Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008449.1 Hibiscus syriacus cultivar Beakdansim tig00111254_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: 1344907
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 6
Found at i:1332 original size:22 final size:20
Alignment explanation
Indices: 1307--1350 Score: 61
Period size: 22 Copynumber: 2.1 Consensus size: 20
1297 ACCCATTTCG
1307 TTTTATTTTAATTCAGTTAATT
1 TTTTATTTTAATTCA-TT-ATT
*
1329 TTTTATTTTCATTCATTATT
1 TTTTATTTTAATTCATTATT
1349 TT
1 TT
1351 CACTCAATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 5 0.24
21 2 0.10
22 14 0.67
ACGTcount: A:0.23, C:0.07, G:0.02, T:0.68
Consensus pattern (20 bp):
TTTTATTTTAATTCATTATT
Found at i:3152 original size:199 final size:200
Alignment explanation
Indices: 2810--3204 Score: 562
Period size: 199 Copynumber: 2.0 Consensus size: 200
2800 TCAACAACCA
* * * * * *
2810 AAAAAGAGCTTTTTTCCATAGTATTTTCTTTAAAAAAATTTATATCATATTTACTTGGAACTAAT
1 AAAAAGAGCTTCTTGCCATAGTATTTGCTTTAAAAAAATATAGATAATATTTACTTGGAACTAAT
* *
2875 ATCGTTATTTTTCTTATCATGCATCGTTAAGACATTTAATGAGAAAGAAAGAAGCAAAACCAAGG
66 ATCGTTATTTTTCTTATAATGCAGCGTTAAGACATTTAATGAGAAAGAAAGAAGCAAAACCAAGG
*
2940 CTTATCTGTTGGATTTTACTTCTTTAA-AATTCAATTTGGAAATCAAAGACAAGAAGCGATGCGT
131 CTTATCCGTTGGATTTTACTTCTTTAAGAATTCAATTTGGAAATCAAAGACAAGAAGCGATGCGT
3004 GGCCT
196 GGCCT
* *
3009 AAAAAGAGCTTCTTGCCATAGTATTTGCTTTAAAAAAA-ATAGATAATATTTATTTGGGACTAAT
1 AAAAAGAGCTTCTTGCCATAGTATTTGCTTTAAAAAAATATAGATAATATTTACTTGGAACTAAT
* * * * * **
3073 ATTGTTGTTTTTTCTTATAATGCAGCGTTACA-ATATTTAATTAGCAAGAAAGAAGCAAAACTGA
66 ATCGTT-ATTTTTCTTATAATGCAGCGTTA-AGACATTTAATGAGAAAGAAAGAAGCAAAACCAA
* * *
3137 GGCTTATCCGTTGGATTTTACTTCTTTAAGAATTCAATTTGGTATTCAAAGACAAGAAGGGATGC
129 GGCTTATCCGTTGGATTTTACTTCTTTAAGAATTCAATTTGGAAATCAAAGACAAGAAGCGATGC
3202 GTG
194 GTG
3205 AATTTGGTTG
Statistics
Matches: 172, Mismatches: 21, Indels: 5
0.87 0.11 0.03
Matches are distributed among these distances:
198 26 0.15
199 110 0.64
200 36 0.21
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (200 bp):
AAAAAGAGCTTCTTGCCATAGTATTTGCTTTAAAAAAATATAGATAATATTTACTTGGAACTAAT
ATCGTTATTTTTCTTATAATGCAGCGTTAAGACATTTAATGAGAAAGAAAGAAGCAAAACCAAGG
CTTATCCGTTGGATTTTACTTCTTTAAGAATTCAATTTGGAAATCAAAGACAAGAAGCGATGCGT
GGCCT
Found at i:19231 original size:39 final size:40
Alignment explanation
Indices: 19149--19231 Score: 123
Period size: 40 Copynumber: 2.1 Consensus size: 40
19139 ACTTCAGTGT
* * *
19149 ATATGGTGGGCATAACCTTATGTGTAATGCACTTTGGTTC
1 ATATGGTGGGCACAACCTTATGTGTAATGCACTATGGTGC
*
19189 ATATGGTGGGCACGACCTTATGTGTAA-GCACTATGGTGC
1 ATATGGTGGGCACAACCTTATGTGTAATGCACTATGGTGC
19228 ATAT
1 ATAT
19232 ATTTTACTCG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
39 14 0.36
40 25 0.64
ACGTcount: A:0.24, C:0.16, G:0.27, T:0.34
Consensus pattern (40 bp):
ATATGGTGGGCACAACCTTATGTGTAATGCACTATGGTGC
Found at i:24710 original size:15 final size:15
Alignment explanation
Indices: 24690--24746 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
24680 CTTCATGGGG
*
24690 TAAGAAGACAATGTC
1 TAAGAAGAAAATGTC
24705 TAAGAAGAAAATGTC
1 TAAGAAGAAAATGTC
* *
24720 GAAGAAGAAAACGTC
1 TAAGAAGAAAATGTC
*
24735 AAAGAAGGAAAA
1 TAAGAA-GAAAA
24747 AGAAAGCATC
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
15 32 0.86
16 5 0.14
ACGTcount: A:0.56, C:0.09, G:0.23, T:0.12
Consensus pattern (15 bp):
TAAGAAGAAAATGTC
Found at i:28611 original size:26 final size:26
Alignment explanation
Indices: 28581--28672 Score: 75
Period size: 26 Copynumber: 3.6 Consensus size: 26
28571 TGTTGAAAAG
28581 GAAGAGGAGAAAGGAGAAGGGACACC
1 GAAGAGGAGAAAGGAGAAGGGACACC
* * * **
28607 GAAGATGGA-AAAAGAGAA-AGAAAAG
1 GAAGA-GGAGAAAGGAGAAGGGACACC
28632 GAAGAGG-GTAAAGGAGAAGGGACACC
1 GAAGAGGAG-AAAGGAGAAGGGACACC
*
28658 GCAA-AGGAAAAAGGA
1 G-AAGAGGAGAAAGGA
28673 AGAGGAGAAA
Statistics
Matches: 49, Mismatches: 11, Indels: 12
0.68 0.15 0.17
Matches are distributed among these distances:
24 2 0.04
25 16 0.33
26 26 0.53
27 5 0.10
ACGTcount: A:0.52, C:0.08, G:0.38, T:0.02
Consensus pattern (26 bp):
GAAGAGGAGAAAGGAGAAGGGACACC
Found at i:28633 original size:51 final size:50
Alignment explanation
Indices: 28575--28670 Score: 151
Period size: 51 Copynumber: 1.9 Consensus size: 50
28565 AGAACTTGTT
28575 GAAAAGGAAGAGGAG-AAAGGAGAAGGGACACCG-AAGATGGAAAAAGAGAAA
1 GAAAAGGAAGAGG-GTAAAGGAGAAGGGACACCGCAA-A-GGAAAAAGAGAAA
28626 GAAAAGGAAGAGGGTAAAGGAGAAGGGACACCGCAAAGGAAAAAG
1 GAAAAGGAAGAGGGTAAAGGAGAAGGGACACCGCAAAGGAAAAAG
28671 GAAGAGGAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
50 9 0.21
51 32 0.74
52 2 0.05
ACGTcount: A:0.53, C:0.07, G:0.38, T:0.02
Consensus pattern (50 bp):
GAAAAGGAAGAGGGTAAAGGAGAAGGGACACCGCAAAGGAAAAAGAGAAA
Found at i:31060 original size:2 final size:2
Alignment explanation
Indices: 31053--31082 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
31043 TTGTCATCTA
31053 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
31083 TATGAAATAC
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:31248 original size:85 final size:85
Alignment explanation
Indices: 31136--31349 Score: 263
Period size: 85 Copynumber: 2.5 Consensus size: 85
31126 AATGATATGT
* *
31136 GCTTCAATGACACGCAATGTAATTCATACATGCGTGTCATAAATTTAGGACACACAAATGTATGT
1 GCTTCAACGACACGCAATGTAAGTCATACATGCGTGTCATAAATTTAGGACACACAAATGTATGT
31201 CAAGCAT-ATTTATGACGGGG
66 C-AGCATAATTTATGACGGGG
* * * * *
31221 GCTTTAACGACGCGCAATGTAAGTCATACATGCGTGTCATAAATTTATGACGCACAAATGTGTGT
1 GCTTCAACGACACGCAATGTAAGTCATACATGCGTGTCATAAATTTAGGACACACAAATGTATGT
* * *
31286 CATCTTAATTTATGATGGGG
66 CAGCATAATTTATGACGGGG
* * *
31306 GCTTCAATGACACTCAATG-AATGTCATTA-ATGCGCGTCATAAAT
1 GCTTCAACGACACGCAATGTAA-GTCA-TACATGCGTGTCATAAAT
31350 ATGTGTCATA
Statistics
Matches: 111, Mismatches: 15, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
84 5 0.05
85 104 0.94
86 2 0.02
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (85 bp):
GCTTCAACGACACGCAATGTAAGTCATACATGCGTGTCATAAATTTAGGACACACAAATGTATGT
CAGCATAATTTATGACGGGG
Found at i:31344 original size:13 final size:13
Alignment explanation
Indices: 31328--31385 Score: 62
Period size: 13 Copynumber: 4.5 Consensus size: 13
31318 CTCAATGAAT
*
31328 GTCATTAATGCGC
1 GTCATAAATGCGC
** *
31341 GTCATAAATATGT
1 GTCATAAATGCGC
* *
31354 GTCATAAATGTGT
1 GTCATAAATGCGC
31367 GTCATAAATGCGC
1 GTCATAAATGCGC
31380 GTCATA
1 GTCATA
31386 GATTTATGAC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 38 1.00
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.33
Consensus pattern (13 bp):
GTCATAAATGCGC
Found at i:47502 original size:40 final size:39
Alignment explanation
Indices: 47444--47520 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 39
47434 ATCGATTAAG
* * *
47444 CACTTCAGTGCATGTGGTGGGCTCGACCTTGTGTGTAATA
1 CACTTCAGTGCATATGGTGGGC-CAACCTTATGTGTAATA
47484 CACTTC-GTTGCATATGGTGGGCCAACCTTATGTGTAA
1 CACTTCAG-TGCATATGGTGGGCCAACCTTATGTGTAA
47521 GCACTATGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
39 14 0.42
40 19 0.58
ACGTcount: A:0.19, C:0.21, G:0.27, T:0.32
Consensus pattern (39 bp):
CACTTCAGTGCATATGGTGGGCCAACCTTATGTGTAATA
Found at i:60276 original size:39 final size:40
Alignment explanation
Indices: 60199--60276 Score: 131
Period size: 40 Copynumber: 2.0 Consensus size: 40
60189 TAACACATTT
*
60199 GTGGGCACGACCTTATGTGTAATGCACTTCGGTGCATATG
1 GTGGGCACGACCTTATGTGTAATGCACTACGGTGCATATG
*
60239 GTGGGCACGACCTTATGTGTTA-GCACTACGGTGCATAT
1 GTGGGCACGACCTTATGTGTAATGCACTACGGTGCATAT
60277 ATTTGACTAG
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
39 15 0.42
40 21 0.58
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (40 bp):
GTGGGCACGACCTTATGTGTAATGCACTACGGTGCATATG
Found at i:65992 original size:18 final size:18
Alignment explanation
Indices: 65969--66004 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
65959 TATGCCTAAG
65969 TACGGAGGTGCGGTCCCT
1 TACGGAGGTGCGGTCCCT
*
65987 TACGGAGGTGTGGTCCCT
1 TACGGAGGTGCGGTCCCT
66005 GAAGAAGCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.25, G:0.39, T:0.25
Consensus pattern (18 bp):
TACGGAGGTGCGGTCCCT
Found at i:97344 original size:19 final size:20
Alignment explanation
Indices: 97320--97381 Score: 65
Period size: 19 Copynumber: 3.1 Consensus size: 20
97310 TGTCCCAACA
97320 AAAAAGAATGAG-GAAGAAG
1 AAAAAGAATGAGAGAAGAAG
* *
97339 AAAAAGAA-GAGAGGAGGAG
1 AAAAAGAATGAGAGAAGAAG
*
97358 AAAGAAGAATAGTGAGAAGAAG
1 AAA-AAGAAT-GAGAGAAGAAG
97380 AA
1 AA
97382 TGAGAAGGAG
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
18 3 0.09
19 16 0.47
20 5 0.15
22 10 0.29
ACGTcount: A:0.61, C:0.00, G:0.34, T:0.05
Consensus pattern (20 bp):
AAAAAGAATGAGAGAAGAAG
Found at i:97400 original size:37 final size:35
Alignment explanation
Indices: 97337--97405 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
97327 ATGAGGAAGA
97337 AGAAAAAGAAGAGAGGAGGAGAAAGAAGAATAGTG
1 AGAAAAAGAAGAGAGGAGGAGAAAGAAGAATAGTG
* *
97372 AGAAGAAGAATGAGAAGGAGGAGGAAGAAGAATA
1 AGAAAAAGAA-GAG-AGGAGGAGAAAGAAGAATA
97406 ACGAAAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
35 9 0.30
36 3 0.10
37 18 0.60
ACGTcount: A:0.57, C:0.00, G:0.38, T:0.06
Consensus pattern (35 bp):
AGAAAAAGAAGAGAGGAGGAGAAAGAAGAATAGTG
Found at i:100252 original size:42 final size:42
Alignment explanation
Indices: 100109--100351 Score: 233
Period size: 42 Copynumber: 5.8 Consensus size: 42
100099 GATAGATCGA
* * * *
100109 GATCTATAGCGGCGTTTTTGAAACAAACACCGCAAAAGGT-T
1 GATCTATAGCGACGTTTTTGGAACAAACGCCGCAAAAGGTCG
* * * *
100150 GCTCTATAGCGGCGTTTTTGGATA-AAATGCTGCAAAAGGTCG
1 GATCTATAGCGACGTTTTTGGA-ACAAACGCCGCAAAAGGTCG
* * *
100192 GAGCTAAAGC-AGCGTTTTTGGAACAAACGCCGCAAAAAGTCG
1 GATCTATAGCGA-CGTTTTTGGAACAAACGCCGCAAAAGGTCG
* * *
100234 GATCTATAACGACATTTTTGGAACAAACGCCGCAATAGGTCG
1 GATCTATAGCGACGTTTTTGGAACAAACGCCGCAAAAGGTCG
** **
100276 AGATCTATAGCGGTGTTTTTGGAGA-AAACGCCGCAAAAGGTAA
1 -GATCTATAGCGACGTTTTTGGA-ACAAACGCCGCAAAAGGTCG
* * *
100319 GATCTATAGTGTCGTTTTTGGAGCAAACGCCGC
1 GATCTATAGCGACGTTTTTGGAACAAACGCCGC
100352 TAATTAACGT
Statistics
Matches: 164, Mismatches: 30, Indels: 15
0.78 0.14 0.07
Matches are distributed among these distances:
41 34 0.21
42 95 0.58
43 34 0.21
44 1 0.01
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (42 bp):
GATCTATAGCGACGTTTTTGGAACAAACGCCGCAAAAGGTCG
Found at i:100323 original size:85 final size:84
Alignment explanation
Indices: 100100--100351 Score: 267
Period size: 85 Copynumber: 3.0 Consensus size: 84
100090 AAATGTCGCG
* * * * * *
100100 ATAGATCGAGATCTATAGCGGCGTTTTTGAAACAAACACCGCAAAAGGTTGCTCTATAGCGGCGT
1 ATAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTAGATCTATAGCGACGT
* *
100165 TTTTGGATA-AAATGCTGCA
66 TTTTGGA-ACAAACGCCGCA
* * * * * * * *
100184 AAAGGTCG-GAGCTAAAGCAGCGTTTTTGGAACAAACGCCGCAAAAAGTCGGATCTATAACGACA
1 ATAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGT-AGATCTATAGCGACG
100248 TTTTTGGAACAAACGCCGCA
65 TTTTTGGAACAAACGCCGCA
* * *
100268 ATAGGTCGAGATCTATAGCGGTGTTTTTGGAGA-AAACGCCGCAAAAGGTAAGATCTATAGTGTC
1 ATAGGTCGAGATCTATAGCGGCGTTTTTGGA-ACAAACGCCGCAAAAGGT-AGATCTATAGCGAC
*
100332 GTTTTTGGAGCAAACGCCGC
64 GTTTTTGGAACAAACGCCGC
100352 TAATTAACGT
Statistics
Matches: 136, Mismatches: 28, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
83 35 0.26
84 39 0.29
85 61 0.45
86 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.24
Consensus pattern (84 bp):
ATAGGTCGAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTAGATCTATAGCGACGT
TTTTGGAACAAACGCCGCA
Found at i:100335 original size:127 final size:125
Alignment explanation
Indices: 100109--100351 Score: 290
Period size: 127 Copynumber: 1.9 Consensus size: 125
100099 GATAGATCGA
* * * * * *
100109 GATCTATAGCGGCGTTTTTGAAACAAACACCGCAAAAGGTTGCTCTATAGCGGCGTTTTTGGATA
1 GATCTATAACGACATTTTTGAAACAAACACCGCAAAAGGTAGATCTATAGCGGCGTTTTTGGAGA
* * **
100174 AAATGCTGCAAAAGGTCGGAGCTAAAGCAGCGTTTTTGGAACAAACGCCGCAAAAAGTCG
66 AAACGCCGCAAAAGGTAAGAGCTAAAGCAGCGTTTTTGGAACAAACGCCGCAAAAAGTCG
* * * *
100234 GATCTATAACGACATTTTTGGAACAAACGCCGCAATAGGTCGAGATCTATAGCGGTGTTTTTGGA
1 GATCTATAACGACATTTTTGAAACAAACACCGCAAAAGGT--AGATCTATAGCGGCGTTTTTGGA
* * * *
100299 GAAAACGCCGCAAAAGGTAAGATCTATAG-TGTCGTTTTTGGAGCAAACGCCGC
64 GAAAACGCCGCAAAAGGTAAGAGCTAAAGCAG-CGTTTTTGGAACAAACGCCGC
100352 TAATTAACGT
Statistics
Matches: 97, Mismatches: 18, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
125 34 0.35
126 1 0.01
127 62 0.64
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.24
Consensus pattern (125 bp):
GATCTATAACGACATTTTTGAAACAAACACCGCAAAAGGTAGATCTATAGCGGCGTTTTTGGAGA
AAACGCCGCAAAAGGTAAGAGCTAAAGCAGCGTTTTTGGAACAAACGCCGCAAAAAGTCG
Found at i:104292 original size:40 final size:40
Alignment explanation
Indices: 104154--104326 Score: 144
Period size: 38 Copynumber: 4.4 Consensus size: 40
104144 GCACTAAAGT
*
104154 CGTTTGTATAAAAACGTCACTAAAGTACTAG----TAGCGG
1 CGTTTGTATAAAAACGCCACTAAAGTA-TAGTCTTTAGCGG
* * * * *
104191 TGTTTGTTTTGAAAACGCCACTAAAGTATGAATCTATAGCGG
1 CGTTTG-TATAAAAACGCCACTAAAGTAT-AGTCTTTAGCGG
* * * *
104233 TG-TT-T-TAAAAATGCAACTAAAGTATAGTCTTTAGCGA
1 CGTTTGTATAAAAACGCCACTAAAGTATAGTCTTTAGCGG
* *
104270 CGTTTGTATAAAAACGCCACTAAAGTACAGTCTTTAGTGG
1 CGTTTGTATAAAAACGCCACTAAAGTATAGTCTTTAGCGG
*
104310 CGTTTGTTCTAAAAACG
1 CGTTTG-TATAAAAACG
104327 ATGCTAAAAA
Statistics
Matches: 108, Mismatches: 18, Indels: 16
0.76 0.13 0.11
Matches are distributed among these distances:
37 16 0.15
38 38 0.35
39 2 0.02
40 33 0.31
41 11 0.10
42 8 0.07
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.32
Consensus pattern (40 bp):
CGTTTGTATAAAAACGCCACTAAAGTATAGTCTTTAGCGG
Found at i:107600 original size:90 final size:87
Alignment explanation
Indices: 107441--107613 Score: 292
Period size: 90 Copynumber: 2.0 Consensus size: 87
107431 CCTAACACAC
*
107441 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTATTATTTCAAATTAATTAAATCTATAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTATTATTTAAAATTAATTAAATCTATAT
*
107506 TTAATTAATTAGAATTTAATAAT
66 TTAATTAATT-GAAATTAATAAT
*
107529 CCTTTTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTAAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGG--TTTATTATTTAAAATTAATTAAATCTAT
107594 ATTTAATTAATTGAAATTAA
64 ATTTAATTAATTGAAATTAA
107614 ATATTCAGGA
Statistics
Matches: 80, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
88 34 0.43
89 7 0.09
90 39 0.49
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.45
Consensus pattern (87 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTATTATTTAAAATTAATTAAATCTATAT
TTAATTAATTGAAATTAATAAT
Found at i:113521 original size:2 final size:2
Alignment explanation
Indices: 113509--113564 Score: 103
Period size: 2 Copynumber: 27.5 Consensus size: 2
113499 AAAAACAAAC
113509 AT AT CAT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
113552 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
113565 CGTTGTTACA
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 51 0.96
3 2 0.04
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:114359 original size:90 final size:88
Alignment explanation
Indices: 114202--114374 Score: 301
Period size: 89 Copynumber: 1.9 Consensus size: 88
114192 CTAACACACA
114202 CTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATAT
1 CTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATAT
*
114267 TTAATTAATTAGAATTTAATAATC
66 TTAATTAATT-GAAATTAATAATC
* *
114291 CTTTTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAGTTAATTAAATCTATA
1 CTTTTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTATA
114356 TTTAATTAATTGAAATTAA
65 TTTAATTAATTGAAATTAA
114375 ATATTCAGGA
Statistics
Matches: 80, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
89 40 0.50
90 40 0.50
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.45
Consensus pattern (88 bp):
CTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATAT
TTAATTAATTGAAATTAATAATC
Found at i:119562 original size:24 final size:24
Alignment explanation
Indices: 119532--119578 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
119522 ATTAAAGTTT
* *
119532 TTTCTTTTTTCTTTTCAAGTTTTA
1 TTTCTTTTATATTTTCAAGTTTTA
119556 TTTCTTTTATATTTTCAAGTTTT
1 TTTCTTTTATATTTTCAAGTTTT
119579 GTTTTTATGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.15, C:0.11, G:0.04, T:0.70
Consensus pattern (24 bp):
TTTCTTTTATATTTTCAAGTTTTA
Found at i:124780 original size:22 final size:23
Alignment explanation
Indices: 124761--124804 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
124751 AAACAAAACA
124761 GCAGTTC-AAAAAAGAAAAAAAT
1 GCAGTTCGAAAAAAGAAAAAAAT
**
124783 GTTGTTCGAAAAAAGAAAAAAA
1 GCAGTTCGAAAAAAGAAAAAAA
124805 AAAGAAAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.61, C:0.07, G:0.16, T:0.16
Consensus pattern (23 bp):
GCAGTTCGAAAAAAGAAAAAAAT
Found at i:124781 original size:23 final size:23
Alignment explanation
Indices: 124750--124805 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
124740 GCTCCATCAG
124750 GAAACAAAACAGCAGTTC-AAAAAA
1 GAAA-AAAA-AGCAGTTCGAAAAAA
* **
124774 GAAAAAAATGTTGTTCGAAAAAA
1 GAAAAAAAAGCAGTTCGAAAAAA
124797 GAAAAAAAA
1 GAAAAAAAA
124806 AAGAAAGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 5 0.19
23 18 0.67
24 4 0.15
ACGTcount: A:0.64, C:0.09, G:0.14, T:0.12
Consensus pattern (23 bp):
GAAAAAAAAGCAGTTCGAAAAAA
Found at i:124829 original size:11 final size:11
Alignment explanation
Indices: 124791--124820 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
124781 ATGTTGTTCG
124791 AAAAAAGAAAA
1 AAAAAAGAAAA
*
124802 AAAAAAGAAAG
1 AAAAAAGAAAA
124813 AAAAAAGA
1 AAAAAAGA
124821 CATAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:125884 original size:25 final size:25
Alignment explanation
Indices: 125856--125903 Score: 80
Period size: 25 Copynumber: 1.9 Consensus size: 25
125846 ATTAAAGCTT
125856 TTTCTT-TTTACTTTTCAAGTTTTTA
1 TTTCTTCTTTA-TTTTCAAGTTTTTA
125881 TTTCTTCTTTATTTTCAAGTTTT
1 TTTCTTCTTTATTTTCAAGTTTT
125904 GTTTTTATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.15, C:0.12, G:0.04, T:0.69
Consensus pattern (25 bp):
TTTCTTCTTTATTTTCAAGTTTTTA
Found at i:127291 original size:21 final size:22
Alignment explanation
Indices: 127244--127362 Score: 91
Period size: 23 Copynumber: 5.3 Consensus size: 22
127234 CACCACAGCT
*
127244 CACATAATTTG-CACCGAAGTG-C
1 CACATAGTTTGTC-CCGAAG-GAC
127266 CACATA-TTTGTCCCGAAGGAC
1 CACATAGTTTGTCCCGAAGGAC
* * *
127287 TACATAGTTTTGTCTCGAAAGAC
1 CACATAG-TTTGTCCCGAAGGAC
*
127310 CACATAGGATTGTCCCGAAGGAC
1 CACATA-GTTTGTCCCGAAGGAC
* * * *
127333 AATATAGGTTTATCCCGAAAGAC
1 CACATA-GTTTGTCCCGAAGGAC
127356 CACATAG
1 CACATAG
127363 ACCATCGACT
Statistics
Matches: 78, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
20 1 0.01
21 16 0.21
22 8 0.10
23 52 0.67
24 1 0.01
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (22 bp):
CACATAGTTTGTCCCGAAGGAC
Found at i:127305 original size:23 final size:23
Alignment explanation
Indices: 127257--127362 Score: 101
Period size: 23 Copynumber: 4.7 Consensus size: 23
127247 ATAATTTGCA
127257 CCGAAGTG-CCACATA--TTTGTC
1 CCGAAG-GACCACATAGGTTTGTC
* *
127278 CCGAAGGACTACATAGTTTTGTC
1 CCGAAGGACCACATAGGTTTGTC
* * *
127301 TCGAAAGACCACATAGGATTGTC
1 CCGAAGGACCACATAGGTTTGTC
* * *
127324 CCGAAGGACAATATAGGTTTATC
1 CCGAAGGACCACATAGGTTTGTC
*
127347 CCGAAAGACCACATAG
1 CCGAAGGACCACATAG
127363 ACCATCGACT
Statistics
Matches: 67, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
20 1 0.01
21 12 0.18
23 54 0.81
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.24
Consensus pattern (23 bp):
CCGAAGGACCACATAGGTTTGTC
Found at i:127325 original size:46 final size:46
Alignment explanation
Indices: 127273--127362 Score: 135
Period size: 46 Copynumber: 2.0 Consensus size: 46
127263 TGCCACATAT
* * * *
127273 TTGTCCCGAAGGACTACATAGTTTTGTCTCGAAAGACCACATAGGA
1 TTGTCCCGAAGGACAACATAGGTTTATCCCGAAAGACCACATAGGA
*
127319 TTGTCCCGAAGGACAATATAGGTTTATCCCGAAAGACCACATAG
1 TTGTCCCGAAGGACAACATAGGTTTATCCCGAAAGACCACATAG
127363 ACCATCGACT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.24
Consensus pattern (46 bp):
TTGTCCCGAAGGACAACATAGGTTTATCCCGAAAGACCACATAGGA
Found at i:150371 original size:30 final size:30
Alignment explanation
Indices: 150337--150395 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
150327 TAGGTTGAGG
*
150337 TCCAGCAGAATCAGCTACAGTAGGGCATGA
1 TCCAGCAGAATCAGCTACAGCAGGGCATGA
* *
150367 TCCAGCAGGATCAGCTACAGCAGTGCATG
1 TCCAGCAGAATCAGCTACAGCAGGGCATG
150396 GTCCTCTACA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.25, G:0.27, T:0.17
Consensus pattern (30 bp):
TCCAGCAGAATCAGCTACAGCAGGGCATGA
Found at i:154800 original size:23 final size:23
Alignment explanation
Indices: 154745--154834 Score: 90
Period size: 23 Copynumber: 3.9 Consensus size: 23
154735 TGCCACATAT
* **
154745 TTGTCCCGAAGGACCACATAGTT
1 TTGTCCTGAAGGACCACATAGGA
* *
154768 TTCTCCTGAAGGAGCACATAGGA
1 TTGTCCTGAAGGACCACATAGGA
* * * *
154791 TTGTCTTGAATGACCACATAAGT
1 TTGTCCTGAAGGACCACATAGGA
*
154814 TTGTCCCGAAGGACCACATAG
1 TTGTCCTGAAGGACCACATAG
154835 AACCCTCGAC
Statistics
Matches: 52, Mismatches: 15, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (23 bp):
TTGTCCTGAAGGACCACATAGGA
Found at i:157909 original size:34 final size:33
Alignment explanation
Indices: 157862--157931 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 33
157852 ATATTACATT
157862 TTAATTTCATTTTGATTATTCACCGATTAAAAA
1 TTAATTTCATTTTGATTATTCACCGATTAAAAA
*
157895 TTAAGTTTCATTTTGATTATTCACTGATTAAAAA
1 TTAA-TTTCATTTTGATTATTCACCGATTAAAAA
157929 TTA
1 TTA
157932 GCATAACTAC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
33 4 0.11
34 31 0.89
ACGTcount: A:0.36, C:0.10, G:0.07, T:0.47
Consensus pattern (33 bp):
TTAATTTCATTTTGATTATTCACCGATTAAAAA
Found at i:160036 original size:94 final size:94
Alignment explanation
Indices: 159809--160029 Score: 327
Period size: 94 Copynumber: 2.4 Consensus size: 94
159799 CTTCGTGGAA
* * * *
159809 ACAGCATATGATTTCCAATTCTTATCACAATACATAAGTATATATTCAACTTTAGATCTGACCAA
1 ACAGCATATGATTACCAATTCTTATCACAATACATAAGTATATATTCAACCTCAGATCTGAACAA
*
159874 CTTGAAATCCAATGGATGAAAAGTGACAT
66 CTCGAAATCCAATGGATGAAAAGTGACAT
*
159903 ACAGCATATGATTACCAATTCTTATCACAATACATAAGTATATATTCAACCCTCAGATTTGAACA
1 ACAGCATATGATTACCAATTCTTATCACAATACATAAGTATATATTCAA-CCTCAGATCTGAACA
* * * *
159968 ACTCGAAGTTCAAT-GATGAAATGTGGCAT
65 ACTCGAAATCCAATGGATGAAAAGTGACAT
*
159997 ACAGCATATAATTACCAATTCTTATCACAATAC
1 ACAGCATATGATTACCAATTCTTATCACAATAC
160030 GCAAGTAAAT
Statistics
Matches: 115, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
94 93 0.81
95 22 0.19
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.30
Consensus pattern (94 bp):
ACAGCATATGATTACCAATTCTTATCACAATACATAAGTATATATTCAACCTCAGATCTGAACAA
CTCGAAATCCAATGGATGAAAAGTGACAT
Found at i:160056 original size:18 final size:18
Alignment explanation
Indices: 160033--160075 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
160023 ACAATACGCA
*
160033 AGTAAATGTTCATCTCTT
1 AGTAAATGTTCAACTCTT
160051 AGTAAATGTTCAACTCTT
1 AGTAAATGTTCAACTCTT
160069 AGTAAAT
1 AGTAAAT
160076 ATCTTTTAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.40
Consensus pattern (18 bp):
AGTAAATGTTCAACTCTT
Found at i:161826 original size:31 final size:31
Alignment explanation
Indices: 161752--161827 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 31
161742 TTTAAAAGTG
* *
161752 ACAAACTGGTCACAAACATTATCGATTTATA
1 ACAAAATGGTCACTAACATTATCGATTTATA
* * * **
161783 AGAAATTTGTCACTAACATTATTTATTTATA
1 ACAAAATGGTCACTAACATTATCGATTTATA
161814 ACAAAATGGTCACT
1 ACAAAATGGTCACT
161828 CTACCCTCAT
Statistics
Matches: 36, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.41, C:0.16, G:0.09, T:0.34
Consensus pattern (31 bp):
ACAAAATGGTCACTAACATTATCGATTTATA
Found at i:163577 original size:13 final size:13
Alignment explanation
Indices: 163559--163592 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 13
163549 TTCTTTGACT
163559 ATGGAATATTTTA
1 ATGGAATATTTTA
163572 ATGGAAGATATTTTA
1 ATGG-A-ATATTTTA
163587 ATGGAA
1 ATGGAA
163593 ATTGGTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 5 0.26
14 2 0.11
15 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.21, T:0.38
Consensus pattern (13 bp):
ATGGAATATTTTA
Found at i:163584 original size:15 final size:15
Alignment explanation
Indices: 163564--163592 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
163554 TGACTATGGA
163564 ATATTTTAATGGAAG
1 ATATTTTAATGGAAG
163579 ATATTTTAATGGAA
1 ATATTTTAATGGAA
163593 ATTGGTAATT
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:0.41, C:0.00, G:0.17, T:0.41
Consensus pattern (15 bp):
ATATTTTAATGGAAG
Found at i:166630 original size:2 final size:2
Alignment explanation
Indices: 166623--166665 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
166613 ATATTCGTAT
166623 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
166665 T
1 T
166666 TTAAATGATT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:169476 original size:21 final size:22
Alignment explanation
Indices: 169450--169490 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
169440 ACAGGACAGG
*
169450 GAGTATCGGTACT-CCTTTAAT
1 GAGTATCAGTACTACCTTTAAT
169471 GAGTATCAGTACTACCTTTA
1 GAGTATCAGTACTACCTTTA
169491 TAATTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.37
Consensus pattern (22 bp):
GAGTATCAGTACTACCTTTAAT
Found at i:170424 original size:23 final size:23
Alignment explanation
Indices: 170385--170429 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
170375 AAATTTGACA
*
170385 TAATTTTTTACTTTGACTAAATT
1 TAATTTGTTACTTTGACTAAATT
170408 TAATTTGTTA-TTGTGACTAAAT
1 TAATTTGTTACTT-TGACTAAAT
170430 CATTTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.31, C:0.07, G:0.09, T:0.53
Consensus pattern (23 bp):
TAATTTGTTACTTTGACTAAATT
Found at i:175205 original size:54 final size:55
Alignment explanation
Indices: 175138--175391 Score: 291
Period size: 55 Copynumber: 4.6 Consensus size: 55
175128 CTAAGCGTGC
* * * *
175138 AAAAACTTAAGAAATCCATACTAAGTGTATGAATTTCGGTAT-GAAACTTTATGTG
1 AAAAAC-TAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGACACTTTGTGTG
* *
175193 AAAAACTAAGAAATTCATACTATGTGTATGAATTTTCGTATAGG-CACTATT-TGTG
1 AAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTAT-GGACACT-TTGTGTG
* * * * *
175248 CAAAACTAAGAAATTCGTACTAGGTGTATGAATTTCCGTATGGGCACTTTGGGTG
1 AAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGACACTTTGTGTG
* * *
175303 CAAAACTAAGAAATTCATACTAAGTGTATGGATTTCCGTATGGACACTATGTGTG
1 AAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGACACTTTGTGTG
* * * *
175358 -CAAACAAAGAAATCCATACTAAGTGTATTAATTT
1 AAAAACTAAGAAATTCATACTAAGTGTATGAATTT
175392 ATGTTTAGGA
Statistics
Matches: 173, Mismatches: 21, Indels: 11
0.84 0.10 0.05
Matches are distributed among these distances:
54 64 0.37
55 106 0.61
56 3 0.02
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (55 bp):
AAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGACACTTTGTGTG
Found at i:175323 original size:110 final size:109
Alignment explanation
Indices: 175134--175391 Score: 331
Period size: 110 Copynumber: 2.3 Consensus size: 109
175124 GGCACTAAGC
* *
175134 GTGCAAAAACTTAAGAAATCCATACTAAGTGTATGAATTTCGGTATGAAACTTTATGTGAAAAAC
1 GTGC-AAAAC-TAAGAAATCCATACTAAGTGTATGAATTTCCGTATGAAACTTTAGGTGAAAAAC
* * *
175199 TAAGAAATTCATACTATGTGTATGAATTTTCGTATAGG-CACTATTT
64 TAAGAAATTCATACTAAGTGTATGAATTTCCGTAT-GGACACTATGT
* * * ** * *
175245 GTGCAAAACTAAGAAATTCGTACTAGGTGTATGAATTTCCGTATGGGCACTTTGGGTGCAAAACT
1 GTGCAAAACTAAGAAATCCATACTAAGTGTATGAATTTCCGTAT-GAAACTTTAGGTGAAAAACT
*
175310 AAGAAATTCATACTAAGTGTATGGATTTCCGTATGGACACTATGT
65 AAGAAATTCATACTAAGTGTATGAATTTCCGTATGGACACTATGT
* *
175355 GTGC-AAACAAAGAAATCCATACTAAGTGTATTAATTT
1 GTGCAAAACTAAGAAATCCATACTAAGTGTATGAATTT
175392 ATGTTTAGGA
Statistics
Matches: 127, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
109 61 0.48
110 62 0.49
111 4 0.03
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (109 bp):
GTGCAAAACTAAGAAATCCATACTAAGTGTATGAATTTCCGTATGAAACTTTAGGTGAAAAACTA
AGAAATTCATACTAAGTGTATGAATTTCCGTATGGACACTATGT
Found at i:175901 original size:68 final size:68
Alignment explanation
Indices: 175517--175883 Score: 536
Period size: 68 Copynumber: 5.4 Consensus size: 68
175507 TGGGCATTAT
* * ** *
175517 AGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAGTGCATTTGATACGTAACTGTGCATTTGACA
1 AGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTGTGCATTTGACA
175582 GAA
66 GAA
* *
175585 AGGTGTCAATTATGCCAGTTAGATGAAAAGCTAAGTGCCTTTGTGGCCTAACTGTGCATTTGACA
1 AGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTGTGCATTTGACA
*
175650 TAA
66 GAA
* * * * *
175653 ATGTATCAATTATGCCAGTTAGATGAAAGGCTAAGTACCTTTGAGTCCTAACTGTGTATTTGACA
1 AGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTGTGCATTTGACA
175718 GAA
66 GAA
*
175721 AGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAAGCCTAACTGTGCATTTGACA
1 AGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTGTGCATTTGACA
175786 GAA
66 GAA
* * * * *
175789 AAGTGTCAATTATACTAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTATGAATTTGACA
1 AGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTGTGCATTTGACA
175854 GAA
66 GAA
* * *
175857 AGGTGTCAGTTATTCTAGTTAGATGAA
1 AGGTGTCAATTATGCCAGTTAGATGAA
175884 CGATTAAAGA
Statistics
Matches: 268, Mismatches: 31, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
68 268 1.00
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.31
Consensus pattern (68 bp):
AGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTGTGCATTTGACA
GAA
Found at i:175982 original size:81 final size:81
Alignment explanation
Indices: 175846--176450 Score: 863
Period size: 81 Copynumber: 7.5 Consensus size: 81
175836 CTAACTATGA
* * * * *
175846 ATTTGACAGAAAGGTGTCAGTTATTCTAGTTAGATGAACGATTAAAGACCATTGAGTAAAAGATA
1 ATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGATTAAAGACCGTTGAGTAAAAGATA
* *
175911 AATAGCTTAGCTGTGC
66 AATGGCCTAGCTGTGC
* *
175927 ATTTGGCA-AAATGTTGTCAATTATGCCAGTTAGATGAACAATTAAAGACCGTTGAGTAAAAGAT
1 ATTTGGCAGAAA-GGTGTCAATTATGCCAGTTAGATGAACGATTAAAGACCGTTGAGTAAAAGAT
* *
175991 AAATGGCCTAGTTGTTC
65 AAATGGCCTAGCTGTGC
* *
176008 ATTTGGCAGAAATGTGTCAATTATGCCAGTTAGATGAACGATTAAAGACCATTGAGTAAAAGATA
1 ATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGATTAAAGACCGTTGAGTAAAAGATA
* *
176073 AATGGCCTAGTTATGC
66 AATGGCCTAGCTGTGC
* *
176089 ATTTCGTAGAAAGGTGTCAATTATGCCAGTTAGATGAACGATTAAAGACCGTTGAGTAAAAGATA
1 ATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGATTAAAGACCGTTGAGTAAAAGATA
***
176154 AATGATATAGCTGTGC
66 AATGGCCTAGCTGTGC
176170 ATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGATTAAAGACCGTTGAGTAAAAGATA
1 ATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGATTAAAGACCGTTGAGTAAAAGATA
** *
176235 AATGGATTAGCTGTGT
66 AATGGCCTAGCTGTGC
176251 ATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGATTAAAGACCGTTGAGTAAAAGATA
1 ATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGATTAAAGACCGTTGAGTAAAAGATA
*
176316 AATGGCCTAGCTATGC
66 AATGGCCTAGCTGTGC
* * * * * *
176332 ATTTGACAGAAAGGTGTCAATTATGACAGTTAGATGAACGGTTAAATATCATTGAGTAAAAGATA
1 ATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGATTAAAGACCGTTGAGTAAAAGATA
*
176397 AATGACCTAGCTGTGC
66 AATGGCCTAGCTGTGC
* * * *
176413 ATTTGGTAGACAA-GTGTCAATCATGCAAGGTAGATGAA
1 ATTTGGCAGA-AAGGTGTCAATTATGCCAGTTAGATGAA
176451 AGGTTAAATG
Statistics
Matches: 471, Mismatches: 50, Indels: 6
0.89 0.09 0.01
Matches are distributed among these distances:
80 3 0.01
81 463 0.98
82 5 0.01
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (81 bp):
ATTTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGATTAAAGACCGTTGAGTAAAAGATA
AATGGCCTAGCTGTGC
Found at i:193674 original size:26 final size:26
Alignment explanation
Indices: 193645--193701 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
193635 GATTAAAGTG
193645 AAAGGTATCCACCAACAGTTGTTTGC
1 AAAGGTATCCACCAACAGTTGTTTGC
193671 AAAGGTATCCACCAACAGTTGTTTGC
1 AAAGGTATCCACCAACAGTTGTTTGC
193697 AAAGG
1 AAAGG
193702 AAAAGGGGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (26 bp):
AAAGGTATCCACCAACAGTTGTTTGC
Found at i:194150 original size:49 final size:49
Alignment explanation
Indices: 194044--194496 Score: 266
Period size: 49 Copynumber: 9.4 Consensus size: 49
194034 TTCAACACCA
* * *
194044 GATCTAACCTACCCTGAAGAGCAGA-AGAGCATATCTCTTT-TTCTTTCTT
1 GATCTGACCTACCCTAAAGAGCAGAGAGAGCATATCTCTTTCTT-TTTC-C
* *
194093 GATCTGACCTACCCTGAAGAGTAGTAGAGTAG-ATATC-CTTTCTTTTTCC
1 GATCTGACCTACCCTAAAGAGCAG-AGAG-AGCATATCTCTTTCTTTTTCC
* * * * *
194142 GATATGACCTACCCTAGAGAGAAGCG-GAGCATATCTCTTTCCTTTTCC
1 GATCTGACCTACCCTAAAGAGCAGAGAGAGCATATCTCTTTCTTTTTCC
* * *
194190 TGATCTGACCTACCCTAAAGAGCAGCG-GAGAATATCTCTTTTCTTTTCCC
1 -GATCTGACCTACCCTAAAGAGCAGAGAGAGCATATCTC-TTTCTTTTTCC
* *
194240 GATCTGACCTACCCTAAAGAGCA-ACAAAGCATATCTCCTTTC-TTTTCTC
1 GATCTGACCTACCCTAAAGAGCAGAGAGAGCATATCT-CTTTCTTTTTC-C
* * * * *
194289 GATCTG-CACTACCTTGAAGAGC--AG-CA-TATATCTCTTT-TTTTCCC
1 GATCTGAC-CTACCCTAAAGAGCAGAGAGAGCATATCTCTTTCTTTTTCC
* * * * * *
194333 GATCTAACCCACCCTAAAGAGCAG-CA-TGCAGATCTTATTTC-TTTTCC
1 GATCTGACCTACCCTAAAGAGCAGAGAGAGCATATC-TCTTTCTTTTTCC
* * * * *
194380 TGATCTAACCTACCCT-AAGAGTAGCG-GAGCAGATATCATTTC-TTTTCC
1 -GATCTGACCTACCCTAAAGAGCAGAGAGAGCATATCTC-TTTCTTTTTCC
** * * * * *
194428 TGATCCAACCTACTCTAAATAGCAGCG-GAGTATATCTCATTTATTTTTCC
1 -GATCTGACCTACCCTAAAGAGCAGAGAGAGCATATCTC-TTTCTTTTTCC
* *
194478 TATCT-ACCTACCTTAAAGA
1 GATCTGACCTACCCTAAAGA
194497 ACAACGAAGC
Statistics
Matches: 323, Mismatches: 55, Indels: 53
0.75 0.13 0.12
Matches are distributed among these distances:
44 17 0.05
45 9 0.03
46 12 0.04
47 24 0.07
48 73 0.23
49 152 0.47
50 25 0.08
51 9 0.03
52 2 0.01
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.33
Consensus pattern (49 bp):
GATCTGACCTACCCTAAAGAGCAGAGAGAGCATATCTCTTTCTTTTTCC
Found at i:194194 original size:98 final size:96
Alignment explanation
Indices: 194044--194489 Score: 346
Period size: 98 Copynumber: 4.6 Consensus size: 96
194034 TTCAACACCA
* * * * * *
194044 GATCTAACCTACCCTGAAGAGCAGAAGAGCATATCTCTTTTTCTTTCTTGATCTGACCTACCCTG
1 GATCTGACCTACCCTAAAGAGAAG-CGAGCATATCTCTTTCT-TTTCCTGATCTGACCTACCCTG
* ** *
194109 AAGAGTAGTAGAGTAGATATC-CTTTCTTTTTCC
64 AAGAGCAGCGGAGTA-ATATCTCTTTCTTTTCCC
* * *
194142 GATATGACCTACCCTAGAGAGAAGCGGAGCATATCTCTTTCCTTTTCCTGATCTGACCTACCCTA
1 GATCTGACCTACCCTAAAGAGAAGC-GAGCATATCTCTTT-CTTTTCCTGATCTGACCTACCCTG
194207 AAGAGCAGCGGAG-AATATCTCTTTTCTTTTCCC
64 AAGAGCAGCGGAGTAATATCTC-TTTCTTTTCCC
*
194240 GATCTGACCTACCCTAAAGAGCAA-CAAAGCATATCTCCTTTCTTTT-CTCGATCTG-CACTACC
1 GATCTGACCTACCCTAAAGAG-AAGC-GAGCATATCT-CTTTCTTTTCCT-GATCTGAC-CTACC
*
194302 TTGAAGAGCAGC--A-T-ATATCTCTTT-TTTTCCC
61 CTGAAGAGCAGCGGAGTAATATCTCTTTCTTTTCCC
* * * * * *
194333 GATCTAACCCACCCTAAAGAGCAGC-ATGCAGATCTTATTTCTTTTCCTGATCTAACCTACCCT-
1 GATCTGACCTACCCTAAAGAGAAGCGA-GCATATC-TCTTTCTTTTCCTGATCTGACCTACCCTG
* * * *
194396 AAGAGTAGCGGAGCAGATATC-ATTTCTTTTCCT
64 AAGAGCAGCGGAGTA-ATATCTCTTTCTTTTCCC
** * * * * *
194429 GATCCAACCTACTCTAAATAGCAGCGGAGTATATCTCATTTATTTTTCCT-ATCT-ACCTACC
1 GATCTGACCTACCCTAAAGAGAAGC-GAGCATATCTC-TTT-CTTTTCCTGATCTGACCTACC
194490 TTAAAGAACA
Statistics
Matches: 286, Mismatches: 38, Indels: 50
0.76 0.10 0.13
Matches are distributed among these distances:
91 9 0.03
92 26 0.09
93 32 0.11
94 3 0.01
95 10 0.03
96 46 0.16
97 17 0.06
98 136 0.48
99 7 0.02
ACGTcount: A:0.26, C:0.27, G:0.14, T:0.33
Consensus pattern (96 bp):
GATCTGACCTACCCTAAAGAGAAGCGAGCATATCTCTTTCTTTTCCTGATCTGACCTACCCTGAA
GAGCAGCGGAGTAATATCTCTTTCTTTTCCC
Found at i:199150 original size:47 final size:44
Alignment explanation
Indices: 199054--199165 Score: 154
Period size: 47 Copynumber: 2.5 Consensus size: 44
199044 GTAAGTATGC
*
199054 AAATAAGCTTACGAGCTTAT-GAATAATGGTAAGTATATTGGTA
1 AAATAAGCTTAAGAGCTTATGGAATAATGGTAAGTATATTGGTA
* * *
199097 AAATAAGCTTATGAGCTTATGGAATTTAAATGTTAAGTATTTTGGTA
1 AAATAAGCTTAAGAGCTTATGGAA--T-AATGGTAAGTATATTGGTA
199144 AAATAAGCTTAAGAGCTTATGG
1 AAATAAGCTTAAGAGCTTATGG
199166 GAAAAAAAGG
Statistics
Matches: 61, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
43 19 0.31
44 3 0.05
46 1 0.02
47 38 0.62
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.35
Consensus pattern (44 bp):
AAATAAGCTTAAGAGCTTATGGAATAATGGTAAGTATATTGGTA
Found at i:199658 original size:20 final size:20
Alignment explanation
Indices: 199633--199682 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
199623 CCGATTCCCC
199633 CACTGTTCATGGGTACTATT
1 CACTGTTCATGGGTACTATT
*
199653 CACTGTTCATGGGTACTGTT
1 CACTGTTCATGGGTACTATT
*
199673 CACTATTCAT
1 CACTGTTCAT
199683 AAAAAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.20, C:0.22, G:0.18, T:0.40
Consensus pattern (20 bp):
CACTGTTCATGGGTACTATT
Found at i:204710 original size:29 final size:29
Alignment explanation
Indices: 204645--204707 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
204635 ACAAGCCTCA
* *
204645 GAAAAATT-GGGATCATTTCGTAAGTTTG
1 GAAAAATTGGGGATAAATTCGTAAGTTTG
*
204673 GAAAAATTGGGGATAAATTCGTAAATTTTG
1 GAAAAATTGGGGATAAATTCGT-AAGTTTG
204703 GAAAA
1 GAAAA
204708 TTGATGAAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 8 0.27
29 11 0.37
30 11 0.37
ACGTcount: A:0.40, C:0.05, G:0.24, T:0.32
Consensus pattern (29 bp):
GAAAAATTGGGGATAAATTCGTAAGTTTG
Found at i:206223 original size:47 final size:44
Alignment explanation
Indices: 206124--206237 Score: 158
Period size: 47 Copynumber: 2.5 Consensus size: 44
206114 GTAAGTATGC
206124 AAATAAGCTTACGAGCTTAT-GAATAATGGCAAGTATATTGATA
1 AAATAAGCTTACGAGCTTATGGAATAATGGCAAGTATATTGATA
** * *
206167 AAATAAGCTTACGAGCTTATGGAATTTAAATGTTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTATGGAA--T-AATGGCAAGTATATTGATA
206214 AAATAAGCTTACGAGCTTATGGAA
1 AAATAAGCTTACGAGCTTATGGAA
206238 AAAAAAGGTA
Statistics
Matches: 63, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
43 20 0.32
44 3 0.05
46 1 0.02
47 39 0.62
ACGTcount: A:0.39, C:0.09, G:0.19, T:0.32
Consensus pattern (44 bp):
AAATAAGCTTACGAGCTTATGGAATAATGGCAAGTATATTGATA
Found at i:207916 original size:29 final size:29
Alignment explanation
Indices: 207872--207940 Score: 120
Period size: 29 Copynumber: 2.4 Consensus size: 29
207862 ACGTCTCGAC
* *
207872 TATAATGCATCGTCTTGTACCATAAAACA
1 TATAATGCATCATCTTGTACCATAAAAAA
207901 TATAATGCATCATCTTGTACCATAAAAAA
1 TATAATGCATCATCTTGTACCATAAAAAA
207930 TATAATGCATC
1 TATAATGCATC
207941 GTCAATAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.32
Consensus pattern (29 bp):
TATAATGCATCATCTTGTACCATAAAAAA
Found at i:216695 original size:17 final size:17
Alignment explanation
Indices: 216685--216737 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
216675 TTAATAAAGT
216685 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
* *
216702 TAGTTCATTCATCAAAC
1 TAGTTCATTAATTAAAC
* *
216719 TAGATCATTTATTAAAC
1 TAGTTCATTAATTAAAC
216736 TA
1 TA
216738 AATCTTAATT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.40, C:0.15, G:0.06, T:0.40
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:224321 original size:21 final size:22
Alignment explanation
Indices: 224274--224324 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
224264 AGGTTTGATC
224274 TTGATTTGGTTCAATTTTTTGA
1 TTGATTTGGTTCAATTTTTTGA
* *
224296 ATGATTTGTTTTC-ATTTTTT-A
1 TTGATTTG-GTTCAATTTTTTGA
224317 TTGATTTG
1 TTGATTTG
224325 ATCAGGTGAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 8 0.32
22 14 0.56
23 3 0.12
ACGTcount: A:0.18, C:0.04, G:0.16, T:0.63
Consensus pattern (22 bp):
TTGATTTGGTTCAATTTTTTGA
Found at i:224797 original size:3 final size:3
Alignment explanation
Indices: 224783--224824 Score: 50
Period size: 3 Copynumber: 14.3 Consensus size: 3
224773 CATGGACCTG
* * *
224783 AAT AAT AA- AAT AAT AAT AAT ATT AAT AAT GAT AAT AAA AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
224825 TAAATGTATA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:224943 original size:22 final size:22
Alignment explanation
Indices: 224909--224966 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 22
224899 TATATGTGAT
224909 ATATATTATATATAA-TATTATA
1 ATATATTATATATAATTA-TATA
224931 ATAT-TTATAATATAATTATATA
1 ATATATTAT-ATATAATTATATA
*
224953 ATATACTAGTATAT
1 ATATATTA-TATAT
224967 GTATATTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
21 4 0.13
22 18 0.58
23 8 0.26
24 1 0.03
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
ATATATTATATATAATTATATA
Found at i:225013 original size:12 final size:12
Alignment explanation
Indices: 224996--225029 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
224986 ATATTTTTCA
224996 AATATAATATAT
1 AATATAATATAT
*
225008 AATATACTATAT
1 AATATAATATAT
225020 AATAT-ATATA
1 AATATAATATA
225030 CTTAGAAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (12 bp):
AATATAATATAT
Found at i:225422 original size:43 final size:43
Alignment explanation
Indices: 225369--225457 Score: 128
Period size: 43 Copynumber: 2.1 Consensus size: 43
225359 ACGGATCAAA
*
225369 CTTCAAATGACTCCCC-TCCT-CAGGTTAAGCTAGGTGAAATGTT
1 CTTCAAATGACTCCCCAT--TGCAAGTTAAGCTAGGTGAAATGTT
*
225412 CTTCAGATGACTCCCCATTGCAAGTTAAGCTAGGTGAAATGTT
1 CTTCAAATGACTCCCCATTGCAAGTTAAGCTAGGTGAAATGTT
225455 CTT
1 CTT
225458 TGGATGACCC
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
42 1 0.02
43 40 0.95
44 1 0.02
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (43 bp):
CTTCAAATGACTCCCCATTGCAAGTTAAGCTAGGTGAAATGTT
Found at i:227520 original size:82 final size:83
Alignment explanation
Indices: 227383--227538 Score: 235
Period size: 82 Copynumber: 1.9 Consensus size: 83
227373 GCAATAATGA
227383 CACCTTACTGCCAAAAATGCACAGCTAGGCATTTAGTCTTTATTCCCAAAAGCATTTAACCTTTA
1 CACCTTACTGCC-AAAATGCACAGCTAGGCATTTAGTCTTTATTCCCAAAAGCATTTAACCTTTA
227448 ATCTAACTGTCATTATTGG
65 ATCTAACTGTCATTATTGG
* * * * *
227467 CACCTTTCTGCC-AAATGCACGGCTAGGCATTTAGTCTTT-TATCCTAAAGGCATTTAACCTTTC
1 CACCTTACTGCCAAAATGCACAGCTAGGCATTTAGTCTTTAT-TCCCAAAAGCATTTAACCTTTA
227530 ATCTAACTG
65 ATCTAACTG
227539 GCACATTTCT
Statistics
Matches: 66, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
81 1 0.02
82 54 0.82
84 11 0.17
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.34
Consensus pattern (83 bp):
CACCTTACTGCCAAAATGCACAGCTAGGCATTTAGTCTTTATTCCCAAAAGCATTTAACCTTTAA
TCTAACTGTCATTATTGG
Found at i:227803 original size:54 final size:54
Alignment explanation
Indices: 227656--228358 Score: 832
Period size: 54 Copynumber: 13.1 Consensus size: 54
227646 ACTCTATAGT
* * ** * * * *
227656 CACATAGTGCCAATATGGTAATTCA-CAACTTATTATGAATTCTGTAGGTTGCA
1 CACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTATGTGGGTTGCA
* ** *
227709 CACTTAGTGCCTATACGGT-GTTCATCAACATATGATGAATTCCGTAGGTTGCA
1 CACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTATGTGGGTTGCA
*** *** ***
227762 TGTATAGTGCCTATACCAACGTTCATCAACATATGATGAATTCCATGGGTTGCA
1 CACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTATGTGGGTTGCA
*** * * *
227816 CAC-TCAGTGCCTATGTTGTGGTTCATCAACATATGATGAATT-CGTGGGTTGAA
1 CACAT-AGTGCCTATACGGTCGTTCATCAACATATGATGAATTATGTGGGTTGCA
* * * **
227869 CACTTAGTGCCTATAC-GTCATTCATTAACATATGATGAATTATGTGGGTTAAA
1 CACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTATGTGGGTTGCA
* * * * *
227922 CACTTAGTGCCTATACAGTCGTTC-TCAACACATGATGAATTTTATGGGTTGCA
1 CACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTATGTGGGTTGCA
* *
227975 CACATAGAGCCTATACGGTTGTTCATCAACATATGATGAATTATGTGGGTTG--
1 CACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTATGTGGGTTGCA
* *
228027 CACATAGTGCCTATATGGTCGTTCATCAACATATGATGAAGTT-CGTGGGTTGCA
1 CACATAGTGCCTATACGGTCGTTCATCAACATATGATGAA-TTATGTGGGTTGCA
* * *
228081 CACATAGTGCCTATAGGGTCGTTCATCAATATATGATGAATT-TCATGGGTTGCA
1 CACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTAT-GTGGGTTGCA
*
228135 CACATAGTGCCTATACGGTCATTCATCAACATATGATGAATTATGTGGGTTGCA
1 CACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTATGTGGGTTGCA
*
228189 CACATAGTGCCTATACGGTCGTTCATCAAAATATGATGAATTATGTGGGTTGCA
1 CACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTATGTGGGTTGCA
*
228243 CACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTATGTGTGTTGCA
1 CACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTATGTGGGTTGCA
** ***
228297 CACATAGTGCCTATACGACCGTTCATCAACATATGATGAATTCCATGGGTTGCA
1 CACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTATGTGGGTTGCA
*
228351 CACTTAGT
1 CACATAGT
228359 ATTGATGTAA
Statistics
Matches: 567, Mismatches: 71, Indels: 23
0.86 0.11 0.03
Matches are distributed among these distances:
52 71 0.13
53 147 0.26
54 348 0.61
55 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.33
Consensus pattern (54 bp):
CACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTATGTGGGTTGCA
Found at i:228269 original size:162 final size:162
Alignment explanation
Indices: 227656--228358 Score: 879
Period size: 160 Copynumber: 4.4 Consensus size: 162
227646 ACTCTATAGT
* * ** * * * *
227656 CACATAGTGCCAATATGGTAATTCA-CAACTTATTATGAATTCTGTAGGTTGCACACTTAGTGCC
1 CACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTATGTGGGTTGCACACTTAGTGCC
* * *** ***
227720 TATACGGT-GTTCATCAACATATGATGAATTCCGTAGGTTGCATGTATAGTGCCTATACCAACGT
66 TATACGGTCGTTCATCAACATATGATGAATTACGTGGGTTGCACACATAGTGCCTATACGGTCGT
*
227784 TCATCAACATATGATGAATTCCATGGGTTGCA
131 TCATCAACATATGATGAATTTCATGGGTTGCA
*** * * *
227816 CAC-TCAGTGCCTATGTTGTGGTTCATCAACATATGATGAATT-CGTGGGTTGAACACTTAGTGC
1 CACAT-AGTGCCTATACGGTCGTTCATCAACATATGATGAATTATGTGGGTTGCACACTTAGTGC
* * * ** * *
227879 CTATAC-GTCATTCATTAACATATGATGAATTATGTGGGTTAAACACTTAGTGCCTATACAGTCG
65 CTATACGGTCGTTCATCAACATATGATGAATTACGTGGGTTGCACACATAGTGCCTATACGGTCG
* *
227943 TTC-TCAACACATGATGAATTTTATGGGTTGCA
130 TTCATCAACATATGATGAATTTCATGGGTTGCA
* *
227975 CACATAGAGCCTATACGGTTGTTCATCAACATATGATGAATTATGTGGGTTGCACA--TAGTGCC
1 CACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTATGTGGGTTGCACACTTAGTGCC
* *
228038 TATATGGTCGTTCATCAACATATGATGAAGTT-CGTGGGTTGCACACATAGTGCCTATAGGGTCG
66 TATACGGTCGTTCATCAACATATGATGAA-TTACGTGGGTTGCACACATAGTGCCTATACGGTCG
*
228102 TTCATCAATATATGATGAATTTCATGGGTTGCA
130 TTCATCAACATATGATGAATTTCATGGGTTGCA
* *
228135 CACATAGTGCCTATACGGTCATTCATCAACATATGATGAATTATGTGGGTTGCACACATAGTGCC
1 CACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTATGTGGGTTGCACACTTAGTGCC
* *
228200 TATACGGTCGTTCATCAAAATATGATGAATTATGTGGGTTGCACACATAGTGCCTATACGGTCGT
66 TATACGGTCGTTCATCAACATATGATGAATTACGTGGGTTGCACACATAGTGCCTATACGGTCGT
228265 TCATCAACATATGATGAA-TT-ATGTGTGTTGCA
131 TCATCAACATATGATGAATTTCATG-G-GTTGCA
** ***
228297 CACATAGTGCCTATACGACCGTTCATCAACATATGATGAATTCCATGGGTTGCACACTTAGT
1 CACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTATGTGGGTTGCACACTTAGT
228359 ATTGATGTAA
Statistics
Matches: 469, Mismatches: 61, Indels: 24
0.85 0.11 0.04
Matches are distributed among these distances:
158 11 0.02
159 114 0.24
160 182 0.39
161 19 0.04
162 143 0.30
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.33
Consensus pattern (162 bp):
CACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTATGTGGGTTGCACACTTAGTGCC
TATACGGTCGTTCATCAACATATGATGAATTACGTGGGTTGCACACATAGTGCCTATACGGTCGT
TCATCAACATATGATGAATTTCATGGGTTGCA
Found at i:228301 original size:27 final size:27
Alignment explanation
Indices: 228163--228302 Score: 71
Period size: 27 Copynumber: 5.2 Consensus size: 27
228153 TCATTCATCA
*
228163 ACATATGATGAATTATGTGGGTTGCAC
1 ACATATGATGAATTATGTGTGTTGCAC
** *
228190 ACATA-G-TGCCTATACG-GTCGTT-CATC
1 ACATATGATGAAT-TATGTGT-GTTGCA-C
* *
228216 AAAATATGATGAATTATGTGGGTTGCAC
1 -ACATATGATGAATTATGTGTGTTGCAC
** *
228244 ACATA-G-TGCCTATACG-GTCGTT-CATC
1 ACATATGATGAAT-TATGTGT-GTTGCA-C
228270 AACATATGATGAATTATGTGTGTTGCAC
1 -ACATATGATGAATTATGTGTGTTGCAC
228298 ACATA
1 ACATA
228303 GTGCCTATAC
Statistics
Matches: 80, Mismatches: 17, Indels: 32
0.62 0.13 0.25
Matches are distributed among these distances:
25 12 0.15
26 16 0.20
27 23 0.29
28 16 0.20
29 13 0.16
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.32
Consensus pattern (27 bp):
ACATATGATGAATTATGTGTGTTGCAC
Found at i:231662 original size:48 final size:48
Alignment explanation
Indices: 231601--231692 Score: 139
Period size: 48 Copynumber: 1.9 Consensus size: 48
231591 CACTGATCCT
* **
231601 CATCTAACCTGCATTAGTGGTACCTTTCTACCAAAAATGCACAGTAGA
1 CATCTAACCTGCATTAATGACACCTTTCTACCAAAAATGCACAGTAGA
* *
231649 CATCTAACTTGCATTAATGACACCTTTCTGCCAAAAATGCACAG
1 CATCTAACCTGCATTAATGACACCTTTCTACCAAAAATGCACAG
231693 CTAGGCATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 39 1.00
ACGTcount: A:0.34, C:0.26, G:0.13, T:0.27
Consensus pattern (48 bp):
CATCTAACCTGCATTAATGACACCTTTCTACCAAAAATGCACAGTAGA
Found at i:231791 original size:82 final size:83
Alignment explanation
Indices: 231649--231878 Score: 311
Period size: 82 Copynumber: 2.8 Consensus size: 83
231639 GCACAGTAGA
* * * *
231649 CATCTAACTTGCATTAATGACACCTTTCTGCCAAAAATGCACAGCTAGGCATTTATTCTTTATTT
1 CATCTAACTGGCATTATTGGCACCTTTCTGCC--AAATGCACAGCTAGGCATTTAGTCTTTATTT
231714 CC-AAAGGCATTTAACCTTT
64 CCTAAAGGCATTTAACCTTT
* * * * *
231733 CATCTAAGTGGTATTATTTGCACCTTTCTGCCAAATGCACAGCTAGGGATTTAGTCTTT-TATCC
1 CATCTAACTGGCATTATTGGCACCTTTCTGCCAAATGCACAGCTAGGCATTTAGTCTTTATTTCC
*
231797 TAAAGGCTTTTAACCTTT
66 TAAAGGCATTTAACCTTT
* *
231815 CATCTAACTGGCATTATTGGCACCTTTCTGCCAAATGAACAGCTAGACATTTAGTCTTTTATTT
1 CATCTAACTGGCATTATTGGCACCTTTCTGCCAAATGCACAGCTAGGCATTTAGTC-TTTATTT
231879 TAGATCAGTT
Statistics
Matches: 126, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
81 4 0.03
82 91 0.72
83 3 0.02
84 28 0.22
ACGTcount: A:0.27, C:0.22, G:0.13, T:0.37
Consensus pattern (83 bp):
CATCTAACTGGCATTATTGGCACCTTTCTGCCAAATGCACAGCTAGGCATTTAGTCTTTATTTCC
TAAAGGCATTTAACCTTT
Found at i:232060 original size:54 final size:53
Alignment explanation
Indices: 231951--232549 Score: 586
Period size: 54 Copynumber: 11.2 Consensus size: 53
231941 ACTCTATAGT
* * ** * * * *
231951 TTGCACACTTAGTGCCAATACGGTAATTCA-CAACTTATTATAAATTACGTGGG
1 TTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATT-TGTGGG
* * * *
232004 TTGCACACTTAGTACCTATACAGTCGTTCATCAATATATGATGAATTATGTGGG
1 TTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATT-TGTGGG
* *
232058 TTGCACACATAGTGCATATATGGTCGTTCATCAACATATGATGAATTCCT-TGGG
1 TTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATT--TGTGGG
* *
232112 TTGCACACTTAGTGCCTATACGGTTGTTCATCAACATATGATGAATTCTGTGGG
1 TTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATT-TGTGGG
* *
232166 TTGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTCGTAGG
1 TTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTT-GTGGG
* * * *
232220 TTGTACACTTAGTGCCTATATGGTCGTTCATCAACATATGATGAATTCCGTGGG
1 TTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATT-TGTGGG
* **
232274 TTG----C--A-TGCCTATACAGTCGTTCATCAACATATGATGAATTCCCTGGG
1 TTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATT-TGTGGG
* * * * *
232321 TTGCTCACATAGTGTCTATACGATCATTCATCAACATATGATGAATTTCATGGG
1 TTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTT-GTGGG
* ** * * * *
232375 TTGCACACATAGTACCTATAATGTTGTTCATGAATATATGATGAATTTCATGGG
1 TTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTT-GTGGG
* * * * *
232429 TTGCACACATAGTACATATACGGTTGTTCATGAACATATGCTGAATTATGTGGG
1 TTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATT-TGTGGG
* * * * * *
232483 TTGTACACATAGTGCATGTATGGTCATTCATCAACATATGATAAATTTCGTGGG
1 TTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTT-GTGGG
*
232537 TTGCACACTTAGT
1 TTGCACACATAGT
232550 ATTGATGTAA
Statistics
Matches: 468, Mismatches: 63, Indels: 29
0.84 0.11 0.05
Matches are distributed among these distances:
47 42 0.09
48 1 0.00
50 1 0.00
51 1 0.00
53 30 0.06
54 391 0.84
55 2 0.00
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (53 bp):
TTGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTGTGGG
Found at i:232132 original size:108 final size:108
Alignment explanation
Indices: 231951--232549 Score: 660
Period size: 108 Copynumber: 5.6 Consensus size: 108
231941 ACTCTATAGT
* * * ** * * * *
231951 TTGCACACTTAGTGCCAATACGGTAATTCA-CAACTTATTATAAATTACGTGGGTTGCACACTTA
1 TTGCACACATAGTGCCTATATGGTCGTTCATCAACATATGATGAATTTCGTGGGTTGCACACTTA
* * *
232015 GTACCTATACAGTCGTTCATCAATATATGATGAATTATGTGGG
66 GTGCCTATACGGTCGTTCATCAACATATGATGAATTATGTGGG
* * *
232058 TTGCACACATAGTGCATATATGGTCGTTCATCAACATATGATGAATTCCTTGGGTTGCACACTTA
1 TTGCACACATAGTGCCTATATGGTCGTTCATCAACATATGATGAATTTCGTGGGTTGCACACTTA
* *
232123 GTGCCTATACGGTTGTTCATCAACATATGATGAATTCTGTGGG
66 GTGCCTATACGGTCGTTCATCAACATATGATGAATTATGTGGG
* * * *
232166 TTGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTCGTAGGTTGTACACTTA
1 TTGCACACATAGTGCCTATATGGTCGTTCATCAACATATGATGAATTTCGTGGGTTGCACACTTA
* **
232231 GTGCCTATATGGTCGTTCATCAACATATGATGAATTCCGTGGG
66 GTGCCTATACGGTCGTTCATCAACATATGATGAATTATGTGGG
** * * * *
232274 TTG----C--A-TGCCTATACAGTCGTTCATCAACATATGATGAATTCCCTGGGTTGCTCACATA
1 TTGCACACATAGTGCCTATATGGTCGTTCATCAACATATGATGAATTTCGTGGGTTGCACACTTA
* * * *
232332 GTGTCTATACGATCATTCATCAACATATGATGAATT-TCATGGG
66 GTGCCTATACGGTCGTTCATCAACATATGATGAATTAT-GTGGG
* * * * * *
232375 TTGCACACATAGTACCTATAAT-GTTGTTCATGAATATATGATGAATTTCATGGGTTGCACACAT
1 TTGCACACATAGTGCCTAT-ATGGTCGTTCATCAACATATGATGAATTTCGTGGGTTGCACACTT
* * * * *
232439 AGTACATATACGGTTGTTCATGAACATATGCTGAATTATGTGGG
65 AGTGCCTATACGGTCGTTCATCAACATATGATGAATTATGTGGG
* * * * *
232483 TTGTACACATAGTGCATGTATGGTCATTCATCAACATATGATAAATTTCGTGGGTTGCACACTTA
1 TTGCACACATAGTGCCTATATGGTCGTTCATCAACATATGATGAATTTCGTGGGTTGCACACTTA
232548 GT
66 GT
232550 ATTGATGTAA
Statistics
Matches: 413, Mismatches: 67, Indels: 23
0.82 0.13 0.05
Matches are distributed among these distances:
101 85 0.21
102 1 0.00
104 1 0.00
105 1 0.00
107 27 0.07
108 296 0.72
109 2 0.00
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (108 bp):
TTGCACACATAGTGCCTATATGGTCGTTCATCAACATATGATGAATTTCGTGGGTTGCACACTTA
GTGCCTATACGGTCGTTCATCAACATATGATGAATTATGTGGG
Found at i:232301 original size:47 final size:47
Alignment explanation
Indices: 232232--232324 Score: 159
Period size: 47 Copynumber: 2.0 Consensus size: 47
232222 GTACACTTAG
** *
232232 TGCCTATATGGTCGTTCATCAACATATGATGAATTCCGTGGGTTGCA
1 TGCCTATACAGTCGTTCATCAACATATGATGAATTCCCTGGGTTGCA
232279 TGCCTATACAGTCGTTCATCAACATATGATGAATTCCCTGGGTTGC
1 TGCCTATACAGTCGTTCATCAACATATGATGAATTCCCTGGGTTGC
232325 TCACATAGTG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.33
Consensus pattern (47 bp):
TGCCTATACAGTCGTTCATCAACATATGATGAATTCCCTGGGTTGCA
Found at i:232487 original size:263 final size:263
Alignment explanation
Indices: 232018--232541 Score: 730
Period size: 263 Copynumber: 2.0 Consensus size: 263
232008 ACACTTAGTA
* ** * *
232018 CCTATACAGTCGTTCATCAATATATGATGAATTATGTGGGTTGCACACATAGTGCATATATGGTC
1 CCTATACAGTCGTTCATCAACATATGATGAATTACCTGGGTTGCACACATAGTGCATATACGATC
* * * * *
232083 GTTCATCAACATATGATGAATTCCTTGGGTTGCACACTTAGTGCCTATACGGTTGTTCATCAACA
66 ATTCATCAACATATGATGAATTCCATGGGTTGCACACATAGTACCTATAAGGTTGTTCATCAACA
* * * *
232148 TATGATGAATTCTGTGGGTTGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATT
131 TATGATGAATTCTATGGGTTGCACACATAGTACATATACGGTCGTTCATCAACATATGATGAATT
* * * *
232213 TCGTAGGTTGTACACTTAGTGCCTATATGGTCGTTCATCAACATATGATGAATTCCGTGGGTTGC
196 TCGTAGGTTGTACACATAGTGCATATATGGTCATTCATCAACATATGATAAATTCCGTGGGTTGC
232278 ATG
261 ATG
* *
232281 CCTATACAGTCGTTCATCAACATATGATGAATTCCCTGGGTTGCTCACATAGTGTC-TATACGAT
1 CCTATACAGTCGTTCATCAACATATGATGAATTACCTGGGTTGCACACATAGTG-CATATACGAT
* * * *
232345 CATTCATCAACATATGATGAATTTCATGGGTTGCACACATAGTACCTATAATGTTGTTCATGAAT
65 CATTCATCAACATATGATGAATTCCATGGGTTGCACACATAGTACCTATAAGGTTGTTCATCAAC
* * *
232410 ATATGATGAATT-TCATGGGTTGCACACATAGTACATATACGGTTGTTCATGAACATATGCTGAA
130 ATATGATGAATTCT-ATGGGTTGCACACATAGTACATATACGGTCGTTCATCAACATATGATGAA
* * *
232474 TTAT-GTGGGTTGTACACATAGTGCATGTATGGTCATTCATCAACATATGATAAATTTCGTGGGT
194 TT-TCGTAGGTTGTACACATAGTGCATATATGGTCATTCATCAACATATGATAAATTCCGTGGGT
232538 TGCA
258 TGCA
232542 CACTTAGTAT
Statistics
Matches: 228, Mismatches: 30, Indels: 6
0.86 0.11 0.02
Matches are distributed among these distances:
262 1 0.00
263 225 0.99
264 2 0.01
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.35
Consensus pattern (263 bp):
CCTATACAGTCGTTCATCAACATATGATGAATTACCTGGGTTGCACACATAGTGCATATACGATC
ATTCATCAACATATGATGAATTCCATGGGTTGCACACATAGTACCTATAAGGTTGTTCATCAACA
TATGATGAATTCTATGGGTTGCACACATAGTACATATACGGTCGTTCATCAACATATGATGAATT
TCGTAGGTTGTACACATAGTGCATATATGGTCATTCATCAACATATGATAAATTCCGTGGGTTGC
ATG
Found at i:233374 original size:45 final size:44
Alignment explanation
Indices: 233324--233486 Score: 220
Period size: 45 Copynumber: 3.6 Consensus size: 44
233314 TTTATGCTGG
* * * *
233324 TAATGCACCCATGTGCATTTCAACTATGGCATCCTTTCATGCCAA
1 TAATGCACCCATATGCATTT-AATTTTGGCATCCTTTCATGCCGA
*
233369 TAATGCACCCATATGCATTATTATTTTGGCATCCTTTCATGCCGA
1 TAATGCACCCATATGCATT-TAATTTTGGCATCCTTTCATGCCGA
233414 TAATGCACCCATATG-ATTTATTATTTTGGCATCCTTTCATGCCGA
1 TAATGCACCCATATGCATTTA--ATTTTGGCATCCTTTCATGCCGA
*
233459 TAATGCACCCATATGCATTATTATTTTG
1 TAATGCACCCATATGCATT-TAATTTTG
233487 TTCATTCGTT
Statistics
Matches: 106, Mismatches: 7, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 97 0.92
46 4 0.04
47 1 0.01
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (44 bp):
TAATGCACCCATATGCATTTAATTTTGGCATCCTTTCATGCCGA
Found at i:240321 original size:45 final size:45
Alignment explanation
Indices: 240272--240408 Score: 202
Period size: 45 Copynumber: 3.0 Consensus size: 45
240262 ATTTCAACTA
*
240272 TGGCATCCTTTCATGCCGATAATGCACCCATATGTATTATTATTT
1 TGGCATCCTTTCATGCCGATAATGCACCCATATGCATTATTATTT
** * * *
240317 TGGCATAATTGCATACCAATAATGCACCCATATGCATTATTATTT
1 TGGCATCCTTTCATGCCGATAATGCACCCATATGCATTATTATTT
* *
240362 TGGAATCCTTTCATGCTGATAATGCACCCATATGCATTATTATTT
1 TGGCATCCTTTCATGCCGATAATGCACCCATATGCATTATTATTT
240407 TG
1 TG
240409 TTCATTCATT
Statistics
Matches: 79, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 79 1.00
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (45 bp):
TGGCATCCTTTCATGCCGATAATGCACCCATATGCATTATTATTT
Found at i:242320 original size:44 final size:45
Alignment explanation
Indices: 242227--242324 Score: 162
Period size: 44 Copynumber: 2.2 Consensus size: 45
242217 AGCTTATTTT
*
242227 GCTTATTTTACCAATATACTTACCATTTACTCCATAAGCTCGTAA
1 GCTTATTTTACCAATATACTTACCATTTACTCCATAAGCTCATAA
* *
242272 GCTTATTTTACCAATATACTTGCCA-TTATTCCATAAGCTCATAA
1 GCTTATTTTACCAATATACTTACCATTTACTCCATAAGCTCATAA
242316 GCTTATTTT
1 GCTTATTTT
242325 CATGTTTACC
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
44 26 0.52
45 24 0.48
ACGTcount: A:0.30, C:0.22, G:0.07, T:0.41
Consensus pattern (45 bp):
GCTTATTTTACCAATATACTTACCATTTACTCCATAAGCTCATAA
Found at i:242477 original size:40 final size:40
Alignment explanation
Indices: 242398--242477 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 40
242388 ATAAGAGTCA
* * *
242398 AATACTGCACCGAAGTGAAGAGGTCGAGCTTTGCTCACCT
1 AATAATGCACCGAAGTGAAGAGGTCGAGCTTTACCCACCT
* ** *
242438 AATAATGCACCGTAGTGCTGAGGTCGGGCTTTACCCACCT
1 AATAATGCACCGAAGTGAAGAGGTCGAGCTTTACCCACCT
242478 TGTACACCGT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.25, C:0.26, G:0.25, T:0.24
Consensus pattern (40 bp):
AATAATGCACCGAAGTGAAGAGGTCGAGCTTTACCCACCT
Found at i:250368 original size:54 final size:54
Alignment explanation
Indices: 250298--250772 Score: 737
Period size: 54 Copynumber: 8.9 Consensus size: 54
250288 ATATTTCATT
* * *
250298 TTACCGTATCGACACTATGTGTGCAACCCACATAATTCATAATGAGTTTTTGAA
1 TTACCGTATCGGCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAA
* *
250352 TTACCGTATCGGCACTATATGTGCAACCCACGTAATTCATAATAAGTTTGTGAA
1 TTACCGTATCGGCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAA
* *
250406 TTACCATATCGACACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAA
1 TTACCGTATCGGCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAA
* *
250460 TTACCGTATCGCCACTATGTGTGCAACCCACGTAATTCATAATGAATTTGTGAA
1 TTACCGTATCGGCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAA
*
250514 TTACCGTATCGGCACTATGTGTGCAACCCACGTAATTCATAATGAATTTGTGAA
1 TTACCGTATCGGCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAA
250568 TTACCGTATCGGCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAA
1 TTACCGTATCGGCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAA
* * *
250622 TTACCGTAT---CACTATGTGTGTAACCCACGTAATTCAAAATGATTTTGTGAA
1 TTACCGTATCGGCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAA
* * * *
250673 TTACCGTATCAGCACTATATGTGCAACTCACGTAATTCATAATGAGTTTGTAAA
1 TTACCGTATCGGCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAA
*
250727 TTACCGTATCGGCACTA--TGTGCAACCCACAG-AATTTATAATGAGTT
1 TTACCGTATCGGCACTATGTGTGCAACCCAC-GTAATTCATAATGAGTT
250773 GTAATATTCA
Statistics
Matches: 391, Mismatches: 26, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
51 48 0.12
52 25 0.06
53 1 0.00
54 317 0.81
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (54 bp):
TTACCGTATCGGCACTATGTGTGCAACCCACGTAATTCATAATGAGTTTGTGAA
Found at i:254306 original size:54 final size:54
Alignment explanation
Indices: 254205--254599 Score: 560
Period size: 54 Copynumber: 7.4 Consensus size: 54
254195 TTATGTATAT
*
254205 TATCGGCACTAAGTGTGCAACCCAC-GAATTCATAATAAGTTTATGAACGACCG
1 TATCGGCACTAAGTGTGCAACCCACAAAATTCATAATAAGTTTATGAACGACCG
* * *
254258 TATCGGCACTAAGTGTTCAACCTACAAAATTCATAGTAAGTTTATGAACGACCG
1 TATCGGCACTAAGTGTGCAACCCACAAAATTCATAATAAGTTTATGAACGACCG
*
254312 TATCGGCACTAAGTGTGCAACCCACAAAATTCATAGTAAGTTTATGAACGACCG
1 TATCGGCACTAAGTGTGCAACCCACAAAATTCATAATAAGTTTATGAACGACCG
* ** **
254366 TATCGGAACTAAGTGTGCAACCCATGAAATTCATAATAAGTTTATGAACGAATG
1 TATCGGCACTAAGTGTGCAACCCACAAAATTCATAATAAGTTTATGAACGACCG
*
254420 TAT-GGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCG
1 TATCGGCACTAAGTGTGCAACCCACAAAATTCATAATAAGTTTATGAACGACCG
* * * *
254473 TATTGGCACTAAGTGTACAACCCACGAAATTCAAAATAAGTTTATGAACGACCG
1 TATCGGCACTAAGTGTGCAACCCACAAAATTCATAATAAGTTTATGAACGACCG
** * * * **
254527 TATCGGCACTAAGTAAGCAACCCACAGAATTCATAATAAGTTTATAAATGATTG
1 TATCGGCACTAAGTGTGCAACCCACAAAATTCATAATAAGTTTATGAACGACCG
* *
254581 TATGGGCACTACGTGTGCA
1 TATCGGCACTAAGTGTGCA
254600 TCCTAAAGAA
Statistics
Matches: 303, Mismatches: 37, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
53 70 0.23
54 233 0.77
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (54 bp):
TATCGGCACTAAGTGTGCAACCCACAAAATTCATAATAAGTTTATGAACGACCG
Found at i:254483 original size:161 final size:161
Alignment explanation
Indices: 254205--254599 Score: 569
Period size: 161 Copynumber: 2.4 Consensus size: 161
254195 TTATGTATAT
**
254205 TATCGGCACTAAGTGTGCAACCCACG-AATTCATAATAAGTTTATGAACGACCGTATCGGCACTA
1 TATCGGCACTAAGTGTGCAACCCA-GAAATTCATAATAAGTTTATGAACGAATGTATCGGCACTA
* * * *
254269 AGTGTTCAACCTACAAAATTCATAGTAAGTTTATGAACGACCGTATCGGCACTAAGTGTGCAACC
65 AGTGTGCAACCCACAAAATTCATAATAAGTTTATGAACGACCGTATCGGCACTAAGTGTACAACC
* *
254334 CACAAAATTCATAGTAAGTTTATGAACGACCG
130 CACAAAATTCAAAATAAGTTTATGAACGACCG
*
254366 TATCGGAACTAAGTGTGCAACCCATGAAATTCATAATAAGTTTATGAACGAATGTAT-GGCACTA
1 TATCGGCACTAAGTGTGCAACCCA-GAAATTCATAATAAGTTTATGAACGAATGTATCGGCACTA
* *
254430 AGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCGTATTGGCACTAAGTGTACAACC
65 AGTGTGCAACCCACAAAATTCATAATAAGTTTATGAACGACCGTATCGGCACTAAGTGTACAACC
*
254495 CACGAAATTCAAAATAAGTTTATGAACGACCG
130 CACAAAATTCAAAATAAGTTTATGAACGACCG
** * * * * *
254527 TATCGGCACTAAGTAAGCAACCCACAGAATTCATAATAAGTTTATAAATGATTGTATGGGCACTA
1 TATCGGCACTAAGTGTGCAACCCAGA-AATTCATAATAAGTTTATGAACGAATGTATCGGCACTA
*
254592 CGTGTGCA
65 AGTGTGCA
254600 TCCTAAAGAA
Statistics
Matches: 210, Mismatches: 21, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
160 1 0.00
161 167 0.80
162 42 0.20
ACGTcount: A:0.36, C:0.20, G:0.18, T:0.26
Consensus pattern (161 bp):
TATCGGCACTAAGTGTGCAACCCAGAAATTCATAATAAGTTTATGAACGAATGTATCGGCACTAA
GTGTGCAACCCACAAAATTCATAATAAGTTTATGAACGACCGTATCGGCACTAAGTGTACAACCC
ACAAAATTCAAAATAAGTTTATGAACGACCG
Found at i:254648 original size:49 final size:49
Alignment explanation
Indices: 254591--254689 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 49
254581 TATGGGCACT
*
254591 ACGTGTGCATCCTAAAGAACTTATAATGAGTTGAAAATAATAAATTTGA
1 ACGTGTGCATCCCAAAGAACTTATAATGAGTTGAAAATAATAAATTTGA
254640 ACGTGTGCATCCCAAAGAACTTATAATGAGTTGAAAATAATAAATTTGA
1 ACGTGTGCATCCCAAAGAACTTATAATGAGTTGAAAATAATAAATTTGA
254689 A
1 A
254690 TTTGATAGTT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.43, C:0.11, G:0.16, T:0.29
Consensus pattern (49 bp):
ACGTGTGCATCCCAAAGAACTTATAATGAGTTGAAAATAATAAATTTGA
Found at i:256296 original size:264 final size:263
Alignment explanation
Indices: 255788--256316 Score: 943
Period size: 264 Copynumber: 2.0 Consensus size: 263
255778 AAGAACAAGC
*
255788 ACATCAGGGAGCAGTATATGAGGTCAATGCTACTGAAGTTCTTAATTTGAAACAAGGCAATCGAG
1 ACATCAGGGAGCAGTATATGAGGTCAATGCTACTAAAGTTCTTAATTTGAAACAAGGCAATCGAG
*
255853 CAGTGCATGAGTATGAGGTTGAATACAACAAACTTAGTCGTTATGCTATTGAGGTAGTTCCTAAT
66 CAGTGCATGAGTATAAGGTTGAATACAACAAACTTAGTCGTTATGCTATTGAGGTAGTTCCTAAT
255918 GATAAAGCCCGACGTGATTGGTTCATTGAAGATTTGAGGCCTAAGTTGAAAGAGATAATGTTAGC
131 GATAAAGCCCGACGTGATTGGTTCATTGAAGATTTGAGGCCTAAGTTGAAAGAGATAATGTTAGC
255983 TTTAAATTTTTCCTAGTTTACAAGAAGTTATTAACCGAGCTAAGGTTATTGAAAAATCTCAAGAT
196 TTTAAATTTTTCCTAGTTTACAAGAAGTTATTAACCGAGCTAAGGTTATTGAAAAATCTCAAGAT
256048 GAG
261 GAG
* * *
256051 ACATCAGGTAGCAGTTTAT-ATGGTCAATGCTACTAAAGTTTCTTAATTTGAAACAAGGCGATCG
1 ACATCAGGGAGCAGTATATGA-GGTCAATGCTACTAAAG-TTCTTAATTTGAAACAAGGCAATCG
256115 AGCAGTGCATGAGTATAAGGTTGAATACAACAAACTTAGTCGTTATGCTATTGAGGTAGTTCCTA
64 AGCAGTGCATGAGTATAAGGTTGAATACAACAAACTTAGTCGTTATGCTATTGAGGTAGTTCCTA
* *
256180 ATGATAAAGCCCGACGTGATTGGTTCATTTAAGGTTTGAGGCCTAAGTTGAAAGAGATAATGTTA
129 ATGATAAAGCCCGACGTGATTGGTTCATTGAAGATTTGAGGCCTAAGTTGAAAGAGATAATGTTA
* * *
256245 GCTTTAAATTTTTCCTAGTTTGCAAGAAGTTATTAACCGAGCTAAGGTTATTGAAATATCTCAAT
194 GCTTTAAATTTTTCCTAGTTTACAAGAAGTTATTAACCGAGCTAAGGTTATTGAAAAATCTCAAG
256310 ATGAG
259 ATGAG
256315 AC
1 AC
256317 TCAAGCAGCG
Statistics
Matches: 254, Mismatches: 10, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
262 1 0.00
263 33 0.13
264 220 0.87
ACGTcount: A:0.33, C:0.13, G:0.22, T:0.31
Consensus pattern (263 bp):
ACATCAGGGAGCAGTATATGAGGTCAATGCTACTAAAGTTCTTAATTTGAAACAAGGCAATCGAG
CAGTGCATGAGTATAAGGTTGAATACAACAAACTTAGTCGTTATGCTATTGAGGTAGTTCCTAAT
GATAAAGCCCGACGTGATTGGTTCATTGAAGATTTGAGGCCTAAGTTGAAAGAGATAATGTTAGC
TTTAAATTTTTCCTAGTTTACAAGAAGTTATTAACCGAGCTAAGGTTATTGAAAAATCTCAAGAT
GAG
Found at i:258426 original size:54 final size:54
Alignment explanation
Indices: 258344--258709 Score: 483
Period size: 54 Copynumber: 6.8 Consensus size: 54
258334 CTATGTTTAT
*
258344 TATCGGCACTAAGTGTGCTACCCACAGAATTCATAATAAGTTTATGAACGACCG
1 TATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCG
*
258398 TATCGGTACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCG
1 TATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCG
* *
258452 TATCGACACTAAGTGTGCAACCCAC-GAAATTCATAATAAGTTTATGAACGATCG
1 TATCGGCACTAAGTGTGCAACCCACAG-AATTCATAATAAGTTTATGAACGACCG
* * *
258506 TATCGGCACTAAGTGTGCAACCCACATAACTT-ATAATAAGTTTATGAAAGACCA
1 TATCGGCACTAAGTGTGCAACCCACAGAA-TTCATAATAAGTTTATGAACGACCG
* * *
258560 TATCGGCACTAAATATGTAACCCAC-GAAATTCATAATAAGTTTATGAACGACCG
1 TATCGGCACTAAGTGTGCAACCCACAG-AATTCATAATAAGTTTATGAACGACCG
* * *
258614 TATCGGCATTTAGTGTGCAACCCAC-GAAATTAATAATAAGTTTATGAACGACCG
1 TATCGGCACTAAGTGTGCAACCCACAG-AATTCATAATAAGTTTATGAACGACCG
* * * *
258668 TAT-GGCCACTATGTGTGCACCCCAAAGAACTT-ATAATGAGTT
1 TATCGG-CACTAAGTGTGCAACCCACAGAA-TTCATAATAAGTT
258710 GAAAATAATA
Statistics
Matches: 276, Mismatches: 28, Indels: 16
0.86 0.09 0.05
Matches are distributed among these distances:
53 5 0.02
54 266 0.96
55 5 0.02
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (54 bp):
TATCGGCACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCG
Found at i:276537 original size:21 final size:22
Alignment explanation
Indices: 276511--276551 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
276501 TGATTATTAT
276511 TATTAT-TATTATTCTTTTTCA
1 TATTATGTATTATTCTTTTTCA
* *
276532 TATTATGTTTTATTTTTTTT
1 TATTATGTATTATTCTTTTT
276552 TACTTTTTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (22 bp):
TATTATGTATTATTCTTTTTCA
Found at i:279956 original size:181 final size:178
Alignment explanation
Indices: 279561--280028 Score: 597
Period size: 179 Copynumber: 2.6 Consensus size: 178
279551 GATCCAAATT
* * **
279561 AAAAATGTATCGATCCAA-AATGATATAACAGGTTAAACA-ATGACAAAACCGGTATTGAAATGA
1 AAAAATGTATCGAT-CAACAATGATATAACAGG-TAAAAATATGATAAAACCGGTATCAAAATGA
* * * * *
279624 TAAAACCGGTAAAGCGTTACCGAATATATTTAAAGTGTCGGTACTTTAATATAAGGATCGACATT
64 T-AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACATT
*
279689 TCGTTAATTTAAAAGAGAAGTTTTAGCGCCTATAAAGTGTCGATACTTTCA
128 TCGTGAATTTAAAAGAGAAGTTTTAGCGCCTATAAAGTGTCGATACTTTCA
* * ** *
279740 AAAAATATATCGATCAACAACGATATAACAGGTAAAAATATGATAAAATTGATATCAAAATGATG
1 AAAAATGTATCGATCAACAATGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGAT-
* * * *
279805 AAACCGGTAAAACGCTATCGGATATATTGAAAGTGTCGAAACTTT-ATATAAGGATCGACACTTT
65 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACA-TTT
* *
279869 -GTGAATTTAAAAGAGAAGCAGTTTTAGCGTCTATAAAGTGTCGATA-TTTTA
129 CGTGAATTTAAAAGAG-A--AGTTTTAGCGCCTATAAAGTGTCGATACTTTCA
*
279920 AAAAATGTATCGATCAAACAATGATATAATAGGTAAAAATATGATAAAACCGGTATCAAAATGAT
1 AAAAATGTATCGATC-AACAATGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGAT
* *
279985 AAAACGGT-AAATGATACCGGATATATTAAAAGTGTCGATACTTT
65 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTT
280029 CGTAAGTACG
Statistics
Matches: 250, Mismatches: 32, Indels: 14
0.84 0.11 0.05
Matches are distributed among these distances:
178 37 0.15
179 118 0.47
180 25 0.10
181 70 0.28
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.28
Consensus pattern (178 bp):
AAAAATGTATCGATCAACAATGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
AACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACATTTCG
TGAATTTAAAAGAGAAGTTTTAGCGCCTATAAAGTGTCGATACTTTCA
Found at i:279974 original size:20 final size:18
Alignment explanation
Indices: 279951--279995 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 18
279941 TGATATAATA
279951 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAA-C
*
279971 GGTATCAAAATGATAAAAC
1 GGTA-AAAAATGATAAAAC
279990 GGTAAA
1 GGTAAA
279996 TGATACCGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 1 0.05
19 5 0.23
20 13 0.59
21 3 0.14
ACGTcount: A:0.53, C:0.09, G:0.18, T:0.20
Consensus pattern (18 bp):
GGTAAAAAATGATAAAAC
Found at i:282159 original size:14 final size:15
Alignment explanation
Indices: 282125--282158 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
282115 TGGTTGTATT
*
282125 GGGGGATGACGGTGA
1 GGGGGACGACGGTGA
282140 GGGGGACGACGGTGA
1 GGGGGACGACGGTGA
282155 GGGG
1 GGGG
282159 AAAACAGTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.18, C:0.09, G:0.65, T:0.09
Consensus pattern (15 bp):
GGGGGACGACGGTGA
Found at i:282263 original size:21 final size:21
Alignment explanation
Indices: 282237--282277 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
282227 AAGACAATCA
282237 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAT
* *
282258 AGAGTCGAAGATACACTTGA
1 AGAGTCGAAGAGAAACTTGA
282278 GAGGCATAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.12, G:0.27, T:0.20
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAT
Found at i:282567 original size:15 final size:15
Alignment explanation
Indices: 282547--282601 Score: 58
Period size: 15 Copynumber: 3.5 Consensus size: 15
282537 AGAGGGAGGA
282547 GGAAGAAGAAGAGAT
1 GGAAGAAGAAGAGAT
*
282562 GGAAGAA-AAGAGGGAGGA
1 GGAAGAAGAAGA--GA--T
282580 GGAAGAAGAAGAGAT
1 GGAAGAAGAAGAGAT
282595 GGAAGAA
1 GGAAGAA
282602 ATGAGGAGGA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 4 0.12
15 14 0.42
16 2 0.06
17 2 0.06
18 7 0.21
19 4 0.12
ACGTcount: A:0.53, C:0.00, G:0.44, T:0.04
Consensus pattern (15 bp):
GGAAGAAGAAGAGAT
Found at i:282588 original size:36 final size:33
Alignment explanation
Indices: 282534--282617 Score: 143
Period size: 33 Copynumber: 2.5 Consensus size: 33
282524 ATATGAAAAA
282534 AAAAGAGGGAGGAGGAAGAAGAAGAGATGGAAG
1 AAAAGAGGGAGGAGGAAGAAGAAGAGATGGAAG
282567 AAAAGAGGGAGGAGGAAGAAGAAGAGATGGAAG
1 AAAAGAGGGAGGAGGAAGAAGAAGAGATGGAAG
*
282600 AAATGA-GGAGGAAGGAAG
1 AAAAGAGGGAGG-AGGAAG
282618 TCGATGTCAT
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
32 5 0.10
33 44 0.90
ACGTcount: A:0.51, C:0.00, G:0.45, T:0.04
Consensus pattern (33 bp):
AAAAGAGGGAGGAGGAAGAAGAAGAGATGGAAG
Found at i:284168 original size:18 final size:20
Alignment explanation
Indices: 284145--284192 Score: 75
Period size: 19 Copynumber: 2.5 Consensus size: 20
284135 AAATGTAGGG
284145 TAATTTTGTATTA-GA-TTA
1 TAATTTTGTATTACGATTTA
284163 TAATTTTGTA-TACGATTTA
1 TAATTTTGTATTACGATTTA
284182 TAATTTTGTAT
1 TAATTTTGTAT
284193 GTGAATGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 2 0.07
18 12 0.44
19 13 0.48
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.56
Consensus pattern (20 bp):
TAATTTTGTATTACGATTTA
Found at i:285114 original size:197 final size:193
Alignment explanation
Indices: 284776--285226 Score: 753
Period size: 197 Copynumber: 2.3 Consensus size: 193
284766 ATGTATCGAC
* *
284776 TTATGAGAGAATATGTGTAATATATGTATTGACACTTTTTAATTTTGTGTCGATACTATTGGTCC
1 TTATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCC
* *
284841 ATAATGAATGGCAAACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAATGTGTCGATCCCA
66 ATAA-GAATGGCAAACAGGGTGCAACCATAAAGTGTCAATCCATATATAAAAGGTGTCGATCCCA
*
284906 GAAACATCGAAACTCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATAAGTATAC
130 GAAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACC-G-----GTATAC
284971 CGGAT
189 CGGAT
*
284976 TTATGAGAGAATAGGTGTAATATATGTATCGACGCTTTTTAATTTTGTGTCGATACTATTGGTCC
1 TTATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCC
*
285041 A-GA-AATGGCAAACAGGGTGCAACCATAAAGTGTCAATCCATATATAAAAGGTGTCGATCCCAG
66 ATAAGAATGGCAAACAGGGTGCAACCATAAAGTGTCAATCCATATATAAAAGGTGTCGATCCCAG
285104 AAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATACCGGAT
131 AAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATACCGGAT
*
285167 TTATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATATTATT
1 TTATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATT
285227 TAAATATCGA
Statistics
Matches: 242, Mismatches: 9, Indels: 9
0.93 0.03 0.03
Matches are distributed among these distances:
191 69 0.29
196 1 0.00
197 108 0.45
199 1 0.00
200 63 0.26
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (193 bp):
TTATGAGAGAATAGGTGTAATATATGTATCGACACTTTTTAATTTTGTGTCGATACTATTGGTCC
ATAAGAATGGCAAACAGGGTGCAACCATAAAGTGTCAATCCATATATAAAAGGTGTCGATCCCAG
AAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAACCGGTATACCGGAT
Found at i:290541 original size:180 final size:181
Alignment explanation
Indices: 290059--290562 Score: 897
Period size: 181 Copynumber: 2.8 Consensus size: 181
290049 TTTTACCTTT
*
290059 TTTAAAAGAGAAGAAGTTATATCGTCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGTCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
*
290124 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
*
290189 CGGTTATGTTGAAAGTGTCGATAATTTATTATATGTATCGACACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGA-ACTTTTGGAA
* *
290241 TTTAAAAGAGAAG-AGTTATAGCGCCAATAAAGTGTCAATACTTTATAAAAATGTATCGATCCAT
1 TTTAAAAGAGAAGAAGTTATAGCGTCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
290305 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
290370 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCG-ACTTTTGGAA
131 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGAACTTTTGGAA
*
290420 -TTAATAAGAGAAGAAGTTATAGCGTCAATAACGTGTCGATACTTTATAAAAATGTATCGATCCA
1 TTTAA-AAGAGAAGAAGTTATAGCGTCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCA
*
290484 TAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAATTGACAAAACAGGTAAAGCGCTA
65 TAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTA
*
290549 CCGGTTATGATGAA
130 CCGGTTATGTTGAA
290563 TTTAAAAGAG
Statistics
Matches: 310, Mismatches: 10, Indels: 6
0.95 0.03 0.02
Matches are distributed among these distances:
178 4 0.01
179 18 0.06
180 124 0.40
181 151 0.49
182 13 0.04
ACGTcount: A:0.41, C:0.14, G:0.17, T:0.27
Consensus pattern (181 bp):
TTTAAAAGAGAAGAAGTTATAGCGTCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGAACTTTTGGAA
Found at i:290675 original size:143 final size:144
Alignment explanation
Indices: 290420--290693 Score: 478
Period size: 143 Copynumber: 1.9 Consensus size: 144
290410 ACTTTTGGAA
* *
290420 TTAATAAGAGAAGAAGTTATAGCGTCAATAACGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTAATAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* *
290485 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAATTGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
290550 CGGTTATGATGAAT
131 CGGTTATGATGAAT
* *
290564 TTAA-AAGAGAAGAAGTTATAGCGCCAATAAAGTGTTGATATTTTATAAAAATGTATCGATCCAT
1 TTAATAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
*
290628 AACAATATAACAGGTAAAAATATGACAAAATCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
66 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
290693 C
131 C
290694 AGATATGTTG
Statistics
Matches: 123, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
143 119 0.97
144 4 0.03
ACGTcount: A:0.44, C:0.14, G:0.17, T:0.25
Consensus pattern (144 bp):
TTAATAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
AACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
CGGTTATGATGAAT
Found at i:290845 original size:323 final size:321
Alignment explanation
Indices: 290238--290884 Score: 1118
Period size: 323 Copynumber: 2.0 Consensus size: 321
290228 GACACTTTTG
290238 GAATTTAAAAGAGAAGAGTTATAGCGCCAATAAAGTGTCAATACTTTATAAAAATGTATCGATCC
1 GAATTTAAAAGAGAAGAGTTATAGCGCCAATAAAGTGTCAATACTTTATAAAAATGTATCGATCC
*
290303 ATAACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCT
66 ATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCT
* * *
290368 ACCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACTTTTGGAATTAATAAGAGAAG
131 ACCAGATATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACCTTTGGAATTAATAAGAGAAG
* * * *
290433 AAGTTATAGCGTCAATAACGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAT
196 AAGTTATAGCGCCAATAAAGTGTAGATACTTTATAAAAATATATCGATCCATAACAATATAACAT
*
290498 GTAAAAATATGACAAAACCGGTCTCGAATTGACAAAACAGGTAAAGCGCTACCGGTTATGAT
261 GTAAAAATATGACAAAACCGGTCTCGAAATGAC-AAACAGGTAAAGCGCTACCGGTTATGAT
** *
290560 GAATTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTTGATATTTTATAAAAATGTATCGATC
1 GAATTTAAAAGAGAAG-AGTTATAGCGCCAATAAAGTGTCAATACTTTATAAAAATGTATCGATC
*
290625 CATAACAATATAACAGGTAAAAATATGACAAAATCGGTCTCGAAATGACAAAACAGGTAAAGCGC
65 CATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGC
290690 TACCAGATATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTGGAATTTAA-AAGAG
130 TACCAGATATGTTGAAAGTGTCGATAATTTATTATAAGTATCGAC-CTTTGGAA-TTAATAAGAG
290754 AAGAAGTTATAGCGCCAATAAAGTGTAGATACTTTATAAAAATATATCGATCCATAACAATATAA
193 AAGAAGTTATAGCGCCAATAAAGTGTAGATACTTTATAAAAATATATCGATCCATAACAATATAA
*
290819 CATGTAAAAATATGACAAAA-CGGTCTCGAAATGACAAACAGGTAAAGCGCTACCGGTTATGTT
258 CATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAACAGGTAAAGCGCTACCGGTTATGAT
290882 GAA
1 GAA
290885 AGTGTCGATA
Statistics
Matches: 308, Mismatches: 14, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
322 46 0.15
323 165 0.54
324 93 0.30
325 4 0.01
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.26
Consensus pattern (321 bp):
GAATTTAAAAGAGAAGAGTTATAGCGCCAATAAAGTGTCAATACTTTATAAAAATGTATCGATCC
ATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCT
ACCAGATATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACCTTTGGAATTAATAAGAGAAG
AAGTTATAGCGCCAATAAAGTGTAGATACTTTATAAAAATATATCGATCCATAACAATATAACAT
GTAAAAATATGACAAAACCGGTCTCGAAATGACAAACAGGTAAAGCGCTACCGGTTATGAT
Found at i:291624 original size:533 final size:529
Alignment explanation
Indices: 290564--291740 Score: 1858
Period size: 533 Copynumber: 2.2 Consensus size: 529
290554 TATGATGAAT
* * *
290564 TTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTTGATATTTTATAAAAATGTATCGATCCATA
1 TTAATAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATA
* *
290629 ACAATATAACAGGTAAAAATATGACAAAATCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACC
66 ACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACC
290694 AGATATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTGGAATTTAAAAGAGAAGAA
131 AGATATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTGGAATTTAAAAGAGAAGAA
*
290759 GTTATAGCGCCAATAAAGTGTAGATACTTTATAAAAATATATCGATCCATAACAATATAACATGT
196 GTTATAGCGCCAATAAAGTGTAGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGT
*
290824 AAAAATATGACAAAACGGTCTCGAAATGACAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTG
261 AAAAATATGACAAAACGGTCTCAAAATGACAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTG
*
290889 TCGATAATTATTATACGTATCGACACTTTAGAATTTAAAAAGAAGATTATAGCGCCAATAAAGTG
326 TCGATAATTATTATAAGTATCGACACTTTAGAATTTAAAAAGAAGATTATAGCGCCAATAAAGTG
* * *
290954 TTGATACGTTATAAAATGTATCTATCCATAACAATATAACATGTAAAAATATGACAAAACCGGTC
391 TCGATACGTTATAAAA--TATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTC
*
291019 TAGAAATGACAAAACATAAAGCGCTCCGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATC
454 TAGAAATGACAAAACATAAAGCGCTCCGGTGATGTTGAAAGTGTCGATAATTTATTATAAGTATC
291084 GACTTTTGGAA
519 GACTTTTGGAA
*
291095 TTAATAGAGAAGAAGTTATAGCGCCAATAACGTGTCGATACTTTATAAAAATGTATCGATCCATA
1 TTAATAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT-
291160 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
65 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTAC
* *
291225 CGGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAG
130 CAGATATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACAC-TTTGGAATTTAAAAGAGAAG
* *
291290 AAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATAAC-ATATAACAG
194 AAGTTATAGCGCCAATAAAGTGTAGATACTTTATAAAAATATATCGATCCATAACAATATAACAG
* *
291354 GTAATAATATGACAAAACCGGTCTCAAAATGACAAAACAGGTAAAGTGCTA-CGGTTATGTTGAA
259 GTAAAAATATGACAAAA-CGGTCTCAAAATGAC-AAACAGGTAAAGCGCTACCGGTTATGTTGAA
*
291418 AGTGTCGATAATTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCCA
322 AGTGTCGATAATTATTATAAGTATCGACAC-TTTAGAATTTAAAA-AGAAG-A-TTATAGCGCCA
*
291483 ATAAAGTGTCGATACTTTATAAAA-ATCGAT-CAT-A-AATATAACAGGT-AAAATATGACAAAA
383 ATAAAGTGTCGATACGTTATAAAATATCGATCCATAACAATATAACAGGTAAAAATATGAC-AAA
* * *
291543 ACCGGTCTCG-AATGACAAAATAGGTAAAGTGCTACCGG-GAT-TTGAAAGTGTCGATAATTTAT
447 ACCGGTCTAGAAATGACAAAACA--TAAAGCGCT-CCGGTGATGTTGAAAGTGTCGATAATTTAT
291605 TATAAGTATCGACACTTTTGGAA
509 TATAAGTATCG--ACTTTTGGAA
291628 TTAATAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTAAT-AGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* * *
291693 AATAATATAACATG-GAAAATATGATAAAACCGGTCT--ATAATGACAAAA
65 AACAATATAACATGTAAAAATATGACAAAACCGGTCTCGA-AATGACAAAA
291741 TGTGAACGCA
Statistics
Matches: 602, Mismatches: 28, Indels: 32
0.91 0.04 0.05
Matches are distributed among these distances:
530 22 0.04
531 125 0.21
532 160 0.27
533 164 0.27
534 92 0.15
535 5 0.01
536 1 0.00
537 33 0.05
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (529 bp):
TTAATAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATA
ACAATATAACATGTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACC
AGATATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTGGAATTTAAAAGAGAAGAA
GTTATAGCGCCAATAAAGTGTAGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGT
AAAAATATGACAAAACGGTCTCAAAATGACAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTG
TCGATAATTATTATAAGTATCGACACTTTAGAATTTAAAAAGAAGATTATAGCGCCAATAAAGTG
TCGATACGTTATAAAATATCGATCCATAACAATATAACAGGTAAAAATATGACAAAACCGGTCTA
GAAATGACAAAACATAAAGCGCTCCGGTGATGTTGAAAGTGTCGATAATTTATTATAAGTATCGA
CTTTTGGAA
Found at i:291654 original size:351 final size:359
Alignment explanation
Indices: 290564--291740 Score: 1814
Period size: 351 Copynumber: 3.3 Consensus size: 359
290554 TATGATGAAT
* *
290564 TTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTTGATATTTTATAAAAATGTATCGATCCATA
1 TTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATA
* *
290629 ACAATATAACAGGTAAAAATATGACAAAATCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACC
66 ACAATATAACAGGTAAAAATATGACAAAACCGGTCT-AAAATGACAAAACAGGTAAAGCGCTA-C
* *
290694 AGATATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACAC-TTTGGAATTTAAAAGAGAAGA
129 GGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGA
*
290758 AGTTATAGCGCCAATAAAGTGTAGATACTTTATAAAAATATATCGATCCATAACAATATAACATG
194 AGTTATAGCGCCAATAAAGTGTCGATACTTTAT-AAAA-ATATCGATCCATAACAATATAACATG
290823 TAAAAATATGACAAAA-CGGTCTCGAAATGAC-AAACAGGTAAAGCGCTACCGGTTATGTTGAAA
257 TAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAA
* *
290886 GTGTCGATAA-TTATTATACGTATCGACAC-TTTAGAA
322 GTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
* * *
290922 TTTAAAA-AGAAG-A-TTATAGCGCCAATAAAGTGTTGATACGTTAT-AAAATGTATCTATCCAT
1 -TTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* *
290983 AACAATATAACATGTAAAAATATGACAAAACCGGTCTAGAAATGACAAAACA--TAAAGCGCTCC
65 AACAATATAACAGGTAAAAATATGACAAAACCGGTCTA-AAATGACAAAACAGGTAAAGCGCTAC
*
291046 GGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCG--ACTTTTGGAA-TTAATAGAGAAGA
129 GGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGA
*
291108 AGTTATAGCGCCAATAACGTGTCGATACTTTATAAAAATGTATCGATCCATAAACAATATAACAT
194 AGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAA--TATCGATCCAT-AACAATATAACAT
291173 GTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAA
256 GTAAAAATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAA
291238 AGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
321 AGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
291277 TTTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 -TTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* *
291342 AAC-ATATAACAGGTAATAATATGACAAAACCGGTCTCAAAATGACAAAACAGGTAAAGTGCTAC
65 AACAATATAACAGGTAAAAATATGACAAAACCGGTCT-AAAATGACAAAACAGGTAAAGCGCTAC
291406 GGTTATGTTGAAAGTGTCGATAA-TTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGA
129 GGTTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGA
*
291470 AGTTATAGCGCCAATAAAGTGTCGATACTTTAT-AAAA-ATCGAT-CAT-A-AATATAACAGGT-
194 AGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATATCGATCCATAACAATATAACATGTA
* * *
291529 AAAATATGACAAAAACCGGTCTCG-AATGACAAAATAGGTAAAGTGCTACCGG-GAT-TTGAAAG
259 AAAATATGAC-AAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAG
291591 TGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
323 TGTCGATAATTTATTATAAGTATCGACACTTTTGGAA
291628 TTAATAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
1 TTAA-AAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCAT
* * *
291693 AATAATATAACATGG--AAAATATGATAAAACCGGTCTATAATGACAAAA
65 AACAATATAACA-GGTAAAAATATGACAAAACCGGTCTAAAATGACAAAA
291741 TGTGAACGCA
Statistics
Matches: 764, Mismatches: 31, Indels: 55
0.90 0.04 0.06
Matches are distributed among these distances:
348 1 0.00
349 4 0.01
350 71 0.09
351 162 0.21
352 63 0.08
353 89 0.12
354 42 0.05
355 78 0.10
356 34 0.04
357 5 0.01
358 84 0.11
359 41 0.05
360 32 0.04
361 14 0.02
362 44 0.06
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (359 bp):
TTAAAAGAGAAGAAGTTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATGTATCGATCCATA
ACAATATAACAGGTAAAAATATGACAAAACCGGTCTAAAATGACAAAACAGGTAAAGCGCTACGG
TTATGTTGAAAGTGTCGATAATTTATTATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAG
TTATAGCGCCAATAAAGTGTCGATACTTTATAAAAATATCGATCCATAACAATATAACATGTAAA
AATATGACAAAACCGGTCTCGAAATGACAAAACAGGTAAAGCGCTACCGGTTATGTTGAAAGTGT
CGATAATTTATTATAAGTATCGACACTTTTGGAA
Found at i:291991 original size:23 final size:23
Alignment explanation
Indices: 291939--291991 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
291929 TCCGGTTAAA
**
291939 TACCTATTTTATTATATAAGCGC
1 TACCTATTACATTATATAAGCGC
* * *
291962 TATCTATTACATTATATAAGTGT
1 TACCTATTACATTATATAAGCGC
291985 TACCTAT
1 TACCTAT
291992 ATGTTATTGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.32, C:0.15, G:0.08, T:0.45
Consensus pattern (23 bp):
TACCTATTACATTATATAAGCGC
Found at i:293601 original size:18 final size:17
Alignment explanation
Indices: 293578--293622 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
293568 TATTTTTAAA
293578 AAAAAACTAATTAA-AAT
1 AAAAAA-TAATTAATAAT
*
293595 GAAAAAATAAATAATAAT
1 -AAAAAATAATTAATAAT
293613 AAAAAATAAT
1 AAAAAATAAT
293623 GTGGTATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (17 bp):
AAAAAATAATTAATAAT
Found at i:309726 original size:29 final size:30
Alignment explanation
Indices: 309667--309727 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
309657 ATTTAACAGC
309667 TCAGTGGTATAATTGAAACAAAAATCAAAGT
1 TCAGTGGTATAATTG-AACAAAAATCAAAGT
* * *
309698 TCAGTGTTATAATTG-ACAAAATTGAAAGT
1 TCAGTGGTATAATTGAACAAAAATCAAAGT
309727 T
1 T
309728 TATTGGTAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
29 13 0.48
31 14 0.52
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.31
Consensus pattern (30 bp):
TCAGTGGTATAATTGAACAAAAATCAAAGT
Found at i:318412 original size:130 final size:131
Alignment explanation
Indices: 318095--318453 Score: 400
Period size: 130 Copynumber: 2.7 Consensus size: 131
318085 AGTTCCAGTC
* * * * * *
318095 ATCTAAGGGTGACACAACTCCTACATGATTAGAAGATATTGTCGGTGGATGACACAGTTCCTACG
1 ATCTAAGGGTGACACGACTCCTACGTGATGAGGAGGTATAGTCGGTGGATGACACAGTTCCTACG
* * * * * * *
318160 CGATGATGAAGGTTGACCATCTTTAGGAATGGTGATAACACGGTTTCTACGCGATGAGGACGGCT
66 TGATGAGGAAGGTAGGCCATCTTTAGG---GATGATAACACGGTTCCTACGCGATGAGGACGACT
318225 GATT
128 GATT
* * * * *
318229 ATCTAGGGGTGACACGGCTCCTACGTGATGAGGAGGTACAGTCAGTGGATGACACGGTTCCTACG
1 ATCTAAGGGTGACACGACTCCTACGTGATGAGGAGGTATAGTCGGTGGATGACACAGTTCCTACG
* * * * *
318294 TGATGAGGATGGTAGGCCATCTTTAGGGATGATAGCACGGTTCCTACGTGATGAGTACGACTGGT
66 TGATGAGGAAGGTAGGCCATCTTTAGGGATGATAACACGGTTCCTACGCGATGAGGACGACTGAT
318359 T
131 T
* * * *
318360 A-CTAAGGGTGACACGACTCCTACGTGATGAGGTGGTATGGTCGGTGGATGACACAGTTCCCA-A
1 ATCTAAGGGTGACACGACTCCTACGTGATGAGGAGGTATAGTCGGTGGATGACACAGTTCCTACG
*
318423 TCGATGA-GAACGGTATGCCATCTTTAGGGAT
66 T-GATGAGGAA-GGTAGGCCATCTTTAGGGAT
318454 AATGTTTCAT
Statistics
Matches: 189, Mismatches: 34, Indels: 8
0.82 0.15 0.03
Matches are distributed among these distances:
129 3 0.02
130 77 0.41
131 33 0.17
134 76 0.40
ACGTcount: A:0.26, C:0.18, G:0.30, T:0.26
Consensus pattern (131 bp):
ATCTAAGGGTGACACGACTCCTACGTGATGAGGAGGTATAGTCGGTGGATGACACAGTTCCTACG
TGATGAGGAAGGTAGGCCATCTTTAGGGATGATAACACGGTTCCTACGCGATGAGGACGACTGAT
T
Found at i:318785 original size:65 final size:66
Alignment explanation
Indices: 318576--318819 Score: 364
Period size: 65 Copynumber: 3.7 Consensus size: 66
318566 TATCTCCTAG
* * *
318576 AGAAATTGTCTCAAGAGAAACAAAACTTTGTTTCCAGAGAAACAGTCTCAAAGATTTTTTTTCTT
1 AGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCCAGAGAAACAGACTCAAAG---TTTTTTCTT
318641 CAAA
63 CAAA
* * * * *
318645 AGAAACTGTCTCAAGAGAGACAAAATTTTGTTTTCAAAGAAACATACTCAAAGATTTTTCTTCAA
1 AGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCCAGAGAAACAGACTCAAAGTTTTTTCTTCAA
318710 A
66 A
318711 AGAAACTGTCTCAAGAGAGACAAAACTTT-TTTCCAGAGAAACAGACTCAAAGTTTTTTCTTCAA
1 AGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCCAGAGAAACAGACTCAAAGTTTTTTCTTCAA
318775 A
66 A
* *
318776 AGAAACTGTCTCAAGAGATACAAAACTTTGTTTCAAGAGAAACA
1 AGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCCAGAGAAACA
318820 ATTTCAAAGT
Statistics
Matches: 159, Mismatches: 15, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
65 60 0.38
66 53 0.33
69 46 0.29
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (66 bp):
AGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCCAGAGAAACAGACTCAAAGTTTTTTCTTCAA
A
Found at i:318844 original size:131 final size:133
Alignment explanation
Indices: 318576--318844 Score: 386
Period size: 131 Copynumber: 2.0 Consensus size: 133
318566 TATCTCCTAG
* *
318576 AGAAATTGTCTCAAGAGAAACAAAACTTTGTTTCCAGAGAAACAGTCTCAAAGATTTTTTTTCTT
1 AGAAACTGTCTCAAGAGAAACAAAACTTTGTTTCCAGAGAAACAGACTCAAAG--TTTTTTTCTT
* *
318641 CAAAAGAAACTGTCTCAAGAGAGACAAAATTTTGTTTTCAAAGAAACATACTCAAAGATTTTTCT
64 CAAAAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTTCAAAGAAACATACTCAAAGATTTGTCT
*
318706 TCAAA
129 TAAAA
*
318711 AGAAACTGTCTCAAGAGAGACAAAACTTT-TTTCCAGAGAAACAGACTCAAAG-TTTTTTCTTCA
1 AGAAACTGTCTCAAGAGAAACAAAACTTTGTTTCCAGAGAAACAGACTCAAAGTTTTTTTCTTCA
* *
318774 AAAGAAACTGTCTCAAGAGATACAAAACTTTG-TTTCAAGAGAAACA-ATTTCAAAG-TTTGTCT
66 AAAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTTCAA-AGAAACATA-CTCAAAGATTTGTCT
318836 TAAGAA
129 TAA-AA
318842 AGA
1 AGA
318845 TTGTCTCAAG
Statistics
Matches: 123, Mismatches: 8, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
130 15 0.12
131 59 0.48
134 22 0.18
135 27 0.22
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (133 bp):
AGAAACTGTCTCAAGAGAAACAAAACTTTGTTTCCAGAGAAACAGACTCAAAGTTTTTTTCTTCA
AAAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTTCAAAGAAACATACTCAAAGATTTGTCTTA
AAA
Found at i:318861 original size:66 final size:66
Alignment explanation
Indices: 318576--318831 Score: 349
Period size: 66 Copynumber: 3.8 Consensus size: 66
318566 TATCTCCTAG
* * * *
318576 AGAAATTGTCTCAAGAGAAACAAAACTTTGTTTCCAGAGAAACAGTCTCAAAGATTTTTTTTCTT
1 AGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACAATCTCAAAG---TTTTTTCTT
318641 CAAA
63 CAAA
* *
318645 AGAAACTGTCTCAAGAGAGACAAAATTTTGTTTTCAA-AGAAAC-ATACTCAAAGATTTTTCTTC
1 AGAAACTGTCTCAAGAGAGACAAAACTTTG-TTTCAAGAGAAACAAT-CTCAAAGTTTTTTCTTC
318708 AAA
64 AAA
*
318711 AGAAACTGTCTCAAGAGAGACAAAACTTT-TTTCCAGAGAAACAGA-CTCAAAGTTTTTTCTTCA
1 AGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACA-ATCTCAAAGTTTTTTCTTCA
318774 AA
65 AA
* *
318776 AGAAACTGTCTCAAGAGATACAAAACTTTGTTTCAAGAGAAACAATTTCAAAGTTT
1 AGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACAATCTCAAAGTTT
318832 GTCTTAAGAA
Statistics
Matches: 168, Mismatches: 12, Indels: 17
0.85 0.06 0.09
Matches are distributed among these distances:
64 5 0.03
65 54 0.32
66 62 0.37
67 1 0.01
68 1 0.01
69 40 0.24
70 5 0.03
ACGTcount: A:0.41, C:0.16, G:0.13, T:0.30
Consensus pattern (66 bp):
AGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACAATCTCAAAGTTTTTTCTTCAA
A
Found at i:319002 original size:40 final size:37
Alignment explanation
Indices: 318942--319059 Score: 112
Period size: 40 Copynumber: 3.1 Consensus size: 37
318932 TATCTCAAAG
* *
318942 GAAAAATGTCTCAAGTGAGACAAAATTTGTTTTGAGA
1 GAAAACTGTCTCAAGCGAGACAAAATTTGTTTTGAGA
* ** * * * *
318979 TAAATTGTTTGTCTCAAGCGAGACCATATTTATTTTTAGA
1 GAAA---ACTGTCTCAAGCGAGACAAAATTTGTTTTGAGA
*
319019 GAAAACTGTCTCAAGCGAGATAAAATTTGTTTTGAG-
1 GAAAACTGTCTCAAGCGAGACAAAATTTGTTTTGAGA
319055 GAAAA
1 GAAAA
319060 AAAACCTCAA
Statistics
Matches: 62, Mismatches: 16, Indels: 7
0.73 0.19 0.08
Matches are distributed among these distances:
36 5 0.08
37 28 0.45
40 29 0.47
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.33
Consensus pattern (37 bp):
GAAAACTGTCTCAAGCGAGACAAAATTTGTTTTGAGA
Found at i:319407 original size:16 final size:16
Alignment explanation
Indices: 319386--319424 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
319376 TTCATGTATC
319386 ATGTATGTGTGTGTTG
1 ATGTATGTGTGTGTTG
*
319402 ATGTATGTTTGTGTTG
1 ATGTATGTGTGTGTTG
319418 ATGTATG
1 ATGTATG
319425 CTTTTCGATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.15, C:0.00, G:0.33, T:0.51
Consensus pattern (16 bp):
ATGTATGTGTGTGTTG
Found at i:323103 original size:18 final size:18
Alignment explanation
Indices: 323067--323104 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
323057 AAAAATAAAT
**
323067 AAATGAGTTAGTATGAAC
1 AAATGAGTTAGTACAAAC
323085 AAATGAGTTAGTACAAAC
1 AAATGAGTTAGTACAAAC
323103 AA
1 AA
323105 GATAATCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.50, C:0.08, G:0.18, T:0.24
Consensus pattern (18 bp):
AAATGAGTTAGTACAAAC
Found at i:324034 original size:19 final size:22
Alignment explanation
Indices: 323993--324035 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
323983 TCATAACCAT
323993 TTTTTGAAACAATTAAAATATTA
1 TTTTTGAAACAA-TAAAATATTA
324016 TTTTT-AAACAA-AAAA-ATTA
1 TTTTTGAAACAATAAAATATTA
324035 T
1 T
324036 GACTTTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
19 5 0.25
20 4 0.20
22 6 0.30
23 5 0.25
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (22 bp):
TTTTTGAAACAATAAAATATTA
Found at i:325700 original size:18 final size:16
Alignment explanation
Indices: 325664--325696 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
325654 ACCTCCCTTA
325664 ACCCGAAAACCACCCC
1 ACCCGAAAACCACCCC
325680 ACCCAGAAAACCACCCC
1 ACCC-GAAAACCACCCC
325697 CACCTAGCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.39, C:0.55, G:0.06, T:0.00
Consensus pattern (16 bp):
ACCCGAAAACCACCCC
Found at i:326825 original size:3 final size:3
Alignment explanation
Indices: 326819--326870 Score: 68
Period size: 3 Copynumber: 17.3 Consensus size: 3
326809 AAATAATTAT
* * * *
326819 TAA TAA TAA CAA TAA CAA TAA CAA CAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
326867 TAA T
1 TAA T
326871 TTTTTTAGAT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (3 bp):
TAA
Found at i:328750 original size:22 final size:22
Alignment explanation
Indices: 328725--328766 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
328715 CGAATTAAGT
*
328725 GGATGATGATGGTCTTGATGAA
1 GGATGATCATGGTCTTGATGAA
* *
328747 GGATGTTCATGGTGTTGATG
1 GGATGATCATGGTCTTGATG
328767 TTGAAATGGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.21, C:0.05, G:0.38, T:0.36
Consensus pattern (22 bp):
GGATGATCATGGTCTTGATGAA
Found at i:334564 original size:9 final size:9
Alignment explanation
Indices: 334552--334578 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
334542 CATTATAGCT
334552 ATATATGTA
1 ATATATGTA
334561 ATATATGTA
1 ATATATGTA
334570 ATATATGTA
1 ATATATGTA
334579 TATGAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (9 bp):
ATATATGTA
Found at i:336006 original size:30 final size:30
Alignment explanation
Indices: 335972--336028 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
335962 ATATATTGAC
335972 TTTATCCTTTACTTTTT-TTA-TTTATATGTT
1 TTTAT-CTTT-CTTTTTATTATTTTATATGTT
*
336002 TTTATCTTTTTTTTTATTATTTTATAT
1 TTTATCTTTCTTTTTATTATTTTATAT
336029 TGTAATTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 5 0.21
29 7 0.29
30 12 0.50
ACGTcount: A:0.18, C:0.07, G:0.02, T:0.74
Consensus pattern (30 bp):
TTTATCTTTCTTTTTATTATTTTATATGTT
Found at i:339866 original size:20 final size:21
Alignment explanation
Indices: 339814--339874 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
339804 TTCCACTGTG
339814 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
*
339837 GGGGGAATCGGTTCCCTC-AT
1 GGGGGAATCGGTTCCCTCAAA
* *
339857 GGGGGTATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
339875 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 17 0.49
21 2 0.06
22 3 0.09
23 13 0.37
ACGTcount: A:0.16, C:0.26, G:0.33, T:0.25
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:346697 original size:94 final size:93
Alignment explanation
Indices: 346522--346804 Score: 321
Period size: 90 Copynumber: 3.1 Consensus size: 93
346512 GTAGACCCTC
* * *
346522 AAAATTTGTAACGGGTCCACATATTCCGT-TACAAAATTTAGAGTTTTTTTTCTAATTACCCGCT
1 AAAATTTGTGACGGGTCCACATGTTCCGTCT-CAAAATTTAGAG--TTTTTT-TAATTACCCTCT
346586 CATTTCCTCCAA--TTCCATCCATTAAAACAT
62 CATTTCCTCCAATTTTCCATCCATTAAAACAT
346616 AAAATTTGTGACGGGTCCACATGTTCC-TCTCAAAATTTAGAG-TTTTTTAATTACCCTCTCATT
1 AAAATTTGTGACGGGTCCACATGTTCCGTCTCAAAATTTAGAGTTTTTTTAATTACCCTCTCATT
*
346679 TCCTCCAATTTTCC-TCCATTGAAACAT
66 TCCTCCAATTTTCCATCCATTAAAACAT
* ** * * * * * *
346706 AGAATTTGTGATAGATTCACATGCTCCGTCACAAAATTTAGAGGTTTTTTTACTT-TCCTCTCAT
1 AAAATTTGTGACGGGTCCACATGTTCCGTCTCAAAATTTAGA-GTTTTTTTAATTACCCTCTCAT
* * *
346770 TTCCTCCAA-TTTCCCTCCACTGAAACAT
65 TTCCTCCAATTTTCCATCCATTAAAACAT
346798 AAAATTT
1 AAAATTT
346805 CAAACATACC
Statistics
Matches: 167, Mismatches: 15, Indels: 16
0.84 0.08 0.08
Matches are distributed among these distances:
89 23 0.14
90 38 0.23
91 22 0.13
92 36 0.22
93 22 0.13
94 26 0.16
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.38
Consensus pattern (93 bp):
AAAATTTGTGACGGGTCCACATGTTCCGTCTCAAAATTTAGAGTTTTTTTAATTACCCTCTCATT
TCCTCCAATTTTCCATCCATTAAAACAT
Found at i:346727 original size:90 final size:92
Alignment explanation
Indices: 346522--346804 Score: 315
Period size: 92 Copynumber: 3.1 Consensus size: 92
346512 GTAGACCCTC
* * * ** * *
346522 AAAATTTGTAACGGGTCCACATATTCCGTTACAAAATTTAGAGTTTTTTTTCTAATTACCCGCTC
1 AAAATTTGTGACAGATCCACATGCTCCGTCACAAAATTTAGAG--TTTTTT-TAATTACCCTCTC
*
346587 ATTTCCTCCAA--TTCCATCCATTAAAACAT
63 ATTTCCTCCAATTTTCC-TCCATTGAAACAT
* * * *
346616 AAAATTTGTGACGGGTCCACATGTTCC-TCTCAAAATTTAGAG-TTTTTTAATTACCCTCTCATT
1 AAAATTTGTGACAGATCCACATGCTCCGTCACAAAATTTAGAGTTTTTTTAATTACCCTCTCATT
346679 TCCTCCAATTTTCCTCCATTGAAACAT
66 TCCTCCAATTTTCCTCCATTGAAACAT
* * * * *
346706 AGAATTTGTGATAGATTCACATGCTCCGTCACAAAATTTAGAGGTTTTTTTACTT-TCCTCTCAT
1 AAAATTTGTGACAGATCCACATGCTCCGTCACAAAATTTAGA-GTTTTTTTAATTACCCTCTCAT
* *
346770 TTCCTCCAATTTCCCTCCACTGAAACAT
65 TTCCTCCAATTTTCCTCCATTGAAACAT
346798 AAAATTT
1 AAAATTT
346805 CAAACATACC
Statistics
Matches: 166, Mismatches: 18, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
89 23 0.14
90 38 0.23
91 17 0.10
92 41 0.25
93 22 0.13
94 25 0.15
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.38
Consensus pattern (92 bp):
AAAATTTGTGACAGATCCACATGCTCCGTCACAAAATTTAGAGTTTTTTTAATTACCCTCTCATT
TCCTCCAATTTTCCTCCATTGAAACAT
Found at i:347294 original size:124 final size:124
Alignment explanation
Indices: 347175--347411 Score: 332
Period size: 124 Copynumber: 1.9 Consensus size: 124
347165 AAAAAATCAT
* ** * **
347175 TTTTAGAA-AAAGTATTTTCAATTTGTGATGGAATTTGTGGACCCATCACAAATTTCTGACTGAT
1 TTTTAGAACAAAGTATTTTAAATTTGTGATAAAATTTGTGGACCCATCACAAATTTCTAACAAAT
* ***
347239 CCACCTATTCTGTCACAAATTTGTGATGGGTCTACATGTTCCGTCACAAAAAAAAAAAA
66 CCACCTATTCCGTCACAAATTTGTGACAAGTCTACATGTTCCGTCACAAAAAAAAAAAA
* * * *
347298 TTTTAGAACAAATTATTTTAAATTTGTGATAAAATTTGTGGACTCGTCACAATTTTCTAACAAAT
1 TTTTAGAACAAAGTATTTTAAATTTGTGATAAAATTTGTGGACCCATCACAAATTTCTAACAAAT
*
347363 CCATCTATTCCGTCACAAATTTGTGACAAGTCTACATGTTCCGTCACAA
66 CCACCTATTCCGTCACAAATTTGTGACAAGTCTACATGTTCCGTCACAA
347412 TTTTTTGGAG
Statistics
Matches: 98, Mismatches: 15, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
123 8 0.08
124 90 0.92
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.35
Consensus pattern (124 bp):
TTTTAGAACAAAGTATTTTAAATTTGTGATAAAATTTGTGGACCCATCACAAATTTCTAACAAAT
CCACCTATTCCGTCACAAATTTGTGACAAGTCTACATGTTCCGTCACAAAAAAAAAAAA
Found at i:347377 original size:31 final size:31
Alignment explanation
Indices: 347342--347415 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 31
347332 TTTGTGGACT
347342 CGTCACAATTTTCTAACAAATCCATC-TATTC
1 CGTCACAATTTTCTAACAAATCCA-CATATTC
* * * * * *
347373 CGTCACAAATTTGTGACAAGTCTACATGTTC
1 CGTCACAATTTTCTAACAAATCCACATATTC
347404 CGTCACAATTTT
1 CGTCACAATTTT
347416 TTGGAGGGTT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
30 1 0.03
31 34 0.97
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.35
Consensus pattern (31 bp):
CGTCACAATTTTCTAACAAATCCACATATTC
Found at i:359456 original size:23 final size:24
Alignment explanation
Indices: 359407--359456 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
359397 GCAATTTTTC
* * *
359407 TTTTTTTAATCACTAACCTTTTTA
1 TTTTTTTAATCACTAAACATTTGA
*
359431 TTTTTTTATTCA-TAAACATTTGA
1 TTTTTTTAATCACTAAACATTTGA
359454 TTT
1 TTT
359457 GACCTTGCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 11 0.50
24 11 0.50
ACGTcount: A:0.26, C:0.12, G:0.02, T:0.60
Consensus pattern (24 bp):
TTTTTTTAATCACTAAACATTTGA
Found at i:360130 original size:14 final size:15
Alignment explanation
Indices: 360113--360145 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
360103 CTTTACCCTC
*
360113 AAAATAT-ATATTTT
1 AAAATATAATATTGT
360127 AAAATATAATATTGT
1 AAAATATAATATTGT
360142 AAAA
1 AAAA
360146 CATTTTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 7 0.41
15 10 0.59
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (15 bp):
AAAATATAATATTGT
Found at i:361739 original size:24 final size:24
Alignment explanation
Indices: 361712--361766 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
361702 GTACACGAAG
* * *
361712 GCACTGATACAGGAGTGGATATTT
1 GCACTAATACAGAAGTGCATATTT
* *
361736 GCACAAATACAGAAGTGCATGTTT
1 GCACTAATACAGAAGTGCATATTT
361760 GCACTAA
1 GCACTAA
361767 CATATGATCA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (24 bp):
GCACTAATACAGAAGTGCATATTT
Found at i:368124 original size:64 final size:63
Alignment explanation
Indices: 368049--368168 Score: 177
Period size: 64 Copynumber: 1.9 Consensus size: 63
368039 ATTGTTCAAG
* * *
368049 GTGTATCGATGCACATGAAGTGCATCGATGCACTCCTTTAAAATAAAAACATCGAATGCCATCA
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCTT-AAATAAAAACATCGAATGCCATCA
* **
368113 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAATGGAAACATCGAAT
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCTTAAATAAAAACATCGAAT
368169 AGGATTTATG
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
63 15 0.30
64 35 0.70
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (63 bp):
GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCTTAAATAAAAACATCGAATGCCATCA
Found at i:377881 original size:17 final size:17
Alignment explanation
Indices: 377861--377910 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
377851 TTTACGGAAG
377861 TAGTTCATTAATTAAAC
1 TAGTTCATTAATTAAAC
* *
377878 TAGTTCATTCATCAAAC
1 TAGTTCATTAATTAAAC
*
377895 TAGTTCATTTATTAAA
1 TAGTTCATTAATTAAA
377911 TTAACTCTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.38, C:0.14, G:0.06, T:0.42
Consensus pattern (17 bp):
TAGTTCATTAATTAAAC
Found at i:378740 original size:20 final size:20
Alignment explanation
Indices: 378715--378759 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
378705 ACTTTATCGG
378715 CTTCAAGATAGTCTTGTAGT
1 CTTCAAGATAGTCTTGTAGT
378735 CTTCAAGATAGTCTTGTAGT
1 CTTCAAGATAGTCTTGTAGT
378755 CTTCA
1 CTTCA
378760 TCCATTTCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40
Consensus pattern (20 bp):
CTTCAAGATAGTCTTGTAGT
Found at i:384065 original size:17 final size:17
Alignment explanation
Indices: 384045--384084 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
384035 AGGGAAGTAT
384045 TTCATTAATCAAACTAG
1 TTCATTAATCAAACTAG
*
384062 TTCATTCATCAAACTAG
1 TTCATTAATCAAACTAG
384079 TTCATT
1 TTCATT
384085 TATTAAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.35, C:0.20, G:0.05, T:0.40
Consensus pattern (17 bp):
TTCATTAATCAAACTAG
Done.