Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015299.1 Kokia drynarioides strain JFW-HI SEQ_130344, 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: 1333876
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 300 characters in sequence are not A, C, G, or T
File 2 of 4
Found at i:305739 original size:14 final size:13
Alignment explanation
Indices: 305697--305739 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
305687 TTTTTGGAAA
305697 AAAGTCAACGGTC
1 AAAGTCAACGGTC
305710 AAAGTCAACGGATC
1 AAAGTCAACGG-TC
*
305724 AATGTTCAACGGTC
1 AAAG-TCAACGGTC
305738 AA
1 AA
305740 CGGTCGGCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 11 0.41
14 9 0.33
15 7 0.26
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.19
Consensus pattern (13 bp):
AAAGTCAACGGTC
Found at i:305836 original size:47 final size:47
Alignment explanation
Indices: 305768--305870 Score: 190
Period size: 47 Copynumber: 2.2 Consensus size: 47
305758 TTGGTTTAGA
*
305768 TTTGGGT-TTGGGCTTTGTTCAATTGGTCAAAAAGTTTGGGTATTTG
1 TTTGGGTATTGGGCTTTGTTCAATTGGTCAAAAAGTTTGGGTATTGG
305814 TTTGGGTATTGGGCTTTGTTCAATTGGTCAAAAAGTTTGGGTATTGG
1 TTTGGGTATTGGGCTTTGTTCAATTGGTCAAAAAGTTTGGGTATTGG
305861 TTTGGGTATT
1 TTTGGGTATT
305871 AAGGGTTTAC
Statistics
Matches: 55, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
46 7 0.13
47 48 0.87
ACGTcount: A:0.17, C:0.06, G:0.31, T:0.46
Consensus pattern (47 bp):
TTTGGGTATTGGGCTTTGTTCAATTGGTCAAAAAGTTTGGGTATTGG
Found at i:313410 original size:23 final size:23
Alignment explanation
Indices: 313379--313459 Score: 63
Period size: 23 Copynumber: 3.5 Consensus size: 23
313369 GAAACAGGAT
313379 TGACGTCCCGACGACGCGACACG
1 TGACGTCCCGACGACGCGACACG
* * * *
313402 TGACTTCCCGATGACGTGACACA
1 TGACGTCCCGACGACGCGACACG
* * * * **
313425 CGACGTCCTGACAATGCGACGTG
1 TGACGTCCCGACGACGCGACACG
*
313448 TGATGTCCCGAC
1 TGACGTCCCGAC
313460 AAGTCGAAAA
Statistics
Matches: 41, Mismatches: 17, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.22, C:0.33, G:0.27, T:0.17
Consensus pattern (23 bp):
TGACGTCCCGACGACGCGACACG
Found at i:316729 original size:97 final size:96
Alignment explanation
Indices: 316554--316736 Score: 237
Period size: 97 Copynumber: 1.9 Consensus size: 96
316544 AAGGATGTTA
* ** * *
316554 GATTATCTCGATTTGAGGAAAGGTTGCACCTAGTAAGTTAAGGCGTAAATTTTCAGAATCGAAGA
1 GATTATCTCGATTTGAGAAAAAATTGCACCTAATAAGTTAAGGCGCAAATTTTCAGAATCGAAGA
*
316619 TAAGTAAACATTGCCTCGATTAAGGGTATTC
66 TAAGAAAACATTGCCTCGATTAAGGGTATTC
*
316650 GATTATTTCGATTTGAAGAAAAAATTGCACCTAATAAGTTAAGGCGCAAATTTTC-GAAACTCGA
1 GATTATCTCGATTTG-AGAAAAAATTGCACCTAATAAGTTAAGGCGCAAATTTTCAG-AA-TCGA
*
316714 A-ATAA-AAGAATATTGCCTCGATT
63 AGATAAGAA-AACATTGCCTCGATT
316737 TTAAAGTTTT
Statistics
Matches: 75, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
96 16 0.21
97 54 0.72
98 5 0.07
ACGTcount: A:0.37, C:0.14, G:0.20, T:0.30
Consensus pattern (96 bp):
GATTATCTCGATTTGAGAAAAAATTGCACCTAATAAGTTAAGGCGCAAATTTTCAGAATCGAAGA
TAAGAAAACATTGCCTCGATTAAGGGTATTC
Found at i:317055 original size:57 final size:58
Alignment explanation
Indices: 316977--317123 Score: 156
Period size: 57 Copynumber: 2.6 Consensus size: 58
316967 GAAATGGTAA
* * *
316977 TTTTAGAT-TCTCGAGGGTAAAATGGTAATTTTAGGAAATTTTGGGGTT-AAAAGGGAAT
1 TTTTAGATAT-TCGAGGGTAAAATGGTAATTTTAAG-AATTTCGAGGTTGAAAAGGGAAT
* * * * *
317035 TTTTAGATATTCG-GGGTAAAAAGGTAATTTCAAGAGTTTCGAGGTTGAAAATGGAGT
1 TTTTAGATATTCGAGGGTAAAATGGTAATTTTAAGAATTTCGAGGTTGAAAAGGGAAT
* * *
317092 TTTTGGATATCCGAGGGCAAAATGGTAATTTT
1 TTTTAGATATTCGAGGGTAAAATGGTAATTTT
317124 TTAAAGTTTT
Statistics
Matches: 73, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
56 9 0.12
57 37 0.51
58 26 0.36
59 1 0.01
ACGTcount: A:0.32, C:0.05, G:0.27, T:0.35
Consensus pattern (58 bp):
TTTTAGATATTCGAGGGTAAAATGGTAATTTTAAGAATTTCGAGGTTGAAAAGGGAAT
Found at i:317075 original size:28 final size:27
Alignment explanation
Indices: 316972--317075 Score: 84
Period size: 28 Copynumber: 3.7 Consensus size: 27
316962 GGGGCGAAAT
*
316972 GGTAATTTT-AGATTCTCGAGGGTAAAAT
1 GGTAATTTTAAGATT-TCG-GGGTAAAAA
* * *
317000 GGTAATTTTAGGAAATTTTGGGGTTAAAA
1 GGTAATTTTA--AGATTTCGGGGTAAAAA
* *
317029 GGGAATTTTTAGATATTCGGGGTAAAAA
1 GGTAATTTTAAGAT-TTCGGGGTAAAAA
*
317057 GGTAATTTCAAGAGTTTCG
1 GGTAATTTTAAGA-TTTCG
317076 AGGTTGAAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
27 3 0.05
28 34 0.58
29 16 0.27
30 2 0.03
31 4 0.07
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.36
Consensus pattern (27 bp):
GGTAATTTTAAGATTTCGGGGTAAAAA
Found at i:317214 original size:59 final size:56
Alignment explanation
Indices: 317127--317322 Score: 178
Period size: 59 Copynumber: 3.3 Consensus size: 56
317117 TAATTTTTTA
* ** * *
317127 AAGTTTTGGGGTCAAAAATGAAAATTTTGGAGGTTCGAGGGTAAAAAATGGAATTTCTGG
1 AAGTTTTAGGGTCAAAAATG-GGATTTTGGAAGTTAG-GGGT-AAAAATGGAATTT-TGG
* * * * *
317187 AAGTTTTTGGGCCAAAAATGGGATTTTGGAAATTTTGGGGTCAAAAATGAGACTTTTGG
1 AAGTTTTAGGGTCAAAAATGGGATTTTGG-AAGTTAGGGGT-AAAAATG-GAATTTTGG
* *
317246 AAGTTTCAGGGTCAAAAATGGGATTTTTTGAAGTTAGGGGTAAAAATGGAATTTTTGG
1 AAGTTTTAGGGTCAAAAATGGGA-TTTTGGAAGTTAGGGGTAAAAATGGAA-TTTTGG
*
317304 AAG-TTTCGAGGTCAAAAAT
1 AAGTTTTAG-GGTCAAAAAT
317323 TGAATTTTTT
Statistics
Matches: 113, Mismatches: 18, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
57 5 0.04
58 26 0.23
59 50 0.44
60 32 0.28
ACGTcount: A:0.34, C:0.06, G:0.29, T:0.32
Consensus pattern (56 bp):
AAGTTTTAGGGTCAAAAATGGGATTTTGGAAGTTAGGGGTAAAAATGGAATTTTGG
Found at i:317331 original size:30 final size:30
Alignment explanation
Indices: 317069--317331 Score: 168
Period size: 30 Copynumber: 8.9 Consensus size: 30
317059 TAATTTCAAG
** *
317069 AGTTTCGAGGTTGAAAATGGAGTTTTTGG-
1 AGTTTCGAGGTCAAAAATGGAATTTTTGGA
* * **
317098 A-TATCCGAGGGC-AAAATGGTAATTTTTTAA
1 AGT-TTCGAGGTCAAAAATGG-AATTTTTGGA
* * * *
317128 AGTTTTGGGGTCAAAAATGAAAATTTTGG-
1 AGTTTCGAGGTCAAAAATGGAATTTTTGGA
* * *
317157 AGGTTCGAGGGTAAAAAATGGAATTTCTGGA
1 AGTTTCGA-GGTCAAAAATGGAATTTTTGGA
* * *
317188 AGTTTTTG-GGCCAAAAATGGGA-TTTTGGA
1 AG-TTTCGAGGTCAAAAATGGAATTTTTGGA
* * * *
317217 AATTTTGGGGTCAAAAAT-GAGACTTTTGGA
1 AGTTTCGAGGTCAAAAATGGA-ATTTTTGGA
* *
317247 AGTTTC-AGGGTCAAAAATGGGATTTTTTGA
1 AGTTTCGA-GGTCAAAAATGGAATTTTTGGA
* *
317277 AG-TTAGGGGT-AAAAATGGAATTTTTGGA
1 AGTTTCGAGGTCAAAAATGGAATTTTTGGA
*
317305 AGTTTCGAGGTCAAAAATTGAATTTTT
1 AGTTTCGAGGTCAAAAATGGAATTTTT
317332 TGACGGATTA
Statistics
Matches: 175, Mismatches: 43, Indels: 31
0.70 0.17 0.12
Matches are distributed among these distances:
28 32 0.18
29 46 0.26
30 84 0.48
31 10 0.06
32 3 0.02
ACGTcount: A:0.32, C:0.06, G:0.28, T:0.34
Consensus pattern (30 bp):
AGTTTCGAGGTCAAAAATGGAATTTTTGGA
Found at i:317333 original size:89 final size:88
Alignment explanation
Indices: 317110--317331 Score: 225
Period size: 89 Copynumber: 2.5 Consensus size: 88
317100 ATCCGAGGGC
**
317110 AAAATGGTAATTTTTTAAAGTTTTGGGGTCAAAAATGAAAATTTTGGAGGTTCGAGGGTAAAAAA
1 AAAATGG-AATTTTTGGAAGTTTTGGGGTCAAAAATG-AAATTTTGGAGGTTCGAGGGTAAAAAA
*
317175 TGGAATTTCTGGAAGTTTTTGGGCCA
64 TGGAATTTCTGGAAG-TTTAGGGCCA
* * * * *
317201 AAAATGGGA-TTTTGGAAATTTTGGGGTCAAAAATGAGACTTTTGGAAGTTTC-AGGGTCAAAAA
1 AAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGA-AATTTTGG-AGGTTCGAGGGTAAAAAA
* * * **
317264 TGGGATTTTTTGAAG-TTAGGGGTA
64 TGGAATTTCTGGAAGTTTAGGGCCA
* * *
317288 AAAATGGAATTTTTGGAAGTTTCGAGGTCAAAAATTGAATTTTT
1 AAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAA-TGAAATTTT
317332 TGACGGATTA
Statistics
Matches: 109, Mismatches: 18, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
87 14 0.13
88 27 0.25
89 55 0.50
90 6 0.06
91 7 0.06
ACGTcount: A:0.34, C:0.05, G:0.27, T:0.35
Consensus pattern (88 bp):
AAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGAAATTTTGGAGGTTCGAGGGTAAAAAATG
GAATTTCTGGAAGTTTAGGGCCA
Found at i:318401 original size:3 final size:3
Alignment explanation
Indices: 318395--318485 Score: 60
Period size: 3 Copynumber: 30.0 Consensus size: 3
318385 TTCGATTTTT
* * *
318395 TTA TTA TTA TTA ATA TCTA TTA TTA TTA TTA -TA TTA TTA ATA ATA
1 TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * *
318440 TTAA TTA -TA GTTG TCA TTA ATA TTG TTA TGA TCA TTA TTA TTA TTA
1 TT-A TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
318486 AGTTAATGTT
Statistics
Matches: 68, Mismatches: 15, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
2 4 0.06
3 57 0.84
4 7 0.10
ACGTcount: A:0.36, C:0.03, G:0.04, T:0.56
Consensus pattern (3 bp):
TTA
Found at i:319157 original size:10 final size:10
Alignment explanation
Indices: 319142--319202 Score: 68
Period size: 10 Copynumber: 5.8 Consensus size: 10
319132 ATTGGACATT
319142 ATTTAAATAA
1 ATTTAAATAA
319152 ATTTAAATTTAA
1 ATTTAAA--TAA
319164 ATTTATAATAA
1 ATTTA-AATAA
**
319175 ATTTAAATTT
1 ATTTAAATAA
*
319185 ATTCAAATAA
1 ATTTAAATAA
319195 ATTTAAAT
1 ATTTAAAT
319203 TTAAAATAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
10 24 0.57
11 8 0.19
12 8 0.19
13 2 0.05
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (10 bp):
ATTTAAATAA
Found at i:319160 original size:6 final size:6
Alignment explanation
Indices: 319149--319237 Score: 59
Period size: 6 Copynumber: 16.0 Consensus size: 6
319139 ATTATTTAAA
*
319149 TAAATT TAAATT TAAATT TATAA-- TAAATT TAAATT T--ATT CAAA--
1 TAAATT TAAATT TAAATT TA-AATT TAAATT TAAATT TAAATT TAAATT
* * * * *
319192 TAAATT TAAATT TAAA-A TAAACT TAATTT TAAA-A TAAATT CAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
319238 CTGTTGGGCC
Statistics
Matches: 64, Mismatches: 10, Indels: 18
0.70 0.11 0.20
Matches are distributed among these distances:
4 8 0.12
5 10 0.16
6 44 0.69
7 2 0.03
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (6 bp):
TAAATT
Found at i:319177 original size:17 final size:17
Alignment explanation
Indices: 319155--319237 Score: 103
Period size: 17 Copynumber: 4.7 Consensus size: 17
319145 TAAATAAATT
*
319155 TAAATTTAAATTTATAA
1 TAAATTTAAATTTAAAA
319172 TAAATTTAAATTTATTCAAA
1 TAAATTTAAATTTA---AAA
319192 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* *
319209 TAAACTTAATTTTAAAA
1 TAAATTTAAATTTAAAA
*
319226 TAAATTCAAATT
1 TAAATTTAAATT
319238 CTGTTGGGCC
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
17 41 0.72
20 16 0.28
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:319199 original size:37 final size:34
Alignment explanation
Indices: 319155--319237 Score: 103
Period size: 37 Copynumber: 2.4 Consensus size: 34
319145 TAAATAAATT
* * *
319155 TAAATTTAAATTTATAATAAATTTAAATTTATTCAAA
1 TAAATTTAAATTTAAAATAAACTT-AA-TT-TTAAAA
319192 TAAATTTAAATTTAAAATAAACTTAATTTTAAAA
1 TAAATTTAAATTTAAAATAAACTTAATTTTAAAA
*
319226 TAAATTCAAATT
1 TAAATTTAAATT
319238 CTGTTGGGCC
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
34 16 0.38
35 2 0.05
36 2 0.05
37 22 0.52
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (34 bp):
TAAATTTAAATTTAAAATAAACTTAATTTTAAAA
Found at i:321268 original size:22 final size:24
Alignment explanation
Indices: 321242--321286 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 24
321232 AAGCTTTCTC
321242 CTTTTCTTA-TTTC-TCTATTTTT
1 CTTTTCTTATTTTCTTCTATTTTT
*
321264 CTTTTTTTATTTTCTTCTATTTT
1 CTTTTCTTATTTTCTTCTATTTT
321287 GATTCATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 8 0.40
23 4 0.20
24 8 0.40
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.76
Consensus pattern (24 bp):
CTTTTCTTATTTTCTTCTATTTTT
Found at i:322779 original size:6 final size:6
Alignment explanation
Indices: 322768--322805 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
322758 TGCAAGTGGG
*
322768 AATGGC AATGGC AATGGC AATGGC AATGG- AATGAC AAT
1 AATGGC AATGGC AATGGC AATGGC AATGGC AATGGC AAT
322806 CTACACTTGC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
5 4 0.13
6 26 0.87
ACGTcount: A:0.39, C:0.13, G:0.29, T:0.18
Consensus pattern (6 bp):
AATGGC
Found at i:325222 original size:84 final size:84
Alignment explanation
Indices: 325069--325224 Score: 215
Period size: 84 Copynumber: 1.9 Consensus size: 84
325059 GGCTAAAGTG
* * * * * * * *
325069 CAATTTCACAATATATTAATTTATAATTTCTTTATTTATAAGATGGTTGAATTGAAATATTTTTA
1 CAATTTCACAATATATTAATTTATAATTTCTCTATTCATAAAAAGGATGAATTAAAAAATTTATA
325134 TTTTGAGGTAGACAAAATA
66 TTTTGAGGTAGACAAAATA
*
325153 CAATTTCACTATATATTAATTTATAATTTCTCTATTCATAAAAAGGATGAATTAAAAAAATTTAT
1 CAATTTCACAATATATTAATTTATAATTTCTCTATTCATAAAAAGGATGAATT-AAAAAATTTAT
325218 -TTTTGAG
65 ATTTTGAG
325225 AGGGGCCCTA
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
84 54 0.87
85 8 0.13
ACGTcount: A:0.40, C:0.07, G:0.09, T:0.44
Consensus pattern (84 bp):
CAATTTCACAATATATTAATTTATAATTTCTCTATTCATAAAAAGGATGAATTAAAAAATTTATA
TTTTGAGGTAGACAAAATA
Found at i:326112 original size:31 final size:31
Alignment explanation
Indices: 326072--326133 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
326062 CTTAATAACC
* *
326072 TAGTGACTTAAATGAAGACTTTTGAAAAGTT
1 TAGTAACTTAAATGAAAACTTTTGAAAAGTT
* *
326103 TAGTAACTTAAATGAAAATTTTTGAATAGTT
1 TAGTAACTTAAATGAAAACTTTTGAAAAGTT
326134 CAATGACCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.40, C:0.05, G:0.16, T:0.39
Consensus pattern (31 bp):
TAGTAACTTAAATGAAAACTTTTGAAAAGTT
Found at i:326293 original size:18 final size:18
Alignment explanation
Indices: 326270--326307 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
326260 ATATAAAACT
326270 AAGTCCTATTTTTTTTCC
1 AAGTCCTATTTTTTTTCC
326288 AAGTCCTATTTTTTTTCC
1 AAGTCCTATTTTTTTTCC
326306 AA
1 AA
326308 ATCGTTTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.21, G:0.05, T:0.53
Consensus pattern (18 bp):
AAGTCCTATTTTTTTTCC
Found at i:354676 original size:14 final size:14
Alignment explanation
Indices: 354655--354691 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
354645 CTTTGTACCT
354655 ACGCGTTAAAACAA
1 ACGCGTTAAAACAA
*
354669 ATGCGTTAAAACAA
1 ACGCGTTAAAACAA
354683 ACGCGTTAA
1 ACGCGTTAA
354692 GTCGGTGAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.19, G:0.16, T:0.19
Consensus pattern (14 bp):
ACGCGTTAAAACAA
Found at i:354911 original size:21 final size:21
Alignment explanation
Indices: 354880--354934 Score: 85
Period size: 21 Copynumber: 2.6 Consensus size: 21
354870 TAAACGGAAC
354880 TAACAGAAAGTACCAAAGTACT
1 TAACAG-AAGTACCAAAGTACT
354902 T-ACTAGAAGTACCAAAGTACT
1 TAAC-AGAAGTACCAAAGTACT
354923 TAACAGAAGTAC
1 TAACAGAAGTAC
354935 ATAACTGTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
21 26 0.84
22 5 0.16
ACGTcount: A:0.47, C:0.18, G:0.15, T:0.20
Consensus pattern (21 bp):
TAACAGAAGTACCAAAGTACT
Found at i:364240 original size:11 final size:12
Alignment explanation
Indices: 364217--364242 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
364207 TTGAATCTTG
364217 AAATTTAAAAAA
1 AAATTTAAAAAA
364229 AAATTTAAAAAA
1 AAATTTAAAAAA
364241 AA
1 AA
364243 CTAACGACAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (12 bp):
AAATTTAAAAAA
Found at i:365143 original size:30 final size:31
Alignment explanation
Indices: 365109--365180 Score: 78
Period size: 31 Copynumber: 2.4 Consensus size: 31
365099 GTCACATTTA
*
365109 ACAAAATAGTCA-TTCAACTT-T-GAAAATGTG
1 ACAAAATAGTCACTAC-ACTTATCGAAAA-GTG
* *
365139 ACAAAACAGTCACTACAGTTATCGAAAAGTG
1 ACAAAATAGTCACTACACTTATCGAAAAGTG
365170 ACAAAATAGTC
1 ACAAAATAGTC
365181 CTCTTGTTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
30 14 0.40
31 16 0.46
32 5 0.14
ACGTcount: A:0.46, C:0.17, G:0.14, T:0.24
Consensus pattern (31 bp):
ACAAAATAGTCACTACACTTATCGAAAAGTG
Found at i:366136 original size:30 final size:31
Alignment explanation
Indices: 366068--366139 Score: 85
Period size: 30 Copynumber: 2.4 Consensus size: 31
366058 ACAACAAGAA
* * *
366068 GACTATTTTGTCACTTTTCGATAATTTTAGT
1 GACTGTTTTGTCACTTTTCGATAAGTTGAGT
*
366099 GATTGTTTTGTCACATTTTC-A-AAGTTGAGT
1 GACTGTTTTGTCAC-TTTTCGATAAGTTGAGT
366129 GACTGTTTTGT
1 GACTGTTTTGT
366140 TAAATGTAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
30 17 0.49
31 13 0.37
32 5 0.14
ACGTcount: A:0.21, C:0.11, G:0.18, T:0.50
Consensus pattern (31 bp):
GACTGTTTTGTCACTTTTCGATAAGTTGAGT
Found at i:373408 original size:33 final size:33
Alignment explanation
Indices: 373366--373431 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
373356 TATATATGTA
373366 TACATAGACATACATTCTGATTTGATTCTTTAT
1 TACATAGACATACATTCTGATTTGATTCTTTAT
373399 TACATAGACATACATTCTGATTTGATTCTTTAT
1 TACATAGACATACATTCTGATTTGATTCTTTAT
373432 GTATTTTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.30, C:0.15, G:0.09, T:0.45
Consensus pattern (33 bp):
TACATAGACATACATTCTGATTTGATTCTTTAT
Found at i:375642 original size:2 final size:2
Alignment explanation
Indices: 375635--375660 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
375625 GATCAAATTA
375635 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
375661 GTGAATCTAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:376443 original size:2 final size:2
Alignment explanation
Indices: 376436--376466 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
376426 ACATTAAAGC
376436 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
376467 AATTAGTGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:386204 original size:26 final size:25
Alignment explanation
Indices: 386136--386206 Score: 63
Period size: 26 Copynumber: 2.8 Consensus size: 25
386126 TTTAAAAAGT
* *
386136 ATATATTAATTTTAATCTAATTTATA
1 ATATA-TAATTTTAATTTAATTAATA
** *
386162 ATATATAA-TACAGATTTGATATAATA
1 ATATATAATTTTA-ATTTAAT-TAATA
386188 ATATATAATTTTAATTTAA
1 ATATATAATTTTAATTTAA
386207 AAAGATATTG
Statistics
Matches: 34, Mismatches: 8, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
24 2 0.06
25 8 0.24
26 22 0.65
27 2 0.06
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (25 bp):
ATATATAATTTTAATTTAATTAATA
Found at i:387128 original size:26 final size:24
Alignment explanation
Indices: 387082--387130 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 24
387072 AATGAATGAA
387082 ATTTTTAATAAAAAAATTTAATTT
1 ATTTTTAATAAAAAAATTTAATTT
387106 ATTTTTATATAAAAAAATATTAATT
1 ATTTTTA-ATAAAAAAAT-TTAATT
387131 CTAATCAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 7 0.30
25 10 0.43
26 6 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
ATTTTTAATAAAAAAATTTAATTT
Found at i:390545 original size:19 final size:19
Alignment explanation
Indices: 390509--390564 Score: 73
Period size: 18 Copynumber: 3.1 Consensus size: 19
390499 TTTTTTAAAA
390509 TATAAATATTTT-AATTTT
1 TATAAATATTTTGAATTTT
390527 TATAAATATTTTGAA-TTT
1 TATAAATATTTTGAATTTT
*
390545 TAAAAATTATTTTG-ATTTT
1 TATAAA-TATTTTGAATTTT
390564 T
1 T
390565 TTTTGTTGAG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
18 21 0.62
19 13 0.38
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.59
Consensus pattern (19 bp):
TATAAATATTTTGAATTTT
Found at i:393262 original size:3 final size:3
Alignment explanation
Indices: 393254--393281 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
393244 TCATTTCAGA
393254 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG A
393282 TTAGCAGGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:396563 original size:10 final size:10
Alignment explanation
Indices: 396529--396562 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
396519 TTTGAAAACA
*
396529 ATTTTCCCTC
1 ATTTTCTCTC
396539 ATTTTCTCTC
1 ATTTTCTCTC
396549 ATTTTCTCT-
1 ATTTTCTCTC
396558 ATTTT
1 ATTTT
396563 TGAAATGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 5 0.22
10 18 0.78
ACGTcount: A:0.12, C:0.26, G:0.00, T:0.62
Consensus pattern (10 bp):
ATTTTCTCTC
Found at i:403650 original size:20 final size:20
Alignment explanation
Indices: 403609--403651 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
403599 TTGTTTGGAA
**
403609 CTTTTTCCAGGATTCTTGAT
1 CTTTTTCCAGGATTCTCCAT
*
403629 CTTTTTCTAGGATTCTCCAT
1 CTTTTTCCAGGATTCTCCAT
403649 CTT
1 CTT
403652 AAAATATTCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.23, G:0.12, T:0.51
Consensus pattern (20 bp):
CTTTTTCCAGGATTCTCCAT
Found at i:419307 original size:43 final size:43
Alignment explanation
Indices: 419177--419307 Score: 112
Period size: 38 Copynumber: 3.0 Consensus size: 43
419167 AAATTTATAA
* *
419177 AAATTTAATTTAATAATTATCTTAATAA-TATTTTATTAATTTAATCTT
1 AAATTTAATTTAATATTTATTTTAATAAGTA--TTA-T-A-TTAAT-TT
* * *
419225 AAATTTAATTTAATGTTTATTTT-GT-AG-A-TA-AATAATTT
1 AAATTTAATTTAATATTTATTTTAATAAGTATTATATTAATTT
*
419263 AAATTTAATCTAATATTTATTTTAATAAGTATTATATTAATTT
1 AAATTTAATTTAATATTTATTTTAATAAGTATTATATTAATTT
419306 AA
1 AA
419308 TATTAAAGTG
Statistics
Matches: 68, Mismatches: 9, Indels: 17
0.72 0.10 0.18
Matches are distributed among these distances:
38 23 0.34
39 5 0.07
40 3 0.04
41 1 0.01
42 2 0.03
43 11 0.16
46 2 0.03
47 1 0.01
48 20 0.29
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (43 bp):
AAATTTAATTTAATATTTATTTTAATAAGTATTATATTAATTT
Found at i:419767 original size:32 final size:33
Alignment explanation
Indices: 419731--419798 Score: 102
Period size: 32 Copynumber: 2.1 Consensus size: 33
419721 TTGGGATCCA
*
419731 TGTGGGTGGTGGGGCAGGGATGGTTTT-AGTCT
1 TGTGGGTGCTGGGGCAGGGATGGTTTTGAGTCT
* *
419763 TGTGGGTTCTGGGGCAGGGATGGTTTTGAGTTT
1 TGTGGGTGCTGGGGCAGGGATGGTTTTGAGTCT
419796 TGT
1 TGT
419799 ACCCGCAACA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 25 0.78
33 7 0.22
ACGTcount: A:0.09, C:0.06, G:0.47, T:0.38
Consensus pattern (33 bp):
TGTGGGTGCTGGGGCAGGGATGGTTTTGAGTCT
Found at i:420070 original size:41 final size:41
Alignment explanation
Indices: 420020--420136 Score: 148
Period size: 41 Copynumber: 2.9 Consensus size: 41
420010 GCTGTGCTTT
* *
420020 CCCAAAAGCGCTGCTATTGCTCTGACCTTTAGCGGCACTTA
1 CCCATAAGCGCTGTTATTGCTCTGACCTTTAGCGGCACTTA
* * *
420061 CCCATAAGCG-TCGTTATTTCTCTGACCTTTAGCGGCGCTTT
1 CCCATAAGCGCT-GTTATTGCTCTGACCTTTAGCGGCACTTA
* *
420102 CCCATAAGCACTGTTATTGCTCT-ACCTTTTGCGGC
1 CCCATAAGCGCTGTTATTGCTCTGACCTTTAGCGGC
420137 GTTTATATAA
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
40 12 0.18
41 53 0.80
42 1 0.02
ACGTcount: A:0.18, C:0.31, G:0.19, T:0.32
Consensus pattern (41 bp):
CCCATAAGCGCTGTTATTGCTCTGACCTTTAGCGGCACTTA
Found at i:422139 original size:20 final size:21
Alignment explanation
Indices: 422101--422203 Score: 88
Period size: 21 Copynumber: 4.9 Consensus size: 21
422091 ATTATATTGT
*
422101 TGTTTT-GGTGTTGTTTTTTAC
1 TGTTTTAGTTGTT-TTTTTTAC
*
422122 TGTTTTAATTGTTTTTTTGT--
1 TGTTTTAGTTGTTTTTTT-TAC
*
422142 TGTTTTTGTGTTGTTTTTTTTAC
1 TG-TTTT-AGTTGTTTTTTTTAC
*
422165 TGTTTT-GGTGTTTTTTTTAC
1 TGTTTTAGTTGTTTTTTTTAC
* *
422185 TATTTTAGTTGTTGTTTTT
1 TGTTTTAGTTGTTTTTTTT
422204 GTGTTGTTTT
Statistics
Matches: 67, Mismatches: 8, Indels: 14
0.75 0.09 0.16
Matches are distributed among these distances:
20 20 0.30
21 26 0.39
22 19 0.28
23 2 0.03
ACGTcount: A:0.07, C:0.03, G:0.18, T:0.72
Consensus pattern (21 bp):
TGTTTTAGTTGTTTTTTTTAC
Found at i:422140 original size:33 final size:33
Alignment explanation
Indices: 422096--422248 Score: 136
Period size: 33 Copynumber: 4.7 Consensus size: 33
422086 AAAAAATTAT
422096 ATTGTTGTTTTGGTGTTGTTTTTTACTGTTTTA
1 ATTGTTGTTTTGGTGTTGTTTTTTACTGTTTTA
** *
422129 ATTGTT-TTTT--TGTTGTTTTTGTGTTGTTTTT
1 ATTGTTGTTTTGGTGTTGTTTTT-TACTGTTTTA
* ** *
422160 TTTACTGTTTTGGTGTT-TTTTTTACTATTTTA
1 ATTGTTGTTTTGGTGTTGTTTTTTACTGTTTTA
* * **
422192 GTTGTTGTTTTTGTGTTGTTTTTTGTTGCTTTTA
1 ATTGTTGTTTTGGTGTTGTTTTTTACTG-TTTTA
*
422226 A-TGTTGTTTTGCTGTTAGTTTTT
1 ATTGTTGTTTTGGTGTT-GTTTTT
422249 GCTGTTGTTT
Statistics
Matches: 93, Mismatches: 20, Indels: 13
0.74 0.16 0.10
Matches are distributed among these distances:
30 10 0.11
31 10 0.11
32 27 0.29
33 31 0.33
34 15 0.16
ACGTcount: A:0.07, C:0.03, G:0.20, T:0.70
Consensus pattern (33 bp):
ATTGTTGTTTTGGTGTTGTTTTTTACTGTTTTA
Found at i:422144 original size:11 final size:11
Alignment explanation
Indices: 422130--422279 Score: 69
Period size: 11 Copynumber: 13.5 Consensus size: 11
422120 ACTGTTTTAA
422130 TTGTTTTTTTG
1 TTGTTTTTTTG
*
422141 TTGTTTTTGTG
1 TTGTTTTTTTG
422152 TTGTTTTTTT-
1 TTGTTTTTTTG
**
422162 TACTGTTTTGGTG
1 T--TGTTTTTTTG
**
422175 TT-TTTTTTAC
1 TTGTTTTTTTG
**
422185 TAT-TTTAGTTG
1 T-TGTTTTTTTG
*
422196 TTGTTTTTGTG
1 TTGTTTTTTTG
422207 TTG-TTTTTTG
1 TTGTTTTTTTG
**
422217 TTGCTTTTAATG
1 TTG-TTTTTTTG
**
422229 TTGTTTTGCTG
1 TTGTTTTTTTG
422240 TTAG--TTTTTG
1 TT-GTTTTTTTG
* *
422250 CTGTTGTTTTGG
1 TTGTT-TTTTTG
422262 TTGTTATTTTTG
1 TTGTT-TTTTTG
422274 TTGTTT
1 TTGTTT
422280 GGATGCTATT
Statistics
Matches: 101, Mismatches: 27, Indels: 22
0.67 0.18 0.15
Matches are distributed among these distances:
9 1 0.01
10 21 0.21
11 43 0.43
12 35 0.35
13 1 0.01
ACGTcount: A:0.05, C:0.03, G:0.21, T:0.71
Consensus pattern (11 bp):
TTGTTTTTTTG
Found at i:422179 original size:41 final size:41
Alignment explanation
Indices: 422097--422181 Score: 118
Period size: 41 Copynumber: 2.0 Consensus size: 41
422087 AAAAATTATA
*
422097 TTGTTGTTTTGGTGTTGTTTTTTACTGTTTTAATTGTTTTT
1 TTGTTGTTTTGGTGTTGTTTTTTACTGTTTTAAGTGTTTTT
* *
422138 TTGTTGTTTTTGTGTTGTTTTTTTTACTGTTTT-GGTGTTTTT
1 TTGTTGTTTTGGTGTTG--TTTTTTACTGTTTTAAGTGTTTTT
422180 TT
1 TT
422182 TACTATTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
41 16 0.41
42 9 0.23
43 14 0.36
ACGTcount: A:0.05, C:0.02, G:0.20, T:0.73
Consensus pattern (41 bp):
TTGTTGTTTTGGTGTTGTTTTTTACTGTTTTAAGTGTTTTT
Found at i:422202 original size:12 final size:12
Alignment explanation
Indices: 422187--422278 Score: 75
Period size: 12 Copynumber: 7.9 Consensus size: 12
422177 TTTTTTACTA
*
422187 TTTTAGTTGTTG
1 TTTTTGTTGTTG
422199 TTTTTG-TGTTG
1 TTTTTGTTGTTG
422210 -TTTT-TTGTTG
1 TTTTTGTTGTTG
* **
422220 CTTTTAATGTTG
1 TTTTTGTTGTTG
*
422232 -TTTTGCTGTTAG
1 TTTTTGTTGTT-G
*
422244 TTTTTGCTGTTG
1 TTTTTGTTGTTG
* *
422256 TTTTGGTTGTTA
1 TTTTTGTTGTTG
422268 TTTTTGTTGTT
1 TTTTTGTTGTT
422279 TGGATGCTAT
Statistics
Matches: 67, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
10 9 0.13
11 17 0.25
12 31 0.46
13 10 0.15
ACGTcount: A:0.05, C:0.03, G:0.23, T:0.68
Consensus pattern (12 bp):
TTTTTGTTGTTG
Found at i:422203 original size:43 final size:42
Alignment explanation
Indices: 422097--422203 Score: 103
Period size: 43 Copynumber: 2.5 Consensus size: 42
422087 AAAAATTATA
* * *
422097 TTGTTGTTTTGGTGTTG-TTTTTTACTGTTTTAATTGTTTTT
1 TTGTTATTTTAGTGTTGTTTTTTTACTGTTTTAAGTGTTTTT
* * *
422138 TTGTTGTTTTTGTGTTGTTTTTTTTACTGTTTT-GGTGTTTTT
1 TTGTTATTTTAGTGTTG-TTTTTTTACTGTTTTAAGTGTTTTT
422180 TT-TACTATTTTAGTTGTTGTTTTT
1 TTGT--TATTTTAG-TGTTGTTTTT
422204 GTGTTGTTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
41 17 0.30
42 9 0.16
43 25 0.45
44 5 0.09
ACGTcount: A:0.07, C:0.03, G:0.19, T:0.72
Consensus pattern (42 bp):
TTGTTATTTTAGTGTTGTTTTTTTACTGTTTTAAGTGTTTTT
Found at i:422278 original size:24 final size:22
Alignment explanation
Indices: 422098--422274 Score: 82
Period size: 22 Copynumber: 8.0 Consensus size: 22
422088 AAAATTATAT
* *
422098 TGTTGTTTTGGTGTTGTTTTT-
1 TGTTGTTTTGTTGTTATTTTTG
** *
422119 TACTGTTTTAATTGTT-TTTTTG
1 TGTTGTTTT-GTTGTTATTTTTG
422141 TTGTT-TTTGTGTTGTT-TTTTT-
1 -TGTTGTTT-TGTTGTTATTTTTG
** *
422162 TACTGTTTTGGTGTT-TTTTT-
1 TGTTGTTTTGTTGTTATTTTTG
** * *
422182 TACTATTTTAGTTGTTGTTTTTG
1 TGTTGTTTT-GTTGTTATTTTTG
* **
422205 TGTTGTTTT-TTGTTGCTTTTAA
1 TGTTGTTTTGTTGTT-ATTTTTG
*
422227 TGTTGTTTTGCTGTTAGTTTTTG
1 TGTTGTTTTGTTGTTA-TTTTTG
422250 CTGTTGTTTTGGTTGTTATTTTTG
1 -TGTTGTTTT-GTTGTTATTTTTG
422274 T
1 T
422275 TGTTTGGATG
Statistics
Matches: 120, Mismatches: 23, Indels: 24
0.72 0.14 0.14
Matches are distributed among these distances:
20 21 0.17
21 25 0.21
22 35 0.29
23 18 0.15
24 15 0.12
25 6 0.05
ACGTcount: A:0.06, C:0.03, G:0.21, T:0.69
Consensus pattern (22 bp):
TGTTGTTTTGTTGTTATTTTTG
Found at i:422293 original size:21 final size:21
Alignment explanation
Indices: 422251--422292 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
422241 TAGTTTTTGC
* *
422251 TGTTGTTTTGGTTGTTATTTT
1 TGTTGTTTTGGATGCTATTTT
422272 TGTTG-TTTGGATGCTATTTT
1 TGTTGTTTTGGATGCTATTTT
422292 T
1 T
422293 TATGCGTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 14 0.74
21 5 0.26
ACGTcount: A:0.07, C:0.02, G:0.24, T:0.67
Consensus pattern (21 bp):
TGTTGTTTTGGATGCTATTTT
Found at i:424117 original size:5 final size:5
Alignment explanation
Indices: 424082--424141 Score: 50
Period size: 5 Copynumber: 11.2 Consensus size: 5
424072 AAAAAGTCTA
* *
424082 ATTTT A-TTA ATTTT ATTTT GACTTT ACTTTT ATTTT ATTTT ATCATTGT
1 ATTTT ATTTT ATTTT ATTTT -ATTTT A-TTTT ATTTT ATTTT AT--TT-T
424131 ATTTT ATTTT A
1 ATTTT ATTTT A
424142 ACAAGAATTC
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
4 3 0.07
5 27 0.60
6 10 0.22
7 2 0.04
8 3 0.07
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.68
Consensus pattern (5 bp):
ATTTT
Found at i:429717 original size:20 final size:20
Alignment explanation
Indices: 429674--429719 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
429664 AATTAAAAAC
429674 TAAAAATAAAATAAAACTGA
1 TAAAAATAAAATAAAACTGA
429694 -AAAAATAGAAAGT-AAACT-A
1 TAAAAATA-AAA-TAAAACTGA
429713 TAAAAAT
1 TAAAAAT
429720 CTTCAAAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
19 8 0.35
20 14 0.61
21 1 0.04
ACGTcount: A:0.70, C:0.04, G:0.07, T:0.20
Consensus pattern (20 bp):
TAAAAATAAAATAAAACTGA
Found at i:445007 original size:13 final size:13
Alignment explanation
Indices: 444989--445014 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
444979 CATTACTATT
444989 GACAATTCTTTTC
1 GACAATTCTTTTC
445002 GACAATTCTTTTC
1 GACAATTCTTTTC
445015 ATTTAAACTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.08, T:0.46
Consensus pattern (13 bp):
GACAATTCTTTTC
Found at i:453654 original size:3 final size:3
Alignment explanation
Indices: 453646--453684 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
453636 CTTTTGATCT
453646 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
453685 AAGCATTAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:456779 original size:23 final size:23
Alignment explanation
Indices: 456753--456800 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
456743 CTAATACTTT
456753 ATTTAATAAAATAAAT-GAAAAAA
1 ATTTAATAAAAT-AATGGAAAAAA
* *
456776 ATTTCATAAAATTATGGAAAAAA
1 ATTTAATAAAATAATGGAAAAAA
456799 AT
1 AT
456801 ATTTAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 2 0.09
23 20 0.91
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.29
Consensus pattern (23 bp):
ATTTAATAAAATAATGGAAAAAA
Found at i:460942 original size:30 final size:29
Alignment explanation
Indices: 460908--461002 Score: 145
Period size: 30 Copynumber: 3.2 Consensus size: 29
460898 ACTTATTTTA
460908 TTGTTAATTTTGTTATTATTTTAAAGATAT
1 TTGTTAATTTTGTTATTATTTTAAAG-TAT
460938 TTGTTAATTTTGTTATTATTTTAGAAGTAT
1 TTGTTAATTTTGTTATTATTTTA-AAGTAT
* *
460968 TTATTAATTTTGTTATTATTTTAAAAGCAT
1 TTGTTAATTTTGTTATTATTTT-AAAGTAT
460998 TTGTT
1 TTGTT
461003 TGTTAAATTT
Statistics
Matches: 60, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
30 56 0.93
31 4 0.07
ACGTcount: A:0.28, C:0.01, G:0.11, T:0.60
Consensus pattern (29 bp):
TTGTTAATTTTGTTATTATTTTAAAGTAT
Found at i:469805 original size:18 final size:18
Alignment explanation
Indices: 469782--469818 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
469772 ACCTTTAATA
*
469782 AATTATTTTTTTTAAATT
1 AATTATATTTTTTAAATT
*
469800 AATTATATTTTTTCAATT
1 AATTATATTTTTTAAATT
469818 A
1 A
469819 TAAAAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (18 bp):
AATTATATTTTTTAAATT
Found at i:488920 original size:18 final size:18
Alignment explanation
Indices: 488905--488952 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
488895 AGGTGGAACC
*
488905 TGAGGAGAAGAAGGAAAT
1 TGAGGAGAAGAAGGAAAA
* *
488923 TGAAGAGGAGAAGGAAGAA
1 TGAGGAGAAGAAGGAA-AA
488942 -GAGGAGAAGAA
1 TGAGGAGAAGAA
488953 TGAAGAGAAG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
18 23 0.96
19 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.42, T:0.06
Consensus pattern (18 bp):
TGAGGAGAAGAAGGAAAA
Found at i:488944 original size:15 final size:15
Alignment explanation
Indices: 488923--488959 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
488913 AGAAGGAAAT
488923 TGAAGAGGAGAAGGAA
1 TGAAGAGGAGAA-GAA
488939 -GAAGAGGAGAAGAA
1 TGAAGAGGAGAAGAA
488953 TGAAGAG
1 TGAAGAG
488960 AAGGAAGATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 3 0.15
15 17 0.85
ACGTcount: A:0.51, C:0.00, G:0.43, T:0.05
Consensus pattern (15 bp):
TGAAGAGGAGAAGAA
Found at i:489286 original size:3 final size:3
Alignment explanation
Indices: 489278--489306 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
489268 GGAGCATCCA
489278 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
489307 AGCCAAGGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:493935 original size:18 final size:19
Alignment explanation
Indices: 493914--493950 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
493904 CTTTTAATAA
*
493914 TTTTGAGACTT-TAATTTT
1 TTTTAAGACTTGTAATTTT
493932 TTTTAAGACTTGTAATTTT
1 TTTTAAGACTTGTAATTTT
493951 GGGGATCATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.24, C:0.05, G:0.11, T:0.59
Consensus pattern (19 bp):
TTTTAAGACTTGTAATTTT
Found at i:494852 original size:25 final size:26
Alignment explanation
Indices: 494823--494891 Score: 70
Period size: 25 Copynumber: 2.6 Consensus size: 26
494813 GCCAAAGAAG
*
494823 AGAAAATTAGT-GAAAAGAATAAA-AA
1 AGAAAATGAGTAGAAAAGAA-AAACAA
*
494848 AGAAAATGAGTAGAAACGAAAAACAA
1 AGAAAATGAGTAGAAAAGAAAAACAA
*
494874 AGAATCATGAGTAAGAAA
1 AGAA-AATGAGT-AGAAA
494892 TATGTGAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
25 13 0.35
26 13 0.35
27 6 0.16
28 5 0.14
ACGTcount: A:0.64, C:0.04, G:0.19, T:0.13
Consensus pattern (26 bp):
AGAAAATGAGTAGAAAAGAAAAACAA
Found at i:500249 original size:37 final size:37
Alignment explanation
Indices: 500155--500253 Score: 112
Period size: 37 Copynumber: 2.7 Consensus size: 37
500145 AATTATGTAC
*
500155 ATGTTCATGCAGTGACA-TTCTTGGGTGCATTCTGGAG
1 ATGTTCATGCAGTGACAGTT-TTGGGTGCAATCTGGAG
* * * *
500192 ATATTCTTGCAATGATAGTTTTGGGTGCAATCTGGA-
1 ATGTTCATGCAGTGACAGTTTTGGGTGCAATCTGGAG
*
500228 AGTGTTCATGCAGCGACAGTTTTGGG
1 A-TGTTCATGCAGTGACAGTTTTGGG
500254 CGTAATTTTG
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
36 1 0.02
37 47 0.94
38 2 0.04
ACGTcount: A:0.21, C:0.14, G:0.29, T:0.35
Consensus pattern (37 bp):
ATGTTCATGCAGTGACAGTTTTGGGTGCAATCTGGAG
Found at i:504814 original size:38 final size:38
Alignment explanation
Indices: 504727--504814 Score: 94
Period size: 38 Copynumber: 2.3 Consensus size: 38
504717 GTACATGTTC
*
504727 ATGCAGCGATA-TTCCTCGGTGTAATTGAAGAATACTT
1 ATGCAGCGATAGTTCCTCGGTGCAATTGAAGAATACTT
* *
504764 ATGCA-CTTATAGTT-CT-GGATGCAATTTGAAGAATATTT
1 ATGCAGC-GATAGTTCCTCGG-TGCAA-TTGAAGAATACTT
504802 ATGCAGCGATAGT
1 ATGCAGCGATAGT
504815 CTTGGGTGCA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
36 3 0.07
37 14 0.33
38 24 0.57
39 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.34
Consensus pattern (38 bp):
ATGCAGCGATAGTTCCTCGGTGCAATTGAAGAATACTT
Found at i:504833 original size:38 final size:37
Alignment explanation
Indices: 504727--504837 Score: 93
Period size: 38 Copynumber: 3.0 Consensus size: 37
504717 GTACATGTTC
* * * * * *
504727 ATGCAGCGATATTCCTCGGTGTAATTGAAGAATACTT
1 ATGCAGCGATAGTCTTGGGTGCATTTGAAGAATATTT
* *
504764 ATGCA-CTTATAGT-TCTGGATGCAATTTGAAGAATATTT
1 ATGCAGC-GATAGTCT-TGGGTGC-ATTTGAAGAATATTT
504802 ATGCAGCGATAGTCTTGGGTGCATTTCGAAG-ATATT
1 ATGCAGCGATAGTCTTGGGTGCATTT-GAAGAATATT
504838 CCTGCGATGA
Statistics
Matches: 58, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
36 1 0.02
37 22 0.38
38 33 0.57
39 2 0.03
ACGTcount: A:0.29, C:0.14, G:0.23, T:0.35
Consensus pattern (37 bp):
ATGCAGCGATAGTCTTGGGTGCATTTGAAGAATATTT
Found at i:505724 original size:30 final size:30
Alignment explanation
Indices: 505690--505748 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
505680 AAAAGAAAAA
* *
505690 CTAAAAATGAAATATATATGCCAAAAATTC
1 CTAAAAATAAAATATACATGCCAAAAATTC
* *
505720 CTAAAAATAAAATTTGCATGCCAAAAATT
1 CTAAAAATAAAATATACATGCCAAAAATT
505749 TTTATGTTAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.53, C:0.14, G:0.07, T:0.27
Consensus pattern (30 bp):
CTAAAAATAAAATATACATGCCAAAAATTC
Found at i:523024 original size:27 final size:27
Alignment explanation
Indices: 522986--523039 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
522976 GCTATTGTGG
522986 TCTTTACCCTCAAGATCTAGAGATACT
1 TCTTTACCCTCAAGATCTAGAGATACT
*
523013 TCTTTGCCCTCAAGATCTAGAGATACT
1 TCTTTACCCTCAAGATCTAGAGATACT
523040 ATCTCTTTGG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (27 bp):
TCTTTACCCTCAAGATCTAGAGATACT
Found at i:525680 original size:34 final size:34
Alignment explanation
Indices: 525640--525705 Score: 132
Period size: 34 Copynumber: 1.9 Consensus size: 34
525630 AAATATTCTC
525640 TTTTTCTTGAAATCGATCTCTTTCGATTAGTCTT
1 TTTTTCTTGAAATCGATCTCTTTCGATTAGTCTT
525674 TTTTTCTTGAAATCGATCTCTTTCGATTAGTC
1 TTTTTCTTGAAATCGATCTCTTTCGATTAGTC
525706 ATACGTTTCG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.18, C:0.18, G:0.12, T:0.52
Consensus pattern (34 bp):
TTTTTCTTGAAATCGATCTCTTTCGATTAGTCTT
Found at i:549674 original size:14 final size:14
Alignment explanation
Indices: 549655--549688 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
549645 TTTCAGCAAT
*
549655 TTTTTCTTTTTTTC
1 TTTTTCTTTTCTTC
549669 TTTTTC-TTTCTTC
1 TTTTTCTTTTCTTC
549682 TTTTTCT
1 TTTTTCT
549689 CATTTTTGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTTCTTTTCTTC
Found at i:550299 original size:17 final size:17
Alignment explanation
Indices: 550269--550309 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
550259 AAACTAAAAT
550269 GAATGCAATGATAATTAA
1 GAATGCAATGATAA-TAA
550287 -AATGCAA-GCATAATAA
1 GAATGCAATG-ATAATAA
550303 GAATGCA
1 GAATGCA
550310 TGAAAACTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.51, C:0.10, G:0.17, T:0.22
Consensus pattern (17 bp):
GAATGCAATGATAATAA
Found at i:550731 original size:3 final size:3
Alignment explanation
Indices: 550723--550760 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
550713 CCTCGACAAG
550723 TTC TTC TTC TTC TTC TTC TTC TT- TTC TT- TTC TTTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC -TTC TTC
550761 CTCGTCTTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 4 0.12
3 25 0.78
4 3 0.09
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (3 bp):
TTC
Found at i:559015 original size:24 final size:24
Alignment explanation
Indices: 558988--559042 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 24
558978 ACAACCAATT
558988 CATTTTATATTACAGTTGCACTGA
1 CATTTTATATTACAGTTGCACTGA
* *
559012 CATTTTGTATTACATTTGCACTGA
1 CATTTTATATTACAGTTGCACTGA
559036 CAATTTT
1 C-ATTTT
559043 TACTCTTAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
24 23 0.82
25 5 0.18
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.45
Consensus pattern (24 bp):
CATTTTATATTACAGTTGCACTGA
Found at i:560396 original size:92 final size:90
Alignment explanation
Indices: 560227--560401 Score: 237
Period size: 92 Copynumber: 1.9 Consensus size: 90
560217 TTGCATTTCA
* * * *
560227 TCCTTTTAAATGATGTCATGAATTGGCCTTTAAGTGCCCTAAAACCGATTAGCATTTGAAGAGTT
1 TCCTTTTAAATGATGCCATGAATTGGCCTTTAAGTGCCC-AAAACCAATCAACATTTGAAGAGTT
560292 TCCTCTTGGTCTTTTGAATAGCCACT
65 TCCTCTTGGTCTTTTGAATAGCCACT
* *
560318 TCCTTTTATAATTGGTGCCATGAATTGGCCTTTAAGTGCACC-AAACTAATCAACATTTGAAGAG
1 TCCTTTTA-AA-TGATGCCATGAATTGGCCTTTAAGTGC-CCAAAACCAATCAACATTTGAAGAG
560382 TCTTCC-CTTGGTCTTTTGAA
63 T-TTCCTCTTGGTCTTTTGAA
560402 GAGTCAGCTT
Statistics
Matches: 74, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
91 8 0.11
92 35 0.47
93 29 0.39
94 2 0.03
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (90 bp):
TCCTTTTAAATGATGCCATGAATTGGCCTTTAAGTGCCCAAAACCAATCAACATTTGAAGAGTTT
CCTCTTGGTCTTTTGAATAGCCACT
Found at i:560811 original size:50 final size:52
Alignment explanation
Indices: 560704--560817 Score: 162
Period size: 50 Copynumber: 2.2 Consensus size: 52
560694 TGGATTACTA
*
560704 AATGCATGACTTGATTTAATGATGCAAACTTAACTAATCATGAGAGTTACAT
1 AATGCATGACTTGATTTAATGATGCAAACTTAACTAATCATGAAAGTTACAT
* * *
560756 TATGCATGTCATT-ATTT-ATGATGCATACTTAACTAA-CATGAAAGTTACAT
1 AATGCATGAC-TTGATTTAATGATGCAAACTTAACTAATCATGAAAGTTACAT
560806 AATGCATGACTT
1 AATGCATGACTT
560818 TAATAAATGC
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
49 2 0.04
50 21 0.38
51 18 0.33
52 12 0.22
53 2 0.04
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (52 bp):
AATGCATGACTTGATTTAATGATGCAAACTTAACTAATCATGAAAGTTACAT
Found at i:567624 original size:34 final size:34
Alignment explanation
Indices: 567581--567676 Score: 120
Period size: 34 Copynumber: 2.8 Consensus size: 34
567571 GCACTTAGTG
* * * *
567581 TGCTAGATGGACTAGCTCTTACGAGTATTTGGTA
1 TGCTGGATGGACTGGCTCATACGAGCATTTGGTA
* *
567615 TGCTGGATGGATTGGCTCATGCGAGCATTTGGTA
1 TGCTGGATGGACTGGCTCATACGAGCATTTGGTA
* *
567649 TGCTGGATGGACTGGCTCACACAAGCAT
1 TGCTGGATGGACTGGCTCATACGAGCAT
567677 CTAGTGTGCT
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 52 1.00
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.30
Consensus pattern (34 bp):
TGCTGGATGGACTGGCTCATACGAGCATTTGGTA
Found at i:570343 original size:16 final size:15
Alignment explanation
Indices: 570307--570345 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
570297 TATACATATT
*
570307 TTTTTCTTCTTTTCC
1 TTTTTCTTATTTTCC
*
570322 TTTTTCTTATTTTTC
1 TTTTTCTTATTTTCC
570337 TCTTTTCTT
1 T-TTTTCTT
570346 TATGTGACTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.67
16 7 0.33
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTCTTATTTTCC
Found at i:576726 original size:14 final size:14
Alignment explanation
Indices: 576707--576740 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
576697 CCTTGACTAG
*
576707 ATGAATTTCCATAT
1 ATGAATTTACATAT
576721 ATGAATTTACATAT
1 ATGAATTTACATAT
*
576735 CTGAAT
1 ATGAAT
576741 GTTGTTGCAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.09, T:0.41
Consensus pattern (14 bp):
ATGAATTTACATAT
Found at i:585115 original size:51 final size:51
Alignment explanation
Indices: 585043--585275 Score: 253
Period size: 51 Copynumber: 4.6 Consensus size: 51
585033 TTTCATTTAA
* * *
585043 TACTCACGATGACA-TATAGTCATCGGACCTCTT-GTTCCATATAGGAATTCA-
1 TACTCACGATGACACT-TAGTCATCGGACCTTTTAATT-CATAAAGG-ATTCAT
* * * *
585094 TACTCACGATGACACTGAGTCATCGGACC-TTTAATCCATCATGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTTAATTCATAAAGGATTCA-T
* * *
585145 TGCTCACGATGACACTTAGTCATCGGA-CTTTTAATTCGTAAAGGGTTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTTAATTCATAAAGGATTCA-T
* *
585196 TACTCACGATGACACTCAGTCATCGG-CCTTTTAATTCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTTAATTCATAAAGGATTCA-T
*
585247 TACTCACGATAACACTTAGTCATCGGACC
1 TACTCACGATGACACTTAGTCATCGGACC
585276 CTTTCGTTTA
Statistics
Matches: 156, Mismatches: 19, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
49 5 0.03
50 8 0.05
51 140 0.90
52 3 0.02
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTTAATTCATAAAGGATTCAT
Found at i:593191 original size:21 final size:21
Alignment explanation
Indices: 593150--593192 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
593140 GTTAAACTTC
*
593150 ACTAAGTTAGAAAATGCAATA
1 ACTAAGTTAGAAAATACAATA
593171 ACTAAGTTA-AAAATACTAATA
1 ACTAAGTTAGAAAATAC-AATA
593192 A
1 A
593193 TGTTTGCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.56, C:0.09, G:0.09, T:0.26
Consensus pattern (21 bp):
ACTAAGTTAGAAAATACAATA
Found at i:598045 original size:52 final size:51
Alignment explanation
Indices: 597963--598207 Score: 242
Period size: 52 Copynumber: 4.7 Consensus size: 51
597953 ATAAACGAAG
* *
597963 AGGTCCAATGATTAAGTGTCATCA-TGAGTATATGAATCCTTTACGGATTAA
1 AGGTCCGATGACTAAGTGTCAT-AGTGAGTATATGAATCCTTTACGGATTAA
* * * *
598014 ATGGTCCAATGACTAAGTGTTATAGTCAGTATATGAATCCTTTATGGATTAA
1 A-GGTCCGATGACTAAGTGTCATAGTGAGTATATGAATCCTTTACGGATTAA
* * * * *
598066 ACGGTCTGATGACTAATTGTCATCA-TGAGTATATGGATCCTTCACAGATTAA
1 A-GGTCCGATGACTAAGTGTCAT-AGTGAGTATATGAATCCTTTACGGATTAA
** * * *
598118 GAGGTCCGATGACTCTGTGTCATCGTGAGTATACGAATCCCTTACGGATTATA
1 -AGGTCCGATGACTAAGTGTCATAGTGAGTATATGAATCCTTTACGGATTA-A
* * * *
598171 AGGTCCGATGGCTATGTGTTATCGTGAGTATATGAAT
1 AGGTCCGATGACTAAGTGTCATAGTGAGTATATGAAT
598208 GAAGTGAAAT
Statistics
Matches: 160, Mismatches: 28, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
51 2 0.01
52 155 0.97
53 3 0.02
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.33
Consensus pattern (51 bp):
AGGTCCGATGACTAAGTGTCATAGTGAGTATATGAATCCTTTACGGATTAA
Found at i:598167 original size:104 final size:104
Alignment explanation
Indices: 597963--598207 Score: 271
Period size: 104 Copynumber: 2.4 Consensus size: 104
597953 ATAAACGAAG
* * * * *
597963 AGGTCCAATGATTAAGTGTCATCATGAGTATATGAATCCTTTACGGATTAAATGGTCCAATGACT
1 AGGTCCGATGACTAATTGTCATCATGAGTATATGAATCCTTCACAGATTAAATGGTCCAATGACT
* * * *
598028 AAGTGTTATAGTCAGTATATGAATCCTTTATGGATTA-A
66 AAGTGTCATAGTCAGTATACGAATCCCTTACGGATTATA
* * *
598066 ACGGTCTGATGACTAATTGTCATCATGAGTATATGGATCCTTCACAGATTAAGA-GGTCCGATGA
1 A-GGTCCGATGACTAATTGTCATCATGAGTATATGAATCCTTCACAGATTAA-ATGGTCCAATGA
** * *
598130 CTCTGTGTCATCGTGAGTATACGAATCCCTTACGGATTATA
64 CTAAGTGTCATAGTCAGTATACGAATCCCTTACGGATTATA
* * *
598171 AGGTCCGATGGCT-ATGTGTTATCGTGAGTATATGAAT
1 AGGTCCGATGACTAAT-TGTCATCATGAGTATATGAAT
598208 GAAGTGAAAT
Statistics
Matches: 117, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
103 3 0.03
104 111 0.95
105 3 0.03
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.33
Consensus pattern (104 bp):
AGGTCCGATGACTAATTGTCATCATGAGTATATGAATCCTTCACAGATTAAATGGTCCAATGACT
AAGTGTCATAGTCAGTATACGAATCCCTTACGGATTATA
Found at i:598713 original size:22 final size:22
Alignment explanation
Indices: 598688--598731 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
598678 CTTGTGTTTG
598688 GTATGAATCTTGAGATTTTGCA
1 GTATGAATCTTGAGATTTTGCA
598710 GTATGAATCTTGAGATTTTGCA
1 GTATGAATCTTGAGATTTTGCA
598732 TACTTGTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.09, G:0.23, T:0.41
Consensus pattern (22 bp):
GTATGAATCTTGAGATTTTGCA
Found at i:598870 original size:21 final size:21
Alignment explanation
Indices: 598844--598883 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
598834 AGTAGTTATA
*
598844 TGTATAGATGTATCGATAGTT
1 TGTATACATGTATCGATAGTT
*
598865 TGTATACTTGTATCGATAG
1 TGTATACATGTATCGATAG
598884 AAGTTATAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.07, G:0.23, T:0.42
Consensus pattern (21 bp):
TGTATACATGTATCGATAGTT
Found at i:603107 original size:36 final size:36
Alignment explanation
Indices: 603066--603148 Score: 148
Period size: 36 Copynumber: 2.3 Consensus size: 36
603056 TGACTGATAT
603066 GACAATAAATATGTGGGTATGTTATTCATGCCATGA
1 GACAATAAATATGTGGGTATGTTATTCATGCCATGA
*
603102 GACAATAAATATGTGGGTATGTTATTCATGCCATGT
1 GACAATAAATATGTGGGTATGTTATTCATGCCATGA
*
603138 GACAGTAAATA
1 GACAATAAATA
603149 ATTTGTGTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.33
Consensus pattern (36 bp):
GACAATAAATATGTGGGTATGTTATTCATGCCATGA
Found at i:603616 original size:69 final size:68
Alignment explanation
Indices: 603543--603873 Score: 333
Period size: 69 Copynumber: 5.1 Consensus size: 68
603533 ATTAAACTTA
*
603543 ATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAATCCAGAAATATTCATTTGATTAAA
1 ATTAAATGTGACTAAACGTGATTAATATGTGATGTGATAAATCC-GAAATATTCATTTGATTAAA
603608 TGTG
65 TGTG
* * * *
603612 ATTAAGTGTGACTAAACGTAATTAATATGTGATGTGATAAATACTAAA-A-T-ATTT-A-T---T
1 ATTAAATGTGACTAAACGTGATTAATATGTGATGTGATAAATCCGAAATATTCATTTGATTAAAT
603669 -TG
66 GTG
* *
603671 ATTAAATGTAACTAAACATGATTAATATGTGATGTGATAAATGCCGAAATATTC-----A-T---
1 ATTAAATGTGACTAAACGTGATTAATATGTGATGTGATAAAT-CCGAAATATTCATTTGATTAAA
603727 T-TG
65 TGTG
* ** *
603730 ATTAAATGTGACTAAACGTAATTAATATGTGATGTGATAAATGCTAAAATATTCATATGATTAAA
1 ATTAAATGTGACTAAACGTGATTAATATGTGATGTGATAAAT-CCGAAATATTCATTTGATTAAA
*
603795 AGTG
65 TGTG
* * *
603799 ATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAAAGCTGAAATATTC-TTGTGATTAA
1 ATTAAATGTGACTAAACGTGATTAATATGTGATGTGAT-AAATCCGAAATATTCATT-TGATTAA
603863 ATGTG
64 ATGTG
*
603868 ACTAAA
1 ATTAAA
603874 GTTGAAATAT
Statistics
Matches: 222, Mismatches: 24, Indels: 32
0.80 0.09 0.12
Matches are distributed among these distances:
59 94 0.42
60 5 0.02
61 1 0.00
62 1 0.00
63 1 0.00
64 2 0.01
65 5 0.02
66 1 0.00
67 1 0.00
68 4 0.02
69 104 0.47
70 3 0.01
ACGTcount: A:0.41, C:0.06, G:0.17, T:0.37
Consensus pattern (68 bp):
ATTAAATGTGACTAAACGTGATTAATATGTGATGTGATAAATCCGAAATATTCATTTGATTAAAT
GTG
Found at i:603673 original size:59 final size:60
Alignment explanation
Indices: 603610--603873 Score: 284
Period size: 59 Copynumber: 4.3 Consensus size: 60
603600 TGATTAAATG
*
603610 TGATTAAGTGTGACTAAACGTAATTAATATGTGATGTGATAAATACTAAAATATT-TATT
1 TGATTAAATGTGACTAAACGTAATTAATATGTGATGTGATAAATACTAAAATATTATATT
* * * * ** *
603669 TGATTAAATGTAACTAAACATGATTAATATGTGATGTGATAAATGCCGAAATATT-CATT
1 TGATTAAATGTGACTAAACGTAATTAATATGTGATGTGATAAATACTAAAATATTATATT
*
603728 TGATTAAATGTGACTAAACGTAATTAATATGTGATGTGATAAATGCTAAAATATTCATATGATT
1 TGATTAAATGTGACTAAACGTAATTAATATGTGATGTGATAAATACTAAAATA-T--TAT-ATT
* * * *
603792 AAAAGTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAA-AGCTGAAATATTCT-T
1 -----TGATTAAATGTGACTAAACGTAATTAATATGTGATGTGATAAATA-CTAAAATATTATAT
*
603855 G
60 T
603856 TGATTAAATGTGACTAAA
1 TGATTAAATGTGACTAAA
603874 GTTGAAATAT
Statistics
Matches: 174, Mismatches: 20, Indels: 22
0.81 0.09 0.10
Matches are distributed among these distances:
59 117 0.67
60 1 0.01
62 1 0.01
64 4 0.02
66 2 0.01
68 1 0.01
69 48 0.28
ACGTcount: A:0.41, C:0.06, G:0.17, T:0.36
Consensus pattern (60 bp):
TGATTAAATGTGACTAAACGTAATTAATATGTGATGTGATAAATACTAAAATATTATATT
Found at i:603709 original size:128 final size:129
Alignment explanation
Indices: 603543--603868 Score: 399
Period size: 128 Copynumber: 2.5 Consensus size: 129
603533 ATTAAACTTA
603543 ATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAATCCAGAAATATTCATTTGATTAAA
1 ATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAATCC-GAAATATTCATTTGATTAAA
603608 TGTGATTAAGTGTGACTAAACGTAATTAATATGTGATGTGATAAATACTAAAATA-T-T-T-ATT
65 TGTGA--AA-TGTGACTAAACGTAATTAATATGTGATGTGATAAATACTAAAATATTATATGATT
603669 -TG
127 ATG
* **
603671 ATTAAATGTAACTAAACATGATTAATATGTGATGTGATAAATGCCGAAATATTCATTTG-----A
1 ATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAAT-CCGAAATATTCATTTGATTAAA
*
603731 T-T-AAATGTGACTAAACGTAATTAATATGTGATGTGATAAATGCTAAAATATTCATATGATTAA
65 TGTGAAATGTGACTAAACGTAATTAATATGTGATGTGATAAATACTAAAATATT-ATATGATT--
603794 AAGTG
127 -A-TG
* *
603799 ATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAAAGCTGAAATATTC-TTGTGATTAA
1 ATTAAATGTGACTAAATGTGATTAATATGTGATGTGAT-AAATCCGAAATATTCATT-TGATTAA
603863 ATGTGA
64 ATGTGA
603869 CTAAAGTTGA
Statistics
Matches: 169, Mismatches: 9, Indels: 33
0.80 0.04 0.16
Matches are distributed among these distances:
118 44 0.26
119 3 0.02
121 2 0.01
122 2 0.01
123 5 0.03
127 2 0.01
128 102 0.60
129 5 0.03
133 2 0.01
134 1 0.01
135 1 0.01
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.37
Consensus pattern (129 bp):
ATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAATCCGAAATATTCATTTGATTAAAT
GTGAAATGTGACTAAACGTAATTAATATGTGATGTGATAAATACTAAAATATTATATGATTATG
Found at i:603830 original size:11 final size:10
Alignment explanation
Indices: 603787--603831 Score: 63
Period size: 10 Copynumber: 4.4 Consensus size: 10
603777 AATATTCATA
*
603787 TGATTAAAAG
1 TGATTAAATG
603797 TGATTAAATG
1 TGATTAAATG
*
603807 TGACTAAATG
1 TGATTAAATG
603817 TGATTAATATG
1 TGATTAA-ATG
603828 TGAT
1 TGAT
603832 GTGATAAAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
10 24 0.77
11 7 0.23
ACGTcount: A:0.40, C:0.02, G:0.20, T:0.38
Consensus pattern (10 bp):
TGATTAAATG
Found at i:603867 original size:33 final size:34
Alignment explanation
Indices: 603830--603906 Score: 131
Period size: 33 Copynumber: 2.3 Consensus size: 34
603820 TTAATATGTG
603830 ATGTGA-TAAAAGCTGAAATATTCTTGTGATTAA
1 ATGTGACTAAAAGCTGAAATATTCTTGTGATTAA
*
603863 ATGTGACT-AAAGTTGAAATATTCTTGTGATTAA
1 ATGTGACTAAAAGCTGAAATATTCTTGTGATTAA
603896 ATGTGACTAAA
1 ATGTGACTAAA
603907 CGTGATTAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
33 38 0.93
34 3 0.07
ACGTcount: A:0.39, C:0.06, G:0.18, T:0.36
Consensus pattern (34 bp):
ATGTGACTAAAAGCTGAAATATTCTTGTGATTAA
Found at i:603898 original size:92 final size:92
Alignment explanation
Indices: 603796--603965 Score: 268
Period size: 92 Copynumber: 1.8 Consensus size: 92
603786 ATGATTAAAA
* * * * *
603796 GTGATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAAAGCTGAAATATTCTTGTGATT
1 GTGATTAAATGTGACTAAACGTGATTAATATGTGACGTGATAAAAGCTGAAACATTCATATGATT
*
603861 AAATGTGACTAAAGTTGAAATATTCTT
66 AAATCTGACTAAAGTTGAAATATTCTT
*
603888 GTGATTAAATGTGACTAAACGTGATTAATATGTGACGTGATAAATGCTGAAACATTCATATGATT
1 GTGATTAAATGTGACTAAACGTGATTAATATGTGACGTGATAAAAGCTGAAACATTCATATGATT
*
603953 AAATCTGATTAAA
66 AAATCTGACTAAA
603966 TGTGACTAAA
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
92 70 1.00
ACGTcount: A:0.38, C:0.07, G:0.19, T:0.36
Consensus pattern (92 bp):
GTGATTAAATGTGACTAAACGTGATTAATATGTGACGTGATAAAAGCTGAAACATTCATATGATT
AAATCTGACTAAAGTTGAAATATTCTT
Found at i:603928 original size:69 final size:69
Alignment explanation
Indices: 603889--604039 Score: 221
Period size: 69 Copynumber: 2.2 Consensus size: 69
603879 AATATTCTTG
*
603889 TGATTAAATGTGACTAAACGTGATTAATATGTGACGTGATAAATGCTGAAACATTCATATGATTA
1 TGATTAAATGTGACTAAACGTGATTAATATGTGACGTGATAAATGCTGAAACATTCAAATGATTA
603954 AATC
66 AATC
* * * * ** *
603958 TGATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAATGCTGCAATATTCACTTGCTTA
1 TGATTAAATGTGACTAAACGTGATTAATATGTGACGTGATAAATGCTGAAACATTCAAATGATTA
*
604023 AATG
66 AATC
604027 TGATTAAATGTGA
1 TGATTAAATGTGA
604040 TTAATATGTG
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 74 1.00
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.36
Consensus pattern (69 bp):
TGATTAAATGTGACTAAACGTGATTAATATGTGACGTGATAAATGCTGAAACATTCAAATGATTA
AATC
Found at i:603928 original size:128 final size:126
Alignment explanation
Indices: 603669--603898 Score: 306
Period size: 128 Copynumber: 1.8 Consensus size: 126
603659 AATATTTATT
*
603669 TGATTAAATGTAACTAAACATGATTAATATGTGATGTGATAAATGCCGAAATATTCATTTGATTA
1 TGATTAAATGTAACTAAACATGATTAATATGTGATGTGATAAAAGCCGAAATATTCATTTGATTA
* * *
603734 AATGTGACTAAACGTAATTAATATGTGATGTGATAAATGCTAAAATATTCATATGATTAAAAG
66 AATGTGACTAAACGT-ATAAATATGTCATGTGATAAATGCTAAAATATTAATATGA-TAAAAG
* ** *
603797 TGATTAAATGTGACTAAATGTGATTAATATGTGATGTGATAAAAGCTGAAATATTC-TTGTGATT
1 TGATTAAATGTAACTAAACATGATTAATATGTGATGTGATAAAAGCCGAAATATTCATT-TGATT
*
603861 AAATGTGACTAAA-GT-TGAAATAT-TCTTGTGATTAAATG
65 AAATGTGACTAAACGTAT-AAATATGTCATGTGA-TAAATG
603899 TGACTAAACG
Statistics
Matches: 91, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
125 7 0.08
126 11 0.12
127 4 0.04
128 69 0.76
ACGTcount: A:0.40, C:0.06, G:0.17, T:0.37
Consensus pattern (126 bp):
TGATTAAATGTAACTAAACATGATTAATATGTGATGTGATAAAAGCCGAAATATTCATTTGATTA
AATGTGACTAAACGTATAAATATGTCATGTGATAAATGCTAAAATATTAATATGATAAAAG
Found at i:603991 original size:11 final size:10
Alignment explanation
Indices: 603948--603992 Score: 63
Period size: 10 Copynumber: 4.4 Consensus size: 10
603938 AACATTCATA
*
603948 TGATTAAATC
1 TGATTAAATG
603958 TGATTAAATG
1 TGATTAAATG
*
603968 TGACTAAATG
1 TGATTAAATG
603978 TGATTAATATG
1 TGATTAA-ATG
603989 TGAT
1 TGAT
603993 GTGATAAATG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
10 24 0.77
11 7 0.23
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40
Consensus pattern (10 bp):
TGATTAAATG
Found at i:604026 original size:161 final size:161
Alignment explanation
Indices: 603702--604068 Score: 510
Period size: 161 Copynumber: 2.3 Consensus size: 161
603692 TTAATATGTG
* *
603702 ATGTGA-TAAATGCCGAAATATTCATT-TGATTAAATGTGACTAAACGTAATTAATATGTGATGT
1 ATGTGACTAAATG-TGAAATATTC-TTGTGATTAAATGTGACTAAACGTAATTAATATGTGACGT
* *
603765 GATAAATGCTAAAATATTCATATGATTAAAAGTGATTAAATGTGACTAAATGTGATTAATATGTG
64 GATAAATGCTAAAACATTCATATGATTAAAACTGATTAAATGTGACTAAATGTGATTAATATGTG
*
603830 ATGTGATAAAAGCTGAAATATTCTTGTGATTAA
129 ATGTGATAAAAGCTGAAATATTCCTGTGATTAA
*
603863 ATGTGACTAAA-GTTGAAATATTCTTGTGATTAAATGTGACTAAACGTGATTAATATGTGACGTG
1 ATGTGACTAAATG-TGAAATATTCTTGTGATTAAATGTGACTAAACGTAATTAATATGTGACGTG
* *
603927 ATAAATGCTGAAACATTCATATGATTAAATCTGATTAAATGTGACTAAATGTGATTAATATGTGA
65 ATAAATGCTAAAACATTCATATGATTAAAACTGATTAAATGTGACTAAATGTGATTAATATGTGA
* * *
603992 TGTGATAAATGCTGCAATATTCACT-TGCTTAA
130 TGTGATAAAAGCTGAAATATTC-CTGTGATTAA
* *
604024 ATGTGATTAAATGTGATTAATATGTGTTGTG-TTAAATGTTGACTA
1 ATGTGACTAAATGTGA--AATAT-TCTTGTGATTAAATG-TGACTA
604069 GTCATGTGAT
Statistics
Matches: 184, Mismatches: 14, Indels: 13
0.87 0.07 0.06
Matches are distributed among these distances:
160 2 0.01
161 152 0.83
162 6 0.03
163 12 0.07
164 12 0.07
ACGTcount: A:0.38, C:0.07, G:0.18, T:0.37
Consensus pattern (161 bp):
ATGTGACTAAATGTGAAATATTCTTGTGATTAAATGTGACTAAACGTAATTAATATGTGACGTGA
TAAATGCTAAAACATTCATATGATTAAAACTGATTAAATGTGACTAAATGTGATTAATATGTGAT
GTGATAAAAGCTGAAATATTCCTGTGATTAA
Found at i:604035 original size:10 final size:10
Alignment explanation
Indices: 604020--604049 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
604010 ATTCACTTGC
604020 TTAAATGTGA
1 TTAAATGTGA
604030 TTAAATGTGA
1 TTAAATGTGA
604040 TTAATATGTG
1 TTAA-ATGTG
604050 TTGTGTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 14 0.74
11 5 0.26
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.43
Consensus pattern (10 bp):
TTAAATGTGA
Found at i:607262 original size:2 final size:2
Alignment explanation
Indices: 607255--607282 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
607245 AATAACATCA
607255 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
607283 GTAAGAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:607699 original size:14 final size:14
Alignment explanation
Indices: 607682--607713 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
607672 TTTTAGCTAC
*
607682 ATAGCGATAGCTTT
1 ATAGCAATAGCTTT
607696 ATAGCAATAGCTTT
1 ATAGCAATAGCTTT
607710 ATAG
1 ATAG
607714 ATGGTCACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.34, C:0.12, G:0.19, T:0.34
Consensus pattern (14 bp):
ATAGCAATAGCTTT
Found at i:608853 original size:29 final size:30
Alignment explanation
Indices: 608806--608878 Score: 121
Period size: 29 Copynumber: 2.5 Consensus size: 30
608796 AATTAAAATT
608806 ATTTAATAATTTTATTATTTCAAAAAATAA
1 ATTTAATAATTTTATTATTTCAAAAAATAA
* *
608836 TTTTAATAATTTTA-TATTTTAAAAAATAA
1 ATTTAATAATTTTATTATTTCAAAAAATAA
608865 ATTTAATAATTTTA
1 ATTTAATAATTTTA
608879 AAATCATTTG
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
29 27 0.68
30 13 0.32
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (30 bp):
ATTTAATAATTTTATTATTTCAAAAAATAA
Found at i:613324 original size:22 final size:22
Alignment explanation
Indices: 613299--613341 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
613289 TATAATTATA
613299 AAATATTGCTTGAATAAAATAG
1 AAATATTGCTTGAATAAAATAG
613321 AAATATTGCTTGAATAAAATA
1 AAATATTGCTTGAATAAAATA
613342 TTTAAATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.05, G:0.12, T:0.33
Consensus pattern (22 bp):
AAATATTGCTTGAATAAAATAG
Found at i:617224 original size:22 final size:22
Alignment explanation
Indices: 617199--617274 Score: 66
Period size: 22 Copynumber: 3.4 Consensus size: 22
617189 ATTATTTGGT
*
617199 TGATTATGCTATATGATATGCA
1 TGATTATGCTATATGATTTGCA
* *
617221 TGA-TATGGTAAATATTATTTG-A
1 TGATTATGCT--ATATGATTTGCA
*
617243 TTGATTATGCTATATGATTTGCT
1 -TGATTATGCTATATGATTTGCA
617266 TGATATATG
1 TGAT-TATG
617275 TTTCACTCAA
Statistics
Matches: 42, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
21 5 0.12
22 17 0.40
23 15 0.36
24 5 0.12
ACGTcount: A:0.30, C:0.05, G:0.18, T:0.46
Consensus pattern (22 bp):
TGATTATGCTATATGATTTGCA
Found at i:617270 original size:45 final size:45
Alignment explanation
Indices: 617136--617271 Score: 164
Period size: 45 Copynumber: 3.0 Consensus size: 45
617126 AACCGATGAG
* * * ** * *
617136 TGGTAAATACTATTTGATTAATTATGCTGTACAATATGCCTAATA
1 TGGTAAATATTATTTGATTGATTATGCTATATGATATGCATGATA
* * *
617181 TGGTGATTATTATTTGGTTGATTATGCTATATGATATGCATGATA
1 TGGTAAATATTATTTGATTGATTATGCTATATGATATGCATGATA
* *
617226 TGGTAAATATTATTTGATTGATTATGCTATATGATTTGCTTGATA
1 TGGTAAATATTATTTGATTGATTATGCTATATGATATGCATGATA
617271 T
1 T
617272 ATGTTTCACT
Statistics
Matches: 76, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 76 1.00
ACGTcount: A:0.30, C:0.07, G:0.18, T:0.46
Consensus pattern (45 bp):
TGGTAAATATTATTTGATTGATTATGCTATATGATATGCATGATA
Found at i:619042 original size:19 final size:22
Alignment explanation
Indices: 619020--619068 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
619010 AGTTTACTTG
619020 TTTAAT-TAT-TTTTTATTT-A
1 TTTAATATATATTTTTATTTCA
619039 TTTAAATTATATATTTTTATTTCA
1 TTT-AA-TATATATTTTTATTTCA
619063 TTTAAT
1 TTTAAT
619069 CAATGTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
19 3 0.12
20 2 0.08
21 1 0.04
22 4 0.16
23 11 0.44
24 4 0.16
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (22 bp):
TTTAATATATATTTTTATTTCA
Found at i:621098 original size:19 final size:19
Alignment explanation
Indices: 621074--621111 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
621064 TCTCACATGC
* *
621074 CAAAGTGAAAAATTGATTT
1 CAAAGTAAAAAAATGATTT
621093 CAAAGTAAAAAAATGATTT
1 CAAAGTAAAAAAATGATTT
621112 ATGTGGCCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.53, C:0.05, G:0.13, T:0.29
Consensus pattern (19 bp):
CAAAGTAAAAAAATGATTT
Found at i:621211 original size:47 final size:47
Alignment explanation
Indices: 621159--621271 Score: 147
Period size: 47 Copynumber: 2.4 Consensus size: 47
621149 AAAGTGGAAG
* * *
621159 ATGTGGCAGTTTATCTGCAAAAAGTGATGGCTTGTCC-TAATATTTTT
1 ATGTGGCAGTTTATTTGCAAAAA-TGATGGCTTGTCCACAATATTATT
* *
621206 ATGTGGAAGTTTATTTGCAAAAATGGTGGCTTGTCCACAATATTATT
1 ATGTGGCAGTTTATTTGCAAAAATGATGGCTTGTCCACAATATTATT
* *
621253 AAGTGGCAATTTATTTGCA
1 ATGTGGCAGTTTATTTGCA
621272 TTACTGGTGA
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
46 12 0.21
47 45 0.79
ACGTcount: A:0.28, C:0.12, G:0.21, T:0.39
Consensus pattern (47 bp):
ATGTGGCAGTTTATTTGCAAAAATGATGGCTTGTCCACAATATTATT
Found at i:622624 original size:4 final size:4
Alignment explanation
Indices: 622610--622656 Score: 60
Period size: 4 Copynumber: 11.8 Consensus size: 4
622600 TTTCTTTCAT
**
622610 TTTA TTATA TTTA TTTA TTTA -TTA TTTA TTTA TTTA AGTA TTTA TTT
1 TTTA TT-TA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
622657 TTTGGTTTAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
3 3 0.08
4 30 0.81
5 4 0.11
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (4 bp):
TTTA
Found at i:622637 original size:15 final size:16
Alignment explanation
Indices: 622617--622656 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
622607 CATTTTATTA
*
622617 TATTTATTTATTT-AT
1 TATTTATTTATTTAAG
622632 TATTTATTTATTTAAG
1 TATTTATTTATTTAAG
622648 TATTTATTT
1 TATTTATTT
622657 TTTGGTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (16 bp):
TATTTATTTATTTAAG
Found at i:622645 original size:23 final size:24
Alignment explanation
Indices: 622610--622655 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
622600 TTTCTTTCAT
**
622610 TTTATTATATTTATTTATTTATTA
1 TTTATTATATTTAAGTATTTATTA
622634 TTTATT-TATTTAAGTATTTATT
1 TTTATTATATTTAAGTATTTATT
622656 TTTTGGTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (24 bp):
TTTATTATATTTAAGTATTTATTA
Found at i:627850 original size:52 final size:52
Alignment explanation
Indices: 627767--627904 Score: 186
Period size: 52 Copynumber: 2.7 Consensus size: 52
627757 CGTAAATAAA
* * * * *
627767 AAAAGGTTCGATGACTATGTGTCACCATGAGTATATGAATCCTTTATGGATT
1 AAAAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTCACGGATT
* * *
627819 AAAAGGTCCGATGACTATATGTCATCGTGAGTGTATGATTCCTTCACGGATT
1 AAAAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTCACGGATT
* *
627871 AAGAGGCCCGATGACTATGTGTCATCGTGAGTAT
1 AAAAGGTCCGATGACTATGTGTCATCGTGAGTAT
627905 TAATTGGAAT
Statistics
Matches: 74, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (52 bp):
AAAAGGTCCGATGACTATGTGTCATCGTGAGTATATGAATCCTTCACGGATT
Found at i:628715 original size:21 final size:21
Alignment explanation
Indices: 628667--628718 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
628657 GGAGTTTTTA
*
628667 GTATCGGTAAAAGCATGACAT
1 GTATCGGTAGAAGCATGACAT
* *
628688 GTTTCGGTAGAAGTCAT-ACTT
1 GTATCGGTAGAAG-CATGACAT
628709 GTATCGGTAG
1 GTATCGGTAG
628719 TATTGTCTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 23 0.88
22 3 0.12
ACGTcount: A:0.29, C:0.13, G:0.27, T:0.31
Consensus pattern (21 bp):
GTATCGGTAGAAGCATGACAT
Found at i:632012 original size:24 final size:24
Alignment explanation
Indices: 631983--632030 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
631973 TGTCATTGCA
*
631983 ATTTTTCTATTAATTT-TTGTCTTTT
1 ATTTTACT-TTAATTTGTT-TCTTTT
632008 ATTTTACTTTAATTTGTTTCTTT
1 ATTTTACTTTAATTTGTTTCTTT
632031 AGTTTTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.17, C:0.08, G:0.04, T:0.71
Consensus pattern (24 bp):
ATTTTACTTTAATTTGTTTCTTTT
Found at i:634298 original size:17 final size:17
Alignment explanation
Indices: 634260--634292 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
634250 ATTTCATCTA
634260 ATTGTCTTTACATTTTT
1 ATTGTCTTTACATTTTT
*
634277 ATTGTCTTTGCATTTT
1 ATTGTCTTTACATTTT
634293 ACTTGTTCTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.12, G:0.09, T:0.64
Consensus pattern (17 bp):
ATTGTCTTTACATTTTT
Found at i:639830 original size:66 final size:67
Alignment explanation
Indices: 639754--639894 Score: 205
Period size: 67 Copynumber: 2.1 Consensus size: 67
639744 TTGATACATA
**
639754 CAAAATATTAATTGTATATATTTTA-TGAATTTAATAACATAAACAA-CTATATTAATTAATTTT
1 CAAAATATTAATTGTATATATTTTACCAAATTTAATAACATAAA-AAGCTATATTAATTAATTTT
639817 GGT
65 GGT
* * * *
639820 CAAACTATTAATTGTATATATTTTACCAAATTTATTAATATAAAAAGTTATATTAATTAATTTTG
1 CAAAATATTAATTGTATATATTTTACCAAATTTAATAACATAAAAAGCTATATTAATTAATTTTG
639885 GT
66 GT
639887 CAAAATAT
1 CAAAATAT
639895 AAAAGAAATG
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
66 26 0.39
67 40 0.61
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (67 bp):
CAAAATATTAATTGTATATATTTTACCAAATTTAATAACATAAAAAGCTATATTAATTAATTTTG
GT
Found at i:639996 original size:125 final size:127
Alignment explanation
Indices: 639825--640051 Score: 386
Period size: 125 Copynumber: 1.8 Consensus size: 127
639815 TTGGTCAAAC
639825 TATTAATTGTATATATTTTACCAAATTTATTAATATAAAAAGTTATATTAATTAATTTTGGTCAA
1 TATTAATTGTATATATTTTACCAAATTTATTAATATAAAAAGTTATATTAATTAATTTTGGTCAA
639890 AATATAAAAGAAATGAAAATTAATATTCTTTT-GAAAAGATATGAATTTGATTCATACACAA
66 AATATAAAAGAAATGAAAATTAATATTCTTTTAGAAAAGATATGAATTTGATTCATACACAA
** * *
639951 TATTAATTGTATATATTTTACTGAA-TTATTAATATAAACATTTATATTAATTAATTTTGGTCAA
1 TATTAATTGTATATATTTTACCAAATTTATTAATATAAAAAGTTATATTAATTAATTTTGGTCAA
* *
640015 AATATAAAAGACATGGAAATTAATATTCTTTTAGAAA
66 AATATAAAAGAAATGAAAATTAATATTCTTTTAGAAA
640052 GAATATAATT
Statistics
Matches: 94, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
125 67 0.71
126 27 0.29
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (127 bp):
TATTAATTGTATATATTTTACCAAATTTATTAATATAAAAAGTTATATTAATTAATTTTGGTCAA
AATATAAAAGAAATGAAAATTAATATTCTTTTAGAAAAGATATGAATTTGATTCATACACAA
Found at i:640130 original size:74 final size:75
Alignment explanation
Indices: 640037--640182 Score: 240
Period size: 75 Copynumber: 2.0 Consensus size: 75
640027 ATGGAAATTA
* * *
640037 ATATTCTTTTAGAAAGAATATAATTT-TTTTTCTAACTTTTCGTTTGCCTTCTCTATTAATAAGG
1 ATATTCTTTTAGAAAGAATATAATTTCTTTTACTAACTTTCCATTTGCCTTCTCTATTAATAAGG
640101 GAATAATCCT
66 GAATAATCCT
* *
640111 ATATTCTTTTGGAAAGAATATAATTTCTTTTACTAACTTTCCATTTGTCTTCTCTATTAATAAGG
1 ATATTCTTTTAGAAAGAATATAATTTCTTTTACTAACTTTCCATTTGCCTTCTCTATTAATAAGG
640176 GAATAAT
66 GAATAAT
640183 TATGGTTCTC
Statistics
Matches: 66, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
74 25 0.38
75 41 0.62
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.47
Consensus pattern (75 bp):
ATATTCTTTTAGAAAGAATATAATTTCTTTTACTAACTTTCCATTTGCCTTCTCTATTAATAAGG
GAATAATCCT
Found at i:643967 original size:30 final size:30
Alignment explanation
Indices: 643933--643989 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
643923 TATAGCTCGT
643933 GGGTACAGAGCTTGCACTTTACATGCTTGC
1 GGGTACAGAGCTTGCACTTTACATGCTTGC
643963 GGGTACAGAGCTTGCACTTTACATGCT
1 GGGTACAGAGCTTGCACTTTACATGCT
643990 CGTAGCTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.30
Consensus pattern (30 bp):
GGGTACAGAGCTTGCACTTTACATGCTTGC
Found at i:658017 original size:30 final size:29
Alignment explanation
Indices: 657991--658175 Score: 144
Period size: 30 Copynumber: 6.2 Consensus size: 29
657981 TCAAAATCTG
* *
657991 ATTTTTGAGGAGTTTAGGGGCTAAAATGTG
1 ATTTTTGA-GAGTTTAGGGGTTAAAATGTA
*
658021 ATTTTT-ATGAAGTTTGGGGGTTAAAATGTA
1 ATTTTTGA-G-AGTTTAGGGGTTAAAATGTA
658051 ATTTTATGA-AGTTTAGGGGTTAAAATGTA
1 ATTTT-TGAGAGTTTAGGGGTTAAAATGTA
* * * ** *
658080 ATTTTTACAAAGTTTAAGGGCCAAAATGTG
1 ATTTTT-GAGAGTTTAGGGGTTAAAATGTA
* *
658110 ATTTTCATGA-AGTTTGGGGGTTAAAATATA
1 ATTTT--TGAGAGTTTAGGGGTTAAAATGTA
* *
658140 GTTTTTGTGAAGTTT-GAGGGTTAAAATGTA
1 ATTTTTGAG-AGTTTAG-GGGTTAAAATGTA
658170 ATTTTT
1 ATTTTT
658176 ACAAAGTTTG
Statistics
Matches: 124, Mismatches: 21, Indels: 20
0.75 0.13 0.12
Matches are distributed among these distances:
28 3 0.02
29 28 0.23
30 89 0.72
31 2 0.02
32 2 0.02
ACGTcount: A:0.31, C:0.03, G:0.25, T:0.41
Consensus pattern (29 bp):
ATTTTTGAGAGTTTAGGGGTTAAAATGTA
Found at i:658055 original size:60 final size:58
Alignment explanation
Indices: 658001--658174 Score: 213
Period size: 60 Copynumber: 2.9 Consensus size: 58
657991 ATTTTTGAGG
* *
658001 AGTTTAGGGGCTAAAATGTGATTTTTATGAAGTTTGGGGGTTAAAATGTAATTTTATGA
1 AGTTTAGGGGTTAAAATGT-ATTTTTATGAAGTTTGAGGGTTAAAATGTAATTTTATGA
** * ** *
658060 AGTTTAGGGGTTAAAATGTAATTTTTACAAAGTTTAAGGGCCAAAATGTGATTTTCATGA
1 AGTTTAGGGGTTAAAATGT-ATTTTTATGAAGTTTGAGGGTTAAAATGTAATTTT-ATGA
* * *
658120 AGTTTGGGGGTTAAAATATAGTTTTTGTGAAGTTTGAGGGTTAAAATGTAATTTT
1 AGTTTAGGGGTTAAAATGTA-TTTTTATGAAGTTTGAGGGTTAAAATGTAATTTT
658175 TACAAAGTTT
Statistics
Matches: 95, Mismatches: 18, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
59 47 0.49
60 48 0.51
ACGTcount: A:0.32, C:0.03, G:0.25, T:0.40
Consensus pattern (58 bp):
AGTTTAGGGGTTAAAATGTATTTTTATGAAGTTTGAGGGTTAAAATGTAATTTTATGA
Found at i:658183 original size:30 final size:30
Alignment explanation
Indices: 658012--658190 Score: 191
Period size: 30 Copynumber: 6.0 Consensus size: 30
658002 GTTTAGGGGC
* *
658012 TAAAATGTGATTTTTATGAAGTTTGGGGGT
1 TAAAATGTAATTTTTATGAAGTTTGAGGGT
658042 TAAAATGTAA-TTTTATGAAGTTT-AGGGGT
1 TAAAATGTAATTTTTATGAAGTTTGA-GGGT
** * *
658071 TAAAATGTAATTTTTACAAAGTTTAAGGGC
1 TAAAATGTAATTTTTATGAAGTTTGAGGGT
* * * *
658101 CAAAATGTGATTTTCATGAAGTTTGGGGGT
1 TAAAATGTAATTTTTATGAAGTTTGAGGGT
* * *
658131 TAAAATATAGTTTTTGTGAAGTTTGAGGGT
1 TAAAATGTAATTTTTATGAAGTTTGAGGGT
** *
658161 TAAAATGTAATTTTTACAAAGTTTGGGGGT
1 TAAAATGTAATTTTTATGAAGTTTGAGGGT
658191 CTTTTAAGTA
Statistics
Matches: 120, Mismatches: 26, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
29 27 0.22
30 92 0.77
31 1 0.01
ACGTcount: A:0.32, C:0.03, G:0.25, T:0.40
Consensus pattern (30 bp):
TAAAATGTAATTTTTATGAAGTTTGAGGGT
Found at i:659182 original size:3 final size:3
Alignment explanation
Indices: 659174--659201 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
659164 CCTCTTTTAT
659174 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
659202 AAAACTGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:659601 original size:19 final size:20
Alignment explanation
Indices: 659574--659615 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
659564 GTAGATTACA
*
659574 GTGGCGGTGGTGC-AACTTG
1 GTGGCGGTGGTGCTAACGTG
*
659593 GTGGTGGTGGTGCTAACGTG
1 GTGGCGGTGGTGCTAACGTG
659613 GTG
1 GTG
659616 AATTTAGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 12 0.60
20 8 0.40
ACGTcount: A:0.10, C:0.12, G:0.50, T:0.29
Consensus pattern (20 bp):
GTGGCGGTGGTGCTAACGTG
Found at i:660311 original size:85 final size:85
Alignment explanation
Indices: 660167--660324 Score: 208
Period size: 85 Copynumber: 1.9 Consensus size: 85
660157 CTCTTGGTCT
* * * * * * *
660167 ACTTCTCTGTATCTCATCAGGAAGATGACTACTTCATTGTTTTAATCCACTTCTTTGTATCTCAT
1 ACTTCTCTGCATCTCATCAAGAAGATGACCACTTCATTGCTTCAACCCACTTCTCTGTATCTCAT
660232 CAAGAAGACGGATTTGGTTC
66 CAAGAAGACGGATTTGGTTC
* * * *
660252 ACTTCTCTGCATCTCATCAAGAAGATGACCACTTTATTGCTTCGACCCATTTCTCTGTATCTTAT
1 ACTTCTCTGCATCTCATCAAGAAGATGACCACTTCATTGCTTCAACCCACTTCTCTGTATCTCAT
*
660317 CAGGAAGA
66 CAAGAAGA
660325 TAGGGTTTGA
Statistics
Matches: 61, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
85 61 1.00
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (85 bp):
ACTTCTCTGCATCTCATCAAGAAGATGACCACTTCATTGCTTCAACCCACTTCTCTGTATCTCAT
CAAGAAGACGGATTTGGTTC
Found at i:660498 original size:85 final size:85
Alignment explanation
Indices: 660376--660533 Score: 190
Period size: 85 Copynumber: 1.9 Consensus size: 85
660366 GAATTGGTCT
* * * ** * * **
660376 ACTTCTCTATATCTCATCAGGAAGATGACCGGTTTATTATTTTAATTCACTTCTCTATATCTCAT
1 ACTTCTCTACATCTCATCAAGAAGATAACCACTTTATTACTTCAACCCACTTCTCTATATCTCAT
*
660441 TAGGAAGACAAATTTGGTTC
66 CAGGAAGACAAATTTGGTTC
* * * *
660461 ACTTCTCTGCATCTCGTCAAGAAGATAACCACTTTATTGCTTCAACCCACTTCTCTGTATCTCAT
1 ACTTCTCTACATCTCATCAAGAAGATAACCACTTTATTACTTCAACCCACTTCTCTATATCTCAT
660526 CAGGAAGA
66 CAGGAAGA
660534 TGGGGTTTTG
Statistics
Matches: 59, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
85 59 1.00
ACGTcount: A:0.28, C:0.23, G:0.13, T:0.36
Consensus pattern (85 bp):
ACTTCTCTACATCTCATCAAGAAGATAACCACTTTATTACTTCAACCCACTTCTCTATATCTCAT
CAGGAAGACAAATTTGGTTC
Found at i:660520 original size:209 final size:209
Alignment explanation
Indices: 660160--660541 Score: 593
Period size: 209 Copynumber: 1.8 Consensus size: 209
660150 ACTTCATCTC
* * * * *
660160 TTGGTCTACTTCTCTGTATCTCATCAGGAAGATGACTACTTCATTGTTTTAATCCACTTCTTTGT
1 TTGGTCTACTTCTCTATATCTCATCAGGAAGATGACCACTTCATTATTTTAATCCACTTCTCTAT
** *
660225 ATCTCATCAAGAAGACGGATTTGGTTCACTTCTCTGCATCTCATCAAGAAGATGACCACTTTATT
66 ATCTCATCAAGAAGACAAATTTGGTTCACTTCTCTGCATCTCATCAAGAAGATAACCACTTTATT
* * *
660290 GCTTCGACCCATTTCTCTGTATCTTATCAGGAAGATAGGGTTTGAAAGTTTCACTCACATTGAGC
131 GCTTCAACCCACTTCTCTGTATCTCATCAGGAAGATAGGGTTTGAAAGTTTCACTCACATTGAGC
660355 TTCGCTTCATTGAA
196 TTCGCTTCATTGAA
** * *
660369 TTGGTCTACTTCTCTATATCTCATCAGGAAGATGACCGGTTTATTATTTTAATTCACTTCTCTAT
1 TTGGTCTACTTCTCTATATCTCATCAGGAAGATGACCACTTCATTATTTTAATCCACTTCTCTAT
* * *
660434 ATCTCATTAGGAAGACAAATTTGGTTCACTTCTCTGCATCTCGTCAAGAAGATAACCACTTTATT
66 ATCTCATCAAGAAGACAAATTTGGTTCACTTCTCTGCATCTCATCAAGAAGATAACCACTTTATT
*
660499 GCTTCAACCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTT
131 GCTTCAACCCACTTCTCTGTATCTCATCAGGAAGATAGGGTTT
660542 TGAATTTTCA
Statistics
Matches: 154, Mismatches: 19, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
209 154 1.00
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (209 bp):
TTGGTCTACTTCTCTATATCTCATCAGGAAGATGACCACTTCATTATTTTAATCCACTTCTCTAT
ATCTCATCAAGAAGACAAATTTGGTTCACTTCTCTGCATCTCATCAAGAAGATAACCACTTTATT
GCTTCAACCCACTTCTCTGTATCTCATCAGGAAGATAGGGTTTGAAAGTTTCACTCACATTGAGC
TTCGCTTCATTGAA
Found at i:660818 original size:78 final size:79
Alignment explanation
Indices: 660665--661188 Score: 497
Period size: 78 Copynumber: 6.7 Consensus size: 79
660655 CCCCGTCGCC
* ** * * * * * * *
660665 GGGTAAGAGATTGGATGACAGTGATCTGCCCCATGATCGAGGTAAAAGATCGAATGGCTGCTATT
1 GGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATTGGATGGCTGCAATC
660730 TG-CCTCAAGCTCG
66 TGACCTCAAGCTCG
** * * * * * * * *
660743 GGGTAAGAGATAAGCTGATGGTGATTTGCCTCAAGATCGGGGTAAAATATTGTATGGTTTCAATC
1 GGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATTGGATGGCTGCAATC
*
660808 TGCCCT-AAGCTCG
66 TGACCTCAAGCTCG
* * * * * *
660821 GGGTAAGAGATTGGCTAATGGTGATCTGCCACAGGCTCGAGGTAAAAGATCGAATAGCTGCAAT-
1 GGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATTGGATGGCTGCAATC
* *
660885 TTACCTCAGGCTCG
66 TGACCTCAAGCTCG
* * * *
660899 AGGTAAGAGATTGGCTGATGGTGATCTGCCCTAGGCTCGGGGTAAAAGATCGGATGGCTGAAATC
1 GGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATTGGATGGCTGCAATC
* **
660964 T-ACCTCAGGCTTA
66 TGACCTCAAGCTCG
* * * * *
660977 GGGTAAGAGATTGACTGATGGTGATCTACCCCAAGCTCGGGATAAAAGATCT-TATGGCTGCAAT
1 GGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGAT-TGGATGGCTGCAAT
*
661041 TTG-CC-CGAAGCTCG
65 CTGACCTC-AAGCTCG
* * * *
661055 GGGTAAGAGATTGGTTGAAGGTGATCTGCCCCAGGCTCGGGGTAAAATATTGGATGGTTGCAATC
1 GGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATTGGATGGCTGCAATC
*
661120 TG-CCTCAGGCTCG
66 TGACCTCAAGCTCG
* * * * * *
661133 GGGTAAGAGATTGGTTTATGGTGATCTACCCCAAGCTTGGGGTAAAAGATCGGATG
1 GGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATTGGATG
661189 ATTTTGATCT
Statistics
Matches: 364, Mismatches: 74, Indels: 16
0.80 0.16 0.04
Matches are distributed among these distances:
77 6 0.02
78 353 0.97
79 5 0.01
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.25
Consensus pattern (79 bp):
GGGTAAGAGATTGGCTGATGGTGATCTGCCCCAGGCTCGGGGTAAAAGATTGGATGGCTGCAATC
TGACCTCAAGCTCG
Found at i:660848 original size:39 final size:38
Alignment explanation
Indices: 660736--661182 Score: 159
Period size: 39 Copynumber: 11.5 Consensus size: 38
660726 TATTTGCCTC
* ** *
660736 AAGCTCGGGGTAAGAGATAAGCTGATGGTGATTTG-CCT
1 AAGCTCGGGGTAAAAGATTGGCT-ATGGTGATCTGCCCT
* * *
660774 CAAGATCGGGGTAAAATATT-G-TATGGTTTCAATCTGCCCT
1 -AAGCTCGGGGTAAAAGATTGGCTATGG--T-GATCTGCCCT
*
660814 AAGCTCGGGGTAAGAGATTGGCTAATGGTGATCTGCCAC-
1 AAGCTCGGGGTAAAAGATTGGCT-ATGGTGATCTGCC-CT
* * * ** * **
660853 AGGCTCGAGGTAAAAGATCGAATA-GCTGCAAT-TTACCT
1 AAGCTCGGGGTAAAAGATTGGCTATGGTG--ATCTGCCCT
* * *
660891 CAGGCTCGAGGTAAGAGATTGGCTGATGGTGATCTGCCCT
1 -AAGCTCGGGGTAAAAGATTGGCT-ATGGTGATCTGCCCT
* * *
660931 AGGCTCGGGGTAAAAGATCGG--ATGGCTGAAATCT-ACCT
1 AAGCTCGGGGTAAAAGATTGGCTATGG-TG--ATCTGCCCT
* ** * * * *
660969 CAGGCTTAGGGTAAGAGATTGACTGATGGTGATCTACCCC
1 -AAGCTCGGGGTAAAAGATTGGCT-ATGGTGATCTGCCCT
* * *
661009 AAGCTCGGGATAAAAGA-T--CTTATGGCTGCAATTTGCCCG
1 AAGCTCGGGGTAAAAGATTGGC-TATGG-TG--ATCTGCCCT
* * * *
661048 AAGCTCGGGGTAAGAGATTGGTTGAAGGTGATCTGCCCC
1 AAGCTCGGGGTAAAAGATTGGCT-ATGGTGATCTGCCCT
* *
661087 AGGCTCGGGGTAAAATATTGG--ATGGTTGCAATCTG-CCT
1 AAGCTCGGGGTAAAAGATTGGCTATGG-TG--ATCTGCCCT
* * * * *
661125 CAGGCTCGGGGTAAGAGATTGGTTTATGGTGATCTACCCC
1 -AAGCTCGGGGTAAAAGATTGG-CTATGGTGATCTGCCCT
*
661165 AAGCTTGGGGTAAAAGAT
1 AAGCTCGGGGTAAAAGAT
661183 CGGATGATTT
Statistics
Matches: 306, Mismatches: 63, Indels: 78
0.68 0.14 0.17
Matches are distributed among these distances:
36 16 0.05
37 12 0.04
38 11 0.04
39 225 0.74
40 16 0.05
41 11 0.04
42 15 0.05
ACGTcount: A:0.26, C:0.18, G:0.31, T:0.26
Consensus pattern (38 bp):
AAGCTCGGGGTAAAAGATTGGCTATGGTGATCTGCCCT
Found at i:660939 original size:156 final size:156
Alignment explanation
Indices: 660635--661184 Score: 631
Period size: 156 Copynumber: 3.5 Consensus size: 156
660625 TTTGTAAGAG
* * * * * * ** * *
660635 ATTGGATGGTTGCAATCTGCCCCCGTCGCCGGGTAAGAGATTGGATGACAGTGATCTGCCCCATG
1 ATTGGATGGTTGCAATCTGCCTCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTACCCCAAG
* * **
660700 ATCGAGGTAAAAGATCGAATGGCTGCTATTTGCCTCAAGCTCGGGGTAAGAGATAAGCTGATGGT
66 CTCGAGGTAAAAGATCGAATGGCTGCAATTTGCCTCAAGCTCGGGGTAAGAGATTGGCTGATGGT
* * *
660765 GATTTG-CCTCAAGATCGGGGTAAAAT
131 GATCTGCCCT-AGGCTCGGGGTAAAAT
* * * * * * *
660791 ATTGTATGGTTTCAATCTGCC-CTAAGCTCGGGGTAAGAGATTGGCTAATGGTGATCTGCCACAG
1 ATTGGATGGTTGCAATCTGCCTC-AGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTACCCCAA
* * * *
660855 GCTCGAGGTAAAAGATCGAATAGCTGCAATTTACCTCAGGCTCGAGGTAAGAGATTGGCTGATGG
65 GCTCGAGGTAAAAGATCGAATGGCTGCAATTTGCCTCAAGCTCGGGGTAAGAGATTGGCTGATGG
*
660920 TGATCTGCCCTAGGCTCGGGGTAAAAG
130 TGATCTGCCCTAGGCTCGGGGTAAAAT
* * * * ** *
660947 ATCGGATGGCTGAAATCTACCTCAGGCTTAGGGTAAGAGATTGACTGATGGTGATCTACCCCAAG
1 ATTGGATGGTTGCAATCTGCCTCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTACCCCAAG
** * *
661012 CTCG-GGATAAAAGATCTTATGGCTGCAATTTGCC-CGAAGCTCGGGGTAAGAGATTGGTTGAAG
66 CTCGAGG-TAAAAGATCGAATGGCTGCAATTTGCCTC-AAGCTCGGGGTAAGAGATTGGCTGATG
*
661075 GTGATCTGCCCCAGGCTCGGGGTAAAAT
129 GTGATCTGCCCTAGGCTCGGGGTAAAAT
* *
661103 ATTGGATGGTTGCAATCTGCCTCAGGCTCGGGGTAAGAGATTGGTTTATGGTGATCTACCCCAAG
1 ATTGGATGGTTGCAATCTGCCTCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTACCCCAAG
* *
661168 CTTGGGGTAAAAGATCG
66 CTCGAGGTAAAAGATCG
661185 GATGATTTTG
Statistics
Matches: 328, Mismatches: 60, Indels: 12
0.82 0.15 0.03
Matches are distributed among these distances:
155 4 0.01
156 318 0.97
157 6 0.02
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (156 bp):
ATTGGATGGTTGCAATCTGCCTCAGGCTCGGGGTAAGAGATTGGCTGATGGTGATCTACCCCAAG
CTCGAGGTAAAAGATCGAATGGCTGCAATTTGCCTCAAGCTCGGGGTAAGAGATTGGCTGATGGT
GATCTGCCCTAGGCTCGGGGTAAAAT
Done.