Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008185.1 Hibiscus syriacus cultivar Beakdansim tig00110788_pilon, 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: 3563405
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 16
Found at i:2387772 original size:19 final size:19
Alignment explanation
Indices: 2387748--2387803 Score: 69
Period size: 19 Copynumber: 3.0 Consensus size: 19
2387738 TTATCGTATA
*
2387748 ATTATTATTATTTTTTATT
1 ATTATTATTATTTTTTAAT
*
2387767 ATTATTATTA-TTGTTAAT
1 ATTATTATTATTTTTTAAT
* *
2387785 AATATTTTTATTTTTTAAT
1 ATTATTATTATTTTTTAAT
2387804 TTTACAGGCC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
18 14 0.45
19 17 0.55
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (19 bp):
ATTATTATTATTTTTTAAT
Found at i:2388924 original size:32 final size:32
Alignment explanation
Indices: 2388887--2388948 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
2388877 TTCATGTTAT
*
2388887 TTTATTTTTATTTTTATTTT-TAACATTTTTAC
1 TTTATTATT-TTTTTATTTTCTAACATTTTTAC
*
2388919 TTTATTATTTTTTTATTTTCTAACCTTTTT
1 TTTATTATTTTTTTATTTTCTAACATTTTT
2388949 TATTCTTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 10 0.37
32 17 0.63
ACGTcount: A:0.19, C:0.08, G:0.00, T:0.73
Consensus pattern (32 bp):
TTTATTATTTTTTTATTTTCTAACATTTTTAC
Found at i:2389101 original size:12 final size:13
Alignment explanation
Indices: 2389079--2389107 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
2389069 CCAATTGAAT
2389079 TTTTAAATTTTAA
1 TTTTAAATTTTAA
2389092 TTTT-AATTTTAA
1 TTTTAAATTTTAA
2389104 TTTT
1 TTTT
2389108 TTCGCAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:2389165 original size:12 final size:12
Alignment explanation
Indices: 2389148--2389173 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2389138 GATACCGAAA
2389148 GGGCAGTACAAG
1 GGGCAGTACAAG
2389160 GGGCAGTACAAG
1 GGGCAGTACAAG
2389172 GG
1 GG
2389174 TGCTAATCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.15, G:0.46, T:0.08
Consensus pattern (12 bp):
GGGCAGTACAAG
Found at i:2391997 original size:7 final size:7
Alignment explanation
Indices: 2391979--2392051 Score: 69
Period size: 7 Copynumber: 10.4 Consensus size: 7
2391969 AATAAGAAGC
2391979 AAAAAAG
1 AAAAAAG
*
2391986 GAAAAA-
1 AAAAAAG
*
2391992 ACAAAAG
1 AAAAAAG
*
2391999 AAAAAACA
1 AAAAAA-G
*
2392007 AAAAAAC
1 AAAAAAG
2392014 AAAAAAGG
1 AAAAAA-G
2392022 AAAAAA-
1 AAAAAAG
*
2392028 ACAAAAG
1 AAAAAAG
2392035 AAAAAAG
1 AAAAAAG
2392042 AAAAAAG
1 AAAAAAG
2392049 AAA
1 AAA
2392052 GAACAAAGAT
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
6 9 0.17
7 32 0.60
8 12 0.23
ACGTcount: A:0.84, C:0.05, G:0.11, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:2392010 original size:8 final size:8
Alignment explanation
Indices: 2391999--2392033 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
2391989 AAAACAAAAG
2391999 AAAAAACA
1 AAAAAACA
2392007 AAAAAACA
1 AAAAAACA
**
2392015 AAAAAGGA
1 AAAAAACA
2392023 AAAAAACA
1 AAAAAACA
2392031 AAA
1 AAA
2392034 GAAAAAAGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.86, C:0.09, G:0.06, T:0.00
Consensus pattern (8 bp):
AAAAAACA
Found at i:2392024 original size:35 final size:36
Alignment explanation
Indices: 2391978--2392047 Score: 124
Period size: 36 Copynumber: 2.0 Consensus size: 36
2391968 CAATAAGAAG
2391978 CAAAAAAGG-AAAAAACAAAAGAAAAAACAAAAAAA
1 CAAAAAAGGAAAAAAACAAAAGAAAAAACAAAAAAA
*
2392013 CAAAAAAGGAAAAAAACAAAAGAAAAAAGAAAAAA
1 CAAAAAAGGAAAAAAACAAAAGAAAAAACAAAAAA
2392048 GAAAGAACAA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
35 9 0.27
36 24 0.73
ACGTcount: A:0.83, C:0.07, G:0.10, T:0.00
Consensus pattern (36 bp):
CAAAAAAGGAAAAAAACAAAAGAAAAAACAAAAAAA
Found at i:2392707 original size:22 final size:22
Alignment explanation
Indices: 2392674--2392717 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
2392664 AGCTACCCCA
2392674 TCAAACATTTGAACATCAAATG
1 TCAAACATTTGAACATCAAATG
*
2392696 TCAAACCA-TTGAGCATCAAATG
1 TCAAA-CATTTGAACATCAAATG
2392718 GACAAAAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.43, C:0.20, G:0.11, T:0.25
Consensus pattern (22 bp):
TCAAACATTTGAACATCAAATG
Found at i:2394250 original size:32 final size:32
Alignment explanation
Indices: 2394204--2394279 Score: 134
Period size: 32 Copynumber: 2.4 Consensus size: 32
2394194 GTCAAGGCTT
* *
2394204 AACTTCACGACGAAGGGGCTATCCGCGATTTC
1 AACTCCACGACGAAGGGGCCATCCGCGATTTC
2394236 AACTCCACGACGAAGGGGCCATCCGCGATTTC
1 AACTCCACGACGAAGGGGCCATCCGCGATTTC
2394268 AACTCCACGACG
1 AACTCCACGACG
2394280 GAGGATATCG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.26, C:0.33, G:0.24, T:0.17
Consensus pattern (32 bp):
AACTCCACGACGAAGGGGCCATCCGCGATTTC
Found at i:2394435 original size:43 final size:43
Alignment explanation
Indices: 2394374--2394523 Score: 155
Period size: 43 Copynumber: 3.4 Consensus size: 43
2394364 CAGAGCCAAT
*
2394374 TTCAACTTCAC-AGCGAAGGATATTGGACTCAAGACAACGCAAG
1 TTCAACTTCACGA-CGAAGGATATTGGACTCAATACAACGCAAG
** ** *
2394417 TTCAACTTCACGACGAAGGGACCTCTGGTTGTCAATA-AA--CAAC
1 TTCAACTTCACGACGAA-GGATAT-TGG-ACTCAATACAACGCAAG
*
2394460 TTCCCAACTTCACAACGAAGGATATTGGACTCAATACAACGCAAG
1 TT--CAACTTCACGACGAAGGATATTGGACTCAATACAACGCAAG
2394505 TTCAACTTCACGACGAAGG
1 TTCAACTTCACGACGAAGG
2394524 GACCGCTGGT
Statistics
Matches: 85, Mismatches: 13, Indels: 18
0.73 0.11 0.16
Matches are distributed among these distances:
42 6 0.07
43 41 0.48
44 9 0.11
45 24 0.28
46 5 0.06
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (43 bp):
TTCAACTTCACGACGAAGGATATTGGACTCAATACAACGCAAG
Found at i:2394470 original size:45 final size:45
Alignment explanation
Indices: 2394419--2394559 Score: 139
Period size: 45 Copynumber: 3.2 Consensus size: 45
2394409 AACGCAAGTT
2394419 CAACTTCACGACGAAGGGACCTCTGGTTGTCAATAAACAACTTCC
1 CAACTTCACGACGAAGGGACCTCTGGTTGTCAATAAACAACTTCC
* ** ** *
2394464 CAACTTCACAACGAA-GGATAT-TGG-ACTCAATACAACGCAAGTT--
1 CAACTTCACGACGAAGGGACCTCTGGTTGTCAATA-AA--CAACTTCC
* *
2394507 CAACTTCACGACGAAGGGACCGCTGGTTGTCAAAAAACAACTTCC
1 CAACTTCACGACGAAGGGACCTCTGGTTGTCAATAAACAACTTCC
*
2394552 CAATTTCA
1 CAACTTCA
2394560 AAGCCAATTT
Statistics
Matches: 73, Mismatches: 15, Indels: 16
0.70 0.14 0.15
Matches are distributed among these distances:
42 6 0.08
43 24 0.33
44 7 0.10
45 31 0.42
46 5 0.07
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.21
Consensus pattern (45 bp):
CAACTTCACGACGAAGGGACCTCTGGTTGTCAATAAACAACTTCC
Found at i:2394525 original size:88 final size:88
Alignment explanation
Indices: 2394376--2394559 Score: 323
Period size: 88 Copynumber: 2.1 Consensus size: 88
2394366 GAGCCAATTT
* *
2394376 CAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCT
1 CAACTTCACAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
*
2394441 CTGGTTGTCAATAAACAACTTCC
66 CTGGTTGTCAAAAAACAACTTCC
*
2394464 CAACTTCACAACGAAGGATATTGGACTCAATACAACGCAAGTTCAACTTCACGACGAAGGGACCG
1 CAACTTCACAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
2394529 CTGGTTGTCAAAAAACAACTTCC
66 CTGGTTGTCAAAAAACAACTTCC
*
2394552 CAATTTCA
1 CAACTTCA
2394560 AAGCCAATTT
Statistics
Matches: 91, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
88 91 1.00
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (88 bp):
CAACTTCACAACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
CTGGTTGTCAAAAAACAACTTCC
Found at i:2394651 original size:106 final size:106
Alignment explanation
Indices: 2394464--2395116 Score: 969
Period size: 106 Copynumber: 6.2 Consensus size: 106
2394454 AACAACTTCC
* * *
2394464 CAACTTCACAACGAAGGATATTGGACTCAATACAACGCAAGTTCAACTTCACGACGAAGGGACCG
1 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
* *
2394529 CTGGTTGTCAAAAAACAACTTCCCAATTTCAAAGCCAATTT
66 CTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
*
2394570 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
1 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
* *
2394635 CTGGTTGTCAACAAACAATTTCCTAATTTCAGAGCCAATTT
66 CTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
*
2394676 TAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
1 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
*
2394741 CTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
66 CTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
2394782 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
1 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
* * *
2394847 CTGGTTGTCAATAAACAATTTCCCAATTTTAGAGCCAATTT
66 CTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
* * * *
2394888 CAACTTCACATCGAAGTATATTGGACTCCAGACAACACAAGTTCAACTTCAGGACGAAGGGACCG
1 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
* *
2394953 CTGGTTGTCAATAAACAACTTCCCAATTTCATAGCCAATTT
66 CTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
** * * * * * *
2394994 TGACTTCTCAGCGAAGGATCTTGGAC-CCAAGACAACACAAGCTCAACTTCACGACGAAGGGGCG
1 CAACTTCACAGCGAAGGATATTGGACTCC-AGACAACGCAAGTTCAACTTCACGACGAAGGGACC
* * *
2395058 GCTGATTGTCAAC-AA-AA-TT-TC-A-TTCAGAGTCAATTT
65 GCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
*
2395094 CAACTTCACAGCGAAGTATATTG
1 CAACTTCACAGCGAAGGATATTG
2395117 ACATCGAAAC
Statistics
Matches: 503, Mismatches: 43, Indels: 8
0.91 0.08 0.01
Matches are distributed among these distances:
100 30 0.06
101 1 0.00
102 1 0.00
103 2 0.00
104 2 0.00
105 4 0.01
106 463 0.92
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG
CTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
Found at i:2395042 original size:318 final size:312
Alignment explanation
Indices: 2394294--2395116 Score: 1134
Period size: 318 Copynumber: 2.7 Consensus size: 312
2394284 ATATCGTACC
* * * *
2394294 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAATAACTTTCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * * *
2394359 AATTGCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACT
66 AATTTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGGACTCCAGACAACACAAGCTCAACT
* * * * *
2394424 TCACGACGAAGGGACCTCTGGTTGTC-A-ATAA----A--CA-A--C--TTCCCAACTTCACAAC
131 TCACGACGAAGGGACCGCTGATTGTCAACAAAATTTCATTCAGAGCCAATT-TCAACTTCACAGC
*
2394476 GAAGGATATTGGACTCAATACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAA
195 GAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAA
2394541 AAACAACTTCCCAATTTCAAAGCCAATTTCAACTTCACAACGAAGGATATTGG
260 AAACAACTTCCCAATTTCAAAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
2394594 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCT
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
2394659 AATTTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
66 AATTTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGGACTCCAGACAACACAAGCTCAACT
*
2394724 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTC
131 TCACGACGAAGGGACCGCTGATTGTCAAC-AA-AA-TT-TC-A-TTCAGAGCCAATTTCAACTTC
*
2394789 ACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
190 ACAGCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTG
* * * * * *
2394854 TCAATAAACAATTTCCCAATTTTAGAGCCAATTTCAACTTCACATCGAAGTATATTGG
255 TCAAAAAACAACTTCCCAATTTCAAAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
2394912 ACTCCAGACAACACAAGTTCAACTTCAGGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * *
2394977 AATTTCATAGCCAATTTTGACTTCTCAGCGAAGGATCTTGGAC-CCAAGACAACACAAGCTCAAC
66 AATTTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGGACTCC-AGACAACACAAGCTCAAC
* * *
2395041 TTCACGACGAAGGGGCGGCTGATTGTCAACAAAATTTCATTCAGAGTCAATTTCAACTTCACAGC
130 TTCACGACGAAGGGACCGCTGATTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAGC
*
2395106 GAAGTATATTG
195 GAAGGATATTG
2395117 ACATCGAAAC
Statistics
Matches: 467, Mismatches: 36, Indels: 28
0.88 0.07 0.05
Matches are distributed among these distances:
300 147 0.31
301 1 0.00
303 1 0.00
304 2 0.00
311 1 0.00
312 35 0.07
313 1 0.00
314 4 0.01
315 3 0.01
316 2 0.00
317 5 0.01
318 263 0.56
319 2 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (312 bp):
ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTTAACTTCACAGCGAAGGATATTGGACTCCAGACAACACAAGCTCAACT
TCACGACGAAGGGACCGCTGATTGTCAACAAAATTTCATTCAGAGCCAATTTCAACTTCACAGCG
AAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAAA
AACAACTTCCCAATTTCAAAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:2396494 original size:2 final size:2
Alignment explanation
Indices: 2396489--2396519 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2396479 TTTTTCATGT
2396489 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
2396520 TCTTCATGTT
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:2396543 original size:10 final size:11
Alignment explanation
Indices: 2396528--2396586 Score: 50
Period size: 11 Copynumber: 5.1 Consensus size: 11
2396518 ATTCTTCATG
2396528 TTATTTTA-TT
1 TTATTTTATTT
2396538 TTATTTTATTT
1 TTATTTTATTT
2396549 TTATTTTTAACATTT
1 TTA-TTTT---ATTT
*
2396564 TTACTTTATTAT
1 TTATTTTATT-T
2396576 TT-TTTTATTT
1 TTATTTTATTT
2396586 T
1 T
2396587 CTAACCTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
10 10 0.24
11 14 0.34
12 7 0.17
14 3 0.07
15 7 0.17
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.76
Consensus pattern (11 bp):
TTATTTTATTT
Found at i:2396552 original size:16 final size:16
Alignment explanation
Indices: 2396531--2396586 Score: 53
Period size: 16 Copynumber: 3.6 Consensus size: 16
2396521 CTTCATGTTA
2396531 TTTTATTTTATTTTAT
1 TTTTATTTTATTTTAT
***
2396547 TTTTATTTT-TAACAT
1 TTTTATTTTATTTTAT
*
2396562 TTTTACTTTATTATT-T
1 TTTTATTTTATT-TTAT
2396578 TTTTATTTT
1 TTTTATTTT
2396587 CTAACCTTTT
Statistics
Matches: 30, Mismatches: 8, Indels: 4
0.71 0.19 0.10
Matches are distributed among these distances:
15 11 0.37
16 19 0.63
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTATTTTATTTTAT
Found at i:2396566 original size:31 final size:32
Alignment explanation
Indices: 2396531--2396597 Score: 93
Period size: 31 Copynumber: 2.1 Consensus size: 32
2396521 CTTCATGTTA
*
2396531 TTTTATTTTATT-TTATTTTTATTTT-TAACAT
1 TTTTACTTTATTATT-TTTTTATTTTCTAACAT
*
2396562 TTTTACTTTATTATTTTTTTATTTTCTAACCT
1 TTTTACTTTATTATTTTTTTATTTTCTAACAT
2396594 TTTT
1 TTTT
2396598 TATTCTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
31 21 0.66
32 11 0.34
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.73
Consensus pattern (32 bp):
TTTTACTTTATTATTTTTTTATTTTCTAACAT
Found at i:2396744 original size:6 final size:6
Alignment explanation
Indices: 2396728--2396762 Score: 61
Period size: 6 Copynumber: 5.7 Consensus size: 6
2396718 CCAATTGAAT
2396728 TTTTAAA TTTTAA TTTTAA TTTTAA TTTTAA TTTT
1 TTTT-AA TTTTAA TTTTAA TTTTAA TTTTAA TTTT
2396763 TTCGCAATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 24 0.86
7 4 0.14
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTTTAA
Found at i:2398279 original size:104 final size:103
Alignment explanation
Indices: 2398100--2398305 Score: 376
Period size: 104 Copynumber: 2.0 Consensus size: 103
2398090 AAATTTATAT
*
2398100 ATTTGATAAATTCAAAAATTCAATTTTATAAAAATAATGTCTAAATCCACATAATATATTATTAA
1 ATTTGATAAATTCAAAAATTCAATTTTATAAAAATAATGTCTAAATCCACAGAATATATTATTAA
2398165 TTTGGTAAATTTTATAAAATTAATCTTAATTATTATTA
66 TTTGGTAAATTTTATAAAATTAATCTTAATTATTATTA
* *
2398203 ATTTGATAAATTCAAAATATTCAATTTTATTAATATAATGTCTAAATCCACAGAATATATTATTA
1 ATTTGATAAATTCAAAA-ATTCAATTTTATAAAAATAATGTCTAAATCCACAGAATATATTATTA
2398268 ATTTGGTAAATTTTATAAAATTAATCTTAATTATTATT
65 ATTTGGTAAATTTTATAAAATTAATCTTAATTATTATT
2398306 CAAAAGTAAT
Statistics
Matches: 99, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
103 17 0.17
104 82 0.83
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (103 bp):
ATTTGATAAATTCAAAAATTCAATTTTATAAAAATAATGTCTAAATCCACAGAATATATTATTAA
TTTGGTAAATTTTATAAAATTAATCTTAATTATTATTA
Found at i:2406072 original size:24 final size:25
Alignment explanation
Indices: 2406041--2406087 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
2406031 ATTTTACCAG
2406041 AAAATAAATCTT-AAGCG-TGTTAC
1 AAAATAAATCTTAAAGCGATGTTAC
*
2406064 AAAACTAAATGTTAAAGCGATGTT
1 AAAA-TAAATCTTAAAGCGATGTT
2406088 TTTAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 7 0.35
25 5 0.25
26 4 0.20
ACGTcount: A:0.45, C:0.11, G:0.15, T:0.30
Consensus pattern (25 bp):
AAAATAAATCTTAAAGCGATGTTAC
Found at i:2410138 original size:24 final size:24
Alignment explanation
Indices: 2410102--2410163 Score: 79
Period size: 24 Copynumber: 2.6 Consensus size: 24
2410092 GATTGAGTTA
* *
2410102 AACATAAATGAACGGACATAAACG
1 AACATAAACGAACGAACATAAACG
*
2410126 AACATAACCGAACGAACATAAACG
1 AACATAAACGAACGAACATAAACG
* *
2410150 AAAATAAATGAACG
1 AACATAAACGAACG
2410164 TTCACGAACG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.56, C:0.18, G:0.15, T:0.11
Consensus pattern (24 bp):
AACATAAACGAACGAACATAAACG
Found at i:2410139 original size:14 final size:14
Alignment explanation
Indices: 2410122--2410151 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2410112 AACGGACATA
*
2410122 AACGAACATAACCG
1 AACGAACATAAACG
2410136 AACGAACATAAACG
1 AACGAACATAAACG
2410150 AA
1 AA
2410152 AATAAATGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.23, G:0.13, T:0.07
Consensus pattern (14 bp):
AACGAACATAAACG
Found at i:2411862 original size:30 final size:29
Alignment explanation
Indices: 2411828--2411885 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
2411818 TATTAAAAGT
2411828 TTAACCATCAATGAC-AGAAGAAAGTTTTTA
1 TTAACCA-CAATGACTA-AAGAAAGTTTTTA
* *
2411858 TTAACTACAATGACTAATGAAAGTTTTT
1 TTAACCACAATGACTAAAGAAAGTTTTT
2411886 TCAATTTCAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (29 bp):
TTAACCACAATGACTAAAGAAAGTTTTTA
Found at i:2422360 original size:80 final size:80
Alignment explanation
Indices: 2422227--2422470 Score: 488
Period size: 80 Copynumber: 3.0 Consensus size: 80
2422217 CATAATTTCA
2422227 TGGTTTGAGCAAGGTTATTTTGGTACAGACTTACCTGTTCGATTGGCAAATGCTCATGATGGATC
1 TGGTTTGAGCAAGGTTATTTTGGTACAGACTTACCTGTTCGATTGGCAAATGCTCATGATGGATC
2422292 GCCTTTCCGAGAACT
66 GCCTTTCCGAGAACT
2422307 TGGTTTGAGCAAGGTTATTTTGGTACAGACTTACCTGTTCGATTGGCAAATGCTCATGATGGATC
1 TGGTTTGAGCAAGGTTATTTTGGTACAGACTTACCTGTTCGATTGGCAAATGCTCATGATGGATC
2422372 GCCTTTCCGAGAACT
66 GCCTTTCCGAGAACT
2422387 TGGTTTGAGCAAGGTTATTTTGGTACAGACTTACCTGTTCGATTGGCAAATGCTCATGATGGATC
1 TGGTTTGAGCAAGGTTATTTTGGTACAGACTTACCTGTTCGATTGGCAAATGCTCATGATGGATC
2422452 GCCTTTCCGAGAACT
66 GCCTTTCCGAGAACT
2422467 TGGT
1 TGGT
2422471 GAAGTGATGC
Statistics
Matches: 164, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 164 1.00
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.34
Consensus pattern (80 bp):
TGGTTTGAGCAAGGTTATTTTGGTACAGACTTACCTGTTCGATTGGCAAATGCTCATGATGGATC
GCCTTTCCGAGAACT
Found at i:2423755 original size:30 final size:29
Alignment explanation
Indices: 2423670--2423774 Score: 86
Period size: 30 Copynumber: 3.5 Consensus size: 29
2423660 ACATCAGTGG
** *
2423670 CAGTTGGAACTTCAGCGATAGCATCAACAT
1 CAGTTGGAACTTCAGCGCGA-CAGCAACAT
* *
2423700 CAGTTGGAATTTCAGCTGCTG-CAGCATCAT
1 CAGTTGGAACTTCAGC-GC-GACAGCAACAT
* *
2423730 CAGTTGGAACTTCAGCGGCGACAGCAGCAG
1 CAGTTGGAACTTCAGC-GCGACAGCAACAT
* *
2423760 CACTTGGAAATTCAG
1 CAGTTGGAACTTCAG
2423775 TGGCAGCAGC
Statistics
Matches: 61, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
29 1 0.02
30 59 0.97
31 1 0.02
ACGTcount: A:0.29, C:0.24, G:0.25, T:0.23
Consensus pattern (29 bp):
CAGTTGGAACTTCAGCGCGACAGCAACAT
Found at i:2432648 original size:31 final size:31
Alignment explanation
Indices: 2432610--2432734 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
2432600 CCCGAAGGAC
* *
2432610 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
2432641 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
2432672 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
2432703 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
2432734 C
1 C
2432735 CCTCGACCCT
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 86 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:2433629 original size:21 final size:21
Alignment explanation
Indices: 2433599--2433643 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2433589 ATTCTGTCGT
* *
2433599 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2433620 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2433641 TTG
1 TTG
2433644 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:2436093 original size:21 final size:21
Alignment explanation
Indices: 2436063--2436107 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2436053 TCTTATTCGT
* *
2436063 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2436084 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2436105 TTG
1 TTG
2436108 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:2439218 original size:22 final size:22
Alignment explanation
Indices: 2439174--2439240 Score: 98
Period size: 22 Copynumber: 3.0 Consensus size: 22
2439164 CTCGTATAAA
2439174 TGCACCGAAGTGCCCTGTAGAAT
1 TGCACCGAAGTGCCC-GTAGAAT
2439197 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
* * *
2439219 TGCACCGTAGAGCCCATAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
2439241 GATGTCCATA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 26 0.63
23 15 0.37
ACGTcount: A:0.28, C:0.27, G:0.25, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:2440965 original size:21 final size:21
Alignment explanation
Indices: 2440935--2440979 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
2440925 TCTTATTCGT
* *
2440935 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
2440956 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
2440977 TTG
1 TTG
2440980 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:2448691 original size:24 final size:24
Alignment explanation
Indices: 2448664--2448709 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
2448654 ACTTCAATTT
2448664 GAACAGCAGCGGCAGCAGCAGCTC
1 GAACAGCAGCGGCAGCAGCAGCTC
** *
2448688 GAACTTCATCGGCAGCAGCAGC
1 GAACAGCAGCGGCAGCAGCAGC
2448710 AGCAGCTGGA
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:0.28, C:0.33, G:0.30, T:0.09
Consensus pattern (24 bp):
GAACAGCAGCGGCAGCAGCAGCTC
Found at i:2448709 original size:30 final size:30
Alignment explanation
Indices: 2448669--2448859 Score: 292
Period size: 30 Copynumber: 6.4 Consensus size: 30
2448659 AATTTGAACA
* *
2448669 GCAGCGGCAGCAGCAGCTCGAACTTCATCG
1 GCAGCAGCAGCAGCAGCTGGAACTTCATCG
2448699 GCAGCAGCAGCAGCAGCTGGAACTTCATCG
1 GCAGCAGCAGCAGCAGCTGGAACTTCATCG
2448729 GCAGCAGCAGCAGCAGCTGGAACTTCATCG
1 GCAGCAGCAGCAGCAGCTGGAACTTCATCG
*
2448759 GCAGCAGCAGCAGCAGCTGGAACTTCAGCG
1 GCAGCAGCAGCAGCAGCTGGAACTTCATCG
* * *
2448789 GCGGCAGCAGCAGCAGCTGGAACTTCAGCA
1 GCAGCAGCAGCAGCAGCTGGAACTTCATCG
* * *
2448819 GCGGCAGCAACAGCAGCTGGAACTTCAACG
1 GCAGCAGCAGCAGCAGCTGGAACTTCATCG
*
2448849 ACAGCAGCAGC
1 GCAGCAGCAGC
2448860 TTGAACTTCA
Statistics
Matches: 150, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 150 1.00
ACGTcount: A:0.27, C:0.31, G:0.31, T:0.11
Consensus pattern (30 bp):
GCAGCAGCAGCAGCAGCTGGAACTTCATCG
Found at i:2448739 original size:60 final size:60
Alignment explanation
Indices: 2448669--2448922 Score: 292
Period size: 60 Copynumber: 4.3 Consensus size: 60
2448659 AATTTGAACA
* * *
2448669 GCAGCGGCAGCAGCAGCTCGAACTTCATCGGCAGCAGCAGCAGCAGCTGGAACTTCATCG
1 GCAGCAGCAGCAGCAGCTGGAACTTCATCGGCAGCAGCAGCAGCAGCTGGAACTTCAACG
*
2448729 GCAGCAGCAGCAGCAGCTGGAACTTCATCGGCAGCAGCAGCAGCAGCTGGAACTTCAGCG
1 GCAGCAGCAGCAGCAGCTGGAACTTCATCGGCAGCAGCAGCAGCAGCTGGAACTTCAACG
* * * * *
2448789 GCGGCAGCAGCAGCAGCTGGAACTTCAGCAGCGGCAGCAACAGCAGCTGGAACTTCAA--
1 GCAGCAGCAGCAGCAGCTGGAACTTCATCGGCAGCAGCAGCAGCAGCTGGAACTTCAACG
* *
2448847 -C-G-A-CAGCAGCAGCTTGAACTTCAGCTACGG-AG--GCAGCAGCAGCTTGAACTTCAGCGAC
1 GCAGCAGCAGCAGCAGCTGGAACTTCA--T-CGGCAGCAGCAGCAGCAGCTGGAACTTCA---AC
2448905 G
60 G
2448906 GCAGCAGCAGCAGCAGC
1 GCAGCAGCAGCAGCAGC
2448923 AGCAACAGCA
Statistics
Matches: 167, Mismatches: 15, Indels: 21
0.82 0.07 0.10
Matches are distributed among these distances:
54 38 0.23
55 1 0.01
56 2 0.01
57 4 0.02
60 110 0.66
61 1 0.01
62 1 0.01
63 10 0.06
ACGTcount: A:0.27, C:0.30, G:0.31, T:0.12
Consensus pattern (60 bp):
GCAGCAGCAGCAGCAGCTGGAACTTCATCGGCAGCAGCAGCAGCAGCTGGAACTTCAACG
Found at i:2448809 original size:90 final size:87
Alignment explanation
Indices: 2448667--2448919 Score: 316
Period size: 90 Copynumber: 2.9 Consensus size: 87
2448657 TCAATTTGAA
* * * * *
2448667 CAGCAGCGGCAGCAGCAGCTCGAACTTCATCGGCAGCAGCAGCAGCAGCTGGAACTTCATCGGCA
1 CAGCAGCAGCAGCAGCAGCTCGAACTTCAGCGGCGGCAGCAGCAGCAGCTGGAACTTCAGCGGCG
2448732 GCAGCAGCAGCAGCTGGAACTT
66 GCAGCAGCAGCAGCTGGAACTT
* *
2448754 CATCGGCAGCAGCAGCAGCAGCTGGAACTTCAGCGGCGGCAGCAGCAGCAGCTGGAACTTCAGCA
1 CA---GCAGCAGCAGCAGCAGCTCGAACTTCAGCGGCGGCAGCAGCAGCAGCTGGAACTTCAGCG
*
2448819 GCGGCAGCAACAGCAGCTGGAACTT
63 GCGGCAGCAGCAGCAGCTGGAACTT
* * ** * *
2448844 CAAC-G-A-CAGCAGCAGCTTGAACTTCAGCTACGG-AGGCAGCAGCAGCTTGAACTTCAGCGAC
1 CAGCAGCAGCAGCAGCAGCTCGAACTTCAGCGGCGGCA-GCAGCAGCAGCTGGAACTTCAGCGGC
2448905 GGCAGCAGCAGCAGC
65 GGCAGCAGCAGCAGC
2448920 AGCAGCAACA
Statistics
Matches: 146, Mismatches: 16, Indels: 11
0.84 0.09 0.06
Matches are distributed among these distances:
83 1 0.01
84 61 0.42
85 1 0.01
86 1 0.01
87 3 0.02
90 79 0.54
ACGTcount: A:0.27, C:0.30, G:0.30, T:0.12
Consensus pattern (87 bp):
CAGCAGCAGCAGCAGCAGCTCGAACTTCAGCGGCGGCAGCAGCAGCAGCTGGAACTTCAGCGGCG
GCAGCAGCAGCAGCTGGAACTT
Found at i:2448817 original size:15 final size:15
Alignment explanation
Indices: 2448769--2448845 Score: 59
Period size: 15 Copynumber: 5.1 Consensus size: 15
2448759 GCAGCAGCAG
2448769 CAGCAGCTGGAACTT
1 CAGCAGCTGGAACTT
* * **
2448784 CAGCGGC-GGCAGCAG
1 CAGCAGCTGG-AACTT
2448799 CAGCAGCTGGAACTT
1 CAGCAGCTGGAACTT
* **
2448814 CAGCAGC-GGCAGCAA
1 CAGCAGCTGG-AACTT
2448829 CAGCAGCTGGAACTT
1 CAGCAGCTGGAACTT
2448844 CA
1 CA
2448846 ACGACAGCAG
Statistics
Matches: 44, Mismatches: 14, Indels: 8
0.67 0.21 0.12
Matches are distributed among these distances:
14 4 0.09
15 36 0.82
16 4 0.09
ACGTcount: A:0.27, C:0.30, G:0.31, T:0.12
Consensus pattern (15 bp):
CAGCAGCTGGAACTT
Found at i:2448884 original size:30 final size:29
Alignment explanation
Indices: 2448674--2448919 Score: 210
Period size: 30 Copynumber: 8.4 Consensus size: 29
2448664 GAACAGCAGC
*
2448674 GGCAGCAGCAGCTCGAACTTCAT-CGGCA
1 GGCAGCAGCAGCTGGAACTTCATACGGCA
2448702 GCAGCAGCAGCAGCTGGAACTTCAT-CGGCA
1 G--GCAGCAGCAGCTGGAACTTCATACGGCA
2448732 GCAGCAGCAGCAGCTGGAACTTCAT-CGGCA
1 G--GCAGCAGCAGCTGGAACTTCATACGGCA
* *
2448762 GCAGCAGCAGCAGCTGGAACTTCA-GCGGCG
1 G--GCAGCAGCAGCTGGAACTTCATACGGCA
*
2448792 GCAGCAGCAGCAGCTGGAACTTCAGCAGCGGCA
1 G--GCAGCAGCAGCTGGAACTTCA-TA-CGGCA
*
2448825 -GCAACAGCAGCTGGAACTTCA-AC-G-A
1 GGCAGCAGCAGCTGGAACTTCATACGGCA
*
2448850 --CAGCAGCAGCTTGAACTTCAGCTACGG-A
1 GGCAGCAGCAGCTGGAACTTCA--TACGGCA
* *
2448878 GGCAGCAGCAGCTTGAACTTCAGCGACGGCA
1 GGCAGCAGCAGCTGGAACTTCA--TACGGCA
2448909 -GCAGCAGCAGC
1 GGCAGCAGCAGC
2448920 AGCAGCAACA
Statistics
Matches: 197, Mismatches: 8, Indels: 24
0.86 0.03 0.10
Matches are distributed among these distances:
24 18 0.09
25 1 0.01
26 1 0.01
27 3 0.02
28 4 0.02
30 165 0.84
31 1 0.01
33 4 0.02
ACGTcount: A:0.27, C:0.30, G:0.30, T:0.12
Consensus pattern (29 bp):
GGCAGCAGCAGCTGGAACTTCATACGGCA
Found at i:2448946 original size:24 final size:24
Alignment explanation
Indices: 2448822--2448960 Score: 72
Period size: 24 Copynumber: 5.7 Consensus size: 24
2448812 TTCAGCAGCG
*
2448822 GCAGCAACAGCAGCTGGAACTTCA
1 GCAGCAACAGCAGCTTGAACTTCA
* *
2448846 AC-GACAGCAGCAGCTTGAACTTCA
1 GCAG-CAACAGCAGCTTGAACTTCA
*
2448870 GCTACGGAGGCAGCAGCAGCTTGAACTTCA
1 G---C--A-GCAACAGCAGCTTGAACTTCA
* * * **
2448900 GC-G--ACGGCAGC-AGCAGCAGCA
1 GCAGCAACAGCAGCTTG-AACTTCA
2448921 GCAGCAACAGCAGCTTGAACTTCA
1 GCAGCAACAGCAGCTTGAACTTCA
* *
2448945 GCGGCAGCAGCAGCTT
1 GCAGCAACAGCAGCTT
2448961 CGTAACCATC
Statistics
Matches: 85, Mismatches: 17, Indels: 26
0.66 0.13 0.20
Matches are distributed among these distances:
20 1 0.01
21 12 0.14
22 1 0.01
23 2 0.02
24 44 0.52
25 1 0.01
27 2 0.02
30 21 0.25
31 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.28, T:0.13
Consensus pattern (24 bp):
GCAGCAACAGCAGCTTGAACTTCA
Found at i:2452114 original size:20 final size:20
Alignment explanation
Indices: 2452076--2452114 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2452066 TTTATAAAAG
* *
2452076 ATAATTATATTTTATTTTTT
1 ATAATTATATTTAAATTTTT
*
2452096 ATAATTCTATTTAAATTTT
1 ATAATTATATTTAAATTTT
2452115 AATTAAATAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (20 bp):
ATAATTATATTTAAATTTTT
Found at i:2455209 original size:17 final size:18
Alignment explanation
Indices: 2455187--2455228 Score: 61
Period size: 17 Copynumber: 2.4 Consensus size: 18
2455177 CAAAGAGGTT
2455187 TTATATTTAATTTT-ATA
1 TTATATTTAATTTTAATA
*
2455204 TTATATTTGATTTTAATA
1 TTATATTTAATTTTAATA
2455222 TTA-ATTT
1 TTATATTT
2455229 TTTAAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 17 0.74
18 6 0.26
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (18 bp):
TTATATTTAATTTTAATA
Found at i:2455292 original size:64 final size:64
Alignment explanation
Indices: 2455192--2455406 Score: 322
Period size: 64 Copynumber: 3.5 Consensus size: 64
2455182 AGGTTTTATA
* *
2455192 TTTAATTTTATATTAT--AT-TTGATTTTAATATTAATTTTTTAAATAAATAAAATATTAATTT
1 TTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATAAAATATTAATTT
*
2455253 TTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTAAAATAAA-ATAAATATTAATTT
1 TTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATA-AAATATTAATTT
2455317 TTTAATATTATATTATAGATATTAATTTTAATATTAA-TTTTT--A-AAATAAAA-ATTAATTT
1 TTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATAAAATATTAATTT
2455376 TTTAATATTATATTATAGATATTTAATTTTA
1 TTTAATATTATATTATAGATA-TTAATTTTA
2455407 TATCATATAA
Statistics
Matches: 144, Mismatches: 4, Indels: 13
0.89 0.02 0.08
Matches are distributed among these distances:
59 29 0.20
60 15 0.10
61 17 0.12
63 7 0.05
64 76 0.53
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (64 bp):
TTTAATATTATATTATAGATATTAATTTTAATATTAATTTTTTAAATAAATAAAATATTAATTT
Found at i:2455422 original size:24 final size:22
Alignment explanation
Indices: 2455371--2455440 Score: 56
Period size: 21 Copynumber: 3.2 Consensus size: 22
2455361 AATAAAAATT
*
2455371 AATTTTTTAATATTATATTATA
1 AATTATTTAATATTATATTATA
* *
2455393 GA-TATTTAATTTTATATCATATA
1 AATTATTTAATATTATAT--TATA
*
2455416 AATTATTTTATA-TATTATTA-A
1 AATTATTTAATATTA-TATTATA
2455437 AATT
1 AATT
2455441 TTATATTTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
21 18 0.47
22 3 0.08
23 7 0.18
24 10 0.26
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (22 bp):
AATTATTTAATATTATATTATA
Found at i:2455461 original size:20 final size:19
Alignment explanation
Indices: 2455401--2455462 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
2455391 TAGATATTTA
*
2455401 ATTTTATATCA-TATAAATT
1 ATTTTATAT-ATTATTAATT
*
2455420 ATTTTATATATTATTAA-A
1 ATTTTATATATTATTAATT
2455438 ATTTTATAT-TTATTTTAATT
1 ATTTTATATATTA--TTAATT
2455458 ATTTT
1 ATTTT
2455463 GATTTAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.08
18 10 0.28
19 18 0.50
20 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATATATTATTAATT
Found at i:2455961 original size:31 final size:31
Alignment explanation
Indices: 2455924--2455983 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
2455914 TAGTTGTATG
*
2455924 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTCAGTATTGTAAAACTAA
2455955 AATTATTTAAATCTCAGTATTGTAAAACT
1 AATTATTTAAATCTCAGTATTGTAAAACT
2455984 CTTTTAAGTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.43, C:0.08, G:0.07, T:0.42
Consensus pattern (31 bp):
AATTATTTAAATCTCAGTATTGTAAAACTAA
Found at i:2456856 original size:14 final size:14
Alignment explanation
Indices: 2456839--2456866 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2456829 AGAAACTATC
2456839 ACAAAGGAAAACTA
1 ACAAAGGAAAACTA
2456853 ACAAAGGAAAACTA
1 ACAAAGGAAAACTA
2456867 GCAAGGGCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.14, G:0.14, T:0.07
Consensus pattern (14 bp):
ACAAAGGAAAACTA
Found at i:2457928 original size:21 final size:18
Alignment explanation
Indices: 2457888--2457959 Score: 63
Period size: 20 Copynumber: 3.7 Consensus size: 18
2457878 GACCCGAAAT
2457888 AATATATATATATTAAAA
1 AATATATATATATTAAAA
*
2457906 AATATTATTTATATTCAATAA
1 AATA-TATATATATT-AA-AA
* * *
2457927 AATAGAGATTTAATTGAAAA
1 AATATATATAT-ATT-AAAA
2457947 AATATATATATAT
1 AATATATATATAT
2457960 AGAGGGGCAT
Statistics
Matches: 41, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
18 4 0.10
19 11 0.27
20 15 0.37
21 11 0.27
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.40
Consensus pattern (18 bp):
AATATATATATATTAAAA
Found at i:2458557 original size:75 final size:76
Alignment explanation
Indices: 2458406--2458614 Score: 271
Period size: 75 Copynumber: 2.8 Consensus size: 76
2458396 CAAAGCCAAA
* * * **
2458406 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATT-CCCCCTAAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGATT--CCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
2458470 TTTTGGCCCCGAG
64 TTTTGGCCCCGAG
*
2458483 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
*
2458548 TT-GCTCCGAG
66 TTGGCCCCGAG
* * * *
2458558 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGAT-TCCCCCATAGGAGGAACCGATTCCCCCCT
2458615 TGTACAACGG
Statistics
Matches: 118, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
75 73 0.62
76 20 0.17
77 25 0.21
ACGTcount: A:0.24, C:0.32, G:0.23, T:0.20
Consensus pattern (76 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
TTGGCCCCGAG
Found at i:2464437 original size:23 final size:23
Alignment explanation
Indices: 2464407--2464491 Score: 111
Period size: 23 Copynumber: 3.7 Consensus size: 23
2464397 CCCCCCCTGA
2464407 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
* **
2464430 GGGAACCGATCCCCCCCCCCTG-A-
1 GGGAACCGAT--TCCCCCTTTGAAG
2464453 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTTGAAG
2464476 GGGAACCGATTCCCCC
1 GGGAACCGATTCCCCC
2464492 CCACAGGGGA
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
21 7 0.13
22 1 0.02
23 36 0.69
24 1 0.02
25 7 0.13
ACGTcount: A:0.20, C:0.39, G:0.25, T:0.16
Consensus pattern (23 bp):
GGGAACCGATTCCCCCTTTGAAG
Found at i:2464458 original size:46 final size:46
Alignment explanation
Indices: 2464397--2464493 Score: 185
Period size: 46 Copynumber: 2.1 Consensus size: 46
2464387 GGGAATCGAT
2464397 CCCCCCCTGAGGGAACCGATTCCCCCTTTGAAGGGGAACCGATCCC
1 CCCCCCCTGAGGGAACCGATTCCCCCTTTGAAGGGGAACCGATCCC
*
2464443 CCCCCCCTGAGGGAACCGATTCCCCCTTTGAAGGGGAACCGATTCC
1 CCCCCCCTGAGGGAACCGATTCCCCCTTTGAAGGGGAACCGATCCC
2464489 CCCCC
1 CCCCC
2464494 ACAGGGGAAT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.19, C:0.43, G:0.23, T:0.15
Consensus pattern (46 bp):
CCCCCCCTGAGGGAACCGATTCCCCCTTTGAAGGGGAACCGATCCC
Found at i:2464499 original size:22 final size:22
Alignment explanation
Indices: 2464428--2464514 Score: 77
Period size: 23 Copynumber: 3.9 Consensus size: 22
2464418 CCCCCTTTGA
* *
2464428 AGGGGAACCGATCCCCCCCCCC
1 AGGGGAACCGATTCCCCCCCAC
* **
2464450 TGAGGGAACCGATTCCCCCTTTGA-
1 AG-GGGAACCGATTCCCCC--CCAC
2464474 AGGGGAACCGATTCCCCCCCAC
1 AGGGGAACCGATTCCCCCCCAC
* *
2464496 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATTCCCCCC
2464515 TGGGGTTCTG
Statistics
Matches: 51, Mismatches: 10, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
21 1 0.02
22 18 0.35
23 31 0.61
24 1 0.02
ACGTcount: A:0.22, C:0.41, G:0.24, T:0.13
Consensus pattern (22 bp):
AGGGGAACCGATTCCCCCCCAC
Found at i:2464514 original size:46 final size:46
Alignment explanation
Indices: 2464397--2464515 Score: 152
Period size: 46 Copynumber: 2.6 Consensus size: 46
2464387 GGGAATCGAT
* *
2464397 CCCCCC-CTGAGGGAACCGATTCCCCCTTTGAAGGGGAACCGATCC
1 CCCCCCACAGAGGGAACCGATCCCCCCTTTGAAGGGGAACCGATCC
* * * *
2464442 CCCCCCCCTGAGGGAACCGATTCCCCCTTTGAAGGGGAACCGATTC
1 CCCCCCACAGAGGGAACCGATCCCCCCTTTGAAGGGGAACCGATCC
*
2464488 CCCCCCACAG-GGGAATCGATACCCCCCT
1 CCCCCCACAGAGGGAACCGAT-CCCCCCT
2464516 GGGGTTCTGT
Statistics
Matches: 67, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
45 15 0.22
46 52 0.78
ACGTcount: A:0.20, C:0.42, G:0.23, T:0.15
Consensus pattern (46 bp):
CCCCCCACAGAGGGAACCGATCCCCCCTTTGAAGGGGAACCGATCC
Found at i:2466132 original size:17 final size:17
Alignment explanation
Indices: 2466110--2466157 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
2466100 TTTCAACACT
2466110 TTTGATATTTTGGATTG
1 TTTGATATTTTGGATTG
2466127 TTTGAT-TTTGTGGATTG
1 TTTGATATTT-TGGATTG
*
2466144 -TTG-GATTTTGGATT
1 TTTGATATTTTGGATT
2466158 TATGAATAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
15 6 0.21
16 9 0.32
17 13 0.46
ACGTcount: A:0.15, C:0.00, G:0.27, T:0.58
Consensus pattern (17 bp):
TTTGATATTTTGGATTG
Found at i:2466894 original size:75 final size:76
Alignment explanation
Indices: 2466743--2466951 Score: 271
Period size: 75 Copynumber: 2.8 Consensus size: 76
2466733 CAAAGCCAAA
* * * **
2466743 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATT-CCCCCTAAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGATT--CCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
2466807 TTTTGGCCCCGAG
64 TTTTGGCCCCGAG
*
2466820 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
*
2466885 TT-GCTCCGAG
66 TTGGCCCCGAG
* * * *
2466895 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGAT-TCCCCCATAGGAGGAACCGATTCCCCCCT
2466952 TGTACAACGG
Statistics
Matches: 118, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
75 73 0.62
76 20 0.17
77 25 0.21
ACGTcount: A:0.24, C:0.32, G:0.23, T:0.20
Consensus pattern (76 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
TTGGCCCCGAG
Found at i:2468542 original size:25 final size:24
Alignment explanation
Indices: 2468508--2468558 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
2468498 TAACCTCAAA
2468508 AAATAATATCACCATT-T-TATAAAT
1 AAATAATAT--CCATTATCTATAAAT
2468532 AAATATATATCCATTATCTATAAAT
1 AAATA-ATATCCATTATCTATAAAT
2468557 AA
1 AA
2468559 CATTTGAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
23 5 0.21
24 6 0.25
25 13 0.54
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (24 bp):
AAATAATATCCATTATCTATAAAT
Found at i:2475487 original size:20 final size:20
Alignment explanation
Indices: 2475462--2475509 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
2475452 GAATTTTTGG
2475462 TTATTAAATTTTTAAAACAA
1 TTATTAAATTTTTAAAACAA
* *
2475482 TTATTAAATTTTTTAAATAA
1 TTATTAAATTTTTAAAACAA
2475502 TTA-TAAAT
1 TTATTAAAT
2475510 AATAATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
TTATTAAATTTTTAAAACAA
Found at i:2478945 original size:2 final size:2
Alignment explanation
Indices: 2478938--2478973 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2478928 AATACCAGGT
2478938 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
2478974 ACACACACAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:2490886 original size:36 final size:36
Alignment explanation
Indices: 2490836--2490935 Score: 155
Period size: 36 Copynumber: 2.8 Consensus size: 36
2490826 GTCCATAAAG
* * **
2490836 AATTATCAGCTTGATCGGTGTTGAACCTATATAAGT
1 AATTAACAGTTTGATCGAAGTTGAACCTATATAAGT
*
2490872 AATTACCAGTTTGATCGAAGTTGAACCTATATAAGT
1 AATTAACAGTTTGATCGAAGTTGAACCTATATAAGT
2490908 AATTAACAGTTTGATCGAAGTTGAACCT
1 AATTAACAGTTTGATCGAAGTTGAACCT
2490936 GTAGAAACTT
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 59 1.00
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (36 bp):
AATTAACAGTTTGATCGAAGTTGAACCTATATAAGT
Found at i:2493571 original size:2 final size:2
Alignment explanation
Indices: 2493564--2493593 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2493554 AATATTTTTA
2493564 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
2493594 GTAAATTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2501148 original size:21 final size:20
Alignment explanation
Indices: 2501124--2501176 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 20
2501114 CAAAACTTCT
2501124 TAAAAAATTATAAAATAGTTA
1 TAAAAAATTATAAAATA-TTA
*
2501145 T-AAAAATATATTAAATTATTA
1 TAAAAAAT-TA-TAAAATATTA
*
2501166 TAAACAATTAT
1 TAAAAAATTAT
2501177 GGGACTTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
20 7 0.26
21 9 0.33
22 11 0.41
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (20 bp):
TAAAAAATTATAAAATATTA
Found at i:2501808 original size:31 final size:31
Alignment explanation
Indices: 2501773--2501835 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
2501763 GGACAAGGCT
2501773 TGTGAGCTTCTCTAACATCTCCTCAGCGCCA
1 TGTGAGCTTCTCTAACATCTCCTCAGCGCCA
2501804 TGTGAGCTTCTCTAACATCTCCTCAGCGCCA
1 TGTGAGCTTCTCTAACATCTCCTCAGCGCCA
2501835 T
1 T
2501836 CGCCTCAACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.19, C:0.35, G:0.16, T:0.30
Consensus pattern (31 bp):
TGTGAGCTTCTCTAACATCTCCTCAGCGCCA
Found at i:2506655 original size:106 final size:106
Alignment explanation
Indices: 2506468--2506733 Score: 426
Period size: 106 Copynumber: 2.5 Consensus size: 106
2506458 AAAAGTTGTC
* * * *
2506468 TGTCAACAGACAATTTCCCAATTTCGGAGCCAATTTCAAACTTCCCAGCGAAGGATATTGGACTC
1 TGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTC-AACTTCACAACGAAGGATATTGGACTC
*
2506533 CAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGT
65 CAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGT
*
2506575 TGTCAATAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
1 TGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
*
2506640 AGACAACGCATGTTCAACTTCACAACGAAGGGACCGCTGGT
66 AGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGT
* *
2506681 TGTCAACAAACAACTTCTCAATATT-AGAGCCAATTTCAACTTCACAACGAAGG
1 TGTCAACAAACAATTTCCCAAT-TTCAGAGCCAATTTCAACTTCACAACGAAGG
2506734 GACCGCTGGT
Statistics
Matches: 148, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
106 112 0.76
107 36 0.24
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (106 bp):
TGTCAACAAACAATTTCCCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCC
AGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGT
Found at i:2506751 original size:63 final size:63
Alignment explanation
Indices: 2506652--2506796 Score: 290
Period size: 63 Copynumber: 2.3 Consensus size: 63
2506642 ACAACGCATG
2506652 TTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATATTAGAGCCAAT
1 TTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATATTAGAGCCAAT
2506715 TTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATATTAGAGCCAAT
1 TTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATATTAGAGCCAAT
2506778 TTCAACTTCACAACGAAGG
1 TTCAACTTCACAACGAAGG
2506797 ATATTGGACT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 82 1.00
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.23
Consensus pattern (63 bp):
TTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATATTAGAGCCAAT
Found at i:2506825 original size:169 final size:169
Alignment explanation
Indices: 2506546--2506902 Score: 628
Period size: 169 Copynumber: 2.1 Consensus size: 169
2506536 ACAACGCAAG
* * *
2506546 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCCAATTT
1 TTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
2506611 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACAACGAAGGGACCG
66 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACAACGAAGGGACCG
2506676 CTGGTTGTCAACAAACAACTTCTCAATATT-AGAGCCAAT
131 CTGGTTGTCAACAAACAACTTCTCAAT-TTCAGAGCCAAT
*
2506715 TTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATATT-AGAGCCAATT
1 TTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAAT-TTCAGAGCCAATT
* *
2506779 TCAACTTCACAACGAAGGATATTGGACTCCTGACAACGCATGTTCAACTTCACGACGAAGGGACC
65 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACAACGAAGGGACC
2506844 GCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAAT
130 GCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAAT
2506884 TTCAACTTCACAACGAAGG
1 TTCAACTTCACAACGAAGG
2506903 ATATTGGACT
Statistics
Matches: 180, Mismatches: 6, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
168 2 0.01
169 176 0.98
170 2 0.01
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.24
Consensus pattern (169 bp):
TTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCATGTTCAACTTCACAACGAAGGGACCG
CTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAAT
Found at i:2506827 original size:106 final size:106
Alignment explanation
Indices: 2506715--2507336 Score: 1039
Period size: 106 Copynumber: 5.9 Consensus size: 106
2506705 TAGAGCCAAT
* *
2506715 TTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATATT-AGAGCCAATT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAAT-TTCAGAGCCAATT
* *
2506779 TCAACTTCACAACGAAGGATATTGGACTCCTGACAACGCATG
65 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
*
2506821 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
2506886 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
66 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* *
2506927 TTCAACTTCACGACGAAGGGACCGCTGGTTATCAACAAACAATTTCCCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
*
2506992 CAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAG
66 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* *
2507033 TTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
2507098 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
66 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* * * *
2507139 TTCAACTTCACGATGAAGGGACCGCTGGTTTTCAATAAACAATTTCCCAATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
*
2507204 CAACTTCACAACGAATGATATTGGACTCCAGACAACGCAAG
66 CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
* * *
2507245 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAGTTCCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
** *
2507310 CAACTTCACGGCGGAGGATATTGGACT
66 CAACTTCACAACGAAGGATATTGGACT
2507337 TAGAACAATA
Statistics
Matches: 489, Mismatches: 26, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
105 2 0.00
106 487 1.00
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.23
Consensus pattern (106 bp):
TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCCAATTTCAGAGCCAATTT
CAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
Found at i:2507729 original size:84 final size:81
Alignment explanation
Indices: 2507540--2507799 Score: 238
Period size: 84 Copynumber: 3.1 Consensus size: 81
2507530 CTAACAAAAT
* * * * * * *
2507540 ACCTTTGAGTTCGACTACGCTCAGC-TCAATGGCACATCATTTGCAGCATAGCTTAAGTCGAGAA
1 ACCTTCGAGTTCGACTACGCTCAGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCGACAA
2507604 GGGCTATCTGCCAAAG
66 GGGCTATCTGCCAAAG
** * * * * * *
2507620 ACCCCCGAGTTCGATTACACTCAGCTTCGAGGGTATATCATTTACAGCATAACTCAAGGCTACAA
1 ACCTTCGAGTTCGACTACGCTCAGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCGACAA
*
2507685 GGGTTATCTGTGACCAAAG
66 GGGCTATC--TG-CCAAAG
* * * * *
2507704 ACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTGA-AGCATAGCTGAAGTCGAAA
1 ACCTTCGAGTTCGACTACGCTCAGCTTCAAGGGCACATCATTT-ACAGCATAACTCAAGGCGACA
2507767 AGGGCTATCTGCCAACCGAAG
65 AGGGCTATCTGCC-A---AAG
2507788 ACCTTCGAGTTC
1 ACCTTCGAGTTC
2507800 AATTACACTC
Statistics
Matches: 141, Mismatches: 30, Indels: 14
0.76 0.16 0.08
Matches are distributed among these distances:
80 22 0.16
81 39 0.28
83 34 0.24
84 46 0.33
ACGTcount: A:0.28, C:0.26, G:0.22, T:0.24
Consensus pattern (81 bp):
ACCTTCGAGTTCGACTACGCTCAGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCGACAA
GGGCTATCTGCCAAAG
Found at i:2512927 original size:21 final size:21
Alignment explanation
Indices: 2512901--2512970 Score: 106
Period size: 21 Copynumber: 3.3 Consensus size: 21
2512891 GCCATCTCCA
*
2512901 CAGGGTTACATTCCGAGCCCG
1 CAGGGTTACATTCCTAGCCCG
2512922 CAGGGTTACATTCCTAGCCCG
1 CAGGGTTACATTCCTAGCCCG
*
2512943 CCA-GGTTACATGCCTAGCCCG
1 -CAGGGTTACATTCCTAGCCCG
2512964 CAGGGTT
1 CAGGGTT
2512971 TTATACCATA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.04
21 41 0.91
22 2 0.04
ACGTcount: A:0.19, C:0.33, G:0.27, T:0.21
Consensus pattern (21 bp):
CAGGGTTACATTCCTAGCCCG
Found at i:2513552 original size:33 final size:34
Alignment explanation
Indices: 2513493--2513589 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 34
2513483 AAATGTTTTT
*
2513493 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
2513527 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
2513560 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
2513590 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:2513596 original size:34 final size:33
Alignment explanation
Indices: 2513491--2513596 Score: 133
Period size: 34 Copynumber: 3.2 Consensus size: 33
2513481 ATAAATGTTT
*
2513491 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTT-AAA
* *
2513525 TAAAAATAAAAATAATATTATTC-AAATTTAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAA
* *
2513557 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTCGAAATTTAA-A
2513592 TTAAA
1 TTAAA
2513597 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAA
Found at i:2514202 original size:126 final size:126
Alignment explanation
Indices: 2513977--2514833 Score: 1651
Period size: 126 Copynumber: 6.8 Consensus size: 126
2513967 TTTAAGTTAT
2513977 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
2514042 GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
2514103 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
2514168 GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
2514229 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
*
2514294 GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTAATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
2514355 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
2514420 GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
2514481 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
2514546 GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
2514607 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
* *
2514672 GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATATGTACTAATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
* * *
2514733 TCCCCGAGGGAGATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGT
1 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
*
2514798 GTGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAA
66 GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAA
2514834 CCGATTATAG
Statistics
Matches: 723, Mismatches: 8, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
126 723 1.00
ACGTcount: A:0.32, C:0.19, G:0.26, T:0.23
Consensus pattern (126 bp):
TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
GCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
Found at i:2514914 original size:8 final size:8
Alignment explanation
Indices: 2514901--2514941 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
2514891 TCACAATCTT
2514901 TCAAATTC
1 TCAAATTC
2514909 TCAAATTC
1 TCAAATTC
* *
2514917 CCAAACTC
1 TCAAATTC
2514925 T-AAATTC
1 TCAAATTC
2514932 TCAAATTC
1 TCAAATTC
2514940 TC
1 TC
2514942 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:2517967 original size:12 final size:13
Alignment explanation
Indices: 2517934--2517971 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
2517924 AAATACATAA
2517934 ATATATTTAATAT
1 ATATATTTAATAT
*
2517947 ATTTATTTAATAT
1 ATATATTTAATAT
2517960 A-ATATTTAATAT
1 ATATATTTAATAT
2517972 TATTAGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATATATTTAATAT
Found at i:2519033 original size:24 final size:24
Alignment explanation
Indices: 2518996--2519056 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
2518986 GTTCGTGAAT
*
2518996 GTTCGGTTATGTTCGTTTATATGC
1 GTTCAGTTATGTTCGTTTATATGC
* *
2519020 GTTTAGTTATGTTCGTTTATGTGC
1 GTTCAGTTATGTTCGTTTATATGC
*
2519044 GTTCATTTATGTT
1 GTTCAGTTATGTT
2519057 TAACCTAATA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.13, C:0.10, G:0.23, T:0.54
Consensus pattern (24 bp):
GTTCAGTTATGTTCGTTTATATGC
Found at i:2520582 original size:10 final size:10
Alignment explanation
Indices: 2520567--2520641 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
2520557 GGGTCTCCAA
2520567 CGTTTATGTT
1 CGTTTATGTT
2520577 CGTTTATGTT
1 CGTTTATGTT
2520587 CG----TGTT
1 CGTTTATGTT
*
2520593 CATTTATGTT
1 CGTTTATGTT
*
2520603 CGTATT-CGTTT
1 CGT-TTATG-TT
* *
2520614 ATGTTTGTGTT
1 -CGTTTATGTT
2520625 CGTTTATGTT
1 CGTTTATGTT
2520635 CGTTTAT
1 CGTTTAT
2520642 TTATTAAATG
Statistics
Matches: 50, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
6 5 0.10
10 34 0.68
11 8 0.16
12 3 0.06
ACGTcount: A:0.11, C:0.11, G:0.20, T:0.59
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:2520598 original size:16 final size:16
Alignment explanation
Indices: 2520573--2520637 Score: 103
Period size: 16 Copynumber: 4.1 Consensus size: 16
2520563 CCAACGTTTA
2520573 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
2520589 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
* *
2520605 TATTCGTTTATGTTTG
1 TGTTCGTTTATGTTCG
2520621 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
2520637 T
1 T
2520638 TTATTTATTA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.09, C:0.11, G:0.22, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:2520728 original size:16 final size:16
Alignment explanation
Indices: 2520707--2520737 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2520697 AAAAAAAATT
2520707 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
2520723 TGTTCGTTTATGTTC
1 TGTTCGTTTATGTTC
2520738 ACTTATTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.13, G:0.23, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:2521646 original size:31 final size:31
Alignment explanation
Indices: 2521611--2521677 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
2521601 TTATAATATG
2521611 TATAAAAATTAGAT-AAATTTAATAATTACTT
1 TATAAAAATTAGATAAAATTTAATAATT-CTT
* * * *
2521642 TATAATATTTTGATAAAATTTAATAATTTTT
1 TATAAAAATTAGATAAAATTTAATAATTCTT
2521673 TATAA
1 TATAA
2521678 TAACTTATGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 18 0.58
32 13 0.42
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.48
Consensus pattern (31 bp):
TATAAAAATTAGATAAAATTTAATAATTCTT
Found at i:2522509 original size:60 final size:58
Alignment explanation
Indices: 2522443--2522603 Score: 153
Period size: 60 Copynumber: 2.7 Consensus size: 58
2522433 TGATATCTAG
* * * *
2522443 TTTAAATTAGTCCCCAAAGTTTTAAATGTTCTAATTTCATCTTTAAACTATAA-CTCTCAT
1 TTTAAATT-GTCCCAAAAATTTTAAATATTCTAATTTCATC-TCAAACTATAACCT-TCAT
* * *
2522503 TTTAAATTGGTCCCAAAAATTTTAAATATTTTAAATTCATGCTCAAACTATGACCTTCAT
1 TTTAAATT-GTCCCAAAAATTTTAAATATTCTAATTTCAT-CTCAAACTATAACCTTCAT
* ** * *
2522563 TCTATGTTGATCCCTAAACTTTTAAATATTCTAATTTCATC
1 TTTAAATTG-TCCCAAAAATTTTAAATATTCTAATTTCATC
2522604 CTCTAACTTT
Statistics
Matches: 83, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
59 2 0.02
60 78 0.94
61 3 0.04
ACGTcount: A:0.34, C:0.18, G:0.06, T:0.43
Consensus pattern (58 bp):
TTTAAATTGTCCCAAAAATTTTAAATATTCTAATTTCATCTCAAACTATAACCTTCAT
Found at i:2551351 original size:15 final size:17
Alignment explanation
Indices: 2551331--2551365 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 17
2551321 TGGTATAGTT
2551331 TGTTTTTTTT-T-TCTC
1 TGTTTTTTTTCTGTCTC
2551346 TGTTTTTTTTCTGTCTC
1 TGTTTTTTTTCTGTCTC
2551363 TGT
1 TGT
2551366 CTCTAGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 10 0.56
16 1 0.06
17 7 0.39
ACGTcount: A:0.00, C:0.14, G:0.11, T:0.74
Consensus pattern (17 bp):
TGTTTTTTTTCTGTCTC
Found at i:2551396 original size:21 final size:21
Alignment explanation
Indices: 2551348--2551398 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
2551338 TTTTTCTCTG
*
2551348 TTTTTTTTCTGTCTCTGTCTC
1 TTTTTTTTCTGTCTCTGCCTC
* *
2551369 TAGTTTTTT-TGTCTCTGCCTT
1 T-TTTTTTTCTGTCTCTGCCTC
2551390 TTTTTTTTC
1 TTTTTTTTC
2551399 AGGTTCGGGT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
20 6 0.25
21 12 0.50
22 6 0.25
ACGTcount: A:0.02, C:0.20, G:0.10, T:0.69
Consensus pattern (21 bp):
TTTTTTTTCTGTCTCTGCCTC
Found at i:2551861 original size:3 final size:3
Alignment explanation
Indices: 2551853--2551923 Score: 124
Period size: 3 Copynumber: 23.7 Consensus size: 3
2551843 AATATATATT
* *
2551853 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAC TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2551901 TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
2551924 TGGATAAAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2552593 original size:113 final size:113
Alignment explanation
Indices: 2552240--2552789 Score: 923
Period size: 113 Copynumber: 4.9 Consensus size: 113
2552230 TGATAGTATC
* *
2552240 AAAC-AAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
** * * *
2552304 TCATTATGAACCTTCTCTGGCAA---AAAT-AATCAAGTGATGAATTC
66 TCATTATGAACCTTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
* *
2552348 AAACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
*
2552413 TCATTCATGAACTTTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
66 TCATT-ATGAACCTTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
2552462 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
*
2552527 TCATTATGAACCTTCTCTGGAAATGTTGATCCATCAAATGATGAATTT
66 TCATTATGAACCTTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
2552575 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
2552640 TCATTATGAACCTTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
66 TCATTATGAACCTTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
2552688 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
1 AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* *
2552753 TCATTATGAA-CTTATCTGGCAATGAATGATCCATCAA
66 TCATTATGAACCTTCTCTGGCAATG-TTGATCCATCAA
2552790 GTGGATTTGA
Statistics
Matches: 420, Mismatches: 15, Indels: 9
0.95 0.03 0.02
Matches are distributed among these distances:
108 4 0.01
109 63 0.15
110 17 0.04
112 13 0.03
113 241 0.57
114 82 0.20
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.37
Consensus pattern (113 bp):
AAACAAAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
TCATTATGAACCTTCTCTGGCAATGTTGATCCATCAAATGATGAATTT
Found at i:2553667 original size:83 final size:84
Alignment explanation
Indices: 2553528--2553860 Score: 582
Period size: 83 Copynumber: 4.0 Consensus size: 84
2553518 AGTTCTTACC
*
2553528 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTTCCCAA
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAA
2553592 TTCAATGATTGGTTCTGCT
66 TTCAATGATTGGTTCTGCT
* *
2553611 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACAAATTCATCTTCTAAA
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAA
2553675 TTCAATGATTGGTTCTG-T
66 TTCAATGATTGGTTCTGCT
*
2553693 CCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAA
1 -AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAA
*
2553758 ATTCAATGATTGGTTCTGCC
65 ATTCAATGATTGGTTCTGCT
*
2553778 AAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAA
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAA
2553843 TTCAATGATTGGTTCTGC
66 TTCAATGATTGGTTCTGC
2553861 CAAATCACAA
Statistics
Matches: 237, Mismatches: 9, Indels: 7
0.94 0.04 0.03
Matches are distributed among these distances:
82 3 0.01
83 117 0.49
84 117 0.49
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (84 bp):
AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAA
TTCAATGATTGGTTCTGCT
Found at i:2553791 original size:167 final size:166
Alignment explanation
Indices: 2553529--2553863 Score: 600
Period size: 167 Copynumber: 2.0 Consensus size: 166
2553519 GTTCTTACCA
*
2553529 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCCAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATT
*
2553594 CAATGATTGGTTCTGCTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAA
66 CAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAA
*
2553658 CAAATTCATCTTCTAAATTCAATGATTGGTTCTGTCC
131 CAAATTCATCTTCCAAATTCAATGATTGGTTCTG-CC
2553695 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCAAAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTTCCAAAT
*
2553760 TCAATGATTGGTTCTGCCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGA
65 TCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGA
*
2553825 GCAAATTCATCTTCCAAATTCAATGATTGGTTCTGCC
130 ACAAATTCATCTTCCAAATTCAATGATTGGTTCTGCC
2553862 AA
1 AA
2553864 ATCACAACAC
Statistics
Matches: 162, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
166 45 0.28
167 81 0.50
168 36 0.22
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (166 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATT
CAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAA
CAAATTCATCTTCCAAATTCAATGATTGGTTCTGCC
Found at i:2553867 original size:84 final size:84
Alignment explanation
Indices: 2553526--2553864 Score: 603
Period size: 84 Copynumber: 4.1 Consensus size: 84
2553516 GTAGTTCTTA
*
2553526 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTTCCC
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCA
2553590 AATTCAATGATTGGTTCTG
66 AATTCAATGATTGGTTCTG
* * *
2553609 CTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAACAAATTCATCTTCTA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCA
2553673 AATTCAATGATTGGTTCTG
66 AATTCAATGATTGGTTCTG
2553692 TCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCC
1 -CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCC
2553756 AAATTCAATGATTGGTTCTG
65 AAATTCAATGATTGGTTCTG
*
2553776 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCA
2553841 AATTCAATGATTGGTTCTG
66 AATTCAATGATTGGTTCTG
2553860 CCAAA
1 CCAAA
2553865 TCACAACACT
Statistics
Matches: 244, Mismatches: 8, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
82 2 0.01
83 120 0.49
84 122 0.50
ACGTcount: A:0.37, C:0.22, G:0.14, T:0.27
Consensus pattern (84 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCA
AATTCAATGATTGGTTCTG
Found at i:2554994 original size:11 final size:10
Alignment explanation
Indices: 2554974--2555046 Score: 62
Period size: 10 Copynumber: 7.1 Consensus size: 10
2554964 ACCTTGACCC
2554974 TCTTTCTTTT
1 TCTTTCTTTT
2554984 TCTTCTCTTTT
1 TCTT-TCTTTT
2554995 T-TTT-TATTT
1 TCTTTCT-TTT
2555004 TCTATT-TATTT
1 TCT-TTCT-TTT
*
2555015 TCTTTTTTTTT
1 TC-TTTCTTTT
*
2555026 TCTTTTTTTT
1 TCTTTCTTTT
2555036 TCTTTCTTTT
1 TCTTTCTTTT
2555046 T
1 T
2555047 TTTTTCAATT
Statistics
Matches: 56, Mismatches: 1, Indels: 12
0.81 0.01 0.17
Matches are distributed among these distances:
8 1 0.02
9 5 0.09
10 25 0.45
11 23 0.41
12 2 0.04
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (10 bp):
TCTTTCTTTT
Found at i:2554995 original size:1 final size:1
Alignment explanation
Indices: 2554991--2555051 Score: 50
Period size: 1 Copynumber: 61.0 Consensus size: 1
2554981 TTTTCTTCTC
* * * * * * * *
2554991 TTTTTTTTTATTTTCTATTTATTTTCTTTTTTTTTTCTTTTTTTTTCTTTCTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2555052 CAATTCTCTT
Statistics
Matches: 44, Mismatches: 16, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
1 44 1.00
ACGTcount: A:0.05, C:0.08, G:0.00, T:0.87
Consensus pattern (1 bp):
T
Found at i:2555005 original size:26 final size:26
Alignment explanation
Indices: 2554976--2555050 Score: 93
Period size: 27 Copynumber: 2.9 Consensus size: 26
2554966 CTTGACCCTC
2554976 TTTCTTTTTCTTCTCTTTTTTTTTAT
1 TTTCTTTTTCTTCTCTTTTTTTTTAT
* *
2555002 TTTCTATTTATTTTCT-TTTTTTTTTCT
1 TTTCT-TTT-TCTTCTCTTTTTTTTTAT
2555029 TTT-TTTTTCTT-TCTTTTTTTTT
1 TTTCTTTTTCTTCTCTTTTTTTTT
2555051 TCAATTCTCT
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
23 1 0.02
24 12 0.28
25 3 0.07
26 6 0.14
27 16 0.37
28 5 0.12
ACGTcount: A:0.04, C:0.12, G:0.00, T:0.84
Consensus pattern (26 bp):
TTTCTTTTTCTTCTCTTTTTTTTTAT
Found at i:2555047 original size:11 final size:11
Alignment explanation
Indices: 2554974--2555052 Score: 62
Period size: 11 Copynumber: 7.5 Consensus size: 11
2554964 ACCTTGACCC
2554974 TCTTTC-TTTT
1 TCTTTCTTTTT
2554984 TC-TTCTCTTTT
1 TCTTTCT-TTTT
*
2554995 T-TTT-TATTT
1 TCTTTCTTTTT
*
2555004 TCTATT-TATTT
1 TCT-TTCTTTTT
*
2555015 TCTTTTTTTTT
1 TCTTTCTTTTT
2555026 TCTTT-TTTTT
1 TCTTTCTTTTT
2555036 TCTTTCTTTTT
1 TCTTTCTTTTT
*
2555047 TTTTTC
1 TCTTTC
2555053 AATTCTCTTC
Statistics
Matches: 59, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
9 7 0.12
10 16 0.27
11 36 0.61
ACGTcount: A:0.04, C:0.14, G:0.00, T:0.82
Consensus pattern (11 bp):
TCTTTCTTTTT
Found at i:2567072 original size:20 final size:17
Alignment explanation
Indices: 2567032--2567066 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
2567022 GAGTTCTGCC
2567032 GCCGACCACCGCCGCCG
1 GCCGACCACCGCCGCCG
2567049 GCCGACCACCGCCGCCG
1 GCCGACCACCGCCGCCG
2567066 G
1 G
2567067 TGGCCGGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.11, C:0.57, G:0.31, T:0.00
Consensus pattern (17 bp):
GCCGACCACCGCCGCCG
Found at i:2567332 original size:18 final size:18
Alignment explanation
Indices: 2567307--2567375 Score: 63
Period size: 16 Copynumber: 3.7 Consensus size: 18
2567297 TGGTATAGTT
2567307 TGTTTTTTTTT-T-TCTC
1 TGTTTTTTTTTCTGTCTC
2567323 TGTTTTTTTTTCTGTCTC
1 TGTTTTTTTTTCTGTCTC
2567341 TGTCTCTAGTTTTTT-TGTCTC
1 TGT-T-T--TTTTTTCTGTCTC
2567362 TGCCTTTTTTTTTC
1 TG--TTTTTTTTTC
2567376 AGGTTCGGGT
Statistics
Matches: 44, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
16 11 0.25
17 1 0.02
18 7 0.16
19 7 0.16
20 1 0.02
21 9 0.20
22 7 0.16
23 1 0.02
ACGTcount: A:0.01, C:0.17, G:0.10, T:0.71
Consensus pattern (18 bp):
TGTTTTTTTTTCTGTCTC
Found at i:2567838 original size:3 final size:3
Alignment explanation
Indices: 2567830--2567905 Score: 136
Period size: 3 Copynumber: 25.7 Consensus size: 3
2567820 AATATATATT
*
2567830 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2567878 T-A TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2567906 TGGATAAAAA
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 68 0.97
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2576359 original size:3 final size:3
Alignment explanation
Indices: 2576351--2576380 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2576341 ATACCCTTTG
2576351 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
2576381 CATGTCTCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:2577461 original size:165 final size:164
Alignment explanation
Indices: 2577273--2577638 Score: 552
Period size: 165 Copynumber: 2.2 Consensus size: 164
2577263 ACTTTTGTGT
* *
2577273 CGTTTTAAGACAAACGCCACAGAAGGTGACATCAATAGTGGCATTTCTTGTAAAAACGCCGCAAT
1 CGTTTTTAGACAAACGCCACAGAAGGTGACATCAATAGTAGCATTTCTTGTAAAAACGCCGCAAT
* * * * *
2577338 AGATATGAAATTTCGTGGCGTTTTAACTCAAATGCCGTAATAGAACTGTAATTTAGCGGCGTTTA
66 AGATATGAAATTTCATGGCGTTTTAACTAAAACGCCGTAACAGAACTGCAATTTAGCGGCGTTTA
* ** *
2577403 GACTAAAAACGTCGTAATATGTAGTTTTTTTACGG
131 GACTAAAAACGCCACAATATGTAG-TTTTTTACAG
*
2577438 CGTTTTTAGACAAACGCCACAGAAGGTGACATCAATAGTAGCGTTTCTTGTAAAAACGCCGCAAT
1 CGTTTTTAGACAAACGCCACAGAAGGTGACATCAATAGTAGCATTTCTTGTAAAAACGCCGCAAT
* * ** *
2577503 AGATATGAAATTTCATGGCGTTTTATCTAAAACGCTGTAACAGATTTGCAATTTAGTGGCGTTTA
66 AGATATGAAATTTCATGGCGTTTTAACTAAAACGCCGTAACAGAACTGCAATTTAGCGGCGTTTA
2577568 GACTAAAAACGCCACAATATGTAGTTTTTTACAG
131 GACTAAAAACGCCACAATATGTAGTTTTTTACAG
* *
2577602 CGTTTTTAGACAAACGCCACAGAATGTGACATTAATA
1 CGTTTTTAGACAAACGCCACAGAAGGTGACATCAATA
2577639 TTGGTGTTTT
Statistics
Matches: 182, Mismatches: 19, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
164 44 0.24
165 138 0.76
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (164 bp):
CGTTTTTAGACAAACGCCACAGAAGGTGACATCAATAGTAGCATTTCTTGTAAAAACGCCGCAAT
AGATATGAAATTTCATGGCGTTTTAACTAAAACGCCGTAACAGAACTGCAATTTAGCGGCGTTTA
GACTAAAAACGCCACAATATGTAGTTTTTTACAG
Found at i:2577534 original size:42 final size:42
Alignment explanation
Indices: 2577488--2577586 Score: 96
Period size: 41 Copynumber: 2.4 Consensus size: 42
2577478 GCGTTTCTTG
*
2577488 TAAAAACGCCGCAATAGATATGAAATTTCA-TGGCGTTTTA-TC
1 TAAAAACGCCGCAATAGATATGAAATTT-AGTGGCG-TTTAGAC
* * * * *
2577530 T-AAAACGCTGTAACAGATTTGCAATTTAGTGGCGTTTAGAC
1 TAAAAACGCCGCAATAGATATGAAATTTAGTGGCGTTTAGAC
*
2577571 TAAAAACGCCACAATA
1 TAAAAACGCCGCAATA
2577587 TGTAGTTTTT
Statistics
Matches: 44, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
40 5 0.11
41 28 0.64
42 11 0.25
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.28
Consensus pattern (42 bp):
TAAAAACGCCGCAATAGATATGAAATTTAGTGGCGTTTAGAC
Found at i:2579250 original size:41 final size:41
Alignment explanation
Indices: 2579180--2579279 Score: 114
Period size: 40 Copynumber: 2.4 Consensus size: 41
2579170 TAAATACTGA
* * *
2579180 ACTTTAGTAGCATTTTTA-TACAAACGCCACAGAAGGTCA-T
1 ACTTTAGTGGCGTTTTTAGCACAAACGCCAC-GAAGGTCACT
* **
2579220 ACTTTCGTGGCGTTTTTAGCACAAACGCCACGAATTTCACTT
1 ACTTTAGTGGCGTTTTTAGCACAAACGCCACGAAGGTCAC-T
2579262 ACTTTAGTGGCGTTTTTA
1 ACTTTAGTGGCGTTTTTA
2579280 AGATAAACGC
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
40 21 0.42
41 11 0.22
42 18 0.36
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (41 bp):
ACTTTAGTGGCGTTTTTAGCACAAACGCCACGAAGGTCACT
Found at i:2579272 original size:42 final size:42
Alignment explanation
Indices: 2579013--2579292 Score: 148
Period size: 42 Copynumber: 6.8 Consensus size: 42
2579003 TAAAATATCG
* * * *
2579013 TACTTTAGTGGCG-TTTTATGTAAAAACGCCGCGAATTTTACA
1 TACTTTAGTGGCGTTTTTA-GCACAAACGCCGCGAATTTCACT
* * * * * ** *
2579055 TACTCTAGCGACATTTTAAGCACAAACGCCGC-AGATAACAAT
1 TACTTTAGTGGCGTTTTTAGCACAAACGCCGCGA-ATTTCACT
* * *
2579097 TACTTTAGTGGCG-TTTTACGCACAAACGTCGCGAAATACACT
1 TACTTTAGTGGCGTTTTTA-GCACAAACGCCGCGAATTTCACT
* ** * ** *
2579139 TACTGTAGTGGCG-TTTTAATATAAACGCCGATAA-AT-ACT
1 TACTTTAGTGGCGTTTTTAGCACAAACGCCGCGAATTTCACT
* * * * * **
2579178 GAACTTTAGTAGCATTTTTA-TACAAACGCCACAGAAGGTCA--
1 -TACTTTAGTGGCGTTTTTAGCACAAACGCCGC-GAATTTCACT
* *
2579219 TACTTTCGTGGCGTTTTTAGCACAAACGCCACGAATTTCACT
1 TACTTTAGTGGCGTTTTTAGCACAAACGCCGCGAATTTCACT
*
2579261 TACTTTAGTGGCGTTTTTAAG-ATAAACGCCGC
1 TACTTTAGTGGCGTTTTT-AGCACAAACGCCGC
2579293 AGGCCATCTT
Statistics
Matches: 176, Mismatches: 49, Indels: 26
0.70 0.20 0.10
Matches are distributed among these distances:
39 3 0.02
40 39 0.22
41 33 0.19
42 93 0.53
43 8 0.05
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (42 bp):
TACTTTAGTGGCGTTTTTAGCACAAACGCCGCGAATTTCACT
Found at i:2581628 original size:15 final size:15
Alignment explanation
Indices: 2581608--2581637 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2581598 CCTGTATCAG
2581608 ATTAATCATATTTGA
1 ATTAATCATATTTGA
2581623 ATTAATCATATTTGA
1 ATTAATCATATTTGA
2581638 TACTGAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (15 bp):
ATTAATCATATTTGA
Found at i:2583152 original size:15 final size:15
Alignment explanation
Indices: 2583132--2583171 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
2583122 TGGATCCAGT
2583132 TCATCACAGTACATG
1 TCATCACAGTACATG
2583147 TCATCACAGTACATG
1 TCATCACAGTACATG
2583162 TCATCACAGT
1 TCATCACAGT
2583172 CTCAATCTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.33, C:0.28, G:0.12, T:0.28
Consensus pattern (15 bp):
TCATCACAGTACATG
Found at i:2583284 original size:21 final size:21
Alignment explanation
Indices: 2583266--2583363 Score: 83
Period size: 21 Copynumber: 4.7 Consensus size: 21
2583256 ATGAAGCAAG
2583266 GGAAGCAGAGAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
*
2583287 GGAAGCA-ACCAGAGCAGCAGC
1 GGAAGCAGA-GAGAGCAGCAGC
* * **
2583308 GGAAACAGAGAGAGAAGCAAT
1 GGAAGCAGAGAGAGCAGCAGC
* *
2583329 GGCAGCACAGAGAG-AGGCAGC
1 GGAAGCAGAGAGAGCA-GCAGC
* *
2583350 GGCAGCACAGAGAG
1 GGAAGCAGAGAGAG
2583364 AAACAACATA
Statistics
Matches: 63, Mismatches: 11, Indels: 6
0.79 0.14 0.08
Matches are distributed among these distances:
20 2 0.03
21 60 0.95
22 1 0.02
ACGTcount: A:0.40, C:0.20, G:0.39, T:0.01
Consensus pattern (21 bp):
GGAAGCAGAGAGAGCAGCAGC
Found at i:2583786 original size:44 final size:43
Alignment explanation
Indices: 2583684--2583767 Score: 123
Period size: 43 Copynumber: 1.9 Consensus size: 43
2583674 AATTATGTAT
*
2583684 TATTTAGCGGCGTTTGTAACAAAAAATGCCGCAATATACCACA
1 TATTTAGCGGCGTTTGTAACAAAAAACGCCGCAATATACCACA
* * *
2583727 TATTTAGCGGCGTTTGTATCCTAAAAACGCCGCTATATACC
1 TATTTAGCGGCGTTTGTA-ACAAAAAACGCCGCAATATACC
2583768 GCACCTATTG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 18 0.50
44 18 0.50
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.29
Consensus pattern (43 bp):
TATTTAGCGGCGTTTGTAACAAAAAACGCCGCAATATACCACA
Found at i:2583838 original size:43 final size:43
Alignment explanation
Indices: 2583769--2583932 Score: 195
Period size: 43 Copynumber: 3.8 Consensus size: 43
2583759 CTATATACCG
* * ** *
2583769 CACCTATTGCGGCGTTTGCGATAAAAACGCCGCTAAATATCAA
1 CACCTACTGCGGCGTTTGTGGGAAAAACGCCGCTAAACATCAA
*
2583812 CATCTACTGCGGCGTTTGTGGGAAAAACGCCGCTAAACATCAA
1 CACCTACTGCGGCGTTTGTGGGAAAAACGCCGCTAAACATCAA
* * *
2583855 CACCTACTACGACGTTTGTGGGAAAAATGCCGCTAAACATCAA
1 CACCTACTGCGGCGTTTGTGGGAAAAACGCCGCTAAACATCAA
* ** *
2583898 CACCTATTGATGCGTTTGT-TGAACAAACGCCGCTA
1 CACCTACTGCGGCGTTTGTGGGAA-AAACGCCGCTA
2583933 TATGGCATCA
Statistics
Matches: 103, Mismatches: 17, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
42 3 0.03
43 100 0.97
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (43 bp):
CACCTACTGCGGCGTTTGTGGGAAAAACGCCGCTAAACATCAA
Found at i:2583977 original size:15 final size:14
Alignment explanation
Indices: 2583957--2583998 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
2583947 TGCCGCGAAC
2583957 TTTAGCGGTGCTATT
1 TTTAGCGGTGCT-TT
2583972 TTTAGCGGTGC-TT
1 TTTAGCGGTGCTTT
2583985 TTT-GCGGTG-TTT
1 TTTAGCGGTGCTTT
2583997 TT
1 TT
2583999 CATAACGCCG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
12 10 0.38
13 5 0.19
15 11 0.42
ACGTcount: A:0.07, C:0.12, G:0.29, T:0.52
Consensus pattern (14 bp):
TTTAGCGGTGCTTT
Found at i:2587813 original size:2 final size:2
Alignment explanation
Indices: 2587806--2587894 Score: 178
Period size: 2 Copynumber: 44.5 Consensus size: 2
2587796 ATTTCCAGCT
2587806 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
2587848 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA
2587890 TA TA T
1 TA TA T
2587895 GCAAGTGAAG
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 87 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2588016 original size:2 final size:2
Alignment explanation
Indices: 2588011--2588050 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
2588001 AAAAGAAAAG
*
2588011 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2588051 CTTAAATATA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2589963 original size:14 final size:16
Alignment explanation
Indices: 2589930--2589966 Score: 51
Period size: 14 Copynumber: 2.4 Consensus size: 16
2589920 TATTTTTGAA
2589930 TTAATATTTTCAAGTTT
1 TTAAT-TTTTCAAGTTT
2589947 TTAATTTTT-AA-TTT
1 TTAATTTTTCAAGTTT
2589961 TTAATT
1 TTAATT
2589967 GAAGTAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 9 0.45
15 2 0.10
16 4 0.20
17 5 0.25
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (16 bp):
TTAATTTTTCAAGTTT
Found at i:2593731 original size:15 final size:15
Alignment explanation
Indices: 2593711--2593739 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2593701 TTGAAGCTTG
2593711 ACTTAAACTCGAAAA
1 ACTTAAACTCGAAAA
2593726 ACTTAAACTCGAAA
1 ACTTAAACTCGAAA
2593740 TATTTTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.21, G:0.07, T:0.21
Consensus pattern (15 bp):
ACTTAAACTCGAAAA
Found at i:2601200 original size:57 final size:57
Alignment explanation
Indices: 2601130--2601241 Score: 206
Period size: 57 Copynumber: 2.0 Consensus size: 57
2601120 CGTTAAGGGA
*
2601130 TGCATCGATACATGGTGTAGTGTATCGATGCATACCTTCATTAAAAGATAAAAATGG
1 TGCATCGATACATGGTGTAGTGCATCGATGCATACCTTCATTAAAAGATAAAAATGG
*
2601187 TGCATTGATACATGGTGTAGTGCATCGATGCATACCTTCATTAAAAGATAAAAAT
1 TGCATCGATACATGGTGTAGTGCATCGATGCATACCTTCATTAAAAGATAAAAAT
2601242 AGCTTTCTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (57 bp):
TGCATCGATACATGGTGTAGTGCATCGATGCATACCTTCATTAAAAGATAAAAATGG
Found at i:2601772 original size:18 final size:18
Alignment explanation
Indices: 2601749--2601821 Score: 58
Period size: 18 Copynumber: 3.9 Consensus size: 18
2601739 AGGGATTGTC
* *
2601749 AGTGGTCCTTCGGGACAT
1 AGTGGTCATTCAGGACAT
*
2601767 AGTGGTTC-TTCAGAACAAT
1 AGTGG-TCATTCAGGAC-AT
* * *
2601786 CGGTGGTCATTCGGGACGT
1 -AGTGGTCATTCAGGACAT
2601805 AGTGGTCATTCAGGACA
1 AGTGGTCATTCAGGACA
2601822 AATATTCAGT
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
18 25 0.60
19 7 0.17
20 10 0.24
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.27
Consensus pattern (18 bp):
AGTGGTCATTCAGGACAT
Found at i:2603342 original size:42 final size:41
Alignment explanation
Indices: 2603319--2603410 Score: 121
Period size: 41 Copynumber: 2.2 Consensus size: 41
2603309 GTCTATGCTG
2603319 AAAGTTATGGCAAAGGCTCCAACCTTTAGCCACTCCACGCT
1 AAAGTTATGGCAAAGGCTCCAACCTTTAGCCACTCCACGCT
* * * * * *
2603360 AAATTTATGGTAAAGGCTTCAACCTTTAACCGCTCCACACT
1 AAAGTTATGGCAAAGGCTCCAACCTTTAGCCACTCCACGCT
2603401 GAAAGTTATG
1 -AAAGTTATG
2603411 TTCATCTCGA
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
41 35 0.81
42 8 0.19
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (41 bp):
AAAGTTATGGCAAAGGCTCCAACCTTTAGCCACTCCACGCT
Found at i:2607756 original size:41 final size:41
Alignment explanation
Indices: 2607703--2607798 Score: 149
Period size: 41 Copynumber: 2.3 Consensus size: 41
2607693 TTACAGTAAA
* *
2607703 AAGATTAGTCGTCAGGTATTCCGAGCAACCTGTACAAAAAT
1 AAGATTAGTCGTCAGATATTCCGAACAACCTGTACAAAAAT
*
2607744 AAGATT-GATCGTCAGATATTCCGAACGACCTGTACAAAAAT
1 AAGATTAG-TCGTCAGATATTCCGAACAACCTGTACAAAAAT
2607785 AAGATTAGTCGTCA
1 AAGATTAGTCGTCA
2607799 AGTGCTCCAG
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
40 1 0.02
41 48 0.96
42 1 0.02
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.25
Consensus pattern (41 bp):
AAGATTAGTCGTCAGATATTCCGAACAACCTGTACAAAAAT
Found at i:2610400 original size:20 final size:20
Alignment explanation
Indices: 2610375--2610413 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
2610365 TATGTCTTTC
2610375 TTTATTTTATTTAATAAAAT
1 TTTATTTTATTTAATAAAAT
2610395 TTTATTTTATTTAATAAAA
1 TTTATTTTATTTAATAAAA
2610414 ATTTGATGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TTTATTTTATTTAATAAAAT
Found at i:2610427 original size:20 final size:20
Alignment explanation
Indices: 2610381--2610427 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
2610371 TTTCTTTATT
* *
2610381 TTATTTAATAAAATTTTATT
1 TTATTTAATAAAATTTGATG
2610401 TTATTTAATAAAAATTTGATG
1 TTATTTAAT-AAAATTTGATG
2610422 TT-TTTA
1 TTATTTA
2610428 TATTCTATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.57
Consensus pattern (20 bp):
TTATTTAATAAAATTTGATG
Found at i:2613162 original size:3 final size:3
Alignment explanation
Indices: 2613154--2613221 Score: 82
Period size: 3 Copynumber: 22.0 Consensus size: 3
2613144 TTTACCCATT
* * * *
2613154 TTA TTA TTA TTA TAA TTA TTA TCA TAA TTA TTA TTA TTA TAA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2613202 TATA TATA TTA TTA TTA TTA
1 T-TA T-TA TTA TTA TTA TTA
2613222 AAAAAATATA
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
3 50 0.88
4 7 0.12
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:2613230 original size:20 final size:20
Alignment explanation
Indices: 2613188--2613236 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
2613178 TAATTATTAT
* * *
2613188 TATTATAATTATTATATATA
1 TATTATAATTATTAAAAAAA
*
2613208 TATTATTATTATTAAAAAAA
1 TATTATAATTATTAAAAAAA
*
2613228 TATAATAAT
1 TATTATAAT
2613237 AATAATAATT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TATTATAATTATTAAAAAAA
Found at i:2613671 original size:18 final size:18
Alignment explanation
Indices: 2613650--2613688 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
2613640 AGAGACCAGC
* *
2613650 AAAAATAGAGAAGAAAAA
1 AAAAACAGAGAACAAAAA
2613668 AAAAACAGAGAACAAAAA
1 AAAAACAGAGAACAAAAA
2613686 AAA
1 AAA
2613689 GAAAACCTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.79, C:0.05, G:0.13, T:0.03
Consensus pattern (18 bp):
AAAAACAGAGAACAAAAA
Found at i:2614577 original size:20 final size:21
Alignment explanation
Indices: 2614531--2614577 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
2614521 CTGCTTTTAA
*
2614531 ATATATCGTTCTAATTGTATT
1 ATATATTGTTCTAATTGTATT
* *
2614552 -TTTATTGTTTTAATTGT-TT
1 ATATATTGTTCTAATTGTATT
2614571 ATATATT
1 ATATATT
2614578 TAAATATTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
19 2 0.10
20 19 0.90
ACGTcount: A:0.26, C:0.04, G:0.09, T:0.62
Consensus pattern (21 bp):
ATATATTGTTCTAATTGTATT
Found at i:2614647 original size:26 final size:24
Alignment explanation
Indices: 2614618--2614671 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
2614608 AAATATATAT
2614618 AATAAATAATAATTT-ATATTTTTTTC
1 AATAAAT--TAATTTAATA-TTTTTTC
*
2614644 AATAAATTATTTTAATATTTTTTC
1 AATAAATTAATTTAATATTTTTTC
2614668 AATA
1 AATA
2614672 TCGAAGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 16 0.62
25 3 0.12
26 7 0.27
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.54
Consensus pattern (24 bp):
AATAAATTAATTTAATATTTTTTC
Found at i:2618693 original size:15 final size:15
Alignment explanation
Indices: 2618673--2618704 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2618663 ATCAATACCT
2618673 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
2618688 TTTTGCATACATTCA
1 TTTTGCATACATGCA
2618703 TT
1 TT
2618705 ATTCATTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:2622307 original size:17 final size:17
Alignment explanation
Indices: 2622285--2622318 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
2622275 GATTCGCCCA
2622285 TGTTTTCCTGGAGAAAC
1 TGTTTTCCTGGAGAAAC
2622302 TGTTTTCCTGGAGAAAC
1 TGTTTTCCTGGAGAAAC
2622319 ACTCAACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.35
Consensus pattern (17 bp):
TGTTTTCCTGGAGAAAC
Found at i:2626073 original size:24 final size:26
Alignment explanation
Indices: 2626044--2626096 Score: 83
Period size: 25 Copynumber: 2.1 Consensus size: 26
2626034 ATTATGCTTG
*
2626044 AAGAG-AAAAAGAAAAAGA-AAAAAA
1 AAGAGAAAAAAGAAAAAAAGAAAAAA
2626068 AAGAGAAAAAAGAAAAAAAGAAAAAA
1 AAGAGAAAAAAGAAAAAAAGAAAAAA
2626094 AAG
1 AAG
2626097 GGGTCAAGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 5 0.19
25 12 0.46
26 9 0.35
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (26 bp):
AAGAGAAAAAAGAAAAAAAGAAAAAA
Done.