Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009175.1 Hibiscus syriacus cultivar Beakdansim tig00112738_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: 10629029
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 51
Found at i:212173 original size:17 final size:15
Alignment explanation
Indices: 212159--212200 Score: 70
Period size: 14 Copynumber: 2.9 Consensus size: 15
212149 TTTTTTTCCT
212159 TTTTCTTTCTTTTTC
1 TTTTCTTTCTTTTTC
212174 TTTTCTTT-TTTTTC
1 TTTTCTTTCTTTTTC
212188 -TTTCTTTCTTTTT
1 TTTTCTTTCTTTTT
212201 TCTTCAAGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.27
14 11 0.42
15 8 0.31
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTCTTTCTTTTTC
Found at i:212185 original size:24 final size:24
Alignment explanation
Indices: 212158--212204 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
212148 CTTTTTTTCC
212158 TTTTTCTTTCTTT-TTCTTTTCTTT
1 TTTTTCTTTCTTTCTT-TTTTCTTT
212182 TTTTTCTTTCTTTCTTTTTTCTT
1 TTTTTCTTTCTTTCTTTTTTCTT
212205 CAAGCATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 20 0.91
25 2 0.09
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (24 bp):
TTTTTCTTTCTTTCTTTTTTCTTT
Found at i:219417 original size:15 final size:15
Alignment explanation
Indices: 219394--219425 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
219384 TGAAATGAAT
219394 AATGAATGTATGCAA
1 AATGAATGTATGCAA
*
219409 AATGCATGTATGCAA
1 AATGAATGTATGCAA
219424 AA
1 AA
219426 AGGTATTGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.25
Consensus pattern (15 bp):
AATGAATGTATGCAA
Found at i:224790 original size:3 final size:3
Alignment explanation
Indices: 224784--224851 Score: 91
Period size: 3 Copynumber: 22.0 Consensus size: 3
224774 ATATTTTTTT
* *
224784 TAA TAA TAA TAA TAA TATA TATA TAA TAA TAA TAA TAA TAA TTA TGA
1 TAA TAA TAA TAA TAA TA-A TA-A TAA TAA TAA TAA TAA TAA TAA TAA
*
224831 TAA TAA TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA
224852 AATGGGTAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
3 52 0.88
4 7 0.12
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:224802 original size:26 final size:26
Alignment explanation
Indices: 224784--224851 Score: 102
Period size: 26 Copynumber: 2.6 Consensus size: 26
224774 ATATTTTTTT
224784 TAATAATAATAATAATATATATATAA
1 TAATAATAATAATAATATATATATAA
224810 TAATAATAATAATAAT-TATGATAATAA
1 TAATAATAATAATAATATAT-AT-ATAA
*
224837 TTATAATAATAATAA
1 TAATAATAATAATAA
224852 AATGGGTAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
25 3 0.08
26 18 0.46
27 18 0.46
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (26 bp):
TAATAATAATAATAATATATATATAA
Found at i:225574 original size:25 final size:25
Alignment explanation
Indices: 225520--225574 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
225510 TAACGTGTAC
225520 TATTTTAATGAATTTTCAACTATTT
1 TATTTTAATGAATTTTCAACTATTT
* *
225545 AATTTTAAAT-AATTTTCGAA-TTTTT
1 TATTTT-AATGAATTTTC-AACTATTT
225570 TATTT
1 TATTT
225575 ATGATTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
25 20 0.80
26 5 0.20
ACGTcount: A:0.33, C:0.05, G:0.04, T:0.58
Consensus pattern (25 bp):
TATTTTAATGAATTTTCAACTATTT
Found at i:225591 original size:24 final size:25
Alignment explanation
Indices: 225564--225617 Score: 69
Period size: 24 Copynumber: 2.2 Consensus size: 25
225554 TAATTTTCGA
225564 ATTTTTTATTT-AT-GATTTTTATTT
1 ATTTTTTATTTAATAG-TTTTTATTT
*
225588 ATTTTATATTTAATAGTTTTTATTT
1 ATTTTTTATTTAATAGTTTTTATTT
225613 -TTTTT
1 ATTTTT
225618 AATGTTCTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 14 0.54
25 11 0.42
26 1 0.04
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.74
Consensus pattern (25 bp):
ATTTTTTATTTAATAGTTTTTATTT
Found at i:226288 original size:27 final size:27
Alignment explanation
Indices: 226250--226302 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
226240 ATGAAGATCT
*
226250 TGATGCTGTGGACTTTCAAGTTCAAAG
1 TGATGCTATGGACTTTCAAGTTCAAAG
*
226277 TGATGCTATGGAGTTTCAAGTTCAAA
1 TGATGCTATGGACTTTCAAGTTCAAA
226303 ATGGTGATGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.28, C:0.13, G:0.25, T:0.34
Consensus pattern (27 bp):
TGATGCTATGGACTTTCAAGTTCAAAG
Found at i:234894 original size:12 final size:11
Alignment explanation
Indices: 234848--234897 Score: 55
Period size: 11 Copynumber: 4.4 Consensus size: 11
234838 CTTTTAATTT
234848 AAATTTTTTTA
1 AAATTTTTTTA
* *
234859 ATATATTTTTA
1 AAATTTTTTTA
*
234870 ATATATTTTTTA
1 AAAT-TTTTTTA
234882 AAATTTTTATTA
1 AAATTTTT-TTA
234894 AAAT
1 AAAT
234898 AATATATTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
11 17 0.52
12 16 0.48
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
AAATTTTTTTA
Found at i:234904 original size:29 final size:31
Alignment explanation
Indices: 234868--234927 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
234858 AATATATTTT
*
234868 TAATATATTTTT-TAAAATTTTTAT-TAAAA
1 TAATATATTTTTATAAAAATTTTATCTAAAA
234897 TAATATATTTTTATAAAAATTTTATCTAAAA
1 TAATATATTTTTATAAAAATTTTATCTAAAA
234928 CTCACCCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 12 0.43
30 11 0.39
31 5 0.18
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (31 bp):
TAATATATTTTTATAAAAATTTTATCTAAAA
Found at i:235254 original size:24 final size:24
Alignment explanation
Indices: 235185--235276 Score: 77
Period size: 23 Copynumber: 4.0 Consensus size: 24
235175 TTAGGGTTAG
*
235185 GGTT-AAATGATTT-GGGTTTTTTA
1 GGTTAAAATGATTTATGG-TTTTTA
* *
235208 GGTTAAAATG-GTTATGATTTTTA
1 GGTTAAAATGATTTATGGTTTTTA
*
235231 TGTTAAAATGATTTATGGTTTTTA
1 GGTTAAAATGATTTATGGTTTTTA
* *
235255 GAG-TAAAGTGGTTTA-GGTTTTT
1 G-GTTAAAATGATTTATGGTTTTT
235277 TTTTTGTTTA
Statistics
Matches: 56, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
23 28 0.50
24 27 0.48
25 1 0.02
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (24 bp):
GGTTAAAATGATTTATGGTTTTTA
Found at i:235972 original size:36 final size:36
Alignment explanation
Indices: 235924--236025 Score: 120
Period size: 36 Copynumber: 2.8 Consensus size: 36
235914 AATGGAAGGC
*
235924 TTATGTCCTTAATGTATTGTGTTA-GGTTTATTGTTT
1 TTATGTCCTTAATGTATTGT-TTATGATTTATTGTTT
* *
235960 TTATGTCTTTAATGTATTGTTTATGATTTGTTGTTT
1 TTATGTCCTTAATGTATTGTTTATGATTTATTGTTT
*
235996 TTATGTCC-TAACTGTAATTG-TTATGGTTTA
1 TTATGTCCTTAA-TGT-ATTGTTTATGATTTA
236026 GGATTTAATG
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
35 6 0.11
36 47 0.82
37 4 0.07
ACGTcount: A:0.19, C:0.06, G:0.18, T:0.58
Consensus pattern (36 bp):
TTATGTCCTTAATGTATTGTTTATGATTTATTGTTT
Found at i:243303 original size:33 final size:33
Alignment explanation
Indices: 243266--243367 Score: 93
Period size: 33 Copynumber: 3.1 Consensus size: 33
243256 GATATATTCG
*
243266 GTTTATATATATTTACGAATAAGCTCATTATTA
1 GTTTATATATATTTACGAATAAGATCATTATTA
* ** *
243299 GTTTATTTATAAAT-CTGAATAGAGAT-A-TATTTG
1 GTTTATATATATTTAC-GAATA-AGATCATTA-TTA
* *
243332 GTTTATATATATTTACAAATAAGTTCATTATTA
1 GTTTATATATATTTACGAATAAGATCATTATTA
243365 GTT
1 GTT
243368 CATTTATGTG
Statistics
Matches: 52, Mismatches: 11, Indels: 12
0.69 0.15 0.16
Matches are distributed among these distances:
32 6 0.12
33 40 0.77
34 6 0.12
ACGTcount: A:0.36, C:0.06, G:0.11, T:0.47
Consensus pattern (33 bp):
GTTTATATATATTTACGAATAAGATCATTATTA
Found at i:243318 original size:66 final size:66
Alignment explanation
Indices: 243248--243374 Score: 209
Period size: 66 Copynumber: 1.9 Consensus size: 66
243238 TAAATAAACA
* * *
243248 TGAATATAGATATATTCGGTTTATATATATTTACGAATAAGCTCATTATTAGTTTATTTATAAAT
1 TGAATAGAGATATATTCGGTTTATATATATTTACAAATAAGCTCATTATTAGTTCATTTATAAAT
243313 C
66 C
* *
243314 TGAATAGAGATATATTTGGTTTATATATATTTACAAATAAGTTCATTATTAGTTCATTTAT
1 TGAATAGAGATATATTCGGTTTATATATATTTACAAATAAGCTCATTATTAGTTCATTTAT
243375 GTGCTCATTT
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 56 1.00
ACGTcount: A:0.36, C:0.06, G:0.11, T:0.46
Consensus pattern (66 bp):
TGAATAGAGATATATTCGGTTTATATATATTTACAAATAAGCTCATTATTAGTTCATTTATAAAT
C
Found at i:243862 original size:23 final size:23
Alignment explanation
Indices: 243822--243868 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
243812 AATAAAAATC
*
243822 TATGTTTTTGTAATACATTTTTT
1 TATGTTTTTGTAACACATTTTTT
**
243845 TATGTTTTTGTGGCACATTTTTT
1 TATGTTTTTGTAACACATTTTTT
243868 T
1 T
243869 CTTCTGCTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.17, C:0.06, G:0.13, T:0.64
Consensus pattern (23 bp):
TATGTTTTTGTAACACATTTTTT
Found at i:250484 original size:18 final size:18
Alignment explanation
Indices: 250437--250489 Score: 74
Period size: 16 Copynumber: 3.1 Consensus size: 18
250427 CACACGTAAC
250437 CCAATCATTTAAATTAAG
1 CCAATCATTTAAATTAAG
*
250455 CCTATC--TTAAATTAAG
1 CCAATCATTTAAATTAAG
*
250471 CCAATCATTTAAATAAAG
1 CCAATCATTTAAATTAAG
250489 C
1 C
250490 ACTCTAAACA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 15 0.50
18 15 0.50
ACGTcount: A:0.43, C:0.19, G:0.06, T:0.32
Consensus pattern (18 bp):
CCAATCATTTAAATTAAG
Found at i:252614 original size:36 final size:37
Alignment explanation
Indices: 252570--252651 Score: 121
Period size: 36 Copynumber: 2.2 Consensus size: 37
252560 TAAAATAGTC
*
252570 ATTTCCAATGCTAGTGGAAAAACCTAACTTGAGCATT
1 ATTTCCAATGCTAGTGGAAAAACCTAACTTGAACATT
* *
252607 -TTTCCAATGCTAGTGGAAATACCTAATTTGAACATT
1 ATTTCCAATGCTAGTGGAAAAACCTAACTTGAACATT
*
252643 AATTCCAAT
1 ATTTCCAAT
252652 AGTCAACTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
36 33 0.82
37 7 0.17
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.33
Consensus pattern (37 bp):
ATTTCCAATGCTAGTGGAAAAACCTAACTTGAACATT
Found at i:253256 original size:31 final size:31
Alignment explanation
Indices: 253221--253283 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
253211 AATTCAGTGA
*
253221 ATTCAATATGTCATTCTCACTAGGAACTCCC
1 ATTCAACATGTCATTCTCACTAGGAACTCCC
253252 ATTCAACATGTCATTCTCACTAGGAACTCCC
1 ATTCAACATGTCATTCTCACTAGGAACTCCC
253283 A
1 A
253284 AACTCTTGGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.30, C:0.30, G:0.10, T:0.30
Consensus pattern (31 bp):
ATTCAACATGTCATTCTCACTAGGAACTCCC
Found at i:256462 original size:29 final size:28
Alignment explanation
Indices: 256399--256495 Score: 104
Period size: 29 Copynumber: 3.4 Consensus size: 28
256389 CATTTTACAG
* **
256399 AAATAGCACCCCTTTTCGAATTAATTACAA
1 AAATAGCACCCATTTT-GAATTAATT-CCC
256429 AAATAGCACCCATTTTGAATTAATTCCC
1 AAATAGCACCCATTTTGAATTAATTCCC
* ** *
256457 ATAATAGCACCAAAATCGAATTAATTCCC
1 A-AATAGCACCCATTTTGAATTAATTCCC
256486 AAATAGCACC
1 AAATAGCACC
256496 GGTCAACGGT
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
28 11 0.19
29 33 0.56
30 15 0.25
ACGTcount: A:0.41, C:0.25, G:0.07, T:0.27
Consensus pattern (28 bp):
AAATAGCACCCATTTTGAATTAATTCCC
Found at i:263688 original size:30 final size:29
Alignment explanation
Indices: 263648--263708 Score: 86
Period size: 30 Copynumber: 2.1 Consensus size: 29
263638 GTCAACCATT
* * *
263648 TTACAGAAATAGTACCCCTTTTCGAATTAA
1 TTACAAAAATAGCACCCATTTT-GAATTAA
263678 TTACAAAAATAGCACCCATTTTGAATTAA
1 TTACAAAAATAGCACCCATTTTGAATTAA
263707 TT
1 TT
263709 CCTATAAAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 9 0.32
30 19 0.68
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.34
Consensus pattern (29 bp):
TTACAAAAATAGCACCCATTTTGAATTAA
Found at i:267778 original size:27 final size:28
Alignment explanation
Indices: 267725--267780 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
267715 GTTTTATGTT
* * * *
267725 TTATATATTTATTTTGTTTGTATTATTA
1 TTATATATTTACTTTGTATATAATATTA
267753 TTATATA-TTACTTTGTATATAATATTA
1 TTATATATTTACTTTGTATATAATATTA
267780 T
1 T
267781 AGCATGATAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 17 0.71
28 7 0.29
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.62
Consensus pattern (28 bp):
TTATATATTTACTTTGTATATAATATTA
Found at i:271918 original size:21 final size:20
Alignment explanation
Indices: 271890--271928 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
271880 CTTTTTTGCT
271890 GAAAAATGAGAAGGAAATAG
1 GAAAAATGAGAAGGAAATAG
271910 GAAATAATGAGAAGGAAAT
1 GAAA-AATGAGAAGGAAAT
271929 CAAAAGAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.59, C:0.00, G:0.28, T:0.13
Consensus pattern (20 bp):
GAAAAATGAGAAGGAAATAG
Found at i:274360 original size:38 final size:37
Alignment explanation
Indices: 274309--274388 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 37
274299 TTTGGTGTTG
*
274309 TTTCTCTCGAAACAAAATGTCGTCTCACTTAAGACATT
1 TTTCTCTCAAAAC-AAATGTCGTCTCACTTAAGACATT
* * * * *
274347 TTTCTCTTAAAACAAATTTTGTTTCACTTGAGACATT
1 TTTCTCTCAAAACAAATGTCGTCTCACTTAAGACATT
274384 TTTCT
1 TTTCT
274389 TCGGAACAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
37 25 0.69
38 11 0.31
ACGTcount: A:0.29, C:0.20, G:0.09, T:0.42
Consensus pattern (37 bp):
TTTCTCTCAAAACAAATGTCGTCTCACTTAAGACATT
Found at i:274383 original size:37 final size:36
Alignment explanation
Indices: 274333--274492 Score: 134
Period size: 37 Copynumber: 4.6 Consensus size: 36
274323 AAATGTCGTC
*
274333 TCACTTAAGACATTTTTCTCTTAAAACAAATTTTGTT
1 TCACTTGAGACATTTTTCT-TTAAAACAAATTTTGTT
*** **
274370 TCACTTGAGACATTTTTCTTCGGAAC-AA--TAATT
1 TCACTTGAGACATTTTTCTTTAAAACAAATTTTGTT
* *** * *
274403 TCA---AAGTTGTTTTTCTTAAAAACAAATTTTGTC
1 TCACTTGAGACATTTTTCTTTAAAACAAATTTTGTT
*
274436 TCACTTGAGACATTTTTCTCTTAAAACAAATTTCGTT
1 TCACTTGAGACATTTTTCT-TTAAAACAAATTTTGTT
*
274473 TCACTTGAGTCATTTTTCTT
1 TCACTTGAGACATTTTTCTT
274493 CGGAACACAA
Statistics
Matches: 92, Mismatches: 24, Indels: 15
0.70 0.18 0.11
Matches are distributed among these distances:
30 13 0.14
31 2 0.02
33 11 0.12
35 2 0.02
36 14 0.15
37 50 0.54
ACGTcount: A:0.29, C:0.17, G:0.09, T:0.45
Consensus pattern (36 bp):
TCACTTGAGACATTTTTCTTTAAAACAAATTTTGTT
Found at i:274487 original size:103 final size:103
Alignment explanation
Indices: 274330--274557 Score: 404
Period size: 103 Copynumber: 2.2 Consensus size: 103
274320 ACAAAATGTC
* *
274330 GTCTCACTTAAGACATTTTTCTCTTAAAACAAATTTTGTTTCACTTGAGACATTTTTCTTCGGAA
1 GTCTCACTTGAGACATTTTTCTCTTAAAACAAATTTCGTTTCACTTGAGACATTTTTCTTCGGAA
274395 CA-ATAATTTCAAAGTTGTTTTTCTTAAAAACAAATTTT
66 CACA-AATTTCAAAGTTGTTTTTCTTAAAAACAAATTTT
*
274433 GTCTCACTTGAGACATTTTTCTCTTAAAACAAATTTCGTTTCACTTGAGTCATTTTTCTTCGGAA
1 GTCTCACTTGAGACATTTTTCTCTTAAAACAAATTTCGTTTCACTTGAGACATTTTTCTTCGGAA
274498 CACAAATTTCAAAGTTGTTTTTCTTAAAAACAAATTTT
66 CACAAATTTCAAAGTTGTTTTTCTTAAAAACAAATTTT
*
274536 GTTTCACTTGAGACATTTTTCT
1 GTCTCACTTGAGACATTTTTCT
274558 TCGGAACAAT
Statistics
Matches: 120, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
103 119 0.99
104 1 0.01
ACGTcount: A:0.30, C:0.17, G:0.10, T:0.44
Consensus pattern (103 bp):
GTCTCACTTGAGACATTTTTCTCTTAAAACAAATTTCGTTTCACTTGAGACATTTTTCTTCGGAA
CACAAATTTCAAAGTTGTTTTTCTTAAAAACAAATTTT
Found at i:274534 original size:66 final size:66
Alignment explanation
Indices: 274448--274623 Score: 266
Period size: 66 Copynumber: 2.7 Consensus size: 66
274438 ACTTGAGACA
* *
274448 TTTTTCTCTTAAAACAAATTTCGTTTCACTTGAGTCATTTTTCTTCGGAACACA-AATTTCAAAG
1 TTTTTCT-TAAAAACAAATTTTGTTTCACTTGAGTCATTTTTCTTCGGAACA-ATAATTTCAAAG
274512 TTG
64 TTG
*
274515 TTTTTCTTAAAAACAAATTTTGTTTCACTTGAGACATTTTTCTTCGGAACAATAATTTCAAAGTT
1 TTTTTCTTAAAAACAAATTTTGTTTCACTTGAGTCATTTTTCTTCGGAACAATAATTTCAAAGTT
274580 G
66 G
* *
274581 TTTTTCTTAAAAACAAATTTTGTCTCGCTTGAGAT-ATTTTTCT
1 TTTTTCTTAAAAACAAATTTTGTTTCACTTGAG-TCATTTTTCT
274624 CTTAATTTTT
Statistics
Matches: 101, Mismatches: 6, Indels: 5
0.90 0.05 0.04
Matches are distributed among these distances:
65 1 0.01
66 93 0.92
67 7 0.07
ACGTcount: A:0.29, C:0.15, G:0.10, T:0.45
Consensus pattern (66 bp):
TTTTTCTTAAAAACAAATTTTGTTTCACTTGAGTCATTTTTCTTCGGAACAATAATTTCAAAGTT
G
Found at i:274645 original size:169 final size:170
Alignment explanation
Indices: 274345--274660 Score: 519
Period size: 169 Copynumber: 1.9 Consensus size: 170
274335 ACTTAAGACA
*
274345 TTTTTCTCTTAAAACAAATTTTGTTTCACTTGAGACATTTTTCTTCGGAACAATAATTTCAAAGT
1 TTTTTCTCTAAAAACAAATTTTGTTTCACTTGAGACATTTTTCTTCGGAACAATAATTTCAAAGT
274410 TGTTTTTCTTAAAAACAAATTTTGTCTCACTTGAGACATTTTTCTCTTAAAACAAATTTCGTTTC
66 TGTTTTTCTTAAAAACAAATTTTGTCTCACTTGAGACATTTTTCTCTTAAAACAAATTTCGTTTC
274475 ACTTGAG-TCATTTTTCTTCGGAACACAAATTTCAAAGTTG
131 ACTTGAGAT-ATTTTTCTTCGGAACACAAATTTCAAAGTTG
274515 TTTTTCT-TAAAAACAAATTTTGTTTCACTTGAGACATTTTTCTTCGGAACAATAATTTCAAAGT
1 TTTTTCTCTAAAAACAAATTTTGTTTCACTTGAGACATTTTTCTTCGGAACAATAATTTCAAAGT
* * ****** *
274579 TGTTTTTCTTAAAAACAAATTTTGTCTCGCTTGAGATATTTTTCTCTTAATTTTTTTTTTGTTTC
66 TGTTTTTCTTAAAAACAAATTTTGTCTCACTTGAGACATTTTTCTCTTAAAACAAATTTCGTTTC
274644 ACTTGAGATATTTTTCT
131 ACTTGAGATATTTTTCT
274661 CTCAAAACAA
Statistics
Matches: 135, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
169 127 0.94
170 8 0.06
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.47
Consensus pattern (170 bp):
TTTTTCTCTAAAAACAAATTTTGTTTCACTTGAGACATTTTTCTTCGGAACAATAATTTCAAAGT
TGTTTTTCTTAAAAACAAATTTTGTCTCACTTGAGACATTTTTCTCTTAAAACAAATTTCGTTTC
ACTTGAGATATTTTTCTTCGGAACACAAATTTCAAAGTTG
Found at i:274914 original size:36 final size:36
Alignment explanation
Indices: 274808--274915 Score: 135
Period size: 36 Copynumber: 3.0 Consensus size: 36
274798 TTTGAATATA
* *
274808 TTTCCCTTGAAACAAAATTTTGTCTCCCATGAGACAG
1 TTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGATAG
* *
274845 TTTCTCTTGAAACAAATTTTGTATCCCTTGAGATAG
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATAG
* * * *
274881 TTTCCCTTAAAACAGACTTTGTCTCGCTTGAGATA
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATA
274916 TTTTTTTCTC
Statistics
Matches: 61, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
36 49 0.80
37 12 0.20
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATAG
Found at i:275221 original size:52 final size:51
Alignment explanation
Indices: 275133--275324 Score: 215
Period size: 52 Copynumber: 3.7 Consensus size: 51
275123 GAAGACTTTT
* * *
275133 AGAAACTAAGCCTGATTTTCAGGGGTTTCTCGATGTTTTCAAATGAACTTGAA
1 AGAAACTAAACCTAATTTTCAGGGGTTTCTTGATGTTTTCAAATGAA-TT-AA
* *
275186 AGAAACTAAACCTAATTTT-AGGGGTTTCTTAATGTTTTTAAATGAATTTCAA
1 AGAAACTAAACCTAATTTTCAGGGGTTTCTTGATGTTTTCAAATGAA-TT-AA
* * * * **
275238 AGAAATTAAACCTAATTTTTAGGGATTTCTTGATATTTTCAAATGAGATTTT
1 AGAAACTAAACCTAATTTTCAGGGGTTTCTTGATGTTTTCAAATGA-ATTAA
* *
275290 AGAAACTAAGCCTGATTTTCAGGGGTTTCTTGATG
1 AGAAACTAAACCTAATTTTCAGGGGTTTCTTGATG
275325 ATGATTTTCA
Statistics
Matches: 117, Mismatches: 20, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
52 75 0.64
53 41 0.35
54 1 0.01
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (51 bp):
AGAAACTAAACCTAATTTTCAGGGGTTTCTTGATGTTTTCAAATGAATTAA
Found at i:275450 original size:22 final size:22
Alignment explanation
Indices: 275425--275485 Score: 83
Period size: 19 Copynumber: 2.9 Consensus size: 22
275415 TCTTGATAAA
*
275425 TAAGTCTTTCGAGCATGATGAG
1 TAAGTCTTTCGAGCATGATCAG
*
275447 TAAGTC-TTCGGGC-T-ATCAG
1 TAAGTCTTTCGAGCATGATCAG
275466 TAAGTCTTTCGAGCATGATC
1 TAAGTCTTTCGAGCATGATC
275486 CTTAAATTCT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
19 10 0.30
20 7 0.21
21 7 0.21
22 9 0.27
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.33
Consensus pattern (22 bp):
TAAGTCTTTCGAGCATGATCAG
Found at i:276588 original size:105 final size:105
Alignment explanation
Indices: 276406--276697 Score: 424
Period size: 105 Copynumber: 2.7 Consensus size: 105
276396 GGATAAACCG
276406 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCTAAAGGAGAAGGTTCGTAATGAG
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCTAAAGGAGAAGGTTCGTAATGAG
* *
276471 AAGAGCATGTTCCTTTCAAATCCACCGC-AGAAGGAGGTAA
66 AAGAACATGTTCCTTTCAAATCCACC-CTAGAAGGAAGTAA
* * *
276511 ATCAACATTTCTAAAAGAGTTCATAATGGGAAGAACTCATCCTAAAGGAGAAGGTTCGTAATGAG
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCTAAAGGAGAAGGTTCGTAATGAG
* * *
276576 AAGAACATGTTCCTTTCAAATTCACCCTAGGAGGAAGTGA
66 AAGAACATGTTCCTTTCAAATCCACCCTAGAAGGAAGTAA
* *
276616 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCAACAAAAGGAGAAGAAGTTCATA
1 ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCAT-C--CTAAAGGAGAAG--GTTCGTA
*
276681 ATGAGAAGAACTTGTTC
61 ATGAGAAGAACATGTTC
276698 AACCTTAGCT
Statistics
Matches: 167, Mismatches: 14, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
104 1 0.01
105 132 0.79
106 1 0.01
108 11 0.07
110 22 0.13
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.23
Consensus pattern (105 bp):
ATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCCTAAAGGAGAAGGTTCGTAATGAG
AAGAACATGTTCCTTTCAAATCCACCCTAGAAGGAAGTAA
Found at i:278272 original size:27 final size:28
Alignment explanation
Indices: 278219--278274 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
278209 GTTTTATGTT
* * * *
278219 TTATATATTTATTTTGTTTGTATTATTA
1 TTATATATTTAATTTGTATATAATATTA
278247 TTATATA-TTAATTTGTATATAATATTA
1 TTATATATTTAATTTGTATATAATATTA
278274 T
1 T
278275 AGCATGATAG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 17 0.71
28 7 0.29
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (28 bp):
TTATATATTTAATTTGTATATAATATTA
Found at i:280222 original size:19 final size:19
Alignment explanation
Indices: 280198--280234 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
280188 AAAAACCTAA
280198 CTTGAGCATTTTTCCAATG
1 CTTGAGCATTTTTCCAATG
280217 CTTGAGCATTTTTCCAAT
1 CTTGAGCATTTTTCCAAT
280235 ACTAGTGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.43
Consensus pattern (19 bp):
CTTGAGCATTTTTCCAATG
Found at i:280264 original size:36 final size:36
Alignment explanation
Indices: 280217--280288 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
280207 TTTTCCAATG
280217 CTTGAGCATTTTTCCAATACTAGTGGAAAAACCTAA
1 CTTGAGCATTTTTCCAATACTAGTGGAAAAACCTAA
* * *
280253 CTTGAGCATTTTTTCAATGCTAGTGGAAATACCTAA
1 CTTGAGCATTTTTCCAATACTAGTGGAAAAACCTAA
280289 TTTAAACATT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (36 bp):
CTTGAGCATTTTTCCAATACTAGTGGAAAAACCTAA
Found at i:283463 original size:22 final size:22
Alignment explanation
Indices: 283438--283485 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
283428 TTTCCCCCTC
283438 TTTTTCTCC-C-TTTTTCTTTACT
1 TTTTTCTCCTCATTTTT-TTT-CT
283460 TTTTTCTCCTCATTTTTTTTCT
1 TTTTTCTCCTCATTTTTTTTCT
283482 TTTT
1 TTTT
283486 CTGTGTATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
22 15 0.62
23 4 0.17
24 5 0.21
ACGTcount: A:0.04, C:0.23, G:0.00, T:0.73
Consensus pattern (22 bp):
TTTTTCTCCTCATTTTTTTTCT
Found at i:284666 original size:38 final size:36
Alignment explanation
Indices: 284618--284739 Score: 129
Period size: 38 Copynumber: 3.3 Consensus size: 36
284608 ATAAAGAGAT
*
284618 TTTAAAAGAAAATATCTCGAGTAAGATATAATTTTTG
1 TTTAAGAGAAAATATCTCGAGTAAGATA-AATTTTTG
* * *
284655 TTTCAAGAGAAATTGTCTCGAGTAAGATGAAATTTAT-
1 TTT-AAGAGAAAATATCTCGAGTAAGAT-AAATTTTTG
* * *
284692 TTTAAGAGAAAATATCTCAAGTGAGATAAAATTTTG
1 TTTAAGAGAAAATATCTCGAGTAAGATAAATTTTTG
*
284728 TTTTGAGAGAAA
1 -TTTAAGAGAAA
284740 TGTTTCAAGT
Statistics
Matches: 70, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
35 6 0.09
36 20 0.29
37 16 0.23
38 27 0.39
39 1 0.01
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.35
Consensus pattern (36 bp):
TTTAAGAGAAAATATCTCGAGTAAGATAAATTTTTG
Found at i:284724 original size:36 final size:36
Alignment explanation
Indices: 284616--284791 Score: 124
Period size: 36 Copynumber: 4.9 Consensus size: 36
284606 AGATAAAGAG
* * * *
284616 ATTTTAAAAGAAAATATCTCGAGTAAGATATAATTT
1 ATTTTAAGAGAAAATATCTCAAGTGAGATAAAATTT
* * * * * *
284652 TTGTTTCAAGAGAAATTGTCTCGAGTAAGATGAAATTT
1 AT-TTT-AAGAGAAAATATCTCAAGTGAGATAAAATTT
284690 ATTTTAAGAGAAAATATCTCAAGTGAGATAAAATTTT
1 ATTTTAAGAGAAAATATCTCAAGTGAGATAAAA-TTT
* * * * * * *
284727 GTTTTGAGAG-AAATGTTTCAAGTGATACAAAA--A
1 ATTTTAAGAGAAAATATCTCAAGTGAGATAAAATTT
* *
284760 ATTTCAAGAGAAAACTATCTCAAGCGAGATAA
1 ATTTTAAGAGAAAA-TATCTCAAGTGAGATAA
284792 TTTTTTTTTT
Statistics
Matches: 108, Mismatches: 27, Indels: 11
0.74 0.18 0.08
Matches are distributed among these distances:
33 7 0.06
34 3 0.03
35 12 0.11
36 42 0.39
37 17 0.16
38 27 0.25
ACGTcount: A:0.43, C:0.08, G:0.16, T:0.32
Consensus pattern (36 bp):
ATTTTAAGAGAAAATATCTCAAGTGAGATAAAATTT
Found at i:284762 original size:74 final size:69
Alignment explanation
Indices: 284616--285030 Score: 174
Period size: 73 Copynumber: 5.7 Consensus size: 69
284606 AGATAAAGAG
* * * * * *
284616 ATTTTAAAAGAAAATATCTCGAGTAAGATATAATTTTTGTTTCAAGAGAAATTGTCTCGAGTAAG
1 ATTTTAAGAGAAAATATCTCAAGTGAGATA-AAATTTTGTTTCAAGAGAAATTGTCTCAAGTAAC
*
284681 ATGAAATTT
65 A--AAA--A
** *
284690 ATTTTAAGAGAAAATATCTCAAGTGAGATAAAATTTTGTTTTGAGAGAAA-TGTTTCAAGTGATA
1 ATTTTAAGAGAAAATATCTCAAGTGAGATAAAATTTTGTTTCAAGAGAAATTGTCTCAAGT-A-A
284754 CAAAAA
64 CAAAAA
* * ** * ** * **
284760 ATTTCAAGAGAAAACTATCTCAAGCGAGATAATTTTTTTTTTTTGAGACAAATTGTCTTGAGTAA
1 ATTTTAAGAGAAAA-TATCTCAAGTGAGATAA-AATTTTGTTTCAAGAGAAATTGTCTCAAGTAA
284825 -AACAAA
64 CAA-AAA
* * * * ** * *
284831 A-TTCAAGAGAAAACTATCTAAAGCGAGAGAAAAAAATTTTGTTTTGAGAGAAACTGTCTCGAGT
1 ATTTTAAGAGAAAA-TATCTCAA--GTGAG-ATAAAATTTTGTTTCAAGAGAAATTGTCTCAAGT
284895 GAGAC-AAAA
62 -A-ACAAAAA
* * * ** * ** ***
284904 ATCTTCAAAAGTAAATTATCTCAAGCAAGATAAATTTTTTGTTTTGAGAGAAGCAGTCTCAAGTG
1 AT-TTTAAGAG-AAAATATCTCAAGTGAGATAAA-ATTTTGTTTCAAGAGAAATTGTCTCAAGT-
**
284969 AGAC-TTAA
62 A-ACAAAAA
* ** *
284977 ATTTTCAAGAGAAAACTATCTCAAGCGAGATAAAAAAATTATTTCAAGAGAAAT
1 ATTTT-AAGAGAAAA-TATCTCAAGTGAGAT-AAAATTTTGTTTCAAGAGAAAT
285031 ATTTCAAGGG
Statistics
Matches: 270, Mismatches: 52, Indels: 39
0.75 0.14 0.11
Matches are distributed among these distances:
70 35 0.13
71 21 0.08
72 64 0.24
73 99 0.37
74 34 0.13
75 14 0.05
76 3 0.01
ACGTcount: A:0.43, C:0.10, G:0.16, T:0.31
Consensus pattern (69 bp):
ATTTTAAGAGAAAATATCTCAAGTGAGATAAAATTTTGTTTCAAGAGAAATTGTCTCAAGTAACA
AAAA
Found at i:284813 original size:145 final size:144
Alignment explanation
Indices: 284621--285016 Score: 356
Period size: 145 Copynumber: 2.7 Consensus size: 144
284611 AAGAGATTTT
* * ** * **
284621 AAAAGAAAA-TATCTCGAGTAAGATATAA-TTTTTGTTTCAAGAGAAATTGTCTCGAGTAAGATG
1 AAAAGAAAACTATCTCAAGCAAGATA-AATTTTTTGTTTTGAGACAAATTGTCTCGAGTAA-AAC
* * * * *
284684 AAATTTATTTTAAGAGAAAA-TATCTCAA-GTGAG-ATAAAATTTTGTTTTGAGAGAAA-TGTTT
64 AAA---A-TTCAAGAGAAAACTATCTAAACGAGAGAAAAAAATTTTGTTTTGAGAGAAACTGTCT
*
284745 CAAGTGATACAAAAAAT-TTC
125 CAAGTGAGAC-AAAAATCTTC
* * * * *
284765 AAGAGAAAACTATCTCAAGCGAGATAATTTTTTTTTTTTGAGACAAATTGTCTTGAGTAAAACAA
1 AAAAGAAAACTATCTCAAGCAAGATAAATTTTTTGTTTTGAGACAAATTGTCTCGAGTAAAACAA
*
284830 AATTCAAGAGAAAACTATCTAAAGCGAGAGAAAAAAATTTTGTTTTGAGAGAAACTGTCTCGAGT
66 AATTCAAGAGAAAACTATCTAAA-CGAGAGAAAAAAATTTTGTTTTGAGAGAAACTGTCTCAAGT
284895 GAGACAAAAATCTTC
130 GAGACAAAAATCTTC
* * * *** * * *
284910 AAAAGTAAATTATCTCAAGCAAGATAAATTTTTTGTTTTGAGAGAAGCAGTCTCAAGTGAGACTT
1 AAAAGAAAACTATCTCAAGCAAGATAAATTTTTTGTTTTGAGACAAATTGTCTCGAGTAAAAC--
* * *
284975 AAATTTTCAAGAGAAAACTATCTCAAGCGAGATAAAAAAATT
64 AAA-ATTCAAGAGAAAACTATCT-AAACGAGAGAAAAAAATT
285017 ATTTCAAGAG
Statistics
Matches: 204, Mismatches: 36, Indels: 20
0.78 0.14 0.08
Matches are distributed among these distances:
140 11 0.05
141 8 0.04
143 4 0.02
144 41 0.20
145 103 0.50
147 3 0.01
148 32 0.16
149 2 0.01
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.31
Consensus pattern (144 bp):
AAAAGAAAACTATCTCAAGCAAGATAAATTTTTTGTTTTGAGACAAATTGTCTCGAGTAAAACAA
AATTCAAGAGAAAACTATCTAAACGAGAGAAAAAAATTTTGTTTTGAGAGAAACTGTCTCAAGTG
AGACAAAAATCTTC
Found at i:284951 original size:73 final size:72
Alignment explanation
Indices: 284690--285010 Score: 328
Period size: 73 Copynumber: 4.5 Consensus size: 72
284680 GATGAAATTT
* * *
284690 ATTTTAAGAGAAAA-TATCTCAAGTGAGATAAA-ATTTTGTTTTGAGAGAAA-TGTTTCAAGTGA
1 ATTTCAAGAGAAAACTATCTCAAGCGAGATAAATATTTTGTTTTGAGAGAAACTGTCTCAAGTGA
*
284752 TACAAAAA
66 GAC-AAAA
* * * * * ** *
284760 ATTTCAAGAGAAAACTATCTCAAGCGAGATAATTTTTTTTTTTTGAGACAAATTGTCTTGAGTAA
1 ATTTCAAGAGAAAACTATCTCAAGCGAGATAAATATTTTGTTTTGAGAGAAACTGTCTCAAGTGA
*
284825 AAC-AAA
66 GACAAAA
* * * *
284831 A-TTCAAGAGAAAACTATCTAAAGCGAGAGAAAAAAATTTTGTTTTGAGAGAAACTGTCTCGAGT
1 ATTTCAAGAGAAAACTATCTCAAGC--GAGATAAATATTTTGTTTTGAGAGAAACTGTCTCAAGT
284895 GAGACAAAA
64 GAGACAAAA
* * * * * * *
284904 ATCTTCAAAAGTAAATTATCTCAAGCAAGATAAATTTTTTGTTTTGAGAGAAGCAGTCTCAAGTG
1 AT-TTCAAGAGAAAACTATCTCAAGCGAGATAAATATTTTGTTTTGAGAGAAACTGTCTCAAGTG
*
284969 AGACTTAAA
65 AGAC-AAAA
*
284978 TTTTCAAGAGAAAACTATCTCAAGCGAGATAAA
1 ATTTCAAGAGAAAACTATCTCAAGCGAGATAAA
285011 AAAATTATTT
Statistics
Matches: 203, Mismatches: 39, Indels: 15
0.79 0.15 0.06
Matches are distributed among these distances:
70 35 0.17
71 20 0.10
72 48 0.24
73 77 0.38
74 4 0.02
75 19 0.09
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.30
Consensus pattern (72 bp):
ATTTCAAGAGAAAACTATCTCAAGCGAGATAAATATTTTGTTTTGAGAGAAACTGTCTCAAGTGA
GACAAAA
Found at i:287148 original size:28 final size:28
Alignment explanation
Indices: 287102--287170 Score: 131
Period size: 27 Copynumber: 2.5 Consensus size: 28
287092 AGGGATTAGG
287102 ATTTTTTTGTTATTTAAAAAATAATAAT
1 ATTTTTTTGTTATTTAAAAAATAATAAT
287130 A-TTTTTTGTTATTTAAAAAATAATAAT
1 ATTTTTTTGTTATTTAAAAAATAATAAT
287157 ATTTTTTTGTTATT
1 ATTTTTTTGTTATT
287171 ACCACGTCAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
27 27 0.68
28 13 0.32
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (28 bp):
ATTTTTTTGTTATTTAAAAAATAATAAT
Found at i:287411 original size:6 final size:6
Alignment explanation
Indices: 287397--287440 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 6
287387 GCCTTCTCCG
* * *
287397 TCCCCT TCCCGT TCCCCT TCCCCT TCTCGT TCCCCT TCCCCT TC
1 TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT TCCCCT TC
287441 TTTTCTCTCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.00, C:0.59, G:0.05, T:0.36
Consensus pattern (6 bp):
TCCCCT
Found at i:287412 original size:12 final size:12
Alignment explanation
Indices: 287383--287440 Score: 55
Period size: 12 Copynumber: 4.8 Consensus size: 12
287373 AAAGACATTT
*
287383 GTTCGCCTTCTCC
1 GTTCCCCTTC-CC
287396 G-TCCCCTTCCC
1 GTTCCCCTTCCC
287407 GTTCCCCTTCCC
1 GTTCCCCTTCCC
* * *
287419 CTTCTCGTTCCC
1 GTTCCCCTTCCC
*
287431 CTTCCCCTTC
1 GTTCCCCTTC
287441 TTTTCTCTCA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
11 3 0.08
12 34 0.89
13 1 0.03
ACGTcount: A:0.00, C:0.55, G:0.09, T:0.36
Consensus pattern (12 bp):
GTTCCCCTTCCC
Found at i:287441 original size:18 final size:18
Alignment explanation
Indices: 287397--287441 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
287387 GCCTTCTCCG
*
287397 TCCCCTTCCCGTTCCCCT
1 TCCCCTTCTCGTTCCCCT
287415 TCCCCTTCTCGTTCCCCT
1 TCCCCTTCTCGTTCCCCT
287433 TCCCCTTCT
1 TCCCCTTCT
287442 TTTCTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.00, C:0.58, G:0.04, T:0.38
Consensus pattern (18 bp):
TCCCCTTCTCGTTCCCCT
Found at i:304551 original size:2 final size:2
Alignment explanation
Indices: 304544--304583 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
304534 AATGTTTACC
304544 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
304584 TATCAGAATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:307328 original size:68 final size:68
Alignment explanation
Indices: 307249--307397 Score: 255
Period size: 68 Copynumber: 2.2 Consensus size: 68
307239 CAAGTGATGA
307249 TTTTT-CACGTTCACAATTCGAGGGCCACCTTCATGCATGGTATAGCAATTATGTAACCATCATT
1 TTTTTCCACGTTCACAATTCGAGGGCCACCTTCATGCATGGTATAGCAATTATGTAACCATCATT
307313 TCC
66 TCC
** *
307316 TTTTTCCACGTTCACAATTCGAGGGCCATTTTCATGCATGGTATAGTAATTATGTAACCATCATT
1 TTTTTCCACGTTCACAATTCGAGGGCCACCTTCATGCATGGTATAGCAATTATGTAACCATCATT
*
307381 TCT
66 TCC
307384 TTTTTCCACGTTCA
1 TTTTTCCACGTTCA
307398 TACAAATGCG
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
67 5 0.06
68 72 0.94
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.38
Consensus pattern (68 bp):
TTTTTCCACGTTCACAATTCGAGGGCCACCTTCATGCATGGTATAGCAATTATGTAACCATCATT
TCC
Found at i:312825 original size:10 final size:10
Alignment explanation
Indices: 312812--312882 Score: 52
Period size: 10 Copynumber: 6.4 Consensus size: 10
312802 GTTCGTGAAC
312812 GTTCGGTTAT
1 GTTCGGTTAT
*
312822 GTTCGTTTAT
1 GTTCGGTTAT
312832 GTTCGTTCGTTAT
1 GTTCG---GTTAT
*
312845 GTTCGTTTAT
1 GTTCGGTTAT
312855 GTTCGTTCTGTTAT
1 GTTCG----GTTAT
*
312869 GTTCGTTTAT
1 GTTCGGTTAT
312879 GTTC
1 GTTC
312883 ATTCATTTAT
Statistics
Matches: 49, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
10 31 0.63
13 9 0.18
14 9 0.18
ACGTcount: A:0.08, C:0.13, G:0.23, T:0.56
Consensus pattern (10 bp):
GTTCGGTTAT
Found at i:312839 original size:14 final size:14
Alignment explanation
Indices: 312822--312875 Score: 57
Period size: 14 Copynumber: 4.2 Consensus size: 14
312812 GTTCGGTTAT
312822 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
312836 GTTCG-TTA---T-
1 GTTCGTTTATGTTC
312845 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
312859 GTTC-TGTTATGTTC
1 GTTCGT-TTATGTTC
312873 GTT
1 GTT
312876 TATGTTCATT
Statistics
Matches: 34, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
9 5 0.15
10 4 0.12
13 5 0.15
14 20 0.59
ACGTcount: A:0.07, C:0.13, G:0.22, T:0.57
Consensus pattern (14 bp):
GTTCGTTTATGTTC
Found at i:312876 original size:24 final size:24
Alignment explanation
Indices: 312811--312895 Score: 129
Period size: 24 Copynumber: 3.6 Consensus size: 24
312801 CGTTCGTGAA
*
312811 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCTGTTATGTTCGTTTATGTT
312835 CGTTC-GTTATGTTCGTTTATGTT
1 CGTTCTGTTATGTTCGTTTATGTT
312858 CGTTCTGTTATGTTCGTTTATGTT
1 CGTTCTGTTATGTTCGTTTATGTT
*
312882 CATTCAT-TTATGTT
1 CGTTC-TGTTATGTT
312896 TAACTCAATC
Statistics
Matches: 58, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
23 23 0.40
24 34 0.59
25 1 0.02
ACGTcount: A:0.11, C:0.13, G:0.20, T:0.56
Consensus pattern (24 bp):
CGTTCTGTTATGTTCGTTTATGTT
Found at i:313996 original size:16 final size:16
Alignment explanation
Indices: 313975--314027 Score: 88
Period size: 16 Copynumber: 3.3 Consensus size: 16
313965 GTCTCCAACT
313975 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCG
*
313991 TTTATGTTCATGTTCG
1 TTTATGTTCGTGTTCG
*
314007 TTTATGTTCGTGTTTG
1 TTTATGTTCGTGTTCG
314023 TTTAT
1 TTTAT
314028 TTATTAAATG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.09, C:0.09, G:0.21, T:0.60
Consensus pattern (16 bp):
TTTATGTTCGTGTTCG
Found at i:315386 original size:12 final size:13
Alignment explanation
Indices: 315339--315395 Score: 60
Period size: 15 Copynumber: 4.1 Consensus size: 13
315329 AATAAAAATA
315339 TAAAATAAATTAT
1 TAAAATAAATTAT
* *
315352 TAAGTAACAAATAAT
1 TAA--AATAAATTAT
315367 TAAAATAAATTAT
1 TAAAATAAATTAT
315380 TAAATAATAAATTAT
1 T-AA-AATAAATTAT
315395 T
1 T
315396 TTTCAATGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
13 12 0.33
14 2 0.06
15 22 0.61
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (13 bp):
TAAAATAAATTAT
Found at i:315491 original size:13 final size:13
Alignment explanation
Indices: 315469--315532 Score: 92
Period size: 13 Copynumber: 4.7 Consensus size: 13
315459 TATTTATTTT
*
315469 TAAATAATTAAAA
1 TAAATTATTAAAA
315482 TAAATTATTAAAA
1 TAAATTATTAAAA
315495 TAAATTATTAAAA
1 TAAATTATTAAAA
315508 TAAATTTATTAAGTAA
1 TAAA-TTATTAA--AA
315524 TAAATTATT
1 TAAATTATT
315533 TTTCAAGTAT
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
13 29 0.62
14 7 0.15
15 5 0.11
16 6 0.13
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (13 bp):
TAAATTATTAAAA
Found at i:315615 original size:137 final size:134
Alignment explanation
Indices: 315331--315612 Score: 293
Period size: 137 Copynumber: 2.0 Consensus size: 134
315321 TGAATTATAA
315331 TAAAAATATAAAATAAATTATTAAGTAACAAATAATTAAAATAAATTATTAAATAATAAATTATT
1 TAAAAAT-TAAAATAAATTATTAAG-AACAAATAATTAAAATAAATTATTAAATAATAAATTATT
* * *
315396 TTTCAATGATGTCAATATTAAATTATTAAGTAATAAACTATGTTAAATATAGATTTTAAATTATA
64 TTTCAATGATGTCAATATTAAATTATTAAG-AATAAAC-ATGTTAAATATAGAGTGTAAACTATA
****
315461 TTTATTTT
127 TTTAAGGG
* * *
315469 TAAATAATTAAAATAAATTATTAA-AATAAATTATTAAAATAAATTTATTAAGTAATAAATTATT
1 TAAA-AATTAAAATAAATTATTAAGAACAAATAATTAAAATAAA-TTATTAAATAATAAATTATT
* * * *
315533 TTTCAA-GTATGTTAATATTAAATTATTAA-AATAAA-ATGTAACTACATAATTGAGTGTAACCT
64 TTTCAATG-ATGTCAATATTAAATTATTAAGAATAAACATGT---TAAAT-ATAGAGTGTAAACT
315595 ATATTAATAAGGG
124 ATATT--TAAGGG
315608 TAAAA
1 TAAAA
315613 TTATAATTTG
Statistics
Matches: 121, Mismatches: 14, Indels: 18
0.79 0.09 0.12
Matches are distributed among these distances:
133 4 0.03
135 6 0.05
136 22 0.18
137 59 0.49
138 21 0.17
139 9 0.07
ACGTcount: A:0.51, C:0.03, G:0.06, T:0.40
Consensus pattern (134 bp):
TAAAAATTAAAATAAATTATTAAGAACAAATAATTAAAATAAATTATTAAATAATAAATTATTTT
TCAATGATGTCAATATTAAATTATTAAGAATAAACATGTTAAATATAGAGTGTAAACTATATTTA
AGGG
Found at i:316344 original size:6 final size:6
Alignment explanation
Indices: 316333--316357 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
316323 CGCCGCCGTC
316333 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
316358 AATACGTGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.36
Consensus pattern (6 bp):
TCGTGG
Found at i:316510 original size:42 final size:41
Alignment explanation
Indices: 316463--316656 Score: 184
Period size: 34 Copynumber: 5.0 Consensus size: 41
316453 GCAACGAATT
*
316463 TGGAAAATCGCAACGACAACTGT-AGACTATCGCACCGCGAAA
1 TGGAAAATCGCAACG-CAACTGTCA-ACTATCGCAACGCGAAA
* * *
316505 TGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCAACTGTCAACTATCGCAACGCGAAA
316546 TGGAAAA--G---CGCAAC-G-CAACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCAACTGTCAACTATCGCAACGCGAAA
*
316580 TAG-AAA----AACGCAAC-G-CAACTATCGCAACGCGAAA
1 TGGAAAATCGCAACGCAACTGTCAACTATCGCAACGCGAAA
* * * *
316614 TGGAAAATCGCAACGCGATTTTCAACTACCGCAACGCGAAA
1 TGGAAAATCGCAACGCAACTGTCAACTATCGCAACGCGAAA
316655 TG
1 TG
316657 CAACGCGAAA
Statistics
Matches: 129, Mismatches: 13, Indels: 21
0.79 0.08 0.13
Matches are distributed among these distances:
33 3 0.02
34 49 0.38
35 3 0.02
36 4 0.03
39 7 0.05
41 47 0.36
42 16 0.12
ACGTcount: A:0.39, C:0.26, G:0.21, T:0.14
Consensus pattern (41 bp):
TGGAAAATCGCAACGCAACTGTCAACTATCGCAACGCGAAA
Found at i:316559 original size:20 final size:20
Alignment explanation
Indices: 316491--316631 Score: 90
Period size: 20 Copynumber: 7.6 Consensus size: 20
316481 ACTGTAGACT
*
316491 ATCGCACCGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
316511 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
316532 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* *
316552 AGCGCAACGC-AACT-----
1 ATCGCAACGCGAAATGGAAA
*
316566 ATCGCAACGCGAAATAGAAA
1 ATCGCAACGCGAAATGGAAA
* *
316586 AACGCAACGC-AACT-----
1 ATCGCAACGCGAAATGGAAA
316600 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
316620 ATCGCAACGCGA
1 ATCGCAACGCGA
316632 TTTTCAACTA
Statistics
Matches: 89, Mismatches: 19, Indels: 26
0.66 0.14 0.19
Matches are distributed among these distances:
14 18 0.20
15 6 0.07
19 6 0.07
20 44 0.49
21 15 0.17
ACGTcount: A:0.40, C:0.26, G:0.21, T:0.12
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:316660 original size:21 final size:21
Alignment explanation
Indices: 316594--316660 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
316584 AAAACGCAAC
316594 GCAACTATCGCAACGCGAAAT
1 GCAACTATCGCAACGCGAAAT
* * **
316615 GGAA-AATCGCAACGCGATTT
1 GCAACTATCGCAACGCGAAAT
* *
316635 TCAACTACCGCAACGCGAAAT
1 GCAACTATCGCAACGCGAAAT
316656 GCAAC
1 GCAAC
316661 GCGAAATTGC
Statistics
Matches: 34, Mismatches: 11, Indels: 2
0.72 0.23 0.04
Matches are distributed among these distances:
20 15 0.44
21 19 0.56
ACGTcount: A:0.37, C:0.28, G:0.19, T:0.15
Consensus pattern (21 bp):
GCAACTATCGCAACGCGAAAT
Found at i:317544 original size:17 final size:18
Alignment explanation
Indices: 317503--317544 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
317493 AACCTTTATA
317503 TATAATA-TTTAATATTT
1 TATAATATTTTAATATTT
*
317520 TA-AATATTTTTAT-TTT
1 TATAATATTTTAATATTT
317536 TATAATATT
1 TATAATATT
317545 AAAATATGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (18 bp):
TATAATATTTTAATATTT
Found at i:317601 original size:20 final size:21
Alignment explanation
Indices: 317541--317601 Score: 70
Period size: 21 Copynumber: 3.0 Consensus size: 21
317531 ATTTTTATAA
* *
317541 TATTAAAATATGTTATTTAAT
1 TATTAAAATATATTATTTTAT
* *
317562 TATTAAAATATAATAATTTAT
1 TATTAAAATATATTATTTTAT
*
317583 TA-TAAAATTTATTATTTTA
1 TATTAAAATATATTATTTTA
317602 ATAATTTATA
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
20 14 0.42
21 19 0.58
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
TATTAAAATATATTATTTTAT
Found at i:318636 original size:21 final size:21
Alignment explanation
Indices: 318607--318646 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
318597 TGTTACTTTT
*
318607 AATGTAATTACAACAATAACG
1 AATGCAATTACAACAATAACG
* *
318628 AATGCAATTATAACGATAA
1 AATGCAATTACAACAATAA
318647 TGGAAGCAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.53, C:0.12, G:0.10, T:0.25
Consensus pattern (21 bp):
AATGCAATTACAACAATAACG
Found at i:335800 original size:87 final size:87
Alignment explanation
Indices: 335654--335827 Score: 321
Period size: 87 Copynumber: 2.0 Consensus size: 87
335644 ATTGAATACT
*
335654 TGGCAATTCGGTGTTGACTCCACTGTGGTTGTCAAGTCGAAGACTTTGTGATGAGATGAATCCTT
1 TGGCAATTCGGTGTTCACTCCACTGTGGTTGTCAAGTCGAAGACTTTGTGATGAGATGAATCCTT
* *
335719 TAGCTACTCCTAAATAAAGGTA
66 CAGCTACGCCTAAATAAAGGTA
335741 TGGCAATTCGGTGTTCACTCCACTGTGGTTGTCAAGTCGAAGACTTTGTGATGAGATGAATCCTT
1 TGGCAATTCGGTGTTCACTCCACTGTGGTTGTCAAGTCGAAGACTTTGTGATGAGATGAATCCTT
335806 CAGCTACGCCTAAATAAAGGTA
66 CAGCTACGCCTAAATAAAGGTA
335828 AAAGAATTTA
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 84 1.00
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.31
Consensus pattern (87 bp):
TGGCAATTCGGTGTTCACTCCACTGTGGTTGTCAAGTCGAAGACTTTGTGATGAGATGAATCCTT
CAGCTACGCCTAAATAAAGGTA
Found at i:346953 original size:2 final size:2
Alignment explanation
Indices: 346946--346972 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
346936 ATTCTATCTT
346946 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
346973 TATTACAGAA
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:357313 original size:21 final size:21
Alignment explanation
Indices: 357289--357332 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
357279 AATATGTAAA
*
357289 TCGCATTGCAATTTTCCAAAT
1 TCGCATTGCAATTTTACAAAT
* *
357310 TCGCGTTGCGATTTTACAAAT
1 TCGCATTGCAATTTTACAAAT
357331 TC
1 TC
357333 ACAACGCAAA
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:0.25, C:0.23, G:0.14, T:0.39
Consensus pattern (21 bp):
TCGCATTGCAATTTTACAAAT
Found at i:357368 original size:20 final size:20
Alignment explanation
Indices: 357345--357417 Score: 64
Period size: 20 Copynumber: 3.6 Consensus size: 20
357335 AACGCAAATC
357345 TGTAAATCGCAACTCGAATT
1 TGTAAATCGCAACTCGAATT
* *
357365 TGTAAATTGCAACACAGAA--
1 TGTAAATCGCAACTC-GAATT
357384 -GTCAAATTCGCAACGT-GAATT
1 TGT-AAA-TCGCAAC-TCGAATT
357405 TGTAAATCGCAAC
1 TGTAAATCGCAAC
357418 ACTAAAGTCA
Statistics
Matches: 42, Mismatches: 4, Indels: 14
0.70 0.07 0.23
Matches are distributed among these distances:
18 2 0.05
19 6 0.14
20 26 0.62
21 6 0.14
22 2 0.05
ACGTcount: A:0.38, C:0.19, G:0.16, T:0.26
Consensus pattern (20 bp):
TGTAAATCGCAACTCGAATT
Found at i:357395 original size:40 final size:41
Alignment explanation
Indices: 357351--357539 Score: 159
Period size: 40 Copynumber: 4.7 Consensus size: 41
357341 AATCTGTAAA
357351 TCGCAACTCGAATTTGTAAATT-GCAACACAGAAGTCAAAT
1 TCGCAACTCGAATTTGTAAATTCGCAACACAGAAGTCAAAT
357391 TCGCAACGT-GAATTTGTAAA-TCGCAACACTA-AAGTCAAAT
1 TCGCAAC-TCGAATTTGTAAATTCGCAACAC-AGAAGTCAAAT
* ** *
357431 TCGCAACAC--ATAAGTCAAATTCGCAACGC-GATAGTCAAAT
1 TCGCAACTCGAATTTGT-AAATTCGCAACACAGA-AGTCAAAT
* *
357471 TCGCAACT-GAATTT-CAAATTCGCAACA-ATGAATTTCAAAT
1 TCGCAACTCGAATTTGTAAATTCGCAACACA-GAA-GTCAAAT
* *
357511 TTGCAACTCG-ATTT-TCGAATTCGCAACAC
1 TCGCAACTCGAATTTGT-AAATTCGCAACAC
357540 GAATTTAATT
Statistics
Matches: 120, Mismatches: 13, Indels: 30
0.74 0.08 0.18
Matches are distributed among these distances:
38 4 0.03
39 17 0.14
40 83 0.69
41 16 0.13
ACGTcount: A:0.38, C:0.22, G:0.14, T:0.26
Consensus pattern (41 bp):
TCGCAACTCGAATTTGTAAATTCGCAACACAGAAGTCAAAT
Found at i:357409 original size:60 final size:60
Alignment explanation
Indices: 357326--357459 Score: 164
Period size: 60 Copynumber: 2.2 Consensus size: 60
357316 TGCGATTTTA
* * *
357326 CAAATTCACAACGCAAATCTGTAAATCGCAACTCGAATTTGT-AAATT-GCAACACAGAAGT
1 CAAATTCGCAACGCAAATCTGTAAATCGCAACACGAA--AGTCAAATTCGCAACACAGAAGT
** * * *
357386 CAAATTCGCAACGTGAATTTGTAAATCGCAACACTAAAGTCAAATTCGCAACACATAAGT
1 CAAATTCGCAACGCAAATCTGTAAATCGCAACACGAAAGTCAAATTCGCAACACAGAAGT
357446 CAAATTCGCAACGC
1 CAAATTCGCAACGC
357460 GATAGTCAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
58 2 0.03
59 5 0.08
60 56 0.89
ACGTcount: A:0.41, C:0.23, G:0.13, T:0.22
Consensus pattern (60 bp):
CAAATTCGCAACGCAAATCTGTAAATCGCAACACGAAAGTCAAATTCGCAACACAGAAGT
Found at i:357434 original size:20 final size:19
Alignment explanation
Indices: 357411--357497 Score: 93
Period size: 20 Copynumber: 4.4 Consensus size: 19
357401 AATTTGTAAA
357411 TCGCAACACTAAAGTCAAAT
1 TCGCAACAC-AAAGTCAAAT
357431 TCGCAACACATAAGTCAAAT
1 TCGCAACACA-AAGTCAAAT
* *
357451 TCGCAACGCGATAGTCAAAT
1 TCGCAACAC-AAAGTCAAAT
** **
357471 TCGCAACTGAATTTCAAAT
1 TCGCAACACAAAGTCAAAT
357490 TCGCAACA
1 TCGCAACA
357498 ATGAATTTCA
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
19 15 0.26
20 41 0.72
21 1 0.02
ACGTcount: A:0.40, C:0.25, G:0.13, T:0.22
Consensus pattern (19 bp):
TCGCAACACAAAGTCAAAT
Found at i:357475 original size:60 final size:61
Alignment explanation
Indices: 357368--357539 Score: 169
Period size: 60 Copynumber: 2.9 Consensus size: 61
357358 TCGAATTTGT
* *
357368 AAATT-GCAACACAGAAGTCAAATTCGCAACGTGAATTTGT-AAA-TCGCAACACT-AAAGTC
1 AAATTCGCAACACATAAGTCAAATTCGCAACGCG-A-TTGTCAAATTCGCAACACTGAAAGTC
* **
357427 AAATTCGCAACACATAAGTCAAATTCGCAACGCGATAGTCAAATTCGC-A-ACTGAATTTC
1 AAATTCGCAACACATAAGTCAAATTCGCAACGCGATTGTCAAATTCGCAACACTGAAAGTC
* * * * *
357486 AAATTCGCAACA-ATGAATTTCAAATTTGCAACTCGATTTTCGAATTCGCAACAC
1 AAATTCGCAACACAT-AA-GTCAAATTCGCAACGCGATTGTCAAATTCGCAACAC
357540 GAATTTAATT
Statistics
Matches: 94, Mismatches: 11, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
58 8 0.09
59 28 0.30
60 55 0.59
61 1 0.01
62 2 0.02
ACGTcount: A:0.40, C:0.22, G:0.13, T:0.25
Consensus pattern (61 bp):
AAATTCGCAACACATAAGTCAAATTCGCAACGCGATTGTCAAATTCGCAACACTGAAAGTC
Found at i:357489 original size:19 final size:19
Alignment explanation
Indices: 357465--357537 Score: 92
Period size: 21 Copynumber: 3.7 Consensus size: 19
357455 AACGCGATAG
357465 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
357484 TCAAATTCGCAACAATGAATT
1 TCAAATTCGCAAC--TGAATT
* *
357505 TCAAATTTGCAACTCGATTT
1 TCAAATTCGCAACT-GAATT
*
357525 TCGAATTCGCAAC
1 TCAAATTCGCAAC
357538 ACGAATTTAA
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
19 14 0.30
20 15 0.32
21 18 0.38
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.32
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:358369 original size:12 final size:12
Alignment explanation
Indices: 358348--358381 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
358338 ACCACATTTC
*
358348 CAATACCAAACA
1 CAATATCAAACA
358360 CAATATCAAACA
1 CAATATCAAACA
*
358372 CAATCTCAAA
1 CAATATCAAA
358382 ACCCACAACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:361089 original size:20 final size:20
Alignment explanation
Indices: 361064--361115 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
361054 GTTTTCCTTG
*
361064 AATTCGCAACGTGAAAGTCA
1 AATTCGCAACGCGAAAGTCA
*
361084 AATTCGCAACGCGGAAGTCA
1 AATTCGCAACGCGAAAGTCA
361104 AATTCGCAACGC
1 AATTCGCAACGC
361116 AAAATCGCAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.37, C:0.25, G:0.21, T:0.17
Consensus pattern (20 bp):
AATTCGCAACGCGAAAGTCA
Found at i:361163 original size:20 final size:20
Alignment explanation
Indices: 361140--361177 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
361130 AAAATCGCAA
*
361140 TGCGAATTTGACTTTCGCGT
1 TGCGAATTTGACTATCGCGT
361160 TGCGAATTTGACTATCGC
1 TGCGAATTTGACTATCGC
361178 AACGATAAAA
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:0.18, C:0.21, G:0.24, T:0.37
Consensus pattern (20 bp):
TGCGAATTTGACTATCGCGT
Found at i:361359 original size:66 final size:65
Alignment explanation
Indices: 361277--361452 Score: 250
Period size: 66 Copynumber: 2.6 Consensus size: 65
361267 AATTTAAAAC
361277 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTAC-ACATCAAAT
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTT-CTACATC-AAT
361341 TA
64 TA
*
361343 AACAAATCAACTTTTACAAATCAATTAAACAAGC-AAAAAATAATTCTTATTTCTTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTCTACATCAATTA
361407 AACAAATCAACTTTCAATGTA-AAATTCAATTAAACAAGCAAAAAAA
1 AACAAATCAAC-TT---T-TACAAA-TCAATTAAACAAGCAAAAAAA
361453 GTGTACCCCA
Statistics
Matches: 101, Mismatches: 1, Indels: 12
0.89 0.01 0.11
Matches are distributed among these distances:
64 17 0.17
65 24 0.24
66 34 0.34
68 4 0.04
69 16 0.16
70 6 0.06
ACGTcount: A:0.53, C:0.16, G:0.02, T:0.28
Consensus pattern (65 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTCTACATCAATTA
Found at i:362756 original size:42 final size:42
Alignment explanation
Indices: 362697--362819 Score: 124
Period size: 42 Copynumber: 2.9 Consensus size: 42
362687 GTGAGTCGGG
362697 CTCTTGAACGGTGGGAGGGACCAATTGAACGATGACAGTG-GC
1 CTCTTGAACGGTGGGAGGGACCAATTGAACGATGACAG-GAGC
* ** * *
362739 CTCTTGAACGGTGGGAGGGGCCTCTTGAATGATGAGAGGAGC
1 CTCTTGAACGGTGGGAGGGACCAATTGAACGATGACAGGAGC
* * * **
362781 CTCTTGAATGATAGGAGGTG-CCTCTTGAACGATGACAGG
1 CTCTTGAACGGTGGGAGG-GACCAATTGAACGATGACAGG
362820 TGAATCGGGC
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
41 1 0.01
42 67 0.97
43 1 0.01
ACGTcount: A:0.24, C:0.18, G:0.36, T:0.22
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGACCAATTGAACGATGACAGGAGC
Found at i:362820 original size:21 final size:21
Alignment explanation
Indices: 362721--362821 Score: 98
Period size: 21 Copynumber: 4.8 Consensus size: 21
362711 GAGGGACCAA
*
362721 TTGAACGATGACA-GTGGCCTC
1 TTGAACGATGAGAGGT-GCCTC
* * *
362742 TTGAACGGTGGGAGGGGCCTC
1 TTGAACGATGAGAGGTGCCTC
* *
362763 TTGAATGATGAGAGGAGCCTC
1 TTGAACGATGAGAGGTGCCTC
*
362784 TTGAATGAT-AGGAGGTGCCTC
1 TTGAACGATGA-GAGGTGCCTC
*
362805 TTGAACGATGACAGGTG
1 TTGAACGATGAGAGGTG
362822 AATCGGGCTT
Statistics
Matches: 66, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
20 1 0.02
21 63 0.95
22 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.36, T:0.24
Consensus pattern (21 bp):
TTGAACGATGAGAGGTGCCTC
Found at i:363121 original size:21 final size:21
Alignment explanation
Indices: 363097--363146 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
363087 TGAAACAATC
* *
363097 TCACGTAGAGTGGTTACCTCA
1 TCACGTAGAGTAGATACCTCA
*
363118 TCACGTAAAGTAGATACCTCA
1 TCACGTAGAGTAGATACCTCA
363139 TCACGTAG
1 TCACGTAG
363147 CGCACCATTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.30, C:0.24, G:0.20, T:0.26
Consensus pattern (21 bp):
TCACGTAGAGTAGATACCTCA
Found at i:363242 original size:63 final size:64
Alignment explanation
Indices: 363112--363269 Score: 155
Period size: 63 Copynumber: 2.5 Consensus size: 64
363102 TAGAGTGGTT
* * * *
363112 ACCTCATCACGTAAAGTA-GATACCTCATCACGTAGCGCACCATTGTCATCGCGTAAAACATCC
1 ACCTCATCACGTAAAGCACCATACCTCATCACGCAGCGCACCATTGTCATCACGTAAAACATCC
* * * **
363175 ACCTCACCACGTAAAG-ACCATACCTCATCACGCCA-TGCACCATTGTCTTCACGTAAAGTA-CC
1 ACCTCATCACGTAAAGCACCATACCTCATCACG-CAGCGCACCATTGTCATCACGTAAAACATCC
* * *
363237 AACCTCATGACGCAAAGCACC-GACCTCATCACG
1 -ACCTCATCACGTAAAGCACCATACCTCATCACG
363270 TAACTCATCC
Statistics
Matches: 79, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
62 3 0.04
63 72 0.91
64 4 0.05
ACGTcount: A:0.32, C:0.35, G:0.13, T:0.20
Consensus pattern (64 bp):
ACCTCATCACGTAAAGCACCATACCTCATCACGCAGCGCACCATTGTCATCACGTAAAACATCC
Found at i:363269 original size:42 final size:41
Alignment explanation
Indices: 363173--363272 Score: 103
Period size: 42 Copynumber: 2.4 Consensus size: 41
363163 CGTAAAACAT
* * *
363173 CCACCTCACCACGTAAAGACCATACCTCATCACGCCATGCA
1 CCACCTCATCACGTAAAGACCATACCTCATCACGCAAAGCA
** * *
363214 CCATTGTCTTCACGTAAAGTACCA-ACCTCATGACGCAAAGCA
1 CCA-CCTCATCACGTAAAG-ACCATACCTCATCACGCAAAGCA
363256 CCGACCTCATCACGTAA
1 CC-ACCTCATCACGTAA
363273 CTCATCCCGT
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
41 3 0.07
42 38 0.83
43 5 0.11
ACGTcount: A:0.32, C:0.38, G:0.12, T:0.18
Consensus pattern (41 bp):
CCACCTCATCACGTAAAGACCATACCTCATCACGCAAAGCA
Found at i:365370 original size:20 final size:21
Alignment explanation
Indices: 365347--365411 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
365337 TCTGAGAGAT
365347 GGAGAT-AGACGGATTTCGCC
1 GGAGATGAGACGGATTTCGCC
* *
365367 GGAGATGGGGACGGATTTCGTC
1 GGAGAT-GAGACGGATTTCGCC
* * *
365389 TGAGATGGGGACGGATGTCGCC
1 GGAGAT-GAGACGGATTTCGCC
365411 G
1 G
365412 TTGAGAGTGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 6 0.16
22 31 0.84
ACGTcount: A:0.20, C:0.17, G:0.43, T:0.20
Consensus pattern (21 bp):
GGAGATGAGACGGATTTCGCC
Found at i:365381 original size:22 final size:22
Alignment explanation
Indices: 365354--365411 Score: 89
Period size: 22 Copynumber: 2.6 Consensus size: 22
365344 GATGGAGATA
365354 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
* *
365376 GACGGATTTCGTCTGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
365398 GACGGATGTCGCCG
1 GACGGATTTCGCCG
365412 TTGAGAGTGA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.17, C:0.19, G:0.43, T:0.21
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:365589 original size:20 final size:21
Alignment explanation
Indices: 365564--365830 Score: 204
Period size: 20 Copynumber: 13.3 Consensus size: 21
365554 TAAACGCGCT
*
365564 TTGCGAATTTGACTATC-GCG
1 TTGCGAATTTGACTATCAGTG
**
365584 TTGCGAATTTGACT-TTTGTG
1 TTGCGAATTTGACTATCAGTG
**
365604 TTGCGAATTT-AAAATTCAGTG
1 TTGCGAATTTGACTA-TCAGTG
*
365625 TTGCGAATTTGACTATC-GCG
1 TTGCGAATTTGACTATCAGTG
* *
365645 TTGCAAATTTGACT-TCTGTG
1 TTGCGAATTTGACTATCAGTG
*
365665 TTGCGAATTTGACT-TCTGTG
1 TTGCGAATTTGACTATCAGTG
* ** *
365685 TTGCG-ATTT-ACAGATTTGCG
1 TTGCGAATTTGAC-TATCAGTG
*
365705 TTGCAAATTTGACT-TCAGTG
1 TTGCGAATTTGACTATCAGTG
* ** *
365725 TTGCG-ATTT-ACAGATTTGCG
1 TTGCGAATTTGAC-TATCAGTG
*
365745 TTGCAAATTTGACT-TCAGTG
1 TTGCGAATTTGACTATCAGTG
*
365765 TTGCGAATTTGACTATC-GCG
1 TTGCGAATTTGACTATCAGTG
*
365785 TTGCGAATTTGACT-TCTGTG
1 TTGCGAATTTGACTATCAGTG
*
365805 TTGCGAATTTGACT-TCTGTG
1 TTGCGAATTTGACTATCAGTG
365825 TTGCGA
1 TTGCGA
365831 TTTACAAATT
Statistics
Matches: 199, Mismatches: 33, Indels: 30
0.76 0.13 0.11
Matches are distributed among these distances:
18 4 0.02
19 14 0.07
20 149 0.75
21 26 0.13
22 6 0.03
ACGTcount: A:0.20, C:0.15, G:0.24, T:0.41
Consensus pattern (21 bp):
TTGCGAATTTGACTATCAGTG
Found at i:365677 original size:40 final size:40
Alignment explanation
Indices: 365564--365830 Score: 255
Period size: 40 Copynumber: 6.7 Consensus size: 40
365554 TAAACGCGCT
**
365564 TTGCGAATTTGACTATC-GCGTTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACT-TCTGCGTTGCGAATTTGACTTCAGTG
* * * * *
365604 TTGCGAATTTAAAATTCAGTGTTGCGAATTTGACTATC-GCG
1 TTGCGAATTT-GACTTCTGCGTTGCGAATTTGACT-TCAGTG
* * *
365645 TTGCAAATTTGACTTCTGTGTTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTCTGCGTTGCGAATTTGACTTCAGTG
*
365685 TTGCG-ATTT-ACAGATT-TGCGTTGCAAATTTGACTTCAGTG
1 TTGCGAATTTGAC---TTCTGCGTTGCGAATTTGACTTCAGTG
*
365725 TTGCG-ATTT-ACAGATT-TGCGTTGCAAATTTGACTTCAGTG
1 TTGCGAATTTGAC---TTCTGCGTTGCGAATTTGACTTCAGTG
*
365765 TTGCGAATTTGACTATC-GCGTTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACT-TCTGCGTTGCGAATTTGACTTCAGTG
*
365805 TTGCGAATTTGACTTCTGTGTTGCGA
1 TTGCGAATTTGACTTCTGCGTTGCGA
365831 TTTACAAATT
Statistics
Matches: 198, Mismatches: 17, Indels: 24
0.83 0.07 0.10
Matches are distributed among these distances:
38 2 0.01
39 9 0.05
40 149 0.75
41 35 0.18
42 3 0.02
ACGTcount: A:0.20, C:0.15, G:0.24, T:0.41
Consensus pattern (40 bp):
TTGCGAATTTGACTTCTGCGTTGCGAATTTGACTTCAGTG
Found at i:365818 original size:60 final size:59
Alignment explanation
Indices: 365564--365830 Score: 258
Period size: 60 Copynumber: 4.4 Consensus size: 59
365554 TAAACGCGCT
** * * *
365564 TTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTAAAATTCAGTG
1 TTGCGAATTTGACT-TCGCGTTGCGAATTTGACTTCAGTGTTGCGAATTT-GACTTCTGTG
* *
365625 TTGCGAATTTGACTATCGCGTTGCAAATTTGACTTCTGTGTTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACT-TCGCGTTGCGAATTTGACTTCAGTGTTGCGAATTTGACTTCTGTG
* * *
365685 TTGCG-ATTT-ACAGATTTGCGTTGCAAATTTGACTTCAGTGTTGCG-ATTT-ACAGATT-TGCG
1 TTGCGAATTTGAC---TTCGCGTTGCGAATTTGACTTCAGTGTTGCGAATTTGAC---TTCTGTG
* * *
365745 TTGCAAATTTGACTTCAGTGTTGCGAATTTGACTATC-GCGTTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTC-GCGTTGCGAATTTGACT-TCAGTGTTGCGAATTTGACTTCTGTG
*
365805 TTGCGAATTTGACTTCTGTGTTGCGA
1 TTGCGAATTTGACTTC-GCGTTGCGA
365831 TTTACAAATT
Statistics
Matches: 177, Mismatches: 16, Indels: 27
0.80 0.07 0.12
Matches are distributed among these distances:
58 4 0.02
59 12 0.07
60 96 0.54
61 61 0.34
62 4 0.02
ACGTcount: A:0.20, C:0.15, G:0.24, T:0.41
Consensus pattern (59 bp):
TTGCGAATTTGACTTCGCGTTGCGAATTTGACTTCAGTGTTGCGAATTTGACTTCTGTG
Found at i:365847 original size:20 final size:20
Alignment explanation
Indices: 365824--365863 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
365814 TGACTTCTGT
365824 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACAAATTCGC
*
365844 GTTGCGATTTACAGATTCGC
1 GTTGCGATTTACAAATTCGC
365864 AACGCGAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGC
Found at i:365870 original size:20 final size:20
Alignment explanation
Indices: 365827--365904 Score: 57
Period size: 20 Copynumber: 3.9 Consensus size: 20
365817 CTTCTGTGTT
***
365827 GCGATTTACAAATTCGCGTT
1 GCGATTTACAAATTCGCAAC
*
365847 GCGATTTACAGATTCGCAAC
1 GCGATTTACAAATTCGCAAC
** * *
365867 GCGAATTTGGAAAATCGCAAT
1 GCG-ATTTACAAATTCGCAAC
* *
365888 ACGATTTACATATTCGC
1 GCGATTTACAAATTCGC
365905 GTTGCGAATT
Statistics
Matches: 43, Mismatches: 14, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
20 29 0.67
21 14 0.33
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (20 bp):
GCGATTTACAAATTCGCAAC
Found at i:365875 original size:100 final size:99
Alignment explanation
Indices: 365564--365848 Score: 364
Period size: 100 Copynumber: 2.8 Consensus size: 99
365554 TAAACGCGCT
* *
365564 TTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTAAAATTCAGTGTTGC
1 TTGCGAATTTGACTATCGCGTTGCGAATTTGAC-TTTGTGTTGCGAATTT-GACTTCAGTGTTGC
* *
365629 GAATTTGAC-TA-TCGCGTTGCAAATTTGACTTCTGTG
64 G-ATTT-ACAAATTCGCGTTGCAAATTTGACTTCAGTG
* * *
365665 TTGCGAATTTGACT-TCTGTGTTGCG-ATTT-ACAGATTTGCGTTGCAAATTTGACTTCAGTGTT
1 TTGCGAATTTGACTATC-GCGTTGCGAATTTGAC---TTTGTGTTGCGAATTTGACTTCAGTGTT
* *
365727 GCGATTTACAGATTTGCGTTGCAAATTTGACTTCAGTG
62 GCGATTTACAAATTCGCGTTGCAAATTTGACTTCAGTG
*
365765 TTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTTGACTTCTGTGTTGCG
1 TTGCGAATTTGACTATCGCGTTGCGAATTTGACTT-TGTGTTGCGAATTTGACTTCAGTGTTGCG
365830 ATTTACAAATTCGCGTTGC
65 ATTTACAAATTCGCGTTGC
365849 GATTTACAGA
Statistics
Matches: 160, Mismatches: 15, Indels: 19
0.82 0.08 0.10
Matches are distributed among these distances:
98 2 0.01
99 9 0.06
100 106 0.66
101 41 0.26
102 2 0.01
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.41
Consensus pattern (99 bp):
TTGCGAATTTGACTATCGCGTTGCGAATTTGACTTTGTGTTGCGAATTTGACTTCAGTGTTGCGA
TTTACAAATTCGCGTTGCAAATTTGACTTCAGTG
Found at i:368170 original size:23 final size:23
Alignment explanation
Indices: 368144--368191 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
368134 ATAAAGTACA
*
368144 ATAACATACTAGGTAGCGTTTAT
1 ATAACATAATAGGTAGCGTTTAT
**
368167 ATAATGTAATAGGTAGCGTTTAT
1 ATAACATAATAGGTAGCGTTTAT
368190 AT
1 AT
368192 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGTTTAT
Found at i:368645 original size:23 final size:23
Alignment explanation
Indices: 368619--368681 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
368609 ATATAACCAC
368619 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
368642 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
368665 TACCTATTACATCATAT
1 TACCTATTACATTATAT
368682 TTTACCTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:369103 original size:23 final size:22
Alignment explanation
Indices: 369037--369108 Score: 90
Period size: 23 Copynumber: 3.2 Consensus size: 22
369027 ATACTTTACA
*
369037 ATATAACCACTACCTATTACATT
1 ATATAA-CGCTACCTATTACATT
* *
369060 ATATAACGATACATATTACATT
1 ATATAACGCTACCTATTACATT
*
369082 ATATAAGCGCTACCTATTACATC
1 ATATAA-CGCTACCTATTACATT
369105 ATAT
1 ATAT
369109 TTTTACCTAT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
22 19 0.45
23 23 0.55
ACGTcount: A:0.40, C:0.21, G:0.04, T:0.35
Consensus pattern (22 bp):
ATATAACGCTACCTATTACATT
Found at i:369288 original size:429 final size:429
Alignment explanation
Indices: 368265--370599 Score: 4383
Period size: 429 Copynumber: 5.4 Consensus size: 429
368255 TTATAATATG
*
368265 TTGAAAGTGTCCATACTTTTTATAAAAATGATCGATACTTTGTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTGTTTAAAGTTATGTAATTTATGTT
* *
368330 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATGAATTTAATAATTTCATTTGCA
66 TCAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
* *
368395 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTTTAATTTAATAATA
130 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAA-TTTAAATTTAACAATA
368460 ATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAA
194 ATATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAA
368525 CTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAA
259 CTCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAA
368590 AAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATT
324 AAAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATT
368655 ATATAAGCGCTACCTATTACATCATA-TTTTACCTATTATA
389 ATATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
368695 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTGTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTGTTTAAAGTTATGTAATTTATGTT
*
368760 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACTTACAATATTAATTTAATAATTTCATTTACAC
66 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC
368825 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAAT
131 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAAT
*
368890 ATATATCGTAACGTAAAAAATAAATCATTAGACGTCTATAATTACTAAATTAATATCTTAAAACT
196 ATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACT
368955 CACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAAA
261 CACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAAA
*
369020 AGGATAGATACTTTACAATATAACCACTACCTATTACATTATAT-AACGATACATATTACATTAT
326 AGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATTAT
369084 ATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
391 ATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
*
369123 TTGAAAGTGTCCATACTTTTTATAAAAAAGATCGATACTTTGTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTGTTTAAAGTTATGTAATTTATGTT
369188 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
66 TCAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
369253 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAA
130 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAA
369318 TATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAAC
195 TATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAAC
*
369383 TCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGGAAAAAGTATAGACACTTTTATAAA
260 TCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAA
369448 AAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATTA
325 AAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATTA
369513 TATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
390 TATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
* *
369553 TTGAAAGTGTCCATACCTTTTATAAAAAGGATCGATACTTTGTTTAAAGTAATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTGTTTAAAGTTATGTAATTTATGTT
*
369618 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAT
66 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC
*
369683 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAATAATAAT
131 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAAT
369748 ATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACT
196 ATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACT
369813 CACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAAA
261 CACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAAA
*
369878 AGGATAGATACTTTACAATATAACCACTATCTATTACATTATATAAACGATACCTATTACATTAT
326 AGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATTAT
369943 ATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
391 ATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
* * *
369982 TTAAAAGTGTTCATACTTTTTATAAAAAGGATTGATACTTTGTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTGTTTAAAGTTATGTAATTTATGTT
*
370047 TCAATTTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCACTTACA
66 TCAA-TTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACA
*
370112 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAATAATAA
130 CAAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAA
370177 TATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATAT-TTAAAAC
195 TATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAAC
*
370241 TCACTCAAAAGATAA-CTTAAATTAATGTTTTCCAGAGTGAAAAAAGTATAGACACTTTTATAAA
260 TCACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAA
* *
370305 AAGGATAGATATTTTACAATATAACCACTACCTATTACATTATATAAACAATACCTATTACATTA
325 AAGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATTA
370370 TATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
390 TATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
370410 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTGTTTAAAGTTATGTAATTTATGTT
1 TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTGTTTAAAGTTATGTAATTTATGTT
*
370475 TTAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAA-TTCATTTACAC
66 TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC
370539 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAA
131 AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAA
370600 CATTAACCAA
Statistics
Matches: 1864, Mismatches: 37, Indels: 12
0.97 0.02 0.01
Matches are distributed among these distances:
426 70 0.04
427 92 0.05
428 486 0.26
429 844 0.45
430 372 0.20
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (429 bp):
TTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATACTTTGTTTAAAGTTATGTAATTTATGTT
TCAATTTTTTTAATAGTGTTTCATGTTTTCCACCTACAATATTAATTTAATAATTTCATTTACAC
AAAAAATTATTTGATTGTTTTGATATTTTATAAAATAATATTTAGAATTTAAATTTAACAATAAT
ATATATCGTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACT
CACTCAAAAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATAGACACTTTTATAAAA
AGGATAGATACTTTACAATATAACCACTACCTATTACATTATATAAACGATACCTATTACATTAT
ATAAGCGCTACCTATTACATCATATTTTTACCTATTATA
Found at i:369502 original size:23 final size:23
Alignment explanation
Indices: 369476--369538 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
369466 ATATAACCAC
369476 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
* *
369499 TACCTATTACATTATATAAGCGC
1 TACCTATTACATTATATAAACGA
*
369522 TACCTATTACATCATAT
1 TACCTATTACATTATAT
369539 TTTTACCTAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:369934 original size:23 final size:23
Alignment explanation
Indices: 369908--369967 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
369898 TAACCACTAT
369908 CTATTACATTATATAAACGATAC
1 CTATTACATTATATAAACGATAC
* *
369931 CTATTACATTATATAAGCGCTAC
1 CTATTACATTATATAAACGATAC
*
369954 CTATTACATCATAT
1 CTATTACATTATAT
369968 TTTTACCTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.38, C:0.20, G:0.05, T:0.37
Consensus pattern (23 bp):
CTATTACATTATATAAACGATAC
Found at i:370349 original size:23 final size:23
Alignment explanation
Indices: 370323--370395 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
370313 ATATTTTACA
*
370323 ATATAACCACTACCTATTACATT
1 ATATAAACACTACCTATTACATT
*
370346 ATATAAACAATACCTATTACATT
1 ATATAAACACTACCTATTACATT
* * *
370369 ATATAAGCGCTACCTATTACATC
1 ATATAAACACTACCTATTACATT
370392 ATAT
1 ATAT
370396 TTTTACCTAT
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:0.41, C:0.22, G:0.03, T:0.34
Consensus pattern (23 bp):
ATATAAACACTACCTATTACATT
Found at i:373658 original size:181 final size:181
Alignment explanation
Indices: 373238--373723 Score: 857
Period size: 181 Copynumber: 2.7 Consensus size: 181
373228 TTAAAATTAC
*
373238 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGATACAAT
1 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
* *
373303 ATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCACTCATAAAACTGGTATATTTATACCGGTT
66 ATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA-TT-TACCGGTT
373368 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
129 ATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
*
373421 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATTAAGTACCGACACAAT
1 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
373486 ATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTACCGGTTAT
66 ATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTACCGGTTAT
* *
373551 ATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAACTGT
131 ATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
* *
373602 CGACACGTTTTGACAAT-GTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
1 CGACACTTTTTTA-AATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAA
*
373666 TATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTA
65 TATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTA
373724 TACCGATAGC
Statistics
Matches: 292, Mismatches: 10, Indels: 4
0.95 0.03 0.01
Matches are distributed among these distances:
181 173 0.59
182 5 0.02
183 114 0.39
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (181 bp):
CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAGTACCGACACAAT
ATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTACCGGTTAT
ATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
Found at i:375708 original size:3 final size:3
Alignment explanation
Indices: 375700--375744 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
375690 ACTTGTTTGG
* *
375700 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC GTC ATC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
375745 GTCAGCTTCA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.29, C:0.33, G:0.02, T:0.36
Consensus pattern (3 bp):
ATC
Found at i:378134 original size:196 final size:200
Alignment explanation
Indices: 377215--378574 Score: 2466
Period size: 199 Copynumber: 6.9 Consensus size: 200
377205 TTTAAATTAA
377215 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
377280 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
* *
377345 TCGACACTTTTTATATATAGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTAGACA
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACA
*
377410 AAAAA
196 AAAAC
377415 TATCGACACAAACT-AAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
377479 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
*
377544 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCAGTTTTCCATTCATTCTGGAC-
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACA
377608 AAAAC
196 AAAAC
* *
377613 TATCGACACAAACTAAAAAAGTGTCAACACATTATTTAGACATATTCTCTCATAAAACCAGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
377678 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
377743 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACA
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACA
377808 AAAAC
196 AAAAC
377813 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
377878 CTTGTACCGGTTAGATTGAAAAATTACATATTACA-T-TAC-TTTGGGTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
*
377940 TCG-CACTTTTTATATATGGATCGACACTTTATGGTTGTACCCTGTTTTCCATTCATTCTGGACA
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACA
378004 AAAAC
196 AAAAC
378009 TATCGAC-CAAACT-AAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
378072 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATG-TTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
*
378136 TCTACAC--TTT-TATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACA
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACA
378198 AAAAC
196 AAAAC
*
378203 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGATATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
378268 CTTGTACCGGTTAGATTGGAAAATTACATATTACATTATAC-TTTGGGTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
378332 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACA
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACA
*
378397 AAAAA
196 AAAAC
378402 TATCGACACAAACT-AAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
* *
378466 CTTGTATCGGTTAGATTGGAAAATTACATA-TACATTATACTTTTGGGTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
* *
378530 TCGACAC-TTTT-TATATGGTTCGACACTTTATTGTTGCACCCTGTT
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTT
378575 GGCCATATTG
Statistics
Matches: 1127, Mismatches: 20, Indels: 30
0.96 0.02 0.03
Matches are distributed among these distances:
194 148 0.13
195 30 0.03
196 220 0.20
197 57 0.05
198 132 0.12
199 423 0.38
200 117 0.10
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (200 bp):
TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTTCGATGTTTTTGGGA
TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACA
AAAAC
Found at i:378738 original size:19 final size:19
Alignment explanation
Indices: 378692--378740 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
378682 TTATATTCAC
*
378692 ATACAAAAATATAAATCAT
1 ATACAAAATTATAAATCAT
*
378711 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCAT
378730 ATACAAAATTA
1 ATACAAAATTA
378741 ACCCTACATT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.31
Consensus pattern (19 bp):
ATACAAAATTATAAATCAT
Found at i:380542 original size:33 final size:33
Alignment explanation
Indices: 380505--380570 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
380495 CATCTTAATA
*
380505 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
380538 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
380571 CCATCTATTT
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:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:380629 original size:21 final size:21
Alignment explanation
Indices: 380604--380668 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
380594 CCCCTTATGC
* *
380604 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
380625 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
*
380646 CTATCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTCTCTTCGACT
380667 CT
1 CT
380669 TGATTGTCTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.17, C:0.31, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTCTCTTCGACT
Found at i:382685 original size:24 final size:24
Alignment explanation
Indices: 382648--382700 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
382638 CCGTTCTATC
382648 TATTTTCAGAGGATAT-TTAGCTTA
1 TATTTTCAGAGGATATGTTA-CTTA
** *
382672 TATTTTCATCGGATATGTTATTTA
1 TATTTTCAGAGGATATGTTACTTA
382696 TATTT
1 TATTT
382701 AATCGATACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 22 0.88
25 3 0.12
ACGTcount: A:0.26, C:0.08, G:0.13, T:0.53
Consensus pattern (24 bp):
TATTTTCAGAGGATATGTTACTTA
Found at i:382886 original size:20 final size:19
Alignment explanation
Indices: 382841--382886 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
382831 TCCGGTATCA
382841 TTTACCGGTTTAATCATTT
1 TTTACCGGTTTAATCATTT
* *
382860 TGATACCGGTTTTATCATATT
1 T-TTACCGGTTTAATCAT-TT
382881 TTTACC
1 TTTACC
382887 TGTTATATCG
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.05
20 18 0.82
21 3 0.14
ACGTcount: A:0.22, C:0.17, G:0.11, T:0.50
Consensus pattern (19 bp):
TTTACCGGTTTAATCATTT
Found at i:383049 original size:20 final size:20
Alignment explanation
Indices: 383022--383068 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
383012 TCCGGTAACG
383022 TTTTACCGGTTTTATCAT-T
1 TTTTACCGGTTTTATCATAT
383041 TTGTTACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCATAT
383062 TTTTACC
1 TTTTACC
383069 TGGTATATCG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.17, C:0.17, G:0.11, T:0.55
Consensus pattern (20 bp):
TTTTACCGGTTTTATCATAT
Found at i:383183 original size:181 final size:182
Alignment explanation
Indices: 382808--383276 Score: 673
Period size: 181 Copynumber: 2.6 Consensus size: 182
382798 CGTACTTACG
* *
382808 AAAGTATCGACACTTTCAATATATCCGGTATC-ATTTACCGGTTTAATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGATTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
382872 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATATATTTTTTTAAAGTATCGACACATTAT
66 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
*
382937 AGGCGCTAAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
131 AGGCGATAAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
* *
382989 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGTTACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGATTTACCGGTTTTATCATTTTGATACCGGTTT
*
383054 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
** *
383119 A-G-GATTTAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
131 AGGCGATAAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
* * * * * *
383170 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTTACCAGTTTTATCATTTCT-ATACCGGTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGATTTACCGGTTTTATCATTT-TGATACCGGTT
* * * *
383234 TTGTCATA-GTTTACAT-GT-TATCGTTTTGGATCGACACATTTTT
65 TTATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTT
383277 AATTTGGATC
Statistics
Matches: 262, Mismatches: 23, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
178 24 0.09
179 2 0.01
180 49 0.19
181 95 0.36
182 92 0.35
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (182 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGATTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
AGGCGATAAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
Found at i:383660 original size:20 final size:20
Alignment explanation
Indices: 383619--383660 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
383609 CAGGTAAAAA
**
383619 TATGACAAAACCAGATTCAT
1 TATGACAAAACCAGATAAAT
383639 TATGACAAAACC-GAATAAAT
1 TATGACAAAACCAG-ATAAAT
383659 TA
1 TA
383661 CTTGATATGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 1 0.05
20 18 0.95
ACGTcount: A:0.50, C:0.17, G:0.10, T:0.24
Consensus pattern (20 bp):
TATGACAAAACCAGATAAAT
Found at i:384466 original size:177 final size:177
Alignment explanation
Indices: 384130--384669 Score: 768
Period size: 178 Copynumber: 3.0 Consensus size: 177
384120 CGATACAAAT
* * * * * *
384130 TAAAAATGTATCGATCCATAGCAATATAACATGTAAAAATATGATAAAACCGATATC-ATTAT-A
1 TAAAAATGTATCGATCCATAGCAATAT-ACAGGTAATAATATGACAAAACAG-TCTCGA-AATGA
** *
384193 TAAAACCGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATAAATTAATAAGTATCGACACTTT
63 TAAAACCGGTAAAAAGATACCGGATATATTGAAAGTGTCGATAAATTAATAAGTATCGACACTTT
384258 TGTAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAGGTGTCGATACTTTA
128 TGTAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAA-GTGTCGATACTTTA
*
384309 TAAAAATGTGTCGATCCATAGCAATATACAGGTAATAATATGAC-AAACAAGTCTCGAAATGATA
1 TAAAAATGTATCGATCCATAGCAATATACAGGTAATAATATGACAAAAC-AGTCTCGAAATGATA
*
384373 AAACCGGTAAAAAGTTACCGGATATATTGAAAGTGTCGATAAA-TAATAAGTATCGACACTTTTG
65 AAACCGGTAAAAAGATACCGGATATATTGAAAGTGTCGATAAATTAATAAGTATCGACACTTTTG
*
384437 TAATTTAAAAGAGAATAAGTTATAGCGCCTGAAAAGTGTCGATACTTTA
130 TAATTTAAAAGAGAAGAAGTTATAGCGCCT-AAAAGTGTCGATACTTTA
* * * *
384486 TACAAATGTATCGATCCATAGTAATATATCCGGTAATAATATGACAAAAGAGGTCTCGAAATGAT
1 TAAAAATGTATCGATCCATAGCAATATA-CAGGTAATAATATGACAAAACA-GTCTCGAAATGAT
* * *
384551 AAAACCGGT-AAAAGATATCGGATATGTTGAAAGTGTCGATAAATTAATAAGTATCGACACTTTC
64 AAAACCGGTAAAAAGATACCGGATATATTGAAAGTGTCGATAAATTAATAAGTATCGACACTTTT
*
384615 GTAATTTAAAAGAGAAGAA-ATATAGCGCCTAAAAAGTGTCGATACTTTAA
129 GTAATTTAAAAGAGAAGAAGTTATAGCGCCT-AAAAGTGTCGATACTTT-A
384665 TAAAA
1 TAAAA
384670 CCGTTTAATT
Statistics
Matches: 328, Mismatches: 24, Indels: 18
0.89 0.06 0.05
Matches are distributed among these distances:
177 98 0.30
178 137 0.42
179 93 0.28
ACGTcount: A:0.43, C:0.12, G:0.17, T:0.28
Consensus pattern (177 bp):
TAAAAATGTATCGATCCATAGCAATATACAGGTAATAATATGACAAAACAGTCTCGAAATGATAA
AACCGGTAAAAAGATACCGGATATATTGAAAGTGTCGATAAATTAATAAGTATCGACACTTTTGT
AATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAGTGTCGATACTTTA
Found at i:386614 original size:23 final size:23
Alignment explanation
Indices: 386588--386633 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
386578 GTTCGGTTTA
386588 AATTTATATATTTAATAAAATTT
1 AATTTATATATTTAATAAAATTT
* **
386611 AATTTTTATATTTTTTAAAATTT
1 AATTTATATATTTAATAAAATTT
386634 TCATATTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
AATTTATATATTTAATAAAATTT
Found at i:386964 original size:21 final size:21
Alignment explanation
Indices: 386940--387066 Score: 127
Period size: 21 Copynumber: 6.1 Consensus size: 21
386930 TGTAACTTAG
386940 TTTCCAAATTCGCAACGCGAT
1 TTTCCAAATTCGCAACGCGAT
**
386961 TTTCCAAATTCGCATTGCGAT
1 TTTCCAAATTCGCAACGCGAT
386982 TTTCCAAATTCGCAACGCGA-
1 TTTCCAAATTCGCAACGCGAT
**
387002 TTTCTGAATTCGCAACGCGAAT
1 TTTCCAAATTCGCAACGCG-AT
*** *
387024 TTT--GTTTTCGCAACTCGAT
1 TTTCCAAATTCGCAACGCGAT
*
387043 TTT-CAAATTCGCAACACGAAT
1 TTTCCAAATTCGCAACGCG-AT
387064 TTT
1 TTT
387067 AATTTCGTGC
Statistics
Matches: 89, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
19 5 0.06
20 38 0.43
21 43 0.48
22 3 0.03
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (21 bp):
TTTCCAAATTCGCAACGCGAT
Found at i:387073 original size:20 final size:20
Alignment explanation
Indices: 387010--387073 Score: 67
Period size: 20 Copynumber: 3.2 Consensus size: 20
387000 GATTTCTGAA
* **
387010 TTCGCAACGCGAATTTTGTT
1 TTCGCAACACGAATTTTAAT
* *
387030 TTCGCAACTCG-ATTTTCAAA
1 TTCGCAACACGAATTTT-AAT
387050 TTCGCAACACGAATTTTAAT
1 TTCGCAACACGAATTTTAAT
387070 TTCG
1 TTCG
387074 TGCAACACAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
19 5 0.14
20 26 0.72
21 5 0.14
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.38
Consensus pattern (20 bp):
TTCGCAACACGAATTTTAAT
Found at i:387073 original size:40 final size:40
Alignment explanation
Indices: 386948--387073 Score: 130
Period size: 40 Copynumber: 3.1 Consensus size: 40
386938 AGTTTCCAAA
** *
386948 TTCGCAACGCGATTTTCCAAATTCGCATTGCG-ATTTTCCAAA
1 TTCGCAACGCGATTTT-CAAATTCGCAACGCGAATTTT--AAT
* **
386990 TTCGCAACGCGA-TTTCTGAATTCGCAACGCGAATTTTGTT
1 TTCGCAACGCGATTTTC-AAATTCGCAACGCGAATTTTAAT
* *
387030 TTCGCAACTCGATTTTCAAATTCGCAACACGAATTTTAAT
1 TTCGCAACGCGATTTTCAAATTCGCAACGCGAATTTTAAT
387070 TTCG
1 TTCG
387074 TGCAACACAA
Statistics
Matches: 70, Mismatches: 11, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
40 35 0.50
41 18 0.26
42 17 0.24
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (40 bp):
TTCGCAACGCGATTTTCAAATTCGCAACGCGAATTTTAAT
Found at i:387975 original size:24 final size:24
Alignment explanation
Indices: 387948--387994 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
387938 GTATTCGAAA
*
387948 TTTGATCTTGGTCAATACCCAGAC
1 TTTGATCTTGCTCAATACCCAGAC
*
387972 TTTGATCTTGCTCAATACTCAGA
1 TTTGATCTTGCTCAATACCCAGA
387995 TTTCAATGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.36
Consensus pattern (24 bp):
TTTGATCTTGCTCAATACCCAGAC
Found at i:390157 original size:18 final size:18
Alignment explanation
Indices: 390134--390169 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
390124 AAGCAAAAGG
390134 AAATCAAAATCGCAATCA
1 AAATCAAAATCGCAATCA
*
390152 AAATCAAAATCTCAATCA
1 AAATCAAAATCGCAATCA
390170 CAACCGACTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCGCAATCA
Found at i:390404 original size:29 final size:29
Alignment explanation
Indices: 390371--390431 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
390361 AAATTCGAAA
*
390371 CGCAAAAACCGCAACGCGAATTTGACTTT
1 CGCAAAAACCGCAACACGAATTTGACTTT
** *
390400 CGCAACCATCGCAACACGAATTTGACTTT
1 CGCAAAAACCGCAACACGAATTTGACTTT
390429 CGC
1 CGC
390432 GTTGCGAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.31, C:0.31, G:0.16, T:0.21
Consensus pattern (29 bp):
CGCAAAAACCGCAACACGAATTTGACTTT
Found at i:390439 original size:20 final size:20
Alignment explanation
Indices: 390415--390459 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
390405 CCATCGCAAC
390415 ACGAATTTGACTTTCGCGTT
1 ACGAATTTGACTTTCGCGTT
* *
390435 GCGAATTTGATTTTCGCGTT
1 ACGAATTTGACTTTCGCGTT
390455 ACGAA
1 ACGAA
390460 AGTATACCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (20 bp):
ACGAATTTGACTTTCGCGTT
Found at i:390619 original size:64 final size:64
Alignment explanation
Indices: 390518--390668 Score: 232
Period size: 64 Copynumber: 2.4 Consensus size: 64
390508 AATTTAAAAC
390518 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
*** * **
390582 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTTATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
*
390646 AATAAATCAAC-TTTACAAATCAA
1 AACAAATCAACTTTTACAAATCAA
390669 CTTTTACAAA
Statistics
Matches: 80, Mismatches: 7, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
63 12 0.15
64 68 0.85
ACGTcount: A:0.52, C:0.17, G:0.02, T:0.29
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAAGAATTATTTACACATCAATTA
Found at i:390665 original size:13 final size:14
Alignment explanation
Indices: 390649--390679 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
390639 TCAATTAAAT
390649 AAATCAAC-TTTAC
1 AAATCAACTTTTAC
390662 AAATCAACTTTTAC
1 AAATCAACTTTTAC
390676 AAAT
1 AAAT
390680 ACATCAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.48, C:0.19, G:0.00, T:0.32
Consensus pattern (14 bp):
AAATCAACTTTTAC
Found at i:392055 original size:21 final size:21
Alignment explanation
Indices: 392031--392130 Score: 98
Period size: 21 Copynumber: 4.8 Consensus size: 21
392021 GTATGAGGAA
*
392031 CCTCTTGAATGATGACAGGGG
1 CCTCTTGAACGATGACAGGGG
* *
392052 CCTCTTGAATGGTGGA-AGGGG
1 CCTCTTGAACGAT-GACAGGGG
* *
392073 CCTCTTGAAGGATGATAGGGG
1 CCTCTTGAACGATGACAGGGG
* *
392094 -CTCTTGAACGAT-AGGAGAGG
1 CCTCTTGAACGATGA-CAGGGG
392114 CCTCTTGAACGATGACA
1 CCTCTTGAACGATGACA
392131 TGTGAATCGA
Statistics
Matches: 67, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
19 1 0.01
20 17 0.25
21 46 0.69
22 3 0.04
ACGTcount: A:0.25, C:0.18, G:0.34, T:0.23
Consensus pattern (21 bp):
CCTCTTGAACGATGACAGGGG
Found at i:392116 original size:41 final size:42
Alignment explanation
Indices: 392031--392130 Score: 123
Period size: 41 Copynumber: 2.4 Consensus size: 42
392021 GTATGAGGAA
* * * *
392031 CCTCTTGAATGATGACAGGGGCCTCTTGAATGGTGGAAGGGG
1 CCTCTTGAACGATGACAGGGGCCTCTTGAACGATGGAAGAGG
* *
392073 CCTCTTGAAGGATGATAGGGG-CTCTTGAACGATAGG-AGAGG
1 CCTCTTGAACGATGACAGGGGCCTCTTGAACGAT-GGAAGAGG
392114 CCTCTTGAACGATGACA
1 CCTCTTGAACGATGACA
392131 TGTGAATCGA
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
41 29 0.58
42 21 0.42
ACGTcount: A:0.25, C:0.18, G:0.34, T:0.23
Consensus pattern (42 bp):
CCTCTTGAACGATGACAGGGGCCTCTTGAACGATGGAAGAGG
Found at i:392291 original size:12 final size:12
Alignment explanation
Indices: 392272--392313 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
392262 GGGCCGCTAA
*
392272 AAATAAATTAAT
1 AAATAAATCAAT
*
392284 ACATAAATCAAT
1 AAATAAATCAAT
392296 AAATAAA-CAATT
1 AAATAAATCAA-T
392308 AAATAA
1 AAATAA
392314 TGCCGAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 3 0.12
12 23 0.88
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.26
Consensus pattern (12 bp):
AAATAAATCAAT
Found at i:393919 original size:14 final size:14
Alignment explanation
Indices: 393900--393934 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
393890 AACAATAAAC
393900 ATACCAAGTTAGAT
1 ATACCAAGTTAGAT
393914 ATACCAAGTTAGAT
1 ATACCAAGTTAGAT
393928 ATACCAA
1 ATACCAA
393935 AAACTACAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.17, G:0.11, T:0.26
Consensus pattern (14 bp):
ATACCAAGTTAGAT
Found at i:394707 original size:22 final size:22
Alignment explanation
Indices: 394662--394707 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
394652 GATGGAGATA
**
394662 GACGGATATCGCCGGAGATTGT
1 GACGGATATCGCCGGAGAGAGT
* *
394684 GACGGATGTCGCCGTAGAGAGT
1 GACGGATATCGCCGGAGAGAGT
394706 GA
1 GA
394708 GAGATGAAGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.24, C:0.17, G:0.39, T:0.20
Consensus pattern (22 bp):
GACGGATATCGCCGGAGAGAGT
Done.