size: 321 Copynumber: 7.5 Consensus size: 317
106654 TTTTTGGTCT
* * * *
106664 AAAAATTAAGAAAAAACTTTTCAAGTCAGTTTTTGCAAATTTTTAGCTGAAATCGTGTACTAACC
1 AAAAATTGAGGAAAAA-TTTTC-GGTCAG-TTTTGCAAATTTTTAGCCGAAATCGTGTACT---C
* * * *
106729 ATCATGGTTTTTGACTAAAAACGCGTTCCGGAGCGC-CGGCTCAAG-TTTGCATGATATTTGGCA
60 ATCATGATTTTTGGCTAAAAACGCGTTCCGG-GC-CTCGACTC-AGTTTTGCATGATTTTTGGCA
* * * * *
106792 -AAAAGACTCCTTGAAATATCTTTATTCATCGAACCAAATATCAGCTAAATTGGATATAAGGATT
122 TAAAA-ACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATTTAAGGATT
*
106856 T-TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAGGAAAAA
186 TGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTC-G--GAAA-GAAAAA
* * * * * * * *
106920 AGATATTAGAATCTTTAAAAGCCCGTCAA---TCTTGGCGTTAAATTATATATTTTTTCTGAGTA
247 TGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATA-TTTTTCTGAGTA
106982 TTGTGGC
311 TTGTGGC
* * * * *
106989 AAAAATTGAGAAAAAACTTT---TCAG--GT-C-AGTTTTTAGCCGAAATCGTGAAC-CAACCTT
1 AAAAATTGAGGAAAAATTTTCGGTCAGTTTTGCAAATTTTTAGCCGAAATCGTGTACTC-A---T
* * * * * * *
107046 CACGGTTTTTCGCTAAAAACGAGTTACGTGGCC-CTAGTTCAGTTTTGCATGATTTTTGGCATAA
62 CATGATTTTTGGCTAAAAACGCGTTCCG-GGCCTCGA-CTCAGTTTTGCATGATTTTTGGCATAA
* * * * * *
107110 AGACTCTTTGAAATATCTATATTCATCTAACCAAATCTCATCCA-AGTTAGATTTAAGGATTTAT
125 AAACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACA-TTGGATTTAAGGATTTGT
* * *
107174 TTTTACGAGCATCTAAATCTGGTTTCGATTTAATTAGAAATTAATTCGGCAA-AAAAATGATATT
189 TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAGAAAAATGATATT
* * *
107238 AGAAGCGTGGAAAATCCTTCAATTTATTTTGGCATTGAATTATATATTTTT-TGAGTATTGTGGC
254 AGAAGCGTGAAAAACCCTTCAATTT-TTTTGGCGTTGAATTATATATTTTTCTGAGTATTGTGGC
*
107302 AAAGAATTGAGGAAAAATTTCTCGGATCAGTTTTCGCAAATTTTTAGCCGAAATCGTTTACTCAT
1 AAA-AATTGAGGAAAAATTT-TCGG-TCAGTTTT-GCAAATTTTTAGCCGAAATCGTGTACTCAT
* * *
107367 CATTATTTATGGCTAAAAACGCGTTCCGGGTCCTCGACTCAGTTTTGCATGATTTTTGGCGTAAA
62 CATGATTTTTGGCTAAAAACGCGTTCCGGG-CCTCGACTCAGTTTTGCATGATTTTTGGCATAAA
* * ** * * * * * *
107432 AACTCCTTAAAATATCTATATTTATAAAACCAAATCCCAACCAAATTTGATTTAATGATTTATTT
126 AACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTT
* * *
107497 TTACGAGCATCTCAATCTTATTTCGATTTAATTAGAAATTAATTCGGAAAAATGGAAAAACGATA
191 TTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGG--AAA--GAAAAATGATA
* * *
107562 TTAGAAGCATGAAAAACCCTTCAATCTTTTTGGCGTTAAATTATATATTTTT-TACGAGTATTGT
252 TTAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTCT--GAGTATTGT
*
107626 GGTA
315 GG-C
* * *
107630 AAAAATTG-GGAAAAAAGTTTGCGG---G-TCTG----TTTTTAGCCGAAATTGTGTACTAGCCA
1 AAAAATTGAGG-AAAAA-TTTTCGGTCAGTTTTGCAAATTTTTAGCCGAAATCGTGTACT---CA
* * * * * *
107686 TCACTG-CTTTTGGCTAAAAACACGTTTCGGGACCTCGACTCAGTTTTTCATGGTTTTTGACATA
61 TCA-TGATTTTTGGCTAAAAACGCGTTCCGGG-CCTCGACTCAGTTTTGCATGATTTTTGGCATA
* * * * * * *
107750 TAGACTTCTTGAAATATCTTTATTCATCTAATCAAATCTCAGCCACATTGAATTTAAGGATTTGT
124 AAAACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATTTAAGGATTTGT
* * *
107815 TTTTACGAGAATTTGAATCTTGTTTCGATTTAATTTA-AAATAAATTCGGAAAAAAAATCGAAAA
189 TTTTACGAGCATCTGAATCTTGTTTCGATTTAA-TTAGAAATTAATTCGG-----AAA--GAAAA
* * * * *
107879 ACGATATTAGAAGTGTGAAAAACCCTTCAATTTTTTTGGTGCTGAGTTATATATTTTTCTGGAGT
246 ATGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTCT-GAGT
*
107944 ATTGTGGG
310 ATTGTGGC
*
107952 AAAAGATTGAGGAAAAACTCTTCAGGTCAGTTTTTGCAAAATTTTT-GCCGAAATCGTGTACTAA
1 AAAA-ATTGAGGAAAAA-TTTTC-GGTCAG-TTTTGC-AAATTTTTAGCCGAAATCGTGTACT--
* * * * * *
108016 CCATCCT-AGTTTTTGGCTAAAAACGAGTTCTGGAGCCAC-ACCTCAATTTTGCATGTTTTTTGG
59 -CATCATGA-TTTTTGGCTAAAAACGCGTTCCGG-GCCTCGA-CTCAGTTTTGCATGATTTTTGG
* * ** * *
108079 CACAAAGACTTTTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGCATATAAGGAT
120 CATAAAAACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATTTAAGGAT
* * * * *
108144 TTGTTTTTAGGAGCATTTGAATCTTATTTCAATCTAATTAGAAATTAATTCGGGAAAAAAAGGAG
185 TTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTC-GG-----AA--AG
* * *
108209 AAAAATGATATTAGAAGCCTGAAAAGCCCGTT-AA-TTTTTTGGCGTTGAATTAT-T-TTTTTTT
242 AAAAATGATATTAGAAGCGTGAAAAACCC-TTCAATTTTTTTGGCGTTGAATTATATATTTTTCT
*
108270 TAGTATTGTGGCC
306 GAGTATTGTGG-C
* ** * * *
108283 AAAATTTCAGAAAAAAAAAATTTTCGG---G---T-C-AGTTTTTAGCTGAAATCGTGTACCCAT
1 AAAAATT--G--AGGAAAAATTTTCGGTCAGTTTTGCAAATTTTTAGCCGAAATCGTGTACTCAT
* ** *
108340 CA-CAGTTTTTGGTCTAAAAACGCGTTCCGGGGTTCCGGCTCAGTTTTGCATGATTTTTGGCGA-
62 CATGA-TTTTTGG-CTAAAAACGCGTTCCGGGCCT-CGACTCAGTTTTGCATGATTTTTGGC-AT
* * * ** * * *
108403 AAAGACTCCCTGAAATATCTTTATTCATTTAATCAAATCTCAGCCATATTGGAATTAAGGATTTG
123 AAAAACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATTTAAGGATTTG
* * *
108468 TTTTTACGAGCATCTGAATCTTGTTTCAATTTACTTAGAAATAAATTCGAGAAAAAATGGAAAAA
188 TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCG-G---AAA--GAAAAA
* * * * *
108533 CGAAATTAGAAGCGTGAAAAACCCTTCAATTTTTTTTGCATTGAATTATATATTTCTTCTGACTA
247 TGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATATTT-TTCTGAGTA
108598 TTGTGGC
311 TTGTGGC
* * * *
108605 AAAAAAAATTTAGGAAAAAAATTTTTGGTCAGTTTTTACAAAATTTTAGCCGAAATCGTGTACTA
1 ---AAAAATTGAGG--AAAAATTTTCGGTCAG-TTTTGCAAATTTTTAGCCGAAATCGTGTACT-
* * * * * * * *
108670 ACCATCACGGTTTTTTGCAAAAAACGCGTTCCGAAGCCCCGTCTCAGTTTTGCATTATTTTTGGC
59 --CATCATGATTTTTGGCTAAAAACGCGTTCCG-GGCCTCGACTCAGTTTTGCATGATTTTTGGC
* * * * * * *
108735 GTAAAGAA-----T-AGA-ATCTATATTCATCGAACTAAATATTAGTCACATTGGATATAAGGAT
121 ATAAA-AACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATTTAAGGAT
*
108793 TTGTTTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAATTAATTCGGAAAATTGGAAAA
185 TTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGG-AAA---GAAAA
* ** * * * *
108858 ATGATATTAGAAGCTTG---AATTCGTCAATCTTTCTT-GTGTTGAATTATATATTTTTTCTTAG
246 ATGATATTAGAAGCGTGAAAAACCCTTCAAT-TTTTTTGGCGTTGAATTATATA-TTTTTCTGAG
*
108919 TATTGTTGC
309 TATTGTGGC
* * * * * *
108928 AAAAAAAT-AGGAATAAAAAATTTCGG---G---T-C-AGTTTTTCGCTGAAATCATGTACTAAC
1 -AAAAATTGAGG---AAAAATTTTCGGTCAGTTTTGCAAATTTTTAGCCGAAATCGTGTACT---
* * *
108984 CATCACGGTTTTTAGGCTAAAAACGCGTTTCGGGGCC-CGGACTCAGTTTTGCATGATTTTTGGC
59 CATCATGATTTTT-GGCTAAAAACGCG-TTCCGGGCCTC-GACTCAGTTTTGCATGATTTTTGGC
* *
109048 A-AAAAAGGTTCCTTGATATATCTATATTCAT
121 ATAAAAA--CTCCTTGAAATATCTATATTCAT
109079 TAGAATGCCA
Statistics
Matches: 1693, Mismatches: 271, Indels: 257
0.76 0.12 0.12
Matches are distributed among these distances:
311 29 0.02
312 40 0.02
313 56 0.03
314 29 0.02
315 134 0.08
316 51 0.03
317 22 0.01
318 4 0.00
319 39 0.02
320 196 0.12
321 307 0.18
322 20 0.01
323 160 0.09
324 38 0.02
325 51 0.03
326 56 0.03
327 26 0.02
328 89 0.05
329 6 0.00
330 14 0.01
331 11 0.01
332 29 0.02
333 179 0.11
334 91 0.05
335 15 0.01
336 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.36
Consensus pattern (317 bp):
AAAAATTGAGGAAAAATTTTCGGTCAGTTTTGCAAATTTTTAGCCGAAATCGTGTACTCATCATG
ATTTTTGGCTAAAAACGCGTTCCGGGCCTCGACTCAGTTTTGCATGATTTTTGGCATAAAAACTC
CTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACG
AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAGAAAAATGATATTAGAAGCG
TGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTCTGAGTATTGTGGC
Found at i:109153 original size:655 final size:646
Alignment explanation
Indices: 106664--109084 Score: 1779
Period size: 653 Copynumber: 3.7 Consensus size: 646
106654 TTTTTGGTCT
* * * * * *
106664 AAAAATT-AAGAAAAAACTTTTCAAGTCAGTTTTTGCAAATTTTTAGCTGAAATCGTGTACTAAC
1 AAAAATTGAGGAAAAAA-TCTTCAGGTCAGTTTTTACAAAATTTTAGCCGAAATCGTGTACTAAC
* * * * * * ** * * *
106728 CATCATGGTTTTTGACTAAAAACGCGTTCCGGAGCGC-CGGCTCAAGTTTGCATGATATTTGGCA
65 CATCCTAGTTTTTGGCAAAAAACGAGTTCCGAAGC-CACACCTCAATTTTGCATGTTTTTTGGCA
* * * * * *
106792 AAAAGACTCCTTGAAATATCTTTATTCATCGAACCAAATATCAGCTAAATTGGATATAAGGATTT
129 CAAAGA-T--ATGAAATATCTATATTCATCGAACCAAATATCAGCCACATTGCATATAAGGATTT
* * * *
106857 -TTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTC-AGAAAAAAGGA-AAA
191 GTTTTTACGAGCATCTGAATCTTATTTCAATCTAATTAGAAATTAATTCGGGAAAAAAGGAGAAA
* * * * * *
106919 AA-GATATTAGAATCTTTAAAAGCCCGTCAA--TCTTGGCGTTAAATTATATATTTTTTCTGAGT
256 AATGATATTAGAAGC-CTGAAAGCCCGTCAATTTTTTGGCGTTGAATTAT-T-TTTTTT-TTAGT
* * * * * * *
106981 ATTGTGGC--AAAAAT-TG-AGAAAAAACTTTTCAGGTCAGTTTTTAGCCGAAATCGTGAACCAA
317 ATTGTGGCAAAAAAATCAGAAAAAAAAAATTTTCGGGTCAGTTTTTAGCTGAAATCATGTA-C--
* * * * * * * *
107042 CCTTCACGGTTTTTCG-CTAAAAACGAGTTACGTGG-CCCTAGTTCAGTTTTGCATGATTTTTGG
379 CCATCACAGTTTTTGGTCTAAAAACGCGTTCCGGGGTCCC-GGCTCAGTTTTGCATGATTTTTGG
* ** * * * * *
107105 CATAAAGACTCTTTGAAATATCTATATTCATCT-AACCAAATCTCATCCA-AGTTA-GATTTAAG
443 CAAAAAGACTCCCTGAAATATCTATATTCAT-TGAATCAAATCTCAGCCATA--AAGGAATTAAC
* ** * * * * * * * *
107167 GATTTATTTTTACGAGCATCTAAATCTGGTTTCGATTTAATTAGAAATTAATTCGGCAAAAAAAT
505 AATTTGCTTCTA-GA-CATCTGAATCTTGCTTCAATTTACTTAGAAATAAATTCGGAAAAAAAAT
* * *
107232 --------GATATTAGAAGCGTGGAAAATCCTTCAATTTATTTTG-GCATTGAATTATATATTTT
568 CGAAAAACGAAATTAGAAGCGTGAAAAACCCTTCAATTT-TTTTGTGC--TGAATTATATATTTT
* *
107288 T-T-GAGTATTGTGGCA
630 TCTGGACTATTGTGGAA
* * ** * * *
107303 AAGAATTGAGG-AAAAAT-TTCTCGGATCAGTTTTCGCAAATTTTTAGCCGAAATCGTTTACTCA
1 AAAAATTGAGGAAAAAATCTTC-AGG-TCAGTTTTTACAAAATTTTAGCCGAAATCGTGTACTAA
* * * * * * * *
107366 TCAT--TA-TTTATGGCTAAAAACGCGTTCCG-GGTCCTCGA-CTCAGTTTTGCATGATTTTTGG
64 CCATCCTAGTTTTTGGCAAAAAACGAGTTCCGAAG-CCAC-ACCTCAATTTTGCATGTTTTTTGG
** * * * * ** ** * * * *
107426 CGTAAAAACTCCTTAAAATATCTATATTTATAAAACCAAATCCCAACCAAATTTG-ATTTAATGA
127 CACAAAGA-T--ATGAAATATCTATATTCATCGAACCAAATATCAGCCACA-TTGCATATAAGGA
* * * * *
107490 TTTATTTTTACGAGCATCTCAATCTTATTTCGATTTAATTAGAAATTAATTC-GG-AAAAATG-G
188 TTTGTTTTTACGAGCATCTGAATCTTATTTCAATCTAATTAGAAATTAATTCGGGAAAAAAGGAG
* * * * * *
107552 AAAAACGATATTAGAAGCATGAAAAACCCTTCAATCTTTTTGGCGTTAAATTATATATTTTTTAC
253 AAAAATGATATTAGAAGCCTG-AAAGCCCGTCAAT-TTTTTGGCGTTGAATTAT-T-TTTTTT-T
* * * ** * * * * **
107617 GAGTATTGTGG-TAAAAAAT-TG-GGAAAAAAGTTTGCGGGTCTGTTTTTAGCCGAAATTGTGTA
313 TAGTATTGTGGCAAAAAAATCAGAAAAAAAAAATTTTCGGGTCAGTTTTTAGCTGAAATCATGTA
* * * * * * * *
107679 CTAGCCATCACTGCTTTTGG-CTAAAAACACGTTTC-GGGACCTCGACTCAGTTTTTCATGGTTT
378 C---CCATCACAGTTTTTGGTCTAAAAACGCGTTCCGGGGTCC-CGGCTCAGTTTTGCATGATTT
* * * * * * * **
107742 TTGACATATAGACTTCTTGAAATATCTTTATTCATCT-AATCAAATCTCAGCCA-CATTGAATTT
439 TTGGCAAAAAGACTCCCTGAAATATCTATATTCAT-TGAATCAAATCTCAGCCATAAAGGAA-TT
** * * * * * * *
107805 AAGGATTTGTTTTTACGAGAATTTGAATCTTGTTTCGATTTAATTTA-AAATAAATTCGGAAAAA
502 AACAATTTGCTTCTA-GA-CATCTGAATCTTGCTTCAATTT-ACTTAGAAATAAATTCGGAAAAA
* * *
107869 AAATCGAAAAACGATATTAGAAGTGTGAAAAACCCTTCAATTTTTTTGGTGCTGAGTTATATATT
564 AAATCGAAAAACGAAATTAGAAGCGTGAAAAACCCTTCAATTTTTTT-GTGCTGAATTATATATT
* *
107934 TTTCTGGAGTATTGTGGGA
628 TTTCTGGACTATTGTGGAA
* * * *
107953 AAAGATTGAGGAAAAACTCTTCAGGTCAGTTTTTGCAAAATTTTTGCCGAAATCGTGTACTAACC
1 AAAAATTGAGGAAAAAATCTTCAGGTCAGTTTTTACAAAATTTTAGCCGAAATCGTGTACTAACC
* * *
108018 ATCCTAGTTTTTGGCTAAAAACGAGTTCTGGAGCCACACCTCAATTTTGCATGTTTTTTGGCACA
66 ATCCTAGTTTTTGGCAAAAAACGAGTTCCGAAGCCACACCTCAATTTTGCATGTTTTTTGGCACA
* *
108083 AAGACTTTTTGAAATATCTATATTCATCGAACCAAATCTCAGCCACATTGCATATAAGGATTTGT
131 AAGA---TATGAAATATCTATATTCATCGAACCAAATATCAGCCACATTGCATATAAGGATTTGT
* *
108148 TTTTAGGAGCATTTGAATCTTATTTCAATCTAATTAGAAATTAATTCGGGAAAAAAAGGAGAAAA
193 TTTTACGAGCATCTGAATCTTATTTCAATCTAATTAGAAATTAATTCGGG-AAAAAAGGAGAAAA
*
108213 ATGATATTAGAAGCCTGAAAAGCCCGTTAATTTTTTGGCGTTGAATTATTTTTTTTTTAGTATTG
257 ATGATATTAGAAGCCTG-AAAGCCCGTCAATTTTTTGGCGTTGAATTATTTTTTTTTTAGTATTG
* ** *
108278 TGGCCAAAATTTCAGAAAAAAAAAATTTTCGGGTCAGTTTTTAGCTGAAATCGTGTACCCATCAC
321 TGGCAAAAAAATCAGAAAAAAAAAATTTTCGGGTCAGTTTTTAGCTGAAATCATGTACCCATCAC
* *
108343 AGTTTTTGGTCTAAAAACGCGTTCCGGGGTTCCGGCTCAGTTTTGCATGATTTTTGGCGAAAAGA
386 AGTTTTTGGTCTAAAAACGCGTTCCGGGGTCCCGGCTCAGTTTTGCATGATTTTTGGCAAAAAGA
* * ** ** * *
108408 CTCCCTGAAATATCTTTATTCATTTAATCAAATCTCAGCCATATTGGAATTAAGGATTTGTTTTT
451 CTCCCTGAAATATCTATATTCATTGAATCAAATCTCAGCCATAAAGGAATTAACAATTTGCTTCT
* * *
108473 ACGAGCATCTGAATCTTGTTTCAATTTACTTAGAAATAAATTC-GAGAAAAAATGGAAAAACGAA
516 A-GA-CATCTGAATCTTGCTTCAATTTACTTAGAAATAAATTCGGAAAAAAAATCGAAAAACGAA
108537 ATTAGAAGCGTGAAAAACCCTTCAATTTTTTT-TGCATTGAATTATATATTTCTTCT-GACTATT
579 ATTAGAAGCGTGAAAAACCCTTCAATTTTTTTGTGC--TGAATTATATATTT-TTCTGGACTATT
108600 GTGGCAAA
641 GTGG--AA
* **
108608 AAAAATTTAGGAAAAAAAT-TTTTGGTCAGTTTTTACAAAATTTTAGCCGAAATCGTGTACTAAC
1 AAAAATTGAGG-AAAAAATCTTCAGGTCAGTTTTTACAAAATTTTAGCCGAAATCGTGTACTAAC
* * * * ** *
108672 CATCAC-GGTTTTTTGCAAAAAACGCGTTCCGAAGCCCCGTCTCAGTTTTGCAT-TATTTTTGGC
65 CATC-CTAGTTTTTGGCAAAAAACGAGTTCCGAAGCCACACCTCAATTTTGCATGT-TTTTTGGC
** * * * * *
108735 GTAAAGA-AT-AGA-ATCTATATTCATCGAACTAAATATTAGTCACATTGGATATAAGGATTTGT
128 ACAAAGATATGAAATATCTATATTCATCGAACCAAATATCAGCCACATTGCATATAAGGATTTGT
* * **
108797 TTTTACGAGCATCTGAATCTTATTTCGATTTAATTAGAAATTAATTC-GG-AAAATTG-GAAAAA
193 TTTTACGAGCATCTGAATCTTATTTCAATCTAATTAGAAATTAATTCGGGAAAAAAGGAGAAAAA
* ** *
108859 TGATATTAGAAGCTTG-AA-TTCGTCAATCTTTCTT-GTGTTGAATTATATATTTTTTCTTAGTA
258 TGATATTAGAAGCCTGAAAGCCCGTCAAT-TTT-TTGGCGTTGAATTAT-T-TTTTTT-TTAGTA
* * * *
108921 TTGTTGCAAAAAAAT-AGGAATAAAAAA-TTTCGGGTCAGTTTTTCGCTGAAATCATGTACTAAC
318 TTGTGGCAAAAAAATCAGAAAAAAAAAATTTTCGGGTCAGTTTTTAGCTGAAATCATGTAC---C
* *
108984 CATCACGGTTTTTAGG-CTAAAAACGCGTTTCGGGG-CCCGGACTCAGTTTTGCATGATTTTTGG
380 CATCACAGTTTTT-GGTCTAAAAACGCGTTCCGGGGTCCCGG-CTCAGTTTTGCATGATTTTTGG
** * *
109047 CAAAAAAGGTTCCTTGATATATCTATATTCATTAGAAT
443 C-AAAAAGACTCCCTGAAATATCTATATTCATT-GAAT
109085 GCCACGAGTC
Statistics
Matches: 1478, Mismatches: 228, Indels: 142
0.80 0.12 0.08
Matches are distributed among these distances:
635 2 0.00
636 103 0.07
637 75 0.05
638 2 0.00
639 48 0.03
640 43 0.03
641 187 0.13
642 11 0.01
643 16 0.01
644 33 0.02
645 37 0.03
646 26 0.02
647 54 0.04
648 48 0.03
649 121 0.08
650 61 0.04
651 11 0.01
652 9 0.01
653 234 0.16
654 145 0.10
655 116 0.08
656 65 0.04
657 31 0.02
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.36
Consensus pattern (646 bp):
AAAAATTGAGGAAAAAATCTTCAGGTCAGTTTTTACAAAATTTTAGCCGAAATCGTGTACTAACC
ATCCTAGTTTTTGGCAAAAAACGAGTTCCGAAGCCACACCTCAATTTTGCATGTTTTTTGGCACA
AAGATATGAAATATCTATATTCATCGAACCAAATATCAGCCACATTGCATATAAGGATTTGTTTT
TACGAGCATCTGAATCTTATTTCAATCTAATTAGAAATTAATTCGGGAAAAAAGGAGAAAAATGA
TATTAGAAGCCTGAAAGCCCGTCAATTTTTTGGCGTTGAATTATTTTTTTTTTAGTATTGTGGCA
AAAAAATCAGAAAAAAAAAATTTTCGGGTCAGTTTTTAGCTGAAATCATGTACCCATCACAGTTT
TTGGTCTAAAAACGCGTTCCGGGGTCCCGGCTCAGTTTTGCATGATTTTTGGCAAAAAGACTCCC
TGAAATATCTATATTCATTGAATCAAATCTCAGCCATAAAGGAATTAACAATTTGCTTCTAGACA
TCTGAATCTTGCTTCAATTTACTTAGAAATAAATTCGGAAAAAAAATCGAAAAACGAAATTAGAA
GCGTGAAAAACCCTTCAATTTTTTTGTGCTGAATTATATATTTTTCTGGACTATTGTGGAA
Found at i:110910 original size:31 final size:31
Alignment explanation
Indices: 110875--110956 Score: 103
Period size: 31 Copynumber: 2.6 Consensus size: 31
110865 CCAATTTCGC
* *
110875 AAGTAGAGGGACTAAATTGGCCCAAACCT-T
1 AAGTAGAGGGACTAAATTGACCAAAACCTAT
* *
110905 AAAGTAAAGGGACTAAATTGACCAAAATCTAT
1 -AAGTAGAGGGACTAAATTGACCAAAACCTAT
*
110937 AAGTAGAGGGACTAACTTGA
1 AAGTAGAGGGACTAAATTGA
110957 TTTTTTTTAG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
31 43 0.98
32 1 0.02
ACGTcount: A:0.43, C:0.15, G:0.22, T:0.21
Consensus pattern (31 bp):
AAGTAGAGGGACTAAATTGACCAAAACCTAT
Found at i:112728 original size:13 final size:13
Alignment explanation
Indices: 112710--112735 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
112700 TTTCTCCAAA
112710 GCTTAATTATGTT
1 GCTTAATTATGTT
112723 GCTTAATTATGTT
1 GCTTAATTATGTT
112736 ATAAACTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.15, T:0.54
Consensus pattern (13 bp):
GCTTAATTATGTT
Found at i:113000 original size:19 final size:18
Alignment explanation
Indices: 112976--113018 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
112966 TATTGACTAT
112976 GAGAGAG-C-AAGTGGGAG
1 GAGAGAGACTAAGTGGG-G
*
112993 GAGAGAGACTTAGTGGGG
1 GAGAGAGACTAAGTGGGG
113011 GAGAGAGA
1 GAGAGAGA
113019 AGAGGGATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 7 0.30
18 10 0.43
19 6 0.26
ACGTcount: A:0.35, C:0.05, G:0.51, T:0.09
Consensus pattern (18 bp):
GAGAGAGACTAAGTGGGG
Done.