Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004834.1 Hibiscus syriacus cultivar Beakdansim tig00010888_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: 393506
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
File 2 of 2
Found at i:325288 original size:23 final size:22
Alignment explanation
Indices: 325255--325335 Score: 78
Period size: 23 Copynumber: 3.6 Consensus size: 22
325245 AATCAAAAAC
*
325255 AAAAAAGAAAAGAAGCAAAAGA
1 AAAAAAAAAAAGAAGCAAAAGA
*
325277 AGAAAAAAAAAAGAAACAAAAGA
1 A-AAAAAAAAAAGAAGCAAAAGA
*
325300 AACAAAAGAAAA-AAG--AAAGA
1 AA-AAAAAAAAAGAAGCAAAAGA
325320 ACAAAAATAAAAAGAA
1 A-AAAAA-AAAAAGAA
325336 AAAGGGACAA
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
20 10 0.20
21 5 0.10
22 6 0.12
23 28 0.57
ACGTcount: A:0.80, C:0.05, G:0.14, T:0.01
Consensus pattern (22 bp):
AAAAAAAAAAAGAAGCAAAAGA
Found at i:325298 original size:32 final size:30
Alignment explanation
Indices: 325249--325313 Score: 85
Period size: 32 Copynumber: 2.1 Consensus size: 30
325239 AGATCCAATC
* * *
325249 AAAAACAAAAAAGAAAAGAAGCAAAAGAAGA
1 AAAAAAAAAAAACAAAAGAAACAAAAGAA-A
325280 AAAAAAAAAGAAACAAAAGAAACAAAAGAAA
1 AAAAAAAAA-AAACAAAAGAAACAAAAGAAA
325311 AAA
1 AAA
325314 GAAAGAACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 12 0.40
32 18 0.60
ACGTcount: A:0.82, C:0.06, G:0.12, T:0.00
Consensus pattern (30 bp):
AAAAAAAAAAAACAAAAGAAACAAAAGAAA
Found at i:325308 original size:29 final size:28
Alignment explanation
Indices: 325250--325338 Score: 94
Period size: 29 Copynumber: 3.2 Consensus size: 28
325240 GATCCAATCA
* *
325250 AAAACAAAAAAGAAA-AGAAGCAAAAGAAG
1 AAAA-AAAAAAGAAACAAAAG-AAAAAAAG
325279 AAAAAAAAAAGAAACAAAAGAAACAAAAG
1 AAAAAAAAAAGAAACAAAAGAAA-AAAAG
* *
325308 AAAAAAGAAAG-AACAAAA-ATAAAAAG
1 AAAAAAAAAAGAAACAAAAGAAAAAAAG
325334 AAAAA
1 AAAAA
325339 GGGACAAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
26 10 0.19
27 2 0.04
28 20 0.37
29 22 0.41
ACGTcount: A:0.81, C:0.06, G:0.12, T:0.01
Consensus pattern (28 bp):
AAAAAAAAAAGAAACAAAAGAAAAAAAG
Found at i:325311 original size:28 final size:27
Alignment explanation
Indices: 325255--325338 Score: 84
Period size: 28 Copynumber: 3.1 Consensus size: 27
325245 AATCAAAAAC
* *
325255 AAAAAAGAAA-AGAAGCAAAAGAAGAAAA
1 AAAAAAGAAACAAAAG-AAAAAAAG-AAA
325283 AAAAAAGAAACAAAAGAAACAAAAGAAA
1 AAAAAAGAAACAAAAGAAA-AAAAGAAA
*
325311 AAAGAAAG-AACAAAA-ATAAAAAGAAA
1 AAA-AAAGAAACAAAAGAAAAAAAGAAA
325337 AA
1 AA
325339 GGGACAAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
26 10 0.20
27 2 0.04
28 26 0.52
29 12 0.24
ACGTcount: A:0.81, C:0.05, G:0.13, T:0.01
Consensus pattern (27 bp):
AAAAAAGAAACAAAAGAAAAAAAGAAA
Found at i:326017 original size:22 final size:22
Alignment explanation
Indices: 325956--326020 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
325946 AACCGTTAAT
*
325956 CATCAAATGCCAAACCTATGAG
1 CATCAAATGCCAAACCTTTGAG
325978 CATCAAATGCCAAACCTTTGAG
1 CATCAAATGCCAAACCTTTGAG
326000 CATCAAATGCCAAACCTTTGA
1 CATCAAATGCCAAACCTTTGA
326021 CCAAACATAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.38, C:0.28, G:0.12, T:0.22
Consensus pattern (22 bp):
CATCAAATGCCAAACCTTTGAG
Found at i:326458 original size:18 final size:19
Alignment explanation
Indices: 326435--326471 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
326425 TCAACATCAA
326435 ATATTGGGGCATT-TTTGG
1 ATATTGGGGCATTATTTGG
326453 ATATTGGGGCATTATTTGG
1 ATATTGGGGCATTATTTGG
326472 GGATTCAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.19, C:0.05, G:0.32, T:0.43
Consensus pattern (19 bp):
ATATTGGGGCATTATTTGG
Found at i:327062 original size:106 final size:106
Alignment explanation
Indices: 326845--328324 Score: 2222
Period size: 106 Copynumber: 14.0 Consensus size: 106
326835 ATATCGTGCC
* * * * * * *
326845 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGTTGGTTGTCAAC-AACAATTTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
326909 AATTTCGGAGCCAATTTTAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
326950 ATTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
327015 AATTTCAGATCCAATTTCAACTTCACATCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
327056 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
327121 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
327162 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
327227 AATTTTAGAGCCAATTTCAACTTCACAACGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
327268 ACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
327333 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
327374 ACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
327439 AATTTCAGAGCCAATTTCAACTTCACCATGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
327480 ACTCCAGACAACGCAAGTTCAACTTTACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
**
327545 AATTTCAGAGCCAATTTCAACTTCACAATTAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
327586 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGTTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
327651 AATTTCAGAGCCAATTTCAACTTCAC-ACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
327691 ACTCAAGACATCGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
327756 AATTTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
327797 ACTCCAGACAACGCAGGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
327862 AATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
327903 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
** *
327968 AATTTCAGAGCCAATTTCAACTTCACAGTGTAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * *
328009 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTAGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * *
328074 AATTTCAGAGCCAATTTCAACTTCTCAGCGAAGGATCTTGA
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * * *
328115 AC-CCAAGGCAACACAAGCTCAACTTCACGACGAAGGGGCGGCTGATTGTCAAC-AA-AA-TT-T
1 ACTCC-AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCC
* *
328175 C-A-TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * *
328215 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * * *
328280 AGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
328321 ACTC
1 ACTC
328325 AGAACAATGC
Statistics
Matches: 1256, Mismatches: 109, Indels: 19
0.91 0.08 0.01
Matches are distributed among these distances:
100 79 0.06
101 4 0.00
102 3 0.00
103 4 0.00
104 3 0.00
105 147 0.12
106 1016 0.81
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:329092 original size:37 final size:37
Alignment explanation
Indices: 329039--329143 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
329029 CTTTTTCGTC
*
329039 CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
329076 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
* * *
329113 CTACTATGATTTAAACTCCTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAAAATAGGAT
329144 CCACAAGCAC
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:329753 original size:2 final size:2
Alignment explanation
Indices: 329746--329772 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
329736 GCATATTATC
329746 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
329773 TGTAATTATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:330003 original size:2 final size:2
Alignment explanation
Indices: 329996--330024 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
329986 TTTACTCATT
329996 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
330025 TATTTATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:330060 original size:13 final size:12
Alignment explanation
Indices: 330032--330080 Score: 55
Period size: 13 Copynumber: 3.9 Consensus size: 12
330022 TATTATTTAT
330032 TTATTTTTCTTT-
1 TTATTTTT-TTTC
330044 TTATTTTTTTTAC
1 TTATTTTTTTT-C
*
330057 TTATTTTTATTC
1 TTATTTTTTTTC
330069 TTTATTTTTTTT
1 -TTATTTTTTTT
330081 TATTTATTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
11 3 0.09
12 9 0.28
13 20 0.62
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (12 bp):
TTATTTTTTTTC
Found at i:330096 original size:18 final size:17
Alignment explanation
Indices: 330031--330084 Score: 51
Period size: 17 Copynumber: 3.4 Consensus size: 17
330021 ATATTATTTA
* *
330031 TTTATT-TTTCTTTTTA
1 TTTATTCTTTATTTTTT
* *
330047 TTT-TT-TTTACTTATT
1 TTTATTCTTTATTTTTT
330062 TTTATTCTTTATTTTTT
1 TTTATTCTTTATTTTTT
330079 TTTATT
1 TTTATT
330085 TATTCATTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
15 11 0.37
16 5 0.17
17 14 0.47
ACGTcount: A:0.13, C:0.06, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTATTCTTTATTTTTT
Found at i:332330 original size:16 final size:16
Alignment explanation
Indices: 332309--332342 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
332299 ATGAGCATCT
*
332309 AGCTTAACGAGTAACA
1 AGCTTAACAAGTAACA
332325 AGCTTAACAAGTAACA
1 AGCTTAACAAGTAACA
332341 AG
1 AG
332343 TCGAGCAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.47, C:0.18, G:0.18, T:0.18
Consensus pattern (16 bp):
AGCTTAACAAGTAACA
Found at i:332409 original size:31 final size:31
Alignment explanation
Indices: 332328--332412 Score: 107
Period size: 32 Copynumber: 2.7 Consensus size: 31
332318 AGTAACAAGC
* *
332328 TTAACAAGTAACAAGTCGAGCAACAAATTTTT
1 TTAACGAGT-ACAAGTCGAGCAACAAAATTTT
* **
332360 TTAACGAGCAACGTGTCGAGCAACAAAATTTT
1 TTAACGAG-TACAAGTCGAGCAACAAAATTTT
332392 TTAACGAGTACAAGTCGAGCA
1 TTAACGAGTACAAGTCGAGCA
332413 CTGCCTTACT
Statistics
Matches: 44, Mismatches: 8, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
31 10 0.23
32 34 0.77
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.25
Consensus pattern (31 bp):
TTAACGAGTACAAGTCGAGCAACAAAATTTT
Found at i:343276 original size:40 final size:42
Alignment explanation
Indices: 343176--343288 Score: 133
Period size: 40 Copynumber: 2.7 Consensus size: 42
343166 GAATATATTA
* *
343176 ATATTTTAAAATAAATAAAACAATATA-TTTATAATTATTTATC
1 ATATTTT-AAAT-AATTAAATAATATATTTTATAATTATTTATC
* *
343219 ATATTTTAAATAGTTAAATAATATGTTTTATAATTA-TT-TC
1 ATATTTTAAATAATTAAATAATATATTTTATAATTATTTATC
* *
343259 TTATTTTTAATAATTAAATAATATATTTTA
1 ATATTTTAAATAATTAAATAATATATTTTA
343289 ATGGTATAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
40 28 0.46
41 12 0.20
42 14 0.23
43 7 0.11
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (42 bp):
ATATTTTAAATAATTAAATAATATATTTTATAATTATTTATC
Found at i:343908 original size:23 final size:23
Alignment explanation
Indices: 343872--343936 Score: 85
Period size: 23 Copynumber: 2.8 Consensus size: 23
343862 ATTATCTAAT
*
343872 TTTTAAAATCATATTATTTATTTA
1 TTTT-AAATAATATTATTTATTTA
*
343896 TTTTAAATAATATTAATTATTTA
1 TTTTAAATAATATTATTTATTTA
* *
343919 TTTGAAATAGTATTATTT
1 TTTTAAATAATATTATTT
343937 TTAAATTGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
23 32 0.89
24 4 0.11
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (23 bp):
TTTTAAATAATATTATTTATTTA
Found at i:347068 original size:14 final size:14
Alignment explanation
Indices: 347049--347075 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
347039 ACAAATAAAC
347049 AATAATAATAATAT
1 AATAATAATAATAT
347063 AATAATAATAATA
1 AATAATAATAATA
347076 AAGTCTCCGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
AATAATAATAATAT
Found at i:348109 original size:27 final size:28
Alignment explanation
Indices: 348052--348111 Score: 113
Period size: 28 Copynumber: 2.2 Consensus size: 28
348042 AGACAACACC
348052 GCTTAAACTTATCCAAGGAAAAAAAGCG
1 GCTTAAACTTATCCAAGGAAAAAAAGCG
348080 GCTTAAACTTATCCAAGG-AAAAAAGCG
1 GCTTAAACTTATCCAAGGAAAAAAAGCG
348107 GCTTA
1 GCTTA
348112 CAGCAGGAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 14 0.44
28 18 0.56
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.20
Consensus pattern (28 bp):
GCTTAAACTTATCCAAGGAAAAAAAGCG
Found at i:348210 original size:30 final size:29
Alignment explanation
Indices: 348176--348254 Score: 72
Period size: 30 Copynumber: 2.7 Consensus size: 29
348166 TGTATTGGGT
* *
348176 GTTATTAAATTATATAAAATATTTTTTGTA
1 GTTATTAAATTATATAAAATA-TATTTATA
* *
348206 GTTATT--ATTATTTTAAATATATTTATA
1 GTTATTAAATTATATAAAATATATTTATA
* *
348233 TTTATTAAAATATTATAAAATA
1 GTTATTAAATTA-TATAAAATA
348255 ATCTTAATTT
Statistics
Matches: 38, Mismatches: 8, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
27 11 0.29
28 11 0.29
29 3 0.08
30 13 0.34
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (29 bp):
GTTATTAAATTATATAAAATATATTTATA
Found at i:348574 original size:12 final size:12
Alignment explanation
Indices: 348541--348574 Score: 59
Period size: 13 Copynumber: 2.8 Consensus size: 12
348531 TTGTATTTCA
348541 TTTTTATTTACT
1 TTTTTATTTACT
348553 TTTCTTATTTACT
1 TTT-TTATTTACT
348566 TTTTTATTT
1 TTTTTATTT
348575 TTTTTCAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTTATTTACT
Found at i:355217 original size:88 final size:88
Alignment explanation
Indices: 355068--355231 Score: 292
Period size: 88 Copynumber: 1.9 Consensus size: 88
355058 TATGTTATAT
*
355068 CATTTAACCGGAAATATTATCAAATACAATAACATATTAGGTAGTGCTTATATAATGTAATAGGT
1 CATTTAACCGGAAATATTATCAAATACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
355133 AGCACTTATATAATAAAAATAGA
66 AGCACTTATATAATAAAAATAGA
* *
355156 CATTTAACCGGAAATATTATTAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
1 CATTTAACCGGAAATATTATCAAATACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
*
355221 AGCGCTTATAT
66 AGCACTTATAT
355232 TGACCTATTT
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
88 72 1.00
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (88 bp):
CATTTAACCGGAAATATTATCAAATACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
AGCACTTATATAATAAAAATAGA
Found at i:355675 original size:200 final size:197
Alignment explanation
Indices: 355256--355714 Score: 602
Period size: 200 Copynumber: 2.3 Consensus size: 197
355246 ACTAAACCGA
* * *
355256 TATATTTATATCGA-TAACATTGCAAATTTACCTATTACATTATAATTATCGGTTTCGATATTTT
1 TATATTTATACCGAGT-ACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
* * *
355320 TGGGATTGATACAATTTTAAATGTATCGACACTTTATGCATACACCTCGTTGGGCATTCATTCTG
65 TGGGATCGATAC-ATTTTAAATGTATCGACACTTTATGCATACACCTCGTTGGACATTCATTATG
* *
355385 GAAAAAAGTATCGACACAAACTTAAAACGTGTCGATACATTATGTAGACCTATTTTCTCATAAAA
129 GAAAAAAGTATCGACACAAACTTAAAACGTGTCGATACATTATGTAGACATATTCTCTCATAAAA
355450 CTGG
194 CTGG
* *
355454 TATATTTCTACCGAGTACATTGTAAATTTACCTATTACATTGTAATTATCGGTTTCGATGTTTTT
1 TATATTTATACCGAGTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTT
* * *
355519 GGGATCGATAC-TTTTAATAACTGTATCGACACTTTATGCGTGCACCTCGTTTGACATTCATTAT
66 GGGATCGATACATTTT-A-AA-TGTATCGACACTTTATGCATACACCTCGTTGGACATTCATTAT
* *** ** * *
355583 GGACAAAATGTATCGACAC-TTTTTAAATTTGTGTCGATACGTTATGTTGACATATTCTCTCATA
128 GGA-AAAAAGTATCGACACAAACTTAAA-ACGTGTCGATACATTATGTAGACATATTCTCTCATA
355647 AAACTGG
191 AAACTGG
* * *
355654 TATATTTATACC-AGTTACATTGTAAATTTACCTATTACATTTTAATTATCGTTTTTGATGT
1 TATATTTATACCGAG-TACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGT
355715 AACATATGCG
Statistics
Matches: 229, Mismatches: 25, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
196 4 0.02
197 1 0.00
198 70 0.31
199 49 0.21
200 105 0.46
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (197 bp):
TATATTTATACCGAGTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTTT
GGGATCGATACATTTTAAATGTATCGACACTTTATGCATACACCTCGTTGGACATTCATTATGGA
AAAAAGTATCGACACAAACTTAAAACGTGTCGATACATTATGTAGACATATTCTCTCATAAAACT
GG
Found at i:356062 original size:327 final size:329
Alignment explanation
Indices: 355416--356120 Score: 1110
Period size: 327 Copynumber: 2.1 Consensus size: 329
355406 TTAAAACGTG
** * *
355416 TCGATACATTATGTAGACCTATTTTCTCATAAAACTGGTATATTTCTACCGAGTACATTGTAAAT
1 TCGATACA-TATGTTTACCTATTTTCTCATAAAACCGATATATTTCTACCGAGTACATTGTAAAT
*
355481 TTACCTATTACATTGTAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAACTGTATC
65 TTACCTATTACATTGTAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATC
*
355546 GACACTTTATGCGTGCACCTCGTTTGACATTCATTATGGACAAAATGTATCGACACTTTTTAAAT
130 GACACTTTATGCGTGCACCTCATTTGACATTCATTATGGACAAAATGTATCGACACTTTTTAAAT
* * *
355611 TTGTGTCGATACGTTATGTTGACATATTCTCTCATAAAACTGGTATATTTATACCAGTTACATTG
195 TTGTGTCGATACATTATGTTGACATATTCTCTCATAAAACCGATATATTTATACCAGTTACATTG
* * *
355676 TAAATTTACCTATTACATTTTAATTATCGTTTTTGATGTAACATATGCGTCGATACTTTTAGAAA
260 TAAATTTACCTATTACATTATAATTATCGGTTTCGATGTAACATATGCGTCGATACTTTTAGAAA
355741 ATGTA
325 ATGTA
* *
355746 TCGATACATATGTTTACCTATTTTCTCATAAAACCGATATA-TT-TATCGGGTACATTGTAAATT
1 TCGATACATATGTTTACCTATTTTCTCATAAAACCGATATATTTCTACCGAGTACATTGTAAATT
* * *
355809 TACCTATTACATTGTAATTATCGGTTTCGATTTTTTTTGGATTGATACTTTTAATAAATGTATCG
66 TACCTATTACATTGTAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCG
* *
355874 ACACTTTATGCGTGCACTTCATTTGACATTCATTATGGACAAAATGTATCGACATTTTTTAAATT
131 ACACTTTATGCGTGCACCTCATTTGACATTCATTATGGACAAAATGTATCGACACTTTTTAAATT
*
355939 TGTGTCGATACATTATGTTGACATATTCTCTCATAAAACCGATATATTTATACCGGTTACATTGT
196 TGTGTCGATACATTATGTTGACATATTCTCTCATAAAACCGATATATTTATACCAGTTACATTGT
* * *
356004 AAATTTATCTATTACATTATACTTATCGGTTTCGATGTAACATATGTGTCGATACTTTTAGAAAA
261 AAATTTACCTATTACATTATAATTATCGGTTTCGATGTAACATATGCGTCGATACTTTTAGAAAA
356069 TGTA
326 TGTA
* * * * * * *
356073 TCGACACATATGTTTACATATTCTGTCATTAAACTGCTATATTT-TACC
1 TCGATACATATGTTTACCTATTTTCTCATAAAACCGATATATTTCTACC
356121 TATTACTTTA
Statistics
Matches: 343, Mismatches: 31, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
327 299 0.87
328 7 0.02
329 29 0.08
330 8 0.02
ACGTcount: A:0.30, C:0.15, G:0.13, T:0.42
Consensus pattern (329 bp):
TCGATACATATGTTTACCTATTTTCTCATAAAACCGATATATTTCTACCGAGTACATTGTAAATT
TACCTATTACATTGTAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCG
ACACTTTATGCGTGCACCTCATTTGACATTCATTATGGACAAAATGTATCGACACTTTTTAAATT
TGTGTCGATACATTATGTTGACATATTCTCTCATAAAACCGATATATTTATACCAGTTACATTGT
AAATTTACCTATTACATTATAATTATCGGTTTCGATGTAACATATGCGTCGATACTTTTAGAAAA
TGTA
Found at i:357495 original size:21 final size:21
Alignment explanation
Indices: 357469--357523 Score: 110
Period size: 21 Copynumber: 2.6 Consensus size: 21
357459 CTACCGGTTC
357469 GTGTCGATCCAAATTAAAAAT
1 GTGTCGATCCAAATTAAAAAT
357490 GTGTCGATCCAAATTAAAAAT
1 GTGTCGATCCAAATTAAAAAT
357511 GTGTCGATCCAAA
1 GTGTCGATCCAAA
357524 ACGATATAAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.27
Consensus pattern (21 bp):
GTGTCGATCCAAATTAAAAAT
Found at i:357567 original size:20 final size:20
Alignment explanation
Indices: 357544--357581 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
357534 AGGTAAAACT
357544 ATGACAAAACCGGTATAGAA
1 ATGACAAAACCGGTATAGAA
*
357564 ATGATAAAACCGGTATAG
1 ATGACAAAACCGGTATAG
357582 CGCTACCGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.13, G:0.21, T:0.18
Consensus pattern (20 bp):
ATGACAAAACCGGTATAGAA
Found at i:357851 original size:181 final size:181
Alignment explanation
Indices: 357505--357971 Score: 654
Period size: 182 Copynumber: 2.6 Consensus size: 181
357495 GATCCAAATT
* * *
357505 AAAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACCGGTAT-AGAAATGAT
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCA-AAATGAT
* * * * *
357569 AAAACCGGT-ATAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACT
65 AAAACCGGTAAAAG-GATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACT
* *
357633 TCGTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTTTTA
129 TCGTGAATTTAAAAGAGAAACAGTTTTAAAGCCTATAAAGTGTCGATAC-TTTA
* ** *
357687 AAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAATTGGTATCAAAACGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* *
357752 AAACCGGTAAAAGGTTACCGGATATATTAAAAGTGTCGATACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAAGGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
* ** *
357816 GTGAATTTAAAAGAGAAATAGTTTTAGCGCCTATAATGTGTCGATACTTTA
131 GTGAATTTAAAAGAGAAACAGTTTTAAAGCCTATAAAGTGTCGATACTTTA
* * *
357867 AAAAA-ATATCGACCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* *
357931 AAACCGGTAAAATGATACCGGATATATTGAAAGTGTCGATA
66 AAACCGGTAAAAGGATACCGGATATATTAAAAGTGTCGATA
357972 TTTTCGTAAG
Statistics
Matches: 254, Mismatches: 29, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
179 90 0.35
180 9 0.04
181 59 0.23
182 92 0.36
183 4 0.02
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (181 bp):
AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACCGGTAAAAGGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAGAGAAACAGTTTTAAAGCCTATAAAGTGTCGATACTTTA
Found at i:357919 original size:20 final size:19
Alignment explanation
Indices: 357896--357942 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
357886 CGATATAACA
357896 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
357916 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
357936 GGTAAAA
1 GGTAAAA
357943 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:357944 original size:17 final size:19
Alignment explanation
Indices: 357905--357947 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
357895 AGGTAAAAAT
357905 ATGATAAAACCGGTATCAAA
1 ATGATAAAACCGG-ATCAAA
357925 ATGATAAAACCGG-T-AAA
1 ATGATAAAACCGGATCAAA
357942 ATGATA
1 ATGATA
357948 CCGGATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.39
18 1 0.04
20 13 0.57
ACGTcount: A:0.51, C:0.12, G:0.16, T:0.21
Consensus pattern (19 bp):
ATGATAAAACCGGATCAAA
Found at i:360181 original size:21 final size:21
Alignment explanation
Indices: 360141--360184 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
360131 AAGACAATCA
*
360141 AGAGTCGAAGAGAAATTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
360162 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
360183 AG
1 AG
360185 GCATAAGGGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.09, G:0.32, T:0.18
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:360260 original size:33 final size:33
Alignment explanation
Indices: 360218--360283 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
360208 AAATAGATGG
*
360218 AGTGGTGAAAGAAGTAGAGGCGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGCGTTAAGGGGTGA
* *
360251 AGTGGTGAAAGAAGTTGAGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGCGTTAAGGGGTGA
360284 TATTAAGATG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.30, C:0.02, G:0.47, T:0.21
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGCGTTAAGGGGTGA
Found at i:362091 original size:17 final size:18
Alignment explanation
Indices: 362069--362112 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 18
362059 AAATGTAGGT
362069 TAATTTTGTATA-ATTTA
1 TAATTTTGTATACATTTA
362086 TAATTTTGTATACGATTTA
1 TAATTTTGTATAC-ATTTA
*
362105 TATTTTTG
1 TAATTTTG
362113 CATGTGAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 12 0.50
19 12 0.50
ACGTcount: A:0.30, C:0.02, G:0.09, T:0.59
Consensus pattern (18 bp):
TAATTTTGTATACATTTA
Found at i:362769 original size:200 final size:200
Alignment explanation
Indices: 362230--363179 Score: 1542
Period size: 200 Copynumber: 4.9 Consensus size: 200
362220 CAATATGGCC
* * *
362230 AACATGGTGCAACCATAAAGTGTCGAACCATATATAAAAAGTGTAGATCCCAAAAACATCGAAAC
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAC
* *
362295 CCAAAAGTATAATATAATATATAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
66 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
362360 GAATATGTCTAAATAATGTGTCGACAC-TTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
131 GAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
362424 TGG-A
196 TGGAA
* *
362428 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAGCATCGAAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAC
362493 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
66 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
*
362558 GAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGTTCCAGAATGAA
131 GAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
362623 TGGAA
196 TGGAA
362628 AACAAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCG-AA
1 AAC-AGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAA
*
362692 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAATATACCGGTTTTATGAG
65 CCCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAG
* * *
362757 AGAATATGTCTAAATAATATGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGTTCCAGACTGA
130 AGAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGA
362822 ATGGAA
195 ATGGAA
*
362828 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAA
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAC
*
362893 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTTTGAGA
66 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
362958 GAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATA-TTTTGGTCCAGAATGAA
131 GAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
363022 TGGAA
196 TGGAA
* * *
363027 AACAGGGTGCAACCATAAAGTGTCGATCC-----CAAAAA----C-AT--C--GAAC--C-CAA-
1 AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAC
363074 ----AAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGG-TTTATGAGA
66 CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
363134 GAATATGTCTAAATAATGTGTCGACAC-TTTTTAGTTTGTGTCGATA
131 GAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATA
363180 CTAATTTAAA
Statistics
Matches: 725, Mismatches: 23, Indels: 31
0.93 0.03 0.04
Matches are distributed among these distances:
175 19 0.03
176 35 0.05
177 51 0.07
182 2 0.00
183 1 0.00
185 3 0.00
187 1 0.00
189 2 0.00
190 1 0.00
194 5 0.01
198 150 0.21
199 146 0.20
200 252 0.35
201 57 0.08
ACGTcount: A:0.37, C:0.15, G:0.17, T:0.31
Consensus pattern (200 bp):
AACAGGGTGCAACCATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAAACATCGAAAC
CCAAAAGTATAATGTAATATGTAATTTTTCAATCTAACCGGTACAAGTATACCGGTTTTATGAGA
GAATATGTCTAAATAATGTGTCGACACTTTTTTAGTTTGTGTCGATATTTTTGGTCCAGAATGAA
TGGAA
Found at i:364589 original size:6 final size:6
Alignment explanation
Indices: 364578--364671 Score: 66
Period size: 6 Copynumber: 15.7 Consensus size: 6
364568 CAAGCGGTCA
* * * *
364578 ATGAAG ATGAAG CT-AACG ATGAAG ATGACG ATGATG ATGACG ATGAAG
1 ATGAAG ATGAAG ATGAA-G ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG
* * * * * *
364626 CTGACA- ATGAAG ATGATG ACGATG ATGATG ATGATG ATGAAG ATGA
1 ATGA-AG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGAAG ATGA
364672 TGATCCAAAC
Statistics
Matches: 72, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
5 3 0.04
6 66 0.92
7 3 0.04
ACGTcount: A:0.40, C:0.07, G:0.31, T:0.21
Consensus pattern (6 bp):
ATGAAG
Found at i:364599 original size:18 final size:18
Alignment explanation
Indices: 364578--364641 Score: 74
Period size: 18 Copynumber: 3.6 Consensus size: 18
364568 CAAGCGGTCA
*
364578 ATGAAGATGAAGCTAACG
1 ATGAAGATGAAGCTGACG
* * *
364596 ATGAAGATGACGATGATG
1 ATGAAGATGAAGCTGACG
* *
364614 ATGACGATGAAGCTGACA
1 ATGAAGATGAAGCTGACG
364632 ATGAAGATGA
1 ATGAAGATGA
364642 TGACGATGAT
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 36 1.00
ACGTcount: A:0.42, C:0.09, G:0.30, T:0.19
Consensus pattern (18 bp):
ATGAAGATGAAGCTGACG
Found at i:364600 original size:12 final size:12
Alignment explanation
Indices: 364578--364671 Score: 80
Period size: 12 Copynumber: 7.8 Consensus size: 12
364568 CAAGCGGTCA
*
364578 ATGAAGATGAAG
1 ATGACGATGAAG
* *
364590 CTAACGATGAAG
1 ATGACGATGAAG
*
364602 ATGACGATGATG
1 ATGACGATGAAG
364614 ATGACGATGAAG
1 ATGACGATGAAG
* *
364626 CTGACAATGAAG
1 ATGACGATGAAG
* * *
364638 ATGATGACGATG
1 ATGACGATGAAG
* *
364650 ATGATGATGATG
1 ATGACGATGAAG
*
364662 ATGAAGATGA
1 ATGACGATGA
364672 TGATCCAAAC
Statistics
Matches: 66, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 66 1.00
ACGTcount: A:0.40, C:0.07, G:0.31, T:0.21
Consensus pattern (12 bp):
ATGACGATGAAG
Found at i:364636 original size:36 final size:36
Alignment explanation
Indices: 364578--364659 Score: 110
Period size: 36 Copynumber: 2.3 Consensus size: 36
364568 CAAGCGGTCA
* *
364578 ATGAAGATGAAGCTAACGATGAAGATGACGATGATG
1 ATGAAGATGAAGCTAACAATGAAGATGACGACGATG
* * *
364614 ATGACGATGAAGCTGACAATGAAGATGATGACGATG
1 ATGAAGATGAAGCTAACAATGAAGATGACGACGATG
*
364650 ATGATGATGA
1 ATGAAGATGA
364660 TGATGAAGAT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 40 1.00
ACGTcount: A:0.40, C:0.09, G:0.30, T:0.21
Consensus pattern (36 bp):
ATGAAGATGAAGCTAACAATGAAGATGACGACGATG
Found at i:364663 original size:9 final size:9
Alignment explanation
Indices: 364595--364675 Score: 72
Period size: 9 Copynumber: 9.0 Consensus size: 9
364585 TGAAGCTAAC
*
364595 GATGAAGAT
1 GATGATGAT
*
364604 GACGATGAT
1 GATGATGAT
*
364613 GATGACGAT
1 GATGATGAT
* * *
364622 GAAGCTGAC
1 GATGATGAT
* *
364631 AATGAAGAT
1 GATGATGAT
*
364640 GATGACGAT
1 GATGATGAT
364649 GATGATGAT
1 GATGATGAT
*
364658 GATGATGAA
1 GATGATGAT
364667 GATGATGAT
1 GATGATGAT
364676 CCAAACAAGT
Statistics
Matches: 54, Mismatches: 18, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
9 54 1.00
ACGTcount: A:0.38, C:0.06, G:0.32, T:0.23
Consensus pattern (9 bp):
GATGATGAT
Found at i:366286 original size:23 final size:23
Alignment explanation
Indices: 366255--366327 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
366245 ATAGGTAAAA
*
366255 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
366278 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
366301 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
366324 ATAT
1 ATAT
366328 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:366979 original size:183 final size:183
Alignment explanation
Indices: 366705--367196 Score: 891
Period size: 183 Copynumber: 2.7 Consensus size: 183
366695 GTAATGCTAT
* *
366705 CGGTATAAATATACCGG-TTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
1 CGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATATT
*
366769 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATA-CATTGTCAAAAAGTGTCGAC
66 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATT-TAAAAAAGTGTCGAC
*
366833 ATTTACACATC-AGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAAC
130 ATTTACACATCGA-AACCCAGAATTATAATGTAATAGATAATTTTGTAATATAAC
366887 CGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATATT
1 CGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATATT
*
366952 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTTGATACCATTTAAAAAAGTGTCGACA
66 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCGACA
*
367017 TTTACACATCGAAACCCAGATTTATAATGTAATAGATAATTTTGTAATATAAC
131 TTTACACATCGAAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAAC
367070 CGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATATT
1 CGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATATT
367135 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCG
66 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCG
367197 GTAATTTTAA
Statistics
Matches: 300, Mismatches: 7, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
182 17 0.06
183 278 0.93
184 5 0.02
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (183 bp):
CGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTCTAATATT
GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCGACA
TTTACACATCGAAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAAC
Found at i:369689 original size:25 final size:25
Alignment explanation
Indices: 369661--369725 Score: 112
Period size: 25 Copynumber: 2.6 Consensus size: 25
369651 TTATCATTAA
369661 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
369686 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
* *
369711 AATTAGGTATATACA
1 ATTTAGGTATGTACA
369726 TCTTTTGAGT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.35
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:370103 original size:23 final size:23
Alignment explanation
Indices: 370072--370134 Score: 92
Period size: 22 Copynumber: 2.8 Consensus size: 23
370062 ATATGTAAAA
*
370072 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
370095 ATATAATGTAATA-GTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
370117 ATATAATGTAATAGGTAG
1 ATATAATGTAATAGGTAG
370135 TAGTTATATT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 20 0.57
23 15 0.43
ACGTcount: A:0.37, C:0.05, G:0.21, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:370142 original size:45 final size:42
Alignment explanation
Indices: 370072--370154 Score: 105
Period size: 45 Copynumber: 1.9 Consensus size: 42
370062 ATATGTAAAA
* *
370072 ATATGATGTAATAGGTAGCGCTTATATAATGTAATAGTATCGTTT
1 ATATAATGTAATAGGTAGAGCTTATAT--TGTAA-AGTATCGTTT
370117 ATATAATGTAATAGGTAGTAG-TTATATTGTAAAGTATC
1 ATATAATGTAATAGGTAG-AGCTTATATTGTAAAGTATC
370155 TATCCTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
42 6 0.17
43 5 0.14
45 23 0.66
46 1 0.03
ACGTcount: A:0.36, C:0.05, G:0.19, T:0.40
Consensus pattern (42 bp):
ATATAATGTAATAGGTAGAGCTTATATTGTAAAGTATCGTTT
Found at i:370171 original size:20 final size:20
Alignment explanation
Indices: 370146--370184 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
370136 AGTTATATTG
*
370146 TAAAGTATCTATCCTTTTTA
1 TAAAGTATCTATACTTTTTA
*
370166 TAAAGTGTCTATACTTTTT
1 TAAAGTATCTATACTTTTT
370185 TACTGTGGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.13, G:0.08, T:0.51
Consensus pattern (20 bp):
TAAAGTATCTATACTTTTTA
Found at i:370530 original size:23 final size:23
Alignment explanation
Indices: 370499--370571 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
370489 ATAGGTAAAA
*
370499 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
370522 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
370545 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
370568 ATAT
1 ATAT
370572 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:370738 original size:428 final size:428
Alignment explanation
Indices: 369877--371158 Score: 2264
Period size: 421 Copynumber: 3.0 Consensus size: 428
369867 TGTTAAATTT
* *
369877 AAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGTAAATGAAATTA
1 AAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTA
*
369942 TTAAATTAATATTGTAGGTGGAAAACATGAAACACTGTT-AAAAAAATTGAAACATAAATTACAT
66 TTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACAT
* *
370006 AACTTTTAAAAAAAGTATCGATCCTTTTTATAAAAAGTATGGACACTTTCAATATAATATGTAAA
131 AAC-TTTAAAAGAAGTATCGATCC-TTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAA
370071 AATATGATGTAATAGGTAGCGCTTATATAATGTAATA-GTATCGTTTATATAATGTAATAGGTAG
194 AATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAG
*
370135 TAGTTATATTGTAAAGTATCTATCCTTTTTAT-AAAGTGTCTATACTTTTTT-ACTGTGGAAAAC
259 TGGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATACTTTTTTCACTGTGGAAAAC
370198 ATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAAT
324 ATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAAT
* **
370263 GATTTATTTTTTACGTTACGATATATATTATTGTTAAATTT
389 GATTTATTTTTTACGTTACGA-ATATATTATTATTAAATAA
*
370304 AAATTCTAAATAATATTTTATAAAATATCAAAACAATTAAATAATTTTTTTGTGCAAATGAAATT
1 AAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAA-TTTTTTGTGCAAATGAAATT
370369 ATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACA
65 ATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACA
370434 TAACTTTAAAAGAAGTATCGATCCTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAA
130 TAACTTTAAAAGAAGTATCGATCCTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAA
370499 ATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGT
195 ATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGT
*
370564 GGTTATATTGTAAAGTATCTATCTTTTTTATAAAAGTGTCTATACTTTTTTCACTGTGGAAAACA
260 GGTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATACTTTTTTCACTGTGGAAAACA
*
370629 TTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATATGCGTCTAATG
325 TTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATG
370694 ATTTA-TTTTTACGTTACG-ATATATTATTATTAAATAAA
390 ATTTATTTTTTACGTTACGAATATATTATTATTAAAT-AA
370732 AAATTCTAAATAATATTTTA-AAAATATCAAAACAATCAAATAA-TTTTTGTGCAAATGAAATTA
1 AAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTA
370795 TTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACAT-AATTACAT
66 TTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACAT
370859 AACTTTAAAAGAAGTATCGATCCTTTTAT-AAAAGTATGGACACTTTCAATATAATAGGT-AAAA
131 AACTTTAAAAGAAGTATCGATCCTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAA
*
370922 -ATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGTTTATATAATGTAATAGGTAGTG
196 TATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGTG
* * * *
370986 CTTATATTGTAAAGTATCTATCCTTTTTATAAAAATGTCCATACTTTTTTCACTGTAGAAAACAT
261 GTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATACTTTTTTCACTGTGGAAAACAT
371051 TAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGA
326 TAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGA
371116 TTTATTTTTTACGTTACGATATATATTATTATTAAATTAA
391 TTTATTTTTTACGTTACGA-ATATATTATTATTAAA-TAA
371156 AAA
1 AAA
371159 CAATAAACAT
Statistics
Matches: 825, Mismatches: 20, Indels: 23
0.95 0.02 0.03
Matches are distributed among these distances:
421 191 0.23
422 17 0.02
423 30 0.04
424 58 0.07
425 77 0.09
427 156 0.19
428 154 0.19
429 60 0.07
430 82 0.10
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.39
Consensus pattern (428 bp):
AAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTTTGTGCAAATGAAATTA
TTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATTGAAACATAAATTACAT
AACTTTAAAAGAAGTATCGATCCTTTTATAAAAAGTATGGACACTTTCAATATAATAGGTAAAAA
TATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTATCGTTTATATAATGTAATAGGTAGTG
GTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCTATACTTTTTTCACTGTGGAAAACAT
TAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCTAATGA
TTTATTTTTTACGTTACGAATATATTATTATTAAATAA
Found at i:370951 original size:23 final size:23
Alignment explanation
Indices: 370925--370992 Score: 118
Period size: 23 Copynumber: 3.0 Consensus size: 23
370915 GGTAAAAATG
370925 ATGTAATAGGTAGCGCTTATATA
1 ATGTAATAGGTAGCGCTTATATA
*
370948 ATGTAATAGGTAGCGTTTATATA
1 ATGTAATAGGTAGCGCTTATATA
*
370971 ATGTAATAGGTAGTGCTTATAT
1 ATGTAATAGGTAGCGCTTATAT
370993 TGTAAAGTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.34, C:0.06, G:0.22, T:0.38
Consensus pattern (23 bp):
ATGTAATAGGTAGCGCTTATATA
Found at i:376524 original size:2 final size:2
Alignment explanation
Indices: 376517--376597 Score: 57
Period size: 2 Copynumber: 43.0 Consensus size: 2
376507 TTCCTTTATT
* * * *
376517 TA TA TA TA TA TA TA TA TA TA TA TA TT TT TA TG TA TA -A T- TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
376557 TA T- TT TA T- TT TA T- TA TA CT- 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
376596 TA
1 TA
376598 CATAATCATC
Statistics
Matches: 65, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
1 6 0.09
2 58 0.89
3 1 0.02
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (2 bp):
TA
Found at i:376726 original size:37 final size:38
Alignment explanation
Indices: 376651--376738 Score: 94
Period size: 37 Copynumber: 2.4 Consensus size: 38
376641 GTATATAAAC
* *
376651 ATATTTTTTT-TCTTTTATTATTATATGTATATTCTTT
1 ATATTTTTTTATCTTTTATTATTATATGTATAGTATTT
* *
376688 ATATTTTTTTAT-TTTTATTTTTTTACTGTAT-GTATTT
1 ATATTTTTTTATCTTTTATTATTATA-TGTATAGTATTT
376725 AT-TTTTATTTATCT
1 ATATTTT-TTTATCT
376739 CTATACATAA
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
36 4 0.09
37 32 0.74
38 7 0.16
ACGTcount: A:0.20, C:0.05, G:0.03, T:0.72
Consensus pattern (38 bp):
ATATTTTTTTATCTTTTATTATTATATGTATAGTATTT
Found at i:377105 original size:27 final size:27
Alignment explanation
Indices: 377026--377115 Score: 76
Period size: 27 Copynumber: 3.3 Consensus size: 27
377016 TTTTTAGTTT
*
377026 TTTATTTATTTATTACTATTATATATATC
1 TTTA-TTA-TTATTACCATTATATATATC
* * * * *
377055 -TTCTTATTTTTCCCATTGTTTATATC
1 TTTATTATTATTACCATTATATATATC
*
377081 TTTATTATTATTACCATCATATATATTC
1 TTTATTATTATTACCATTATATATA-TC
377109 TTT-TTAT
1 TTTATTAT
377116 ATTCTATATT
Statistics
Matches: 47, Mismatches: 12, Indels: 6
0.72 0.18 0.09
Matches are distributed among these distances:
26 15 0.32
27 25 0.53
28 7 0.15
ACGTcount: A:0.26, C:0.12, G:0.01, T:0.61
Consensus pattern (27 bp):
TTTATTATTATTACCATTATATATATC
Found at i:387582 original size:55 final size:57
Alignment explanation
Indices: 387489--387597 Score: 159
Period size: 56 Copynumber: 1.9 Consensus size: 57
387479 AATACTTCGC
* * *
387489 TTAGGATGAAAACCCGAGAGGGCGTCCTAAGTTGAAAAAAAA-AAAAAAAAAAACGT
1 TTAGGATGAAAACCCGAGAGGGCGCCCTAAATTAAAAAAAAAGAAAAAAAAAAACGT
* *
387545 TTAGGGTGAAAACCCGA-AGGGCGCCCTAAATTAAAAAAAAAGAAAAAGAAAAA
1 TTAGGATGAAAACCCGAGAGGGCGCCCTAAATTAAAAAAAAAGAAAAAAAAAAA
387598 GAAGAGAAAA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
55 21 0.45
56 26 0.55
ACGTcount: A:0.53, C:0.13, G:0.21, T:0.13
Consensus pattern (57 bp):
TTAGGATGAAAACCCGAGAGGGCGCCCTAAATTAAAAAAAAAGAAAAAAAAAAACGT
Found at i:388750 original size:209 final size:211
Alignment explanation
Indices: 388335--389231 Score: 1456
Period size: 209 Copynumber: 4.3 Consensus size: 211
388325 AGGTTTTACC
388335 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
388400 ACGAAGGGACCGCTGGTTGTCAACAAATATTTCTC-AATGTCAGAGCCAATTTCAACTTCACAAC
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAAT-TCAGAGCCAATTTCAACTTCACAAC
*
388464 GAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
130 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
* *
388529 AAAC-ATTTCTCAA-TA
195 AAACAACTTCTCAATTT
*
388544 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
388609 ACGAAGGGACCGCTGGTTGTCAAC-AACATTTCTCAAATACAGAGCCAATTTCAACTTCACAACG
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACG
*
388673 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATA
131 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
*
388738 AGCAACTTCTCAATTT
196 AACAACTTCTCAATTT
388754 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
388819 ACGAAGGGACCGCTGGTTGTCAAC-AACATTTCTCAAATTCATAGCCAATTTCAACTTCAC-ACG
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACG
388882 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
131 AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
388947 AACAACTTCTCAATTT
196 AACAACTTCTCAATTT
* *
388963 CAGAGCCAATTTCAACTTCACATCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * * *
389028 GCGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACGTCACAAC
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAAATTCAGAGCCAATTTCAACTTCACAAC
*
389093 GAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTC-A-
130 GAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAAC
*
389156 ATA-AA-----CAATTT
195 AAACAACTTCTCAATTT
*
389167 C----CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTAC-C-AGTTCAACTTCA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACA--ACGCAAGTTCAACTTCA
389226 CGACGA
64 CGACGA
389232 GGATGTCATT
Statistics
Matches: 656, Mismatches: 24, Indels: 25
0.93 0.03 0.04
Matches are distributed among these distances:
200 57 0.09
201 1 0.00
202 2 0.00
204 7 0.01
208 99 0.15
209 269 0.41
210 128 0.20
211 30 0.05
212 63 0.10
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (211 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATTCAGAGCCAATTTCAACTTCACAACG
AAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACA
AACAACTTCTCAATTT
Found at i:388800 original size:106 final size:105
Alignment explanation
Indices: 388335--389231 Score: 1427
Period size: 106 Copynumber: 8.7 Consensus size: 105
388325 AGGTTTTACC
388335 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
388400 ACGAAGGGACCGCTGGTTGTCAACAA-ATATTTCTCAATGT
66 ACGAAGGGACCGCTGGTTGTCAACAACA-ATTTCTCAATTT
*
388440 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
388505 ACGAAGGGACCGCTGGTTGTCAACAA-ACATTTCTCAA-TA
66 ACGAAGGGACCGCTGGTTGTCAACAACA-ATTTCTCAATTT
*
388544 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
388609 ACGAAGGGACCGCTGGTTGTCAACAAC-ATTTCTCAAATA
66 ACGAAGGGACCGCTGGTTGTCAACAACAATTTCTCAATTT
388648 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
388713 ACGAAGGGACCGCTGGTTGTCAATAAGCAACTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAA-CAATTTCTCAATTT
388754 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
388819 ACGAAGGGACCGCTGGTTGTCAACAAC-ATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAACAATTTCTCAATTT
*
388858 CATAGCCAATTTCAACTTCAC-ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
388922 ACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAAC-AACAATTTCTCAATTT
* *
388963 CAGAGCCAATTTCAACTTCACATCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
389028 GCGAAGGGACCGCTGGTTGTCAACAAACAACTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAAC-AACAATTTCTCAATTT
* *
389069 CAGAGCCAATTTCAACGTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
389134 ACGAAGGGACCGCTGGTTGTCAA-TA-AA-----CAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAACAATTTCTCAATTT
*
389167 C----CCAATTTCAACTTCACAACGAAGGATATTGGACTCAAGACAGTAC-C-AGTTCAACTTCA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACA--ACGCAAGTTCAACTTCA
389226 CGACGA
64 CGACGA
389232 GGATGTCATT
Statistics
Matches: 756, Mismatches: 27, Indels: 29
0.93 0.03 0.04
Matches are distributed among these distances:
94 57 0.08
95 1 0.00
96 2 0.00
98 7 0.01
103 78 0.10
104 216 0.29
105 132 0.17
106 263 0.35
ACGTcount: A:0.34, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAACAATTTCTCAATTT
Found at i:390592 original size:2 final size:2
Alignment explanation
Indices: 390585--390613 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
390575 ATTCCTTTAT
390585 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
390614 TTTATGTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:391832 original size:49 final size:50
Alignment explanation
Indices: 391775--391879 Score: 151
Period size: 49 Copynumber: 2.1 Consensus size: 50
391765 TATATAACTT
*
391775 TTAATATCATATTTAATATT-AAA-ATTTTTGATACATTTTAGAGCTAATA
1 TTAATATCATATTTAATATTAAAATATTTTTGATACATTTTA-AACTAATA
* *
391824 TTAATATCATGTTTAATATTAAAATTATTTTTGATAGATTTTAAACTAATA
1 TTAATATCATATTTAATATTAAAA-TATTTTTGATACATTTTAAACTAATA
391875 TTAAT
1 TTAAT
391880 TTTTGAAGAG
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
49 19 0.38
50 3 0.06
51 12 0.24
52 16 0.32
ACGTcount: A:0.41, C:0.05, G:0.06, T:0.49
Consensus pattern (50 bp):
TTAATATCATATTTAATATTAAAATATTTTTGATACATTTTAAACTAATA
Done.